Genetic evidence for landscape effects on dispersal in the army ant Eciton burchellii.

PubMed

Soare, Thomas W; Kumar, Anjali; Naish, Kerry A; O'Donnell, Sean

2014-01-01

Inhibited dispersal, leading to reduced gene flow, threatens populations with inbreeding depression and local extinction. Fragmentation may be especially detrimental to social insects because inhibited gene flow has important consequences for cooperation and competition within and among colonies. Army ants have winged males and permanently wingless queens; these traits imply male-biased dispersal. However, army ant colonies are obligately nomadic and have the potential to traverse landscapes. Eciton burchellii, the most regularly nomadic army ant, is a forest interior species: colony raiding activities are limited in the absence of forest cover. To examine whether nomadism and landscape (forest clearing and elevation) affect population genetic structure in a montane E. burchellii population, we reconstructed queen and male genotypes from 25 colonies at seven polymorphic microsatellite loci. Pairwise genetic distances among individuals were compared to pairwise geographical and resistance distances using regressions with permutations, partial Mantel tests and random forests analyses. Although there was no significant spatial genetic structure in queens or males in montane forest, dispersal may be male-biased. We found significant isolation by landscape resistance for queens based on land cover (forest clearing), but not on elevation. Summed colony emigrations over the lifetime of the queen may contribute to gene flow in this species and forest clearing impedes these movements and subsequent gene dispersal. Further forest cover removal may increasingly inhibit Eciton burchellii colony dispersal. We recommend maintaining habitat connectivity in tropical forests to promote population persistence for this keystone species. © 2013 John Wiley & Sons Ltd.

Inferring population structure and demographic history using Y-STR data from worldwide populations.

PubMed

Xu, Hongyang; Wang, Chuan-Chao; Shrestha, Rukesh; Wang, Ling-Xiang; Zhang, Manfei; He, Yungang; Kidd, Judith R; Kidd, Kenneth K; Jin, Li; Li, Hui

2015-02-01

The Y chromosome is one of the best genetic materials to explore the evolutionary history of human populations. Global analyses of Y chromosomal short tandem repeats (STRs) data can reveal very interesting world population structures and histories. However, previous Y-STR works tended to focus on small geographical ranges or only included limited sample sizes. In this study, we have investigated population structure and demographic history using 17 Y chromosomal STRs data of 979 males from 44 worldwide populations. The largest genetic distances have been observed between pairs of African and non-African populations. American populations with the lowest genetic diversities also showed large genetic distances and coancestry coefficients with other populations, whereas Eurasian populations displayed close genetic affinities. African populations tend to have the oldest time to the most recent common ancestors (TMRCAs), the largest effective population sizes and the earliest expansion times, whereas the American, Siberian, Melanesian, and isolated Atayal populations have the most recent TMRCAs and expansion times, and the smallest effective population sizes. This clear geographic pattern is well consistent with serial founder model for the origin of populations outside Africa. The Y-STR dataset presented here provides the most detailed view of worldwide population structure and human male demographic history, and additionally will be of great benefit to future forensic applications and population genetic studies.

24 CFR 1000.162 - How will a recipient know that non-dwelling structures assisted under the IHBG program meet the...

Code of Federal Regulations, 2010 CFR

2010-04-01

..., design, features, amenities, performance or other factors. The standards for such structures must be able to support the reasonableness and necessity for these factors and to clearly identify the affordable... change; (vi) Cultural relevance of design; (vii) Size and scope supported by population and need; (viii...

Genetic diversity and relationships among the tribes of Meghalaya compared to other Indian and Continental populations.

PubMed

Langstieh, B T; Reddy, B Mohan; Thangaraj, K; Kumar, V; Singh, Lalji

2004-08-01

The autosomal AmpFLSTR markers validated and widely used for forensic applications are used in this study to examine the extent of diversity and genetic relationships among nine Meghalaya populations. Altogether, 932 chromosomes from 9 populations were analyzed using 9 tetrameric AmpFLSTR loci. The included populations were all seven subtribes of the Austro-Asiatic Mon-Khmer-speaking Khasi and the neighboring Tibeto-Burman Garo. The Lyngngam, which are linguistically closer to the Khasi but are culturally intermediate between the Khasi and the Garo, are also included in the study. Although most of the microsatellite loci are highly polymorphic in each of these populations, the allele distributions are fairly uniform across the Meghalaya populations, suggesting relative homogeneity among them. Concurrent with this, the coefficient of gene differentiation (G(ST)) is observed to be low (0.026+/-0.002). This is naturally reflected in the lack of clear differentiation and clustering pattern of the Meghalaya tribes based on either geographic proximity or the historical or current affiliations of these tribes. Analysis of molecular variance (AMOVA) suggests no significant population structure. The structure analysis further suggests that, barring War-Khasi and Pnar, no other population shows any semblance of genetic identity. Even the position of the linguistically distinct Garo is not portrayed as separate from the Khasi. However, when comparable data from other Indian, Southeast Asian, and other continental populations were analyzed, the Meghalaya populations formed a compact cluster clearly separated from other populations, suggesting genetic identity of the Meghalaya populations as a whole. These results are concurrent with the hypothesis of a common and recent origin of these Meghalaya populations, whose genetic differentiation is overwhelmed by the homogenizing effect of continuous gene flow.

Genetic structure and diversity of Japanese kokanee Oncorhynchus nerka stocks as revealed by microsatellite and mitochondrial DNA markers.

PubMed

Yamamoto, S; Kitamura, S; Sakano, H; Morita, K

2011-11-01

Genetic structure and diversity of nine Japanese kokanee (landlocked) Oncorhynchus nerka stocks and anadromous O. nerka from the North Pacific and the Canadian Lake Cultus population were examined using microsatellite and mitochondrial DNA. Sequence analyses of the cytochrome b region of mtDNA for Japanese kokanee O. nerka stocks on Honshu and Hokkaido islands revealed that most Japanese stocks were monomorphic of one major haplotype, which was also dominant in the Lake Cultus population and anadromous O. nerka in the North Pacific. Assignment tests using microsatellite DNA revealed that there was no clear-cut population structure in Japanese kokanee O. nerka stocks. © 2011 The Authors. Journal of Fish Biology © 2011 The Fisheries Society of the British Isles.

Morphological and molecular dissection of wild rices from eastern India suggests distinct speciation between O. rufipogon and O. nivara populations.

PubMed

Samal, Rashmita; Roy, Pritesh Sundar; Sahoo, Auromira; Kar, Meera Kumari; Patra, Bhaskar Chandra; Marndi, Bishnu Charan; Gundimeda, Jwala Narasimha Rao

2018-02-09

The inter relationships between the two progenitors is interesting as both wild relatives are known to be the great untapped gene reservoirs. The debate continues on granting a separate species status to Oryza nivara. The present study was conducted on populations of Oryza rufipogon and Oryza nivara from Eastern India employing morphological and molecular characteristics. The cluster analysis of the data on morphological traits could clearly classify the two wild forms into two separate discrete groups without any overlaps i.e. lack of intermediate forms, suggesting the non-sympatric existence of the wild forms. Amplification of hyper variable regions of the genome could reveal 144 alleles suggesting high genetic diversity values (average He = 0.566). Moreover, with 42.37% of uncommon alleles between the two wild relatives, the molecular variance analysis (AMOVA) could detect only 21% of total variation (p < 0.001) among them and rest 59% was within them. The population structure analysis clearly classified these two wild populations into two distinct sub-populations (K = 2) without any overlaps i.e. lack of intermediate forms, suggesting the non-sympatric existence of the wild forms. Clear differentiation into two distinct groups indicates that O. rufipogon and O. nivara could be treated as two different species.

Population structure of Venturia inaequalis, a causal agent of apple scab, in response to heterogeneous apple tree cultivation.

PubMed

Michalecka, Monika; Masny, Sylwester; Leroy, Thibault; Puławska, Joanna

2018-01-19

Tracking newly emergent virulent populations in agroecosystems provides an opportunity to increase our understanding of the co-evolution dynamics of pathogens and their hosts. On the one hand host plants exert selective pressure on pathogen populations, thus dividing them into subpopulations of different virulence, while on the other hand they create an opportunity for secondary contact between the two divergent populations on one tree. The main objectives of the study were to explore whether the previously reported structure between two Venturia inaequalis population types, virulent or avirulent towards Malus x domestica cultivars carrying Rvi6 gene, is maintained or broken several years after the first emergence of new virulent strains in Poland, and to investigate the relationship between 'new' and 'native' populations derived from the same commercial orchards. For this purpose, we investigated the genetic structure of populations of the apple scab fungus, occurring on apple tree cultivars containing Rvi6, Rvi1 or Rvi17 resistance gene or no resistance at all, based on microsatellite data obtained from 606 strains sampled in 10 orchards composed of various host cultivars. Application of genetic distance inferring and clustering methods allowed us to observe clear genetic distinctness of the populations virulent towards cultivars carrying Rvi6 gene from the Rvi6-avirulent populations and substructures within the Rvi6-group as a consequence of independent immigration events followed by rare, long-distance dispersals. We did not observe such a structuring effect of other genes determining apple scab resistance on any other populations, which in turn were genetically homogenous. However, in two orchards the co-occurrence of strains of different virulence pattern on the same trees was detected, blurring the genetic boundaries between populations. Among several resistance genes studied, only Rvi6 exerted selective pressure on pathogens populations: those virulent toward Rvi6 hosts show unique and clear genetic and virulence pattern. For the first time in commercial Malus x domestica orchards, we reported secondary contacts between populations virulent and avirulent toward Rvi6 hosts. These two populations, first diverged in allopatry, second came into contact and subsequently began interbreeding, in such way that they show unambiguous footprints of gene flow today.

Native fishes in the Truckee River: Are in-stream structures and patterns of population genetic structure related?

PubMed

Peacock, Mary M; Gustin, Mae S; Kirchoff, Veronica S; Robinson, Morgan L; Hekkala, Evon; Pizzarro-Barraza, Claudia; Loux, Tim

2016-09-01

In-stream structures are recognized as significant impediments to movement for freshwater fishes. Apex predators such as salmonids have been the focus of much research on the impacts of such barriers to population dynamics and population viability however much less research has focused on native fishes, where in-stream structures may have a greater impact on long term population viability of these smaller, less mobile species. Patterns of genetic structure on a riverscape can provide information on which structures represent real barriers to movement for fish species and under what specific flow conditions. Here we characterize the impact of 41 dam and diversion structures on movement dynamics under varying flow conditions for a suite of six native fishes found in the Truckee River of California and Nevada. Microsatellite loci were used to estimate total allelic diversity, effective population size and assess genetic population structure. Although there is spatial overlap among species within the river there are clear differences in species distributions within the watershed. Observed population genetic structure was associated with in-stream structures, but only under low flow conditions. High total discharge in 2006 allowed fish to move over potential barriers resulting in no observed population genetic structure for any species in 2007. The efficacy of in-stream structures to impede movement and isolate fish emerged only after multiple years of low flow conditions. Our results suggest that restricted movement of fish species, as a result of in-stream barriers, can be mitigated by flow management. However, as flow dynamics are likely to be altered under global climate change, fragmentation due to barriers could isolate stream fishes into small subpopulations susceptible to both demographic losses and losses of genetic variation. Copyright © 2016 Elsevier B.V. All rights reserved.

Comparison of genetic diversity and population structure between two Schistosoma japonicum isolates--the field and the laboratory.

PubMed

Bian, Chao-Rong; Gao, Yu-Meng; Lamberton, Poppy H L; Lu, Da-Bing

2015-06-01

Schistosomiasis japonicum is one of the most important human parasitic diseases, and a number of studies have recently elucidated the difference in biological characteristics of S. japonicum among different parasite isolates, for example, between the field and the laboratory isolates. Therefore, the understanding of underlying genetic mechanism is of both theoretical and practical importance. In this study, we used six microsatellite markers to assess genetic diversity, population structure, and the bottleneck effect (a sharp reduction in population size) of two parasite populations, one field and one laboratory. A total of 136 S. japonicum cercariae from the field and 86 from the laboratory, which were genetically unique within single snails, were analyzed. The results showed bigger numbers of alleles and higher allelic richness in the field parasite population than in the laboratory indicating lower genetic diversity in the laboratory parasites. A bottleneck effect was detected in the laboratory population. When the field and laboratory isolates were combined, there was a clear distinction between two parasite populations using the software Structure. These genetic differences may partially explain the previously observed contrasted biological traits.

Successive range expansion promotes diversity and accelerates evolution in spatially structured microbial populations.

PubMed

Goldschmidt, Felix; Regoes, Roland R; Johnson, David R

2017-09-01

Successive range expansions occur within all domains of life, where one population expands first (primary expansion) and one or more secondary populations then follow (secondary expansion). In general, genetic drift reduces diversity during range expansion. However, it is not clear whether the same effect applies during successive range expansion, mainly because the secondary population must expand into space occupied by the primary population. Here we used an experimental microbial model system to show that, in contrast to primary range expansion, successive range expansion promotes local population diversity. Because of mechanical constraints imposed by the presence of the primary population, the secondary population forms fractal-like dendritic structures. This divides the advancing secondary population into many small sub-populations and promotes intermixing between the primary and secondary populations. We further developed a mathematical model to simulate the formation of dendritic structures in the secondary population during succession. By introducing mutations in the primary or dendritic secondary populations, we found that mutations are more likely to accumulate in the dendritic secondary populations. Our results thus show that successive range expansion can promote intermixing over the short term and increase genetic diversity over the long term. Our results therefore have potentially important implications for predicting the ecological processes and evolutionary trajectories of microbial communities.

Improving supplementary feeding in species conservation.

PubMed

Ewen, John G; Walker, Leila; Canessa, Stefano; Groombridge, Jim J

2015-04-01

Supplementary feeding is often a knee-jerk reaction to population declines, and its application is not critically evaluated, leading to polarized views among managers on its usefulness. Here, we advocate a more strategic approach to supplementary feeding so that the choice to use it is clearly justified over, or in combination with, other management actions and the predicted consequences are then critically assessed following implementation. We propose combining methods from a set of specialist disciplines that will allow critical evaluation of the need, benefit, and risks of food supplementation. Through the use of nutritional ecology, population ecology, and structured decision making, conservation managers can make better choices about what and how to feed by estimating consequences on population recovery across a range of possible actions. This structured approach also informs targeted monitoring and more clearly allows supplementary feeding to be integrated in recovery plans and reduces the risk of inefficient decisions. In New Zealand, managers of the endangered Hihi (Notiomystis cincta) often rely on supplementary feeding to support reintroduced populations. On Kapiti island the reintroduced Hihi population has responded well to food supplementation, but the logistics of providing an increasing demand recently outstretched management capacity. To decide whether and how the feeding regime should be revised, managers used a structured decision making approach informed by population responses to alternative feeding regimes. The decision was made to reduce the spatial distribution of feeders and invest saved time in increasing volume of food delivered into a smaller core area. The approach used allowed a transparent and defendable management decision in regard to supplementary feeding, reflecting the multiple objectives of managers and their priorities. © 2014 The Authors. Conservation Biology published by Wiley Periodicals, Inc., on behalf of Society for Conservation Biology.

Evidence for population bottlenecks and subtle genetic structure in the yellow rail

USGS Publications Warehouse

Popper, Kenneth J.; Miller, Leonard F.; Green, Michael; Haig, Susan M.; Mullins, Thomas D.

2012-01-01

The Yellow Rail (Coturnicops noveboracencis) is among the most enigmatic and least studied North American birds. Nesting exclusively in marshes and wetlands, it breeds largely east of the Rocky Mountains in the northern United States and Canada, but there is an isolated population in southern Oregon once believed extirpated. The degree of connectivity of the Oregon population with the main population is unknown. We used mitochondrial DNA sequences (mtDNA) and six microsatellite loci to characterize the Yellow Rail's genetic structure and diversity patterns in six areas. Our mtDNA-based analyses of genetic structure identified significant population differentiation, but pairwise comparison of regions identified no clear geographic trends. In contrast, microsatellites suggested subtle genetic structure differentiating the Oregon population from those in the five regions sampled in the Yellow Rail's main breeding range. The genetic diversity of the Oregon population was also the lowest of the six regions sampled, and Oregon was one of three regions that demonstrated evidence of recent population bottlenecks. Factors that produced population reductions may include loss of wetlands to development and agricultural conversion, drought, and wildfire. At this time, we are unable to determine if the high percentage (50%) of populations having experienced bottlenecks is representative of the Yellow Rail's entire range. Further genetic data from additional breeding populations will be required for this issue to be addressed.

Population structure of the Yersinia pseudotuberculosis complex according to multilocus sequence typing

PubMed Central

Laukkanen-Ninios, Riikka; Didelot, Xavier; Jolley, Keith A.; Morelli, Giovanna; Sangal, Vartul; Kristo, Paula; Imori, Priscilla F. M.; Fukushima, Hiroshi; Siitonen, Anja; Tseneva, Galina; Voskressenskaya, Ekaterina; Falcao, Juliana P.; Korkeala, Hannu; Maiden, Martin C. J.; Mazzoni, Camila; Carniel, Elisabeth; Skurnik, Mikael; Achtman, Mark

2014-01-01

Summary Multilocus sequence analysis of 417 strains of Yersinia pseudotuberculosis revealed that it is a complex of four populations, three of which have been previously assigned species status [Y. pseudotuberculosis sensu stricto (s.s.), Yersinia pestis and Yersinia similis] and a fourth population, which we refer to as the Korean group, which may be in the process of speciation. We detected clear signs of recombination within Y. pseudotuberculosis s.s. as well as imports from Y. similis and the Korean group. The sources of genetic diversification within Y. pseudotuberculosis s.s. were approximately equally divided between recombination and mutation, whereas recombination has not yet been demonstrated in Y. pestis, which is also much more genetically monomorphic than is Y. pseudotuberculosis s.s. Most Y. pseudotuberculosis s.s. belong to a diffuse group of sequence types lacking clear population structure, although this species contains a melibiose-negative clade that is present globally in domesticated animals. Yersinia similis corresponds to the previously identified Y. pseudotuberculosis genetic type G4, which is probably not pathogenic because it lacks the virulence factors that are typical for Y. pseudotuberculosis s.s. In contrast, Y. pseudotuberculosis s.s., the Korean group and Y. pestis can all cause disease in humans. PMID:21951486

Environmental Variables Explain Genetic Structure in a Beetle-Associated Nematode

PubMed Central

McGaughran, Angela; Morgan, Katy; Sommer, Ralf J.

2014-01-01

The distribution of a species is a complex expression of its ecological and evolutionary history and integrating population genetic, environmental, and ecological data can provide new insights into the effects of the environment on the population structure of species. Previous work demonstrated strong patterns of genetic differentiation in natural populations of the hermaphroditic nematode Pristionchus pacificus in its La Réunion Island habitat, but gave no clear understanding of the role of the environment in structuring this variation. Here, we present what is to our knowledge the first study to statistically evaluate the role of the environment in shaping the structure and distribution of nematode populations. We test the hypothesis that genetic structure in P. pacificus is influenced by environmental variables, by combining population genetic analyses of microsatellite data from 18 populations and 370 strains, with multivariate statistics on environmental data, and species distribution modelling. We assess and quantify the relative importance of environmental factors (geographic distance, altitude, temperature, precipitation, and beetle host) on genetic variation among populations. Despite the fact that geographic populations of P. pacificus comprise vast genetic diversity sourced from multiple ancestral lineages, we find strong evidence for local associations between environment and genetic variation. Further, we show that significantly more genetic variation in P. pacificus populations is explained by environmental variation than by geographic distances. This supports a strong role for environmental heterogeneity vs. genetic drift in the divergence of populations, which we suggest may be influenced by adaptive forces. PMID:24498073

Genetic perspectives on northern population cycles: bridging the gap between theory and empirical studies.

PubMed

Norén, Karin; Angerbjörn, Anders

2014-05-01

Many key species in northern ecosystems are characterised by high-amplitude cyclic population demography. In 1924, Charles Elton described the ecology and evolution of cyclic populations in a classic paper and, since then, a major focus has been the underlying causes of population cycles. Elton hypothesised that fluctuations reduced population genetic variation and influenced the direction of selection pressures. In concordance with Elton, present theories concern the direct consequences of population cycles for genetic structure due to the processes of genetic drift and selection, but also include feedback models of genetic composition on population dynamics. Most of these theories gained mathematical support during the 1970s and onwards, but due to methodological drawbacks, difficulties in long-term sampling and a complex interplay between microevolutionary processes, clear empirical data allowing the testing of these predictions are still scarce. Current genetic tools allow for estimates of genetic variation and identification of adaptive genomic regions, making this an ideal time to revisit this subject. Herein, we attempt to contribute towards a consensus regarding the enigma described by Elton almost 90 years ago. We present nine predictions covering the direct and genetic feedback consequences of population cycles on genetic variation and population structure, and review the empirical evidence. Generally, empirical support for the predictions was low and scattered, with obvious gaps in the understanding of basic population processes. We conclude that genetic variation in northern cyclic populations generally is high and that the geographic distribution and amount of diversity are usually suggested to be determined by various forms of context- and density-dependent dispersal exceeding the impact of genetic drift. Furthermore, we found few clear signatures of selection determining genetic composition in cyclic populations. Dispersal is assumed to have a strong impact on genetic structuring and we suggest that the signatures of other microevolutionary processes such as genetic drift and selection are weaker and have been over-shadowed by density-dependent dispersal. We emphasise that basic biological and demographical questions still need to be answered and stress the importance of extensive sampling, appropriate choice of tools and the value of standardised protocols. © 2013 The Authors. Biological Reviews © 2013 Cambridge Philosophical Society.

Effective Population Size Dynamics and the Demographic Collapse of Bornean Orang-Utans

PubMed Central

Goossens, Benoit; Nater, Alexander; Morf, Nadja; Salmona, Jordi; Bruford, Michael W.; Van Schaik, Carel P.; Krützen, Michael; Chikhi, Lounès

2012-01-01

Bornean orang-utans experienced a major demographic decline and local extirpations during the Pleistocene and Holocene due to climate change, the arrival of modern humans, of farmers and recent commercially-driven habitat loss and fragmentation. The recent loss of habitat and its dramatic fragmentation has affected the patterns of genetic variability and differentiation among the remaining populations and increased the extinction risk of the most isolated ones. However, the contribution of recent demographic events to such genetic patterns is still not fully clear. Indeed, it can be difficult to separate the effects of recent anthropogenic fragmentation from the genetic signature of prehistoric demographic events. Here, we investigated the genetic structure and population size dynamics of orang-utans from different sites. Altogether 126 individuals were analyzed and a full-likelihood Bayesian approach was applied. All sites exhibited clear signals of population decline. Population structure is known to generate spurious bottleneck signals and we found that it does indeed contribute to the signals observed. However, population structure alone does not easily explain the observed patterns. The dating of the population decline varied across sites but was always within the 200–2000 years period. This suggests that in some sites at least, orang-utan populations were affected by demographic events that started before the recent anthropogenic effects that occurred in Borneo. These results do not mean that the recent forest exploitation did not leave its genetic mark on orang-utans but suggests that the genetic pool of orang-utans is also impacted by more ancient events. While we cannot identify the main cause for this decline, our results suggests that the decline may be related to the arrival of the first farmers or climatic events, and that more theoretical work is needed to understand how multiple demographic events impact the genome of species and how we can assess their relative contributions. PMID:23166666

Genetic diversity and structure of a rare endemic cactus and an assessment of its genetic relationship with a more common congener.

PubMed

Rayamajhi, Niraj; Sharma, Jyotsna

2018-06-01

Endemic, obligate outcrossing plant species with narrow geographic distributions and disjunct populations are prone to loss of genetic diversity. Simultaneously, delineating clear species boundaries is important for targeted conservation efforts. The rare and endemic cactus, Sclerocactus brevihamatus subsp. tobuschii (SBT), has a parapatric relationship with Sclerocactus brevihamatus subsp. brevihamatus (SBB) but genetic distance between the two taxa is unknown. We: (1) developed taxon-specific polymorphic microsatellites, (2) assessed genetic diversity within and among nine populations of SBT, and within one population of SBB, and (3) estimated the genetic relationship between the two subspecies. Within-population genetic diversity of SBT was moderate to high (mean H o  = 0.37; mean H e  = 0.59). Indirect estimate of inbreeding corrected for null alleles (F is-INEst ) was low for SBT, ranging from 0.03 to 0.14 (mean F is-INEst  = 0.07). Genetic differentiation among populations of SBT was low based on F st (0.08) and AMOVA (Ф PT  = 0.10). Lack of genetic and spatial correlation in SBT populations coupled with the presence of private alleles and bottleneck events in several populations suggests that reproductive isolation is occurring but that sufficient time may not have yet passed to manifest strong differentiation. Cluster analyses segregated the 10 populations into three distinct groups, and separated SBB genotypes clearly. Results suggest that while hybridization between the two subspecies may occur, SBT is clearly differentiated genetically from SBB to retain its current taxonomic status.

Geographic structure of genetic variation in the widespread woodland grass Milium effusum L. A comparison between two regions with contrasting history and geomorphology.

PubMed

Tyler, Torbjörn

2002-12-01

Allozyme variation in the forest grass Milium effusum L. was studied in 21-23 populations within each of two equally sized densely sampled areas in northern and southern Sweden. In addition, 25 populations from other parts of Eurasia were studied for comparison. The structure of variation was analysed with both diversity statistics and measures based on allelic richness at a standardised sample size. The species was found to be highly variable, but no clear geographic patterns in the distribution of alleles or in overall genetic differentiation were found, either within the two regions or within the whole sample. Thus, no inferences about the direction of postglacial migration could be made. Obviously, migration and gene flow must have taken place in a manner capable of randomising the distribution of alleles. However, there were clear differences in levels and structuring of the variation between the two regions. Levels of variation, both in terms of genetic diversity and allelic richness, were lower in northern Sweden as compared with southern Sweden. In contrast, different measures of geographic structure all showed higher levels of population differentiation in the northern region. This is interpreted as due to different geomorphological conditions in the two regions, creating a relatively continuous habitat and gene flow in the southern region as compared with the northern region where the species, although common, is confined to narrow and mutually isolated corridors in the landscape.

Host specificity and genealogy of the louse Polyplax serrata on field mice, Apodemus species: a case of parasite duplication or colonisation?

PubMed

Stefka, Jan; Hypsa, Václav

2008-05-01

The genealogy, population structure and population dynamics of the sucking louse Polyplax serrata were analysed across four host species of the genus Apodemus. An analysis of 126 sequences of cytochrome c oxidase subunit I using phylogenetic approaches and haplotype networking revealed a clear structure of European samples, forming three distinct and genetically distant clades with different host specificities. Although a clear connection was detected between the host and parasite genealogies/phylogenies, a uniform pattern of co-speciation was not found. For example, a dramatic shift in the degree of host specificity was demonstrated for two related louse lineages living in sympatry and sharing one of their host species. While one of the louse lineages frequently parasitised two different host taxa (Apodemus sylvaticus and Apodemus flavicollis), the other louse lineage was strictly specific to A. flavicollis. The estimate of divergence time between the two louse lineages indicates that they may have arisen due to parasite duplication on A. flavicollis.

Survival and Population Dynamics of the Marabou Stork in an Isolated Population, Swaziland

PubMed Central

Monadjem, Ara; Kane, Adam; Botha, Andre; Dalton, Desire; Kotze, Antoinette

2012-01-01

Investigating the ecology of long lived birds is particularly challenging owing to the time scales involved. Here an analysis is presented of a long term study of the survival and population dynamics of the marabou stork (Leptoptilos crumeniferus), a wide ranging scavenging bird from Sub-Saharan Africa. Using resightings data of tagged nestlings and free flying birds we show that the stork population can be divided into three general life stages with unique survival probabilities and fecundities. Fecundity of the storks is inversely related to rainfall during their breeding season. Corroborative evidence for a metapopulation structure is discussed highlighting the impact of the Swaziland birds on the ecology of the species in the broader region. The importance of tag loss or illegibility over time is highlighted. Clearly, any attempt at conserving a species will require a detailed understanding of its population structure, of the sort examined here. PMID:23029517

Implications for management and conservation of the population genetic structure of the wedge clam Donax trunculus across two biogeographic boundaries

PubMed Central

Marie, Amandine D.; Lejeusne, Christophe; Karapatsiou, Evgenia; Cuesta, José A.; Drake, Pilar; Macpherson, Enrique; Bernatchez, Louis; Rico, Ciro

2016-01-01

In a resource management perspective, the understanding of the relative influence of the physical factors on species connectivity remains a major challenge and is also of great ecological and conservation biology interest. Despite the overfishing threat on the wedge clam Donax trunculus in Europe, relatively little information is known about its population genetic structure and connectivity and their consequences on conservation policies. We employed 16 microsatellite loci to characterise the genetic diversity and population structure of D. trunculus. A total of 514 samples from seven different localities along the Atlantic-Mediterranean transition, from the Atlantic (Gulf of Cádiz) to the north-western Mediterranean were genotyped. The analysis of the population genetic structure displayed a clear distinction along the Atlantic-Mediterranean transition with different clusters in the Atlantic Ocean, the Alboran Sea and the northwestern Mediterranean. Consequently, we recommend that these three areas should be considered as different management units. We showed that all populations seem to be at high long-term risk of extinction with the exception of the protected Doñana National Park population which still seems to have evolutionary potential. Therefore, our results emphasized the necessity of protection of this economic resource and the validity of molecular tools to evaluate the population dynamics. PMID:27991535

Implications for management and conservation of the population genetic structure of the wedge clam Donax trunculus across two biogeographic boundaries.

PubMed

Marie, Amandine D; Lejeusne, Christophe; Karapatsiou, Evgenia; Cuesta, José A; Drake, Pilar; Macpherson, Enrique; Bernatchez, Louis; Rico, Ciro

2016-12-19

In a resource management perspective, the understanding of the relative influence of the physical factors on species connectivity remains a major challenge and is also of great ecological and conservation biology interest. Despite the overfishing threat on the wedge clam Donax trunculus in Europe, relatively little information is known about its population genetic structure and connectivity and their consequences on conservation policies. We employed 16 microsatellite loci to characterise the genetic diversity and population structure of D. trunculus. A total of 514 samples from seven different localities along the Atlantic-Mediterranean transition, from the Atlantic (Gulf of Cádiz) to the north-western Mediterranean were genotyped. The analysis of the population genetic structure displayed a clear distinction along the Atlantic-Mediterranean transition with different clusters in the Atlantic Ocean, the Alboran Sea and the northwestern Mediterranean. Consequently, we recommend that these three areas should be considered as different management units. We showed that all populations seem to be at high long-term risk of extinction with the exception of the protected Doñana National Park population which still seems to have evolutionary potential. Therefore, our results emphasized the necessity of protection of this economic resource and the validity of molecular tools to evaluate the population dynamics.

Implications for management and conservation of the population genetic structure of the wedge clam Donax trunculus across two biogeographic boundaries

NASA Astrophysics Data System (ADS)

Marie, Amandine D.; Lejeusne, Christophe; Karapatsiou, Evgenia; Cuesta, José A.; Drake, Pilar; MacPherson, Enrique; Bernatchez, Louis; Rico, Ciro

2016-12-01

In a resource management perspective, the understanding of the relative influence of the physical factors on species connectivity remains a major challenge and is also of great ecological and conservation biology interest. Despite the overfishing threat on the wedge clam Donax trunculus in Europe, relatively little information is known about its population genetic structure and connectivity and their consequences on conservation policies. We employed 16 microsatellite loci to characterise the genetic diversity and population structure of D. trunculus. A total of 514 samples from seven different localities along the Atlantic-Mediterranean transition, from the Atlantic (Gulf of Cádiz) to the north-western Mediterranean were genotyped. The analysis of the population genetic structure displayed a clear distinction along the Atlantic-Mediterranean transition with different clusters in the Atlantic Ocean, the Alboran Sea and the northwestern Mediterranean. Consequently, we recommend that these three areas should be considered as different management units. We showed that all populations seem to be at high long-term risk of extinction with the exception of the protected Doñana National Park population which still seems to have evolutionary potential. Therefore, our results emphasized the necessity of protection of this economic resource and the validity of molecular tools to evaluate the population dynamics.

Sulfolobus islandicus meta-populations in Yellowstone National Park hot springs

USGS Publications Warehouse

Campbell, Kate M.; Kouris, Angela; England, Whitney; Anderson, Rika E.; McCleskey, R. Blaine; Nordstrom, D. Kirk; Whitaker, Rachel J.

2017-01-01

Abiotic and biotic forces shape the structure and evolution of microbial populations. We investigated forces that shape the spatial and temporal population structure of Sulfolobus islandicus by comparing geochemical and molecular analysis from seven hot springs in five regions sampled over 3 years in Yellowstone National Park. Through deep amplicon sequencing, we uncovered 148 unique alleles at two loci whose relative frequency provides clear evidence for independent populations in different hot springs. Although geography controls regional geochemical composition and population differentiation, temporal changes in population were not explained by corresponding variation in geochemistry. The data suggest that the influence of extinction, bottleneck events and/or selective sweeps within a spring and low migration between springs shape these populations. We suggest that hydrologic events such as storm events and surface snowmelt runoff destabilize smaller hot spring environments with smaller populations and result in high variation in the S. islandicus population over time. Therefore, physical abiotic features such as hot spring size and position in the landscape are important factors shaping the stability and diversity of the S. islandicus meta-population within Yellowstone National Park.

Loss of Genetic Diversity Means Loss of Geological Information: The Endangered Japanese Crayfish Exhibits Remarkable Historical Footprints

PubMed Central

Koizumi, Itsuro; Usio, Nisikawa; Kawai, Tadashi; Azuma, Noriko; Masuda, Ryuichi

2012-01-01

Intra-specific genetic diversity is important not only because it influences population persistence and evolutionary potential, but also because it contains past geological, climatic and environmental information. In this paper, we show unusually clear genetic structure of the endangered Japanese crayfish that, as a sedentary species, provides many insights into lesser-known past environments in northern Japan. Over the native range, most populations consisted of unique 16S mtDNA haplotypes, resulting in significant genetic divergence (overall F ST = 0.96). Owing to the simple and clear structure, a new graphic approach unraveled a detailed evolutionary history; regional crayfish populations were comprised of two distinct lineages that had experienced contrasting demographic processes (i.e. rapid expansion vs. slow stepwise range expansion) following differential drainage topologies and past climate events. Nuclear DNA sequences also showed deep separation between the lineages. Current ocean barriers to dispersal did not significantly affect the genetic structure of the freshwater crayfish, indicating the formation of relatively recent land bridges. This study provides one of the best examples of how phylogeographic analysis can unravel a detailed evolutionary history of a species and how this history contributes to the understanding of the past environment in the region. Ongoing local extinctions of the crayfish lead not only to loss of biodiversity but also to the loss of a significant information regarding past geological and climatic events. PMID:22470505

Investigating the population structure and genetic differentiation of livestock guard dog breeds.

PubMed

Bigi, D; Marelli, S P; Liotta, L; Frattini, S; Talenti, A; Pagnacco, G; Polli, M; Crepaldi, P

2018-01-14

Livestock guarding dogs are a valuable adjunct to the pastoral community. Having been traditionally selected for their working ability, they fulfil their function with minimal interaction or command from their human owners. In this study, the population structure and the genetic differentiation of three Italian livestock guardian breeds (Sila's Dog, Maremma and Abruzzese Sheepdog and Mannara's Dog) and three functionally and physically similar breeds (Cane Corso, Central Asian Shepherd Dog and Caucasian Shepherd Dog), totalling 179 dogs unrelated at the second generation, were investigated with 18 autosomal microsatellite markers. Values for the number of alleles per locus, observed and expected heterozygosity, Hardy-Weinberg Equilibrium, F stats, Nei's and Reynold's genetic distances, clustering and sub-population formation abilities and individual genetic structures were calculated. Our results show clear breed differentiation, whereby all the considered breeds show reasonable genetic variability despite small population sizes and variable selection schemes. These results provide meaningful data to stakeholders in specific breed and environmental conservation programmes.

Age, growth and population structure of invasive lionfish (Pterois volitans/miles) in northeast Florida using a length-based, age-structured population model.

PubMed

Johnson, Eric G; Swenarton, Mary Katherine

2016-01-01

The effective management of invasive species requires detailed understanding of the invader's life history. This information is essential for modeling population growth and predicting rates of expansion, quantifying ecological impacts and assessing the efficacy of removal and control strategies. Indo-Pacific lionfish ( Pterois volitans/miles ) have rapidly invaded the western Atlantic, Gulf of Mexico and Caribbean Sea with documented negative impacts on native ecosystems. To better understand the life history of this species, we developed and validated a length-based, age-structured model to investigate age, growth and population structure in northeast Florida. The main findings of this study were: (1) lionfish exhibited rapid growth with seasonal variation in growth rates; (2) distinct cohorts were clearly identifiable in the length-frequency data, suggesting that lionfish are recruiting during a relatively short period in summer; and (3) the majority of lionfish were less than two years old with no lionfish older than three years of age, which may be the result of culling efforts as well as ontogenetic habitat shifts to deeper water.

Age, growth and population structure of invasive lionfish (Pterois volitans/miles) in northeast Florida using a length-based, age-structured population model

PubMed Central

2016-01-01

The effective management of invasive species requires detailed understanding of the invader’s life history. This information is essential for modeling population growth and predicting rates of expansion, quantifying ecological impacts and assessing the efficacy of removal and control strategies. Indo-Pacific lionfish (Pterois volitans/miles) have rapidly invaded the western Atlantic, Gulf of Mexico and Caribbean Sea with documented negative impacts on native ecosystems. To better understand the life history of this species, we developed and validated a length-based, age-structured model to investigate age, growth and population structure in northeast Florida. The main findings of this study were: (1) lionfish exhibited rapid growth with seasonal variation in growth rates; (2) distinct cohorts were clearly identifiable in the length-frequency data, suggesting that lionfish are recruiting during a relatively short period in summer; and (3) the majority of lionfish were less than two years old with no lionfish older than three years of age, which may be the result of culling efforts as well as ontogenetic habitat shifts to deeper water. PMID:27920953

Turkish Population Structure and Genetic Ancestry Reveal Relatedness among Eurasian Populations

PubMed Central

Hodoğlugil, Uğur; Mahley, Robert W.

2013-01-01

Summary Turkey connects the Middle East, Europe, and Asia and has experienced major population movements. We examined the population structure and genetic relatedness of samples from three regions of Turkey using over 500,000 SNP genotypes. The data were analyzed together with Human Genome Diversity Panel data. To obtain a more representative sampling from Central Asia, Kyrgyz samples (Bishkek, Kyrgyzstan) were genotyped and analyzed. Principal component (PC) analysis reveals a significant overlap between Turks and Middle Easterners and a relationship with Europeans and South and Central Asians; however, the Turkish genetic structure is unique. FRAPPE, STRUCTURE, and phylogenetic analyses support the PC analysis depending upon the number of parental ancestry components chosen. For example, supervised STRUCTURE (K = 3) illustrates a genetic ancestry for the Turks of 45% Middle Eastern (95% CI, 42–49), 40% European (95% CI, 36–44), and 15% Central Asian (95% CI, 13–16), whereas at K = 4 the genetic ancestry of the Turks was 38% European (95% CI, 35–42), 35% Middle Eastern (95% CI, 33–38), 18% South Asian (95% CI, 16–19), and 9% Central Asian (95% CI, 7–11). PC analysis and FRAPPE/STRUCTURE results from three regions in Turkey (Aydin, Istanbul, and Kayseri) were superimposed, without clear subpopulation structure, suggesting the selected samples were rather homogeneous. Thus, this study demonstrates admixture of Turkish people reflecting the population migration patterns. PMID:22332727

Hierarchical Genetic Analysis of German Cockroach (Blattella germanica) Populations from within Buildings to across Continents

PubMed Central

Vargo, Edward L.; Crissman, Jonathan R.; Booth, Warren; Santangelo, Richard G.; Mukha, Dmitry V.; Schal, Coby

2014-01-01

Understanding the population structure of species that disperse primarily by human transport is essential to predicting and controlling human-mediated spread of invasive species. The German cockroach (Blattella germanica) is a widespread urban invader that can actively disperse within buildings but is spread solely by human-mediated dispersal over longer distances; however, its population structure is poorly understood. Using microsatellite markers we investigated population structure at several spatial scales, from populations within single apartment buildings to populations from several cities across the U.S. and Eurasia. Both traditional measures of genetic differentiation and Bayesian clustering methods revealed increasing levels of genetic differentiation at greater geographic scales. Our results are consistent with active dispersal of cockroaches largely limited to movement within a building. Their low levels of genetic differentiation, yet limited active spread between buildings, suggests a greater likelihood of human-mediated dispersal at more local scales (within a city) than at larger spatial scales (within and between continents). About half the populations from across the U.S. clustered together with other U.S. populations, and isolation by distance was evident across the U.S. Levels of genetic differentiation among Eurasian cities were greater than those in the U.S. and greater than those between the U.S. and Eurasia, but no clear pattern of structure at the continent level was detected. MtDNA sequence variation was low and failed to reveal any geographical structure. The weak genetic structure detected here is likely due to a combination of historical admixture among populations and periodic population bottlenecks and founder events, but more extensive studies are needed to determine whether signatures of global movement may be present in this species. PMID:25020136

Characteristics and Roles of Literacy Clinic Directors

ERIC Educational Resources Information Center

Ortlieb, Evan; Pearce, Daniel L.

2013-01-01

A literacy clinic is an ideal setting where research and exploration often lead to breakthroughs in reading remediation; that information can then be transferred to classroom instruction (Morris, 2003). Although it is clear that literacy clinics should be structured around what works for their student populations, there remains ambiguity…

Region, landscape, and host plant effects on reproduction by a mobile, multivoltine arthropod herbivore

USDA-ARS?s Scientific Manuscript database

Community structure, species abundance, and biotic interactions of invertebrate species in farmlands are influenced by larger-scale processes at region and landscape levels. While previous work makes clear the importance of landscape factors for natural enemy populations, relatively less is known ab...

Evaluations of Structural Interventions for HIV Prevention: A Review of Approaches and Methods.

PubMed

Iskarpatyoti, Brittany S; Lebov, Jill; Hart, Lauren; Thomas, Jim; Mandal, Mahua

2018-04-01

Structural interventions alter the social, economic, legal, political, and built environments that underlie processes affecting population health. We conducted a systematic review of evaluations of structural interventions for HIV prevention in low- and middle-income countries (LMICs) to better understand methodological and other challenges and identify effective evaluation strategies. We included 27 peer-reviewed articles on interventions related to economic empowerment, education, and substance abuse in LMICs. Twenty-one evaluations included clearly articulated theories of change (TOCs); 14 of these assessed the TOC by measuring intermediary variables in the causal pathway between the intervention and HIV outcomes. Although structural interventions address complex interactions, no evaluation included methods designed to evaluate complex systems. To strengthen evaluations of structural interventions, we recommend clearly articulating a TOC and measuring intermediate variables between the predictor and outcome. We additionally recommend adapting study designs and analytic methods outside traditional epidemiology to better capture complex results, influences external to the intervention, and unintended consequences.

Effects of landscape matrix on population connectivity of an arboreal mammal, Petaurus breviceps.

PubMed

Malekian, Mansoureh; Cooper, Steven J B; Saint, Kathleen M; Lancaster, Melanie L; Taylor, Andrea C; Carthew, Susan M

2015-09-01

Ongoing habitat loss and fragmentation is considered a threat to biodiversity as it can create small, isolated populations that are at increased risk of extinction. Tree-dependent species are predicted to be highly sensitive to forest and woodland loss and fragmentation, but few studies have tested the influence of different types of landscape matrix on gene flow and population structure of arboreal species. Here, we examine the effects of landscape matrix on population structure of the sugar glider (Petaurus breviceps) in a fragmented landscape in southeastern South Australia. We collected 250 individuals across 12 native Eucalyptus forest remnants surrounded by cleared agricultural land or exotic Pinus radiata plantations and a large continuous eucalypt forest. Fifteen microsatellite loci were genotyped and analyzed to infer levels of population differentiation and dispersal. Genetic differentiation among most forest patches was evident. We found evidence for female philopatry and restricted dispersal distances for females relative to males, suggesting there is male-biased dispersal. Among the environmental variables, spatial variables including geographic location, minimum distance to neighboring patch, and degree of isolation were the most important in explaining genetic variation. The permeability of a cleared agricultural matrix to dispersing gliders was significantly higher than that of a pine matrix, with the gliders dispersing shorter distances across the latter. Our results added to previous findings for other species of restricted dispersal and connectivity due to habitat fragmentation in the same region, providing valuable information for the development of strategies to improve the connectivity of populations in the future.

Plasmodium vivax Diversity and Population Structure across Four Continents

PubMed Central

Koepfli, Cristian; Rodrigues, Priscila T.; Antao, Tiago; Orjuela-Sánchez, Pamela; Van den Eede, Peter; Gamboa, Dionicia; van Hong, Nguyen; Bendezu, Jorge; Erhart, Annette; Barnadas, Céline; Ratsimbasoa, Arsène; Menard, Didier; Severini, Carlo; Menegon, Michela; Nour, Bakri Y. M.; Karunaweera, Nadira; Mueller, Ivo; Ferreira, Marcelo U.; Felger, Ingrid

2015-01-01

Plasmodium vivax is the geographically most widespread human malaria parasite. To analyze patterns of microsatellite diversity and population structure across countries of different transmission intensity, genotyping data from 11 microsatellite markers was either generated or compiled from 841 isolates from four continents collected in 1999–2008. Diversity was highest in South-East Asia (mean allelic richness 10.0–12.8), intermediate in the South Pacific (8.1–9.9) Madagascar and Sudan (7.9–8.4), and lowest in South America and Central Asia (5.5–7.2). A reduced panel of only 3 markers was sufficient to identify approx. 90% of all haplotypes in South Pacific, African and SE-Asian populations, but only 60–80% in Latin American populations, suggesting that typing of 2–6 markers, depending on the level of endemicity, is sufficient for epidemiological studies. Clustering analysis showed distinct clusters in Peru and Brazil, but little sub-structuring was observed within Africa, SE-Asia or the South Pacific. Isolates from Uzbekistan were exceptional, as a near-clonal parasite population was observed that was clearly separated from all other populations (F ST>0.2). Outside Central Asia F ST values were highest (0.11–0.16) between South American and all other populations, and lowest (0.04–0.07) between populations from South-East Asia and the South Pacific. These comparisons between P. vivax populations from four continents indicated that not only transmission intensity, but also geographical isolation affect diversity and population structure. However, the high effective population size results in slow changes of these parameters. This persistency must be taken into account when assessing the impact of control programs on the genetic structure of parasite populations. PMID:26125189

Plasmodium vivax Diversity and Population Structure across Four Continents.

PubMed

Koepfli, Cristian; Rodrigues, Priscila T; Antao, Tiago; Orjuela-Sánchez, Pamela; Van den Eede, Peter; Gamboa, Dionicia; van Hong, Nguyen; Bendezu, Jorge; Erhart, Annette; Barnadas, Céline; Ratsimbasoa, Arsène; Menard, Didier; Severini, Carlo; Menegon, Michela; Nour, Bakri Y M; Karunaweera, Nadira; Mueller, Ivo; Ferreira, Marcelo U; Felger, Ingrid

2015-01-01

Plasmodium vivax is the geographically most widespread human malaria parasite. To analyze patterns of microsatellite diversity and population structure across countries of different transmission intensity, genotyping data from 11 microsatellite markers was either generated or compiled from 841 isolates from four continents collected in 1999-2008. Diversity was highest in South-East Asia (mean allelic richness 10.0-12.8), intermediate in the South Pacific (8.1-9.9) Madagascar and Sudan (7.9-8.4), and lowest in South America and Central Asia (5.5-7.2). A reduced panel of only 3 markers was sufficient to identify approx. 90% of all haplotypes in South Pacific, African and SE-Asian populations, but only 60-80% in Latin American populations, suggesting that typing of 2-6 markers, depending on the level of endemicity, is sufficient for epidemiological studies. Clustering analysis showed distinct clusters in Peru and Brazil, but little sub-structuring was observed within Africa, SE-Asia or the South Pacific. Isolates from Uzbekistan were exceptional, as a near-clonal parasite population was observed that was clearly separated from all other populations (FST>0.2). Outside Central Asia FST values were highest (0.11-0.16) between South American and all other populations, and lowest (0.04-0.07) between populations from South-East Asia and the South Pacific. These comparisons between P. vivax populations from four continents indicated that not only transmission intensity, but also geographical isolation affect diversity and population structure. However, the high effective population size results in slow changes of these parameters. This persistency must be taken into account when assessing the impact of control programs on the genetic structure of parasite populations.

Genetic diversity and structure of the threatened species Sinopodophyllum hexandrum (Royle) Ying.

PubMed

Liu, W; Wang, J; Yin, D X; Yang, M; Wang, P; Han, Q S; Ma, Q Q; Liu, J J; Wang, J X

2016-06-10

Sinopodophyllum hexandrum is an important medicinal plant that has been listed as an endangered species, making the conservation of its genetic diversity a priority. Therefore, the genetic diversity and population structure of S. hexandrum was investigated through inter-simple sequence repeat analysis of eight natural populations. Eleven selected primers generated 141 discernible fragments. The percentage of polymorphic bands was 37.59% at the species level, and 7.66-24.32% at the population level. Genetic diversity of S. hexandrum was low within populations (average HE = 0.0366), but higher at the species level (HE = 0.0963). Clear structure and high genetic differentiation were detected between populations using unweighted pair groups mean arithmetic and principle coordinate analysis. Clustering approaches clustered the eight sampled populations into three major groups, and AMOVA confirmed there to be significant variation between populations (63.27%). Genetic differentiation may have arisen through limited gene flow (Nm = 0.3317) in this species. Isolation by distance among populations was determined by comparing genetic distance versus geographical distance using the Mantel test. The results revealed no correlation between spatial pattern and geographic location. Given the low within-population genetic diversity, high differentiation among populations, and the increasing anthropogenic pressure on this species, in situ conservation measures, in addition to sampling and ex situ preservation, are recommended to preserve S. hexandrum populations and to retain their genetic diversity.

Gone with the currents: lack of genetic differentiation at the circum-continental scale in the Antarctic krill Euphausia superba

PubMed Central

2011-01-01

Background Southern Ocean fauna represent a significant amount of global biodiversity, whose origin may be linked to glacial cycles determining local extinction/eradication with ice advance, survival of refugee populations and post-glacial re-colonization. This pattern implies high potential for differentiation in benthic shelf species with limited dispersal, yet consequences for pelagic organisms are less clear. The present study investigates levels of genetic variation and population structure of the Antarctic krill Euphausia superba using mitochondrial DNA and EST-linked microsatellite markers for an unprecedentedly comprehensive sampling of its populations over a circum-Antarctic range. Results MtDNA (ND1) sequences and EST-linked microsatellite markers indicated no clear sign of genetic structure among populations over large geographic scales, despite considerable power to detect differences inferred from forward-time simulations. Based on ND1, few instances of genetic heterogeneity, not significant after correction for multiple tests, were detected between geographic or temporal samples. Neutrality tests and mismatch distribution based on mtDNA sequences revealed strong evidence of past population expansion. Significant positive values of the parameter g (a measure of population growth) were obtained from microsatellite markers using a coalescent-based genealogical method and suggested a recent start (60 000 - 40 000 years ago) for the expansion. Conclusions The results provide evidence of lack of genetic heterogeneity of Antarctic krill at large geographic scales and unequivocal support for recent population expansion. Lack of genetic structuring likely reflects the tight link between krill and circum-Antarctic ocean currents and is consistent with the hypothesis that differentiation processes in Antarctic species are largely influenced by dispersal potential, whereas small-scale spatial and temporal differentiation might be due to local conditions leading to genetic patchiness. The signal of recent population growth suggests differential impact of glacial cycles on pelagic Antarctic species, which experienced population expansion during glaciations with increased available habitat, versus sedentary benthic shelf species. EST-linked microsatellites provide new perspectives to complement the results based on mtDNA and suggest that data-mining of EST libraries will be a useful approach to facilitate use of microsatellites for additional species. PMID:21486439

The fine-scale genetic structure of the two-spotted spider mite in a commercial greenhouse.

PubMed

Uesugi, R; Kunimoto, Y; Osakabe, Mh

2009-02-01

The fine-scale genetic structure of Tetranychus urticae Koch was studied to estimate local gene flow within a rose tree habitat in a commercial greenhouse using seven microsatellite markers. Two beds of rose trees with different population densities were selected and 18 consecutive quadrats of 1.2 m length were sequentially established in each bed. Heterozygote deficiency was positive within quadrats, which was most likely a result of the Wahlund effect because the mites usually form small breeding colonies. Low population density and frequent inbreeding could also accelerate genetic differentiation among the breeding colonies. A short-range (2.4-3.6 m) positive autocorrelation and clear genetic cline among quadrat populations was detected within a bed. This suggests that gene flow was limited to a short range even if population density was substantially increased. Therefore, large-scale dispersal such as aerial dispersal contributed very little to gene flow in the greenhouse.

Cross-amplified microsatellites in the European cherry fly, Rhagoletis cerasi: medium polymorphic-highly informative markers.

PubMed

Augustinos, A A; Asimakopoulou, A K; Papadopoulos, N T; Bourtzis, K

2011-02-01

The European cherry fruit fly, Rhagoletis cerasi (Diptera: Tephritidae), is a major pest of cherries in Europe and parts of Asia. Despite its big economic significance, there is a lack of studies on the genetic structure of its natural populations. Knowledge about an insect pest on molecular, genetic and population levels facilitates the development of environmentally friendly control methods. In this study, we present the development of 13 microsatellite markers for R. cerasi, through cross-species amplification. These markers have been used for the genotyping of 130 individuals from five different sampling sites in Greece. Our results indicate that (i) cross-species amplification is a versatile and rapid tool for developing microsatellite markers in Rhagoletis spp., (ii) the microsatellite markers presented here constitute an important tool for population studies on this pest, and (iii) there is clear structuring of natural European cherry fly populations.

Genomic population structure of freshwater-resident and anadromous ide (Leuciscus idus) in north-western Europe.

PubMed

Skovrind, Mikkel; Olsen, Morten Tange; Vieira, Filipe Garrett; Pacheco, George; Carl, Henrik; Gilbert, M Thomas P; Møller, Peter Rask

2016-02-01

Climate change experts largely agree that future climate change and associated rises in oceanic water levels over the upcoming decades, will affect marine salinity levels. The subsequent effects on fish communities in estuarine ecosystems however, are less clear. One species that is likely to become increasingly affected by changes in salinity is the ide (Leuciscus idus). The ide is a stenohaline freshwater fish that primarily inhabits rivers, with frequent anadromous behavior when sea salinity does not exceed 15%. Unlike most other anadromous Baltic Sea fish species, the ide has yet to be subjected to large-scale stocking programs, and thus provides an excellent opportunity for studying the natural population structure across the current salinity gradient in the Danish Belts. To explore this, we used Genotyping-by-Sequencing to determine genomic population structure of both freshwater resident and anadromous ide populations in the western Baltic Sea region, and relate the results to the current salinity gradient and the demographic history of ide in the region. The sample sites separate into four clusters, with all anadromous populations in one cluster and the freshwater resident populations in the remaining three. Results demonstrate high level of differentiation between sites hosting freshwater resident populations, but little differentiation among anadromous populations. Thus ide exhibit the genomic population structure of both a typical freshwater species, and a typical anadromous species. In addition to providing a first insight into the population structure of north-western European ide, our data also (1) provide indications of a single illegal introduction by man; (2) suggest limited genetic effects of heavy pollution in the past; and (3) indicate possible historical anadromous behavior in a now isolated freshwater population.

Genome-wide genetic diversity, population structure and admixture analysis in African and Asian cattle breeds.

PubMed

Edea, Z; Bhuiyan, M S A; Dessie, T; Rothschild, M F; Dadi, H; Kim, K S

2015-02-01

Knowledge about genetic diversity and population structure is useful for designing effective strategies to improve the production, management and conservation of farm animal genetic resources. Here, we present a comprehensive genome-wide analysis of genetic diversity, population structure and admixture based on 244 animals sampled from 10 cattle populations in Asia and Africa and genotyped for 69,903 autosomal single-nucleotide polymorphisms (SNPs) mainly derived from the indicine breed. Principal component analysis, STRUCTURE and distance analysis from high-density SNP data clearly revealed that the largest genetic difference occurred between the two domestic lineages (taurine and indicine), whereas Ethiopian cattle populations represent a mosaic of the humped zebu and taurine. Estimation of the genetic influence of zebu and taurine revealed that Ethiopian cattle were characterized by considerable levels of introgression from South Asian zebu, whereas Bangladeshi populations shared very low taurine ancestry. The relationships among Ethiopian cattle populations reflect their history of origin and admixture rather than phenotype-based distinctions. The high within-individual genetic variability observed in Ethiopian cattle represents an untapped opportunity for adaptation to changing environments and for implementation of within-breed genetic improvement schemes. Our results provide a basis for future applications of genome-wide SNP data to exploit the unique genetic makeup of indigenous cattle breeds and to facilitate their improvement and conservation.

Origin, Migration Routes and Worldwide Population Genetic Structure of the Wheat Yellow Rust Pathogen Puccinia striiformis f.sp. tritici

PubMed Central

Ali, Sajid; Gladieux, Pierre; Leconte, Marc; Gautier, Angélique; Justesen, Annemarie F.; Hovmøller, Mogens S.; Enjalbert, Jérôme; de Vallavieille-Pope, Claude

2014-01-01

Analyses of large-scale population structure of pathogens enable the identification of migration patterns, diversity reservoirs or longevity of populations, the understanding of current evolutionary trajectories and the anticipation of future ones. This is particularly important for long-distance migrating fungal pathogens such as Puccinia striiformis f.sp. tritici (PST), capable of rapid spread to new regions and crop varieties. Although a range of recent PST invasions at continental scales are well documented, the worldwide population structure and the center of origin of the pathogen were still unknown. In this study, we used multilocus microsatellite genotyping to infer worldwide population structure of PST and the origin of new invasions based on 409 isolates representative of distribution of the fungus on six continents. Bayesian and multivariate clustering methods partitioned the set of multilocus genotypes into six distinct genetic groups associated with their geographical origin. Analyses of linkage disequilibrium and genotypic diversity indicated a strong regional heterogeneity in levels of recombination, with clear signatures of recombination in the Himalayan (Nepal and Pakistan) and near-Himalayan regions (China) and a predominant clonal population structure in other regions. The higher genotypic diversity, recombinant population structure and high sexual reproduction ability in the Himalayan and neighboring regions suggests this area as the putative center of origin of PST. We used clustering methods and approximate Bayesian computation (ABC) to compare different competing scenarios describing ancestral relationship among ancestral populations and more recently founded populations. Our analyses confirmed the Middle East-East Africa as the most likely source of newly spreading, high-temperature-adapted strains; Europe as the source of South American, North American and Australian populations; and Mediterranean-Central Asian populations as the origin of South African populations. Although most geographic populations are not markedly affected by recent dispersal events, this study emphasizes the influence of human activities on recent long-distance spread of the pathogen. PMID:24465211

Ancestry informative markers for distinguishing between Thai populations based on genome-wide association datasets

PubMed Central

Vongpaisarnsin, Kornkiat; Listman, Jennifer Beth; Malison, Robert T; Gelernter, Joel

2015-01-01

The main purpose of this work was to identify a set of AIMs that stratify the genetic structure and diversity of the Thai population from a high-throughput autosomal genome-wide association study. In this study, more than one million SNPs from the International HapMap database and the Thai depression genome-wide association study have been examined to identify ancestry informative markers (AIMs) that distinguish between Thai populations. An efficient strategy is proposed to identify and characterize such SNPs and to test high-resolution SNP data from international HapMap populations. The best AIMs are identified to stratify the population and to infer genetic ancestry structure. A total of 124 AIMs were clearly clustered geographically across the continent, whereas only 89 AIMs stratified the Thai population from East Asian populations. Finally, a set of 273 AIMs was able to distinguish northern from southern Thai subpopulations. These markers will be of particular value in identifying the ethnic origins in regions where matching by self-reports is unavailable or unreliable, which usually occurs in real forensic cases. PMID:25759192

Ancestry informative markers for distinguishing between Thai populations based on genome-wide association datasets.

PubMed

Vongpaisarnsin, Kornkiat; Listman, Jennifer Beth; Malison, Robert T; Gelernter, Joel

2015-07-01

The main purpose of this work was to identify a set of AIMs that stratify the genetic structure and diversity of the Thai population from a high-throughput autosomal genome-wide association study. In this study, more than one million SNPs from the international HapMap database and the Thai depression genome-wide association study have been examined to identify ancestry informative markers (AIMs) that distinguish between Thai populations. An efficient strategy is proposed to identify and characterize such SNPs and to test high-resolution SNP data from international HapMap populations. The best AIMs are identified to stratify the population and to infer genetic ancestry structure. A total of 124 AIMs were clearly clustered geographically across the continent, whereas only 89 AIMs stratified the Thai population from East Asian populations. Finally, a set of 273 AIMs was able to distinguish northern from southern Thai subpopulations. These markers will be of particular value in identifying the ethnic origins in regions where matching by self-reports is unavailable or unreliable, which usually occurs in real forensic cases. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Plague circulation and population genetics of the reservoir Rattus rattus: the influence of topographic relief on the distribution of the disease within the Madagascan focus.

PubMed

Brouat, Carine; Rahelinirina, Soanandrasana; Loiseau, Anne; Rahalison, Lila; Rajerison, Minoariso; Laffly, Dominique; Handschumacher, Pascal; Duplantier, Jean-Marc

2013-01-01

Landscape may affect the distribution of infectious diseases by influencing the population density and dispersal of hosts and vectors. Plague (Yersinia pestis infection) is a highly virulent, re-emerging disease, the ecology of which has been scarcely studied in Africa. Human seroprevalence data for the major plague focus of Madagascar suggest that plague spreads heterogeneously across the landscape as a function of the relief. Plague is primarily a disease of rodents. We therefore investigated the relationship between disease distribution and the population genetic structure of the black rat, Rattus rattus, the main reservoir of plague in Madagascar. We conducted a comparative study of plague seroprevalence and genetic structure (15 microsatellite markers) in rat populations from four geographic areas differing in topology, each covering about 150-200 km(2) within the Madagascan plague focus. The seroprevalence levels in the rat populations mimicked those previously reported for humans. As expected, rat populations clearly displayed a more marked genetic structure with increasing relief. However, the relationship between seroprevalence data and genetic structure differs between areas, suggesting that plague distribution is not related everywhere to the effective dispersal of rats. Genetic diversity estimates suggested that plague epizootics had only a weak impact on rat population sizes. In the highlands of Madagascar, plague dissemination cannot be accounted for solely by the effective dispersal of the reservoir. Human social activities may also be involved in spreading the disease in rat and human populations.

Genetic structuring and recent demographic history of red pandas (Ailurus fulgens) inferred from microsatellite and mitochondrial DNA.

PubMed

Hu, Yibo; Guo, Yu; Qi, Dunwu; Zhan, Xiangjiang; Wu, Hua; Bruford, Michael W; Wei, Fuwen

2011-07-01

Clarification of the genetic structure and population history of a species can shed light on the impacts of landscapes, historical climate change and contemporary human activities and thus enables evidence-based conservation decisions for endangered organisms. The red panda (Ailurus fulgens) is an endangered species distributing at the edge of the Qinghai-Tibetan Plateau and is currently subject to habitat loss, fragmentation and population decline, thus representing a good model to test the influences of the above-mentioned factors on a plateau edge species. We combined nine microsatellite loci and 551 bp of mitochondrial control region (mtDNA CR) to explore the genetic structure and demographic history of this species. A total of 123 individuals were sampled from 23 locations across five populations. High levels of genetic variation were identified for both mtDNA and microsatellites. Phylogeographic analyses indicated little geographic structure, suggesting historically wide gene flow. However, microsatellite-based Bayesian clustering clearly identified three groups (Qionglai-Liangshan, Xiaoxiangling and Gaoligong-Tibet). A significant isolation-by-distance pattern was detected only after removing Xiaoxiangling. For mtDNA data, there was no statistical support for a historical population expansion or contraction for the whole sample or any population except Xiaoxiangling where a signal of contraction was detected. However, Bayesian simulations of population history using microsatellite data did pinpoint population declines for Qionglai, Xiaoxiangling and Gaoligong, demonstrating significant influences of human activity on demography. The unique history of the Xiaoxiangling population plays a critical role in shaping the genetic structure of this species, and large-scale habitat loss and fragmentation is hampering gene flow among populations. The implications of our findings for the biogeography of the Qinghai-Tibetan Plateau, subspecies classification and conservation of red pandas are discussed. © 2011 Blackwell Publishing Ltd.

Possible ancestral structure in human populations.

PubMed

Plagnol, Vincent; Wall, Jeffrey D

2006-07-01

Determining the evolutionary relationships between fossil hominid groups such as Neanderthals and modern humans has been a question of enduring interest in human evolutionary genetics. Here we present a new method for addressing whether archaic human groups contributed to the modern gene pool (called ancient admixture), using the patterns of variation in contemporary human populations. Our method improves on previous work by explicitly accounting for recent population history before performing the analyses. Using sequence data from the Environmental Genome Project, we find strong evidence for ancient admixture in both a European and a West African population (p approximately 10(-7)), with contributions to the modern gene pool of at least 5%. While Neanderthals form an obvious archaic source population candidate in Europe, there is not yet a clear source population candidate in West Africa.

Long-distance dispersal and recolonization of a fire-destroyed niche by a mite-associated fungus.

PubMed

Aylward, Janneke; Dreyer, Léanne L; Steenkamp, Emma T; Wingfield, Michael J; Roets, Francois

2015-04-01

The Fynbos Biome in the Core Cape Subregion of South Africa is prone to recurrent fires that can clear vast areas of vegetation. Between periods of fire, ophiostomatoid fungi colonize the fruiting structures of serotinous Protea species through arthropod-mediated dispersal. Using microsatellite markers, this study considered the process whereby a Protea-associated ophiostomatoid fungus, Knoxdaviesia proteae, recolonizes a burnt area. The genetic diversity, composition and structure of fungal populations from young P. repens plants in a recently burnt area were compared to populations from the adjacent, unburnt Protea population. The only difference between K. proteae populations from the two areas was found in the number of private alleles, which was significantly higher in the unburnt population. The population structure, although weak, indicated that most K. proteae individuals from recently burnt areas originated from the unburnt population. However, individuals from unsampled source populations were also detected. This, together with the lack of isolation-by-distance across the landscape, suggested that long-distance dispersal is important for K. proteae to recolonize burnt areas. Similarly, the high level of gene flow and low differentiation observed between two distantly separated K. proteae populations also supported the existence of long-distance dispersal. The genetic cohesiveness of populations over long distances and the genetic diversity within populations could be attributed to frequent multiple fungal migration events mediated primarily by arthropods but, potentially, also by birds. Copyright © 2015 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

The microgeographical patterns of morphological and molecular variation of a mixed ploidy population in the species complex Actinidia chinensis.

PubMed

Liu, Yifei; Li, Dawei; Yan, Ling; Huang, Hongwen

2015-01-01

Polyploidy and hybridization are thought to have significant impacts on both the evolution and diversification of the genus Actinidia, but the structure and patterns of morphology and molecular diversity relating to ploidy variation of wild Actinidia plants remain much less understood. Here, we examine the distribution of morphological variation and ploidy levels along geographic and environmental variables of a large mixed-ploidy population of the A. chinensis species complex. We then characterize the extent of both genetic and epigenetic diversity and differentiation exhibited between individuals of different ploidy levels. Our results showed that while there are three ploidy levels in this population, hexaploids were constituted the majority (70.3%). Individuals with different ploidy levels were microgeographically structured in relation to elevation and extent of niche disturbance. The morphological characters examined revealed clear difference between diploids and hexaploids, however tetraploids exhibited intermediate forms. Both genetic and epigenetic diversity were high but the differentiation among cytotypes was weak, suggesting extensive gene flow and/or shared ancestral variation occurred in this population even across ploidy levels. Epigenetic variation was clearly correlated with changes in altitudes, a trend of continuous genetic variation and gradual increase of epigenomic heterogeneities of individuals was also observed. Our results show that complex interactions between the locally microgeographical environment, ploidy and gene flow impact A. chinensis genetic and epigenetic variation. We posit that an increase in ploidy does not broaden the species habitat range, but rather permits A. chinensis adaptation to specific niches.

Islands within an island: Population genetic structure of the endemic Sardinian newt, Euproctus platycephalus.

PubMed

Ball, Sarah E; Bovero, Stefano; Sotgiu, Giuseppe; Tessa, Giulia; Angelini, Claudio; Bielby, Jon; Durrant, Christopher; Favelli, Marco; Gazzaniga, Enrico; Garner, Trenton W J

2017-02-01

The identification of historic and contemporary barriers to dispersal is central to the conservation of endangered amphibians, but may be hindered by their complex life history and elusive nature. The complementary information generated by mitochondrial (mtDNA) and microsatellite markers generates a valuable tool in elucidating population structure and the impact of habitat fragmentation. We applied this approach to the study of an endangered montane newt, Euproctus platycephalus . Endemic to the Mediterranean island of Sardinia, it is threatened by anthropogenic activity, disease, and climate change. We have demonstrated a clear hierarchy of structure across genetically divergent and spatially distinct subpopulations. Divergence between three main mountain regions dominated genetic partitioning with both markers. Mitochondrial phylogeography revealed a deep division dating to ca. 1 million years ago (Mya), isolating the northern region, and further differentiation between the central and southern regions ca. 0.5 Mya, suggesting an association with Pleistocene severe glacial oscillations. Our findings are consistent with a model of southward range expansion during glacial periods, with postglacial range retraction to montane habitat and subsequent genetic isolation. Microsatellite markers revealed further strong population structure, demonstrating significant divergence within the central region, and partial differentiation within the south. The northern population showed reduced genetic diversity. Discordance between mitochondrial and microsatellite markers at this scale indicated a further complexity of population structure, in keeping with male-biased dispersal and female philopatry. Our study underscores the need to elucidate cryptic population structure in the ecology and conservation strategies for endangered island-restricted amphibians, especially in the context of disease and climate change.

Psychometric properties of the Compulsive Exercise Test in an adolescent eating disorder population.

PubMed

Formby, Pam; Watson, Hunna J; Hilyard, Anna; Martin, Kate; Egan, Sarah J

2014-12-01

The objective of this study was to evaluate the factor structure, validity, and reliability of the Compulsive Exercise Test (CET) in an adolescent clinical eating disorder population. The data source was the Helping to Outline Paediatric Eating Disorders (HOPE) Project, a prospective ongoing registry study comprising consecutive pediatric tertiary eating disorder referrals. Adolescents (N=104; 12-17years) with eating disorders completed the CET and other measures. Factor structure, convergent validity, and internal consistency were evaluated. Despite failing to identify a factor structure, the study provided clear evidence of the multidimensionality of the measure. The total score correlated significantly with measures of eating pathology, perfectionism, and frequency of exercise for shape and weight control (r=0.32-0.70, ps<0.05). More research into the multidimensional nature of compulsive exercise in clinical populations is needed. Further, research into compulsive exercise offers promise as an addition to existing cognitive behavioral models and treatments for eating disorders. Copyright © 2014 Elsevier Ltd. All rights reserved.

Genetic Diversity and Population Structure of the Pelagic Thresher Shark (Alopias pelagicus) in the Pacific Ocean: Evidence for Two Evolutionarily Significant Units

PubMed Central

Cardeñosa, Diego; Hyde, John; Caballero, Susana

2014-01-01

There has been an increasing concern about shark overexploitation in the last decade, especially for open ocean shark species, where there is a paucity of data about their life histories and population dynamics. Little is known regarding the population structure of the pelagic thresher shark, Alopias pelagicus. Though an earlier study using mtDNA control region data, showed evidence for differences between eastern and western Pacific populations, the study was hampered by low sample size and sparse geographic coverage, particularly a lack of samples from the central Pacific. Here, we present the population structure of Alopias pelagicus analyzing 351 samples from six different locations across the Pacific Ocean. Using data from mitochondrial DNA COI sequences and seven microsatellite loci we found evidence of strong population differentiation between western and eastern Pacific populations and evidence for reciprocally monophyly for organelle haplotypes and significant divergence of allele frequencies at nuclear loci, suggesting the existence of two Evolutionarily Significant Units (ESU) in the Pacific Ocean. Interestingly, the population in Hawaii appears to be composed of both ESUs in what seems to be clear sympatry with reproductive isolation. These results may indicate the existence of a new cryptic species in the Pacific Ocean. The presence of these distinct ESUs highlights the need for revised management plans for this highly exploited shark throughout its range. PMID:25337814

Genetic diversity and population structure of the pelagic thresher shark (Alopias pelagicus) in the Pacific Ocean: evidence for two evolutionarily significant units.

PubMed

Cardeñosa, Diego; Hyde, John; Caballero, Susana

2014-01-01

There has been an increasing concern about shark overexploitation in the last decade, especially for open ocean shark species, where there is a paucity of data about their life histories and population dynamics. Little is known regarding the population structure of the pelagic thresher shark, Alopias pelagicus. Though an earlier study using mtDNA control region data, showed evidence for differences between eastern and western Pacific populations, the study was hampered by low sample size and sparse geographic coverage, particularly a lack of samples from the central Pacific. Here, we present the population structure of Alopias pelagicus analyzing 351 samples from six different locations across the Pacific Ocean. Using data from mitochondrial DNA COI sequences and seven microsatellite loci we found evidence of strong population differentiation between western and eastern Pacific populations and evidence for reciprocally monophyly for organelle haplotypes and significant divergence of allele frequencies at nuclear loci, suggesting the existence of two Evolutionarily Significant Units (ESU) in the Pacific Ocean. Interestingly, the population in Hawaii appears to be composed of both ESUs in what seems to be clear sympatry with reproductive isolation. These results may indicate the existence of a new cryptic species in the Pacific Ocean. The presence of these distinct ESUs highlights the need for revised management plans for this highly exploited shark throughout its range.

Supporting Students with Incarcerated Parents in Schools: A Group Intervention

ERIC Educational Resources Information Center

Lopez, Caroline; Bhat, Christine Suniti

2007-01-01

Although it is clear that parental incarceration has adverse effects on children, there is limited information about effective services for helping this population. With an increase in the number of parents of minor children in jail, there is a need for schools to assist affected students in a structured and comprehensive manner. The purpose of…

Using Snorkeling to Quantify Fish Assemblage Structure in Arkansas Streams

Treesearch

David G. Lonzarich; Mary E. Lonzarich; Melvin L. Warren

2004-01-01

Abstract - As a technique for surveying fish populations in low diversity, clear streams of the Pacific Northwest, snorkeling is a commonly used alternative to electrofishing. While the method is becoming more widely used in the high diversity streams of eastern North America, its efficacy as a tool for surveying fish assemblages in these streams is...

Heterogeneous road networks have no apparent effect on the genetic structure of small mammal populations.

PubMed

Grilo, Clara; Del Cerro, Irene; Centeno-Cuadros, Alejandro; Ramiro, Victor; Román, Jacinto; Molina-Vacas, Guillem; Fernández-Aguilar, Xavier; Rodríguez, Juan; Porto-Peter, Flávia; Fonseca, Carlos; Revilla, Eloy; Godoy, José A

2016-09-15

Roads are widely recognized to represent a barrier to individual movements and, conversely, verges can act as potential corridors for the dispersal of many small mammals. Both barrier and corridor effects should generate a clear spatial pattern in genetic structure. Nevertheless, the effect of roads on the genetic structure of small mammal populations still remains unclear. In this study, we examine the barrier effect that different road types (4-lane highway, 2-lane roads and single-lane unpaved roads) may have on the population genetic structure of three species differing in relevant life history traits: southern water vole Arvicola sapidus, the Mediterranean pine vole Microtus duodecimcostatus and the Algerian mouse Mus spretus. We also examine the corridor effect of highway verges on the Mediterranean pine vole and the Algerian mouse. We analysed the population structure through pairwise estimates of FST among subpopulations bisected by roads, identified genetic clusters through Bayesian assignment approaches, and used simple and partial Mantel tests to evaluate the relative barrier or corridor effect of roads. No strong evidences were found for an effect of roads on population structure of these three species. The barrier effect of roads seems to be site-specific and no corridor effect of verges was found for the pine vole and Algerian mouse populations. The lack of consistent results among species and for each road type lead us to believe that the ability of individual dispersers to use those crossing structures or the habitat quality in the highway verges may have a relatively higher influence on gene flow among populations than the presence of crossing structures per se. Further research should include microhabitat analysis and the estimates of species abundance to understand the mechanisms that underlie the genetic structure observed at some sites. Copyright © 2016 Elsevier B.V. All rights reserved.

Understanding protein evolution: from protein physics to Darwinian selection.

PubMed

Zeldovich, Konstantin B; Shakhnovich, Eugene I

2008-01-01

Efforts in whole-genome sequencing and structural proteomics start to provide a global view of the protein universe, the set of existing protein structures and sequences. However, approaches based on the selection of individual sequences have not been entirely successful at the quantitative description of the distribution of structures and sequences in the protein universe because evolutionary pressure acts on the entire organism, rather than on a particular molecule. In parallel to this line of study, studies in population genetics and phenomenological molecular evolution established a mathematical framework to describe the changes in genome sequences in populations of organisms over time. Here, we review both microscopic (physics-based) and macroscopic (organism-level) models of protein-sequence evolution and demonstrate that bridging the two scales provides the most complete description of the protein universe starting from clearly defined, testable, and physiologically relevant assumptions.

Genetic diversity and structure of managed and semi-natural populations of cocoa (Theobroma cacao) in the Huallaga and Ucayali Valleys of Peru.

PubMed

Zhang, Dapeng; Arevalo-Gardini, Enrique; Mischke, Sue; Zúñiga-Cernades, Luis; Barreto-Chavez, Alejandro; Del Aguila, Jorge Adriazola

2006-09-01

Cocoa (Theobroma cacao) is indigenous to the Amazon region of South America, and it is well known that the Peruvian Amazon harbours a large number of diverse cocoa populations. A small fraction of the diversity has been collected and maintained as an ex-situ germplasm repository in Peru. However, incorrect labelling of accessions and lack of information on genetic diversity have hindered efficient conservation and use of this germplasm. This study targeted assessment of genetic diversity and population structure in a managed and a semi-natural population. Using a capillary electrophoresis genotyping system, 105 cocoa accessions collected from the Huallaga and Ucayali valleys of Peru were fingerprinted. Based on 15 loci SSR profiles, genetic identity was examined for each accession and duplicates identified, population structure assessed and genetic diversity analysed in these two populations. Ten synonymous mislabelled groups were identified among the 105 accessions. The germplasm group in the Huallaga valley was clearly separated from the group in Ucayali valley by the Bayesian assignment test. The Huallaga group has lower genetic diversity, both in terms of allelic richness and of gene diversity, than the Ucayali group. Analysis of molecular variance suggested genetic substructure in the Ucayali group. Significant spatial correlation between genetic distance and geographical distances was detected in the Ucayali group by Mantel tests. These results substantiate the hypothesis that the Peruvian Amazon hosts a high level of cocoa genetic diversity, and the diversity has a spatial structure. The introduction of exotic seed populations into the Peruvian Amazon is changing the cocoa germplasm spectrum in this region. The spatial structure of cocoa diversity recorded here highlights the need for additional collecting and conservation measures for natural and semi-natural cocoa populations.

In situ population structure and ex situ representation of the endangered Amur tiger.

PubMed

Henry, P; Miquelle, D; Sugimoto, T; McCullough, D R; Caccone, A; Russello, M A

2009-08-01

The Amur tiger (Panthera tigris altaica) is a critically endangered felid that suffered a severe demographic contraction in the 1940s. In this study, we sampled 95 individuals collected throughout their native range to investigate questions relative to population genetic structure and demographic history. Additionally, we sampled targeted individuals from the North American ex situ population to assess the genetic representation found in captivity. Population genetic and Bayesian structure analyses clearly identified two populations separated by a development corridor in Russia. Despite their well-documented 20th century decline, we failed to find evidence of a recent population bottleneck, although genetic signatures of a historical contraction were detected. This disparity in signal may be due to several reasons, including historical paucity in population genetic variation associated with postglacial colonization and potential gene flow from a now extirpated Chinese population. Despite conflicting signatures of a bottleneck, our estimates of effective population size (N(e) = 27-35) and N(e)/N ratio (0.07-0.054) were substantially lower than the only other values reported for a wild tiger population. Lastly, the extent and distribution of genetic variation in captive and wild populations were similar, yet gene variants persisted ex situ that were lost in situ. Overall, our results indicate the need to secure ecological connectivity between the two Russian populations to minimize loss of genetic diversity and overall susceptibility to stochastic events, and support a previous study suggesting that the captive population may be a reservoir of gene variants lost in situ.

Age and condition of juvenile catostomids in Clear Lake Reservoir, California

USGS Publications Warehouse

Burdick, Summer M.; Rasmussen, Josh

2013-01-01

Although infrequent recruitment of new individuals into the adult spawning populations of Lost River suckers (Deltistes luxatus) and shortnose suckers (Chasmistes brevirostris) limits recovery of these species in Upper Klamath Lake, it is not clear that populations are recruitment limited in Clear Lake Reservoir (hereafter Clear Lake). Specifically, some evidence indicates that shortnose suckers may regularly recruit to the adult spawning population in Clear Lake. Therefore, a study of early life history patterns and recruitment dynamics in Clear Lake may lead to a better understanding of what is limiting recovery of suckers in both lakes. Adult suckers in Clear Lake migrate up Willow Creek and its tributaries to spawn in some years, but low flow in Willow Creek may inhibit spawning migrations in other years. It is unclear whether spawning is successful, larvae survive, or how frequently juveniles persist to adulthood. Environmental variables associated with successful spawning or young-of-year survival have not been identified, and early life history for these populations is poorly understood. The U.S. Geological Survey, in cooperation with the U.S. Fish and Wildlife Service, initiated a study in 2011 to better understand juvenile sucker life history in Clear Lake, and to identify constraints in the early life history that may limit recruitment to the adult spawning populations. The relative weights of shortnose suckers from Clear Lake and Upper Klamath Lake were compared to examine differences in condition. However, it is unclear whether the disparity in relative weights between the populations reflects differences in condition, phenotype, or both. Approximately 80 percent of juvenile suckers in Clear Lake are shortnose suckers with some morphologic features similar to Klamath largescale suckers (Catostomus snyderi), whereas juvenile suckers in Upper Klamath Lake can be clearly classified as either shortnose or Lost River suckers. The presence of juvenile suckers age-3 and older indicate that production, larval survival, and juvenile survival are at least periodically sufficient to lead to recruitment into the adult population of shortnose suckers in Clear Lake.

The factor structure of the illness attitude scales in a German population.

PubMed

Weck, Florian; Bleichhardt, Gaby; Hiller, Wolfgang

2009-01-01

The illness attitudes scales (IAS) were developed to identify different dimensions of hypochondrical attitudes, fears, beliefs, and abnormal illness behavior (Kellner 1986). Although there are several studies which focus on the scale structure of the IAS, the factor structure has not yet been made quite clear. Therefore, the aim of this study was to investigate the factor structure of the IAS on a large representative sample. Participants (N = 1,575) comparable with the general German population regarding sex, age, and education level completed the IAS. For the data analyses, a principal components analyses with subsequent oblique rotations was used. The minimum average partial method suggested a three-factor solution. The three factors were named (1) health anxiety, (2) health behavior, and (3) health habits. Internal consistency (Cronbach's alpha) for the three scales were (1) alpha = 0.88, (2) alpha = 0.75, and (3) alpha = 0.56. The results support previous findings, namely that the IAS factor structure appears to be less complex than originally suggested by the author. For a sample of the general German population, a three-factor solution fit best. Further items should be added to improve the internal consistency, especially for the third scale (health habits).

Plague Circulation and Population Genetics of the Reservoir Rattus rattus: The Influence of Topographic Relief on the Distribution of the Disease within the Madagascan Focus

PubMed Central

Brouat, Carine; Rahelinirina, Soanandrasana; Loiseau, Anne; Rahalison, Lila; Rajerison, Minoariso; Laffly, Dominique; Handschumacher, Pascal; Duplantier, Jean-Marc

2013-01-01

Background Landscape may affect the distribution of infectious diseases by influencing the population density and dispersal of hosts and vectors. Plague (Yersinia pestis infection) is a highly virulent, re-emerging disease, the ecology of which has been scarcely studied in Africa. Human seroprevalence data for the major plague focus of Madagascar suggest that plague spreads heterogeneously across the landscape as a function of the relief. Plague is primarily a disease of rodents. We therefore investigated the relationship between disease distribution and the population genetic structure of the black rat, Rattus rattus, the main reservoir of plague in Madagascar. Methodology/Principal Findings We conducted a comparative study of plague seroprevalence and genetic structure (15 microsatellite markers) in rat populations from four geographic areas differing in topology, each covering about 150–200 km2 within the Madagascan plague focus. The seroprevalence levels in the rat populations mimicked those previously reported for humans. As expected, rat populations clearly displayed a more marked genetic structure with increasing relief. However, the relationship between seroprevalence data and genetic structure differs between areas, suggesting that plague distribution is not related everywhere to the effective dispersal of rats. Conclusions/Significance Genetic diversity estimates suggested that plague epizootics had only a weak impact on rat population sizes. In the highlands of Madagascar, plague dissemination cannot be accounted for solely by the effective dispersal of the reservoir. Human social activities may also be involved in spreading the disease in rat and human populations. PMID:23755317

Comparing two forms of a childhood perspective-taking measure using CFA and IRT.

PubMed

Carey, Jasmine M; Cassels, Tracy G

2013-09-01

Deficits in perspective-taking ability have been linked to social problems associated with disorders such as autism spectrum disorders (ASD) and conduct disorder. Even subtle deficits in perspective-taking are related to social adjustment and moral development. A common measure of perspective-taking abilities in children is the "Reading the Mind in the Eyes Task" ("Eyes task"; Baron-Cohen, Wheelwright, Spong, Scahill, & Lawson, 2001). The Eyes task was primarily developed for use in identifying individuals with ASDs, while its function with nonclinical populations has not been clearly addressed. Additionally, it is unknown whether the Eyes task can be used to measure specific deficits or abilities in the cognitive or emotional components of perspective-taking. In this article we assessed the structure and function of the Eyes task and an open ended or generative format of the same task (Generative Eyes Task; GET) found to measure emotional perspective-taking specifically. Confirmatory factor analyses found the traditional Eyes task to have the assumed single factor structure, while the GET has a clear 2-factor structure corresponding to emotionally valenced or neutral items. The Eyes task and the GET were also compared using item response theory. The Eyes task provided the most measurement accuracy at 2 standard deviations below the mean making it most accurate for populations with severe deficits, while the GET was most accurate at the mean level of perspective-taking. Based on these analyses, we conclude that the GET is more appropriate for use in nonclinical populations and when emotional perspective-taking abilities are of interest.

Investigating Concordance among Genetic Data, Subspecies Circumscriptions and Hostplant Use in the Nymphalid Butterfly Polygonia faunus

PubMed Central

Janz, Niklas; Leski, Michael; Slove, Jessica; Warren, Andrew; Nylin, Sören

2012-01-01

Subspecies are commonly used taxonomic units to formally describe intraspecific geographic variation in morphological traits. However, the concept of subspecies is not clearly defined, and there is little agreement about what they represent in terms of evolutionary units, and whether they can be used as reliably useful units in conservation, evolutionary theory and taxonomy. We here investigate whether the morphologically well-characterized subspecies in the North American butterfly Polygonia faunus are supported by genetic data from mitochondrial sequences and eight microsatellite loci. We also investigate the phylogeographic structure of P. faunus and test whether similarities in host-plant use among populations are related to genetic similarity. Neither the nuclear nor the mitochondrial data corroborated subspecies groupings. We found three well defined genetic clusters corresponding to California, Arizona and (New Mexico+Colorado). There was little structuring among the remaining populations, probably due to gene flow across populations. We found no support for the hypothesis that similarities in host use are related to genetic proximity. The results indicate that the species underwent a recent rapid expansion, probably from two glacial refugia in western North America. The mitochondrial haplotype network indicates at least two independent expansion phases into eastern North America. Our results clearly demonstrate that subspecies in P. faunus do not conform to the structuring of genetic variation. More studies on insects and other invertebrates are needed to better understand the scope of this phenomenon. The results of this study will be crucial in designing further experiments to understand the evolution of hostplant utilization in this species. PMID:22844425

Determinants of childhood obesity: need for a trans-sectoral convergent approach.

PubMed

Kiranmala, Naorem; Das, Manoja K; Arora, Narendra K

2013-03-01

The emerging burden of non communicable diseases is likely to erode the "Demographic-Dividend" of India and compromise the national growth and development. Increasing rates of childhood obesity globally and in India is a cause for serious public health concern. It is becoming increasingly apparent that obesity is result of complex interplay between multiple genes, environmental factors and human behavior. Clear comprehension of this interaction and pathway is still not clear, making the prevention and management of obesity especially challenging. Globalization and rapid economic growth has led to dramatic changes in the life style of the population including food intake, physical activity, market, environmental factors and social structures. A growing economy, urbanization and motorized transport have increased physical inactivity. A systematic multi-sectoral approach with population health as the center of discourse and attention is the only key to tackle this problem.

Matching genetics with oceanography: directional gene flow in a Mediterranean fish species.

PubMed

Schunter, C; Carreras-Carbonell, J; Macpherson, E; Tintoré, J; Vidal-Vijande, E; Pascual, A; Guidetti, P; Pascual, M

2011-12-01

Genetic connectivity and geographic fragmentation are two opposing mechanisms determining the population structure of species. While the first homogenizes the genetic background across populations the second one allows their differentiation. Therefore, knowledge of processes affecting dispersal of marine organisms is crucial to understand their genetic distribution patterns and for the effective management of their populations. In this study, we use genetic analyses of eleven microsatellites in combination with oceanographic satellite and dispersal simulation data to determine distribution patterns for Serranus cabrilla, a ubiquitous demersal broadcast spawner, in the Mediterranean Sea. Pairwise population F(ST) values ranged between -0.003 and 0.135. Two genetically distinct clusters were identified, with a clear division located between the oceanographic discontinuities at the Ibiza Channel (IC) and the Almeria-Oran Front (AOF), revealing an admixed population in between. The Balearic Front (BF) also appeared to dictate population structure. Directional gene flow on the Spanish coast was observed as S. cabrilla dispersed from west to east over the AOF, from north to south on the IC and from south of the IC towards the Balearic Islands. Correlations between genetic and oceanographic data were highly significant. Seasonal changes in current patterns and the relationship between ocean circulation patterns and spawning season may also play an important role in population structure around oceanographic fronts. © 2011 Blackwell Publishing Ltd.

Fine-scale population structure in Atlantic salmon from Maine's Penobscot River drainage

USGS Publications Warehouse

Spidle, A.P.; Bane, Schill W.; Lubinski, B.A.; King, T.L.

2001-01-01

We report a survey of micro satellite DNA variation in Atlantic salmon from the unimpounded lower reaches of Maine's Penobscot River. Our analysis indicates that Atlantic salmon in the Penobscot River are distinct from other populations that have little or no history of human-mediated repopulation, including two of its tributaries, Cove Brook and Kenduskeag Stream, another Maine river, the Ducktrap, and Canada's Miramichi and Gander rivers. Significant heterogeneity was detected in allele frequency among all three subpopulations sampled in the Penobscot drainage. The high resolution of the 12-locus suite was quantified using maximum likelihood assignment tests, which correctly identified the source of 90.4-96.1% of individuals from within the Penobscot drainage. Current populations are clearly isolated from each other, however we are unable to determine from the present data whether the populations in Cove Brook and Kenduskeag Stream are recently diverged from populations stocked into the Penobscot River over the last century, or are aboriginal in origin. The degree of population structure identified in the Penobscot drainage is noteworthy in light of its lengthy history of systematic restocking, the geographic proximity of the subpopulations, and the extent of the differentiation. Similar population structure on this extremely limited geographic scale could exist among Atlantic salmon runs elsewhere in Maine and throughout the species' range and should be taken into account for future management decisions.

Evaluating the genetic impact of South and Southeast Asia on the peopling of Bangladesh.

PubMed

Sultana, Gazi Nurun Nahar; Sharif, Mohd Istiaq; Asaduzzaman, Md; Chaubey, Gyaneshwer

2015-11-01

Despite rapidly growing understandings and dependency on single nucleotide polymorphisms (SNPs), highly variable autosomal short tandem repeats (STRs) are still regarded as the most established method to differentiate individuals at forensic level. Here with large number of various ethnic groups we undertook this study to reveal the genetic structure of the most densely populated part of South Asia i.e. the Bangladesh. The purpose of this work was to estimate population parameters based on the allele frequencies obtained for 15 polymorphic autosomal STR loci investigated in caste and tribal populations from Bangladesh (n=706). We compared the results in a broader context by merging 24 different populations of Asia to pertain their affinity. Various statistical analyses suggested a clear cut demarcation of tribal and non-tribal in Bangladesh. Moreover, beside the phylogenetic structure of the studied populations, it is found that the mean heterozygosity value was highest among the populations of Bangladesh, likely because of gene flow from different directions. However, Tonchangya, Adi and Khumi showed sign of genetic isolation and reduced diversity, possibly as a result of genetic drift and/or strong founder effects working on small endogamous populations. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Genetic Diversity and Population Structure of Ethiopian Sheep Populations Revealed by High-Density SNP Markers

PubMed Central

Edea, Zewdu; Dessie, Tadelle; Dadi, Hailu; Do, Kyoung-Tag; Kim, Kwan-Suk

2017-01-01

Sheep in Ethiopia are adapted to a wide range of environments, including extreme habitats. Elucidating their genetic diversity is critical for improving breeding strategies and mapping quantitative trait loci associated with productivity. To this end, the present study investigated the genetic diversity and population structure of five Ethiopian sheep populations exhibiting distinct phenotypes and sampled from distinct production environments, including arid lowlands and highlands. To investigate the genetic relationships in greater detail and infer population structure of Ethiopian sheep breeds at the continental and global levels, we analyzed genotypic data of selected sheep breeds from the Ovine SNP50K HapMap dataset. All Ethiopian sheep samples were genotyped with Ovine Infinium HD SNP BeadChip (600K). Mean genetic diversity ranged from 0.29 in Arsi-Bale to 0.32 in Menz sheep, while estimates of genetic differentiation among populations ranged from 0.02 to 0.07, indicating low to moderate differentiation. An analysis of molecular variance revealed that 94.62 and 5.38% of the genetic variation was attributable to differences within and among populations, respectively. Our population structure analysis revealed clustering of five Ethiopian sheep populations according to tail phenotype and geographic origin—i.e., short fat-tailed (very cool high-altitude), long fat-tailed (mid to high-altitude), and fat-rumped (arid low-altitude), with clear evidence of admixture between long fat-tailed populations. North African sheep breeds showed higher levels of within-breed diversity, but were less differentiated than breeds from Eastern and Southern Africa. When African breeds were grouped according to geographic origin (North, South, and East), statistically significant differences were detected among groups (regions). A comparison of population structure between Ethiopian and global sheep breeds showed that fat-tailed breeds from Eastern and Southern Africa clustered together, suggesting that these breeds were introduced to the African continent via the Horn and migrated further south. PMID:29312441

Short-range phenotypic divergence among genetically distinct parapatric populations of an Australian funnel-web spider.

PubMed

Wong, Mark K L; Woodman, James D; Rowell, David M

2017-07-01

Speciation involves divergence at genetic and phenotypic levels. Where substantial genetic differentiation exists among populations, examining variation in multiple phenotypic characters may elucidate the mechanisms by which divergence and speciation unfold. Previous work on the Australian funnel-web spider Atrax sutherlandi Gray (2010; Records of the Australian Museum 62 , 285-392; Mygalomorphae: Hexathelidae: Atracinae) has revealed a marked genetic structure along a 110-kilometer transect, with six genetically distinct, parapatric populations attributable to past glacial cycles. In the present study, we explore variation in three classes of phenotypic characters (metabolic rate, water loss, and morphological traits) within the context of this phylogeographic structuring. Variation in metabolic and water loss rates shows no detectable association with genetic structure; the little variation observed in these rates may be due to the spiders' behavioral adaptations (i.e., burrowing), which buffer the effects of climatic gradients across the landscape. However, of 17 morphological traits measured, 10 show significant variation among genetic populations, in a disjunct manner that is clearly not latitudinal. Moreover, patterns of variation observed for morphological traits serving different organismic functions (e.g., prey capture, burrowing, and locomotion) are dissimilar. In contrast, a previous study of an ecologically similar sympatric spider with little genetic structure indicated a strong latitudinal response in 10 traits over the same range. The congruence of morphological variation with deep phylogeographic structure in Tallaganda's A. sutherlandi populations, as well as the inconsistent patterns of variation across separate functional traits, suggest that the spiders are likely in early stages of speciation, with parapatric populations independently responding to local selective forces.

Multi-Genetic Marker Approach and Spatio-Temporal Analysis Suggest There Is a Single Panmictic Population of Swordfish Xiphias gladius in the Indian Ocean

PubMed Central

Muths, Delphine; Le Couls, Sarah; Evano, Hugues; Grewe, Peter; Bourjea, Jerome

2013-01-01

Genetic population structure of swordfish Xiphias gladius was examined based on 2231 individual samples, collected mainly between 2009 and 2010, among three major sampling areas within the Indian Ocean (IO; twelve distinct sites), Atlantic (two sites) and Pacific (one site) Oceans using analysis of nineteen microsatellite loci (n = 2146) and mitochondrial ND2 sequences (n = 2001) data. Sample collection was stratified in time and space in order to investigate the stability of the genetic structure observed with a special focus on the South West Indian Ocean. Significant AMOVA variance was observed for both markers indicating genetic population subdivision was present between oceans. Overall value of F-statistics for ND2 sequences confirmed that Atlantic and Indian Oceans swordfish represent two distinct genetic stocks. Indo-Pacific differentiation was also significant but lower than that observed between Atlantic and Indian Oceans. However, microsatellite F-statistics failed to reveal structure even at the inter-oceanic scale, indicating that resolving power of our microsatellite loci was insufficient for detecting population subdivision. At the scale of the Indian Ocean, results obtained from both markers are consistent with swordfish belonging to a single unique panmictic population. Analyses partitioned by sampling area, season, or sex also failed to identify any clear structure within this ocean. Such large spatial and temporal homogeneity of genetic structure, observed for such a large highly mobile pelagic species, suggests as satisfactory to consider swordfish as a single panmictic population in the Indian Ocean. PMID:23717447

Working Memory Structure in 10- and 15-Year Old Children with Mild to Borderline Intellectual, Disabilities

ERIC Educational Resources Information Center

van der Molen, Mariet J.

2010-01-01

The validity of Baddeley's working memory model within the typically developing population, was tested. However, it is not clear if this model also holds in children and adolescents with mild to, borderline intellectual disabilities (ID; IQ score 55-85). The main purpose of this study was therefore, to explore the model's validity in this…

Conserving and managing the trees of the future: genetic resources for Pacific Northwest forests.

Treesearch

Sally Duncan

2003-01-01

Genetic resource management has historically called for altering the genetic structure of plant populations through selection for traits of interest such as rapid growth. Although this is still a principal component of tree breeding programs in the Pacific Northwest, managing genetic resources now also brings a clear focus on retaining a broad diversity within and...

Bipartite graphs as models of population structures in evolutionary multiplayer games.

PubMed

Peña, Jorge; Rochat, Yannick

2012-01-01

By combining evolutionary game theory and graph theory, "games on graphs" study the evolutionary dynamics of frequency-dependent selection in population structures modeled as geographical or social networks. Networks are usually represented by means of unipartite graphs, and social interactions by two-person games such as the famous prisoner's dilemma. Unipartite graphs have also been used for modeling interactions going beyond pairwise interactions. In this paper, we argue that bipartite graphs are a better alternative to unipartite graphs for describing population structures in evolutionary multiplayer games. To illustrate this point, we make use of bipartite graphs to investigate, by means of computer simulations, the evolution of cooperation under the conventional and the distributed N-person prisoner's dilemma. We show that several implicit assumptions arising from the standard approach based on unipartite graphs (such as the definition of replacement neighborhoods, the intertwining of individual and group diversity, and the large overlap of interaction neighborhoods) can have a large impact on the resulting evolutionary dynamics. Our work provides a clear example of the importance of construction procedures in games on graphs, of the suitability of bigraphs and hypergraphs for computational modeling, and of the importance of concepts from social network analysis such as centrality, centralization and bipartite clustering for the understanding of dynamical processes occurring on networked population structures.

Contrasts in genetic structure and historical demography of marine and riverine populations of Atherina at similar geographical scales

NASA Astrophysics Data System (ADS)

Francisco, Sara M.; Cabral, Henrique; Vieira, Maria Natividade; Almada, Vítor C.

2006-09-01

In this paper, we compare the genetic structure and the historical demography of two populations of the sand smelt Atherina boyeri from the rivers Tagus and Mondego (Portugal) with two groups of samples of the closely related marine Atherina presbyter collected on the shore at comparable latitudes. A. presbyter is a pelagic marine inshore fish, while A. boyeri is typically found in coastal lagoons, estuaries and freshwaters bodies. Analysis of mtDNA control region sequences showed that the marine A. presbyter did not display signs of genetic differentiation between sites some hundreds of kilometers apart. On the contrary, A. boyeri showed clear differences between populations. The populations of A. boyeri showed a much lower genetic diversity and younger coalescence times when compared with A. presbyter. We suggest that these differences reflect the interplay between differences in ecology between the two species and the historical impact of the glaciations. While A. presbyter likely moved to the south evading the cold periods, A. boyeri probably went extinct and its populations in Western Europe are recent recolonizations from western Mediterranean refugia.

Impact of Human Management on the Genetic Variation of Wild Pepper, Capsicum annuum var. glabriusculum

PubMed Central

González-Jara, Pablo; Moreno-Letelier, Alejandra; Fraile, Aurora; Piñero, Daniel; García-Arenal, Fernando

2011-01-01

Management of wild peppers in Mexico has occurred for a long time without clear phenotypic signs of domestication. However, pre-domestication management could have implications for the population's genetic richness. To test this hypothesis we analysed 27 wild (W), let standing (LS) and cultivated (C) populations, plus 7 samples from local markets (LM), with nine polymorphic microsatellite markers. Two hundred and fifty two alleles were identified, averaging 28 per locus. Allele number was higher in W, and 15 and 40% less in LS and C populations, respectively. Genetic variation had a significant population structure. In W populations, structure was associated with ecological and geographic areas according to isolation by distance. When LM and C populations where included in the analysis, differentiation was no longer apparent. Most LM were related to distant populations from Sierra Madre Oriental, which represents their probable origin. Historical demography shows a recent decline in all W populations. Thus, pre-domestication human management is associated with a significant reduction of genetic diversity and with a loss of differentiation suggesting movement among regions by man. Measures to conserve wild and managed populations should be implemented to maintain the source and the architecture of genetic variation in this important crop relative. PMID:22163053

Identifying currents in the gene pool for bacterial populations using an integrative approach.

PubMed

Tang, Jing; Hanage, William P; Fraser, Christophe; Corander, Jukka

2009-08-01

The evolution of bacterial populations has recently become considerably better understood due to large-scale sequencing of population samples. It has become clear that DNA sequences from a multitude of genes, as well as a broad sample coverage of a target population, are needed to obtain a relatively unbiased view of its genetic structure and the patterns of ancestry connected to the strains. However, the traditional statistical methods for evolutionary inference, such as phylogenetic analysis, are associated with several difficulties under such an extensive sampling scenario, in particular when a considerable amount of recombination is anticipated to have taken place. To meet the needs of large-scale analyses of population structure for bacteria, we introduce here several statistical tools for the detection and representation of recombination between populations. Also, we introduce a model-based description of the shape of a population in sequence space, in terms of its molecular variability and affinity towards other populations. Extensive real data from the genus Neisseria are utilized to demonstrate the potential of an approach where these population genetic tools are combined with an phylogenetic analysis. The statistical tools introduced here are freely available in BAPS 5.2 software, which can be downloaded from http://web.abo.fi/fak/mnf/mate/jc/software/baps.html.

Ethnicity and Population Structure in Personal Naming Networks

PubMed Central

Mateos, Pablo; Longley, Paul A.; O'Sullivan, David

2011-01-01

Personal naming practices exist in all human groups and are far from random. Rather, they continue to reflect social norms and ethno-cultural customs that have developed over generations. As a consequence, contemporary name frequency distributions retain distinct geographic, social and ethno-cultural patterning that can be exploited to understand population structure in human biology, public health and social science. Previous attempts to detect and delineate such structure in large populations have entailed extensive empirical analysis of naming conventions in different parts of the world without seeking any general or automated methods of population classification by ethno-cultural origin. Here we show how ‘naming networks’, constructed from forename-surname pairs of a large sample of the contemporary human population in 17 countries, provide a valuable representation of cultural, ethnic and linguistic population structure around the world. This innovative approach enriches and adds value to automated population classification through conventional national data sources such as telephone directories and electoral registers. The method identifies clear social and ethno-cultural clusters in such naming networks that extend far beyond the geographic areas in which particular names originated, and that are preserved even after international migration. Moreover, one of the most striking findings of this approach is that these clusters simply ‘emerge’ from the aggregation of millions of individual decisions on parental naming practices for their children, without any prior knowledge introduced by the researcher. Our probabilistic approach to community assignment, both at city level as well as at a global scale, helps to reveal the degree of isolation, integration or overlap between human populations in our rapidly globalising world. As such, this work has important implications for research in population genetics, public health, and social science adding new understandings of migration, identity, integration and social interaction across the world. PMID:21909399

Spatial Genetic Structure and Mitochondrial DNA Phylogeography of Argentinean Populations of the Grasshopper Dichroplus elongatus

PubMed Central

Rosetti, Natalia; Remis, Maria Isabel

2012-01-01

Many grasshopper species are considered of agronomical importance because they cause damage to pastures and crops. Comprehension of pest population dynamics requires a clear understanding of the genetic diversity and spatial structure of populations. In this study we report on patterns of genetic variation in the South American grasshopper Dichroplus elongatus which is an agricultural pest of crops and forage grasses of great economic significance in Argentina. We use Direct Amplification of Minisatellite Regions (DAMD) and partial sequences of the cytochrome oxydase 1 (COI) mitochondrial gene to investigate intraspecific structure, demographic history and gene flow patterns in twenty Argentinean populations of this species belonging to different geographic and biogeographic regions. DAMD data suggest that, although genetic drift and migration occur within and between populations, measurable relatedness among neighbouring populations declines with distance and dispersal over distances greater than 200 km is not typical, whereas effective gene flow may occur for populations separated by less than 100 km. Landscape analysis was useful to detect genetic discontinuities associated with environmental heterogeneity reflecting the changing agroecosystem. The COI results indicate the existence of strong genetic differentiation between two groups of populations located at both margins of the Paraná River which became separated during climate oscillations of the Middle Pleistocene, suggesting a significant restriction in effective dispersion mediated by females and large scale geographic differentiation. The number of migrants between populations estimated through mitochondrial and DAMD markers suggest that gene flow is low prompting a non-homogeneous spatial structure and justifying the variation through space. Moreover, the genetic analysis of both markers allows us to conclude that males appear to disperse more than females, reducing the chance of the genetic loss associated with recent anthropogenic fragmentation of the D. elongatus studied range. PMID:22859953

Phylogenetic information in polymorphic L1 and Alu insertions from East Asians and Native American populations.

PubMed

Mateus Pereira, L H; Socorro, A; Fernandez, I; Masleh, M; Vidal, D; Bianchi, N O; Bonatto, S L; Salzano, F M; Herrera, R J

2005-09-01

This study attempts to ascertain genetic affinities between Native American and East Asian populations by analyzing four polymorphic Alu insertions (PAIs) and three L1 polymorphic loci. These two genetic systems demonstrated strong congruence when levels of diversity and genetic distances were considered. Overall, genetic relatedness within Native American groups does not correlate with geographical and linguistic structure, although strong grouping for Native Americans with East Asians was demonstrated, with clear discrimination from African and European groups. Most of the variation was assigned to differences occurring within groups, but the interpopulation variation found for South Amerindians was recognizably higher in comparison to the other sampled groups of populations. Our data suggest that bottleneck events followed by strong influence of genetic drift in the process of the peopling of the Americas may have been determinant factors in delineating the genetic background of present-day South Amerindians. Since no clear subgroups were detected within Native Americans and East Asians, there is no indication of multiple waves in the early colonization of the New World. (c) 2005 Wiley-Liss, Inc.

Genetic diversity and population structure of Prunus mira (Koehne) from the Tibet plateau in China and recommended conservation strategies

PubMed Central

Bao, Wenquan; Li, Tiezhu; Liu, Huimin; Jiang, Zhongmao; Zhu, Xuchun; Du, Hongyan; Bai, Yu-e

2017-01-01

Prunus mira Koehne, an important economic fruit crop with high breeding and medicinal values, and an ancestral species of many cultivated peach species, has recently been declared an endangered species. However, basic information about genetic diversity, population structure, and morphological variation is still limited for this species. In this study, we sampled 420 P. mira individuals from 21 wild populations in the Tibet plateau to conduct a comprehensive analysis of genetic and morphological characteristics. The results of molecular analyses based on simple sequence repeat (SSR) markers indicated moderate genetic diversity and inbreeding (A = 3.8, Ae = 2.5, He = 0.52, Ho = 0.44, I = 0.95, FIS = 0.17) within P. mira populations. STRUCTURE, GENELAND, and phylogenetic analyses assigned the 21 populations to three genetic clusters that were moderately correlated with geographic altitudes, and this may have resulted from significantly different climatic and environmental factors at different altitudinal ranges. Significant isolation-by-distance was detected across the entire distribution of P. mira populations, but geographic altitude might have more significant effects on genetic structure than geographic distance in partial small-scale areas. Furthermore, clear genetic structure, high genetic differentiation, and restricted gene flow were detected between pairwise populations from different geographic groups, indicating that geographic barriers and genetic drift have significant effects on P. mira populations. Analyses of molecular variance based on the SSR markers indicated high variation (83.7% and 81.7%), whereas morphological analyses revealed low variation (1.30%–36.17%) within the populations. Large and heavy fruits were better adapted than light fruits and nutlets to poor climate and environmental conditions at high altitudes. Based on the results of molecular and morphological analyses, we classified the area into three conservation units and proposed several conservation strategies for wild P. mira populations in the Tibet plateau. PMID:29186199

Genetic diversity and population structure of Prunus mira (Koehne) from the Tibet plateau in China and recommended conservation strategies.

PubMed

Bao, Wenquan; Wuyun, Tana; Li, Tiezhu; Liu, Huimin; Jiang, Zhongmao; Zhu, Xuchun; Du, Hongyan; Bai, Yu-E

2017-01-01

Prunus mira Koehne, an important economic fruit crop with high breeding and medicinal values, and an ancestral species of many cultivated peach species, has recently been declared an endangered species. However, basic information about genetic diversity, population structure, and morphological variation is still limited for this species. In this study, we sampled 420 P. mira individuals from 21 wild populations in the Tibet plateau to conduct a comprehensive analysis of genetic and morphological characteristics. The results of molecular analyses based on simple sequence repeat (SSR) markers indicated moderate genetic diversity and inbreeding (A = 3.8, Ae = 2.5, He = 0.52, Ho = 0.44, I = 0.95, FIS = 0.17) within P. mira populations. STRUCTURE, GENELAND, and phylogenetic analyses assigned the 21 populations to three genetic clusters that were moderately correlated with geographic altitudes, and this may have resulted from significantly different climatic and environmental factors at different altitudinal ranges. Significant isolation-by-distance was detected across the entire distribution of P. mira populations, but geographic altitude might have more significant effects on genetic structure than geographic distance in partial small-scale areas. Furthermore, clear genetic structure, high genetic differentiation, and restricted gene flow were detected between pairwise populations from different geographic groups, indicating that geographic barriers and genetic drift have significant effects on P. mira populations. Analyses of molecular variance based on the SSR markers indicated high variation (83.7% and 81.7%), whereas morphological analyses revealed low variation (1.30%-36.17%) within the populations. Large and heavy fruits were better adapted than light fruits and nutlets to poor climate and environmental conditions at high altitudes. Based on the results of molecular and morphological analyses, we classified the area into three conservation units and proposed several conservation strategies for wild P. mira populations in the Tibet plateau.

Validity and feasibility of a satellite imagery-based method for rapid estimation of displaced populations

PubMed Central

2013-01-01

Background Estimating the size of forcibly displaced populations is key to documenting their plight and allocating sufficient resources to their assistance, but is often not done, particularly during the acute phase of displacement, due to methodological challenges and inaccessibility. In this study, we explored the potential use of very high resolution satellite imagery to remotely estimate forcibly displaced populations. Methods Our method consisted of multiplying (i) manual counts of assumed residential structures on a satellite image and (ii) estimates of the mean number of people per structure (structure occupancy) obtained from publicly available reports. We computed population estimates for 11 sites in Bangladesh, Chad, Democratic Republic of Congo, Ethiopia, Haiti, Kenya and Mozambique (six refugee camps, three internally displaced persons’ camps and two urban neighbourhoods with a mixture of residents and displaced) ranging in population from 1,969 to 90,547, and compared these to “gold standard” reference population figures from census or other robust methods. Results Structure counts by independent analysts were reasonably consistent. Between one and 11 occupancy reports were available per site and most of these reported people per household rather than per structure. The imagery-based method had a precision relative to reference population figures of <10% in four sites and 10–30% in three sites, but severely over-estimated the population in an Ethiopian camp with implausible occupancy data and two post-earthquake Haiti sites featuring dense and complex residential layout. For each site, estimates were produced in 2–5 working person-days. Conclusions In settings with clearly distinguishable individual structures, the remote, imagery-based method had reasonable accuracy for the purposes of rapid estimation, was simple and quick to implement, and would likely perform better in more current application. However, it may have insurmountable limitations in settings featuring connected buildings or shelters, a complex pattern of roofs and multi-level buildings. Based on these results, we discuss possible ways forward for the method’s development. PMID:23343099

Validity and feasibility of a satellite imagery-based method for rapid estimation of displaced populations.

PubMed

Checchi, Francesco; Stewart, Barclay T; Palmer, Jennifer J; Grundy, Chris

2013-01-23

Estimating the size of forcibly displaced populations is key to documenting their plight and allocating sufficient resources to their assistance, but is often not done, particularly during the acute phase of displacement, due to methodological challenges and inaccessibility. In this study, we explored the potential use of very high resolution satellite imagery to remotely estimate forcibly displaced populations. Our method consisted of multiplying (i) manual counts of assumed residential structures on a satellite image and (ii) estimates of the mean number of people per structure (structure occupancy) obtained from publicly available reports. We computed population estimates for 11 sites in Bangladesh, Chad, Democratic Republic of Congo, Ethiopia, Haiti, Kenya and Mozambique (six refugee camps, three internally displaced persons' camps and two urban neighbourhoods with a mixture of residents and displaced) ranging in population from 1,969 to 90,547, and compared these to "gold standard" reference population figures from census or other robust methods. Structure counts by independent analysts were reasonably consistent. Between one and 11 occupancy reports were available per site and most of these reported people per household rather than per structure. The imagery-based method had a precision relative to reference population figures of <10% in four sites and 10-30% in three sites, but severely over-estimated the population in an Ethiopian camp with implausible occupancy data and two post-earthquake Haiti sites featuring dense and complex residential layout. For each site, estimates were produced in 2-5 working person-days. In settings with clearly distinguishable individual structures, the remote, imagery-based method had reasonable accuracy for the purposes of rapid estimation, was simple and quick to implement, and would likely perform better in more current application. However, it may have insurmountable limitations in settings featuring connected buildings or shelters, a complex pattern of roofs and multi-level buildings. Based on these results, we discuss possible ways forward for the method's development.

The population structure and recent colonization history of Oregon threespine stickleback determined using RAD-seq

PubMed Central

Catchen, Julian; Bassham, Susan; Wilson, Taylor; Currey, Mark; O’Brien, Conor; Yeates, Quick; Cresko, William A.

2013-01-01

Understanding how genetic variation is partitioned across genomes within and among populations is a fundamental problem in ecological and evolutionary genetics. To address this problem we are studied the threespine stickleback fish, which has repeatedly undergone parallel phenotypic and genetic differentiation when oceanic fish have invaded freshwater habitats. While significant evolutionary genetic research has been performed using stickleback from geographic regions that have been de-glaciated in the last 20,000 years, less research has focused on freshwater populations that predate the last glacial maximum. We performed RAD-seq based population genomic analyses on stickleback from across Oregon, which was not glaciated during the last maximum. We sampled stickleback from coastal, Willamette Basin, and central Oregon sites, analyzed their genetic diversity using RAD-seq, performed STRUCTURE analyses, reconstructed their phylogeographic history, and tested the hypothesis of recent stickleback introduction into central Oregon, where incidence of this species was only recently documented. Our results showed a clear phylogeographic break between coastal and inland populations, with oceanic populations exhibiting the lowest levels of divergence from one another. Willamette Basin and central Oregon populations formed a clade of closely related populations, a finding consistent with a recent introduction of stickleback into central Oregon. Finally, genome wide analysis of genetic diversity (π) and correlations of alleles within individuals in subpopulations (FIS) supported a role for introgressive hybridization in coastal populations and a recent expansion in central Oregon. Our results exhibit the power of next generation sequencing genomic approaches such as RAD-seq to identify both historical population structure and recent colonization history. PMID:23718143

Isolated populations of a rare alpine plant show high genetic diversity and considerable population differentiation.

PubMed

Aegisdóttir, Hafdís Hanna; Kuss, Patrick; Stöcklin, Jürg

2009-12-01

Gene flow and genetic variability within and among alpine plant populations can be greatly influenced by the steep environmental gradients and heterogeneous topography of alpine landscapes. In this study, the effects are examined of natural isolation of alpine habitats on genetic diversity and geographic structure in populations of C. thyrsoides, a rare and isolated European Alpine monocarpic perennial with limited seed dispersal capacity. Molecular diversity was analysed for 736 individuals from 32 populations in the Swiss Alps and adjacent Jura mountains using five polymorphic microsatellite loci. Pollen flow was estimated using pollen grain-sized fluorescent powder. In addition, individual-based Bayesian approaches were applied to examine population structure. High within-population genetic diversity (H(E) = 0.76) and a relatively low inbreeding coefficient (F(IS) = 0.022) were found. Genetic differentiation among populations measured with a standardized measure was considerable (G'(ST) = 0.53). A significant isolation-by-distance relationship was found (r = 0.62, P < 0.001) and a significant geographic sub-structure, coinciding with proposed postglacial migration patterns. Altitudinal location and size of populations did not influence molecular variation. Direct measures of pollen flow revealed that insect-mediated pollen dispersal was restricted to short distances within a population. The natural isolation of suitable habitats for C. thyrsoides restricts gene flow among the populations as expected for a monocarpic species with very limited seed dispersal capacities. The observed high within-population genetic diversity in this rare monocarpic perennial is best explained by its outcrossing behaviour, long-lived individuals and overlapping generations. Despite the high within-population genetic diversity, the considerable genetic differentiation and the clear western-eastern differentiation in this species merits consideration in future conservation efforts.

Genetic structure of Quechua-speakers of the Central Andes and geographic patterns of gene frequencies in South Amerindian populations.

PubMed

Luiselli, D; Simoni, L; Tarazona-Santos, E; Pastor, S; Pettener, D

2000-09-01

A sample of 141 Quechua-speaking individuals of the population of Tayacaja, in the Peruvian Central Andes, was typed for the following 16 genetic systems: ABO, Rh, MNSs, P, Duffy, AcP1, EsD, GLOI, PGM1, AK, 6-PGD, Hp, Gc, Pi, C3, and Bf. The genetic structure of the population was analyzed in relation to the allele frequencies available for other South Amerindian populations, using a combination of multivariate and multivariable techniques. Spatial autocorrelation analysis was performed independently for 13 alleles to identify patterns of gene flow in South America as a whole and in more specific geographic regions. We found a longitudinal cline for the AcP1*a and EsD*1 alleles which we interpreted as the result of an ancient longitudinal expansion of a putative ancestral population of modern Amerindians. Monmonnier's algorithm, used to identify areas of sharp genetic discontinuity, suggested a clear east-west differentiation of native South American populations, which was confirmed by analysis of the distribution of genetic distances. We suggest that this pattern of genetic structures is the consequence of the independent peopling of western and eastern South America or to low levels of gene flow between these regions, related to different environmental and demographic histories. Copyright 2000 Wiley-Liss, Inc.

Genetic structure of Tibetan populations in Gansu revealed by forensic STR loci.

PubMed

Yao, Hong-Bing; Wang, Chuan-Chao; Wang, Jiang; Tao, Xiaolan; Shang, Lei; Wen, Shao-Qing; Du, Qiajun; Deng, Qiongying; Xu, Bingying; Huang, Ying; Wang, Hong-Dan; Li, Shujin; Bin Cong; Ma, Liying; Jin, Li; Krause, Johannes; Li, Hui

2017-01-23

The origin and diversification of Sino-Tibetan speaking populations have been long-standing hot debates. However, the limited genetic information of Tibetan populations keeps this topic far from clear. In the present study, we genotyped 15 forensic autosomal short tandem repeats (STRs) from 803 unrelated Tibetan individuals from Gansu Province (635 from Gannan and 168 from Tianzhu) in northwest China. We combined these data with published dataset to infer a detailed population affinities and genetic substructure of Sino-Tibetan populations. Our results revealed Tibetan populations in Gannan and Tianzhu are genetically very similar with Tibetans from other regions. The Tibetans in Tianzhu have received more genetic influence from surrounding lowland populations. The genetic structure of Sino-Tibetan populations was strongly correlated with linguistic affiliations. Although the among-population variances are relatively small, the genetic components for Tibetan, Lolo-Burmese, and Han Chinese were quite distinctive, especially for the Deng, Nu, and Derung of Lolo-Burmese. Han Chinese but not Tibetans are suggested to share substantial genetic component with southern natives, such as Tai-Kadai and Hmong-Mien speaking populations, and with other lowland East Asian populations, which implies there might be extensive gene flow between those lowland groups and Han Chinese after Han Chinese were separated from Tibetans. The dataset generated in present study is also valuable for forensic identification and paternity tests in China.

Genetic structure of Tibetan populations in Gansu revealed by forensic STR loci

PubMed Central

Yao, Hong-Bing; Wang, Chuan-Chao; Wang, Jiang; Tao, Xiaolan; Shang, Lei; Wen, Shao-Qing; Du, Qiajun; Deng, Qiongying; Xu, Bingying; Huang, Ying; Wang, Hong-Dan; Li, Shujin; Bin Cong; Ma, Liying; Jin, Li; Krause, Johannes; Li, Hui

2017-01-01

The origin and diversification of Sino-Tibetan speaking populations have been long-standing hot debates. However, the limited genetic information of Tibetan populations keeps this topic far from clear. In the present study, we genotyped 15 forensic autosomal short tandem repeats (STRs) from 803 unrelated Tibetan individuals from Gansu Province (635 from Gannan and 168 from Tianzhu) in northwest China. We combined these data with published dataset to infer a detailed population affinities and genetic substructure of Sino-Tibetan populations. Our results revealed Tibetan populations in Gannan and Tianzhu are genetically very similar with Tibetans from other regions. The Tibetans in Tianzhu have received more genetic influence from surrounding lowland populations. The genetic structure of Sino-Tibetan populations was strongly correlated with linguistic affiliations. Although the among-population variances are relatively small, the genetic components for Tibetan, Lolo-Burmese, and Han Chinese were quite distinctive, especially for the Deng, Nu, and Derung of Lolo-Burmese. Han Chinese but not Tibetans are suggested to share substantial genetic component with southern natives, such as Tai-Kadai and Hmong-Mien speaking populations, and with other lowland East Asian populations, which implies there might be extensive gene flow between those lowland groups and Han Chinese after Han Chinese were separated from Tibetans. The dataset generated in present study is also valuable for forensic identification and paternity tests in China. PMID:28112227

History and structure of sub-Saharan populations of Drosophila melanogaster.

PubMed

Pool, John E; Aquadro, Charles F

2006-10-01

Drosophila melanogaster is an important model organism in evolutionary genetics, yet little is known about the population structure and the demographic history of this species within sub-Saharan Africa, which is thought to contain its ancestral range. We surveyed nucleotide variation at four 1-kb fragments in 240 individual lines representing 21 sub-Saharan and 4 Palearctic population samples of D. melanogaster. In agreement with recent studies, we find a small but significant level of genetic differentiation within sub-Saharan Africa. A clear geographic pattern is observed, with eastern and western African populations composing two genetically distinct groups. This pattern may have resulted from a relatively recent establishment of D. melanogaster in western Africa. Eastern populations show greater evidence for long-term stability, consistent with the hypothesis that eastern Africa contains the ancestral range of the species. Three sub-Saharan populations show evidence for cosmopolitan introgression. Apart from those cases, the closest relationships between Palearctic and sub-Saharan populations involve a sample from the rift zone (Uganda), suggesting that the progenitors of Palearctic D. melanogaster might have come from this region. Finally, we find a large excess of singleton polymorphisms in the full data set, which is best explained by a combination of population growth and purifying selection.

Phylogeography and recolonization of the Swiss Alps by the Valais shrew (Sorex antinorii), inferred with autosomal and sex-specific markers.

PubMed

Yannic, G; Basset, P; Hausser, J

2008-09-01

Using one male-inherited, one female-inherited and eight biparentally inherited markers, we investigate the population genetic structure of the Valais shrew (Sorex antinorii) in the Swiss Alps. Bayesian analysis on autosomal microsatellites suggests a clear genetic differentiation between two groups of populations. This geographically based structure is consistent with two separate postglacial recolonization routes of the species into Switzerland from Italian refugia after the last Pleistocene glaciations. Sex-specific markers also confirm genetic structuring among western and eastern areas, since very few haplotypes for either Y chromosome or mtDNA genome are shared between the two regions. Overall, these results suggest that two already well-differentiated genetic lineages colonized the Swiss Alps and came into secondary contact in the Rhône Valley. Low level of admixture between the two lineages is likely explained by the mountainous landscape structure of lateral valleys orthogonal to the main Rhône valley.

Genomic Tools for Evolution and Conservation in the Chimpanzee: Pan troglodytes ellioti Is a Genetically Distinct Population

PubMed Central

Myers, Simon; Hellenthal, Garrett; Nerrienet, Eric; Bontrop, Ronald E.; Freeman, Colin; Donnelly, Peter; Mundy, Nicholas I.

2012-01-01

In spite of its evolutionary significance and conservation importance, the population structure of the common chimpanzee, Pan troglodytes, is still poorly understood. An issue of particular controversy is whether the proposed fourth subspecies of chimpanzee, Pan troglodytes ellioti, from parts of Nigeria and Cameroon, is genetically distinct. Although modern high-throughput SNP genotyping has had a major impact on our understanding of human population structure and demographic history, its application to ecological, demographic, or conservation questions in non-human species has been extremely limited. Here we apply these tools to chimpanzee population structure, using ∼700 autosomal SNPs derived from chimpanzee genomic data and a further ∼100 SNPs from targeted re-sequencing. We demonstrate conclusively the existence of P. t. ellioti as a genetically distinct subgroup. We show that there is clear differentiation between the verus, troglodytes, and ellioti populations at the SNP and haplotype level, on a scale that is greater than that separating continental human populations. Further, we show that only a small set of SNPs (10–20) is needed to successfully assign individuals to these populations. Tellingly, use of only mitochondrial DNA variation to classify individuals is erroneous in 4 of 54 cases, reinforcing the dangers of basing demographic inference on a single locus and implying that the demographic history of the species is more complicated than that suggested analyses based solely on mtDNA. In this study we demonstrate the feasibility of developing economical and robust tests of individual chimpanzee origin as well as in-depth studies of population structure. These findings have important implications for conservation strategies and our understanding of the evolution of chimpanzees. They also act as a proof-of-principle for the use of cheap high-throughput genomic methods for ecological questions. PMID:22396655

Genomic tools for evolution and conservation in the chimpanzee: Pan troglodytes ellioti is a genetically distinct population.

PubMed

Bowden, Rory; MacFie, Tammie S; Myers, Simon; Hellenthal, Garrett; Nerrienet, Eric; Bontrop, Ronald E; Freeman, Colin; Donnelly, Peter; Mundy, Nicholas I

2012-01-01

In spite of its evolutionary significance and conservation importance, the population structure of the common chimpanzee, Pan troglodytes, is still poorly understood. An issue of particular controversy is whether the proposed fourth subspecies of chimpanzee, Pan troglodytes ellioti, from parts of Nigeria and Cameroon, is genetically distinct. Although modern high-throughput SNP genotyping has had a major impact on our understanding of human population structure and demographic history, its application to ecological, demographic, or conservation questions in non-human species has been extremely limited. Here we apply these tools to chimpanzee population structure, using ∼700 autosomal SNPs derived from chimpanzee genomic data and a further ∼100 SNPs from targeted re-sequencing. We demonstrate conclusively the existence of P. t. ellioti as a genetically distinct subgroup. We show that there is clear differentiation between the verus, troglodytes, and ellioti populations at the SNP and haplotype level, on a scale that is greater than that separating continental human populations. Further, we show that only a small set of SNPs (10-20) is needed to successfully assign individuals to these populations. Tellingly, use of only mitochondrial DNA variation to classify individuals is erroneous in 4 of 54 cases, reinforcing the dangers of basing demographic inference on a single locus and implying that the demographic history of the species is more complicated than that suggested analyses based solely on mtDNA. In this study we demonstrate the feasibility of developing economical and robust tests of individual chimpanzee origin as well as in-depth studies of population structure. These findings have important implications for conservation strategies and our understanding of the evolution of chimpanzees. They also act as a proof-of-principle for the use of cheap high-throughput genomic methods for ecological questions.

Determination of the genetic structure of remnant Morus boninensis Koidz. trees to establish a conservation program on the Bonin Islands, Japan.

PubMed

Tani, Naoki; Yoshimaru, Hiroshi; Kawahara, Takayuki; Hoshi, Yoshio; Nobushima, Fuyuo; Yasui, Takaya

2006-10-11

Morus boninensis, is an endemic plant of the Bonin (Ogasawara) Islands of Japan and is categorized as "critically endangered" in the Japanese red data book. However, little information is available about its ecological, evolutionary and genetic status, despite the urgent need for guidelines for the conservation of the species. Therefore, we adopted Moritz's MU concept, based on the species' current genetic structure, to define management units and to select mother tree candidates for seed orchards. Nearly all individuals of the species were genotyped on the basis of seven microsatellite markers. Genetic diversity levels in putative natural populations were higher than in putative man-made populations with the exception of those on Otouto-jima Island. This is because a limited number of maternal trees are likely to have been used for seed collection to establish the man-made populations. A model-based clustering analysis clearly distinguished individuals into nine clusters, with a large difference in genetic composition between the population on Otouto-jima Island, the putative natural populations and the putative man-made populations. The Otouto-jima population appeared to be genetically differentiated from the others; a finding that was also supported by pairwise FST and RST analysis. Although multiple clusters were detected in the putative man-made populations, the pattern of genetic diversity was monotonous in comparison to the natural populations. The genotyping by microsatellite markers revealed strong genetic structures. Typically, artificial propagation of this species has ignored the genetic structure, relying only on seeds from Otouto-jima for replanting on other islands, because of a problem with inter-specific hybridization on Chichi-jima and Haha-jima Islands. However, this study demonstrates that we should be taking into consideration the genetic structure of the species when designing a propagation program for the conservation of this species.

Determination of the genetic structure of remnant Morus boninensis Koidz. trees to establish a conservation program on the Bonin Islands, Japan

PubMed Central

Tani, Naoki; Yoshimaru, Hiroshi; Kawahara, Takayuki; Hoshi, Yoshio; Nobushima, Fuyuo; Yasui, Takaya

2006-01-01

Background Morus boninensis, is an endemic plant of the Bonin (Ogasawara) Islands of Japan and is categorized as "critically endangered" in the Japanese red data book. However, little information is available about its ecological, evolutionary and genetic status, despite the urgent need for guidelines for the conservation of the species. Therefore, we adopted Moritz's MU concept, based on the species' current genetic structure, to define management units and to select mother tree candidates for seed orchards. Results Nearly all individuals of the species were genotyped on the basis of seven microsatellite markers. Genetic diversity levels in putative natural populations were higher than in putative man-made populations with the exception of those on Otouto-jima Island. This is because a limited number of maternal trees are likely to have been used for seed collection to establish the man-made populations. A model-based clustering analysis clearly distinguished individuals into nine clusters, with a large difference in genetic composition between the population on Otouto-jima Island, the putative natural populations and the putative man-made populations. The Otouto-jima population appeared to be genetically differentiated from the others; a finding that was also supported by pairwise FST and RST analysis. Although multiple clusters were detected in the putative man-made populations, the pattern of genetic diversity was monotonous in comparison to the natural populations. Conclusion The genotyping by microsatellite markers revealed strong genetic structures. Typically, artificial propagation of this species has ignored the genetic structure, relying only on seeds from Otouto-jima for replanting on other islands, because of a problem with inter-specific hybridization on Chichi-jima and Haha-jima Islands. However, this study demonstrates that we should be taking into consideration the genetic structure of the species when designing a propagation program for the conservation of this species. PMID:17034624

Urban Perceptions of the Natural Landscape: Implications for Public Awareness of Wilderness as a Distinct Resource

Treesearch

George W. Duffy

1992-01-01

As more and more of our population move from rural to suburban to urban to metropolitan settings, the connections between people and the land of which they are a part become less obvious, less immediately important and less clearly understood. The contrast between a complex, highly structured social and cultural urban environment and the natural world seems bipolar....

The Trouble with Boys: Observations about Boys' Post-Secondary Aspirations, Attendance and Success

ERIC Educational Resources Information Center

Johnston, J. Howard

2012-01-01

Boys have a slight advantage in the number of live births in the US (about 101:100), so, all things being equal, it is reasonable to assume that they would populate institutions at about the same rate as girls. However, institutions are social structures, and in social systems all things are almost "never" equal, so, clearly, there are other…

Fluorescent-Protein Stabilization and High-Resolution Imaging of Cleared, Intact Mouse Brains

PubMed Central

Schwarz, Martin K.; Scherbarth, Annemarie; Sprengel, Rolf; Engelhardt, Johann; Theer, Patrick; Giese, Guenter

2015-01-01

In order to observe and quantify long-range neuronal connections in intact mouse brain by light microscopy, it is first necessary to clear the brain, thus suppressing refractive-index variations. Here we describe a method that clears the brain and preserves the signal from proteinaceous fluorophores using a pH-adjusted non-aqueous index-matching medium. Successful clearing is enabled through the use of either 1-propanol or tert-butanol during dehydration whilst maintaining a basic pH. We show that high-resolution fluorescence imaging of entire, structurally intact juvenile and adult mouse brains is possible at subcellular resolution, even following many months in clearing solution. We also show that axonal long-range projections that are EGFP-labelled by modified Rabies virus can be imaged throughout the brain using a purpose-built light-sheet fluorescence microscope. To demonstrate the viability of the technique, we determined a detailed map of the monosynaptic projections onto a target cell population in the lateral entorhinal cortex. This example demonstrates that our method permits the quantification of whole-brain connectivity patterns at the subcellular level in the uncut brain. PMID:25993380

Genetic structure and hierarchical population divergence history of Acer mono var. mono in South and Northeast China.

PubMed

Liu, Chunping; Tsuda, Yoshiaki; Shen, Hailong; Hu, Lijiang; Saito, Yoko; Ide, Yuji

2014-01-01

Knowledge of the genetic structure and evolutionary history of tree species across their ranges is essential for the development of effective conservation and forest management strategies. Acer mono var. mono, an economically and ecologically important maple species, is extensively distributed in Northeast China (NE), whereas it has a scattered and patchy distribution in South China (SC). In this study, the genetic structure and demographic history of 56 natural populations of A. mono var. mono were evaluated using seven nuclear microsatellite markers. Neighbor-joining tree and STRUCTURE analysis clearly separated populations into NE and SC groups with two admixed-like populations. Allelic richness significantly decreased with increasing latitude within the NE group while both allelic richness and expected heterozygosity showed significant positive correlation with latitude within the SC group. Especially in the NE region, previous studies in Quercus mongolica and Fraxinus mandshurica have also detected reductions in genetic diversity with increases in latitude, suggesting this pattern may be common for tree species in this region, probably due to expansion from single refugium following the last glacial maximum (LGM). Approximate Bayesian Computation-based analysis revealed two major features of hierarchical population divergence in the species' evolutionary history. Recent divergence between the NE group and the admixed-like group corresponded to the LGM period and ancient divergence of SC groups took place during mid-late Pleistocene period. The level of genetic differentiation was moderate (FST  = 0.073; G'ST  = 0.278) among all populations, but significantly higher in the SC group than the NE group, mirroring the species' more scattered distribution in SC. Conservation measures for this species are proposed, taking into account the genetic structure and past demographic history identified in this study.

Rapid divergence of mussel populations despite incomplete barriers to dispersal.

PubMed

Maas, Diede L; Prost, Stefan; Bi, Ke; Smith, Lydia L; Armstrong, Ellie E; Aji, Ludi P; Toha, Abdul Hamid A; Gillespie, Rosemary G; Becking, Leontine E

2018-04-01

Striking genetic structure among marine populations at small spatial scales is becoming evident with extensive molecular studies. Such observations suggest isolation at small scales may play an important role in forming patterns of genetic diversity within species. Isolation-by-distance, isolation-by-environment and historical priority effects are umbrella terms for a suite of processes that underlie genetic structure, but their relative importance at different spatial and temporal scales remains elusive. Here, we use marine lakes in Indonesia to assess genetic structure and assess the relative roles of the processes in shaping genetic differentiation in populations of a bivalve mussel (Brachidontes sp.). Marine lakes are landlocked waterbodies of similar age (6,000-10,000 years), but with heterogeneous environments and varying degrees of connection to the sea. Using a population genomic approach (double-digest restriction-site-associated DNA sequencing), we show strong genetic structuring across populations (range F ST : 0.07-0.24) and find limited gene flow through admixture plots. At large spatial scales (>1,400 km), a clear isolation-by-distance pattern was detected. At smaller spatial scales (<200 km), this pattern is maintained, but accompanied by an association of genetic divergence with degree of connection. We hypothesize that (incomplete) dispersal barriers can cause initial isolation, allowing priority effects to give the numerical advantage necessary to initiate strong genetic structure. Priority effects may be strengthened by local adaptation, which the data may corroborate by showing a high correlation between mussel genotypes and temperature. Our study indicates an often-neglected role of (evolution-mediated) priority effects in shaping population divergence. © 2018 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.

Genetic Structure and Hierarchical Population Divergence History of Acer mono var. mono in South and Northeast China

PubMed Central

Shen, Hailong; Hu, Lijiang; Saito, Yoko; Ide, Yuji

2014-01-01

Knowledge of the genetic structure and evolutionary history of tree species across their ranges is essential for the development of effective conservation and forest management strategies. Acer mono var. mono, an economically and ecologically important maple species, is extensively distributed in Northeast China (NE), whereas it has a scattered and patchy distribution in South China (SC). In this study, the genetic structure and demographic history of 56 natural populations of A. mono var. mono were evaluated using seven nuclear microsatellite markers. Neighbor-joining tree and STRUCTURE analysis clearly separated populations into NE and SC groups with two admixed-like populations. Allelic richness significantly decreased with increasing latitude within the NE group while both allelic richness and expected heterozygosity showed significant positive correlation with latitude within the SC group. Especially in the NE region, previous studies in Quercus mongolica and Fraxinus mandshurica have also detected reductions in genetic diversity with increases in latitude, suggesting this pattern may be common for tree species in this region, probably due to expansion from single refugium following the last glacial maximum (LGM). Approximate Bayesian Computation-based analysis revealed two major features of hierarchical population divergence in the species’ evolutionary history. Recent divergence between the NE group and the admixed-like group corresponded to the LGM period and ancient divergence of SC groups took place during mid-late Pleistocene period. The level of genetic differentiation was moderate (FST = 0.073; G′ST = 0.278) among all populations, but significantly higher in the SC group than the NE group, mirroring the species’ more scattered distribution in SC. Conservation measures for this species are proposed, taking into account the genetic structure and past demographic history identified in this study. PMID:24498039

Variation in Brain Regions Associated with Fear and Learning in Contrasting Climates

PubMed Central

Roth, Timothy C.; Gallagher, Caitlin M.; LaDage, Lara D.; Pravosudov, Vladimir V.

2012-01-01

In environments where resources are difficult to obtain and enhanced cognitive capabilities might be adaptive, brain structures associated with cognitive traits may also be enhanced. In our previous studies, we documented a clear and significant relationship among environmental conditions, memory and hippocampal structure using ten populations of black-capped chickadees (Poecile atricapillus) over a large geographic range. In addition, focusing on just the two populations from the geographical extremes of our large-scale comparison, Alaska and Kansas, we found enhanced problem-solving capabilities and reduced neophobia in a captive-raised population of black-capped chickadees originating from the energetically demanding environment (Alaska) relative to conspecifics from the milder environment (Kansas). Here, we focused on three brain regions, the arcopallium (AP), the nucleus taeniae of the amygdala and the lateral striatum (LSt), that have been implicated to some extent in aspects of these behaviors in order to investigate whether potential differences in these brain areas may be associated with our previously detected differences in cognition. We compared the variation in neuron number and volumes of these regions between these populations, in both wild-caught birds and captive-raised individuals. Consistent with our behavioral observations, wild-caught birds from Kansas had a larger AP volume than their wild-caught conspecifics from Alaska, which possessed a higher density of neurons in the LSt. However, there were no other significant differences between populations in the wild-caught and captive-raised groups. Interestingly, individuals from the wild had larger LSt and AP volumes with more neurons than those raised in captivity. Overall, we provide some evidence that population-related differences in problem solving and neophobia may be associated with differences in volume and neuron numbers of our target brain regions. However, the relationship is not completely clear, and our study raises numerous questions about the relationship between the brain and behavior, especially in captive animals. PMID:22286546

Y-chromosome diversity in Native Mexicans reveals continental transition of genetic structure in the Americas.

PubMed

Sandoval, Karla; Moreno-Estrada, Andres; Mendizabal, Isabel; Underhill, Peter A; Lopez-Valenzuela, Maria; Peñaloza-Espinosa, Rosenda; Lopez-Lopez, Marisol; Buentello-Malo, Leonor; Avelino, Heriberto; Calafell, Francesc; Comas, David

2012-07-01

The genetic characterization of Native Mexicans is important to understand multiethnic based features influencing the medical genetics of present Mexican populations, as well as to the reconstruct the peopling of the Americas. We describe the Y-chromosome genetic diversity of 197 Native Mexicans from 11 populations and 1,044 individuals from 44 Native American populations after combining with publicly available data. We found extensive heterogeneity among Native Mexican populations and ample segregation of Q-M242* (46%) and Q-M3 (54%) haplogroups within Mexico. The northernmost sampled populations falling outside Mesoamerica (Pima and Tarahumara) showed a clear differentiation with respect to the other populations, which is in agreement with previous results from mtDNA lineages. However, our results point toward a complex genetic makeup of Native Mexicans whose maternal and paternal lineages reveal different narratives of their population history, with sex-biased continental contributions and different admixture proportions. At a continental scale, we found that Arctic populations and the northernmost groups from North America cluster together, but we did not find a clear differentiation within Mesoamerica and the rest of the continent, which coupled with the fact that the majority of individuals from Central and South American samples are restricted to the Q-M3 branch, supports the notion that most Native Americans from Mesoamerica southwards are descendants from a single wave of migration. This observation is compatible with the idea that present day Mexico might have constituted an area of transition in the diversification of paternal lineages during the colonization of the Americas. Copyright © 2012 Wiley Periodicals, Inc.

Genetic structure of colline and montane populations of an endangered plant species

PubMed Central

Maurice, Tiphaine; Matthies, Diethart; Muller, Serge; Colling, Guy

2016-01-01

Due to land-use intensification, lowland and colline populations of many plants of nutrient-poor grasslands have been strongly fragmented in the last decades, with potentially negative consequences for their genetic diversity and persistence. Populations in mountains might represent a genetic reservoir for grassland plants, because they have been less affected by land-use changes. We studied the genetic structure and diversity of colline and montane Vosges populations of the threatened perennial plant Arnica montana in western central Europe using AFLP markers. Our results indicate that in contrast to our expectation even strongly fragmented colline populations of A. montana have conserved a considerable amount of genetic diversity. However, mean seed mass increased with the proportion of polymorphic loci, suggesting inbreeding effects in low diversity populations. At a similar small geographical scale, there was a clear IBD pattern for the montane Vosges but not for the colline populations. However, there was a strong IBD-pattern for the colline populations at a large geographical scale suggesting that this pattern is a legacy of historical gene flow, as most of the colline populations are today strongly isolated from each other. Genetic differentiation between colline and montane Vosges populations was strong. Moreover, results of a genome scan study indicated differences in loci under selection, suggesting that plants from montane Vosges populations might be maladapted to conditions at colline sites. Our results suggest caution in using material from montane populations of rare plants for the reinforcement of small genetically depauperate lowland populations. PMID:27519913

Fundamental differences in diversity and genomic population structure between Atlantic and Pacific Prochlorococcus.

PubMed

Kashtan, Nadav; Roggensack, Sara E; Berta-Thompson, Jessie W; Grinberg, Maor; Stepanauskas, Ramunas; Chisholm, Sallie W

2017-09-01

The Atlantic and Pacific Oceans represent different biogeochemical regimes in which the abundant marine cyanobacterium Prochlorococcus thrives. We have shown that Prochlorococcus populations in the Atlantic are composed of hundreds of genomically, and likely ecologically, distinct coexisting subpopulations with distinct genomic backbones. Here we ask if differences in the ecology and selection pressures between the Atlantic and Pacific are reflected in the diversity and genomic composition of their indigenous Prochlorococcus populations. We applied large-scale single-cell genomics and compared the cell-by-cell genomic composition of wild populations of co-occurring cells from samples from Station ALOHA off Hawaii, and from Bermuda Atlantic Time Series Station off Bermuda. We reveal fundamental differences in diversity and genomic structure of populations between the sites. The Pacific populations are more diverse than those in the Atlantic, composed of significantly more coexisting subpopulations and lacking dominant subpopulations. Prochlorococcus from the two sites seem to be composed of mostly non-overlapping distinct sets of subpopulations with different genomic backbones-likely reflecting different sets of ocean-specific micro-niches. Furthermore, phylogenetically closely related strains carry ocean-associated nutrient acquisition genes likely reflecting differences in major selection pressures between the oceans. This differential selection, along with geographic separation, clearly has a significant role in shaping these populations.

The Story of a Hitchhiker: Population Genetic Patterns in the Invasive Barnacle Balanus(Amphibalanus) improvisus Darwin 1854

PubMed Central

Wrange, Anna-Lisa; Charrier, Gregory; Thonig, Anne; Alm Rosenblad, Magnus; Blomberg, Anders; Havenhand, Jonathan N.; Jonsson, Per R.; André, Carl

2016-01-01

Understanding the ecological and evolutionary forces that determine the genetic structure and spread of invasive species is a key component of invasion biology. The bay barnacle, Balanus improvisus (= Amphibalanus improvisus), is one of the most successful aquatic invaders worldwide, and is characterised by broad environmental tolerance. Although the species can spread through natural larval dispersal, human-mediated transport through (primarily) shipping has almost certainly contributed to the current global distribution of this species. Despite its worldwide distribution, little is known about the phylogeography of this species. Here, we characterize the population genetic structure and model dispersal dynamics of the barnacle B. improvisus, and describe how human-mediated spreading via shipping as well as natural larval dispersal may have contributed to observed genetic variation. We used both mitochondrial DNA (cytochrome c oxidase subunit I: COI) and nuclear microsatellites to characterize the genetic structure in 14 populations of B. improvisus on a global and regional scale (Baltic Sea). Genetic diversity was high in most populations, and many haplotypes were shared among populations on a global scale, indicating that long-distance dispersal (presumably through shipping and other anthropogenic activities) has played an important role in shaping the population genetic structure of this cosmopolitan species. We could not clearly confirm prior claims that B. improvisus originates from the western margins of the Atlantic coasts; although there were indications that Argentina could be part of a native region. In addition to dispersal via shipping, we show that natural larval dispersal may play an important role for further colonisation following initial introduction. PMID:26821161

Rivers influence the population genetic structure of bonobos (Pan paniscus).

PubMed

Eriksson, J; Hohmann, G; Boesch, C; Vigilant, L

2004-11-01

Bonobos are large, highly mobile primates living in the relatively undisturbed, contiguous forest south of the Congo River. Accordingly, gene flow among populations is assumed to be extensive, but may be impeded by large, impassable rivers. We examined mitochondrial DNA control region sequence variation in individuals from five distinct localities separated by rivers in order to estimate relative levels of genetic diversity and assess the extent and pattern of population genetic structure in the bonobo. Diversity estimates for the bonobo exceed those for humans, but are less than those found for the chimpanzee. All regions sampled are significantly differentiated from one another, according to genetic distances estimated as pairwise FSTs, with the greatest differentiation existing between region East and each of the two Northern populations (N and NE) and the least differentiation between regions Central and South. The distribution of nucleotide diversity shows a clear signal of population structure, with some 30% of the variance occurring among geographical regions. However, a geographical patterning of the population structure is not obvious. Namely, mitochondrial haplotypes were shared among all regions excepting the most eastern locality and the phylogenetic analysis revealed a tree in which haplotypes were intermixed with little regard to geographical origin, with the notable exception of the close relationships among the haplotypes found in the east. Nonetheless, genetic distances correlated with geographical distances when the intervening distances were measured around rivers presenting effective current-day barriers, but not when straight-line distances were used, suggesting that rivers are indeed a hindrance to gene flow in this species.

Population genetics of the malaria vector Anopheles aconitus in China and Southeast Asia

PubMed Central

Chen, Bin; Harbach, Ralph E.; Walton, Catherine; He, Zhengbo; Zhong, Daibin; Yan, Guiyun; Butlin, Roger K.

2012-01-01

Anopheles aconitus is a well-known vector of malaria and is broadly distributed in the Oriental Region, yet there is no information on its population genetic characteristics. In this study, the genetic differentiation among populations was examined using 140 mtDNA COII sequences from 21 sites throughout southern China, Myanmar, Vietnam, Thailand, Laos and Sri Lanka. The population in Sri Lanka has characteristic rDNA D3 and ITS2, mtDNA COII and ND5 haplotypes, and may be considered a distinct subspecies. Clear genetic structure was observed with highly significant genetic variation present among population groups in Southeast Asia. The greatest genetic diversity exists in Yunnan and Myanmar population groups. All population groups are significantly different from one another in pairwise Fst values, except northern Thailand with central Thailand. Mismatch distributions and extremely significant Fs values suggest that the populations passed through a recent demographic expansion. These patterns are discussed in relation to the likely biogeographic history of the region and compared to other Anopheles species. PMID:22982161

Bipartite Graphs as Models of Population Structures in Evolutionary Multiplayer Games

PubMed Central

Peña, Jorge; Rochat, Yannick

2012-01-01

By combining evolutionary game theory and graph theory, “games on graphs” study the evolutionary dynamics of frequency-dependent selection in population structures modeled as geographical or social networks. Networks are usually represented by means of unipartite graphs, and social interactions by two-person games such as the famous prisoner’s dilemma. Unipartite graphs have also been used for modeling interactions going beyond pairwise interactions. In this paper, we argue that bipartite graphs are a better alternative to unipartite graphs for describing population structures in evolutionary multiplayer games. To illustrate this point, we make use of bipartite graphs to investigate, by means of computer simulations, the evolution of cooperation under the conventional and the distributed N-person prisoner’s dilemma. We show that several implicit assumptions arising from the standard approach based on unipartite graphs (such as the definition of replacement neighborhoods, the intertwining of individual and group diversity, and the large overlap of interaction neighborhoods) can have a large impact on the resulting evolutionary dynamics. Our work provides a clear example of the importance of construction procedures in games on graphs, of the suitability of bigraphs and hypergraphs for computational modeling, and of the importance of concepts from social network analysis such as centrality, centralization and bipartite clustering for the understanding of dynamical processes occurring on networked population structures. PMID:22970237

Patterns of molecular genetic variation among cat breeds.

PubMed

Menotti-Raymond, Marilyn; David, Victor A; Pflueger, Solveig M; Lindblad-Toh, Kerstin; Wade, Claire M; O'Brien, Stephen J; Johnson, Warren E

2008-01-01

Genetic variation in cat breeds was assessed utilizing a panel of short tandem repeat (STR) loci genotyped in 38 cat breeds and 284 single-nucleotide polymorphisms (SNPs) genotyped in 24 breeds. Population structure in cat breeds generally reflects their recent ancestry and absence of strong breed barriers between some breeds. There is a wide range in the robustness of population definition, from breeds demonstrating high definition to breeds with as little as a third of their genetic variation partitioning into a single population. Utilizing the STRUCTURE algorithm, there was no clear demarcation of the number of population subdivisions; 16 breeds could not be resolved into independent populations, the consequence of outcrossing in established breeds to recently developed breeds with common ancestry. These 16 breeds were divided into 6 populations. Ninety-six percent of cats in a sample set of 1040 were correctly assigned to their classified breed or breed group/population. Average breed STR heterozygosities ranged from moderate (0.53; Havana, Korat) to high (0.85; Norwegian Forest Cat, Manx). Most of the variation in cat breeds was observed within a breed population (83.7%), versus 16.3% of the variation observed between populations. The hierarchical relationships of cat breeds is poorly defined as demonstrated by phylogenetic trees generated from both STR and SNP data, though phylogeographic grouping of breeds derived completely or in part from Southeast Asian ancestors was apparent.

Genetic Diversity and Structure of Managed and Semi-natural Populations of Cocoa (Theobroma cacao) in the Huallaga and Ucayali Valleys of Peru

PubMed Central

ZHANG, DAPENG; AREVALO-GARDINI, ENRIQUE; MISCHKE, SUE; ZÚÑIGA-CERNADES, LUIS; BARRETO-CHAVEZ, ALEJANDRO; AGUILA, JORGE ADRIAZOLA DEL

2006-01-01

• Background and Aims Cocoa (Theobroma cacao) is indigenous to the Amazon region of South America, and it is well known that the Peruvian Amazon harbours a large number of diverse cocoa populations. A small fraction of the diversity has been collected and maintained as an ex-situ germplasm repository in Peru. However, incorrect labelling of accessions and lack of information on genetic diversity have hindered efficient conservation and use of this germplasm. This study targeted assessment of genetic diversity and population structure in a managed and a semi-natural population. •Methods Using a capillary electrophoresis genotyping system, 105 cocoa accessions collected from the Huallaga and Ucayali valleys of Peru were fingerprinted. Based on 15 loci SSR profiles, genetic identity was examined for each accession and duplicates identified, population structure assessed and genetic diversity analysed in these two populations. •Key Results Ten synonymous mislabelled groups were identified among the 105 accessions. The germplasm group in the Huallaga valley was clearly separated from the group in Ucayali valley by the Bayesian assignment test. The Huallaga group has lower genetic diversity, both in terms of allelic richness and of gene diversity, than the Ucayali group. Analysis of molecular variance suggested genetic substructure in the Ucayali group. Significant spatial correlation between genetic distance and geographical distances was detected in the Ucayali group by Mantel tests. •Conclusions These results substantiate the hypothesis that the Peruvian Amazon hosts a high level of cocoa genetic diversity, and the diversity has a spatial structure. The introduction of exotic seed populations into the Peruvian Amazon is changing the cocoa germplasm spectrum in this region. The spatial structure of cocoa diversity recorded here highlights the need for additional collecting and conservation measures for natural and semi-natural cocoa populations. PMID:16845139

Sky island bird populations isolated by ancient genetic barriers are characterized by different song traits than those isolated by recent deforestation.

PubMed

Purushotham, Chetana B; Robin, V V

2016-10-01

Various mechanisms of isolation can structure populations and result in cultural and genetic differentiation. Similar to genetic markers, for songbirds, culturally transmitted sexual signals such as breeding song can be used as a measure of differentiation as songs can also be impacted by geographic isolation resulting in population-level differences in song structure. Several studies have found differences in song structure either across ancient geographic barriers or across contemporary habitat barriers owing to deforestation. However, very few studies have examined the effect of both ancient barriers and recent deforestation in the same system. In this study, we examined the geographic variation in song structure across six populations of the White-bellied Shortwing, a threatened and endemic songbird species complex found on isolated mountaintops or "sky islands" of the Western Ghats. While some sky islands in the system are isolated by ancient valleys, others are separated by deforestation. We examined 14 frequency and temporal spectral traits and two syntax traits from 835 songs of 38 individuals across the six populations. We identified three major song clusters based on a discriminant model of spectral traits, degree of similarity of syntax features, as well as responses of birds to opportunistic playback. However, some traits like complex vocal mechanisms (CVM), relating to the use of syrinxes, clearly differentiated both ancient and recently fragmented populations. We suggest that CVMs may have a cultural basis and can be used to identify culturally isolated populations that cannot be differentiated using genetic markers or commonly used frequency-based song traits. Our results demonstrate the use of bird songs to reconstruct phylogenetic groups and impacts of habitat fragmentation even in complex scenarios of historic and contemporary isolation.

Sex-specific genetic diversity is shaped by cultural factors in Inner Asian human populations.

PubMed

Marchi, Nina; Hegay, Tatyana; Mennecier, Philippe; Georges, Myriam; Laurent, Romain; Whitten, Mark; Endicott, Philipp; Aldashev, Almaz; Dorzhu, Choduraa; Nasyrova, Firuza; Chichlo, Boris; Ségurel, Laure; Heyer, Evelyne

2017-04-01

Sex-specific genetic structures have been previously documented worldwide in humans, even though causal factors have not always clearly been identified. In this study, we investigated the impact of ethnicity, geography and social organization on the sex-specific genetic structure in Inner Asia. Furthermore, we explored the process of ethnogenesis in multiple ethnic groups. We sampled DNA in Central and Northern Asia from 39 populations of Indo-Iranian and Turkic-Mongolic native speakers. We focused on genetic data of the Y chromosome and mitochondrial DNA. First, we compared the frequencies of haplogroups to South European and East Asian populations. Then, we investigated the genetic differentiation for eight Y-STRs and the HVS1 region, and tested for the effect of geography and ethnicity on such patterns. Finally, we reconstructed the male demographic history, inferred split times and effective population sizes of different ethnic groups. Based on the haplogroup data, we observed that the Indo-Iranian- and Turkic-Mongolic-speaking populations have distinct genetic backgrounds. However, each population showed consistent mtDNA and Y chromosome haplogroups patterns. As expected in patrilocal populations, we found that the Y-STRs were more structured than the HVS1. While ethnicity strongly influenced the genetic diversity on the Y chromosome, geography better explained that of the mtDNA. Furthermore, when looking at various ethnic groups, we systematically found a genetic split time older than historical records, suggesting a cultural rather than biological process of ethnogenesis. This study highlights that, in Inner Asia, specific cultural behaviors, especially patrilineality and patrilocality, leave a detectable signature on the sex-specific genetic structure. © 2017 Wiley Periodicals, Inc.

Conservation genetics of evolutionary lineages of the endangered mountain yellow-legged frog, Rana muscosa (Amphibia: Ranidae), in southern California

USGS Publications Warehouse

Schoville, Sean D.; Tustall, Tate S.; Vredenburg, Vance T.; Backlin, Adam R.; Gallegos, Elizabeth; Wood, Dustin A.; Fisher, Robert N.

2011-01-01

Severe population declines led to the listing of southern California Rana muscosa (Ranidae) as endangered in 2002. Nine small populations inhabit watersheds in three isolated mountain ranges, the San Gabriel, San Bernardino and San Jacinto. One population from the Dark Canyon tributary in the San Jacinto Mountains has been used to establish a captive breeding population at the San Diego Zoo Institute for Conservation Research. Because these populations may still be declining, it is critical to gather information on how genetic variation is structured in these populations and what historical inter-population connectivity existed between populations. Additionally, it is not clear whether these populations are rapidly losing genetic diversity due to population bottlenecks. Using mitochondrial and microsatellite data, we examine patterns of genetic variation in southern California and one of the last remaining populations of R. muscosa in the southern Sierra Nevada. We find low levels of genetic variation within each population and evidence of genetic bottlenecks. Additionally, substantial population structure is evident, suggesting a high degree of historical isolation within and between mountain ranges. Based on estimates from a multi-population isolation with migration analysis, these populations diversified during glacial episodes of the Pleistocene, with little gene flow during population divergence. Our data demonstrate that unique evolutionary lineages of R. muscosa occupy each mountain range in southern California and should be managed separately. The captive breeding program at Dark Canyon is promising, although mitigating the loss of neutral genetic diversity relative to the natural population might require additional breeding frogs.

The correlation between ancestry and color in two cities of Northeast Brazil with contrasting ethnic compositions

PubMed Central

Magalhães da Silva, Thiago; Sandhya Rani, M R; de Oliveira Costa, Gustavo Nunes; Figueiredo, Maria A; Melo, Paulo S; Nascimento, João F; Molyneaux, Neil D; Barreto, Maurício L; Reis, Mitermayer G; Teixeira, M Glória; Blanton, Ronald E

2015-01-01

The degree of admixture in Brazil between historically isolated populations is complex and geographically variable. Studies differ as to what the genetic and phenotypic consequences of this mixing have been. In Northeastern Brazil, we enrolled 522 residents of Salvador and 620 of Fortaleza whose distributions of self-declared color were comparable to those in the national census. Using the program Structure and principal components analysis there was a clear correlation between biogeographic ancestry and categories of skin color. This correlation with African ancestry was stronger in Salvador (r=0.585; P<0.001) than in Fortaleza (r=0.236; P<0.001). In Fortaleza, although self-declared blacks had a greater proportion of European ancestry, they had more African ancestry than the other categories. When the populations were analyzed without pseudoancestors, as in some studies, the relationship of ‘race' to genetic ancestry tended to diffuse or disappear. The inclusion of different African populations also influenced ancestry estimates. The percentage of unlinked ancestry informative markers in linkage disequilibrium, a measure of population structure, was 3–5 times higher in both Brazilian populations than expected by chance. We propose that certain methods, ascertainment bias and population history of the specific populations surveyed can result in failure to demonstrate a correlation between skin color and genetic ancestry. Population structure in Brazil has important implications for genetic studies, but genetic ancestry is irrelevant for how individuals are treated in society, their health, their income or their inclusion. These track more closely with perceived skin color than genetic ancestry. PMID:25293718

GENETIC STRUCTURE OF NORWAY SPRUCE (PICEA ABIES): CONCORDANCE OF MORPHOLOGICAL AND ALLOZYMIC VARIATION.

PubMed

Lagercrantz, Ulf; Ryman, Nils

1990-02-01

This study describes the population structure of Norway spruce (Picea abies) as revealed by protein polymorphisms and morphological variation. Electrophoretically detectable genetic variability was examined at 22 protein loci in 70 populations from the natural range of the species in Europe. Like other conifers, Norway spruce exhibits a relatively large amount of genetic variability and little differentiation among populations. Sixteen polymorphic loci (73%) segregate for a total of 51 alleles, and average heterozygosity per population is 0.115. Approximately 5% of the total genetic diversity is explained by differences between populations (G ST = 0.052), and Nei's standard genetic distance is less than 0.04 in all cases. We suggest that the population structure largely reflects relatively recent historical events related to the last glaciation and that Norway spruce is still in a process of adaptation and differentiation. There is a clear geographic pattern in the variation of allele frequencies. A major part of the allelefrequency variation can be accounted for by a few synthetic variables (principal components), and 80% of the variation of the first principal component is "explained" by latitude and longitude. The central European populations are consistently depauperate of genetic variability, most likely as an effect of severe restrictions of population size during the last glaciation. The pattern of differentiation at protein loci is very similar to that observed for seven morphological traits examined. This similarity suggests that the same evolutionary forces have acted upon both sets of characters. © 1990 The Society for the Study of Evolution.

The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing.

PubMed

Catchen, Julian; Bassham, Susan; Wilson, Taylor; Currey, Mark; O'Brien, Conor; Yeates, Quick; Cresko, William A

2013-06-01

Understanding how genetic variation is partitioned across genomes within and among populations is a fundamental problem in ecological and evolutionary genetics. To address this problem, we studied the threespine stickleback fish, which has repeatedly undergone parallel phenotypic and genetic differentiation when oceanic fish have invaded freshwater habitats. While significant evolutionary genetic research has been performed using stickleback from geographic regions that have been deglaciated in the last 20 000 years, less research has focused on freshwater populations that predate the last glacial maximum. We performed restriction-site associated DNA-sequencing (RAD-seq) based population genomic analyses on stickleback from across Oregon, which was not glaciated during the last maximum. We sampled stickleback from coastal, Willamette Basin and central Oregon sites, analysed their genetic diversity using RAD-seq, performed structure analyses, reconstructed their phylogeographic history and tested the hypothesis of recent stickleback introduction into central Oregon, where incidence of this species was only recently documented. Our results showed a clear phylogeographic break between coastal and inland populations, with oceanic populations exhibiting the lowest levels of divergence from one another. Willamette Basin and central Oregon populations formed a clade of closely related populations, a finding consistent with a recent introduction of stickleback into central Oregon. Finally, genome-wide analysis of genetic diversity (π) and correlations of alleles within individuals in subpopulations (FIS) supported a role for introgressive hybridization in coastal populations and a recent expansion in central Oregon. Our results exhibit the power of next-generation sequencing genomic approaches such as RAD-seq to identify both historical population structure and recent colonization history. © 2013 John Wiley & Sons Ltd.

Genetic diversity and structure of Sinopodophyllum hexandrum (Royle) Ying in the Qinling Mountains, China.

PubMed

Liu, Wei; Yin, Dongxue; Liu, Jianjun; Li, Na

2014-01-01

Sinopodophyllum hexandrum is an important medicinal plant whose genetic diversity must be conserved because it is endangered. The Qinling Mts. are a S. hexandrum distribution area that has unique environmental features that highly affect the evolution of the species. To provide the reference data for evolutionary and conservation studies, the genetic diversity and population structure of S. hexandrum in its overall natural distribution areas in the Qinling Mts. were investigated through inter-simple sequence repeats analysis of 32 natural populations. The 11 selected primers generated a total of 135 polymorphic bands. S. hexandrum genetic diversity was low within populations (average He = 0.0621), but higher at the species level (He = 0.1434). Clear structure and high genetic differentiation among populations were detected by using the unweighted pair group method for arithmetic averages, principle coordinate analysis and Bayesian clustering. The clustering approaches supported a division of the 32 populations into three major groups, for which analysis of molecular variance confirmed significant variation (63.27%) among populations. The genetic differentiation may have been attributed to the limited gene flow (Nm = 0.3587) in the species. Isolation by distance among populations was determined by comparing genetic distance versus geographic distance by using the Mantel test. Result was insignificant (r = 0.212, P = 0.287) at 0.05, showing that their spatial pattern and geographic locations are not correlated. Given the low within-population genetic diversity, high differentiation among populations and the increasing anthropogenic pressure on the species, in situ conservation measures were recommended to preserve S. hexandrum in Qinling Mts., and other populations must be sampled to retain as much genetic diversity of the species to achieve ex situ preservation as a supplement to in situ conservation.

Genetic Diversity and Structure of Sinopodophyllum hexandrum (Royle) Ying in the Qinling Mountains, China

PubMed Central

Liu, Wei; Yin, Dongxue; Liu, Jianjun; Li, Na

2014-01-01

Sinopodophyllum hexandrum is an important medicinal plant whose genetic diversity must be conserved because it is endangered. The Qinling Mts. are a S. hexandrum distribution area that has unique environmental features that highly affect the evolution of the species. To provide the reference data for evolutionary and conservation studies, the genetic diversity and population structure of S. hexandrum in its overall natural distribution areas in the Qinling Mts. were investigated through inter-simple sequence repeats analysis of 32 natural populations. The 11 selected primers generated a total of 135 polymorphic bands. S. hexandrum genetic diversity was low within populations (average He = 0.0621), but higher at the species level (He = 0.1434). Clear structure and high genetic differentiation among populations were detected by using the unweighted pair group method for arithmetic averages, principle coordinate analysis and Bayesian clustering. The clustering approaches supported a division of the 32 populations into three major groups, for which analysis of molecular variance confirmed significant variation (63.27%) among populations. The genetic differentiation may have been attributed to the limited gene flow (Nm = 0.3587) in the species. Isolation by distance among populations was determined by comparing genetic distance versus geographic distance by using the Mantel test. Result was insignificant (r = 0.212, P = 0.287) at 0.05, showing that their spatial pattern and geographic locations are not correlated. Given the low within-population genetic diversity, high differentiation among populations and the increasing anthropogenic pressure on the species, in situ conservation measures were recommended to preserve S. hexandrum in Qinling Mts., and other populations must be sampled to retain as much genetic diversity of the species to achieve ex situ preservation as a supplement to in situ conservation. PMID:25333788

The fine-scale genetic structure and evolution of the Japanese population.

PubMed

Takeuchi, Fumihiko; Katsuya, Tomohiro; Kimura, Ryosuke; Nabika, Toru; Isomura, Minoru; Ohkubo, Takayoshi; Tabara, Yasuharu; Yamamoto, Ken; Yokota, Mitsuhiro; Liu, Xuanyao; Saw, Woei-Yuh; Mamatyusupu, Dolikun; Yang, Wenjun; Xu, Shuhua; Teo, Yik-Ying; Kato, Norihiro

2017-01-01

The contemporary Japanese populations largely consist of three genetically distinct groups-Hondo, Ryukyu and Ainu. By principal-component analysis, while the three groups can be clearly separated, the Hondo people, comprising 99% of the Japanese, form one almost indistinguishable cluster. To understand fine-scale genetic structure, we applied powerful haplotype-based statistical methods to genome-wide single nucleotide polymorphism data from 1600 Japanese individuals, sampled from eight distinct regions in Japan. We then combined the Japanese data with 26 other Asian populations data to analyze the shared ancestry and genetic differentiation. We found that the Japanese could be separated into nine genetic clusters in our dataset, showing a marked concordance with geography; and that major components of ancestry profile of Japanese were from the Korean and Han Chinese clusters. We also detected and dated admixture in the Japanese. While genetic differentiation between Ryukyu and Hondo was suggested to be caused in part by positive selection, genetic differentiation among the Hondo clusters appeared to result principally from genetic drift. Notably, in Asians, we found the possibility that positive selection accentuated genetic differentiation among distant populations but attenuated genetic differentiation among close populations. These findings are significant for studies of human evolution and medical genetics.

Investigating the anatomy of magnetosheath jets - MMS observations

NASA Astrophysics Data System (ADS)

Karlsson, Tomas; Plaschke, Ferdinand; Hietala, Heli; Archer, Martin; Blanco-Cano, Xóchitl; Kajdič, Primož; Lindqvist, Per-Arne; Marklund, Göran; Gershman, Daniel J.

2018-04-01

We use Magnetosphere Multiscale (MMS) mission data to investigate a small number of magnetosheath jets, which are localized and transient increases in dynamic pressure, typically due to a combined increase in plasma velocity and density. For two approximately hour-long intervals in November, 2015 we found six jets, which are of two distinct types. (a) Two of the jets are associated with the magnetic field discontinuities at the boundary between the quasi-parallel and quasi-perpendicular magnetosheath. Straddling the boundary, the leading part of these jets contains an ion population similar to the quasi-parallel magnetosheath, while the trailing part contains ion populations similar to the quasi-perpendicular magnetosheath. Both populations are, however, cooler than the surrounding ion populations. These two jets also have clear increases in plasma density and magnetic field strength, correlated with a velocity increase. (b) Three of the jets are found embedded within the quasi-parallel magnetosheath. They contain ion populations similar to the surrounding quasi-parallel magnetosheath, but with a lower temperature. Out of these three jets, two have a simple structure. For these two jets, the increases in density and magnetic field strength are correlated with the dynamic pressure increases. The other jet has a more complicated structure, and no clear correlations between density, magnetic field strength and dynamic pressure. This jet has likely interacted with the magnetosphere, and contains ions similar to the jets inside the quasi-parallel magnetosheath, but shows signs of adiabatic heating. All jets are associated with emissions of whistler, lower hybrid, and broadband electrostatic waves, as well as approximately 10 s period electromagnetic waves with a compressional component. The latter have a Poynting flux of up to 40 µW m-2 and may be energetically important for the evolution of the jets, depending on the wave excitation mechanism. Only one of the jets is likely to have modified the surrounding magnetic field into a stretched configuration, as has recently been reported in other studies. None of the jets are associated with clear signatures of either magnetic or thermal pressure gradient forces acting on them. The different properties of the two types also point to different generation mechanisms, which are discussed here. Their different properties and origins suggest that the two types of jets need to be separated in future statistical and simulation studies.

Absence of geographical structure of chloroplast DNA variation in sallow, Salix caprea L.

PubMed

Palmé, A E; Semerikov, V; Lascoux, M

2003-11-01

In the present study, we have used PCR-RFLP markers to investigate the chloroplast DNA variation in 24 European populations of Salix caprea L. A subset of these populations has also been analysed with chloroplast microsatellites. The main feature of both markers is the absence of a clear geographic structure (G(ST(PCR-RFLP))=0.090, G(ST(microsatellites))=-0.017) and high levels of variation within populations. This lack of phylogeographic structure in S. caprea is suggested to be the consequence of the joint action of several factors: (i) presence of intermediate latitude refugia with large population sizes during the last glacial maximum, (ii) a high speed of recolonisation and dispersal ability, (iii) a high mutation rate and (iv) extensive hybridisation with other willow species. In addition to the S. caprea samples, a limited number of individuals from several other Salix species were also analysed with PCR-RFLP: S. cinerea, S. aurita, S. purpurea, S. atrocinerea, S. appendiculata, S. elaeagnos, S. fragilis and S. alba. Many of the haplotypes found in Salix caprea were also detected in S. cinerea, S. aurita, S. purpurea, S. atrocinerea and/ or S. appendiculata but not in S. alba, S. elaeagnos or S. fragilis. Our data suggest that hybridisation and gene flow have occurred within these two groups but not between them.

Major Land Clearing Fires, Kalimantan, Borneo, Indonesia

NASA Technical Reports Server (NTRS)

1991-01-01

These many and intense land clearing fires in the Kalimantan region of the island of Borneo, Indonesia (3.5S, 113.5E) are indicative of the many deforestation activities on a worldwide scale. In order to feed and house ever increasing populations, more cleared land is required for agriculture to feed ever increasing populations. More pasture lands are needed for livestock. And, more cleared lands are needed for housing.

Excavating past population structures by surname-based sampling: the genetic legacy of the Vikings in northwest England

PubMed Central

Bowden, Georgina R.; Balaresque, Patricia; King, Turi E.; Hansen, Ziff; Lee, Andrew C.; Pergl-Wilson, Giles; Hurley, Emma; Roberts, Stephen J.; Waite, Patrick; Jesch, Judith; Jones, Abigail L.; Thomas, Mark G.; Harding, Stephen E.; Jobling, Mark A.

2009-01-01

The genetic structures of past human populations are obscured by recent migrations and expansions, and can been observed only indirectly by inference from modern samples. However, the unique link between a heritable cultural marker, the patrilineal surname, and a genetic marker, the Y chromosome, provides a means to target sets of modern individuals that might resemble populations at the time of surname establishment. As a test case, we studied samples from the Wirral peninsula and West Lancashire, in northwest England. Place names and archaeology show clear evidence of a past Viking presence, but heavy immigration and population growth since the Industrial Revolution are likely to have weakened the genetic signal of a thousand-year-old Scandinavian contribution. Samples ascertained on the basis of two generations of residence were compared with independent samples based on known ancestry in the region, plus the possession of a surname known from historical records to have been present there in medieval times. The Y-chromosomal haplotypes of these two sets of samples are significantly different, and in admixture analyses the surname-ascertained samples show markedly greater Scandinavian ancestry proportions, supporting the idea that northwest England was once heavily populated by Scandinavian settlers. The method of historical surname-based ascertainment promises to allow investigation of the influence of migration and drift over the last few centuries in changing the population structure of Britain, and will have general utility in other regions where surnames are patrilineal and suitable historical records survive. PMID:18032405

Fine-scaled human genetic structure revealed by SNP microarrays.

PubMed

Xing, Jinchuan; Watkins, W Scott; Witherspoon, David J; Zhang, Yuhua; Guthery, Stephen L; Thara, Rangaswamy; Mowry, Bryan J; Bulayeva, Kazima; Weiss, Robert B; Jorde, Lynn B

2009-05-01

We report an analysis of more than 240,000 loci genotyped using the Affymetrix SNP microarray in 554 individuals from 27 worldwide populations in Africa, Asia, and Europe. To provide a more extensive and complete sampling of human genetic variation, we have included caste and tribal samples from two states in South India, Daghestanis from eastern Europe, and the Iban from Malaysia. Consistent with observations made by Charles Darwin, our results highlight shared variation among human populations and demonstrate that much genetic variation is geographically continuous. At the same time, principal components analyses reveal discernible genetic differentiation among almost all identified populations in our sample, and in most cases, individuals can be clearly assigned to defined populations on the basis of SNP genotypes. All individuals are accurately classified into continental groups using a model-based clustering algorithm, but between closely related populations, genetic and self-classifications conflict for some individuals. The 250K data permitted high-level resolution of genetic variation among Indian caste and tribal populations and between highland and lowland Daghestani populations. In particular, upper-caste individuals from Tamil Nadu and Andhra Pradesh form one defined group, lower-caste individuals from these two states form another, and the tribal Irula samples form a third. Our results emphasize the correlation of genetic and geographic distances and highlight other elements, including social factors that have contributed to population structure.

De novo transcriptome assembly, development of EST-SSR markers and population genetic analyses for the desert biomass willow, Salix psammophila

PubMed Central

Jia, Huixia; Yang, Haifeng; Sun, Pei; Li, Jianbo; Zhang, Jin; Guo, Yinghua; Han, Xiaojiao; Zhang, Guosheng; Lu, Mengzhu; Hu, Jianjun

2016-01-01

Salix psammophila, a sandy shrub known as desert willow, is regarded as a potential biomass feedstock and plays an important role in maintaining local ecosystems. However, a lack of genomic data and efficient molecular markers limit the study of its population evolution and genetic breeding. In this study, chromosome counts, flow cytometry and SSR analyses indicated that S. psammophila is tetraploid. A total of 6,346 EST-SSRs were detected based on 71,458 de novo assembled unigenes from transcriptome data. Twenty-seven EST-SSR markers were developed to evaluate the genetic diversity and population structure of S. psammophila from eight natural populations in Northern China. High levels of genetic diversity (mean 10.63 alleles per locus; mean HE 0.689) were dectected in S. psammophila. The weak population structure and little genetic differentiation (pairwise FST = 0.006–0.016) were found among Population 1-Population 7 (Pop1-Pop7; Inner Mongolia and Shaanxi), but Pop8 (Ningxia) was clearly separated from Pop1-Pop7 and moderate differentiation (pairwise FST = 0.045–0.055) was detected between them, which may be influenced by local habitat conditions. Molecular variance analyses indicated that most of the genetic variation (94.27%) existed within populations. These results provide valuable genetic informations for natural resource conservation and breeding programme optimisation of S. psammophila. PMID:27995985

Photometric Application of the Gram Stain Method To Characterize Natural Bacterial Populations in Aquatic Environments

PubMed Central

Saida, H.; Ytow, N.; Seki, H.

1998-01-01

The Gram stain method was applied to the photometric characterization of aquatic bacterial populations with a charge-coupled device camera and an image analyzer. Escherichia coli and Bacillus subtilis were used as standards of typical gram-negative and gram-positive bacteria, respectively. A mounting agent to obtain clear images of Gram-stained bacteria on Nuclepore membrane filters was developed. The bacterial stainability by the Gram stain was indicated by the Gram stain index (GSI), which was applicable not only to the dichotomous classification of bacteria but also to the characterization of cell wall structure. The GSI spectra of natural bacterial populations in water with various levels of eutrophication showed a distinct profile, suggesting possible staining specificity that indicates the presence of a particular bacterial population in the aquatic environment. PMID:9464416

Deep sequencing of evolving pathogen populations: applications, errors, and bioinformatic solutions

PubMed Central

2014-01-01

Deep sequencing harnesses the high throughput nature of next generation sequencing technologies to generate population samples, treating information contained in individual reads as meaningful. Here, we review applications of deep sequencing to pathogen evolution. Pioneering deep sequencing studies from the virology literature are discussed, such as whole genome Roche-454 sequencing analyses of the dynamics of the rapidly mutating pathogens hepatitis C virus and HIV. Extension of the deep sequencing approach to bacterial populations is then discussed, including the impacts of emerging sequencing technologies. While it is clear that deep sequencing has unprecedented potential for assessing the genetic structure and evolutionary history of pathogen populations, bioinformatic challenges remain. We summarise current approaches to overcoming these challenges, in particular methods for detecting low frequency variants in the context of sequencing error and reconstructing individual haplotypes from short reads. PMID:24428920

Contributions of historical and contemporary geographic and environmental factors to phylogeographic structure in a Tertiary relict species, Emmenopterys henryi (Rubiaceae)

PubMed Central

Zhang, Yong-Hua; Wang, Ian J.; Comes, Hans Peter; Peng, Hua; Qiu, Ying-Xiong

2016-01-01

Examining how historical and contemporary geographic and environmental factors contribute to genetic divergence at different evolutionary scales is a central yet largely unexplored question in ecology and evolution. Here, we examine this key question by investigating how environmental and geographic factors across different epochs have driven genetic divergence at deeper (phylogeographic) and shallower (landscape genetic) evolutionary scales in the Chinese Tertiary relict tree Emmenopterys henryi. We found that geography played a predominant role at all levels – phylogeographic clades are broadly geographically structured, the deepest levels of divergence are associated with major geological or pre-Quaternary climatic events, and isolation by distance (IBD) primarily explained population genetic structure. However, environmental factors are clearly also important – climatic fluctuations since the Last Interglacial (LIG) have likely contributed to phylogeographic structure, and the population genetic structure (in our AFLP dataset) was partly explained by isolation by environment (IBE), which may have resulted from natural selection in environments with divergent climates. Thus, historical and contemporary geography and historical and contemporary environments have all shaped patterns of genetic structure in E. henryi, and, in fact, changes in the landscape through time have also been critical factors. PMID:27137438

Contributions of historical and contemporary geographic and environmental factors to phylogeographic structure in a Tertiary relict species, Emmenopterys henryi (Rubiaceae).

PubMed

Zhang, Yong-Hua; Wang, Ian J; Comes, Hans Peter; Peng, Hua; Qiu, Ying-Xiong

2016-05-03

Examining how historical and contemporary geographic and environmental factors contribute to genetic divergence at different evolutionary scales is a central yet largely unexplored question in ecology and evolution. Here, we examine this key question by investigating how environmental and geographic factors across different epochs have driven genetic divergence at deeper (phylogeographic) and shallower (landscape genetic) evolutionary scales in the Chinese Tertiary relict tree Emmenopterys henryi. We found that geography played a predominant role at all levels - phylogeographic clades are broadly geographically structured, the deepest levels of divergence are associated with major geological or pre-Quaternary climatic events, and isolation by distance (IBD) primarily explained population genetic structure. However, environmental factors are clearly also important - climatic fluctuations since the Last Interglacial (LIG) have likely contributed to phylogeographic structure, and the population genetic structure (in our AFLP dataset) was partly explained by isolation by environment (IBE), which may have resulted from natural selection in environments with divergent climates. Thus, historical and contemporary geography and historical and contemporary environments have all shaped patterns of genetic structure in E. henryi, and, in fact, changes in the landscape through time have also been critical factors.

Substructure of a Tunisian Berber population as inferred from 15 autosomal short tandem repeat loci.

PubMed

Khodjet-El-Khil, Houssein; Fadhlaoui-Zid, Karima; Gusmão, Leonor; Alves, Cíntia; Benammar-Elgaaied, Amel; Amorim, Antonio

2008-08-01

Currently, language and cultural practices are the only criteria to distinguish between Berber autochthonous Tunisian populations. To evaluate these populations' possible genetic structure and differentiation, we have analyzed 15 autosomal short tandem repeat loci (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, TH01, TPOX, VWA, D2S1338, and D19S433) in three southern Tunisian Berber groups: Sened, Matmata, and Chenini-Douiret. The exact test of population differentiation based on allele frequencies at the 15 loci shows significant P values at 7 loci between Chenini-Douiret and both Sened and Matmata, whereas just 5 loci show significant P values between Sened and Matmata. Comparative analyses between the three Berber groups based on genetic distances show that P values for F(ST) distances are significant between the three Berber groups. Population analysis performed using Structure shows a clear differentiation between these Berber groups, with strong genetic isolation of Chenini-Douiret. These results confirm at the autosomal level the high degree of heterogeneity of Tunisian Berber populations that had been previously reported for uniparental markers.

Population structure and temporal maintenance of the multihost fungal pathogen Botrytis cinerea: causes and implications for disease management.

PubMed

Walker, Anne-Sophie; Gladieux, Pierre; Decognet, Véronique; Fermaud, Marc; Confais, Johann; Roudet, Jean; Bardin, Marc; Bout, Alexandre; Nicot, Philippe C; Poncet, Christine; Fournier, Elisabeth

2015-04-01

Understanding the causes of population subdivision is of fundamental importance, as studying barriers to gene flow between populations may reveal key aspects of the process of adaptive divergence and, for pathogens, may help forecasting disease emergence and implementing sound management strategies. Here, we investigated population subdivision in the multihost fungus Botrytis cinerea based on comprehensive multiyear sampling on different hosts in three French regions. Analyses revealed a weak association between population structure and geography, but a clear differentiation according to the host plant of origin. This was consistent with adaptation to hosts, but the distribution of inferred genetic clusters and the frequency of admixed individuals indicated a lack of strict host specificity. Differentiation between individuals collected in the greenhouse (on Solanum) and outdoor (on Vitis and Rubus) was stronger than that observed between individuals from the two outdoor hosts, probably reflecting an additional isolating effect associated with the cropping system. Three genetic clusters coexisted on Vitis but did not persist over time. Linkage disequilibrium analysis indicated that outdoor populations were regularly recombining, whereas clonality was predominant in the greenhouse. Our findings open up new perspectives for disease control by managing plant debris in outdoor conditions and reinforcing prophylactic measures indoor. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Genetic structure and seed-mediated dispersal rates of an endangered shrub in a fragmented landscape: a case study for Juniperus communis in northwestern Europe

PubMed Central

2011-01-01

Background Population extinction risk in a fragmented landscape is related to the differential ability of the species to spread its genes across the landscape. The impact of landscape fragmentation on plant population dynamics will therefore vary across different spatial scales. We quantified successful seed-mediated dispersal of the dioecious shrub Juniperus communis in a fragmented landscape across northwestern Europe by using amplified fragment length polymorphism (AFLP) markers. Furthermore we investigated the genetic diversity and structure on two spatial scales: across northwestern Europe and across Flanders (northern Belgium). We also studied whether seed viability and populations size were correlated with genetic diversity. Results Unexpectedly, estimated seed-mediated dispersal rates were quite high and ranged between 3% and 14%. No population differentiation and no spatial genetic structure were detected on the local, Flemish scale. A significant low to moderate genetic differentiation between populations was detected at the regional, northwest European scale (PhiPT = 0.10). In general, geographically nearby populations were also genetically related. High levels of within-population genetic diversity were detected but no correlation was found between any genetic diversity parameter and population size or seed viability. Conclusions In northwestern Europe, landscape fragmentation has lead to a weak isolation-by-distance pattern but not to genetic impoverishment of common juniper. Substantial rates of successful migration by seed-mediated gene flow indicate a high dispersal ability which could enable Juniperus communis to naturally colonize suitable habitats. However, it is not clear whether the observed levels of migration will suffice to counterbalance the effects of genetic drift in small populations on the long run. PMID:21859457

Genetic structure and seed-mediated dispersal rates of an endangered shrub in a fragmented landscape: a case study for Juniperus communis in northwestern Europe.

PubMed

Vanden-Broeck, An; Gruwez, Robert; Cox, Karen; Adriaenssens, Sandy; Michalczyk, Inga M; Verheyen, Kris

2011-08-22

Population extinction risk in a fragmented landscape is related to the differential ability of the species to spread its genes across the landscape. The impact of landscape fragmentation on plant population dynamics will therefore vary across different spatial scales. We quantified successful seed-mediated dispersal of the dioecious shrub Juniperus communis in a fragmented landscape across northwestern Europe by using amplified fragment length polymorphism (AFLP) markers. Furthermore we investigated the genetic diversity and structure on two spatial scales: across northwestern Europe and across Flanders (northern Belgium). We also studied whether seed viability and populations size were correlated with genetic diversity. Unexpectedly, estimated seed-mediated dispersal rates were quite high and ranged between 3% and 14%. No population differentiation and no spatial genetic structure were detected on the local, Flemish scale. A significant low to moderate genetic differentiation between populations was detected at the regional, northwest European scale (PhiPT = 0.10). In general, geographically nearby populations were also genetically related. High levels of within-population genetic diversity were detected but no correlation was found between any genetic diversity parameter and population size or seed viability. In northwestern Europe, landscape fragmentation has lead to a weak isolation-by-distance pattern but not to genetic impoverishment of common juniper. Substantial rates of successful migration by seed-mediated gene flow indicate a high dispersal ability which could enable Juniperus communis to naturally colonize suitable habitats. However, it is not clear whether the observed levels of migration will suffice to counterbalance the effects of genetic drift in small populations on the long run.

Forest clearing in the Ecuadorian Amazon: A study of patterns over space and time

PubMed Central

Pan, William; Carr, David; Barbieri, Alisson; Bilsborrow, Richard; Suchindran, Chirayath

2010-01-01

This study tests four hypotheses related to forest clearing over time in Ecuador’s northern Amazon: (1) a larger increase in population over time on a farm (finca) leads to more deforestation; (2) rates of forest clearing surrounding four primary reference communities differ (spatial heterogeneity); (3) fincas farther from towns/communities experience lower rates of forest clearing over time; and (4) forest clearing differs by finca settlement cohort, viz., by year of establishment of the finca. In this paper, we examine the relationship between forest clearing and key variables over time, and compare three statistical models—OLS, random effects, and spatial regression—to test hypotheses. Descriptive analyses indicate that 7–15% of forest area was cleared on fincas between 1990 and 1999; that more recently established fincas experienced more rapid forest clearing; and that population size and forest clearing are both related to distance from a major community. Controlling for key variables, model results indicate that an increase in population size is significantly related to more forest clearing; rates of forest clearing around the four major communities are not significantly different; distances separating fincas and communities are not significantly related to deforestation; and deforestation rates are higher among more recently established fincas. Key policy implications include the importance of reducing population growth and momentum through measures such as improving information about and provision of family planning services; increasing the low level of girls education to delay and reduce fertility; and expanding credit and agricultural extension services to increase agricultural intensification. PMID:20703367

Local scale connectivity in the cave-dwelling brooding fish Apogon imberbis

NASA Astrophysics Data System (ADS)

Muths, Delphine; Rastorgueff, Pierre-Alexandre; Selva, Marjorie; Chevaldonné, Pierre

2015-01-01

A lower degree of population connectivity is generally expected for species living in a naturally fragmented habitat than for species living in a continuum of suitable environment. Due to clear-cut environmental conditions with the surrounding littoral zone, underwater marine caves of the Mediterranean Sea constitute a good model to explore the effect of habitat discontinuity on the population structure of their inhabitants. With this goal, the genetic population structure of Apogon imberbis, a mouth-brooding teleost, was explored using the mitochondrial cytochrome b gene and 7 nuclear microsatellite loci from 164 fishes sampled at the micro-scale (ca. 40 km) of the Marseille area (Bay of Marseille and Calanques coast, in NW Mediterranean). Both marker types indicated a low level of genetic structure within the studied area. We propose that each suitable crack and cavity is used as a stepping-stone habitat between disconnected large cave-habitats. This, together with larval dispersal, ensures enough gene flow between caves to homogenize the genetic pattern at microscale while isolation by distance and by open waters could explain the small structure observed. The present study indicates that the effect of natural fragmentation in connectivity disruption can largely be counter-balanced by life history traits and overlooked details in habitat preferences.

Investigation of Structure in the Light Curves of a Sample of Newly Discovered Long Period Variable Stars

NASA Astrophysics Data System (ADS)

Craine, E. R.; Culver, R. B.; Eykholt, R.; Flurchick, K. M.; Kraus, A. L.; Tucker, R. A.; Walker, D. K.

2015-09-01

Long period variable stars exhibit hump structures, and possibly flares, in their light curves. While the existence of humps is not controversial, the presence of flaring activity is less clear. Mining of a sky survey database of new variable star discoveries (the first MOTESS-GNAT Variable Star Catalog (MG1-VSC)) has led to identification of 47 such stars for which there are sufficient data to explore the presence of anomalous light curve features. We find a number of hump structures, and see one possible flare, suggesting that they are rare events. We present light curves and measured parameters for these stars, and a population statistical analysis.

Multi-scale temporal and spatial variation in genotypic composition of Cladophora-borne Escherichia coli populations in Lake Michigan.

PubMed

Badgley, Brian D; Ferguson, John; Vanden Heuvel, Amy; Kleinheinz, Gregory T; McDermott, Colleen M; Sandrin, Todd R; Kinzelman, Julie; Junion, Emily A; Byappanahalli, Muruleedhara N; Whitman, Richard L; Sadowsky, Michael J

2011-01-01

High concentrations of Escherichia coli in mats of Cladophora in the Great Lakes have raised concern over the continued use of this bacterium as an indicator of microbial water quality. Determining the impacts of these environmentally abundant E. coli, however, necessitates a better understanding of their ecology. In this study, the population structure of 4285 Cladophora-borne E. coli isolates, obtained over multiple three day periods from Lake Michigan Cladophora mats in 2007-2009, was examined by using DNA fingerprint analyses. In contrast to previous studies that have been done using isolates from attached Cladophora obtained over large time scales and distances, the extensive sampling done here on free-floating mats over successive days at multiple sites provided a large dataset that allowed for a detailed examination of changes in population structure over a wide range of spatial and temporal scales. While Cladophora-borne E. coli populations were highly diverse and consisted of many unique isolates, multiple clonal groups were also present and accounted for approximately 33% of all isolates examined. Patterns in population structure were also evident. At the broadest scales, E. coli populations showed some temporal clustering when examined by year, but did not show good spatial distinction among sites. E. coli population structure also showed significant patterns at much finer temporal scales. Populations were distinct on an individual mat basis at a given site, and on individual days within a single mat. Results of these studies indicate that Cladophora-borne E. coli populations consist of a mixture of stable, and possibly naturalized, strains that persist during the life of the mat, and more unique, transient strains that can change over rapid time scales. It is clear that further study of microbial processes at fine spatial and temporal scales is needed, and that caution must be taken when interpolating short term microbial dynamics from results obtained from weekly or monthly samples. Copyright © 2010 Elsevier Ltd. All rights reserved.

Multi-scale temporal and spatial variation in genotypic composition of Cladophora-borne Escherichia coli populations in Lake Michigan

USGS Publications Warehouse

Badgley, B.D.; Ferguson, J.; Heuvel, A.V.; Kleinheinz, G.T.; McDermott, C.M.; Sandrin, T.R.; Kinzelman, J.; Junion, E.A.; Byappanahalli, M.N.; Whitman, R.L.; Sadowsky, M.J.

2011-01-01

High concentrations of Escherichia coli in mats of Cladophora in the Great Lakes have raised concern over the continued use of this bacterium as an indicator of microbial water quality. Determining the impacts of these environmentally abundant E. coli, however, necessitates a better understanding of their ecology. In this study, the population structure of 4285 Cladophora-borne E. coli isolates, obtained over multiple three day periods from Lake Michigan Cladophora mats in 2007-2009, was examined by using DNA fingerprint analyses. In contrast to previous studies that have been done using isolates from attached Cladophora obtained over large time scales and distances, the extensive sampling done here on free-floating mats over successive days at multiple sites provided a large dataset that allowed for a detailed examination of changes in population structure over a wide range of spatial and temporal scales. While Cladophora-borne E. coli populations were highly diverse and consisted of many unique isolates, multiple clonal groups were also present and accounted for approximately 33% of all isolates examined. Patterns in population structure were also evident. At the broadest scales, E. coli populations showed some temporal clustering when examined by year, but did not show good spatial distinction among sites. E. coli population structure also showed significant patterns at much finer temporal scales. Populations were distinct on an individual mat basis at a given site, and on individual days within a single mat. Results of these studies indicate that Cladophora-borne E. coli populations consist of a mixture of stable, and possibly naturalized, strains that persist during the life of the mat, and more unique, transient strains that can change over rapid time scales. It is clear that further study of microbial processes at fine spatial and temporal scales is needed, and that caution must be taken when interpolating short term microbial dynamics from results obtained from weekly or monthly samples.

A Parallel Population Genomic and Hydrodynamic Approach to Fishery Management of Highly-Dispersive Marine Invertebrates: The Case of the Fijian Black-Lip Pearl Oyster Pinctada margaritifera.

PubMed

Lal, Monal M; Southgate, Paul C; Jerry, Dean R; Bosserelle, Cyprien; Zenger, Kyall R

2016-01-01

Fishery management and conservation of marine species increasingly relies on genetic data to delineate biologically relevant stock boundaries. Unfortunately for high gene flow species which may display low, but statistically significant population structure, there is no clear consensus on the level of differentiation required to resolve distinct stocks. The use of fine-scale neutral and adaptive variation, considered together with environmental data can offer additional insights to this problem. Genome-wide genetic data (4,123 SNPs), together with an independent hydrodynamic particle dispersal model were used to inform farm and fishery management in the Fijian black-lip pearl oyster Pinctada margaritifera, where comprehensive fishery management is lacking, and the sustainability of exploitation uncertain. Weak fine-scale patterns of population structure were detected, indicative of broad-scale panmixia among wild oysters, while a hatchery-sourced farmed population exhibited a higher degree of genetic divergence (Fst = 0.0850-0.102). This hatchery-produced population had also experienced a bottleneck (NeLD = 5.1; 95% C.I. = [5.1-5.3]); compared to infinite NeLD estimates for all wild oysters. Simulation of larval transport pathways confirmed the existence of broad-scale mixture by surface ocean currents, correlating well with fine-scale patterns of population structuring. Fst outlier tests failed to detect large numbers of loci supportive of selection, with 2-5 directional outlier SNPs identified (average Fst = 0.116). The lack of biologically significant population genetic structure, absence of evidence for local adaptation and larval dispersal simulation, all indicate the existence of a single genetic stock of P. margaritifera in the Fiji Islands. This approach using independent genomic and oceanographic tools has allowed fundamental insights into stock structure in this species, with transferability to other highly-dispersive marine taxa for their conservation and management.

Population structure and genetic variability within isolates of Grapevine fanleaf virus from a naturally infected vineyard in France: evidence for mixed infection and recombination.

PubMed

Vigne, Emmanuelle; Bergdoll, Marc; Guyader, Sébastien; Fuchs, Marc

2004-08-01

The nematode-borne Grapevine fanleaf virus, from the genus Nepovirus in the family Comoviridae, causes severe degeneration of grapevines in most vineyards worldwide. We characterized 347 isolates from transgenic and conventional grapevines from two vineyard sites in the Champagne region of France for their molecular variant composition. The population structure and genetic diversity were examined in the coat protein gene by IC-RT-PCR-RFLP analysis with EcoRI and StyI, and nucleotide sequencing, respectively. RFLP data suggested that 55 % (191 of 347) of the isolates had a population structure consisting of one predominant variant. Sequencing data of 51 isolates representing the different restrictotypes confirmed the existence of mixed infection with a frequency of 33 % (17 of 51) and showed two major predominant haplotypes representing 71 % (60 of 85) of the sequence variants. Comparative nucleotide diversity among population subsets implied a lack of genetic differentiation according to host (transgenic vs conventional) or field site for most restrictotypes (17 of 18 and 13 of 18) and for haplotypes in most phylogenetic groups (seven of eight and six of eight), respectively. Interestingly, five of the 85 haplotypes sequenced had an intermediate divergence (0.036-0.066) between the lower (0.005-0.028) and upper range (0.083-0.138) of nucleotide variability, suggesting the occurrence of homologous RNA recombination. Sequence alignments clearly indicated a mosaic structure for four of these five variants, for which recombination sites were identified and parental lineages proposed. This is the first in-depth characterization of the population structure and genetic diversity in a nepovirus.

Phenotypic differentiation in love song traits among sibling species of the Lutzomyia longipalpis complex in Brazil.

PubMed

Vigoder, Felipe M; Souza, Nataly A; Brazil, Reginaldo P; Bruno, Rafaela V; Costa, Pietra L; Ritchie, Michael G; Klaczko, Louis B; Peixoto, Alexandre A

2015-05-28

Brazilian populations of Lutzomyia longipalpis may constitute a complex of cryptic species, and this report investigates the distribution and number of potential sibling species. One of the main differences observed among Brazilian populations is the type of acoustic signal produced by males during copulation. These copulation song differences seem to be evolving faster than neutral molecular markers and have been suggested to contribute to insemination failure observed in crosses between these sibling species. In previous studies, two main types of copulation songs were found, burst-type and pulse-type. The latter type can, in turn, be further subdivided into five different patterns. We recorded male song from 13 new populations of the L. longipalpis complex from Brazil and compared the songs with 12 already available. Out of these 25 populations, 16 produce burst-type and 9 produce pulse-type songs. We performed a principal component analysis in these two main groups separately and an additional discriminant analysis in the pulse-type group. The pulse-type populations showed a clear separation between the five known patterns with a high correspondence of individuals to their correct group, confirming the differentiation between them. The distinctiveness of the burst-type subgroups was much lower than that observed among the pulse-type groups and no clear population structure was observed. This suggests that the burst-type populations represent a single species. Overall, our results are consistent with the existence in Brazil of at least six species of the L. longipalpis complex, one with a wide distribution comprising all the populations with burst-type songs, and five more closely related allopatric siblings with different pulse-type song patterns and more restricted distribution ranges.

Characterization of Cs vapor cell coated with octadecyltrichlorosilane using coherent population trapping spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hafiz, Moustafa Abdel; Maurice, Vincent; Chutani, Ravinder

2015-05-14

We report the realization and characterization using coherent population trapping (CPT) spectroscopy of an octadecyltrichlorosilane (OTS)-coated centimeter-scale Cs vapor cell. The dual-structure of the resonance lineshape, with presence of a narrow structure line at the top of a Doppler-broadened structure, is clearly observed. The linewidth of the narrow resonance is compared to the linewidth of an evacuated Cs cell and of a buffer gas Cs cell of similar size. The Cs-OTS adsorption energy is measured to be (0.42 ± 0.03) eV, leading to a clock frequency shift rate of 2.7 × 10{sup −9}/K in fractional unit. A hyperfine population lifetime, T{sub 1}, and amore » microwave coherence lifetime, T{sub 2}, of 1.6 and 0.5 ms are reported, corresponding to about 37 and 12 useful bounces, respectively. Atomic-motion induced Ramsey narrowing of dark resonances is observed in Cs-OTS cells by reducing the optical beam diameter. Ramsey CPT fringes are detected using a pulsed CPT interrogation scheme. Potential applications of the Cs-OTS cell to the development of a vapor cell atomic clock are discussed.« less

Genetic and Morphological Differentiation of the Semiterrestrial Crab Armases angustipes (Brachyura: Sesarmidae) along the Brazilian Coast.

PubMed

Marochi, Murilo Zanetti; Masunari, Setuko; Schubart, Christoph D

2017-02-01

The genetic and morphometric population structures of the semiterrestrial crab Armases angustipes from along the Brazilian coast were examined. The influence of the Central South Equatorial Current on larval dispersal of A. angustipes also was evaluated. Six populations were sampled from estuarine areas in São Luis do Maranhão, Maranhão; Natal, Rio Grande do Norte; Maceió, Alagoas; Ilhéus, Bahia; Aracruz, Espírito Santo; and Guaratuba, Paraná. Patterns of genetic differentiation were assessed using DNA sequence data corresponding to parts of the mitochondrial cytochrome c oxidase subunit 1. Geometric morphometric techniques were used to evaluate morphological variation in shape and size of the carapace and right cheliped propodus. Our results revealed low genetic variability and lack of phylogeographic structure; geometric morphometrics showed statistically significant morphological differentiation and geographic structuring. Our data indicate the absence of possible barriers to gene flow for this mobile species, and no clear correlation of morphological or genetic variation with ocean currents and/or geographic distance. Our results also suggest that historical geological and climatological events and/or possible bottleneck effects influenced the current low genetic variability among the populations of A. angustipes.

Low Genetic Variation of Red-Crowned Cranes on Hokkaido Island, Japan, Over the Hundred Years.

PubMed

Akiyama, Takuya; Momose, Kunikazu; Onuma, Manabu; Matsumoto, Fumio; Masuda, Ryuichi

2017-06-01

The red-crowned crane (Grus japonensis) is recognized internationally as an endangered species. Migratory populations breed in eastern Russia and northeastern China, whereas the resident population inhabits the island of Hokkaido, Japan. Although the population inhabiting Hokkaido had experienced a severe bottleneck by the end of the 19th century, the population size has recovered to about 1500 and continues to increase now thanks to conservation efforts. A previous study reported that no marked genetic differences were seen in the island population, and that the genetic variation of the whole population on Hokkaido was lower than that of the continental population. However, the precise genetic structure of the island population in the past or near present remains unclear. To better understand the spatiotemporal changes in the genetic structure of the island population, we performed mitochondrial DNA (mtDNA) analyses using stuffed specimens (years 1878-2001) and tissue or blood samples (years 1970-2014). We found three haplotypes in the island population, one of which was a novel mtDNA haplotype in 1997 and 2007 samples. In addition, there was no clear difference in the haplotype frequency through the time span. These results suggest that the low genetic variation of the island population persisted for the last hundred years. It is thus nearly impossible for the island population to recover its genetic variation in isolation. Conservation plans for this species should therefore include the promotion of genetic exchanges between the continental and island populations, such as through artificial introduction to Hokkaido.

Remotely sensed indicators of habitat heterogeneity and biological diversity: A preliminary report

NASA Technical Reports Server (NTRS)

Imhoff, Marc; Sisk, Thomas; Milne, Anthony; Morgan, Garth; Orr, Tony

1995-01-01

The relationship between habitat area, spatial dynamics of the landscape, and species diversity is an important theme in population and conservation biology. Of particular interest is how populations of various species are affected by increasing habitat edges due to fragmentation. Over the last decade, assumptions regarding the effects of habitat edges on biodiversity have fluctuated wildly, from the belief that they have a positive effect to the belief that they have a clearly negative effect. This change in viewpoint has been brought about by an increasing recognition of the importance of geographic scale and a reinterpretation of natural history observations. In this preliminary report from an ongoing project, we explore the use of remote sensing technology and geographic information systems to further our understanding of how species diversity and population density are affected by habitat heterogeneity and landscape composition. A primary feature of this study is the investigation of SAR for making more rigorous investigations of habitat structure by exploiting the interaction between radar backscatter and vegetation structure and biomass. A major emphasis will be on the use of SAR data to define relative structural types based on measures of structural consolidation using the vegetation surface area to volume ratio (SA/V). Past research has shown that SAR may be sensitive to this form of structural expression which may affect biodiversity.

G-quadruplex dynamics.

PubMed

Harkness, Robert W; Mittermaier, Anthony K

2017-11-01

G-quadruplexes (GQs) are four-stranded nucleic acid secondary structures formed by guanosine (G)-rich DNA and RNA sequences. It is becoming increasingly clear that cellular processes including gene expression and mRNA translation are regulated by GQs. GQ structures have been extensively characterized, however little attention to date has been paid to their conformational dynamics, despite the fact that many biological GQ sequences populate multiple structures of similar free energies, leading to an ensemble of exchanging conformations. The impact of these dynamics on biological function is currently not well understood. Recently, structural dynamics have been demonstrated to entropically stabilize GQ ensembles, potentially modulating gene expression. Transient, low-populated states in GQ ensembles may additionally regulate nucleic acid interactions and function. This review will underscore the interplay of GQ dynamics and biological function, focusing on several dynamic processes for biological GQs and the characterization of GQ dynamics by nuclear magnetic resonance (NMR) spectroscopy in conjunction with other biophysical techniques. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 Elsevier B.V. All rights reserved.

Consequences of a demographic bottleneck on genetic structure and variation in the Scandinavian brown bear.

PubMed

Xenikoudakis, G; Ersmark, E; Tison, J-L; Waits, L; Kindberg, J; Swenson, J E; Dalén, L

2015-07-01

The Scandinavian brown bear went through a major decline in population size approximately 100 years ago, due to intense hunting. After being protected, the population subsequently recovered and today numbers in the thousands. The genetic diversity in the contemporary population has been investigated in considerable detail, and it has been shown that the population consists of several subpopulations that display relatively high levels of genetic variation. However, previous studies have been unable to resolve the degree to which the demographic bottleneck impacted the contemporary genetic structure and diversity. In this study, we used mitochondrial and microsatellite DNA markers from pre- and postbottleneck Scandinavian brown bear samples to investigate the effect of the bottleneck. Simulation and multivariate analysis suggested the same genetic structure for the historical and modern samples, which are clustered into three subpopulations in southern, central and northern Scandinavia. However, the southern subpopulation appears to have gone through a marked change in allele frequencies. When comparing the mitochondrial DNA diversity in the whole population, we found a major decline in haplotype numbers across the bottleneck. However, the loss of autosomal genetic diversity was less pronounced, although a significant decline in allelic richness was observed in the southern subpopulation. Approximate Bayesian computations provided clear support for a decline in effective population size during the bottleneck, in both the southern and northern subpopulations. These results have implications for the future management of the Scandinavian brown bear because they indicate a recent loss in genetic diversity and also that the current genetic structure may have been caused by historical ecological processes rather than recent anthropogenic persecution. © 2015 John Wiley & Sons Ltd.

Genetic Diversity and Population Structure of Two Tomato Species from the Galapagos Islands

PubMed Central

Pailles, Yveline; Ho, Shwen; Pires, Inês S.; Tester, Mark; Negrão, Sónia; Schmöckel, Sandra M.

2017-01-01

Endemic flora of the Galapagos Islands has adapted to thrive in harsh environmental conditions. The wild tomato species from the Galapagos Islands, Solanum cheesmaniae and S. galapagense, are tolerant to various stresses, and can be crossed with cultivated tomato. However, information about genetic diversity and relationships within and between populations is necessary to use these resources efficiently in plant breeding. In this study, we analyzed 3,974 polymorphic SNP markers, obtained through the genotyping-by-sequencing technique, DArTseq, to elucidate the genetic diversity and population structure of 67 accessions of Galapagos tomatoes (compared to two S. lycopersicum varieties and one S. pimpinellifolium accession). Two clustering methods, Principal Component Analysis and STRUCTURE, showed clear distinction between the two species and a subdivision in the S. cheesmaniae group corresponding to geographical origin and age of the islands. High genetic variation among the accessions within each species was suggested by the AMOVA. High diversity in the S. cheesmaniae group and its correlation with the islands of origin were also suggested. This indicates a possible influence of the movement of the islands, from west to east, on the gene flow. Additionally, the absence of S. galapagense populations in the eastern islands points to the species divergence occurring after the eastern islands became isolated. Based on these results, it can be concluded that the population structure of the Galapagos tomatoes collection partially explains the evolutionary history of both species, knowledge that facilitates exploitation of their genetic potential for the identification of novel alleles contributing to stress tolerance. PMID:28261227

Genetic structure of pike (Esox lucius) reveals a complex and previously unrecognized colonization history of Ireland

PubMed Central

Pedreschi, Debbi; Kelly-Quinn, Mary; Caffrey, Joe; O’Grady, Martin; Mariani, Stefano; Phillimore, Albert

2014-01-01

Aim We investigated genetic variation of Irish pike populations and their relationship with European outgroups, in order to elucidate the origin of this species to the island, which is largely assumed to have occurred as a human-mediated introduction over the past few hundred years. We aimed thereby to provide new insights into population structure to improve fisheries and biodiversity management in Irish freshwaters. Location Ireland, Britain and continental Europe. Methods A total of 752 pike (Esox lucius) were sampled from 15 locations around Ireland, and 9 continental European sites, and genotyped at six polymorphic microsatellite loci. Patterns and mechanisms of population genetic structure were assessed through a diverse array of methods, including Bayesian clustering, hierarchical analysis of molecular variance, and approximate Bayesian computation. Results Varying levels of genetic diversity and a high degree of population genetic differentiation were detected. Clear substructure within Ireland was identified, with two main groups being evident. One of the Irish populations showed high similarity with British populations. The other, more widespread, Irish strain did not group with any European population examined. Approximate Bayesian computation suggested that this widespread Irish strain is older, and may have colonized Ireland independently of humans. Main conclusions Population genetic substructure in Irish pike is high and comparable to the levels observed elsewhere in Europe. A comparison of evolutionary scenarios upholds the possibility that pike may have colonized Ireland in two ‘waves’, the first of which, being independent of human colonization, would represent the first evidence for natural colonization of a non-anadromous freshwater fish to the island of Ireland. Although further investigations using comprehensive genomic techniques will be necessary to confirm this, the present results warrant a reappraisal of current management strategies for this species. PMID:25435649

Genetic structure of pike (Esox lucius) reveals a complex and previously unrecognized colonization history of Ireland.

PubMed

Pedreschi, Debbi; Kelly-Quinn, Mary; Caffrey, Joe; O'Grady, Martin; Mariani, Stefano; Phillimore, Albert

2014-03-01

We investigated genetic variation of Irish pike populations and their relationship with European outgroups, in order to elucidate the origin of this species to the island, which is largely assumed to have occurred as a human-mediated introduction over the past few hundred years. We aimed thereby to provide new insights into population structure to improve fisheries and biodiversity management in Irish freshwaters. Ireland, Britain and continental Europe. A total of 752 pike ( Esox lucius ) were sampled from 15 locations around Ireland, and 9 continental European sites, and genotyped at six polymorphic microsatellite loci. Patterns and mechanisms of population genetic structure were assessed through a diverse array of methods, including Bayesian clustering, hierarchical analysis of molecular variance, and approximate Bayesian computation. Varying levels of genetic diversity and a high degree of population genetic differentiation were detected. Clear substructure within Ireland was identified, with two main groups being evident. One of the Irish populations showed high similarity with British populations. The other, more widespread, Irish strain did not group with any European population examined. Approximate Bayesian computation suggested that this widespread Irish strain is older, and may have colonized Ireland independently of humans. Population genetic substructure in Irish pike is high and comparable to the levels observed elsewhere in Europe. A comparison of evolutionary scenarios upholds the possibility that pike may have colonized Ireland in two 'waves', the first of which, being independent of human colonization, would represent the first evidence for natural colonization of a non-anadromous freshwater fish to the island of Ireland. Although further investigations using comprehensive genomic techniques will be necessary to confirm this, the present results warrant a reappraisal of current management strategies for this species.

Contrasting effects of geographical separation on the genetic population structure of sympatric species of mites in avocado orchards.

PubMed

Guzman-Valencia, S; Santillán-Galicia, M T; Guzmán-Franco, A W; González-Hernández, H; Carrillo-Benítez, M G; Suárez-Espinoza, J

2014-10-01

Oligonychus punicae and Oligonychus perseae (Acari: Tetranychidae) are the most important mite species affecting avocado orchards in Mexico. Here we used nucleotide sequence data from segments of the nuclear ribosomal internal transcribed spacers (ITS1 and ITS2) and mitochondrial cytochrome oxidase subunit I (COI) genes to assess the phylogenetic relationships between both sympatric mite species and, using only ITS sequence data, examine genetic variation and population structure in both species, to test the hypothesis that, although both species co-occur, their genetic population structures are different in both Michoacan state (main producer) and Mexico state. Phylogenetic analysis showed a clear separation between both species using ITS and COI sequence information. Haplotype network analysis done on 24 samples of O. punicae revealed low genetic diversity with only three haplotypes found but a significant geographical population structure confirmed by analysis of molecular variance (AMOVA) and Kimura-2-parameter (K2P) analyses. In addition, a Mantel test revealed that geographical isolation was a factor responsible for the genetic differentiation. In contrast, analyses of 22 samples of O. perseae revealed high genetic diversity with 15 haplotypes found but no geographical structure confirmed by the AMOVA, K2P and Mantel test analyses. We have suggested that geographical separation is one of the most important factors driving genetic variation, but that it affected each species differently. The role of the ecology of these species on our results, and the importance of our findings in the development of monitoring and control strategies are discussed.

Impact of anthropogenic pressure on the formation of population structure and genetic diversity of raccoon dog Nyctereutes procyonoides

PubMed Central

Griciuvienė, Loreta; Paulauskas, Algimantas; Radzijevskaja, Jana; Žukauskienė, Judita; Pūraitė, Irma

2016-01-01

Abstract The raccoon dog Nyctereutes procyonoides experienced an active introduction and acclimatization in the European part of Russia followed by its migration to and colonization in the neighboring countries. Eventually, it has spread rapidly into many European countries. N. procyonoides probably invaded Lithuania from the neighboring countries of Belarus and Latvia where the species was introduced. However, the data on genetic diversity and population structure of the raccoon dogs in the recently invaded territories are still scarce. The objectives of this study were to investigate genetic diversity of N. procyonoides in Lithuania after acclimatization, and to assess the impact of anthropogenic pressure on the formation of population structure. A total of 147 N. procyonoides individuals collected from different regions of Lithuania were genotyped using 17 microsatellite markers. The microsatellite analysis of raccoon dogs indicated high levels of genetic diversity within the population. The Bayesian clustering analysis in STRUCTURE identified 4 genetic clusters among sampled raccoon dogs that could not reveal a clear separation between subpopulations. The widespread distribution of raccoon dogs in Lithuania, high level of genetic variation observed within subpopulations, and low level of variation portioned among subpopulations suggest migration and gene flow among locations. The significant correlation between genetic and geographic distances indicated isolation that reflected the distance between locations. The fencing of highways and very intensive traffic could be barriers to gene flow between the western and eastern sampling areas of raccoon dogs. PMID:29491930

Discordant genetic diversity and geographic patterns between Crassicutis cichlasomae (Digenea: Apocreadiidae) and its cichlid host, "Cichlasoma" urophthalmus (Osteichthyes: Cichlidae), in Middle-America.

PubMed

Razo-Mendivil, Ulises; Vázquez-Domínguez, Ella; de León, Gerardo Pérez-Ponce

2013-12-01

Genetic analyses of hosts and their parasites are key to understand the evolutionary patterns and processes that have shaped host-parasite associations. We evaluated the genetic structure of the digenean Crassicutis cichlasomae and its most common host, the Mayan cichlid "Cichlasoma" urophthalmus, encompassing most of their geographical range in Middle-America (river basins in southeastern Mexico, Belize, and Guatemala together with the Yucatan Peninsula). Genetic diversity and structure analyses were done based on 167 cytochrome c oxidase subunit 1 sequences (330 bp) for C. cichlasomae from 21 populations and 161 cytochrome b sequences (599 bp) for "C." urophthalmus from 26 populations. Analyses performed included phylogenetic tree estimation under Bayesian inference and maximum likelihood analysis, genetic diversity, distance and structure estimates, haplotype networks, and demographic evaluations. Crassicutis cichlasomae showed high genetic diversity values and genetic structuring, corresponding with 4 groups clearly differentiated and highly divergent. Conversely, "C." urophthalmus showed low levels of genetic diversity and genetic differentiation, defined as 2 groups with low divergence and with no correspondence with geographical distribution. Our results show that species of cichlids parasitized by C. cichlasomae other than "C." urophthalmus, along with multiple colonization events and subsequent isolation in different basins, are likely factors that shaped the genetic structure of the parasite. Meanwhile, historical long-distance dispersal and drought periods during the Holocene, with significant population size reductions and fragmentations, are factors that could have shaped the genetic structure of the Mayan cichlid.

Desmophyllum dianthus (Esper, 1794) in the scleractinian phylogeny and its intraspecific diversity.

PubMed

Addamo, Anna M; Reimer, James D; Taviani, Marco; Freiwald, André; Machordom, Annie

2012-01-01

The cosmopolitan solitary deep-water scleractinian coral Desmophyllum dianthus (Esper, 1794) was selected as a representative model species of the polyphyletic Caryophylliidae family to (1) examine phylogenetic relationships with respect to the principal Scleractinia taxa, (2) check population structure, (3) test the widespread connectivity hypothesis and (4) assess the utility of different nuclear and mitochondrial markers currently in use. To carry out these goals, DNA sequence data from nuclear (ITS and 28S) and mitochondrial (16S and COI) markers were analyzed for several coral species and for Mediterranean populations of D. dianthus. Three phylogenetic methodologies (ML, MP and BI), based on data from the four molecular markers, all supported D. dianthus as clearly belonging to the "robust" clade, in which the species Lophelia pertusa and D. dianthus not only grouped together, but also shared haplotypes for some DNA markers. Molecular results also showed shared haplotypes among D. dianthus populations distributed in regions separated by several thousands of kilometers and by clear geographic barriers. These results could reflect limited molecular and morphological taxonomic resolution rather than real widespread connectivity. Additional studies are needed in order to find molecular markers and morphological features able to disentangle the complex phylogenetic relationship in the Order Scleractinia and to differentiate isolated populations, thus avoiding the homoplasy found in some morphological characters that are still considered in the literature.

Recovery Potential of a Western Lowland Gorilla Population following a Major Ebola Outbreak: Results from a Ten Year Study

PubMed Central

Gatti, Sylvain; Levréro, Florence; Bigot, Elodie; Caillaud, Damien; Pierre, Jean-Sébastien; Ménard, Nelly

2012-01-01

Investigating the recovery capacity of wildlife populations following demographic crashes is of great interest to ecologists and conservationists. Opportunities to study these aspects are rare due to the difficulty of monitoring populations both before and after a demographic crash. Ebola outbreaks in central Africa have killed up to 95% of the individuals in affected western lowland gorilla (Gorilla gorilla gorilla) populations. Assessing whether and how fast affected populations recover is essential for the conservation of this critically endangered taxon. The gorilla population visiting Lokoué forest clearing, Odzala-Kokoua National Park, Republic of the Congo, has been monitored before, two years after and six years after Ebola affected it in 2004. This allowed us to describe Ebola's short-term and long-term impacts on the structure of the population. The size of the population, which included around 380 gorillas before the Ebola outbreak, dropped to less than 40 individuals after the outbreak. It then remained stable for six years after the outbreak. However, the demographic structure of this small population has significantly changed. Although several solitary males have disappeared, the immigration of adult females, the formation of new breeding groups, and several birth events suggest that the population is showing potential to recover. During the outbreak, surviving adult and subadult females joined old solitary silverbacks. Those females were subsequently observed joining young silverbacks, forming new breeding groups where they later gave birth. Interestingly, some females were observed joining silverbacks that were unlikely to have sired their infant, but no infanticide was observed. The consequences of the Ebola outbreak on the population structure were different two years and six years after the outbreak. Therefore, our results could be used as demographic indicators to detect and date outbreaks that have happened in other, non-monitored gorilla populations. PMID:22649511

Three Decades of Farmed Escapees in the Wild: A Spatio-Temporal Analysis of Atlantic Salmon Population Genetic Structure throughout Norway

PubMed Central

Glover, Kevin A.; Quintela, María; Wennevik, Vidar; Besnier, François; Sørvik, Anne G. E.; Skaala, Øystein

2012-01-01

Each year, hundreds of thousands of domesticated farmed Atlantic salmon escape into the wild. In Norway, which is the world’s largest commercial producer, many native Atlantic salmon populations have experienced large numbers of escapees on the spawning grounds for the past 15–30 years. In order to study the potential genetic impact, we conducted a spatio-temporal analysis of 3049 fish from 21 populations throughout Norway, sampled in the period 1970–2010. Based upon the analysis of 22 microsatellites, individual admixture, FST and increased allelic richness revealed temporal genetic changes in six of the populations. These changes were highly significant in four of them. For example, 76% and 100% of the fish comprising the contemporary samples for the rivers Vosso and Opo were excluded from their respective historical samples at P = 0.001. Based upon several genetic parameters, including simulations, genetic drift was excluded as the primary cause of the observed genetic changes. In the remaining 15 populations, some of which had also been exposed to high numbers of escapees, clear genetic changes were not detected. Significant population genetic structuring was observed among the 21 populations in the historical (global FST = 0.038) and contemporary data sets (global FST = 0.030), although significantly reduced with time (P = 0.008). This reduction was especially distinct when looking at the six populations displaying temporal changes (global FST dropped from 0.058 to 0.039, P = 0.006). We draw two main conclusions: 1. The majority of the historical population genetic structure throughout Norway still appears to be retained, suggesting a low to modest overall success of farmed escapees in the wild; 2. Genetic introgression of farmed escapees in native salmon populations has been strongly population-dependent, and it appears to be linked with the density of the native population. PMID:22916215

Recovery potential of a western lowland gorilla population following a major Ebola outbreak: results from a ten year study.

PubMed

Genton, Céline; Cristescu, Romane; Gatti, Sylvain; Levréro, Florence; Bigot, Elodie; Caillaud, Damien; Pierre, Jean-Sébastien; Ménard, Nelly

2012-01-01

Investigating the recovery capacity of wildlife populations following demographic crashes is of great interest to ecologists and conservationists. Opportunities to study these aspects are rare due to the difficulty of monitoring populations both before and after a demographic crash. Ebola outbreaks in central Africa have killed up to 95% of the individuals in affected western lowland gorilla (Gorilla gorilla gorilla) populations. Assessing whether and how fast affected populations recover is essential for the conservation of this critically endangered taxon. The gorilla population visiting Lokoué forest clearing, Odzala-Kokoua National Park, Republic of the Congo, has been monitored before, two years after and six years after Ebola affected it in 2004. This allowed us to describe Ebola's short-term and long-term impacts on the structure of the population. The size of the population, which included around 380 gorillas before the Ebola outbreak, dropped to less than 40 individuals after the outbreak. It then remained stable for six years after the outbreak. However, the demographic structure of this small population has significantly changed. Although several solitary males have disappeared, the immigration of adult females, the formation of new breeding groups, and several birth events suggest that the population is showing potential to recover. During the outbreak, surviving adult and subadult females joined old solitary silverbacks. Those females were subsequently observed joining young silverbacks, forming new breeding groups where they later gave birth. Interestingly, some females were observed joining silverbacks that were unlikely to have sired their infant, but no infanticide was observed. The consequences of the Ebola outbreak on the population structure were different two years and six years after the outbreak. Therefore, our results could be used as demographic indicators to detect and date outbreaks that have happened in other, non-monitored gorilla populations.

The voyage of an invasive species across continents: genetic diversity of North American and European Colorado potato beetle populations.

PubMed

Grapputo, Alessandro; Boman, Sanna; Lindström, Leena; Lyytinen, Anne; Mappes, Johanna

2005-12-01

The paradox of successful invading species is that they are likely to be genetically depauperate compared to their source population. This study on Colorado potato beetles is one of the few studies of the genetic consequences of continent-scale invasion in an insect pest. Understanding gene flow, population structure and the potential for rapid evolution in native and invasive populations offers insights both into the dynamics of small populations that become successful invaders and for their management as pests. We used this approach to investigate the invasion of the Colorado potato beetle (Leptinotarsa decemlineata) from North America to Europe. The beetles invaded Europe at the beginning of the 20th century and expanded almost throughout the continent in about 30 years. From the analysis of mitochondrial DNA (mtDNA) and amplified fragment length polymorphism (AFLP) markers, we found the highest genetic diversity in beetle populations from the central United States. The European populations clearly contained only a fraction of the genetic variability observed in North American populations. European populations show a significant reduction at nuclear markers (AFLPs) and are fixed for one mitochondrial haplotype, suggesting a single successful founder event. Despite the high vagility of the species and the reduction of genetic diversity in Europe, we found a similar, high level of population structure and low gene flow among populations on both continents. Founder events during range expansion, agricultural management with crop rotation, and selection due to insecticide applications are most likely the causes partitioning genetic diversity in this species.

Mating system and gene flow in the red seaweed Gracilaria gracilis: effect of haploid-diploid life history and intertidal rocky shore landscape on fine-scale genetic structure.

PubMed

Engel, C R; Destombe, C; Valero, M

2004-04-01

The impact of haploid-diploidy and the intertidal landscape on a fine-scale genetic structure was explored in a red seaweed Gracilaria gracilis. The pattern of genetic structure was compared in haploid and diploid stages at a microgeographic scale (< 5 km): a total of 280 haploid and 296 diploid individuals located in six discrete, scattered rock pools were genotyped using seven microsatellite loci. Contrary to the theoretical expectation of predominantly endogamous mating systems in haploid-diploid organisms, G. gracilis showed a clearly allogamous mating system. Although within-population allele frequencies were similar between haploids and diploids, genetic differentiation among haploids was more than twice that of diploids, suggesting that there may be a lag between migration and (local) breeding due to the long generation times in G. gracilis. Weak, but significant, population differentiation was detected in both haploids and diploids and varied with landscape features, and not with geographic distance. Using an assignment test, we establish that effective migration rates varied according to height on the shore. In this intertidal species, biased spore dispersal may occur during the transport of spores and gametes at low tide when small streams flow from high- to lower-shore pools. The longevity of both haploid and diploid free-living stages and the long generation times typical of G. gracilis populations may promote the observed pattern of high genetic diversity within populations relative to that among populations.

Assessing the Genetic Influence of Ancient Sociopolitical Structure: Micro-differentiation Patterns in the Population of Asturias (Northern Spain)

PubMed Central

Pardiñas, Antonio F.; Roca, Agustín; García-Vazquez, Eva; López, Belén

2012-01-01

The human populations of the Iberian Peninsula are the varied result of a complex mixture of cultures throughout history, and are separated by clear social, cultural, linguistic or geographic barriers. The stronger genetic differences between closely related populations occur in the northern third of Spain, a phenomenon commonly known as “micro-differentiation”. It has been argued and discussed how this form of genetic structuring can be related to both the rugged landscape and the ancient societies of Northern Iberia, but this is difficult to test in most regions due to the intense human mobility of previous centuries. Nevertheless, the Spanish autonomous community of Asturias shows a complex history which hints of a certain isolation of its population. This, joined together with a difficult terrain full of deep valleys and steep mountains, makes it suitable for performing a study of genetic structure, based on mitochondrial DNA and Y-Chromosome markers. Our analyses do not only show that there are micro-differentiation patterns inside the Asturian territory, but that these patterns are strikingly similar between both uniparental markers. The inference of barriers to gene flow also indicates that Asturian populations from the coastal north and the mountainous south seem to be relatively isolated from the rest of the territory. These findings are discussed in light of historic and geographic data and, coupled with previous evidence, show that the origin of the current genetic patterning might indeed lie in Roman and Pre-Roman sociopolitical divisions. PMID:23209673

Clear: Composition of Likelihoods for Evolve and Resequence Experiments.

PubMed

Iranmehr, Arya; Akbari, Ali; Schlötterer, Christian; Bafna, Vineet

2017-06-01

The advent of next generation sequencing technologies has made whole-genome and whole-population sampling possible, even for eukaryotes with large genomes. With this development, experimental evolution studies can be designed to observe molecular evolution "in action" via evolve-and-resequence (E&R) experiments. Among other applications, E&R studies can be used to locate the genes and variants responsible for genetic adaptation. Most existing literature on time-series data analysis often assumes large population size, accurate allele frequency estimates, or wide time spans. These assumptions do not hold in many E&R studies. In this article, we propose a method-composition of likelihoods for evolve-and-resequence experiments (Clear)-to identify signatures of selection in small population E&R experiments. Clear takes whole-genome sequences of pools of individuals as input, and properly addresses heterogeneous ascertainment bias resulting from uneven coverage. Clear also provides unbiased estimates of model parameters, including population size, selection strength, and dominance, while being computationally efficient. Extensive simulations show that Clear achieves higher power in detecting and localizing selection over a wide range of parameters, and is robust to variation of coverage. We applied the Clear statistic to multiple E&R experiments, including data from a study of adaptation of Drosophila melanogaster to alternating temperatures and a study of outcrossing yeast populations, and identified multiple regions under selection with genome-wide significance. Copyright © 2017 by the Genetics Society of America.

The fine-scale genetic structure and evolution of the Japanese population

PubMed Central

Katsuya, Tomohiro; Kimura, Ryosuke; Nabika, Toru; Isomura, Minoru; Ohkubo, Takayoshi; Tabara, Yasuharu; Yamamoto, Ken; Yokota, Mitsuhiro; Liu, Xuanyao; Saw, Woei-Yuh; Mamatyusupu, Dolikun; Yang, Wenjun; Xu, Shuhua

2017-01-01

The contemporary Japanese populations largely consist of three genetically distinct groups—Hondo, Ryukyu and Ainu. By principal-component analysis, while the three groups can be clearly separated, the Hondo people, comprising 99% of the Japanese, form one almost indistinguishable cluster. To understand fine-scale genetic structure, we applied powerful haplotype-based statistical methods to genome-wide single nucleotide polymorphism data from 1600 Japanese individuals, sampled from eight distinct regions in Japan. We then combined the Japanese data with 26 other Asian populations data to analyze the shared ancestry and genetic differentiation. We found that the Japanese could be separated into nine genetic clusters in our dataset, showing a marked concordance with geography; and that major components of ancestry profile of Japanese were from the Korean and Han Chinese clusters. We also detected and dated admixture in the Japanese. While genetic differentiation between Ryukyu and Hondo was suggested to be caused in part by positive selection, genetic differentiation among the Hondo clusters appeared to result principally from genetic drift. Notably, in Asians, we found the possibility that positive selection accentuated genetic differentiation among distant populations but attenuated genetic differentiation among close populations. These findings are significant for studies of human evolution and medical genetics. PMID:29091727

Y-chromosome lineages in native South American population.

PubMed

Blanco-Verea, A; Jaime, J C; Brión, M; Carracedo, A

2010-04-01

The present work tries to investigate the population structure and variation of the Amerindian indigenous populations living in Argentina. A total of 134 individuals from three ethnic groups (Kolla, Mapuche and Diaguitas) living in four different regions were collected and analysed for 26 Y-SNPs and 11 Y-STRs. Intra-population variability was analysed, looking for population substructure and neighbour populations were considered for genetic comparative analysis, in order to estimate the contribution of the Amerindian and the European pool, to the current population. We observe a high frequency of R1b1 and Q1a3a* Y-chromosome haplogroups, in the ethnic groups Mapuche, Diaguita and Kolla, characteristic of European and Native American populations, respectively. When we compare our native Argentinean population with other from the South America we also observe that frequency values for Amerindian lineages are relatively lower in our population. These results show a clear Amerindian genetic component but we observe a predominant European influence too, suggesting that typically European male lineages have given rise to the displacement of genuinely Amerindian male lineages in our South American population. Copyright 2009 Elsevier Ireland Ltd. All rights reserved.

Optimal control of Atlantic population Canada geese

USGS Publications Warehouse

Hauser, C.E.; Runge, M.C.; Cooch, E.G.; Johnson, F.A.; Harvey, W.F.

2007-01-01

Management of Canada geese (Branta canadensis) can be a balance between providing sustained harvest opportunity while not allowing populations to become overabundant and cause damage. In this paper, we focus on the Atlantic population of Canada geese and use stochastic dynamic programming to determine the optimal harvest strategy over a range of plausible models for population dynamics. There is evidence to suggest that the population exhibits significant age structure, and it is possible to reconstruct age structure from surveys. Consequently the harvest strategy is a function of the age composition, as well as the abundance, of the population. The objective is to maximize harvest while maintaining the number of breeding adults in the population between specified upper and lower limits. In addition, the total harvest capacity is limited and there is uncertainty about the strength of density-dependence. We find that under a density-independent model, harvest is maximized by maintaining the breeding population at the highest acceptable abundance. However if harvest capacity is limited, then the optimal long-term breeding population size is lower than the highest acceptable level, to reduce the risk of the population growing to an unacceptably large size. Under the proposed density-dependent model, harvest is maximized by maintaining the breeding population at an intermediate level between the bounds on acceptable population size; limits to harvest capacity have little effect on the optimal long-term population size. It is clear that the strength of density-dependence and constraints on harvest significantly affect the optimal harvest strategy for this population. Model discrimination might be achieved in the long term, while continuing to meet management goals, by adopting an adaptive management strategy.

Sex structure and potential female fecundity in a Epinephelus guttatus spawning aggregation: Applying ultrasonic imaging

USGS Publications Warehouse

Whiteman, E.A.; Jennings, C.A.; Nemeth, R.S.

2005-01-01

Ultrasonic imaging was used to determine the spawning population structure and develop a fecundity estimation model for a red hind Epinephelus guttatus spawning aggregation within the Red Hind Bank Marine Conservation District, St Thomas, U.S.V.I. The spawning population showed considerable within-month and between-month variation in population size- and sex-structure. In the spawning season studied, males appeared to arrive at the aggregation site first in December although females represented a large proportion of the catch early in the aggregation periods in January and February. Spawning occurred in January and February, and size frequency distributions suggested that an influx of small females occurred during the second spawning month. An overall sex ratio of 2.9:1 (female:male) was recorded for the whole reproductive season. The sex ratio, however, differed between months and days within months. More females per male were recorded in January than in February when the sex ratio was male biased. Fecundity estimates for this species predicted very high potential fecundities (2.4 ?? 105-2.4 ?? 106 oocytes). The ultrasound model also illustrated a rapid increase in potential female fecundity with total length. Ultrasonic imaging may prove a valuable tool in population assessment for many species and locations in which invasive fishing methods are clearly undesirable. ?? 2005 The Fisheries Society of the British Isles.

Population Genetic Structure of the People of Qatar

PubMed Central

Hunter-Zinck, Haley; Musharoff, Shaila; Salit, Jacqueline; Al-Ali, Khalid A.; Chouchane, Lotfi; Gohar, Abeer; Matthews, Rebecca; Butler, Marcus W.; Fuller, Jennifer; Hackett, Neil R.; Crystal, Ronald G.; Clark, Andrew G.

2010-01-01

People of the Qatar peninsula represent a relatively recent founding by a small number of families from three tribes of the Arabian Peninsula, Persia, and Oman, with indications of African admixture. To assess the roles of both this founding effect and the customary first-cousin marriages among the ancestral Islamic populations in Qatar's population genetic structure, we obtained and genotyped with Affymetrix 500k SNP arrays DNA samples from 168 self-reported Qatari nationals sampled from Doha, Qatar. Principal components analysis was performed along with samples from the Human Genetic Diversity Project data set, revealing three clear clusters of genotypes whose proximity to other human population samples is consistent with Arabian origin, a more eastern or Persian origin, and individuals with African admixture. The extent of linkage disequilibrium (LD) is greater than that of African populations, and runs of homozygosity in some individuals reflect substantial consanguinity. However, the variance in runs of homozygosity is exceptionally high, and the degree of identity-by-descent sharing generally appears to be lower than expected for a population in which nearly half of marriages are between first cousins. Despite the fact that the SNPs of the Affymetrix 500k chip were ascertained with a bias toward SNPs common in Europeans, the data strongly support the notion that the Qatari population could provide a valuable resource for the mapping of genes associated with complex disorders and that tests of pairwise interactions are particularly empowered by populations with elevated LD like the Qatari. PMID:20579625

Evolution over time of the Milky Way's disc shape

NASA Astrophysics Data System (ADS)

Amôres, E. B.; Robin, A. C.; Reylé, C.

2017-06-01

Context. Galactic structure studies can be used as a path to constrain the scenario of formation and evolution of our Galaxy. The dependence with the age of stellar population parameters would be linked with the history of star formation and dynamical evolution. Aims: We aim to investigate the structures of the outer Galaxy, such as the scale length, disc truncation, warp and flare of the thin disc and study their dependence with age by using 2MASS data and a population synthesis model (the so-called Besançon Galaxy Model). Methods: We have used a genetic algorithm to adjust the parameters on the observed colour-magnitude diagrams at longitudes 80° ≤ ℓ ≤ 280° for | b | ≤ 5.5°. We explored parameter degeneracies and uncertainties. Results: We identify a clear dependence of the thin disc scale length, warp and flare shapes with age. The scale length is found to vary between 3.8 kpc for the youngest to about 2 kpc for the oldest. The warp shows a complex structure, clearly asymmetrical with a node angle changing with age from approximately 165° for old stars to 195° for young stars. The outer disc is also flaring with a scale height that varies by a factor of two between the solar neighbourhood and a Galactocentric distance of 12 kpc. Conclusions: We conclude that the thin disc scale length is in good agreement with the inside-out formation scenario and that the outer disc is not in dynamical equilibrium. The warp deformation with time may provide some clues to its origin.

Is central dogma a global property of cellular information flow?

PubMed Central

Piras, Vincent; Tomita, Masaru; Selvarajoo, Kumar

2012-01-01

The central dogma of molecular biology has come under scrutiny in recent years. Here, we reviewed high-throughput mRNA and protein expression data of Escherichia coli, Saccharomyces cerevisiae, and several mammalian cells. At both single cell and population scales, the statistical comparisons between the entire transcriptomes and proteomes show clear correlation structures. In contrast, the pair-wise correlations of single transcripts to proteins show nullity. These data suggest that the organizing structure guiding cellular processes is observed at omics-wide scale, and not at single molecule level. The central dogma, thus, globally emerges as an average integrated flow of cellular information. PMID:23189060

Is central dogma a global property of cellular information flow?

PubMed

Piras, Vincent; Tomita, Masaru; Selvarajoo, Kumar

2012-01-01

The central dogma of molecular biology has come under scrutiny in recent years. Here, we reviewed high-throughput mRNA and protein expression data of Escherichia coli, Saccharomyces cerevisiae, and several mammalian cells. At both single cell and population scales, the statistical comparisons between the entire transcriptomes and proteomes show clear correlation structures. In contrast, the pair-wise correlations of single transcripts to proteins show nullity. These data suggest that the organizing structure guiding cellular processes is observed at omics-wide scale, and not at single molecule level. The central dogma, thus, globally emerges as an average integrated flow of cellular information.

Limited Genetic Connectivity between Gorgonian Morphotypes along a Depth Gradient

PubMed Central

Gori, Andrea; Lopez-González, Pablo; Bramanti, Lorenzo; Rossi, Sergio; Gili, Josep-Maria; Abbiati, Marco

2016-01-01

Gorgonian species show a high morphological variability in relation to the environment in which they live. In coastal areas, parameters such as temperature, light, currents, and food availability vary significantly with depth, potentially affecting morphology of the colonies and the structure of the populations, as well as their connectivity patterns. In tropical seas, the existence of connectivity between shallow and deep populations supported the hypothesis that the deep coral reefs could potentially act as (reproductive) refugia fostering re-colonization of shallow areas after mortality events. Moreover, this hypothesis is not so clear accepted in temperate seas. Eunicella singularis is one of the most common gorgonian species in Northwestern Mediterranean Sea, playing an important role as ecosystem engineer by providing biomass and complexity to the coralligenous habitats. It has a wide bathymetric distribution ranging from about 10 m to 100 m. Two depth-related morphotypes have been identified, differing in colony morphology, sclerite size and shape, and occurrence of symbiotic algae, but not in mitochondrial DNA haplotypes. In the present study the genetic structure of E. singularis populations along a horizontal and bathymetric gradient was assessed using microsatellites and ITS1 sequences. Restricted gene flow was found at 30–40 m depth between the two Eunicella morphotypes. Conversely, no genetic structuring has been found among shallow water populations within a spatial scale of ten kilometers. The break in gene flow between shallow and deep populations contributes to explain the morphological variability observed at different depths. Moreover, the limited vertical connectivity hinted that the refugia hypothesis does not apply to E. singularis. Re-colonization of shallow water populations, occasionally affected by mass mortality events, should then be mainly fueled by larvae from other shallow water populations. PMID:27490900

Genetic structuring of northern myotis (Myotis septentrionalis) at multiple spatial scales

USGS Publications Warehouse

Johnson, Joshua B.; Roberts, James H.; King, Timothy L.; Edwards, John W.; Ford, W. Mark; Ray, David A.

2014-01-01

Although groups of bats may be genetically distinguishable at large spatial scales, the effects of forest disturbances, particularly permanent land use conversions on fine-scale population structure and gene flow of summer aggregations of philopatric bat species are less clear. We genotyped and analyzed variation at 10 nuclear DNA microsatellite markers in 182 individuals of the forest-dwelling northern myotis (Myotis septentrionalis) at multiple spatial scales, from within first-order watersheds scaling up to larger regional areas in West Virginia and New York. Our results indicate that groups of northern myotis were genetically indistinguishable at any spatial scale we considered, and the collective population maintained high genetic diversity. It is likely that the ability to migrate, exploit small forest patches, and use networks of mating sites located throughout the Appalachian Mountains, Interior Highlands, and elsewhere in the hibernation range have allowed northern myotis to maintain high genetic diversity and gene flow regardless of forest disturbances at local and regional spatial scales. A consequence of maintaining high gene flow might be the potential to minimize genetic founder effects following population declines caused currently by the enzootic White-nose Syndrome.

Molecular Evidence of Demographic Expansion of the Chagas Disease Vector Triatoma dimidiata (Hemiptera, Reduviidae, Triatominae) in Colombia

PubMed Central

Gómez-Palacio, Andrés; Triana, Omar

2014-01-01

Background Triatoma dimidiata is one of the most significant vectors of Chagas disease in Central America and Colombia, and, as in most species, its pattern of genetic variation within and among populations is strongly affected by its phylogeographic history. A putative origin from Central America has been proposed for Colombian populations, and high genetic differentiation among three biographically different population groups has recently been evidenced. Analyses based on putatively neutral markers provide data from which past events, such as population expansions and colonization, can be inferred. We analyzed the genealogies of the nicotinamide adenine dinucleotide dehydrogenase 4 (ND4) and the cytochrome oxidase subunit 1-mitochondrial genes, as well as partial nuclear ITS-2 DNA sequences obtained across most of the eco-geographical range in Colombia, to assess the population structure and demographic factors that may explain the geographical distribution of T. dimidiata in this country. Results The population structure results support a significant association between genetic divergence and the eco-geographical location of population groups, suggesting that clear signals of demographic expansion can explain the geographical distribution of haplotypes of population groups. Additionally, empirical date estimation of the event suggests that the population's expansion can be placed after the emergence of the Panama Isthmus, and that it was possibly followed by a population fragmentation process, perhaps resulting from local adaptation accomplished by orographic factors such as geographical isolation. Conclusion Inferences about the historical population processes in Colombian T. dimidiata populations are generally in accordance with population expansions that may have been accomplished by two important biotic and orographic events such as the Great American Interchange and the uplift of the eastern range of the Andes mountains in central Colombia. PMID:24625572

Positron lifetime studies of defect structures in Ba(1-x)K(x)BiO3

NASA Astrophysics Data System (ADS)

Obrien, J. C.; Howell, R. H.; Radousky, H. B.; Sterne, P. A.; Hinks, D. G.; Folkerts, T. J.; Shelton, R. N.

1990-12-01

Temperature-dependent positron lifetime experiments have been performed from room temperature to cryogenic temperatures on Ba(1-x)K(x)BiO3, for x = 0.4 and 0.5. From the temperature dependence of the positron lifetime in the normal state, we observe a clear signature of competition between separate defect populations to trap the positron. Theoretical calculations of lifetimes of free or trapped positrons have been performed on Ba(1-x)K(x)BiO3, to help identify these defects. Lifetime measurements separated by long times have been performed and evidence of aging effects in the sample defect populations is seen in these materials.

Development and testing of the questionnaire CEC-61: Knowledge about cervical cancer in Chilean adolescents.

PubMed

Urrutia, María Teresa; Gajardo, Macarena; Padilla, Oslando

2017-05-22

Despite a clear association between human papillomavirus and cervical cancer, knowledge in adolescent populations regarding the disease and methods for its detection and prevention is deficient. The aim of this study was to develop and test a new questionnaire concerning knowledge on cervical cancer. An instrument was developed and validated to measure knowledge in 226 Chilean adolescents between April and June 2011. Content validity, construct validity, and reliability analysis of the instrument were performed. The new, validated instrument, called CEC-61 (Conocimientos en Cancer Cérvicouterino-61 items/Knowledge in Cervical Cancer-61 items), contains nine factors and 61 items. The new questionnaire explained 81% of the variance with a reliability of 0.96. The assessment of knowledge with a valid and reliable instrument is the first step in creating interventions for a population and to encourage appropriate preventive behavior. CEC-61 is highly reliable and has a clear factorial structure to evaluate knowledge in nine domains related to cervical cancer disease, cervical cancer risk, papilloma virus infection, the Papanicolaou test, and the papilloma virus vaccine.

Detecting and modelling delayed density-dependence in abundance time series of a small mammal (Didelphis aurita)

NASA Astrophysics Data System (ADS)

Brigatti, E.; Vieira, M. V.; Kajin, M.; Almeida, P. J. A. L.; de Menezes, M. A.; Cerqueira, R.

2016-02-01

We study the population size time series of a Neotropical small mammal with the intent of detecting and modelling population regulation processes generated by density-dependent factors and their possible delayed effects. The application of analysis tools based on principles of statistical generality are nowadays a common practice for describing these phenomena, but, in general, they are more capable of generating clear diagnosis rather than granting valuable modelling. For this reason, in our approach, we detect the principal temporal structures on the bases of different correlation measures, and from these results we build an ad-hoc minimalist autoregressive model that incorporates the main drivers of the dynamics. Surprisingly our model is capable of reproducing very well the time patterns of the empirical series and, for the first time, clearly outlines the importance of the time of attaining sexual maturity as a central temporal scale for the dynamics of this species. In fact, an important advantage of this analysis scheme is that all the model parameters are directly biologically interpretable and potentially measurable, allowing a consistency check between model outputs and independent measurements.

Comparison of SSR and SNP Markers in Estimation of Genetic Diversity and Population Structure of Indian Rice Varieties

PubMed Central

Singh, Amit Kumar; Kumar, Sundeep; Srinivasan, Kalyani; Tyagi, R. K.; Singh, N. K.; Singh, Rakesh

2013-01-01

Simple sequence repeat (SSR) and Single Nucleotide Polymorphic (SNP), the two most robust markers for identifying rice varieties were compared for assessment of genetic diversity and population structure. Total 375 varieties of rice from various regions of India archived at the Indian National GeneBank, NBPGR, New Delhi, were analyzed using thirty six genetic markers, each of hypervariable SSR (HvSSR) and SNP which were distributed across 12 rice chromosomes. A total of 80 alleles were amplified with the SSR markers with an average of 2.22 alleles per locus whereas, 72 alleles were amplified with SNP markers. Polymorphic information content (PIC) values for HvSSR ranged from 0.04 to 0.5 with an average of 0.25. In the case of SNP markers, PIC values ranged from 0.03 to 0.37 with an average of 0.23. Genetic relatedness among the varieties was studied; utilizing an unrooted tree all the genotypes were grouped into three major clusters with both SSR and SNP markers. Analysis of molecular variance (AMOVA) indicated that maximum diversity was partitioned between and within individual level but not between populations. Principal coordinate analysis (PCoA) with SSR markers showed that genotypes were uniformly distributed across the two axes with 13.33% of cumulative variation whereas, in case of SNP markers varieties were grouped into three broad groups across two axes with 45.20% of cumulative variation. Population structure were tested using K values from 1 to 20, but there was no clear population structure, therefore Ln(PD) derived Δk was plotted against the K to determine the number of populations. In case of SSR maximum Δk was at K=5 whereas, in case of SNP maximum Δk was found at K=15, suggesting that resolution of population was higher with SNP markers, but SSR were more efficient for diversity analysis. PMID:24367635

Genetic structure and viability selection in the golden eagle (Aquila chrysaetos), a vagile raptor with a Holarctic distribution

USGS Publications Warehouse

Doyle, Jacqueline M.; Katzner, Todd E.; Roemer, Gary; Cain, James W.; Millsap, Brian; McIntyre, Carol; Sonsthagen, Sarah A.; Fernandez, Nadia B.; Wheeler, Maria; Bulut, Zafer; Bloom, Peter; DeWoody, J. Andrew

2016-01-01

Molecular markers can reveal interesting aspects of organismal ecology and evolution, especially when surveyed in rare or elusive species. Herein, we provide a preliminary assessment of golden eagle (Aquila chrysaetos) population structure in North America using novel single nucleotide polymorphisms (SNPs). These SNPs included one molecular sexing marker, two mitochondrial markers, 85 putatively neutral markers that were derived from noncoding regions within large intergenic intervals, and 74 putatively nonneutral markers found in or very near protein-coding genes. We genotyped 523 eagle samples at these 162 SNPs and quantified genotyping error rates and variability at each marker. Our samples corresponded to 344 individual golden eagles as assessed by unique multilocus genotypes. Observed heterozygosity of known adults was significantly higher than of chicks, as was the number of heterozygous loci, indicating that mean zygosity measured across all 159 autosomal markers was an indicator of fitness as it is associated with eagle survival to adulthood. Finally, we used chick samples of known provenance to test for population differentiation across portions of North America and found pronounced structure among geographic sampling sites. These data indicate that cryptic genetic population structure is likely widespread in the golden eagle gene pool, and that extensive field sampling and genotyping will be required to more clearly delineate management units within North America and elsewhere.

Population Genetic Structure of Listeria monocytogenes Strains as Determined by Pulsed-Field Gel Electrophoresis and Multilocus Sequence Typing

PubMed Central

Henri, Clémentine; Félix, Benjamin; Guillier, Laurent; Leekitcharoenphon, Pimlapas; Michelon, Damien; Mariet, Jean-François; Aarestrup, Frank M.; Mistou, Michel-Yves; Hendriksen, René S.

2016-01-01

ABSTRACT Listeria monocytogenes is a ubiquitous bacterium that may cause the foodborne illness listeriosis. Only a small amount of data about the population genetic structure of strains isolated from food is available. This study aimed to provide an accurate view of the L. monocytogenes food strain population in France. From 1999 to 2014, 1,894 L. monocytogenes strains were isolated from food at the French National Reference Laboratory for L. monocytogenes and classified according to the five risk food matrices defined by the European Food Safety Authority (EFSA). A total of 396 strains were selected on the basis of different pulsed-field gel electrophoresis (PFGE) clusters, serotypes, and strain origins and typed by multilocus sequence typing (MLST), and the MLST results were supplemented with MLST data available from Institut Pasteur, representing human and additional food strains from France. The distribution of sequence types (STs) was compared between food and clinical strains on a panel of 675 strains. High congruence between PFGE and MLST was found. Out of 73 PFGE clusters, the two most prevalent corresponded to ST9 and ST121. Using original statistical analysis, we demonstrated that (i) there was not a clear association between ST9 and ST121 and the food matrices, (ii) serotype IIc, ST8, and ST4 were associated with meat products, and (iii) ST13 was associated with dairy products. Of the two major STs, ST121 was the ST that included the fewest clinical strains, which might indicate lower virulence. This observation may be directly relevant for refining risk analysis models for the better management of food safety. IMPORTANCE This study showed a very useful backward compatibility between PFGE and MLST for surveillance. The results enabled better understanding of the population structure of L. monocytogenes strains isolated from food and management of the health risks associated with L. monocytogenes food strains. Moreover, this work provided an accurate view of L. monocytogenes strain populations associated with specific food matrices. We clearly showed that some STs were associated with food matrices, such as meat, meat products, and dairy products. We opened the way to source attribution modeling in order to quantify the relative importance of the main food matrices. PMID:27235443

Intraspecific Genetic Admixture and the Morphological Diversification of an Estuarine Fish Population Complex

PubMed Central

Legault, Michel

2015-01-01

The North-east American Rainbow smelt (Osmerus mordax) is composed of two glacial races first identified through the spatial distribution of two distinct mtDNA lineages. Contemporary breeding populations of smelt in the St. Lawrence estuary comprise contrasting mixtures of both lineages, suggesting that the two races came into secondary contact in this estuary. The overall objective of this study was to assess the role of intraspecific genetic admixture in the morphological diversification of the estuarine rainbow smelt population complex. The morphology of mixed-ancestry populations varied as a function of the relative contribution of the two races to estuarine populations, supporting the hypothesis of genetic admixture. Populations comprising both ancestral mtDNA races did not exhibit intermediate morphologies relative to pure populations but rather exhibited many traits that exceeded the parental trait values, consistent with the hypothesis of transgressive segregation. Evidence for genetic admixture at the level of the nuclear gene pool, however, provided only partial support for this hypothesis. Variation at nuclear AFLP markers revealed clear evidence of the two corresponding mtDNA glacial races. The admixture of the two races at the nuclear level is only pronounced in mixed-ancestry populations dominated by one of the mtDNA lineages, the same populations showing the greatest degree of morphological diversification and population structure. In contrast, mixed-ancestry populations dominated by the alternate mtDNA lineage showed little evidence of introgression of the nuclear genome, little morphological diversification and little contemporary population genetic structure. These results only partially support the hypothesis of transgressive segregation and may be the result of the differential effects of natural selection acting on admixed genomes from different sources. PMID:25856193

Spatial and temporal variation in population genetic structure of wild Nile tilapia (Oreochromis niloticus) across Africa

PubMed Central

2011-01-01

Background Reconstructing the evolutionary history of a species is challenging. It often depends not only on the past biogeographic and climatic events but also the contemporary and ecological factors, such as current connectivity and habitat heterogeneity. In fact, these factors might interact with each other and shape the current species distribution. However, to what extent the current population genetic structure reflects the past and the contemporary factors is largely unknown. Here we investigated spatio-temporal genetic structures of Nile tilapia (Oreochromis niloticus) populations, across their natural distribution in Africa. While its large biogeographic distribution can cause genetic differentiation at the paleo-biogeographic scales, its restricted dispersal capacity might induce a strong genetic structure at micro-geographic scales. Results Using nine microsatellite loci and 350 samples from ten natural populations, we found the highest genetic differentiation among the three ichthyofaunal provinces and regions (Ethiopian, Nilotic and Sudano-Sahelian) (RST = 0.38 - 0.69). This result suggests the predominant effect of paleo-geographic events at macro-geographic scale. In addition, intermediate divergences were found between rivers and lakes within the regions, presumably reflecting relatively recent interruptions of gene flow between hydrographic basins (RST = 0.24 - 0.32). The lowest differentiations were observed among connected populations within a basin (RST = 0.015 in the Volta basin). Comparison of temporal sample series revealed subtle changes in the gene pools in a few generations (F = 0 - 0.053). The estimated effective population sizes were 23 - 143 and the estimated migration rate was moderate (m ~ 0.094 - 0.097) in the Volta populations. Conclusions This study revealed clear hierarchical patterns of the population genetic structuring of O. niloticus in Africa. The effects of paleo-geographic and climatic events were predominant at macro-geographic scale, and the significant effect of geographic connectivity was detected at micro-geographic scale. The estimated effective population size, the moderate level of dispersal and the rapid temporal change in genetic composition might reflect a potential effect of life history strategy on population dynamics. This hypothesis deserves further investigation. The dynamic pattern revealed at micro-geographic and temporal scales appears important from a genetic resource management as well as from a biodiversity conservation point of view. PMID:22151746

Genetic homogeneity across Bantu-speaking groups from Mozambique and Angola challenges early split scenarios between East and West Bantu populations.

PubMed

Alves, Isabel; Coelho, Margarida; Gignoux, Christopher; Damasceno, Albertino; Prista, Antonio; Rocha, Jorge

2011-02-01

The large scale spread of Bantu-speaking populations remains one of the most debated questions in African population history. In this work we studied the genetic structure of 19 Bantu-speaking groups from Mozambique and Angola using a multilocus approach based on 14 newly developed compound haplotype systems (UEPSTRs), each consisting of a rapidly evolving short tandem repeat (STR) closely linked to a unique event polymorphism (UEP). We compared the ability of UEPs, STRs and UEPSTRs to document genetic variation at the intercontinental level and among the African Bantu populations, and found that UEPSTR systems clearly provided more resolution than UEPs or STRs alone. The observed patterns of genetic variation revealed high levels of genetic homogeneity between major populations from Angola and Mozambique, with two main outliers: the Kuvale from Angola and the Chopi from Mozambique. Within Mozambique, two Kaskazi-speaking populations from the far north (Yao and Mwani) and two Nyasa-speaking groups from the Zambezi River basin (Nyungwe and Sena) could be differentiated from the remaining groups, but no further population structure was observed across the country. The close genetic relationship between most sampled Bantu populations is consistent with high degrees of interaction between peoples living in savanna areas located to the south of the rainforest. Our results highlight the role of gene flow during the Bantu expansions and show that the genetic evidence accumulated so far is becoming increasingly difficult to reconcile with widely accepted models postulating an early split between eastern and western Bantu populations.

Locating Noctiluca Miliaris in the Arabian Sea: An Optical Proxy Approach

NASA Technical Reports Server (NTRS)

Thibodeau, Patricia S.; Roesler, Collin S.; Drapeau, Susan L.; Matondkar, S. G. Prabhu; Goes, Joaquim I.; Werdell, P. Jeremy

2014-01-01

Coincident with shifting monsoon weather patterns over India, the phytoplankter Noctiluca miliaris has recently been observed to be dominating phytoplankton blooms in the northeastern Arabian Sea during the winter monsoons. Identifying the exact environmental and/or ecological conditions that favor this species has been hampered by the lack of concurrent environmental and biological observations on time and space scales relevant to ecologic and physiologic processes. We present a bio-optical proxy for N. miliaris measured on highly resolved depth scales coincident with hydrographic observations with the goal to identify conducive hydrographic conditions for the bloom. The proxy is derived from multichannel excitation chlorophyll a fluorescence and is validated with microscopy, pigment composition, and spectral absorption. Phytoplankton populations dominated by either diatoms or other dinoflagellates were additionally discerned. N. miliaris populations in full bloom were identified offshore in low-nutrient and low-N : P ratio surface waters within a narrow temperature and salinity range. These populations transitioned to high-biomass diatom-dominated coastal upwelling populations. A week later, the N. miliaris blooms were observed in declining phase, transitioning to very-low-biomass populations of non-N. miliaris dinoflagellates. There were no clear hydrographic conditions uniquely associated with the N. miliaris populations, although N. miliaris was not found in the upwelling or extremely oligotrophic waters. Taxonomic transitions were not discernible in the spatial structure of the bloom as identified by the ocean color Chl imagery, indicating that in situ observations may be necessary to resolve community structure, particularly for populations below the surface.

Positive correlation between genetic diversity and fitness in a large, well-connected metapopulation.

PubMed

Vandewoestijne, Sofie; Schtickzelle, Nicolas; Baguette, Michel

2008-11-05

Theory predicts that lower dispersal, and associated gene flow, leads to decreased genetic diversity in small isolated populations, which generates adverse consequences for fitness, and subsequently for demography. Here we report for the first time this effect in a well-connected natural butterfly metapopulation with high population densities at the edge of its distribution range. We demonstrate that: (1) lower genetic diversity was coupled to a sharp decrease in adult lifetime expectancy, a key component of individual fitness; (2) genetic diversity was positively correlated to the number of dispersing individuals (indicative of landscape functional connectivity) and adult population size; (3) parameters inferred from capture-recapture procedures (population size and dispersal events between patches) correlated much better with genetic diversity than estimates usually used as surrogates for population size (patch area and descriptors of habitat quality) and dispersal (structural connectivity index). Our results suggest that dispersal is a very important factor maintaining genetic diversity. Even at a very local spatial scale in a metapopulation consisting of large high-density populations interconnected by considerable dispersal rates, genetic diversity can be decreased and directly affect the fitness of individuals. From a biodiversity conservation perspective, this study clearly shows the benefits of both in-depth demographic and genetic analyses. Accordingly, to ensure the long-term survival of populations, conservation actions should not be blindly based on patch area and structural isolation. This result may be especially pertinent for species at their range margins, particularly in this era of rapid environmental change.

Trans-Atlantic exchanges have shaped the population structure of the Lyme disease agent Borrelia burgdorferi sensu stricto.

PubMed

Castillo-Ramírez, S; Fingerle, V; Jungnick, S; Straubinger, R K; Krebs, S; Blum, H; Meinel, D M; Hofmann, H; Guertler, P; Sing, A; Margos, G

2016-03-09

The origin and population structure of Borrelia burgdorferi sensu stricto (s.s.), the agent of Lyme disease, remain obscure. This tick-transmitted bacterial species occurs in both North America and Europe. We sequenced 17 European isolates (representing the most frequently found sequence types in Europe) and compared these with 17 North American strains. We show that trans-Atlantic exchanges have occurred in the evolutionary history of this species and that a European origin of B. burgdorferi s.s. is marginally more likely than a USA origin. The data further suggest that some European human patients may have acquired their infection in North America. We found three distinct genetically differentiated groups: i) the outgroup species Borrelia bissettii, ii) two divergent strains from Europe, and iii) a group composed of strains from both the USA and Europe. Phylogenetic analysis indicated that different genotypes were likely to have been introduced several times into the same area. Our results demonstrate that irrespective of whether B. burgdorferi s.s. originated in Europe or the USA, later trans-Atlantic exchange(s) have occurred and have shaped the population structure of this genospecies. This study clearly shows the utility of next generation sequencing to obtain a better understanding of the phylogeography of this bacterial species.

Driving force analysis of the agricultural water footprint in China based on the LMDI method.

PubMed

Zhao, Chunfu; Chen, Bin

2014-11-04

China's water scarcity problems have become more severe because of the unprecedented economic development and population explosion. Considering agriculture's large share of water consumption, obtaining a clear understanding of Chinese agricultural consumptive water use plays a key role in addressing China's water resource stress and providing appropriate water mitigation policies. We account for the Chinese agricultural water footprint from 1990 to 2009 based on bottom up approach. Then, the underlying driving forces are decomposed into diet structure effect, efficiency effect, economic activity effect, and population effect, and analyzed by applying a log-mean Divisia index (LMDI) model. The results reveal that the Chinese agricultural water footprint has risen from the 94.1 Gm3 in 1990 to 141 Gm3 in 2009. The economic activity effect is the largest positive contributor to promoting the water footprint growth, followed by the population effect and diet structure effect. Although water efficiency improvement as a significant negative effect has reduced overall water footprint, the water footprint decline from water efficiency improvement cannot compensate for the huge increase from the three positive driving factors. The combination of water efficiency improvement and dietary structure adjustment is the most effective approach for controlling the Chinese agricultural water footprint's further growth.

Trans-Atlantic exchanges have shaped the population structure of the Lyme disease agent Borrelia burgdorferi sensu stricto

PubMed Central

Castillo-Ramírez, S.; Fingerle, V.; Jungnick, S.; Straubinger, R. K.; Krebs, S.; Blum, H.; Meinel, D. M.; Hofmann, H.; Guertler, P.; Sing, A.; Margos, G.

2016-01-01

The origin and population structure of Borrelia burgdorferi sensu stricto (s.s.), the agent of Lyme disease, remain obscure. This tick-transmitted bacterial species occurs in both North America and Europe. We sequenced 17 European isolates (representing the most frequently found sequence types in Europe) and compared these with 17 North American strains. We show that trans-Atlantic exchanges have occurred in the evolutionary history of this species and that a European origin of B. burgdorferi s.s. is marginally more likely than a USA origin. The data further suggest that some European human patients may have acquired their infection in North America. We found three distinct genetically differentiated groups: i) the outgroup species Borrelia bissettii, ii) two divergent strains from Europe, and iii) a group composed of strains from both the USA and Europe. Phylogenetic analysis indicated that different genotypes were likely to have been introduced several times into the same area. Our results demonstrate that irrespective of whether B. burgdorferi s.s. originated in Europe or the USA, later trans-Atlantic exchange(s) have occurred and have shaped the population structure of this genospecies. This study clearly shows the utility of next generation sequencing to obtain a better understanding of the phylogeography of this bacterial species. PMID:26955886

The world's most isolated and distinct whale population? Humpback whales of the Arabian Sea.

PubMed

Pomilla, Cristina; Amaral, Ana R; Collins, Tim; Minton, Gianna; Findlay, Ken; Leslie, Matthew S; Ponnampalam, Louisa; Baldwin, Robert; Rosenbaum, Howard

2014-01-01

A clear understanding of population structure is essential for assessing conservation status and implementing management strategies. A small, non-migratory population of humpback whales in the Arabian Sea is classified as "Endangered" on the IUCN Red List of Threatened Species, an assessment constrained by a lack of data, including limited understanding of its relationship to other populations. We analysed 11 microsatellite markers and mitochondrial DNA sequences extracted from 67 Arabian Sea humpback whale tissue samples and compared them to equivalent datasets from the Southern Hemisphere and North Pacific. Results show that the Arabian Sea population is highly distinct; estimates of gene flow and divergence times suggest a Southern Indian Ocean origin but indicate that it has been isolated for approximately 70,000 years, remarkable for a species that is typically highly migratory. Genetic diversity values are significantly lower than those obtained for Southern Hemisphere populations and signatures of ancient and recent genetic bottlenecks were identified. Our findings suggest this is the world's most isolated humpback whale population, which, when combined with low population abundance estimates and anthropogenic threats, raises concern for its survival. We recommend an amendment of the status of the population to "Critically Endangered" on the IUCN Red List.

Genetic divergence in nuclear genomes between populations of Fagus crenata along the Japan Sea and Pacific sides of Japan.

PubMed

Hiraoka, Koichi; Tomaru, Nobuhiro

2009-05-01

Genetic diversity and structure in Fagus crenata were studied by analyzing 14 nuclear microsatellite loci in 23 populations distributed throughout the species' range. Although population differentiation was very low (F (ST) = 0.027; R (ST) = 0.041), both neighbor-joining tree and Bayesian clustering analyses provided clear evidence of genetic divergence between populations along the Japan Sea (Japan Sea lineage) and Pacific (Pacific lineage) sides of Japan, indicating that physical barriers to migration and gene flow, notably the mountain ranges separating the populations along the Japan Sea and Pacific sides, have promoted genetic divergence between these populations. The two lineages of the nuclear genome are generally consistent with those of the chloroplast genome detected in a previous study, with several discrepancies between the two genomes. Within-population genetic diversity was generally very high (average H (E) = 0.839), but decreased in a clinal fashion from southwest to northeast, largely among populations of the Japan Sea lineage. This geographical gradient may have resulted from the late-glacial and postglacial recolonization to the northeast, which led to a loss of within-population genetic diversity due to cumulative founder effects.

THE VELOCITY DISTRIBUTION OF NEARBY STARS FROM HIPPARCOS DATA. II. THE NATURE OF THE LOW-VELOCITY MOVING GROUPS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bovy, Jo; Hogg, David W., E-mail: jo.bovy@nyu.ed

2010-07-10

The velocity distribution of nearby stars ({approx}<100 pc) contains many overdensities or 'moving groups', clumps of comoving stars, that are inconsistent with the standard assumption of an axisymmetric, time-independent, and steady-state Galaxy. We study the age and metallicity properties of the low-velocity moving groups based on the reconstruction of the local velocity distribution in Paper I of this series. We perform stringent, conservative hypothesis testing to establish for each of these moving groups whether it could conceivably consist of a coeval population of stars. We conclude that they do not: the moving groups are neither trivially associated with their eponymousmore » open clusters nor with any other inhomogeneous star formation event. Concerning a possible dynamical origin of the moving groups, we test whether any of the moving groups has a higher or lower metallicity than the background population of thin disk stars, as would generically be the case if the moving groups are associated with resonances of the bar or spiral structure. We find clear evidence that the Hyades moving group has higher than average metallicity and weak evidence that the Sirius moving group has lower than average metallicity, which could indicate that these two groups are related to the inner Lindblad resonance of the spiral structure. Further, we find weak evidence that the Hercules moving group has higher than average metallicity, as would be the case if it is associated with the bar's outer Lindblad resonance. The Pleiades moving group shows no clear metallicity anomaly, arguing against a common dynamical origin for the Hyades and Pleiades groups. Overall, however, the moving groups are barely distinguishable from the background population of stars, raising the likelihood that the moving groups are associated with transient perturbations.« less

Phylogeography and spatial structure of the lowland tapir (Tapirus terrestris, Perissodactyla: Tapiridae) in South America.

PubMed

Ruiz-García, Manuel; Vásquez, Catalina; Sandoval, Sergio; Kaston, Franz; Luengas-Villamil, Kelly; Shostell, Joseph Mark

2016-07-01

We sequenced the mitochondrial cytochrome b gene of 141 lowland tapirs (Tapirus terrestris) - representing the largest geographical distribution sample of this species studied across of South America to date. We compare our new data regard to two previous works on population structure and molecular systematics of T. terrestris. Our data agree with the Thoisy et al.'s work in (1) the Northern Western Amazon basin was the area with the highest gene diversity levels in T. terrestris, being probably the area of initial diversification; (2) there was no clear association between haplogroups and specific geographical areas; (3) there were clear population decreases during the last glacial maximum for the different haplogroups detected, followed by population expansions during the Holocene; and (4) our temporal splits among different T. terrestris haplogroups coincided with the first molecular clock approach carried out by these authors (fossil calibration). Nevertheless, our study disagreed regard to other aspects of the Thoisy et al.'s claims: (1) meanwhile, they detected four relevant clades in their data, we put forward six different relevant clades; (2) the Amazon River was not a strong barrier for haplotype dispersion in T. terrestris; and (3) we found reciprocal monophyly between T. terrestris and T. pinchaque. Additionally, we sequenced 42 individuals (T. terrestris, T. pinchaque, T. bairdii, and the alleged "new species", T. kabomani) for three concatenated mitochondrial genes (Cyt-b, COI, and COII) agreeing quite well with the view of Voss et al., and against of the claims of Cozzuol et al. Tapirus kabomani should be not considered as a full species with the results obtained throughout the mitochondrial sequences.

Sky island diversification meets the multispecies coalescent - divergence in the spruce-fir moss spider (Microhexura montivaga, Araneae, Mygalomorphae) on the highest peaks of southern Appalachia.

PubMed

Hedin, Marshal; Carlson, Dave; Coyle, Fred

2015-07-01

Microhexura montivaga is a miniature tarantula-like spider endemic to the highest peaks of the southern Appalachian mountains and is known only from six allopatric, highly disjunct montane populations. Because of severe declines in spruce-fir forest in the late 20th century, M. montivaga was formally listed as a US federally endangered species in 1995. Using DNA sequence data from one mitochondrial and seven nuclear genes, patterns of multigenic genetic divergence were assessed for six montane populations. Independent mitochondrial and nuclear discovery analyses reveal obvious genetic fragmentation both within and among montane populations, with five to seven primary genetic lineages recovered. Multispecies coalescent validation analyses [guide tree and unguided Bayesian Phylogenetics and Phylogeography (BPP), Bayes factor delimitation (BFD)] using nuclear-only data congruently recover six or seven distinct lineages; BFD analyses using combined nuclear plus mitochondrial data favour seven or eight lineages. In stark contrast to this clear genetic fragmentation, a survey of secondary sexual features for available males indicates morphological conservatism across montane populations. While it is certainly possible that morphologically cryptic speciation has occurred in this taxon, this system may alternatively represent a case where extreme population genetic structuring (but not speciation) leads to an oversplitting of lineage diversity by multispecies coalescent methods. Our results have clear conservation implications for this federally endangered taxon and illustrate a methodological issue expected to become more common as genomic-scale data sets are gathered for taxa found in naturally fragmented habitats. © 2015 John Wiley & Sons Ltd.

[Postspawning survival in lacustrine sock-eyed salmon Oncorhynchus nerka Walb].

PubMed

Markevich, G N; Ivashkin, E G; Pavlov, E D

2011-01-01

The state of gonads, age, structure of scales, and size of specimens of the resident lacustrine form of sock-eyed salmon--kokanee Onchorhynchus nerka--are analyzed. In stocked, previously fishless, lakes, there are specimens that have survived spawning and have remained active for a year or several years. No evidence was found of the possibility of repeated spawning. Thus, such fish do not belong to the spawning stock of the population, and their ecological function is not clear.

Distribution and Catabolic Diversity of 3-Chlorobenzoic Acid Degrading Bacteria Isolated from Geographically-Separated Pristine Soils

DTIC Science & Technology

1994-08-01

influence on the structure of 3-CBA degrading populations. This suggests that if substrate exposure is important, secondary metabolites produced during the...enrichments were treated with 50 gIg 3-CBAgodry-soil- 1 and secondary enrichments were performed with 50 p.g 3-CBA ml-1 d•tfined medium. Isolates were...not attempt to determine metabolites or if transformations were biologically mediated. As a result, it was not clear whether disappearance of a

Dynamics of a black-capped chickadee population, 1958-1983

USGS Publications Warehouse

Loery, G.; Nichols, J.D.

1985-01-01

The dynamics of a wintering population of Black-capped Chickadees (Parus atricapillus) were studied from 1958-1983 using capture-recapture methods. The Jolly-Seber model was used to obtain annual estimates of population size, survival rate, and recruitment. The average estimated population size over this period was ?160 birds. The average estimated number of new birds entering the population each year and alive at the time of sampling was ?57. The arithmetic mean annual survival rate estimate was ?0.59. We tested hypothesis about possible relationships between these population parameters and (1) the natural introduction of Tufted Titmice (Parus bicolor) to the area, (2) the clear-cutting of portions of nearby red pine (Pinus resinosa) plantations, and (3) natural variations in winter temperatures. The chickadee population exhibited a substantial short-term decline following titmouse establishment, produced by decreases in both survival rate and number of new recruits. Survival rate decline somewhat after the initiation of the pine clear-cutting, but population size was very similar before and after clear-cutting. Weighted least squares analyses provided no evidence of a relationship between survival rate and either of two winter temperature variables.

Genetic structure and demographic history of the endangered tree species Dysoxylum malabaricum (Meliaceae) in Western Ghats, India: implications for conservation in a biodiversity hotspot.

PubMed

Bodare, Sofia; Tsuda, Yoshiaki; Ravikanth, Gudasalamani; Uma Shaanker, Ramanan; Lascoux, Martin

2013-09-01

The impact of fragmentation by human activities on genetic diversity of forest trees is an important concern in forest conservation, especially in tropical forests. Dysoxylum malabaricum (white cedar) is an economically important tree species, endemic to the Western Ghats, India, one of the world's eight most important biodiversity hotspots. As D. malabaricum is under pressure of disturbance and fragmentation together with overharvesting, conservation efforts are required in this species. In this study, range-wide genetic structure of twelve D. malabaricum populations was evaluated to assess the impact of human activities on genetic diversity and infer the species' evolutionary history, using both nuclear and chloroplast (cp) DNA simple sequence repeats (SSR). As genetic diversity and population structure did not differ among seedling, juvenile and adult age classes, reproductive success among the old-growth trees and long distance seed dispersal by hornbills were suggested to contribute to maintain genetic diversity. The fixation index (F IS) was significantly correlated with latitude, with a higher level of inbreeding in the northern populations, possibly reflecting a more severe ecosystem disturbance in those populations. Both nuclear and cpSSRs revealed northern and southern genetic groups with some discordance of their distributions; however, they did not correlate with any of the two geographic gaps known as genetic barriers to animals. Approximate Bayesian computation-based inference from nuclear SSRs suggested that population divergence occurred before the last glacial maximum. Finally we discussed the implications of these results, in particular the presence of a clear pattern of historical genetic subdivision, on conservation policies.

Genetic structure and demographic history of the endangered tree species Dysoxylum malabaricum (Meliaceae) in Western Ghats, India: implications for conservation in a biodiversity hotspot

PubMed Central

Bodare, Sofia; Tsuda, Yoshiaki; Ravikanth, Gudasalamani; Uma Shaanker, Ramanan; Lascoux, Martin

2013-01-01

The impact of fragmentation by human activities on genetic diversity of forest trees is an important concern in forest conservation, especially in tropical forests. Dysoxylum malabaricum (white cedar) is an economically important tree species, endemic to the Western Ghats, India, one of the world's eight most important biodiversity hotspots. As D. malabaricum is under pressure of disturbance and fragmentation together with overharvesting, conservation efforts are required in this species. In this study, range-wide genetic structure of twelve D. malabaricum populations was evaluated to assess the impact of human activities on genetic diversity and infer the species’ evolutionary history, using both nuclear and chloroplast (cp) DNA simple sequence repeats (SSR). As genetic diversity and population structure did not differ among seedling, juvenile and adult age classes, reproductive success among the old-growth trees and long distance seed dispersal by hornbills were suggested to contribute to maintain genetic diversity. The fixation index (FIS) was significantly correlated with latitude, with a higher level of inbreeding in the northern populations, possibly reflecting a more severe ecosystem disturbance in those populations. Both nuclear and cpSSRs revealed northern and southern genetic groups with some discordance of their distributions; however, they did not correlate with any of the two geographic gaps known as genetic barriers to animals. Approximate Bayesian computation-based inference from nuclear SSRs suggested that population divergence occurred before the last glacial maximum. Finally we discussed the implications of these results, in particular the presence of a clear pattern of historical genetic subdivision, on conservation policies. PMID:24223264

Demography and population dynamics of the mouse opossum (Thylamys elegans) in semi-arid Chile: seasonality, feedback structure and climate.

PubMed Central

Lima, M.; Stenseth, N. C.; Yoccoz, N. G.; Jaksic, F. M.

2001-01-01

Here we present, to the authors' knowledge for the very first time for a small marsupial, a thorough analysis of the demography and population dynamics of the mouse opossum (Thylamys elegans) in western South America. We test the relative importance of feedback structure and climatic factors (rainfall and the Southern Oscillation Index) in explaining the temporal variation in the demography of the mouse opossum. The demographic information was incorporated into a stage-structured population dynamics model and the model's predictions were compared with observed patterns. The mouse opossum's capture rates showed seasonal (within-year) and between-year variability, with individuals having higher capture rates during late summer and autumn and lower capture rates during winter and spring. There was also a strong between-year effect on capture probabilities. The reproductive (the fraction of reproductively active individuals) and recruitment rates showed a clear seasonal and a between-year pattern of variation with the peak of reproductive activity occuring during winter and early spring. In addition, the fraction of reproductive individuals was positively related to annual rainfall, while population density and annual rainfall positively influenced the recruitment rate. The survival rates were negatively related to annual rainfall. The average finite population growth rate during the study period was estimated to be 1.011 +/- 0.0019 from capture-recapture estimates. While the annual growth rate estimated from the seasonal linear matrix models was 1.026, the subadult and adult survival and maturation rates represent between 54% (winter) and 81% (summer) of the impact on the annual growth rate. PMID:11571053

Phylogeographic structure and historical demography of the western diamondback rattlesnake (Crotalus atrox): A perspective on North American desert biogeography.

PubMed

Castoe, Todd A; Spencer, Carol L; Parkinson, Christopher L

2007-01-01

The western diamondback rattlesnake (Crotalus atrox) is a prominent member of North American desert and semi-arid ecosystems, and its importance extends from its impact on the region's ecology and imagery, to its medical relevance as a large deadly venomous snake. We used mtDNA sequences to identify population genetic structure and historical demographic patterns across the range of this species, and relate these to broader patterns of historical biogeography of desert and semi-arid regions of the southwestern USA and adjacent Mexico. We inferred a Late Pliocene divergence between peninsular and continental lineages of Crotalus, followed by an Early Mid Pleistocene divergence across the continental divide within C. atrox. Within desert regions (Sonoran and Chihuahuan Deserts, Southern Plains, and Tamaulipan Plain) we observed population structure indicating isolation of populations in multiple Pleistocene refugia on either side of the continental divide, which we attempt to identify. Evidence of post-glacial population growth and range expansion was inferred, particularly in populations east of the continental divide. We observed clear evidence of (probably recent) gene flow across the continental divide and secondary contact of haplotype lineages. This recent gene flow appears to be particularly strong in the West-to-East direction. Our results also suggest that Crotalus tortugensis (Tortuga Island rattlesnake) and a population of 'C. atrox' inhabiting Santa Cruz Island (in the Gulf of California) previously suggested to be an unnamed species, are in fact deeply phylogenetically nested within continental lineages of C. atrox. Accordingly, we suggest C. tortugensis and 'C. atrox' from Santa Cruz Island be placed in the synonymy of C. atrox.

How Often Do They Have Sex? A Comparative Analysis of the Population Structure of Seven Eukaryotic Microbial Pathogens

PubMed Central

Tomasini, Nicolás; Lauthier, Juan José; Ayala, Francisco José; Tibayrenc, Michel; Diosque, Patricio

2014-01-01

The model of predominant clonal evolution (PCE) proposed for micropathogens does not state that genetic exchange is totally absent, but rather, that it is too rare to break the prevalent PCE pattern. However, the actual impact of this “residual” genetic exchange should be evaluated. Multilocus Sequence Typing (MLST) is an excellent tool to explore the problem. Here, we compared online available MLST datasets for seven eukaryotic microbial pathogens: Trypanosoma cruzi, the Fusarium solani complex, Aspergillus fumigatus, Blastocystis subtype 3, the Leishmania donovani complex, Candida albicans and Candida glabrata. We first analyzed phylogenetic relationships among genotypes within each dataset. Then, we examined different measures of branch support and incongruence among loci as signs of genetic structure and levels of past recombination. The analyses allow us to identify three types of genetic structure. The first was characterized by trees with well-supported branches and low levels of incongruence suggesting well-structured populations and PCE. This was the case for the T. cruzi and F. solani datasets. The second genetic structure, represented by Blastocystis spp., A. fumigatus and the L. donovani complex datasets, showed trees with weakly-supported branches but low levels of incongruence among loci, whereby genetic structuration was not clearly defined by MLST. Finally, trees showing weakly-supported branches and high levels of incongruence among loci were observed for Candida species, suggesting that genetic exchange has a higher evolutionary impact in these mainly clonal yeast species. Furthermore, simulations showed that MLST may fail to show right clustering in population datasets even in the absence of genetic exchange. In conclusion, these results make it possible to infer variable impacts of genetic exchange in populations of predominantly clonal micro-pathogens. Moreover, our results reveal different problems of MLST to determine the genetic structure in these organisms that should be considered. PMID:25054834

Sensitivity of Marine Warm Cloud Retrieval Statistics to Algorithm Choices: Examples from MODIS Collection 6

NASA Astrophysics Data System (ADS)

Platnick, S.; Wind, G.; Zhang, Z.; Ackerman, S. A.; Maddux, B. C.

2012-12-01

The optical and microphysical structure of warm boundary layer marine clouds is of fundamental importance for understanding a variety of cloud radiation and precipitation processes. With the advent of MODIS (Moderate Resolution Imaging Spectroradiometer) on the NASA EOS Terra and Aqua platforms, simultaneous global/daily 1km retrievals of cloud optical thickness and effective particle size are provided, as well as the derived water path. In addition, the cloud product (MOD06/MYD06 for MODIS Terra and Aqua, respectively) provides separate effective radii results using the 1.6, 2.1, and 3.7 μm spectral channels. Cloud retrieval statistics are highly sensitive to how a pixel identified as being "not-clear" by a cloud mask (e.g., the MOD35/MYD35 product) is determined to be useful for an optical retrieval based on a 1-D cloud model. The Collection 5 MODIS retrieval algorithm removed pixels associated with cloud edges (defined by immediate adjacency to "clear" MOD/MYD35 pixels) as well as ocean pixels with partly cloudy elements in the 250m MODIS cloud mask - part of the so-called Clear Sky Restoral (CSR) algorithm. Collection 6 attempts retrievals for those two pixel populations, but allows a user to isolate or filter out the populations via CSR pixel-level Quality Assessment (QA) assignments. In this paper, using the preliminary Collection 6 MOD06 product, we present global and regional statistical results of marine warm cloud retrieval sensitivities to the cloud edge and 250m partly cloudy pixel populations. As expected, retrievals for these pixels are generally consistent with a breakdown of the 1D cloud model. While optical thickness for these suspect pixel populations may have some utility for radiative studies, the retrievals should be used with extreme caution for process and microphysical studies.

The effects of behavioral and structural assumptions in artificial stock market

NASA Astrophysics Data System (ADS)

Liu, Xinghua; Gregor, Shirley; Yang, Jianmei

2008-04-01

Recent literature has developed the conjecture that important statistical features of stock price series, such as the fat tails phenomenon, may depend mainly on the market microstructure. This conjecture motivated us to investigate the roles of both the market microstructure and agent behavior with respect to high-frequency returns and daily returns. We developed two simple models to investigate this issue. The first one is a stochastic model with a clearing house microstructure and a population of zero-intelligence agents. The second one has more behavioral assumptions based on Minority Game and also has a clearing house microstructure. With the first model we found that a characteristic of the clearing house microstructure, namely the clearing frequency, can explain fat tail, excess volatility and autocorrelation phenomena of high-frequency returns. However, this feature does not cause the same phenomena in daily returns. So the Stylized Facts of daily returns depend mainly on the agents’ behavior. With the second model we investigated the effects of behavioral assumptions on daily returns. Our study implicates that the aspects which are responsible for generating the stylized facts of high-frequency returns and daily returns are different.

Population differences in allele frequencies at the OLR1 locus may suggest geographic disparities in cardiovascular risk events.

PubMed

Predazzi, Irene M; Martínez-Labarga, Cristina; Vecchione, Lucia; Mango, Ruggiero; Ciccacci, Cinzia; Amati, Francesca; Ottoni, Claudio; Crawford, Michael H; Rickards, Olga; Romeo, Francesco; Novelli, Giuseppe

2010-04-01

Several studies have demonstrated a link between cardiovascular disease (CVD) susceptibility and the genetic background of populations. Endothelial activation and dysfunction induced by oxidized low-density lipoprotein (ox-LDL) is one of the key steps in the initiation of atherosclerosis. The oxidized low density lipoprotein (lectin-like) receptor 1 (OLR1) gene is the main receptor of ox-LDL. We have previously characterized two polymorphisms (rs3736235 and rs11053646) associated with the risk for coronary artery disease (CAD) and acute myocardial infarction (AMI). Given their clinical significance, it is of interest to know the distribution of these variants in populations from different continents. A total of 1229 individuals from 17 different African, Asian and European populations was genotyped for the two considered markers. The high frequencies of ancestral alleles in South-Saharan populations is concordant with the African origin of our species. The results highlight that African populations are closer to Asians, and clearly separated from the Europeans. The results confirm significant genetic structuring among populations and suggest a possible basis for varying susceptibility to CVD among groups correlated with the geographical location of populations linked with the migrations out of Africa, or with different lifestyle.

Philopatry and migration of Pacific white sharks

PubMed Central

Jorgensen, Salvador J.; Reeb, Carol A.; Chapple, Taylor K.; Anderson, Scot; Perle, Christopher; Van Sommeran, Sean R.; Fritz-Cope, Callaghan; Brown, Adam C.; Klimley, A. Peter; Block, Barbara A.

2010-01-01

Advances in electronic tagging and genetic research are making it possible to discern population structure for pelagic marine predators once thought to be panmictic. However, reconciling migration patterns and gene flow to define the resolution of discrete population management units remains a major challenge, and a vital conservation priority for threatened species such as oceanic sharks. Many such species have been flagged for international protection, yet effective population assessments and management actions are hindered by lack of knowledge about the geographical extent and size of distinct populations. Combining satellite tagging, passive acoustic monitoring and genetics, we reveal how eastern Pacific white sharks (Carcharodon carcharias) adhere to a highly predictable migratory cycle. Individuals persistently return to the same network of coastal hotspots following distant oceanic migrations and comprise a population genetically distinct from previously identified phylogenetic clades. We hypothesize that this strong homing behaviour has maintained the separation of a northeastern Pacific population following a historical introduction from Australia/New Zealand migrants during the Late Pleistocene. Concordance between contemporary movement and genetic divergence based on mitochondrial DNA demonstrates a demographically independent management unit not previously recognized. This population's fidelity to discrete and predictable locations offers clear population assessment, monitoring and management options. PMID:19889703

Long-range gene flow and the effects of climatic and ecological factors on genetic structuring in a large, solitary carnivore: the Eurasian lynx.

PubMed

Ratkiewicz, Mirosław; Matosiuk, Maciej; Saveljev, Alexander P; Sidorovich, Vadim; Ozolins, Janis; Männil, Peep; Balciauskas, Linas; Kojola, Ilpo; Okarma, Henryk; Kowalczyk, Rafał; Schmidt, Krzysztof

2014-01-01

Due to their high mobility, large terrestrial predators are potentially capable of maintaining high connectivity, and therefore low genetic differentiation among populations. However, previous molecular studies have provided contradictory findings in relation to this. To elucidate patterns of genetic structure in large carnivores, we studied the genetic variability of the Eurasian lynx, Lynx lynx throughout north-eastern Europe using microsatellite, mitochondrial DNA control region and Y chromosome-linked markers. Using SAMOVA we found analogous patterns of genetic structure based on both mtDNA and microsatellites, which coincided with a relatively little evidence for male-biased dispersal. No polymorphism for the cytochrome b and ATP6 mtDNA genes and Y chromosome-linked markers were found. Lynx inhabiting a large area encompassing Finland, the Baltic countries and western Russia formed a single genetic unit, while some marginal populations were clearly divergent from others. The existence of a migration corridor was suggested to correspond with distribution of continuous forest cover. The lowest variability (in both markers) was found in lynx from Norway and Białowieża Primeval Forest (BPF), which coincided with a recent demographic bottleneck (Norway) or high habitat fragmentation (BPF). The Carpathian population, being monomorphic for the control region, showed relatively high microsatellite diversity, suggesting the effect of a past bottleneck (e.g. during Last Glacial Maximum) on its present genetic composition. Genetic structuring for the mtDNA control region was best explained by latitude and snow cover depth. Microsatellite structuring correlated with the lynx's main prey, especially the proportion of red deer (Cervus elaphus) in its diet. Eurasian lynx are capable of maintaining panmictic populations across eastern Europe unless they are severely limited by habitat continuity or a reduction in numbers. Different correlations of mtDNA and microsatellite population divergence patterns with climatic and ecological factors may suggest separate selective pressures acting on males and females in this solitary carnivore.

[TRENDS IN HEALTH OF THE POPULATION IN THE AREA OF THE TENGIZ FIELD].

PubMed

Kenessaryiev, U I; Yerzhanova, A E; Kenessary, D U; Amrin, M K; Dosmukhametov, A T; Baimukhamedov, A A

2015-01-01

At the present the Caspian oil and gas field became extremely important for the economy of Kazakhstan and it has entered a qualitatively new stage of its development. In connection with the intensive development of these fields the attention of both scientists and health practitioners is attracted by problems of populations' health. In the article there are presented data of a study of the quality of main objects of environment, health condition, demographic indices of and morbidity rate of the population of the Zhylyoi district of the Atyrau region. The population resides in the region of influence of the Tengiz oil and gas field. The level of mortality in Zhylyoi for the periodfrom 2006 to 2013 was establishe to decline, as birth rate rather increased. Indices of the population's structure retain the tendency to the progressive type, possibly in relation with urbanization and industrial migration of population, that increased in last years. The district mortality rates are below national, regional and urban values. Natural population growth in Zhylyoi has increased by 27.6%. The analysis of primary morbidity of the population of the Zhylyoi district in dynamics from 2006 to 2013 shows a some decrease. In the structure of the morbidity there was noted a decrease in the proportion of diseases of the skin and subcutaneous tissue, respiratory diseases, digestive organs. However, the proportion of blood diseases, diseases of the hematopoietic system and blood flow has increased. Alongside this in the region there is clearly discernible the scarcity of doctors, qualified nurses and beds.

Population genetic structure of the people of Qatar.

PubMed

Hunter-Zinck, Haley; Musharoff, Shaila; Salit, Jacqueline; Al-Ali, Khalid A; Chouchane, Lotfi; Gohar, Abeer; Matthews, Rebecca; Butler, Marcus W; Fuller, Jennifer; Hackett, Neil R; Crystal, Ronald G; Clark, Andrew G

2010-07-09

People of the Qatar peninsula represent a relatively recent founding by a small number of families from three tribes of the Arabian Peninsula, Persia, and Oman, with indications of African admixture. To assess the roles of both this founding effect and the customary first-cousin marriages among the ancestral Islamic populations in Qatar's population genetic structure, we obtained and genotyped with Affymetrix 500k SNP arrays DNA samples from 168 self-reported Qatari nationals sampled from Doha, Qatar. Principal components analysis was performed along with samples from the Human Genetic Diversity Project data set, revealing three clear clusters of genotypes whose proximity to other human population samples is consistent with Arabian origin, a more eastern or Persian origin, and individuals with African admixture. The extent of linkage disequilibrium (LD) is greater than that of African populations, and runs of homozygosity in some individuals reflect substantial consanguinity. However, the variance in runs of homozygosity is exceptionally high, and the degree of identity-by-descent sharing generally appears to be lower than expected for a population in which nearly half of marriages are between first cousins. Despite the fact that the SNPs of the Affymetrix 500k chip were ascertained with a bias toward SNPs common in Europeans, the data strongly support the notion that the Qatari population could provide a valuable resource for the mapping of genes associated with complex disorders and that tests of pairwise interactions are particularly empowered by populations with elevated LD like the Qatari. Copyright 2010 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Genetic Population Structure of Local Populations of the Endangered Saltmarsh Sesarmid Crab Clistocoeloma sinense in Japan

PubMed Central

Yuhara, Takeshi; Kawane, Masako; Furota, Toshio

2014-01-01

During recent decades, over 40% of Japanese estuarine tidal flats have been lost due to coastal developments. Local populations of the saltmarsh sesarmid crab Clistocoeloma sinense, designated as an endangered species due to the limited suitable saltmarsh habitat available, have decreased accordingly, being now represented as small remnant populations. Several such populations in Tokyo Bay, have been recognised as representing distributional limits of the species. To clarify the genetic diversity and connectivity among local coastal populations of Japanese Clistocoeloma sinense, including those in Tokyo Bay, mitochondrial DNA analyses were conducted in the hope of providing fundamental information for future conservation studies and an understanding of metapopulation dynamics through larval dispersal among local populations. All of the populations sampled indicated low levels of genetic diversity, which may have resulted from recent population bottlenecks or founder events. However, the results also revealed clear genetic differentiation between two enclosed-water populations in Tokyo Bay and Ise-Mikawa Bay, suggesting the existence of a barrier to larval transport between these two water bodies. Since the maintenance of genetic connectivity is a requirement of local population stability, the preservation of extant habitats and restoration of saltmarshes along the coast of Japan may be the most effective measures for conservation of this endangered species. PMID:24400112

Genetic drift and rapid evolution of viviparity in insular fire salamanders (Salamandra salamandra)

PubMed Central

Velo-Antón, G; Zamudio, K R; Cordero-Rivera, A

2012-01-01

Continental islands offer an excellent opportunity to investigate adaptive processes and to time microevolutionary changes that precede macroevolutionary events. We performed a population genetic study of the fire salamander (Salamandra salamandra), a species that displays unique intraspecific diversity of reproductive strategies, to address the microevolutionary processes leading to phenotypic and genetic differentiation of island, coastal and interior populations. We used eight microsatellite markers to estimate genetic diversity, population structure and demographic parameters in viviparous insular populations and ovoviviparous coastal and interior populations. Our results show considerable genetic differentiation (FST range: 0.06–0.27), and no clear signs of gene flow among populations, except between the large and admixed interior populations. We find no support for island colonization by rafting or intentional/accidental anthropogenic introductions, indicating that rising sea levels were responsible for isolation of the island populations approximately 9000 years ago. Our study provides evidence of rapid genetic differentiation between island and coastal populations, and rapid evolution of viviparity driven by climatic selective pressures on island populations, geographic isolation with genetic drift, or a combination of these factors. Studies of these viviparous island populations in early stages of divergence help us better understand the microevolutionary processes involved in rapid phenotypic shifts. PMID:22086081

Genetic drift and rapid evolution of viviparity in insular fire salamanders (Salamandra salamandra).

PubMed

Velo-Antón, G; Zamudio, K R; Cordero-Rivera, A

2012-04-01

Continental islands offer an excellent opportunity to investigate adaptive processes and to time microevolutionary changes that precede macroevolutionary events. We performed a population genetic study of the fire salamander (Salamandra salamandra), a species that displays unique intraspecific diversity of reproductive strategies, to address the microevolutionary processes leading to phenotypic and genetic differentiation of island, coastal and interior populations. We used eight microsatellite markers to estimate genetic diversity, population structure and demographic parameters in viviparous insular populations and ovoviviparous coastal and interior populations. Our results show considerable genetic differentiation (F(ST) range: 0.06-0.27), and no clear signs of gene flow among populations, except between the large and admixed interior populations. We find no support for island colonization by rafting or intentional/accidental anthropogenic introductions, indicating that rising sea levels were responsible for isolation of the island populations approximately 9000 years ago. Our study provides evidence of rapid genetic differentiation between island and coastal populations, and rapid evolution of viviparity driven by climatic selective pressures on island populations, geographic isolation with genetic drift, or a combination of these factors. Studies of these viviparous island populations in early stages of divergence help us better understand the microevolutionary processes involved in rapid phenotypic shifts.

Population Genetics of Plasmodium vivax in Four High Malaria Endemic Areas in Thailand.

PubMed

Congpuong, Kanungnit; Ubalee, Ratawan

2017-10-01

Recent trends of malaria in Thailand illustrate an increasing proportion of Plasmodium vivax, indicating the importance of P. vivax as a major causative agent of malaria. P. vivax malaria is usually considered a benign disease so the knowledge of this parasite has been limited, especially the genetic diversity and genetic structure of isolates from different endemic areas. The aim of this study was to examine the population genetics and structure of P. vivax isolates from 4 provinces with different malaria endemic settings in Thailand using 6 microsatellite markers. Total 234 blood samples from P. vivax mono-infected patients were collected. Strong genetic diversity was observed across all study sites; the expected heterozygosity values ranged from 0.5871 to 0.9033. Genetic variability in this study divided P. vivax population into 3 clusters; first was P. vivax isolates from Mae Hong Son and Kanchanaburi Provinces located on the western part of Thailand; second, Yala isolates from the south; and third, Chanthaburi isolates from the east. P. vivax isolates from patients having parasite clearance time (PCT) longer than 24 hr after the first dose of chloroquine treatment had higher diversity when compared with those having PCT within 24 hr. This study revealed a clear evidence of different population structure of P. vivax from different malaria endemic areas of Thailand. The findings provide beneficial information to malaria control programme as it is a useful tool to track the source of infections and current malaria control efforts.

Responses of bat social groups to roost loss: More questions than answers

USGS Publications Warehouse

Silvis, Alexander; Abaid, Nicole; Ford, W. Mark; Britzke, Eric R.; Ortega, Jorge

2016-01-01

Though characterization of, and understanding determinants of, social structure in bats is increasing, little is known about how bat social groups respond to disturbance resulting in roost loss. Given that many species of bats roost in ephemeral or transitory resources such as plants, it is clear that bat social groups can tolerate some level of roost loss. Understanding responses of bat social groups to roost loss can provide insight into social structure that have applied conservation use. Herein, we review the existing literature on the effects of disturbance on bat social groups, and present a parameterizable agent-based model that can be used to explore the relationships among roost dynamics, population dynamics, and social behavior.

Detection of a novel, integrative aging process suggests complex physiological integration.

PubMed

Cohen, Alan A; Milot, Emmanuel; Li, Qing; Bergeron, Patrick; Poirier, Roxane; Dusseault-Bélanger, Francis; Fülöp, Tamàs; Leroux, Maxime; Legault, Véronique; Metter, E Jeffrey; Fried, Linda P; Ferrucci, Luigi

2015-01-01

Many studies of aging examine biomarkers one at a time, but complex systems theory and network theory suggest that interpretations of individual markers may be context-dependent. Here, we attempted to detect underlying processes governing the levels of many biomarkers simultaneously by applying principal components analysis to 43 common clinical biomarkers measured longitudinally in 3694 humans from three longitudinal cohort studies on two continents (Women's Health and Aging I & II, InCHIANTI, and the Baltimore Longitudinal Study on Aging). The first axis was associated with anemia, inflammation, and low levels of calcium and albumin. The axis structure was precisely reproduced in all three populations and in all demographic sub-populations (by sex, race, etc.); we call the process represented by the axis "integrated albunemia." Integrated albunemia increases and accelerates with age in all populations, and predicts mortality and frailty--but not chronic disease--even after controlling for age. This suggests a role in the aging process, though causality is not yet clear. Integrated albunemia behaves more stably across populations than its component biomarkers, and thus appears to represent a higher-order physiological process emerging from the structure of underlying regulatory networks. If this is correct, detection of this process has substantial implications for physiological organization more generally.

Genetic structure and evolution of natural populations of viruses causing the tomato yellow leaf curl disease in Spain.

PubMed

Font, María Isabel; Rubio, Luis; Martínez-Culebras, Pedro Vicente; Jordá, Concepción

2007-09-01

The population structure and genetic variation of two begomoviruses: tomato yellow leaf curl Sardinia virus (TYLCSV) and tomato yellow leaf curl virus (TYLCV) in tomato crops of Spain were studied from 1997 until 2001. Restriction digestion of a genomic region comprised of the CP coat protein gene (CPR) of 358 TYLC virus isolates enabled us to classify them into 14 haplotypes. Nucleotide sequences of two genomic regions: CPR, and the surrounding intergenic region (SIR) were determined for at least two isolates per haplotype. SIR was more variable than CPR and showed multiple recombination events whereas no recombination was detected within CPR. In all geographic regions except Murcia, the population was, or evolved to be composed of one predominant haplotype with a low genetic diversity (<0.0180). In Murcia, two successive changes of the predominant haplotype were observed in the best studied population. Phylogenetic analysis showed that the TYLCSV sequences determined clustered with sequences obtained from the GenBank of other TYLCSV Spanish isolates which were clearly separated from TYLCSV Italian isolates. Most of our TYLCV sequences were similar to those of isolates from Japan and Portugal, and the sequences obtained from TYLCV isolates from the Canary island of Lanzarote were similar to those of Caribbean TYLCV isolates.

Hi-Tech for Archeology

NASA Technical Reports Server (NTRS)

1987-01-01

Remote sensing is the process of acquiring physical information from a distance, obtaining data on Earth features from a satellite or an airplane. Advanced remote sensing instruments detect radiations not visible to the ordinary camera or the human eye in several bands of the spectrum. These data are computer processed to produce multispectral images that can provide enormous amounts of information about Earth objects or phenomena. Since every object on Earth emits or reflects radiation in its own unique signature, remote sensing data can be interpreted to tell the difference between one type of vegetation and another, between densely populated urban areas and lightly populated farmland, between clear and polluted water or in the archeological application between rain forest and hidden man made structures.

Bifidobacterial Succession and Correlation Networks in a Large Unselected Cohort of Mothers and Their Children

PubMed Central

Storrø, O.; Øien, T.; Johnsen, R.; Wilson, R.; Egeland, T.; Rudi, K.

2013-01-01

Bifidobacteria are a major microbial component of infant gut microbiota, which is believed to promote health benefits for the host and stimulate maturation of the immune system. Despite their perceived importance, very little is known about the natural development of and possible correlations between bifidobacteria in human populations. To address this knowledge gap, we analyzed stool samples from a randomly selected healthy cohort of 87 infants and their mothers with >90% of vaginal delivery and nearly 100% breast-feeding at 4 months. Fecal material was sampled during pregnancy, at 3 and 10 days, at 4 months, and at 1 and 2 years after birth. Stool samples were predicted to be rich in the species Bifidobacterium adolescentis, B. bifidum, B. dentium, B. breve, and B. longum. Due to high variation, we did not identify a clear age-related structure at the individual level. Within the population as a whole, however, there were clear age-related successions. Negative correlations between the B. longum group and B. adolescentis were detected in adults and in 1- and 2-year-old children, whereas negative correlations between B. longum and B. breve were characteristic for newborns and 4-month-old infants. The highly structured age-related development of and correlation networks between bifidobacterial species during the first 2 years of life mirrors their different or competing nutritional requirements, which in turn may be associated with specific biological functions in the development of healthy gut. PMID:23124244

Nuclear DNA microsatellites reveal genetic variation but a lack of phylogeographical structure in an endangered species, Fraxinus mandshurica, across North-east China.

PubMed

Hu, Li-Jiang; Uchiyama, Kentaro; Shen, Hai-Long; Saito, Yoko; Tsuda, Yoshiaki; Ide, Yuji

2008-08-01

The widely accepted paradigm that the modern genetic structure of plant species in the northern hemisphere has been largely determined by recolonization from refugia after the last glacial maximum fails to explain the presence of cold-tolerant species at intermediate latitudes. Another generally accepted paradigm is that mountain ridges act as important barriers causing genetic isolation of species, but this too has been challenged in recent studies. The aims of the work reported here were to determine the genetic diversity and distribution patterns of extant natural populations of an endangered cool temperate species, Faxinus mandshurica, and to examine whether these two paradigms are appropriate when applied to this species over a wide geographical scale. 1435 adult individuals were sampled from 30 natural populations across the main and central range of the species, covering major mountain ranges across North-east China (NEC). Genetic variation was estimated based on nine polymorphic nuclear microsatellite loci. Phylogeographical analyses were employed using various approaches, including Bayesian clustering, spatial analysis of molecular variance, Monmonier's algorithm, neighbor-joining trees, principal co-ordinate analysis and isolation by distance. Genetic diversity within populations was relatively high, and no significant recent bottlenecks were detected in any of the populations. A significant negative correlation between intra-population genetic diversity and latitude was identified. In contrast, genetic differentiation among all the populations examined was extremely low and no clear geographic genetic structure was identified, with the exception of one distinct population. The modern genetic structure in this species can be explained by extensive gene flow, an absence of mountains acting as barriers, and the presence of a wide refuge across NEC rather than multiple small refugia. Intra-population genetic variation along latitudes is probably associated with the systematically northward shifts of forest biomes in eastern China during the mid-Holocene. To determine important genetic patterns and identify resources for conservation, however, it will be necessary to examine differentially inherited genetic markers exposed to selection pressures (e.g. chloroplast DNA) and to investigate different generations.

Predation and fragmentation portrayed in the statistical structure of prey time series

PubMed Central

Hendrichsen, Ditte K; Topping, Chris J; Forchhammer, Mads C

2009-01-01

Background Statistical autoregressive analyses of direct and delayed density dependence are widespread in ecological research. The models suggest that changes in ecological factors affecting density dependence, like predation and landscape heterogeneity are directly portrayed in the first and second order autoregressive parameters, and the models are therefore used to decipher complex biological patterns. However, independent tests of model predictions are complicated by the inherent variability of natural populations, where differences in landscape structure, climate or species composition prevent controlled repeated analyses. To circumvent this problem, we applied second-order autoregressive time series analyses to data generated by a realistic agent-based computer model. The model simulated life history decisions of individual field voles under controlled variations in predator pressure and landscape fragmentation. Analyses were made on three levels: comparisons between predated and non-predated populations, between populations exposed to different types of predators and between populations experiencing different degrees of habitat fragmentation. Results The results are unambiguous: Changes in landscape fragmentation and the numerical response of predators are clearly portrayed in the statistical time series structure as predicted by the autoregressive model. Populations without predators displayed significantly stronger negative direct density dependence than did those exposed to predators, where direct density dependence was only moderately negative. The effects of predation versus no predation had an even stronger effect on the delayed density dependence of the simulated prey populations. In non-predated prey populations, the coefficients of delayed density dependence were distinctly positive, whereas they were negative in predated populations. Similarly, increasing the degree of fragmentation of optimal habitat available to the prey was accompanied with a shift in the delayed density dependence, from strongly negative to gradually becoming less negative. Conclusion We conclude that statistical second-order autoregressive time series analyses are capable of deciphering interactions within and across trophic levels and their effect on direct and delayed density dependence. PMID:19419539

The meta-epigenomic structure of purified human stem cell populations is defined at cis-regulatory sequences

PubMed Central

Zhao, Yong Mei; Golden, Aaron; Mar, Jessica C.; Einstein, Francine H.; Greally, John M.

2014-01-01

The mechanism and significance of epigenetic variability in the same cell type between healthy individuals are not clear. Here, we purify human CD34+ hematopoietic stem and progenitor cells (HSPCs) from different individuals and find that there is increased variability of DNA methylation at loci with properties of promoters and enhancers. The variability is especially enriched at candidate enhancers near genes transitioning between silent and expressed states, and encoding proteins with leukocyte differentiation properties. Our findings of increased variability at loci with intermediate DNA methylation values, at candidate “poised” enhancers, and at genes involved in HSPC lineage commitment suggest that CD34+ cell subtype heterogeneity between individuals is a major mechanism for the variability observed. Epigenomic studies performed on cell populations, even when purified, are testing collections of epigenomes, or meta-epigenomes. Our findings show that meta-epigenomic approaches to data analysis can provide insights into cell subpopulation structure. PMID:25327398

QSAR modeling and chemical space analysis of antimalarial compounds

NASA Astrophysics Data System (ADS)

Sidorov, Pavel; Viira, Birgit; Davioud-Charvet, Elisabeth; Maran, Uko; Marcou, Gilles; Horvath, Dragos; Varnek, Alexandre

2017-05-01

Generative topographic mapping (GTM) has been used to visualize and analyze the chemical space of antimalarial compounds as well as to build predictive models linking structure of molecules with their antimalarial activity. For this, a database, including 3000 molecules tested in one or several of 17 anti- Plasmodium activity assessment protocols, has been compiled by assembling experimental data from in-house and ChEMBL databases. GTM classification models built on subsets corresponding to individual bioassays perform similarly to the earlier reported SVM models. Zones preferentially populated by active and inactive molecules, respectively, clearly emerge in the class landscapes supported by the GTM model. Their analysis resulted in identification of privileged structural motifs of potential antimalarial compounds. Projection of marketed antimalarial drugs on this map allowed us to delineate several areas in the chemical space corresponding to different mechanisms of antimalarial activity. This helped us to make a suggestion about the mode of action of the molecules populating these zones.

QSAR modeling and chemical space analysis of antimalarial compounds.

PubMed

Sidorov, Pavel; Viira, Birgit; Davioud-Charvet, Elisabeth; Maran, Uko; Marcou, Gilles; Horvath, Dragos; Varnek, Alexandre

2017-05-01

Generative topographic mapping (GTM) has been used to visualize and analyze the chemical space of antimalarial compounds as well as to build predictive models linking structure of molecules with their antimalarial activity. For this, a database, including ~3000 molecules tested in one or several of 17 anti-Plasmodium activity assessment protocols, has been compiled by assembling experimental data from in-house and ChEMBL databases. GTM classification models built on subsets corresponding to individual bioassays perform similarly to the earlier reported SVM models. Zones preferentially populated by active and inactive molecules, respectively, clearly emerge in the class landscapes supported by the GTM model. Their analysis resulted in identification of privileged structural motifs of potential antimalarial compounds. Projection of marketed antimalarial drugs on this map allowed us to delineate several areas in the chemical space corresponding to different mechanisms of antimalarial activity. This helped us to make a suggestion about the mode of action of the molecules populating these zones.

Sea lice levels on wild Atlantic salmon, Salmo salar L., returning to the coast of Ireland.

PubMed

Jackson, D; Kane, F; O'Donohoe, P; Mc Dermott, T; Kelly, S; Drumm, A; Newell, J

2013-03-01

The sea lice population structure, prevalence and intensity of Lepeophtheirus salmonis have been studied over a period extending from 2004 to 2011. Infestation data were collected from the interceptor drift net fishery from 2004 until it was closed in 2006. From 2010, data were collected from the inshore draft net fishery. In all, 34 samples from the drift and draft net fisheries have been analysed to date. Prevalence of infestation with L. salmonis regularly approached 100% in samples of hosts recovered from the offshore drift net fishery. Abundance was variable both within and between years with a maximum mean abundance of 25.8 lice per fish recorded in 2004. The population structure of L. salmonis on hosts recovered in the inshore and estuarine draft net fisheries was different from that observed in the more offshore drift net samples. There is clear evidence of recent infestation with L. salmonis in the draft net samples. © 2013 Blackwell Publishing Ltd.

Genetic structure of Zymoseptoria tritici in northern France at region, field, plant and leaf layer scales.

PubMed

Siah, Ali; Bomble, Myriam; Tisserant, Benoit; Cadalen, Thierry; Holvoet, Maxime; Hilbert, Jean-Louis; Halama, Patrice; Reignault, Philippe Lucien

2018-04-16

Population genetic structure of the worldwide-distributed wheat pathogen Zymoseptoria tritici has been extensively studied at large geographical scales, but to a much less extent at small or local spatial scales. A total of 627 single-conidial fungal isolates were sampled from several locations in northern France (Hauts-de-France Region) to assess fungal genetic structure at region, field, plant and leaf layer scales, using highly polymorphic microsatellite markers and mating type idiomorphs. Important and overall similar levels of both gene and genotype diversities (gene diversity values ≥ 0.44 and haplotype frequencies ≥ 94 %) were found at all the examined scales. Such rates of diversity are likely due to an active sexual recombination in the investigated areas, as revealed by equal proportions of the two mating types scored in all sampled populations. Interestingly, a rare occurrence of clones among lesions from a same leaf, as well as among leaves from different plant leaf layers (e.g. upper vs lower leaves), was highlighted, indicating that ascospores contribute much more than expected to Z. tritci epidemics, compared to pycnidiospores. Population structure and AMOVA analyses revealed significant genetic differentiation at the regional scale (GST = 0.23) and, as expected, not at the other more local scales (GST ≤ 0.01). Further analyses using Bayesian and unweighted neighbor-joining statistical methods detected six genetic clusters within the regional population, overall distributed according to the locations from which the isolates were sampled. Neither clear directional relative migration linked to the geographical distribution of the locations, nor isolation by distance, were observed. Separate evolutionary trajectories caused by selection and adaptations to habitat heterogeneity could be the main forces shaping such structuration. This study provides new insights into the epidemiology and the genetic structure of Z. tritici at small local and, for the first time, at single plant and leaf layer scales. Such findings would be helpful in implementing effective control strategies.

Population structure of the Korean gizzard shad, Konosirus punctatus (Clupeiformes, Clupeidae) using multivariate morphometric analysis

NASA Astrophysics Data System (ADS)

Myoung, Se Hun; Kim, Jin-Koo

2016-03-01

The gizzard shad, Konosirus punctatus, is one of the most important fish species in Korea, China, Japan and Taiwan, and therefore the implementation of an appropriate population structure analysis is both necessary and fitting. In order to clarify the current distribution range for the two lineages of the Korean gizzard shad (Myoung and Kim 2014), we conducted a multivariate morphometric analysis by locality and lineage. We analyzed 17 morphometric and 5 meristic characters of 173 individuals, which were sampled from eight localities in the East Sea, the Yellow Sea and the Korean Strait. Unlike population genetics studies, the canonical discriminant analysis (CDA) results showed that the two morphotypes were clearly segregated by the center value "0" of CAN1, of which morphotype A occurred from the Yellow Sea to the western Korean Strait with negative values, and morphotype B occurred from the East Sea to the eastern Korean Strait with positive values even though there exists an admixture zone in the eastern Korean Strait. Further studies using more sensitive markers such as microsatellite DNA are required in order to define the true relationship between the two lineages.

Positive correlation between genetic diversity and fitness in a large, well-connected metapopulation

PubMed Central

Vandewoestijne, Sofie; Schtickzelle, Nicolas; Baguette, Michel

2008-01-01

Background Theory predicts that lower dispersal, and associated gene flow, leads to decreased genetic diversity in small isolated populations, which generates adverse consequences for fitness, and subsequently for demography. Here we report for the first time this effect in a well-connected natural butterfly metapopulation with high population densities at the edge of its distribution range. Results We demonstrate that: (1) lower genetic diversity was coupled to a sharp decrease in adult lifetime expectancy, a key component of individual fitness; (2) genetic diversity was positively correlated to the number of dispersing individuals (indicative of landscape functional connectivity) and adult population size; (3) parameters inferred from capture-recapture procedures (population size and dispersal events between patches) correlated much better with genetic diversity than estimates usually used as surrogates for population size (patch area and descriptors of habitat quality) and dispersal (structural connectivity index). Conclusion Our results suggest that dispersal is a very important factor maintaining genetic diversity. Even at a very local spatial scale in a metapopulation consisting of large high-density populations interconnected by considerable dispersal rates, genetic diversity can be decreased and directly affect the fitness of individuals. From a biodiversity conservation perspective, this study clearly shows the benefits of both in-depth demographic and genetic analyses. Accordingly, to ensure the long-term survival of populations, conservation actions should not be blindly based on patch area and structural isolation. This result may be especially pertinent for species at their range margins, particularly in this era of rapid environmental change. PMID:18986515

Neural and Behavioral Mechanisms of Clear Speech

ERIC Educational Resources Information Center

Luque, Jenna Silver

2017-01-01

Clear speech is a speaking style that has been shown to improve intelligibility in adverse listening conditions, for various listener and talker populations. Clear-speech phonetic enhancements include a slowed speech rate, expanded vowel space, and expanded pitch range. Although clear-speech phonetic enhancements have been demonstrated across a…

Geographic variation and genetic structure in Spotted Owls

USGS Publications Warehouse

Haig, Susan M.; Wagner, R.S.; Forsman, E.D.; Mullins, Thomas D.

2001-01-01

We examined genetic variation, population structure, and definition of conservation units in Spotted Owls (Strix occidentalis). Spotted Owls are mostly non-migratory, long-lived, socially monogamous birds that have decreased population viability due to their occupation of highly-fragmented late successional forests in western North America. To investigate potential effects of habitat fragmentation on population structure, we used random amplified polymorphic DNA (RAPD) to examine genetic variation hierarchically among local breeding areas, subregional groups, regional groups, and subspecies via sampling of 21 breeding areas (276 individuals) among the three subspecies of Spotted Owls. Data from 11 variable bands suggest a significant relationship between geographic distance among local breeding groups and genetic distance (Mantel r = 0.53, P < 0.02) although multi-dimensional scaling of three significant axes did not identify significant grouping at any hierarchical level. Similarly, neighbor-joining clustering of Manhattan distances indicated geographic structure at all levels and identified Mexican Spotted Owls as a distinct clade. RAPD analyses did not clearly differentiate Northern Spotted Owls from California Spotted Owls. Among Northern Spotted Owls, estimates of population differentiation (FST) ranged from 0.27 among breeding areas to 0.11 among regions. Concordantly, within-group agreement values estimated via multi-response permutation procedures of Jaccarda??s distances ranged from 0.22 among local sites to 0.11 among regions. Pairwise comparisons of FST and geographic distance within regions suggested only the Klamath region was in equilibrium with respect to gene flow and genetic drift. Merging nuclear data with recent mitochondrial data provides support for designation of an Evolutionary Significant Unit for Mexican Spotted Owls and two overlapping Management Units for Northern and California Spotted Owls.

Claustrum of the short-tailed fruit bat, Carollia perspicillata: Alignment of cellular orientation and functional connectivity.

PubMed

Orman, Rena; Kollmar, Richard; Stewart, Mark

2017-04-15

The claustrum is a gray-matter structure that underlies neocortex and reciprocates connections with cortical and subcortical targets. In lower mammals, the claustrum is directly adjacent to neocortex, making the definition of claustral boundaries challenging. Latexin, an endogenous inhibitor of metallocarboxypeptidases, localizes to claustral cells, enabling a clear delineation of claustrum. Given its proportionately large claustrum, we hypothesized that the short-tailed fruit bat, Carollia perspicillata, can be a useful model for claustral structure-function relations. We used latexin immunohistochemistry to identify claustral boundaries and intrinsic structure and multielectrode recordings from brain slices to explore intrinsic excitatory connectivity of the claustrum. Carollia's claustrum contains cells whose intrinsic connectivity and alignment permit the generation of spontaneous, synchronous population events and mirror their pattern of spread in disinhibited brain slices over millimeters. Carollia shows cellular alignment and spontaneous population-activity spread along both horizontal and dorsoventral axes. Carollia claustrum possesses intrinsic excitatory connectivity sufficient to: 1) generate single, spontaneous, synchronized burst discharges, 2) support activity spread along axes where claustral cells are aligned, and 3), because of multiple axes for cell alignment, support activity spread along both rostrocaudal and dorsoventral axes. The smaller event sizes in bat claustrum compared with rat claustrum are consistent with events occurring in population subsets rather than the full claustral cell population. The overall size of claustrum, its pronounced vascularity, and its more complex intrinsic connectivity than rat suggest that the bat is an animal model for claustral structure and function that will permit unique access to claustrum's processing capabilities. J. Comp. Neurol. 525:1459-1474, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Feral pig populations are structured at fine spatial scales in tropical Queensland, Australia.

PubMed

Lopez, Jobina; Hurwood, David; Dryden, Bart; Fuller, Susan

2014-01-01

Feral pigs occur throughout tropical far north Queensland, Australia and are a significant threat to biodiversity and World Heritage values, agriculture and are a vector of infectious diseases. One of the constraints on long-lasting, local eradication of feral pigs is the process of reinvasion into recently controlled areas. This study examined the population genetic structure of feral pigs in far north Queensland to identify the extent of movement and the scale at which demographically independent management units exist. Genetic analysis of 328 feral pigs from the Innisfail to Tully region of tropical Queensland was undertaken. Seven microsatellite loci were screened and Bayesian clustering methods used to infer population clusters. Sequence variation at the mitochondrial DNA control region was examined to identify pig breed. Significant population structure was identified in the study area at a scale of 25 to 35 km, corresponding to three demographically independent management units (MUs). Distinct natural or anthropogenic barriers were not found, but environmental features such as topography and land use appear to influence patterns of gene flow. Despite the strong, overall pattern of structure, some feral pigs clearly exhibited ancestry from a MU outside of that from which they were sampled indicating isolated long distance dispersal or translocation events. Furthermore, our results suggest that gene flow is restricted among pigs of domestic Asian and European origin and non-random mating influences management unit boundaries. We conclude that the three MUs identified in this study should be considered as operational units for feral pig control in far north Queensland. Within a MU, coordinated and simultaneous control is required across farms, rainforest areas and National Park Estates to prevent recolonisation from adjacent localities.

Multiplex, quantitative cellular analysis in large tissue volumes with clearing-enhanced 3D microscopy (Ce3D)

PubMed Central

Li, Weizhe; Germain, Ronald N.

2017-01-01

Organ homeostasis, cellular differentiation, signal relay, and in situ function all depend on the spatial organization of cells in complex tissues. For this reason, comprehensive, high-resolution mapping of cell positioning, phenotypic identity, and functional state in the context of macroscale tissue structure is critical to a deeper understanding of diverse biological processes. Here we report an easy to use method, clearing-enhanced 3D (Ce3D), which generates excellent tissue transparency for most organs, preserves cellular morphology and protein fluorescence, and is robustly compatible with antibody-based immunolabeling. This enhanced signal quality and capacity for extensive probe multiplexing permits quantitative analysis of distinct, highly intermixed cell populations in intact Ce3D-treated tissues via 3D histo-cytometry. We use this technology to demonstrate large-volume, high-resolution microscopy of diverse cell types in lymphoid and nonlymphoid organs, as well as to perform quantitative analysis of the composition and tissue distribution of multiple cell populations in lymphoid tissues. Combined with histo-cytometry, Ce3D provides a comprehensive strategy for volumetric quantitative imaging and analysis that bridges the gap between conventional section imaging and disassociation-based techniques. PMID:28808033

Contextual Modulation is Related to Efficiency in a Spiking Network Model of Visual Cortex.

PubMed

Sharifian, Fariba; Heikkinen, Hanna; Vigário, Ricardo; Vanni, Simo

2015-01-01

In the visual cortex, stimuli outside the classical receptive field (CRF) modulate the neural firing rate, without driving the neuron by themselves. In the primary visual cortex (V1), such contextual modulation can be parametrized with an area summation function (ASF): increasing stimulus size causes first an increase and then a decrease of firing rate before reaching an asymptote. Earlier work has reported increase of sparseness when CRF stimulation is extended to its surroundings. However, there has been no clear connection between the ASF and network efficiency. Here we aimed to investigate possible link between ASF and network efficiency. In this study, we simulated the responses of a biomimetic spiking neural network model of the visual cortex to a set of natural images. We varied the network parameters, and compared the V1 excitatory neuron spike responses to the corresponding responses predicted from earlier single neuron data from primate visual cortex. The network efficiency was quantified with firing rate (which has direct association to neural energy consumption), entropy per spike and population sparseness. All three measures together provided a clear association between the network efficiency and the ASF. The association was clear when varying the horizontal connectivity within V1, which influenced both the efficiency and the distance to ASF, DAS. Given the limitations of our biophysical model, this association is qualitative, but nevertheless suggests that an ASF-like receptive field structure can cause efficient population response.

On valuing patches: Estimating contributions to metapopulation growth with reverse-time capture-recapture modelling

USGS Publications Warehouse

Sanderlin, J.S.; Waser, P.M.; Hines, J.E.; Nichols, J.D.

2012-01-01

Metapopulation ecology has historically been rich in theory, yet analytical approaches for inferring demographic relationships among local populations have been few. We show how reverse-time multi-state capture-recapture models can be used to estimate the importance of local recruitment and interpopulation dispersal to metapopulation growth. We use 'contribution metrics' to infer demographic connectedness among eight local populations of banner-tailed kangaroo rats, to assess their demographic closure, and to investigate sources of variation in these contributions. Using a 7 year dataset, we show that: (i) local populations are relatively independent demographically, and contributions to local population growth via dispersal within the system decline with distance; (ii) growth contributions via local survival and recruitment are greater for adults than juveniles, while contributions involving dispersal are greater for juveniles; (iii) central populations rely more on local recruitment and survival than peripheral populations; (iv) contributions involving dispersal are not clearly related to overall metapopulation density; and (v) estimated contributions from outside the system are unexpectedly large. Our analytical framework can classify metapopulations on a continuum between demographic independence and panmixia, detect hidden population growth contributions, and make inference about other population linkage forms, including rescue effects and source-sink structures. Finally, we discuss differences between demographic and genetic population linkage patterns for our system. ?? 2011 The Royal Society.

The history of human populations in the Japanese Archipelago inferred from genome-wide SNP data with a special reference to the Ainu and the Ryukyuan populations.

PubMed

Jinam, Timothy; Nishida, Nao; Hirai, Momoki; Kawamura, Shoji; Oota, Hiroki; Umetsu, Kazuo; Kimura, Ryosuke; Ohashi, Jun; Tajima, Atsushi; Yamamoto, Toshimichi; Tanabe, Hideyuki; Mano, Shuhei; Suto, Yumiko; Kaname, Tadashi; Naritomi, Kenji; Yanagi, Kumiko; Niikawa, Norio; Omoto, Keiichi; Tokunaga, Katsushi; Saitou, Naruya

2012-12-01

The Japanese Archipelago stretches over 4000 km from north to south, and is the homeland of the three human populations; the Ainu, the Mainland Japanese and the Ryukyuan. The archeological evidence of human residence on this Archipelago goes back to >30 000 years, and various migration routes and root populations have been proposed. Here, we determined close to one million single-nucleotide polymorphisms (SNPs) for the Ainu and the Ryukyuan, and compared these with existing data sets. This is the first report of these genome-wide SNP data. Major findings are: (1) Recent admixture with the Mainland Japanese was observed for more than one third of the Ainu individuals from principal component analysis and frappe analyses; (2) The Ainu population seems to have experienced admixture with another population, and a combination of two types of admixtures is the unique characteristics of this population; (3) The Ainu and the Ryukyuan are tightly clustered with 100% bootstrap probability followed by the Mainland Japanese in the phylogenetic trees of East Eurasian populations. These results clearly support the dual structure model on the Japanese Archipelago populations, though the origins of the Jomon and the Yayoi people still remain to be solved.

The World's Most Isolated and Distinct Whale Population? Humpback Whales of the Arabian Sea

PubMed Central

Collins, Tim; Minton, Gianna; Findlay, Ken; Leslie, Matthew S.; Ponnampalam, Louisa; Baldwin, Robert; Rosenbaum, Howard

2014-01-01

A clear understanding of population structure is essential for assessing conservation status and implementing management strategies. A small, non-migratory population of humpback whales in the Arabian Sea is classified as “Endangered” on the IUCN Red List of Threatened Species, an assessment constrained by a lack of data, including limited understanding of its relationship to other populations. We analysed 11 microsatellite markers and mitochondrial DNA sequences extracted from 67 Arabian Sea humpback whale tissue samples and compared them to equivalent datasets from the Southern Hemisphere and North Pacific. Results show that the Arabian Sea population is highly distinct; estimates of gene flow and divergence times suggest a Southern Indian Ocean origin but indicate that it has been isolated for approximately 70,000 years, remarkable for a species that is typically highly migratory. Genetic diversity values are significantly lower than those obtained for Southern Hemisphere populations and signatures of ancient and recent genetic bottlenecks were identified. Our findings suggest this is the world's most isolated humpback whale population, which, when combined with low population abundance estimates and anthropogenic threats, raises concern for its survival. We recommend an amendment of the status of the population to “Critically Endangered” on the IUCN Red List. PMID:25470144

THE MILKY WAY HAS NO DISTINCT THICK DISK

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bovy, Jo; Rix, Hans-Walter; Hogg, David W., E-mail: bovy@ias.edu

2012-06-01

Different stellar sub-populations of the Milky Way's stellar disk are known to have different vertical scale heights, their thickness increasing with age. Using SEGUE spectroscopic survey data, we have recently shown that mono-abundance sub-populations, defined in the [{alpha}/Fe]-[Fe/H] space, are well described by single-exponential spatial-density profiles in both the radial and the vertical direction; therefore, any star of a given abundance is clearly associated with a sub-population of scale height h{sub z} . Here, we work out how to determine the stellar surface-mass density contributions at the solar radius R{sub 0} of each such sub-population, accounting for the survey selectionmore » function, and for the fraction of the stellar population mass that is reflected in the spectroscopic target stars given populations of different abundances and their presumed age distributions. Taken together, this enables us to derive {Sigma}{sub R{sub 0}}(h{sub z}), the surface-mass contributions of stellar populations with scale height h{sub z} . Surprisingly, we find no hint of a thin-thick disk bi-modality in this mass-weighted scale-height distribution, but a smoothly decreasing function, approximately {Sigma}{sub R{sub 0}}(h{sub z}){proportional_to} exp(-h{sub z}), from h{sub z} Almost-Equal-To 200 pc to h{sub z} Almost-Equal-To 1 kpc. As h{sub z} is ultimately the structurally defining property of a thin or thick disk, this shows clearly that the Milky Way has a continuous and monotonic distribution of disk thicknesses: there is no 'thick disk' sensibly characterized as a distinct component. We discuss how our result is consistent with evidence for seeming bi-modality in purely geometric disk decompositions or chemical abundances analyses. We constrain the total visible stellar surface-mass density at the solar radius to be {Sigma}{sub R{sub 0}}* = 30 {+-} 1 M{sub Sun} pc{sup -2}.« less

Determinants of echolocation call frequency variation in the Formosan lesser horseshoe bat (Rhinolophus monoceros)

PubMed Central

Chen, Shiang-Fan; Jones, Gareth; Rossiter, Stephen J.

2009-01-01

The origin and maintenance of intraspecific variation in vocal signals is important for population divergence and speciation. Where vocalizations are transmitted by vertical cultural inheritance, similarity will reflect co-ancestry, and thus vocal divergence should reflect genetic structure. Horseshoe bats are characterized by echolocation calls dominated by a constant frequency component that is partly determined by maternal imprinting. Although previous studies showed that constant frequency calls are also influenced by some non-genetic factors, it is not known how frequency relates to genetic structure. To test this, we related constant frequency variation to genetic and non-genetic variables in the Formosan lesser horseshoe bat (Rhinolophus monoceros). Recordings of bats from across Taiwan revealed that females called at higher frequencies than males; however, we found no effect of environmental or morphological factors on call frequency. By comparison, variation showed clear population structure, with frequencies lower in the centre and east, and higher in the north and south. Within these regions, frequency divergence was directional and correlated with geographical distance, suggesting that call frequencies are subject to cultural drift. However, microsatellite clustering analysis showed that broad differences in constant frequency among populations corresponded to discontinuities in allele frequencies resulting from vicariant events. Our results provide evidence that the processes shaping genetic subdivision have concomitant consequences for divergence in echolocation call frequency. PMID:19692399

The Experience of Cognitive Intrusion of Pain: scale development and validation

PubMed Central

Attridge, Nina; Crombez, Geert; Van Ryckeghem, Dimitri; Keogh, Edmund; Eccleston, Christopher

2015-01-01

Abstract Patients with chronic pain often report their cognition to be impaired by pain, and this observation has been supported by numerous studies measuring the effects of pain on cognitive task performance. Furthermore, cognitive intrusion by pain has been identified as one of 3 components of pain anxiety, alongside general distress and fear of pain. Although cognitive intrusion is a critical characteristic of pain, no specific measure designed to capture its effects exists. In 3 studies, we describe the initial development and validation of a new measure of pain interruption: the Experience of Cognitive Intrusion of Pain (ECIP) scale. In study 1, the ECIP scale was administered to a general population sample to assess its structure and construct validity. In study 2, the factor structure of the ECIP scale was confirmed in a large general population sample experiencing no pain, acute pain, or chronic pain. In study 3, we examined the predictive value of the ECIP scale in pain-related disability in fibromyalgia patients. The ECIP scale scores followed a normal distribution with good variance in a general population sample. The scale had high internal reliability and a clear 1-component structure. It differentiated between chronic pain and control groups, and it was a significant predictor of pain-related disability over and above pain intensity. Repairing attentional interruption from pain may become a novel target for pain management interventions, both pharmacologic and nonpharmacologic. PMID:26067388

A comparative study of the structural organization of spheres derived from the adult human subventricular zone and glioblastoma biopsies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vik-Mo, Einar Osland, E-mail: e.o.vik-mo@medisin.uio.no; Department of Neurosurgery, Oslo University Hospital, Oslo; Sandberg, Cecilie

2011-04-15

Sphere forming assays have been useful to enrich for stem like cells in a range of tumors. The robustness of this system contrasts the difficulties in defining a stem cell population based on cell surface markers. We have undertaken a study to describe the cellular and organizational composition of tumorspheres, directly comparing these to neurospheres derived from the adult human subventricular zone (SVZ). Primary cell cultures from brain tumors were found to contain variable fractions of cells positive for tumor stem cell markers (CD133 (2-93%)/SSEA1 (3-15%)/CXCR4 (1-72%)). All cultures produced tumors upon xenografting. Tumorspheres contained a heterogeneous population of cells,more » but were structurally organized with stem cell markers present at the core of spheres, with markers of more mature glial progenitors and astrocytes at more peripheral location. Ultrastructural studies showed that tumorspheres contained a higher fraction of electron dense cells in the core than the periphery (36% and 19%, respectively). Neurospheres also contained a heterogeneous cell population, but did not have an organization similar to tumorspheres. Although tumorspheres clearly display irregular and neoplastic cells, they establish an organized structure with an outward gradient of differentiation. We suggest that this organization is central in maintaining the tumor stem cell pool.« less

Recent Admixture in an Indian Population of African Ancestry

PubMed Central

Narang, Ankita; Jha, Pankaj; Rawat, Vimal; Mukhopadhayay, Arijit; Dash, Debasis; Basu, Analabha; Mukerji, Mitali

2011-01-01

Identification and study of genetic variation in recently admixed populations not only provides insight into historical population events but also is a powerful approach for mapping disease loci. We studied a population (OG-W-IP) that is of African-Indian origin and has resided in the western part of India for 500 years; members of this population are believed to be descendants of the Bantu-speaking population of Africa. We have carried out this study by using a set of 18,534 autosomal markers common between Indian, CEPH-HGDP, and HapMap populations. Principal-components analysis clearly revealed that the African-Indian population derives its ancestry from Bantu-speaking west-African as well as Indo-European-speaking north and northwest Indian population(s). STRUCTURE and ADMIXTURE analyses show that, overall, the OG-W-IPs derive 58.7% of their genomic ancestry from their African past and have very little inter-individual ancestry variation (8.4%). The extent of linkage disequilibrium also reveals that the admixture event has been recent. Functional annotation of genes encompassing the ancestry-informative markers that are closer in allele frequency to the Indian ancestral population revealed significant enrichment of biological processes, such as ion-channel activity, and cadherins. We briefly examine the implications of determining the genetic diversity of this population, which could provide opportunities for studies involving admixture mapping. PMID:21737057

Genetic profile based upon 15 microsatellites of four caste groups of the eastern Indian state, Bihar.

PubMed

Ashma, R; Kashyap, V K

2003-01-01

The formation of caste groups among the Hindu community and the practice of endogamy exert a great impact on the genetic structure and diversity of the Indian population. Allele frequency data of 15 microsatellite loci clearly portray the genetic diversity and relatedness among four socio-culturally advanced caste groups: Brahmin, Bhumihar, Rajput and Kayasth of Caucasoid ethnicity of Bihar. The study seeks to understand the impact of the man-made caste system on the genetic profile of the four major caste groups of Bihar. Computation of average heterozygosity, most frequent allele, allele diversity and coefficient of gene differentiation (Gst), along with genetic distance (DA)and principal coordinate analysis were performed to assess intra-population and inter-population diversity. The average Gst value for all the loci was 0.012 +/- 0.0033, and the level of average heterozygosity was approximately 75.5%, indicating genetic similarity and intra-population diversity. Genetic distance (DA) values and the phylogenetic tree along with other higher caste groups of India indicate the relative distance between them. The present study clearly depicts the genetic profile of these caste groups, their inherent closeness in the past, and the impact of the imposed caste system that later restricted the gene flow. The study highlights the status of Bhumihar and Kayasth in the Hindu caste system. The former was found clustering with the Brahmin group (as expected, since Bhumihar is known to be a subclass of Brahmin), whereas the distance between the Brahmin and Kayasth caste groups was found to be large. North-eastern Indian Mongoloids form a separate cluster.

Genetic signs of multiple colonization events in Baltic ciscoes with radiation into sympatric spring- and autumn-spawners confined to early postglacial arrival

PubMed Central

Delling, Bo; Palm, Stefan; Palkopoulou, Eleftheria; Prestegaard, Tore

2014-01-01

Presence of sympatric populations may reflect local diversification or secondary contact of already distinct forms. The Baltic cisco (Coregonus albula) normally spawns in late autumn, but in a few lakes in Northern Europe sympatric autumn and spring- or winter-spawners have been described. So far, the evolutionary relationships and taxonomic status of these main life history forms have remained largely unclear. With microsatellites and mtDNA sequences, we analyzed extant and extinct spring- and autumn-spawners from a total of 23 Swedish localities, including sympatric populations. Published sequences from Baltic ciscoes in Germany and Finland, and Coregonus sardinella from North America were also included together with novel mtDNA sequences from Siberian C. sardinella. A clear genetic structure within Sweden was found that included two population assemblages markedly differentiated at microsatellites and apparently fixed for mtDNA haplotypes from two distinct clades. All sympatric Swedish populations belonged to the same assemblage, suggesting parallel evolution of spring-spawning rather than secondary contact. The pattern observed further suggests that postglacial immigration to Northern Europe occurred from at least two different refugia. Previous results showing that mtDNA in Baltic cisco is paraphyletic with respect to North American C. sardinella were confirmed. However, the inclusion of Siberian C. sardinella revealed a more complicated pattern, as these novel haplotypes were found within one of the two main C. albula clades and were clearly distinct from those in North American C. sardinella. The evolutionary history of Northern Hemisphere ciscoes thus seems to be more complex than previously recognized. PMID:25540695

Genetic signs of multiple colonization events in Baltic ciscoes with radiation into sympatric spring- and autumn-spawners confined to early postglacial arrival.

PubMed

Delling, Bo; Palm, Stefan; Palkopoulou, Eleftheria; Prestegaard, Tore

2014-11-01

Presence of sympatric populations may reflect local diversification or secondary contact of already distinct forms. The Baltic cisco (Coregonus albula) normally spawns in late autumn, but in a few lakes in Northern Europe sympatric autumn and spring- or winter-spawners have been described. So far, the evolutionary relationships and taxonomic status of these main life history forms have remained largely unclear. With microsatellites and mtDNA sequences, we analyzed extant and extinct spring- and autumn-spawners from a total of 23 Swedish localities, including sympatric populations. Published sequences from Baltic ciscoes in Germany and Finland, and Coregonus sardinella from North America were also included together with novel mtDNA sequences from Siberian C. sardinella. A clear genetic structure within Sweden was found that included two population assemblages markedly differentiated at microsatellites and apparently fixed for mtDNA haplotypes from two distinct clades. All sympatric Swedish populations belonged to the same assemblage, suggesting parallel evolution of spring-spawning rather than secondary contact. The pattern observed further suggests that postglacial immigration to Northern Europe occurred from at least two different refugia. Previous results showing that mtDNA in Baltic cisco is paraphyletic with respect to North American C. sardinella were confirmed. However, the inclusion of Siberian C. sardinella revealed a more complicated pattern, as these novel haplotypes were found within one of the two main C. albula clades and were clearly distinct from those in North American C. sardinella. The evolutionary history of Northern Hemisphere ciscoes thus seems to be more complex than previously recognized.

Development and Application of Genomic Resources in an Endangered Palaeoendemic Tree, Parrotia subaequalis (Hamamelidaceae) From Eastern China

PubMed Central

Zhang, Yun-Yan; Shi, En; Yang, Zhao-Ping; Geng, Qi-Fang; Qiu, Ying-Xiong; Wang, Zhong-Sheng

2018-01-01

Parrotia subaequalis is an endangered palaeoendemic tree from disjunct montane sites in eastern China. Due to the lack of effective genomic resources, the genetic diversity and population structure of this endangered species are not clearly understood. In this study, we conducted paired-end shotgun sequencing (2 × 125 bp) of genomic DNA for two individuals of P. subaequalis on the Illumina HiSeq platform. Based on the resulting sequences, we have successfully assembled the complete chloroplast genome of P. subaequalis, as well as identified the polymorphic chloroplast microsatellites (cpSSRs), nuclear microsatellites (nSSRs) and mutational hotspots of chloroplast. Ten polymorphic cpSSR loci and 12 polymorphic nSSR loci were used to genotype 96 individuals of P. subaequalis from six populations to estimate genetic diversity and population structure. Our results revealed that P. subaequalis exhibited abundant genetic diversity (e.g., cpSSRs: Hcp = 0.862; nSSRs: HT = 0.559) and high genetic differentiation (e.g., cpSSRs: RST = 0.652; nSSRs: RST = 0.331), and characterized by a low pollen-to-seed migration ratio (r ≈ 1.78). These genetic patterns are attributable to its long evolutionary histories and low levels of contemporary inter-population gene flow by pollen and seed. In addition, lack of isolation-by-distance pattern and strong population genetic structuring in both marker systems, suggests that long-term isolation and/or habitat fragmentation as well as genetic drift may have also contributed to the geographic differentiation of P. subaequalis. Therefore, long-term habitat protection is the most important methods to prevent further loss of genetic variation and a decrease in effective population size. Furthermore, both cpSSRs and nSSRs revealed that P. subaequalis populations consisted of three genetic clusters, which should be considered as separated conservation units. PMID:29545814

Genetic Diversity and Demographic History of Wild and Cultivated/Naturalised Plant Populations: Evidence from Dalmatian Sage (Salvia officinalis L., Lamiaceae).

PubMed

Rešetnik, Ivana; Baričevič, Dea; Batîr Rusu, Diana; Carović-Stanko, Klaudija; Chatzopoulou, Paschalina; Dajić-Stevanović, Zora; Gonceariuc, Maria; Grdiša, Martina; Greguraš, Danijela; Ibraliu, Alban; Jug-Dujaković, Marija; Krasniqi, Elez; Liber, Zlatko; Murtić, Senad; Pećanac, Dragana; Radosavljević, Ivan; Stefkov, Gjoshe; Stešević, Danijela; Šoštarić, Ivan; Šatović, Zlatko

2016-01-01

Dalmatian sage (Salvia officinalis L., Lamiaceae) is a well-known aromatic and medicinal Mediterranean plant that is native in coastal regions of the western Balkan and southern Apennine Peninsulas and is commonly cultivated worldwide. It is widely used in the food, pharmaceutical and cosmetic industries. Knowledge of its genetic diversity and spatiotemporal patterns is important for plant breeding programmes and conservation. We used eight microsatellite markers to investigate evolutionary history of indigenous populations as well as genetic diversity and structure within and among indigenous and cultivated/naturalised populations distributed across the Balkan Peninsula. The results showed a clear separation between the indigenous and cultivated/naturalised groups, with the cultivated material originating from one restricted geographical area. Most of the genetic diversity in both groups was attributable to differences among individuals within populations, although spatial genetic analysis of indigenous populations indicated the existence of isolation by distance. Geographical structuring of indigenous populations was found using clustering analysis, with three sub-clusters of indigenous populations. The highest level of gene diversity and the greatest number of private alleles were found in the central part of the eastern Adriatic coast, while decreases in gene diversity and number of private alleles were evident towards the northwestern Adriatic coast and southern and eastern regions of the Balkan Peninsula. The results of Ecological Niche Modelling during Last Glacial Maximum and Approximate Bayesian Computation suggested two plausible evolutionary trajectories: 1) the species survived in the glacial refugium in southern Adriatic coastal region with subsequent colonization events towards northern, eastern and southern Balkan Peninsula; 2) species survived in several refugia exhibiting concurrent divergence into three genetic groups. The insight into genetic diversity and structure also provide the baseline data for conservation of S. officinalis genetic resources valuable for future breeding programmes.

Genetic Diversity and Demographic History of Wild and Cultivated/Naturalised Plant Populations: Evidence from Dalmatian Sage (Salvia officinalis L., Lamiaceae)

PubMed Central

Rešetnik, Ivana; Baričevič, Dea; Batîr Rusu, Diana; Carović-Stanko, Klaudija; Chatzopoulou, Paschalina; Dajić-Stevanović, Zora; Gonceariuc, Maria; Grdiša, Martina; Greguraš, Danijela; Ibraliu, Alban; Jug-Dujaković, Marija; Krasniqi, Elez; Liber, Zlatko; Murtić, Senad; Pećanac, Dragana; Radosavljević, Ivan; Stefkov, Gjoshe; Stešević, Danijela; Šoštarić, Ivan; Šatović, Zlatko

2016-01-01

Dalmatian sage (Salvia officinalis L., Lamiaceae) is a well-known aromatic and medicinal Mediterranean plant that is native in coastal regions of the western Balkan and southern Apennine Peninsulas and is commonly cultivated worldwide. It is widely used in the food, pharmaceutical and cosmetic industries. Knowledge of its genetic diversity and spatiotemporal patterns is important for plant breeding programmes and conservation. We used eight microsatellite markers to investigate evolutionary history of indigenous populations as well as genetic diversity and structure within and among indigenous and cultivated/naturalised populations distributed across the Balkan Peninsula. The results showed a clear separation between the indigenous and cultivated/naturalised groups, with the cultivated material originating from one restricted geographical area. Most of the genetic diversity in both groups was attributable to differences among individuals within populations, although spatial genetic analysis of indigenous populations indicated the existence of isolation by distance. Geographical structuring of indigenous populations was found using clustering analysis, with three sub-clusters of indigenous populations. The highest level of gene diversity and the greatest number of private alleles were found in the central part of the eastern Adriatic coast, while decreases in gene diversity and number of private alleles were evident towards the northwestern Adriatic coast and southern and eastern regions of the Balkan Peninsula. The results of Ecological Niche Modelling during Last Glacial Maximum and Approximate Bayesian Computation suggested two plausible evolutionary trajectories: 1) the species survived in the glacial refugium in southern Adriatic coastal region with subsequent colonization events towards northern, eastern and southern Balkan Peninsula; 2) species survived in several refugia exhibiting concurrent divergence into three genetic groups. The insight into genetic diversity and structure also provide the baseline data for conservation of S. officinalis genetic resources valuable for future breeding programmes. PMID:27441834

Effects of magnetic field on electron-electron intersubband scattering rates in quantum wells.

NASA Astrophysics Data System (ADS)

Kempa, K.; Zhou, Y.; Engelbrecht, J.; Bakshi, P.

2001-03-01

Electron-electron scattering dominates the physics of carrier relaxation in quantum nano-structures used as active regions of THz radiation sources. This is the limiting mechanism in achieving population inversion, and reducing its deleterious effects could clear the way to a THz laser. We study here the inter-subband relaxation processes due to the electron-electron scattering in quantum well structures, in a magnetic field. We obtain the scattering rate from the imaginary part of the electron self-energy in the random phase approximation, extending our earlier studies [1] to nonzero magnetic fields. We find that the scattering rate is peaked at two possible sets of arrangements of the Landau levels (LL) of the two subbands of interest. The first set occurs when the LL of both subbands align, and the other when the LL misalign, so that the LL of one subband lie exactly in the middle between those of the other subband. Experiments on various quantum cascade structures show that the misaligned set of transitions is completely suppressed. >From our calculations this implies that there is no population inversion in those structures. Work supported by US Army Research Office. [1] K. Kempa, P. Bakshi, J. R. Engelbrecht, and Y. Zhou, Phys. Rev. B61, 11083 (2000).

Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness.

PubMed

Mangin, B; Siberchicot, A; Nicolas, S; Doligez, A; This, P; Cierco-Ayrolles, C

2012-03-01

Among the several linkage disequilibrium measures known to capture different features of the non-independence between alleles at different loci, the most commonly used for diallelic loci is the r(2) measure. In the present study, we tackled the problem of the bias of r(2) estimate, which results from the sample structure and/or the relatedness between genotyped individuals. We derived two novel linkage disequilibrium measures for diallelic loci that are both extensions of the usual r(2) measure. The first one, r(S)(2), uses the population structure matrix, which consists of information about the origins of each individual and the admixture proportions of each individual genome. The second one, r(V)(2), includes the kinship matrix into the calculation. These two corrections can be applied together in order to correct for both biases and are defined either on phased or unphased genotypes.We proved that these novel measures are linked to the power of association tests under the mixed linear model including structure and kinship corrections. We validated them on simulated data and applied them to real data sets collected on Vitis vinifera plants. Our results clearly showed the usefulness of the two corrected r(2) measures, which actually captured 'true' linkage disequilibrium unlike the usual r(2) measure.

Characterizing polymorphic inversions in human genomes by single-cell sequencing

PubMed Central

Sanders, Ashley D.; Hills, Mark; Porubský, David; Guryev, Victor; Falconer, Ester; Lansdorp, Peter M.

2016-01-01

Identifying genomic features that differ between individuals and cells can help uncover the functional variants that drive phenotypes and disease susceptibilities. For this, single-cell studies are paramount, as it becomes increasingly clear that the contribution of rare but functional cellular subpopulations is important for disease prognosis, management, and progression. Until now, studying these associations has been challenged by our inability to map structural rearrangements accurately and comprehensively. To overcome this, we coupled single-cell sequencing of DNA template strands (Strand-seq) with custom analysis software to rapidly discover, map, and genotype genomic rearrangements at high resolution. This allowed us to explore the distribution and frequency of inversions in a heterogeneous cell population, identify several polymorphic domains in complex regions of the genome, and locate rare alleles in the reference assembly. We then mapped the entire genomic complement of inversions within two unrelated individuals to characterize their distinct inversion profiles and built a nonredundant global reference of structural rearrangements in the human genome. The work described here provides a powerful new framework to study structural variation and genomic heterogeneity in single-cell samples, whether from individuals for population studies or tissue types for biomarker discovery. PMID:27472961

Differentiation of Cognitive Abilities across the Lifespan

PubMed Central

Tucker-Drob, Elliot M.

2009-01-01

Existing representations of cognitive ability structure are exclusively based on linear patterns of interrelations. However, a number of developmental and cognitive theories predict that abilities are differentially related across ages (age differentiation-dedifferentiation) and across levels of functioning (ability differentiation). Nonlinear factor analytic models were applied to multivariate cognitive ability data from 6,273 individuals, ages 4 to 101 years, who were selected to be nationally representative of the United States population. Results consistently supported ability differentiation, but were less clear with respect to age differentiation-dedifferentiation. Little evidence for age modification of ability differentiation was found. These findings are particularly informative about the nature of individual differences in cognition, and the developmental course of cognitive ability level and structure. PMID:19586182

Proto-Clusters with Evolved Populations around Radio Galaxies at 2

NASA Astrophysics Data System (ADS)

Kodama, T.; Tanaka, M.; Tanaka, I.; Kajisawa, M.

2007-12-01

We present an on-going near-infrared survey of proto-clusters around high-z radio-loud galaxies at 2 ≲ z ≲ 3 with a new wide-field instrument MOIRCS on Subaru. Most of these field are known to show a large number of Lyα and/or Hα emitters at the same redshifts of the radio galaxies. We see a clear excess of near-infrared selected galaxies (JHK_s-selected galaxies as well as DRG) in these fields, and they are indeed proto-clusters with not only young emitters but also evolved populations. Spatial distribution of such NIR selected galaxies is filamentary and track similar structures traced by the emitters. There is an hint that the bright-end of the red sequence first appeared between z=3 and 2.

The Size Distribution Of Cluster Galaxies

NASA Astrophysics Data System (ADS)

Kuchner, U.; Ziegler, B.; Bamford, S.; Verdugo, M.; Haeussler, B.

2017-06-01

We establish a sample of 560 spectroscopically confirmed cluster members of MACS J1206.2- 0847 at z = 0.45 and utilize multi-wavelength and multi-component Sersic profile fitting to provide luminosities and sizes for the key structural components bulge and disk. While the difference between field and cluster galaxy properties are mostly due to a preference for cluster members to be early-type (quiescent, bulge-dominated), we see evidence for an outer disk fading and a sharp rise in the number of red disks with smaller effective radii at the tidally active cluster region around R200. Even though red disks are already virialized according to their velocity distribution, they are clearly not part of the old population found in the innermost region; they represent an important population of transitional objects in clusters.

Eco-geographical differentiation among Colombian populations of the Chagas disease vector Triatoma dimidiata (Hemiptera: Reduviidae).

PubMed

Gómez-Palacio, Andrés; Triana, Omar; Jaramillo-O, Nicolás; Dotson, Ellen M; Marcet, Paula L

2013-12-01

Triatoma dimidiata is currently the main vector of Chagas disease in Mexico, most Central American countries and several zones of Ecuador and Colombia. Although this species has been the subject of several recent phylogeographic studies, the relationship among different populations within the species remains unclear. To elucidate the population genetic structure of T. dimidiata in Colombia, we analyzed individuals from distinct geographical locations using the cytochrome c oxidase subunit 1 gene and 7 microsatellite loci. A clear genetic differentiation was observed among specimens from three Colombian eco-geographical regions: Inter Andean Valleys, Caribbean Plains and Sierra Nevada de Santa Marta mountain (SNSM). Additionally, evidence of genetic subdivision was found within the Caribbean Plains region as well as moderate gene flow between the populations from the Caribbean Plains and SNSM regions. The genetic differentiation found among Colombian populations correlates, albeit weakly, with an isolation-by-distance model (IBD). The genetic heterogeneity among Colombian populations correlates with the eco-epidemiological and morphological traits observed in this species across regions within the country. Such genetic and epidemiological diversity should be taken into consideration for the development of vector control strategies and entomological surveillance. Copyright © 2013. Published by Elsevier B.V.

Eco-geographical differentiation among Colombian populations of the Chagas disease vector Triatoma dimidiata (Hemiptera: Reduviidae)

PubMed Central

Gómez-Palacio, Andrés; Triana, Omar; Jaramillo-O, Nicolás; Dotson, Ellen M.; Marcet, Paula L.

2016-01-01

Triatoma dimidiata is currently the main vector of Chagas disease in Mexico, most Central American countries and several zones of Ecuador and Colombia. Although this species has been the subject of several recent phylogeographic studies, the relationship among different populations within the species remains unclear. To elucidate the population genetic structure of T. dimidiata in Colombia, we analyzed individuals from distinct geographical locations using the cytochrome c oxidase subunit 1 gene and 7 microsatellite loci. A clear genetic differentiation was observed among specimens from three Colombian eco-geographical regions: Inter Andean Valleys, Caribbean Plains and Sierra Nevada de Santa Marta mountain (SNSM). Additionally, evidence of genetic subdivision was found within the Caribbean Plains region as well as moderate gene flow between the populations from the Caribbean Plains and SNSM regions. The genetic differentiation found among Colombian populations correlates, albeit weakly, with an isolation-by-distance model (IBD). The genetic heterogeneity among Colombian populations correlates with the eco-epidemiological and morphological traits observed in this species across regions within the country. Such genetic and epidemiological diversity should be taken into consideration for the development of vector control strategies and entomological surveillance. PMID:24035810

Brain structure differences between Chinese and Caucasian cohorts: A comprehensive morphometry study.

PubMed

Tang, Yuchun; Zhao, Lu; Lou, Yunxia; Shi, Yonggang; Fang, Rui; Lin, Xiangtao; Liu, Shuwei; Toga, Arthur

2018-05-01

Numerous behavioral observations and brain function studies have demonstrated that neurological differences exist between East Asians and Westerners. However, the extent to which these factors relate to differences in brain structure is still not clear. As the basis of brain functions, the anatomical differences in brain structure play a primary and critical role in the origination of functional and behavior differences. To investigate the underlying differences in brain structure between the two cultural/ethnic groups, we conducted a comparative study on education-matched right-handed young male adults (age = 22-29 years) from two cohorts, Han Chinese (n = 45) and Caucasians (n = 45), using high-dimensional structural magnetic resonance imaging (MRI) data. Using two well-validated imaging analysis techniques, surface-based morphometry (SBM) and voxel-based morphometry (VBM), we performed a comprehensive vertex-wise morphometric analysis of the brain structures between Chinese and Caucasian cohorts. We identified consistent significant between-group differences in cortical thickness, volume, and surface area in the frontal, temporal, parietal, occipital, and insular lobes as well as the cingulate cortices. The SBM analyses revealed that compared with Caucasians, the Chinese population showed larger cortical structures in the temporal and cingulate regions, and smaller structural measures in the frontal and parietal cortices. The VBM data of the same sample was well-aligned with the SBM findings. Our findings systematically revealed comprehensive brain structural differences between young male Chinese and Caucasians, and provided new neuroanatomical insights to the behavioral and functional distinctions in the two cultural/ethnic populations. © 2018 Wiley Periodicals, Inc.

Large-Scale Genetic Structuring of a Widely Distributed Carnivore - The Eurasian Lynx (Lynx lynx)

PubMed Central

Rueness, Eli K.; Naidenko, Sergei; Trosvik, Pål; Stenseth, Nils Chr.

2014-01-01

Over the last decades the phylogeography and genetic structure of a multitude of species inhabiting Europe and North America have been described. The flora and fauna of the vast landmasses of north-eastern Eurasia are still largely unexplored in this respect. The Eurasian lynx is a large felid that is relatively abundant over much of the Russian sub-continent and the adjoining countries. Analyzing 148 museum specimens collected throughout its range over the last 150 years we have described the large-scale genetic structuring in this highly mobile species. We have investigated the spatial genetic patterns using mitochondrial DNA sequences (D-loop and cytochrome b) and 11 microsatellite loci, and describe three phylogenetic clades and a clear structuring along an east-west gradient. The most likely scenario is that the contemporary Eurasian lynx populations originated in central Asia and that parts of Europe were inhabited by lynx during the Pleistocene. After the Last Glacial Maximum (LGM) range expansions lead to colonization of north-western Siberia and Scandinavia from the Caucasus and north-eastern Siberia from a refugium further east. No evidence of a Berinigan refugium could be detected in our data. We observed restricted gene flow and suggest that future studies of the Eurasian lynx explore to what extent the contemporary population structure may be explained by ecological variables. PMID:24695745

Predicting free-space occupancy on novel artificial structures by an invasive intertidal barnacle using a removal experiment.

PubMed

Bracewell, Sally A; Robinson, Leonie A; Firth, Louise B; Knights, Antony M

2013-01-01

Artificial structures can create novel habitat in the marine environment that has been associated with the spread of invasive species. They are often located in areas of high disturbance and can vary significantly in the area of free space provided for settlement of marine organisms. Whilst correlation between the amount of free space available and recruitment success has been shown in populations of several marine benthic organisms, there has been relatively little focus on invasive species, a group with the potential to reproduce in vast numbers and colonise habitats rapidly. Invasion success following different scales of disturbance was examined in the invasive acorn barnacle, Austrominiusmodestus, on a unique art installation located in Liverpool Bay. Population growth and recruitment success were examined by comparing recruitment rates within disturbance clearings of 4 different sizes and by contrasting population development with early recruitment rates over a 10 week period. Disturbed areas were rapidly recolonised and monocultures of A. modestus formed within 6 weeks. The size of patch created during disturbance had no effect on the rate of recruitment, while a linear relationship between recruit density and patch size was observed. Density-dependent processes mediated initial high recruitment resulting in population stability after 8-10 weeks, but densities continued to greatly exceed those reported in natural habitats. Given that artificial structures are likely to continue to proliferate in light of climate change projections, free-space is likely to become more available more frequently in the future supporting the expansion of fast-colonising species.

Within-Range Translocations and Their Consequences in European Larch

PubMed Central

Wagner, Stefanie; Liepelt, Sascha; Gerber, Sophie; Petit, Rémy J.

2015-01-01

In contrast to biological invasions, translocations of individuals within a species range are understudied, due to difficulties in systematically detecting them. This results in limited knowledge about the corresponding processes and uncertainties regarding the status of extant populations. European larch, a forest tree whose fragmented native distribution is restricted to the Alps and to other Central European mountains, has been massively planted for at least 300 years. Here we focus on the genetic characterization of translocations having taken place within its native range. Microsatellite variation at 13 nuclear loci and sequence data of two mitochondrial DNA fragments were analyzed on the basis of a comprehensive range-wide population sample. Two complementary methods (Geneclass and Structure) were used to infer translocation events based on nuclear data whereas mitochondrial data were used for validation of these inferences. Using Geneclass, we found translocation events in a majority of populations. Additional cases of translocation and many instances of admixture were identified using Structure, thanks to the clear-cut ancestral genetic structure detected in this species. In particular, a strong divide between Alpine and Central European populations, also apparent at mitochondrial markers, helped uncover details on translocation events and related processes. Translocations and associated admixture events were found to be heterogeneously distributed across the species range, with a particularly high frequency in Central Europe. Furthermore, translocations frequently involved multiple geographic sources, some of which were over-represented. Our study illustrates the importance of range-wide investigations for tracing translocations back to their origins and for revealing some of their consequences. It provides some first clues for developing suitable conservation and management strategies. PMID:26000791

Human-mediated and natural dispersal of an invasive fish in the eastern Great Lakes.

PubMed

Johansson, Mattias L; Dufour, Bradley A; Wellband, Kyle W; Corkum, Lynda D; MacIsaac, Hugh J; Heath, Daniel D

2018-06-01

The globally invasive Round Goby (Neogobius melanostomus) was introduced to the Great Lakes around 1990, spreading widely and becoming the dominant benthic fish in many areas. The speed and scope of this invasion is remarkable and calls into question conventional secondary spread models and scenarios. We utilized nine microsatellites to identify large-scale genetic structure in Round Goby populations in the eastern Great Lakes, and assessed the role of colonization vs. secondary transport and dispersal in developing this structure. We identified three clusters, corresponding with Lake Huron, eastern Lake Erie, and western Lake Erie plus eastern Lake Ontario, along with three highly divergent populations. Bottleneck analysis identified founder effects in two divergent populations. Regression analyses of isolation by distance and allelic richness vs. distance from the initial invasion site were consistent with limited migration. However, some populations in eastern Lake Erie and Lake Ontario showed anomalously low genetic distance from the original site of colonization, consistent with secondary transport of large numbers of individuals via ballast water. We conclude that genetic structure of Round Goby in the Great Lakes principally resulted from long-distance secondary transport via ballast water with additional movement of individual via bait buckets and natural dispersal. The success of Round Gobies represents an interesting model for colonization characterization; however, those same attributes present significant challenges for conservation and fisheries management. Current management likely prevents many new species from arriving in the Great Lakes, but fails to address the transport of species within the lakes after they arrive; this is an issue of clear and pressing importance.

Species delimitation and conservation genetics of the Canarian endemic Bethencourtia (Asteraceae).

PubMed

Rodríguez-Rodríguez, Priscila; Pérez de Paz, Pedro Luis; Sosa, Pedro A

2018-04-01

Bethencourtia Choisy ex Link is an endemic genus of the Canary Islands and comprises three species. Bethencourtia hermosae and Bethencourtia rupicola are restricted to La Gomera, while Bethencourtia palmensis is present in Tenerife and La Palma. Despite the morphological differences previously found between the species, there are still taxonomic incongruities in the group, with evident consequences for its monitoring and conservation. The objectives of this study were to define the species differentiation, perform population genetic analysis and propose conservation strategies for Bethencourtia. To achieve these objectives, we characterized 10 polymorphic SSR markers. Eleven natural populations (276 individuals) were analyzed (three for B. hermosae, five for B. rupicola and three for B. palmensis). The results obtained by AMOVA, PCoA and Bayesian analysis on STRUCTURE confirmed the evidence of well-structured groups corresponding to the three species. At the intra-specific level, B. hermosae and B. rupicola did not show a clear population structure, while B. palmensis was aggregated according to island of origin. This is consistent with self-incompatibility in the group and high gene flow within species. Overall, the genetic diversity of the three species was low, with expected heterozygosity values of 0.302 (B. hermosae), 0.382 (B. rupicola) and 0.454 (B. palmensis). Recent bottleneck events and a low number of individuals per population are probably the causes of the low genetic diversity. We consider that they are naturally rare species associated with specific habitats. The results given in this article will provide useful information to assist in conservation genetics programs for this endemic genus.

Isolation by distance across the Hawaiian Archipelago in the reef-building coral Porites lobata.

PubMed

Polato, Nicholas R; Concepcion, Gregory T; Toonen, Robert J; Baums, Iliana B

2010-11-01

There is an ongoing debate on the scale of pelagic larval dispersal in promoting connectivity among populations of shallow, benthic marine organisms. The linearly arranged Hawaiian Islands are uniquely suited to study scales of population connectivity and have been used extensively as a natural laboratory in terrestrial systems. Here, we focus on Hawaiian populations of the lobe coral Porites lobata, an ecosystem engineer of shallow reefs throughout the Pacific. Patterns of recent gene flow and population structure in P. lobata samples (n = 318) from two regions, the Hawaiian Islands (n = 10 sites) and from their nearest neighbour Johnston Atoll, were analysed with nine microsatellite loci. Despite its massive growth form, ∼ 6% of the samples from both regions were the product of asexual reproduction via fragmentation. Cluster analysis and measures of genetic differentiation indicated that P. lobata from the Hawaiian Islands are strongly isolated from those on Johnston Atoll (F(ST)  = 0.311; P < 0.001), with the descendants of recent migrants (n = 6) being clearly identifiable. Within the Hawaiian Islands, P. lobata conforms to a pattern of isolation by distance. Here, over 37% (P = 0.001) of the variation in genetic distance was explained by geographical distance. This pattern indicates that while the majority of ongoing gene flow in Hawaiian P. lobata occurs among geographically proximate reefs, inter-island distances are insufficient to generate strong population structure across the archipelago. © 2010 Blackwell Publishing Ltd.

Consequences of extreme life history traits on population persistence: do short-lived gobies face demographic bottlenecks?

NASA Astrophysics Data System (ADS)

Lefèvre, Carine D.; Nash, Kirsty L.; González-Cabello, Alonso; Bellwood, David R.

2016-06-01

The majority of coral reef goby species are short-lived, with some highly abundant species living less than 100 d. To understand the role and consequences of this extreme life history in shaping coral reef fish populations, we quantitatively documented the structure of small reef fish populations over a 26-month period (>14 short-lived fish generations) at an inshore reef on the Great Barrier Reef, Australia. Most species with life spans >1 yr, such as pomacentrids, exhibited a peak in recruitment during the austral summer, driving seasonal changes in the small fish community composition. In contrast, there were no clear changes in goby community composition, despite the abundance of short-lived, high turnover species. Species of Eviota, the most abundant gobiid genus observed, showed remarkably similar demographic profiles year-round, with consistent densities of adults as well as recently recruited juveniles. Our results demonstrate ongoing recruitment of these small cryptic fishes, which appears to compensate for an exceptionally short life span on the reef. Our results suggest that gobiid populations are able to overcome demographic limitations, and by maintaining reproduction, larval survival and recruitment throughout the year, they may avoid population bottlenecks. These findings also underline the potential trophodynamic importance of these small species; because of this constant turnover, Eviota species and other short-lived fishes may be particularly valuable contributors to the flow of energy on coral reefs, underpinning the year-round trophic structure.

Genetic diversity among brazilian isolates of beauveria bassiana: comparisons with non-brazilian isolates and other beauveria species

USGS Publications Warehouse

Fernandes, E.K.K.; Moraes, A.M.L.; Pacheco, R.S.; Rangel, D.E.N.; Miller, M.P.; Bittencourt, V.R.E.P.; Roberts, D.W.

2009-01-01

Aims: The genetic diversity of Beauveria bassiana was investigated by comparing isolates of this species to each other (49 from different geographical regions of Brazil and 4 from USA) and to other Beauveria spp. Methods and Results: The isolates were examined by multilocus enzyme electrophoresis (MLEE), amplified fragment length polymorphism (AFLP), and rDNA sequencing. MLEE and AFLP revealed considerable genetic variability among B. bassiana isolates. Several isolates from South and Southeast Brazil had high similarity coefficients, providing evidence of at least one population with clonal structure. There were clear genomic differences between most Brazilian and USA B. bassiana isolates. A Mantel test using data generated by AFLP provided evidence that greater geographical distances were associated with higher genetic distances. AFLP and rDNA sequencing demonstrated notable genotypic variation between B. bassiana and other Beauveria spp. Conclusion: Geographical distance between populations apparently is an important factor influencing genotypic variability among B. bassiana populations in Brazil. Significance and Impact of the Study: This study characterized many B. bassiana isolates. The results indicate that certain Brazilian isolates are considerably different from others and possibly should be regarded as separate species from B. bassiana sensu latu. The information on genetic variation among the Brazilian isolates, therefore, will be important to comprehending the population structure of B. bassiana in Brazil. ?? 2009 The Society for Applied Microbiology.

An Inventory of International Clearing House Services in Population/Family Planning With Special Reference to Audio-Visual Aids and Educational Materials.

ERIC Educational Resources Information Center

Radel, David

This paper provides an inventory and summary of current and planned international information clearing house services in the field of population/family planning, worldwide. Special emphasis is placed on services relating to audio-visual aids, educational materials, and information/education/communication support, as these items and activities have…

Scale growth of structures in the turbulent boundary layer with a rod-roughened wall

NASA Astrophysics Data System (ADS)

Lee, Jin; Kim, Jung Hoon; Lee, Jae Hwa

2016-01-01

Direct numerical simulation of a turbulent boundary layer over a rod-roughened wall is performed with a long streamwise domain to examine the streamwise-scale growth mechanism of streamwise velocity fluctuating structures in the presence of two-dimensional (2-D) surface roughness. An instantaneous analysis shows that there is a slightly larger population of long structures with a small helix angle (spanwise inclinations relative to streamwise) and a large spanwise width over the rough-wall compared to that over a smooth-wall. Further inspection of time-evolving instantaneous fields clearly exhibits that adjacent long structures combine to form a longer structure through a spanwise merging process over the rough-wall; moreover, spanwise merging for streamwise scale growth is expected to occur frequently over the rough-wall due to the large spanwise scales generated by the 2-D roughness. Finally, we examine the influence of a large width and a small helix angle of the structures over the rough-wall with regard to spatial two-point correlation. The results show that these factors can increase the streamwise coherence of the structures in a statistical sense.

A Resolution to the Blue Whiting (Micromesistius poutassou) Population Paradox?

PubMed Central

Pointin, Fabien; Payne, Mark R.

2014-01-01

We provide the strongest evidence to date supporting the existence of two independent blue whiting (Micromesistius poutassou (Risso, 1827)) populations in the North Atlantic. In spite of extensive data collected in conjunction with the fishery, the population structure of blue whiting is poorly understood. On one hand, genetic, morphometric, otolith and drift modelling studies point towards the existence of two populations, but, on the other hand, observations of adult distributions point towards a single population. A paradox therefore arises in attempting to reconcile these two sets of information. Here we analyse 1100 observations of blue whiting larvae from the Continuous Plankton Recorder (CPR) from 1948–2005 using modern statistical techniques. We show a clear spatial separation between a northern spawning area, in the Rockall Trough, and a southern one, off the Porcupine Seabight. We further show a difference in the timing of spawning between these sites of at least a month, and meaningful differences in interannual variability. The results therefore support the two-population hypothesis. Furthermore, we resolve the paradox by showing that the acoustic observations cited in support of the single-population model are not capable of resolving both populations, as they occur too late in the year and do not extend sufficiently far south to cover the southern population: the confusion is the result of a simple observational artefact. We conclude that blue whiting in the North Atlantic comprises two populations. PMID:25184302

Differential co-localization with choline acetyltransferase in nervus terminalis suggests functional differences for GnRH isoforms in bonnethead sharks (Sphyrna tiburo)

PubMed Central

Moeller, John F.; Meredith, Michael

2010-01-01

The nervus terminalis (NT) is a vertebrate cranial nerve whose function in adults is unknown. In bonnethead sharks the nerve is anatomically independent of the olfactory system, with two major cell populations within one or more ganglia along its exposed length. Most cells are immunoreactive for either gonadotropin-releasing hormone (GnRH) or RFamide-like peptides. To define further the cell populations and connectivity, we used double-label immuno-cytochemistry with antisera to different isoforms of GnRH and to choline acetyltransferase (ChAT). The labeling patterns of two GnRH antisera revealed different populations of GnRH immunoreactive (ir) cell-profiles in the NT ganglion. One antiserum labeled a large group of cells and fibers, which likely contain mammalian GnRH (GnRH-I) as described in previous studies, and which were ChAT immunoreactive. The other antiserum labeled large club-like structures, which were anuclear, and a sparse number of fibers, but with no clear labeling of cell bodies in the ganglion. These club structures were choline acetyltrasferase (ChAT) negative, and preabsorption control tests suggest they may contain chicken-GnRH-II (GnRH-II) or dogfish GnRH. The second major NT ganglion cell-type was immunoreactive for RF-amides, which regulate GnRH release in other vertebrates, and may provide an intraganglionic influence on GnRH release. The immunocytochemical and anatomical differences between the two GnRH immunoreactive profile types indicate possible functional differences for these isoforms in the NT. The club-like structures may be sites of GnRH release into the general circulation since these structures were observed near blood vessels and resembled structures seen in the median eminence of rats. PMID:20950589

Differential co-localization with choline acetyltransferase in nervus terminalis suggests functional differences for GnRH isoforms in bonnethead sharks (Sphyrna tiburo).

PubMed

Moeller, John F; Meredith, Michael

2010-12-17

The nervus terminalis (NT) is a vertebrate cranial nerve whose function in adults is unknown. In bonnethead sharks, the nerve is anatomically independent of the olfactory system, with two major cell populations within one or more ganglia along its exposed length. Most cells are immunoreactive for either gonadotropin-releasing hormone (GnRH) or RF-amide-like peptides. To define further the cell populations and connectivity, we used double-label immunocytochemistry with antisera to different isoforms of GnRH and to choline acetyltransferase (ChAT). The labeling patterns of two GnRH antisera revealed different populations of GnRH-immunoreactive (ir) cell profiles in the NT ganglion. One antiserum labeled a large group of cells and fibers, which likely contain mammalian GnRH (GnRH-I) as described in previous studies and which were ChAT immunoreactive. The other antiserum labeled large club-like structures, which were anuclear, and a sparse number of fibers, but with no clear labeling of cell bodies in the ganglion. These club structures were choline acetyltrasferase (ChAT)-negative, and preabsorption control tests suggest they may contain chicken-GnRH-II (GnRH-II) or dogfish GnRH. The second major NT ganglion cell-type was immunoreactive for RF-amides, which regulate GnRH release in other vertebrates, and may provide an intraganglionic influence on GnRH release. The immunocytochemical and anatomical differences between the two GnRH-immunoreactive profile types indicate possible functional differences for these isoforms in the NT. The club-like structures may be sites of GnRH release into the general circulation since these structures were observed near blood vessels and resembled structures seen in the median eminence of rats. Copyright © 2010 Elsevier B.V. All rights reserved.

Life history and viability of a long-lived marine invertebrate: the octocoral Paramuricea clavata.

PubMed

Linares, Cristina; Doak, Daniel F; Coma, Rafel; Díaz, David; Zabala, Mikel

2007-04-01

The red gorgonian Paramuricea clavata is a long-lived, slow-growing sessile invertebrate of ecological and conservation importance in the northwestern Mediterranean Sea. We develop a series of size-based matrix models for two Paramuricea clavata populations. These models were used to estimate basic life history traits for this species and to evaluate the viability of the red gorgonian populations we studied. As for many other slow-growing species, sensitivity and elasticity analysis demonstrate that gorgonian population growth is far more sensitive to changes in survival rates than to growth, shrinkage, or reproductive rates. The slow growth and low mortality of red gorgonians results in low damping ratios, indicating slow convergence to stable size structures (at least 50 years). The stable distributions predicted by the model did not differ from the observed ones. However, our simulations point out the fragility of this species, showing both populations in decline and high risk of extinction over moderate time horizons. These declines appear to be related to a recent increase in anthropogenic disturbances. Relative to their life span, the values of recruitment elasticity for Paramuricea clavata are lower than those reported for other marine organisms but are similar to those reported for some long-lived plants. These values and the delayed age of sexual maturity, in combination with the longevity of the species, show a clear fecundity/mortality trade-off. Full demographic studies of sessile marine species are quite scarce but can provide insight into population dynamics and life history patterns for these difficult and under-studied species. While our work shows clear results for the red gorgonian, the variability in some of our estimates suggest that future work should include data collection over longer temporal and spatial scales to better understand the long-term effects of natural and anthropogenic disturbances on red gorgonian populations.

Multilocus Phylogeography of the Treefrog Scinax eurydice (Anura, Hylidae) Reveals a Plio-Pleistocene Diversification in the Atlantic Forest.

PubMed

Menezes, Lucas; Canedo, Clarissa; Batalha-Filho, Henrique; Garda, Adrian Antonio; Gehara, Marcelo; Napoli, Marcelo Felgueiras

2016-01-01

We aim to evaluate the genetic structure of an Atlantic Forest amphibian species, Scinax eurydice, testing the congruence among patterns identified and proposed by the literature for Pleistocene refugia, microrefugia, and geographic barriers to gene flow such as major rivers. Furthermore, we aim to evaluate predictions of such barriers and refugia on the genetic structure of the species, such as presence/absence of dispersal, timing since separation, and population expansions/contractions. We sequenced mitochondrial and nuclear genetic markers on 94 tissue samples from 41 localities. We inferred a gene tree and estimated genetic distances using mtDNA sequences. We then ran population clustering and assignment methods, AMOVA, and estimated migration rates among populations identified through mtDNA and nDNA analyses. We used a dated species tree, skyline plots, and summary statistics to evaluate concordance between population's distributions and geographic barriers and Pleistocene refugia. Scinax eurydice showed high mtDNA divergences and four clearly distinct mtDNA lineages. Species tree and population assignment tests supported the existence of two major clades corresponding to northeastern and southeastern Atlantic Forest in Brazil, each one composed of two other clades. Lineage splitting events occurred from late Pliocene to Pleistocene. We identified demographic expansions in two clades, and inexistent to low levels of migrations among different populations. Genetic patterns and demographic data support the existence of two northern Refuge and corroborate microrefugia south of the Doce/Jequitinhonha Rivers biogeographic divide. The results agree with a scenario of recent demographic expansion of lowland taxa. Scinax eurydice comprises a species complex, harboring undescribed taxa consistent with Pleistocene refugia. Two rivers lie at the boundaries among populations and endorse their role as secondary barriers to gene flow.

Surface vibrational structure at alkane liquid/vapor interfaces

NASA Astrophysics Data System (ADS)

Esenturk, Okan; Walker, Robert A.

2006-11-01

Broadband vibrational sum frequency spectroscopy (VSFS) has been used to examine the surface structure of alkane liquid/vapor interfaces. The alkanes range in length from n-nonane (C9H20) to n-heptadecane (C17H36), and all liquids except heptadecane are studied at temperatures well above their bulk (and surface) freezing temperatures. Intensities of vibrational bands in the CH stretching region acquired under different polarization conditions show systematic, chain length dependent changes. Data provide clear evidence of methyl group segregation at the liquid/vapor interface, but two different models of alkane chain structure can predict chain length dependent changes in band intensities. Each model leads to a different interpretation of the extent to which different chain segments contribute to the anisotropic interfacial region. One model postulates that changes in vibrational band intensities arise solely from a reduced surface coverage of methyl groups as alkane chain length increases. The additional methylene groups at the surface must be randomly distributed and make no net contribution to the observed VSF spectra. The second model considers a simple statistical distribution of methyl and methylene groups populating a three dimensional, interfacial lattice. This statistical picture implies that the VSF signal arises from a region extending several functional groups into the bulk liquid, and that the growing fraction of methylene groups in longer chain alkanes bears responsibility for the observed spectral changes. The data and resulting interpretations provide clear benchmarks for emerging theories of molecular structure and organization at liquid surfaces, especially for liquids lacking strong polar ordering.

Collection and characterization of grapevine genetic resources (Vitis vinifera) in the Holy Land, towards the renewal of ancient winemaking practices.

PubMed

Drori, Elyashiv; Rahimi, Oshrit; Marrano, Annarita; Henig, Yakov; Brauner, Hodaya; Salmon-Divon, Mali; Netzer, Yishay; Prazzoli, Maria Lucia; Stanevsky, Maria; Failla, Osvaldo; Weiss, Ehud; Grando, Maria Stella

2017-03-17

The importance and extent of wine consumption in all life aspects at the Holy Land is well documented. The Muslim influence in this region led to the abandonment of winemaking practices, and possible loss of indigenous wine varieties. Here we present a country wide collection of the local grapevine population including wild and cultivated forms, and its characterization by genetic, ampelographic and enological methods. The ampelographic analysis shows clear differences between Sativa and Sylvestris groups in flower, leaf and cluster parameters, and that most Sativa belong to proles orientalis. Genetic population analysis was conducted by analyzing 22 common SSR markers, determining first the unique genotypes, and internally assessing the population's structure, showing the existence of two distinct Sativa and Sylvestris populations, and a third mixed one. Likewise, the relationship between the Israeli grapevine population and grapevine populations in Europe and parts of Asia was investigated, showing that the Israeli Sativa and Sylvestris populations cluster closely together, suggesting a common genetic source. Lastly, the enological characteristics of selected Sativa and Sylvestris genotypes are presented, demonstrating their potential for quality wine production. This research significantly contributes toward the re-establishment of indigenous and traditional local grapevine varieties into the modern international wine industry.

The genetic relationship between extirpated and contemporary Atlantic salmon Salmo salar L. lines from the southern Baltic Sea.

PubMed

Bernaś, Rafał; Poćwierz-Kotus, Anita; Dębowski, Piotr; Wenne, Roman

2016-04-01

The genetic relationship between original Atlantic salmon populations that are now extinct in the southern Baltic Sea and the present-day populations has long been controversial. To investigate and clarify this issue, we successfully genotyped individuals of the historical populations from the Oder and Vistula Rivers using DNA extracted from dried scales with the Atlantic salmon single nucleotide polymorphism array. Our results showed a global F ST of 0.2515 for all pairs of loci, which indicates a high level of genetic differentiation among the groups analyzed in this study. Pairwise F ST values were significant for all comparisons and the highest values were found between present-day reintroduced Slupia River salmon and extinct Vistula River Atlantic salmon. Bayesian analysis of genetic structure revealed the existence of substructures in the extirpated Polish populations and three main clades among studied stocks. The historical salmon population from the Oder River was genetically closer to present-day salmon from the Neman River than to the historical salmon from the Vistula River. Vistula salmon clearly separated from all other analyzed salmon stocks. It is likely that the origins of the Atlantic salmon population from the Morrum River and the Polish historical native populations are different.

Aboriginal and Torres Strait Islander community governance of health research: Turning principles into practice.

PubMed

Gwynn, Josephine; Lock, Mark; Turner, Nicole; Dennison, Ray; Coleman, Clare; Kelly, Brian; Wiggers, John

2015-08-01

Gaps exist in researchers' understanding of the 'practice' of community governance in relation to research with Aboriginal and Torres Strait Islander peoples. We examine Aboriginal community governance of two rural NSW research projects by applying principles-based criteria from two independent sources. One research project possessed a strong Aboriginal community governance structure and evaluated a 2-year healthy lifestyle program for children; the other was a 5-year cohort study examining factors influencing the mental health and well-being of participants. The National Health and Medical Research Council of Australia's 'Values and ethics: guidelines for ethical conduct in Aboriginal and Torres Strait Islander research' and 'Ten principles relevant to health research among Indigenous Australian populations' described by experts in the field. Adopt community-based participatory research constructs. Develop clear governance structures and procedures at the beginning of the study and allow sufficient time for their establishment. Capacity-building must be a key component of the research. Ensure sufficient resources to enable community engagement, conduct of research governance procedures, capacity-building and results dissemination. The implementation of governance structures and procedures ensures research addresses the priorities of the participating Aboriginal and Torres Strait Islander communities, minimises risks and improves outcomes for the communities. Principles-based Aboriginal and Torres Strait Islander community governance of research is very achievable. Next steps include developing a comprehensive evidence base for appropriate governance structures and procedures, and consolidating a suite of practical guides for structuring clear governance in health research. © 2015 National Rural Health Alliance Inc.

Population structure and fruit production of Pyrus bourgaeana D. are affected by land-use

NASA Astrophysics Data System (ADS)

Arenas-Castro, Salvador; Fernández-Haeger, Juan; Jordano-Barbudo, Diego

2016-11-01

The Iberian wild pear (Pyrus bourgaeana D.) is a rare, fleshy-fruited tree restricted to dehesas and evergreen sclerophyllous Mediterranean forests in the southwestern Iberian Peninsula. It produces palatable fruits and leaves attractive to different species groups, playing an important trophic role in the ecological networks of Mediterranean ecosystems. However, the intensification in the traditional land-use linked to these areas could threaten the stability of the wild pear populations in the short/medium-term. In order to determine the population dynamics of this relevant species in relation to the land-use history, we selected two populations (southern Spain) subjected to different land-use management, dehesa (D) and abandoned olive grove (AOG). An analysis of 122 adult trees reported an overall density of 0.6 trees ha-1. The tree age was estimated by tree-rings analysis in all adult trees. Dendrometric parameters, reproductive features, and germination rates were also measured. Regeneration was clearly biased, as evidenced by the truncated age structure. A low correlation (R2 = 34%) between age and DBH (diameter at breast height) (244 cores analysed) showed that diameter seems not to be a reliable predictor of tree age. Trees from AOG populations had significantly-higher values of DBH, height and crown diameter, but were less productive in terms of fruits and seeds. Nested analysis of variance showed significant variation in fruit production, fruit size, dry mass, water content and seed viability. There were also significant differences in masting. No evidence was found to demonstrate that fruit production, seed viability, or germination rate influence the low natural recruitment of this species. These findings indicate that the traditional agrosilvopastoral practices carried out in the study area for decades, and its subsequent intensification, have strongly influenced the ecological structure of the Iberian wild pear populations at the local scale, which could compromise its stability in the near future.

Contrasting Genetic Structure among Populations of Two Amphidromous Fish Species (Sicydiinae) in the Central West Pacific

PubMed Central

Taillebois, Laura; Castelin, Magalie; Ovenden, Jennifer R.; Bonillo, Céline; Keith, Philippe

2013-01-01

Both present-day and past processes can shape connectivity of populations. Pleistocene vicariant events and dispersal have shaped the present distribution and connectivity patterns of aquatic species in the Indo-Pacific region. In particular, the processes that have shaped distribution of amphidromous goby species still remain unknown. Previous studies show that phylogeographic breaks are observed between populations in the Indian and Pacific Oceans where the shallow Sunda shelf constituted a geographical barrier to dispersal, or that the large spans of open ocean that isolate the Hawaiian or Polynesian Islands are also barriers for amphidromous species even though they have great dispersal capacity. Here we assess past and present genetic structure of populations of two amphidromous fish (gobies of the Sicydiinae) that are widely distributed in the Central West Pacific and which have similar pelagic larval durations. We analysed sections of mitochondrial COI, Cytb and nuclear Rhodospine genes in individuals sampled from different locations across their entire known range. Similar to other Sicydiinae fish, intraspecific mtDNA genetic diversity was high for all species (haplotype diversity between 0.9–0.96). Spatial analyses of genetic variation in Sicyopus zosterophorum demonstrated strong isolation across the Torres Strait, which was a geologically intermittent land barrier linking Australia to Papua New Guinea. There was a clear genetic break between the northwestern and the southwestern clusters in Si. zosterophorum (φST = 0.67502 for COI) and coalescent analyses revealed that the two populations split at 306 Kyr BP (95% HPD 79–625 Kyr BP), which is consistent with a Pleistocene separation caused by the Torres Strait barrier. However, this geographical barrier did not seem to affect Sm. fehlmanni. Historical and demographic hypotheses are raised to explain the different patterns of population structure and distribution between these species. Strategies aiming to conserve amphidromous fish should consider the presence of cryptic evolutionary lineages to prevent stock depletion. PMID:24130714

Genetic Diversity and Population Structure of Leishmania infantum from Southeastern France: Evaluation Using Multi-Locus Microsatellite Typing

PubMed Central

Pomares, Christelle; Marty, Pierre; Bañuls, Anne Laure; Lemichez, Emmanuel; Pratlong, Francine; Faucher, Benoît; Jeddi, Fakhri; Moore, Sandy; Michel, Grégory; Aluru, Srikanth; Piarroux, Renaud; Hide, Mallorie

2016-01-01

In the south of France, Leishmania infantum is responsible for numerous cases of canine leishmaniasis (CanL), sporadic cases of human visceral leishmaniasis (VL) and rare cases of cutaneous and muco-cutaneous leishmaniasis (CL and MCL, respectively). Several endemic areas have been clearly identified in the south of France including the Pyrénées-Orientales, Cévennes (CE), Provence (P), Alpes-Maritimes (AM) and Corsica (CO). Within these endemic areas, the two cities of Nice (AM) and Marseille (P), which are located 150 km apart, and their surroundings, concentrate the greatest number of French autochthonous leishmaniasis cases. In this study, 270 L. infantum isolates from an extended time period (1978–2011) from four endemic areas, AM, P, CE and CO, were assessed using Multi-Locus Microsatellite Typing (MLMT). MLMT revealed a total of 121 different genotypes with 91 unique genotypes and 30 repeated genotypes. Substantial genetic diversity was found with a strong genetic differentiation between the Leishmania populations from AM and P. However, exchanges were observed between these two endemic areas in which it seems that strains spread from AM to P. The genetic differentiations in these areas suggest strong epidemiological structuring. A model-based analysis using STRUCTURE revealed two main populations: population A (consisting of samples primarily from the P and AM endemic areas with MON-1 and non-MON-1 strains) and population B consisting of only MON-1 strains essentially from the AM endemic area. For four patients, we observed several isolates from different biological samples which provided insight into disease relapse and re-infection. These findings shed light on the transmission dynamics of parasites in humans. However, further data are required to confirm this hypothesis based on a limited sample set. This study represents the most extensive population analysis of L. infantum strains using MLMT conducted in France. PMID:26808522

Divergence, hybridization, and recombination in the mitochondrial genome of the human pathogenic yeast Cryptococcus gattii.

PubMed

Xu, Jianping; Yan, Zhun; Guo, Hong

2009-06-01

The inheritance of mitochondrial genes and genomes are uniparental in most sexual eukaryotes. This pattern of inheritance makes mitochondrial genomes in natural populations effectively clonal. Here, we examined the mitochondrial population genetics of the emerging human pathogenic fungus Cryptococcus gattii. The DNA sequences for five mitochondrial DNA fragments were obtained from each of 50 isolates belonging to two evolutionary divergent lineages, VGI and VGII. Our analyses revealed a greater sequence diversity within VGI than that within VGII, consistent with observations of the nuclear genes. The combined analyses of all five gene fragments indicated significant divergence between VGI and VGII. However, the five individual genealogies showed different relationships among the isolates, consistent with recent hybridization and mitochondrial gene transfer between the two lineages. Population genetic analyses of the multilocus data identified evidence for predominantly clonal mitochondrial population structures within both lineages. Interestingly, there were clear signatures of recombination among mitochondrial genes within the VGII lineage. Our analyses suggest historical mitochondrial genome divergence within C. gattii, but there is evidence for recent hybridization and recombination in the mitochondrial genome of this important human yeast pathogen.

Use of regenerative tissue for urinary diversion.

PubMed

Sopko, Nikolai A; Kates, Max; Bivalacqua, Trinity J

2015-11-01

There is a large interest in developing tissue engineered urinary diversions (TEUDs) in order to reduce the significant morbidity that results from utilization of the alimentary tract in the urinary system. Preclinical trials have been favorable but durable clinical results have not been realized. The present article will review the pertinent concepts for the clinical development of a successful TEUD. Studies continue to identify novel scaffold materials and cell populations that are combined to generate TEUDs. Scaffold composition range from synthetic material to decelluarized bladder tissue. Cell types vary from fully differentiated adult populations such as smooth muscle cells isolated from the bladder to stem cell populations including mesenchymal stem cells and induced pluripotent stem cells. Each scaffold and cell type has its advantages and disadvantages with no clear superior component having been identified. Recent clinical trials have been disappointing, supporting the need for additional investigation. Successful application of TEUDs requires a complex interplay of scaffold, cells, and host environment. Studies continue to investigate candidate scaffold materials, cell populations, and combinations thereof to determine which will best recapitulate the complex structure of the human genitourinary tract.

Toward a new history and geography of human genes informed by ancient DNA

PubMed Central

Pickrell, Joseph K.; Reich, David

2014-01-01

Genetic information contains a record of the history of our species, and technological advances have transformed our ability to access this record. Many studies have used genome-wide data from populations today to learn about the peopling of the globe and subsequent adaptation to local conditions. Implicit in this research is the assumption that the geographic locations of people today are informative about the geographic locations of their ancestors in the distant past. However, it is now clear that long-range migration, admixture and population replacement subsequent to the initial out-of-Africa expansion have altered the genetic structure of most of the world’s human populations. In light of this, we argue that it is time to critically re-evaluate current models of the peopling of the globe, as well as the importance of natural selection in determining the geographic distribution of phenotypes. We specifically highlight the transformative potential of ancient DNA. By accessing the genetic make-up of populations living at archaeologically-known times and places, ancient DNA makes it possible to directly track migrations and responses to natural selection. PMID:25168683

The effect of habitat patch size on small mammal populations

Treesearch

Mark D. Yates; Susan C. Loeb; David C. Guynn

1997-01-01

Habitat fragmentation is one of the greatest threats to the conservation of bio­diversity and has 3 components: habitat loss, patch isolation, and patch size. The authors tested the effects of forest-clearing size on small mammal populations in the Upper Coastal Plain of South Carolina. These clearings act as islands for many species of small mam­mals, particularly old...

Review of conventional and novel food processing methods on food allergens.

PubMed

Vanga, Sai Kranthi; Singh, Ashutosh; Raghavan, Vijaya

2017-07-03

With the turn of this century, novel food processing techniques have become commercially very important because of their profound advantages over the traditional methods. These novel processing methods tend to preserve the characteristic properties of food including their organoleptic and nutritional qualities better when compared with the conventional food processing methods. During the same period of time, there is a clear rise in the populations suffering from food allergies, especially infants and children. Though, this fact is widely attributed to the changing livelihood of population in both developed and developing nations and to the introduction of new food habits with advent of novel foods and new processing techniques, their complete role is still uncertain. Under the circumstance, it is very important to understand the structural changes in the protein as food is processed to comprehend whether the specific processing technique (conventional and novel) is increasing or mitigating the allergenicity. Various modern means are now being employed to understand the conformational changes in the protein which can affect the allergenicity. In this review, the processing effects on protein structure and allergenicity are discussed along with the insinuations of recent studies and techniques for establishing a platform to investigate future pathway to reduce or eliminate allergenicity in the population.

Population Genetics of Verticillium dahliae in Iran Based on Microsatellite and Single Nucleotide Polymorphism Markers.

PubMed

Rafiei, Vahideh; Banihashemi, Ziaeddin; Bautista-Jalon, Laura S; Del Mar Jiménez-Gasco, Maria; Turgeon, B Gillian; Milgroom, Michael G

2018-06-01

Verticillium dahliae is a plant pathogenic fungus that reproduces asexually and its population structure is highly clonal. In the present study, 78 V. dahliae isolates from Iran were genotyped for mating type, single nucleotide polymorphisms (SNPs), and microsatellites to assign them to clonal lineages and to determine population genetic structure in Iran. The mating type of all isolates was MAT1-2. Based on neighbor-joining analysis and minimum spanning networks constructed from SNPs and microsatellite genotypes, respectively, all but four isolates were assigned to lineage 2B 824 ; four isolates were assigned to lineage 4B. The inferred coalescent genealogy of isolates in lineage 2B 824 showed a clear divergence into two clades that corresponded to geographic origin and host. Haplotypes of cotton and pistachio isolates sampled from central Iran were in one clade, and those of isolates from Prunus spp. sampled from northwestern Iran were in the other. The strong divergence in haplotypes between the two clades suggests that there were at least two separate introductions of lineage 2B 824 to different parts of Iran. Given the history of cotton and pistachio cultivation and Verticillium wilt in Iran, these results are consistent with the hypothesis that cotton was historically a likely source inoculum causing Verticillium wilt in pistachio.

Structure of the microfilarial reservoir of Loa loa in the human host and its implications for monitoring the progr,ammes of Community-Directed Treatment with Ivermectin carried out in Africa.

PubMed

Pion, D S S; Gardon, J; Kamgno, J; Gardon-Wendel, N; Chippaux, J P; Boussinesq, M

2004-11-01

This paper describes the structure of the microfilarial reservoir of Loa loa in an endemic population of central Cameroon. The possible effects of age and sex on the prevalence and intensity of microfilaraemia have been explored. Logistic analysis showed that the prevalence of microfilaraemia increased significantly with age, reaching 60 % in the oldest males. This result suggests that the figure commonly reported, according to which only one third of the infected individuals were microfilaraemic, should be reconsidered; in addition, as part of surveys of loiasis, crude microfilaraemia prevalence values should be replaced by adjusted ones. The intensity of infection did not show any age-specific change. As a result, even if the oldest members of the male population are clearly the most at risk of developing post-ivermectin serious adverse reactions, especially Loa-encephalopathy, the other members of the population are not risk-free. Therefore, in those areas where the African Programme for Onchocerciasis Control is undertaking regular mass distributions of ivermectin for onchocerciasis control, and where loiasis is co-endemic, no subpopulation should be excluded from surveillance and monitoring during community directed treatments with ivermectin.

Associations among depressive symptoms, childhood abuse, neuroticism, and adult stressful life events in the general adult population.

PubMed

Ono, Kotaro; Takaesu, Yoshikazu; Nakai, Yukiei; Shimura, Akiyoshi; Ono, Yasuyuki; Murakoshi, Akiko; Matsumoto, Yasunori; Tanabe, Hajime; Kusumi, Ichiro; Inoue, Takeshi

2017-01-01

Recent studies have suggested that the interactions among several factors affect the onset, progression, and prognosis of major depressive disorder. This study investigated how childhood abuse, neuroticism, and adult stressful life events interact with one another and affect depressive symptoms in the general adult population. A total of 413 participants from the nonclinical general adult population completed the Patient Health Questionnaire-9, the Child Abuse and Trauma Scale, the neuroticism subscale of the shortened Eysenck Personality Questionnaire - Revised, and the Life Experiences Survey, which are self-report scales. Structural equation modeling (Mplus version 7.3) and single and multiple regressions were used to analyze the data. Childhood abuse, neuroticism, and negative evaluation of life events increased the severity of the depressive symptoms directly. Childhood abuse also indirectly increased the negative appraisal of life events and the severity of the depressive symptoms through enhanced neuroticism in the structural equation modeling. There was recall bias in this study. The causal relationship was not clear because this study was conducted using a cross-sectional design. This study suggested that neuroticism is the mediating factor for the two effects of childhood abuse on adulthood depressive symptoms and negative evaluation of life events. Childhood abuse directly and indirectly predicted the severity of depressive symptoms.

Phylogeography of Japanese horse chestnut (Aesculus turbinata) in the Japanese Archipelago based on chloroplast DNA haplotypes.

PubMed

Sugahara, Kanako; Kaneko, Yuko; Ito, Satoshi; Yamanaka, Keisuke; Sakio, Hitoshi; Hoshizaki, Kazuhiko; Suzuki, Wajiro; Yamanaka, Norikazu; Setoguchi, Hiroaki

2011-01-01

Japanese horse chestnut (Aesculus turbinata: Hippocastanaceae) is one of the typical woody plants that grow in temperate riparian forests in the Japanese Archipelago. To analyze the phylogeography of this plant in the Japanese Archipelago, we determined cpDNA haplotypes for 337 samples from 55 populations covering the entire distribution range. Based on 1,313 bp of two spacers, we determined ten haplotypes that are distinguished from adjacent haplotypes by one or two steps. Most of the populations had a single haplotype, suggesting low diversity. Spatial analysis of molecular variance suggested three obvious phylogeographic structures in western Japan, where Japanese horse chestnut is scattered and isolated in mountainous areas. Conversely, no clear phylogeographic structure was observed from the northern to the southern limit of this species, including eastern Japan, where this plant is more common. Rare and private haplotypes were also found in southwestern Japan, where Japanese horse chestnuts are distributed sparsely. These findings imply that western Japan might have maintained a relatively large habitat for A. turbinata during the Quaternary climatic oscillations, while northerly regions could not.

Sulfate-reducing bacteria inhabiting natural corrosion deposits from marine steel structures.

PubMed

Païssé, Sandrine; Ghiglione, Jean-François; Marty, Florence; Abbas, Ben; Gueuné, Hervé; Amaya, José Maria Sanchez; Muyzer, Gerard; Quillet, Laurent

2013-08-01

In the present study, investigations were conducted on natural corrosion deposits to better understand the role of sulfate-reducing bacteria (SRB) in the accelerated corrosion process of carbon steel sheet piles in port environments. We describe the abundance and diversity of total and metabolically active SRB within five natural corrosion deposits located within tidal or low water zone and showing either normal or accelerated corrosion. By using molecular techniques, such as quantitative real-time polymerase chain reaction, denaturing gel gradient electrophoresis, and sequence cloning based on 16S rRNA, dsrB genes, and their transcripts, we demonstrated a clear distinction between SRB population structure inhabiting normal or accelerated low-water corrosion deposits. Although SRB were present in both normal and accelerated low-water corrosion deposits, they dominated and were exclusively active in the inner and intermediate layers of accelerated corrosion deposits. We also highlighted that some of these SRB populations are specific to the accelerated low-water corrosion deposit environment in which they probably play a dominant role in the sulfured corrosion product enrichment.

The fine scale genetic structure of the British population

PubMed Central

Davison, Dan; Boumertit, Abdelhamid; Day, Tammy; Hutnik, Katarzyna; Royrvik, Ellen C; Cunliffe, Barry; Lawson, Daniel J; Falush, Daniel; Freeman, Colin; Pirinen, Matti; Myers, Simon; Robinson, Mark; Donnelly, Peter; Bodmer, Walter

2015-01-01

Summary Fine-scale genetic variation between human populations is interesting as a signature of historical demographic events and because of its potential for confounding disease studies. We use haplotype-based statistical methods to analyse genome-wide SNP data from a carefully chosen geographically diverse sample of 2,039 individuals from the United Kingdom (UK). This reveals a rich and detailed pattern of genetic differentiation with remarkable concordance between genetic clusters and geography. The regional genetic differentiation and differing patterns of shared ancestry with 6,209 individuals from across Europe carry clear signals of historical demographic events. We estimate the genetic contribution to SE England from Anglo-Saxon migrations to be under half, identify the regions not carrying genetic material from these migrations, suggest significant pre-Roman but post-Mesolithic movement into SE England from the Continent, and show that in non-Saxon parts of the UK there exist genetically differentiated subgroups rather than a general “Celtic” population. PMID:25788095

Intraspecific differences in plant chemotype determine the structure of arthropod food webs.

PubMed

Bálint, János; Zytynska, Sharon E; Salamon, Rozália Veronika; Mehrparvar, Mohsen; Weisser, Wolfgang W; Schmitz, Oswald J; Benedek, Klára; Balog, Adalbert

2016-03-01

It is becoming increasingly appreciated that the structure and functioning of ecological food webs are controlled by the nature and level of plant chemicals. It is hypothesized that intraspecific variation in plant chemical resistance, in which individuals of a host-plant population exhibit genetic differences in their chemical contents (called 'plant chemotypes'), may be an important determinant of variation in food web structure and functioning. We evaluated this hypothesis using field assessments and plant chemical assays in the tansy plant Tanacetum vulgare L. (Asteraceae). We examined food webs in which chemotypes of tansy plants are the resource for two specialized aphids, their predators and mutualistic ants. The density of the ant-tended aphid Metopeurum fuscoviride was significantly higher on particular chemotypes (borneol) than others. Clear chemotype preferences between predators were also detected. Aphid specialist seven-spotted ladybird beetles (Coccinella septempunctata) were more often found on camphor plants, while significantly higher numbers of the polyphagous nursery web spider (Pisaura mirabilis) were observed on borneol plants. The analysis of plant chemotype effects on the arthropod community clearly demonstrates a range of possible outcomes between plant-aphid-predator networks. The findings help to offer a deeper insight into how one important factor--plant chemical content--influences which species coexist within a food web on a particular host plant and the nature of their trophic linkages.

Structure of a designed, right-handed coiled-coil tetramer containing all biological amino acids

PubMed Central

Sales, Mark; Plecs, Joseph J.; Holton, James M.; Alber, Tom

2007-01-01

The previous design of an unprecedented family of two-, three-, and four-helical, right-handed coiled coils utilized nonbiological amino acids to efficiently pack spaces in the oligomer cores. Here we show that a stable, right-handed parallel tetrameric coiled coil, called RH4B, can be designed entirely using biological amino acids. The X-ray crystal structure of RH4B was determined to 1.1 Å resolution using a designed metal binding site to coordinate a single Yb2+ ion per 33-amino acid polypeptide chain. The resulting experimental phases were particularly accurate, and the experimental electron density map provided an especially clear, unbiased view of the molecule. The RH4B structure closely matched the design, with equivalent core rotamers and an overall root-mean-square deviation for the N-terminal repeat of the tetramer of 0.24 Å. The clarity and resolution of the electron density map, however, revealed alternate rotamers and structural differences between the three sequence repeats in the molecule. These results suggest that the RH4B structure populates an unanticipated variety of structures. PMID:17766380

Structure of a designed, right-handed coiled-coil tetramer containing all biological amino acids.

PubMed

Sales, Mark; Plecs, Joseph J; Holton, James M; Alber, Tom

2007-10-01

The previous design of an unprecedented family of two-, three-, and four-helical, right-handed coiled coils utilized nonbiological amino acids to efficiently pack spaces in the oligomer cores. Here we show that a stable, right-handed parallel tetrameric coiled coil, called RH4B, can be designed entirely using biological amino acids. The X-ray crystal structure of RH4B was determined to 1.1 Angstrom resolution using a designed metal binding site to coordinate a single Yb(2+) ion per 33-amino acid polypeptide chain. The resulting experimental phases were particularly accurate, and the experimental electron density map provided an especially clear, unbiased view of the molecule. The RH4B structure closely matched the design, with equivalent core rotamers and an overall root-mean-square deviation for the N-terminal repeat of the tetramer of 0.24 Angstrom. The clarity and resolution of the electron density map, however, revealed alternate rotamers and structural differences between the three sequence repeats in the molecule. These results suggest that the RH4B structure populates an unanticipated variety of structures.

Population genomics and the causes of local differentiation.

PubMed

Tonsor, Stephen J

2012-11-01

Exactly 50 years ago, a revolution in empirical population genetics began with the introduction of methods for detecting allelic variation using protein electrophoresis (Throckmorton 1962; Hubby 1963; Lewontin & Hubby 1966). These pioneering scientists showed that populations are chock-full of genetic variation. This variation was a surprise that required a re-thinking of evolutionary genetic heuristics. Understanding the causes for the maintenance of this variation became and remains a major area of research. In the process of addressing the causes, this same group of scientists documented geographical genetic structure (Prakash et al. 1969), spawning the continued accumulation of what is now a huge case study catalogue of geographical differentiation (e.g. Loveless & Hamrick 1984; Linhart & Grant 1996). Geographical differentiation is clearly quite common. Yet, a truly general understanding of the patterns in and causes of spatial genetic structure across the genome remains elusive. To what extent is spatial structure driven by drift and phylogeography vs. geographical differences in environmental sources of selection? What proportion of the genome participates? A general understanding requires range-wide data on spatial patterning of variation across the entire genome. In this issue of Molecular Ecology, Lasky et al. (2012) make important strides towards addressing these issues, taking advantage of three contemporary revolutions in evolutionary biology. Two are technological: high-throughput sequencing and burgeoning computational power. One is cultural: open access to data from the community of scientists and especially data sets that result from large collaborative efforts. Together, these developments may at last put answers within reach.

Comparative genomics of the bacterial genus Streptococcus illuminates evolutionary implications of species groups.

PubMed

Gao, Xiao-Yang; Zhi, Xiao-Yang; Li, Hong-Wei; Klenk, Hans-Peter; Li, Wen-Jun

2014-01-01

Members of the genus Streptococcus within the phylum Firmicutes are among the most diverse and significant zoonotic pathogens. This genus has gone through considerable taxonomic revision due to increasing improvements of chemotaxonomic approaches, DNA hybridization and 16S rRNA gene sequencing. It is proposed to place the majority of streptococci into "species groups". However, the evolutionary implications of species groups are not clear presently. We use comparative genomic approaches to yield a better understanding of the evolution of Streptococcus through genome dynamics, population structure, phylogenies and virulence factor distribution of species groups. Genome dynamics analyses indicate that the pan-genome size increases with the addition of newly sequenced strains, while the core genome size decreases with sequential addition at the genus level and species group level. Population structure analysis reveals two distinct lineages, one including Pyogenic, Bovis, Mutans and Salivarius groups, and the other including Mitis, Anginosus and Unknown groups. Phylogenetic dendrograms show that species within the same species group cluster together, and infer two main clades in accordance with population structure analysis. Distribution of streptococcal virulence factors has no obvious patterns among the species groups; however, the evolution of some common virulence factors is congruous with the evolution of species groups, according to phylogenetic inference. We suggest that the proposed streptococcal species groups are reasonable from the viewpoints of comparative genomics; evolution of the genus is congruent with the individual evolutionary trajectories of different species groups.

Comparative Genomics of the Bacterial Genus Streptococcus Illuminates Evolutionary Implications of Species Groups

PubMed Central

Gao, Xiao-Yang; Zhi, Xiao-Yang; Li, Hong-Wei; Klenk, Hans-Peter; Li, Wen-Jun

2014-01-01

Members of the genus Streptococcus within the phylum Firmicutes are among the most diverse and significant zoonotic pathogens. This genus has gone through considerable taxonomic revision due to increasing improvements of chemotaxonomic approaches, DNA hybridization and 16S rRNA gene sequencing. It is proposed to place the majority of streptococci into “species groups”. However, the evolutionary implications of species groups are not clear presently. We use comparative genomic approaches to yield a better understanding of the evolution of Streptococcus through genome dynamics, population structure, phylogenies and virulence factor distribution of species groups. Genome dynamics analyses indicate that the pan-genome size increases with the addition of newly sequenced strains, while the core genome size decreases with sequential addition at the genus level and species group level. Population structure analysis reveals two distinct lineages, one including Pyogenic, Bovis, Mutans and Salivarius groups, and the other including Mitis, Anginosus and Unknown groups. Phylogenetic dendrograms show that species within the same species group cluster together, and infer two main clades in accordance with population structure analysis. Distribution of streptococcal virulence factors has no obvious patterns among the species groups; however, the evolution of some common virulence factors is congruous with the evolution of species groups, according to phylogenetic inference. We suggest that the proposed streptococcal species groups are reasonable from the viewpoints of comparative genomics; evolution of the genus is congruent with the individual evolutionary trajectories of different species groups. PMID:24977706

Genetic, morphological, and acoustic evidence reveals lack of diversification in the colonization process in an island bird.

PubMed

Illera, Juan Carlos; Palmero, Ana M; Laiolo, Paola; Rodríguez, Felipe; Moreno, Ángel C; Navascués, Miguel

2014-08-01

Songbirds with recently (i.e., early Holocene) founded populations are suitable models for studying incipient differentiation in oceanic islands. On such systems each colonization event represents a different evolutionary episode that can be studied by addressing sets of diverging phenotypic and genetic traits. We investigate the process of early differentiation in the spectacled warbler (Sylvia conspicillata) in 14 populations separated by sea barriers from three Atlantic archipelagos and from continental regions spanning from tropical to temperate latitudes. Our approach involved the study of sexual acoustic signals, morphology, and genetic data. Mitochondrial DNA did not provide clear population structure. However, microsatellites analyses consistently identified two genetic groups, albeit without correspondence to subspecies classification and little correspondence to geography. Coalescent analyses showed significant evidence for gene flow between the two genetic groups. Discriminant analyses could not correctly assign morphological or acoustic traits to source populations. Therefore, although theory predicting that in isolated populations genetic, morphological, or acoustic traits can lead to radiation, we have strikingly failed to document differentiation on these attributes in a resident passerine throughout three oceanic archipelagos. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Genetic variation and geographic differentiation in the marine triclad Bdelloura candida (Platyhelminthes, Tricladida, Maricola), ectocommensal on the American horseshoe crab Limulus polyphemus.

PubMed

Riesgo, Ana; Burke, Emily A; Laumer, Christopher; Giribet, Gonzalo

2017-01-01

Bdelloura candida (Platyhelminthes, Tricladida, Maricola) is an ectocommensal symbiont on the American horseshoe crab Limulus polyphemus , living on the book gills and appendages, where it spends its entire life. Given its limited dispersal capabilities and its inability to live outside of the host, we hypothesized a genetic structure that parallels that of its host. We obtained 84 planarian individuals from 19 horseshoe crabs collected from 10 sites from Massachusetts to Florida. We amplified the mitochondrial 16S rRNA and the nuclear internal transcribed spacer 2 and conducted phylogeographic and population genetic analyses, which show a clear and strong genetic break between the populations in the Atlantic and the Gulf coasts. Among the Atlantic populations, two additional, weaker barriers located along Cape Hatteras and Cape Cod restrict gene flow. Even though previous studies have suggested that the populations of the host may be in decline, those of B. candida remain stable, and some even shows signatures of expansion. Our results indicate that the phylogeography of these marine ectocommensal triclads closely mirrors that of its Limulus host, and highlight the challenges to both host and symbiont to genetically connect populations across their distribution.

The genetic admixture in Tibetan-Yi Corridor.

PubMed

Yao, Hong-Bing; Tang, Senwei; Yao, Xiaotian; Yeh, Hui-Yuan; Zhang, Wanhu; Xie, Zhiyan; Du, Qiajun; Ma, Liying; Wei, Shuoyun; Gong, Xue; Zhang, Zilong; Li, Quanfang; Xu, Bingying; Zhang, Hu-Qin; Chen, Gang; Wang, Chuan-Chao

2017-11-01

The Tibetan-Yi Corridor located on the eastern edge of Tibetan Plateau is suggested to be the key region for the origin and diversification of Tibeto-Burman speaking populations and the main route of the peopling of the Plateau. However, the genetic history of the populations in the Corridor is far from clear due to limited sampling in the northern part of the Corridor. We collected blood samples from 10 Tibetan and 10 Han Chinese individuals from Gansu province and genotyped about 600,000 genome-wide single nucleotide polymorphisms (SNPs). Our data revealed that the populations in the Corridor are all admixed on a genetic cline of deriving ancestry from Tibetans on the Plateau and surrounding lowland East Asians. The Tibetan and Han Chinese groups in the north of the Plateau show significant evidence of low-level West Eurasian admixture that could be probably traced back to 600∼900 years ago. We conclude that there have been huge population migrations from surrounding lowland onto the Tibetan Plateau via the Tibetan-Yi Corridor since the initial formation of Tibetans probably in Neolithic Time, which leads to the current genetic structure of Tibeto-Burman speaking populations. © 2017 Wiley Periodicals, Inc.

The distribution and abundance of reef-associated predatory fishes on the Great Barrier Reef

NASA Astrophysics Data System (ADS)

Emslie, Michael J.; Cheal, Alistair J.; Logan, Murray

2017-09-01

Predatory fishes are important components of coral-reef ecosystems of the Great Barrier Reef (GBR) through both the ecological functions they perform and their high value to recreational and commercial fisheries, estimated at 30 million in 2014. However, management of GBR predatory fish populations is hampered by a lack of knowledge of their distribution and abundance, aside from that of the highly targeted coral trout ( Plectropomus spp. and Variola spp.). Furthermore, there is little information on how these fishes respond to environmental stressors such as coral bleaching, outbreaks of coral-feeding starfishes ( Acanthaster planci) and storms, which limits adaptive management of their populations as the frequency or severity of such natural disturbances increases under climate change. Here, we document the distribution and abundance of 48 species of reef-associated predatory fishes and assess their vulnerability to a range of natural disturbances. There were clear differences in predatory fish assemblages across the continental shelf, but many species were widespread, with few species restricted to either inshore or offshore waters. There was weak latitudinal structure with only a few species restricted to either the northern or southern GBR. On the whole, predatory fishes were surprisingly resistant to the effects of disturbance, with few clear changes in abundance or species richness following 66 documented disturbances of varying magnitudes.

NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers.

PubMed

Sekhar, Ashok; Kay, Lewis E

2013-08-06

The importance of dynamics to biomolecular function is becoming increasingly clear. A description of the structure-function relationship must, therefore, include the role of motion, requiring a shift in paradigm from focus on a single static 3D picture to one where a given biomolecule is considered in terms of an ensemble of interconverting conformers, each with potentially diverse activities. In this Perspective, we describe how recent developments in solution NMR spectroscopy facilitate atomic resolution studies of sparsely populated, transiently formed biomolecular conformations that exchange with the native state. Examples of how this methodology is applied to protein folding and misfolding, ligand binding, and molecular recognition are provided as a means of illustrating both the power of the new techniques and the significant roles that conformationally excited protein states play in biology.

Transport properties of epitaxial lift off films

NASA Technical Reports Server (NTRS)

Mena, R. A.; Schacham, S. E.; Young, P. G.; Haugland, E. J.; Alterovitz, S. A.

1993-01-01

Transport properties of epitaxially lifted-off (ELO) films were characterized using conductivity, Hall, and Shubnikov-de Haas measurements. A 10-15 percent increase in the 2D electron gas concentration was observed in these films as compared with adjacent conventional samples. We believe this result to be caused by a backgating effect produced by a charge build up at the interface of the ELO film and the quartz substrate. This increase results in a substantial decrease in the quantum lifetime in the ELO samples, by 17-30 percent, but without a degradation in carrier mobility. Under persistent photoconductivity, only one subband was populated in the conventional structure, while in the ELO films the population of the second subband was clearly visible. However, the increase of the second subband concentration with increasing excitation is substantially smaller than anticipated due to screening of the backgating effect.

Criteria for assessment of bridge aesthetic and visual quality

NASA Astrophysics Data System (ADS)

Rozentale, I.; Paeglitis, A.

2017-10-01

The bridge designers should find an ideal balance between structure, economy, buildability, aesthetics, durability and harmony with industrial or natural landscape. During the last years, the society has adopted documents providing procedures for evaluation of the impact of the structural appearance on surrounding landscape. The European Landscape Convention defines the landscape as an area perceived by people, whose character is the result of the action and interaction of natural and/or human factors. The Convention indicates the methods for clear and objective assessment of the landscape’s visual qualities. The esthetical qualities of bridge structures, appearance and attraction should satisfy not only the technicians - engineers and architects, but mostly the surrounding population. Each of these groups has a different perception of esthetical qualities of structure. Many authors have used different methods and criteria for assessment of bridge aesthetics. The aim of this paper is to provide an overview of the bridge aesthetic and visual quality assessment methods and criteria.

[POLYMORPHISM IN THE PHENOTYPIC STRUCTURE OF A POPULATION OF TAIGA TICK AND ITS EPIDEMIOLOGICAL SIGNIFICANCE].

PubMed

Morozov, I M; Alekseev, A N; Dubinina, E V; Nikitin, A Ya; Melnikova, O V; Andaev, E I

2015-01-01

The paper presents the results of 10-year (2005-2014) observations of an Ixodespersulcatus Schulze population. The purpose of this investigation was to trace long-term changes in the structure of the taiga tick population from the proportion of specimens with external skeletal anomalies and to assess a relationship between the pattern of imago phenotypic variation and the virus percentage of a carrier. There were a total of reports of the external skeletal structure of 1123 females gathered from plants to a flag in an area at 43 km from the Baikal Road connecting Irkutsk and the settlement of Listvyanka (Irkutsk Region). The proportion of specimens with anomalies averaged 37.8 +/- 1.88%. Four-to-seven varying anomalies were annually recorded. There was a preponderance of scutum impairment (an average of 17.0 +/- 3.08% of all females) that was a conglomerate of prominences and indentations along the entire clypeus surface and that was denoted P9. The nature of a change in the proportion of ticks with two anomalies (average monthly registration rate, 2.5 +/- 0.66%) is exhibited by three-year high-frequency oscillations whereas the specimens with P9 anomalies fail to show so clear cycling. The percentage of virus-containing taiga ticks was individually determined estimating the level of tick-borne encephalitis virus antigen by an enzyme immunoassay. A total of 4022 ticks were examined. The male and female data were pooled. There was a positive correlation between the change in the proportion of females with P9 anomaly and the infection of ticks in the examined population (Spearman's correlation coefficient, 0.88; P < 0.01). This supports the earlier observation of the greater epidemiological significance of the imago of a taiga tick with external skeletal anomalies particularly with considerably marked ones.

[Comparative analysis of ISSR markers polymorphism in populations of yak (Bos mutus) and in F1 hybrids between yak and cattle in the Sayan-Altai region].

PubMed

Stolpovsky, Yu A; Kol, N V; Evsyukov, A N; Nesteruk, L V; Dorzhu, Ch M; Tsendsuren, Ts; Sulimova, G E

2014-10-01

The genetic variability in seven yak populations from the Sayan-Altai region and in F1 hybrids between yak and cattle (khainags) was investigated with the help of a technique that involves the use of inter simple sequence repeat (ISSR) markers generated with PCR primers (AG)9C and (GA)9C. Samples for the analysis were collected in Mongolia, Tuva, and Altai from 2008 through 2012. The examined yak populations differed in in the presence/absence of ISSR fragments, as well as in their frequency. In total, 46 ISSR fragments were identified using two marker systems; the proportion of polymorphic loci constituted 76% and 90% for the AG-ISSR and GA-ISSR markers, respectively. For the total sample of yaks, total genetic diversity (Ht), within-population diversity (Hs), and interpopulation diversity (Gst) constituted 0.081, 0.044, and 0.459 for the AG-ISSR and 0.137, 0.057, and 0.582 for the GA-ISSR markers, respectively. Based on ISSR finger printing, species- and breed-specific DNA patterns were described for the three groups of animals (yaks, cattle, khainags). For the domestic yak, the species-specific profile was represented by eight ISSR fragments. Genetic relationships between the yak populations, cattle breeds, and khainags were examined with the help of four different approaches used in the analysis of population structure: estimation of phylogenetic similarity, multidimensional scaling, principal component analysis, and cluster analysis. Clear evidence on the differentiation of the populations examined at the interspecific, as well as at intraspecific, level were obtained. Similar (relative); as well as remote (isolated), yak populations were identified. Khainags occupy an intermediate position between yak and cattle. However, the data on the ISSR-PCR marker polymorphism (genome polymorphism, population structure).indicate that part of the analyzed khainag genome was more similar to the yak genome than to the cattle genome.

Epidemic Process over the Commute Network in a Metropolitan Area

PubMed Central

Yashima, Kenta; Sasaki, Akira

2014-01-01

An understanding of epidemiological dynamics is important for prevention and control of epidemic outbreaks. However, previous studies tend to focus only on specific areas, indicating that application to another area or intervention strategy requires a similar time-consuming simulation. Here, we study the epidemic dynamics of the disease-spread over a commute network, using the Tokyo metropolitan area as an example, in an attempt to elucidate the general properties of epidemic spread over a commute network that could be used for a prediction in any metropolitan area. The model is formulated on the basis of a metapopulation network in which local populations are interconnected by actual commuter flows in the Tokyo metropolitan area and the spread of infection is simulated by an individual-based model. We find that the probability of a global epidemic as well as the final epidemic sizes in both global and local populations, the timing of the epidemic peak, and the time at which the epidemic reaches a local population are mainly determined by the joint distribution of the local population sizes connected by the commuter flows, but are insensitive to geographical or topological structure of the network. Moreover, there is a strong relation between the population size and the time that the epidemic reaches this local population and we are able to determine the reason for this relation as well as its dependence on the commute network structure and epidemic parameters. This study shows that the model based on the connection between the population size classes is sufficient to predict both global and local epidemic dynamics in metropolitan area. Moreover, the clear relation of the time taken by the epidemic to reach each local population can be used as a novel measure for intervention; this enables efficient intervention strategies in each local population prior to the actual arrival. PMID:24905831

Clinal variation at microsatellite loci reveals historical secondary intergradation between glacial races of Coregonus artedi (Teleostei: Coregoninae).

PubMed

Turgeon, J; Bernatchez, L

2001-11-11

Classical models of the spatial structure of population genetics rely on the assumption of migration-drift equilibrium, which is seldom met in natural populations having only recently colonized their current range (e.g., postglacial). Population structure then depicts historical events, and counfounding effects due to recent secondary contact between recently differentiated lineages can further counfound analyses of association between geographic and genetic distances. Mitochondrial polymorphisms have revealed the existence of two closely related lineages of the lake cisco, Coregonus artedi, whose significantly different but overlaping geographical distributions provided a weak signal of past range fragmentation blurred by putative subsequent extensive secondary contacts. In this study, we analyzed geographical patterns of genetic variation at seven microsatellite loci among 22 populations of lake cisco located along the axis of an area covered by proglacial lakes 12,000-8,000 years ago in North America. The results clearly confirmed the existence of two genetically distinct races characterized by different sets of microsatellite alleles whose frequencies varied clinally across some 3000 km. Equilibrium and nonequilibrium analyses of isolation by distance revealed historical signal of gene flow resulting from the nearly complete admixture of these races following neutral secondary contacts in their historical habitat and indicated that the colonization process occurred by a stepwise expansion of an eastern (Atlantic) race into a previously established Mississippian race. This historical signal of equilibrium contrasted with the current migration-drift disequilibrium within major extant watersheds and was apparently maintained by high effective population sizes and low migration regimes.

Welcome mats? The role of seagrass meadow structure in controlling post-settlement survival in a keystone sea-urchin species

NASA Astrophysics Data System (ADS)

Prado, Patricia; Romero, Javier; Alcoverro, Teresa

2009-11-01

Processes acting on the early-life histories of marine organisms can have important consequences for the structuring of benthic communities. In particular, the degree of coupling between larval supply and adult abundances can wield considerable influence on the strength of trophic interactions in the ecosystem. These processes have been relatively well described in rocky systems and soft-sediment communities, and it is clear that they are governed by very different bottlenecks. Seagrass meadows make interesting study systems because they bear structural affinities to both soft sediments as well as rocky substrates. We examined the early-life history of Paracentrotus lividus, one of the dominant herbivores in Mediterranean seagrass meadows, to identify the drivers of population dynamics in this species. We measured spatial and temporal variability in sea urchin post-settlement in 10 Posidonia oceanica meadows in the North-Western Mediterranean over a period of two years, and compared the numbers with the one-year old cohort a year later (i.e. the new population recruitment) as well as between successive size-age groups. Urchin post-settlers differed substantially between meadows but were present in both years in all meadows surveyed, suggesting that larval supply was not limiting for any of the studied sites. However, in six of the studied meadows, the one-year cohort of urchins was absent in both years, indicating that post-settlement processes strongly affected urchins in these meadows. In contrast, in four of the studied meadows, there was a strong coupling between post-settlers and one-year cohort individuals. These meadows were structurally different from the others in that they were characterised by an exposed matrix of rhizomes forming a dense seagrass mat. This mat apparently strongly mediates post-settlement mortality, and its presence or absence dictates the successful establishment of urchin populations in seagrass meadows. As the population aged, the relationship between size-age groups decreased evidencing the action of other processes. Yet, these results indicate that differences in physical structure are a vital bottleneck for sea urchin populations in seagrass meadows. Exploring the interaction between ecosystem structure and early-life history may provide a broader and more unified framework to understand the dynamics of a range of benthic habitats, including rocky substrates, soft sediments and seagrass meadows.

Multilocus Phylogeography of the Treefrog Scinax eurydice (Anura, Hylidae) Reveals a Plio-Pleistocene Diversification in the Atlantic Forest

PubMed Central

Menezes, Lucas; Canedo, Clarissa; Batalha-Filho, Henrique; Garda, Adrian Antonio; Gehara, Marcelo; Napoli, Marcelo Felgueiras

2016-01-01

We aim to evaluate the genetic structure of an Atlantic Forest amphibian species, Scinax eurydice, testing the congruence among patterns identified and proposed by the literature for Pleistocene refugia, microrefugia, and geographic barriers to gene flow such as major rivers. Furthermore, we aim to evaluate predictions of such barriers and refugia on the genetic structure of the species, such as presence/absence of dispersal, timing since separation, and population expansions/contractions. We sequenced mitochondrial and nuclear genetic markers on 94 tissue samples from 41 localities. We inferred a gene tree and estimated genetic distances using mtDNA sequences. We then ran population clustering and assignment methods, AMOVA, and estimated migration rates among populations identified through mtDNA and nDNA analyses. We used a dated species tree, skyline plots, and summary statistics to evaluate concordance between population’s distributions and geographic barriers and Pleistocene refugia. Scinax eurydice showed high mtDNA divergences and four clearly distinct mtDNA lineages. Species tree and population assignment tests supported the existence of two major clades corresponding to northeastern and southeastern Atlantic Forest in Brazil, each one composed of two other clades. Lineage splitting events occurred from late Pliocene to Pleistocene. We identified demographic expansions in two clades, and inexistent to low levels of migrations among different populations. Genetic patterns and demographic data support the existence of two northern Refuge and corroborate microrefugia south of the Doce/Jequitinhonha Rivers biogeographic divide. The results agree with a scenario of recent demographic expansion of lowland taxa. Scinax eurydice comprises a species complex, harboring undescribed taxa consistent with Pleistocene refugia. Two rivers lie at the boundaries among populations and endorse their role as secondary barriers to gene flow. PMID:27248688

No Evidence of Chemical Abundance Variations in the Intermediate-age Cluster NGC 1783

NASA Astrophysics Data System (ADS)

Zhang, Hao; de Grijs, Richard; Li, Chengyuan; Wu, Xiaohan

2018-02-01

We have analyzed multi-passband photometric observations, obtained with the Hubble Space Telescope, of the massive (1.8 × 105 M ⊙), intermediate-age (1.8 Gyr-old) Large Magellanic Cloud star cluster NGC 1783. The morphology of the cluster’s red giant branch does not exhibit a clear broadening beyond its intrinsic width; the observed width is consistent with that owing to photometric uncertainties alone and independent of the photometric selection boundaries we applied to obtain our sample of red giant stars. The color dispersion of the cluster’s red giant stars around the best-fitting ridgeline is 0.062 ± 0.009 mag, which is equivalent to the width of 0.080 ± 0.001 mag derived from artificial simple stellar population tests, that is, tests based on single-age, single-metallicity stellar populations. NGC 1783 is comparably as massive as other star clusters that show clear evidence of multiple stellar populations. After incorporating mass-loss recipes from its current age of 1.8 Gyr to an age of 6 Gyr, NGC 1783 is expected to remain as massive as some other clusters that host clear multiple populations at these intermediate ages. If we were to assume that mass is an important driver of multiple population formation, then NGC 1783 should have exhibited clear evidence of chemical abundance variations. However, our results support the absence of any chemical abundance variations in NGC 1783.

Are Isolated Indigenous Populations Headed toward Extinction?

PubMed

Walker, Robert S; Kesler, Dylan C; Hill, Kim R

2016-01-01

At least 50 indigenous groups spread across lowland South America remain isolated and have only intermittent and mostly hostile interactions with the outside world. Except in emergency situations, the current policy of governments in Brazil, Colombia, and Peru towards isolated tribes is a "leave them alone" strategy, in which isolated groups are left uncontacted. However, these no-contact policies are based on the assumption that isolated populations are healthy and capable of persisting in the face of mounting external threats, and that they can maintain population viability in the long-term. Here, we test this assumption by tracking the sizes and movements of cleared horticultural areas made by 8 isolated groups over the last 10-14 years. We used deforestation data derived from remote sensing Landsat satellite sensors to identify clearings, and those were then validated and assessed with high-resolution imagery. We found only a single example of a relatively large and growing population (c. 50 cleared ha and 400 people), whereas all of the other 7 groups exhibited much smaller villages and gardens with no sizable growth through time. These results indicated that the smaller groups are critically endangered, and it prompts an urgent re-thinking of policies toward isolated populations, including plans for well-organized contacts that may help save lives and rescue isolated indigenous populations from imminent extinction.

Glacial Refugia in Pathogens: European Genetic Structure of Anther Smut Pathogens on Silene latifolia and Silene dioica

PubMed Central

Vercken, Elodie; Fontaine, Michael C.; Gladieux, Pierre; Hood, Michael E.; Jonot, Odile; Giraud, Tatiana

2010-01-01

Climate warming is predicted to increase the frequency of invasions by pathogens and to cause the large-scale redistribution of native host species, with dramatic consequences on the health of domesticated and wild populations of plants and animals. The study of historic range shifts in response to climate change, such as during interglacial cycles, can help in the prediction of the routes and dynamics of infectious diseases during the impending ecosystem changes. Here we studied the population structure in Europe of two Microbotryum species causing anther smut disease on the plants Silene latifolia and Silene dioica. Clustering analyses revealed the existence of genetically distinct groups for the pathogen on S. latifolia, providing a clear-cut example of European phylogeography reflecting recolonization from southern refugia after glaciation. The pathogen genetic structure was congruent with the genetic structure of its host species S. latifolia, suggesting dependence of the migration pathway of the anther smut fungus on its host. The fungus, however, appeared to have persisted in more numerous and smaller refugia than its host and to have experienced fewer events of large-scale dispersal. The anther smut pathogen on S. dioica also showed a strong phylogeographic structure that might be related to more northern glacial refugia. Differences in host ecology probably played a role in these differences in the pathogen population structure. Very high selfing rates were inferred in both fungal species, explaining the low levels of admixture between the genetic clusters. The systems studied here indicate that migration patterns caused by climate change can be expected to include pathogen invasions that follow the redistribution of their host species at continental scales, but also that the recolonization by pathogens is not simply a mirror of their hosts, even for obligate biotrophs, and that the ecology of hosts and pathogen mating systems likely affects recolonization patterns. PMID:21187901

Genetic structure of the date palm (Phoenix dactylifera) in the Old World reveals a strong differentiation between eastern and western populations

PubMed Central

Zehdi-Azouzi, Salwa; Cherif, Emira; Moussouni, Souhila; Gros-Balthazard, Muriel; Abbas Naqvi, Summar; Ludeña, Bertha; Castillo, Karina; Chabrillange, Nathalie; Bouguedoura, Nadia; Bennaceur, Malika; Si-Dehbi, Farida; Abdoulkader, Sabira; Daher, Abdourahman; Terral, Jean-Frederic; Santoni, Sylvain; Ballardini, Marco; Mercuri, Antonio; Ben Salah, Mohamed; Kadri, Karim; Othmani, Ahmed; Littardi, Claudio; Salhi-Hannachi, Amel; Pintaud, Jean-Christophe; Aberlenc-Bertossi, Frédérique

2015-01-01

Background and Aims Date palms (Phoenix dactylifera, Arecaceae) are of great economic and ecological value to the oasis agriculture of arid and semi-arid areas. However, despite the availability of a large date palm germplasm spreading from the Atlantic shores to Southern Asia, improvement of the species is being hampered by a lack of information on global genetic diversity and population structure. In order to contribute to the varietal improvement of date palms and to provide new insights on the influence of geographic origins and human activity on the genetic structure of the date palm, this study analysed the diversity of the species. Methods Genetic diversity levels and population genetic structure were investigated through the genotyping of a collection of 295 date palm accessions ranging from Mauritania to Pakistan using a set of 18 simple sequence repeat (SSR) markers and a plastid minisatellite. Key Results Using a Bayesian clustering approach, the date palm genotypes can be structured into two different gene pools: the first, termed the Eastern pool, consists of accessions from Asia and Djibouti, whilst the second, termed the Western pool, consists of accessions from Africa. These results confirm the existence of two ancient gene pools that have contributed to the current date palm diversity. The presence of admixed genotypes is also noted, which points at gene flows between eastern and western origins, mostly from east to west, following a human-mediated diffusion of the species. Conclusions This study assesses the distribution and level of genetic diversity of accessible date palm resources, provides new insights on the geographic origins and genetic history of the cultivated component of this species, and confirms the existence of at least two domestication origins. Furthermore, the strong genetic structure clearly established here is a prerequisite for any breeding programme exploiting the effective polymorphism related to each gene pool. PMID:26113618

Population Structure, Diversity and Trait Association Analysis in Rice (Oryza sativa L.) Germplasm for Early Seedling Vigor (ESV) Using Trait Linked SSR Markers

PubMed Central

Anandan, Annamalai; Anumalla, Mahender; Pradhan, Sharat Kumar; Ali, Jauhar

2016-01-01

Early seedling vigor (ESV) is the essential trait for direct seeded rice to dominate and smother the weed growth. In this regard, 629 rice genotypes were studied for their morphological and physiological responses in the field under direct seeded aerobic situation on 14th, 28th and 56th days after sowing (DAS). It was determined that the early observations taken on 14th and 28th DAS were reliable estimators to study ESV as compared to56th DAS. Further, 96 were selected from 629 genotypes by principal component (PCA) and discriminate function analyses. The selected genotypes were subjected to decipher the pattern of genetic diversity in terms of both phenotypic and genotypic by using ESV QTL linked simple sequence repeat (SSR) markers. To assess the genetic structure, model and distance based approaches were used. Genotyping of 96 rice lines using 39 polymorphic SSRs produced a total of 128 alleles with the phenotypic information content (PIC) value of 0.24. The model based population structure approach grouped the accession into two distinct populations, whereas unrooted tree grouped the genotypes into three clusters. Both model based and structure based approach had clearly distinguished the early vigor genotypes from non-early vigor genotypes. Association analysis revealed that 16 and 10 SSRs showed significant association with ESV traits by general linear model (GLM) and mixed linear model (MLM) approaches respectively. Marker alleles on chromosome 2 were associated with shoot dry weight on 28 DAS, vigor index on 14 and 28 DAS. Improvement in the rate of seedling growth will be useful for identifying rice genotypes acquiescent to direct seeded conditions through marker-assisted selection. PMID:27031620

Fishing degrades size structure of coral reef fish communities.

PubMed

Robinson, James P W; Williams, Ivor D; Edwards, Andrew M; McPherson, Jana; Yeager, Lauren; Vigliola, Laurent; Brainard, Russell E; Baum, Julia K

2017-03-01

Fishing pressure on coral reef ecosystems has been frequently linked to reductions of large fishes and reef fish biomass. Associated impacts on overall community structure are, however, less clear. In size-structured aquatic ecosystems, fishing impacts are commonly quantified using size spectra, which describe the distribution of individual body sizes within a community. We examined the size spectra and biomass of coral reef fish communities at 38 US-affiliated Pacific islands that ranged in human presence from near pristine to human population centers. Size spectra 'steepened' steadily with increasing human population and proximity to market due to a reduction in the relative biomass of large fishes and an increase in the dominance of small fishes. Reef fish biomass was substantially lower on inhabited islands than uninhabited ones, even at inhabited islands with the lowest levels of human presence. We found that on populated islands size spectra exponents decreased (analogous to size spectra steepening) linearly with declining biomass, whereas on uninhabited islands there was no relationship. Size spectra were steeper in regions of low sea surface temperature but were insensitive to variation in other environmental and geomorphic covariates. In contrast, reef fish biomass was highly sensitive to oceanographic conditions, being influenced by both oceanic productivity and sea surface temperature. Our results suggest that community size structure may be a more robust indicator than fish biomass to increasing human presence and that size spectra are reliable indicators of exploitation impacts across regions of different fish community compositions, environmental drivers, and fisheries types. Size-based approaches that link directly to functional properties of fish communities, and are relatively insensitive to abiotic variation across biogeographic regions, offer great potential for developing our understanding of fishing impacts in coral reef ecosystems. © 2016 John Wiley & Sons Ltd.

Direct folding simulation of helical proteins using an effective polarizable bond force field.

PubMed

Duan, Lili; Zhu, Tong; Ji, Changge; Zhang, Qinggang; Zhang, John Z H

2017-06-14

We report a direct folding study of seven helical proteins (, Trpcage, , C34, N36, , ) ranging from 17 to 53 amino acids through standard molecular dynamics simulations using a recently developed polarizable force field-Effective Polarizable Bond (EPB) method. The backbone RMSDs, radius of gyrations, native contacts and native helix content are in good agreement with the experimental results. Cluster analysis has also verified that these folded structures with the highest population are in good agreement with their corresponding native structures for these proteins. In addition, the free energy landscape of seven proteins in the two dimensional space comprised of RMSD and radius of gyration proved that these folded structures are indeed of the lowest energy conformations. However, when the corresponding simulations were performed using the standard (nonpolarizable) AMBER force fields, no stable folded structures were observed for these proteins. Comparison of the simulation results based on a polarizable EPB force field and a nonpolarizable AMBER force field clearly demonstrates the importance of polarization in the folding of stable helical structures.

Human impact on genetic diversity of Toxoplasma gondii: example of the anthropized environment from French Guiana.

PubMed

Mercier, A; Ajzenberg, D; Devillard, S; Demar, M P; de Thoisy, B; Bonnabau, H; Collinet, F; Boukhari, R; Blanchet, D; Simon, S; Carme, B; Dardé, M-L

2011-08-01

In French Guiana, severe cases of toxoplasmosis in immunocompetent patients are associated with atypical strains of Toxoplasma gondii linked to a wild neotropical rainforest cycle and a higher genetic diversity than usually observed for T. gondii isolates from anthropized environment. This raises the question of the impact of anthropization of the natural environment, on genetic diversity and on the population structure of T. gondii. However, few data are available on strains circulating in the anthropized areas from French Guiana. Seropositive animals originating mainly from anthropized sub-urban areas and punctually from wild environment in French Guiana were analyzed for T. gondii isolation and genotyping. Thirty-three strains were obtained by bioassay in mice and compared with 18 previously reported isolates chiefly originating from the Amazon rainforest. The genotyping analysis performed with 15 microsatellite markers located on 12 different chromosomes revealed a lower genetic diversity in the anthropized environment. Results were analyzed in terms of population structure by clustering methods, Neighbor-joining trees reconstruction based on genetic distances, F(ST,) Mantel's tests and linkage disequilibrium. They clearly showed a genetic differentiation between strains associated to the anthropized environment and those associated to the wild, but with some inbreeding between them. The majority of strains from the anthropized environment were clustered into additional lineages of T. gondii that are common in the Caribbean. In conclusion the two environmental populations "wild" and "anthropized" were genetically well differentiated. The anthropization of the environment seems to be accompanied with a decreased diversity of T. gondii associated with a greater structure of the populations. We detected potential interpenetration and genetic exchanges between these two environmental populations. As a higher pathogenicity in human of "wild" genotypes has been described, the interpenetration of both environments leads to hybridization between strains that may be at risk for human health. Copyright © 2011 Elsevier B.V. All rights reserved.

Predator cannibalism can intensify negative impacts on heterospecific prey.

PubMed

Takatsu, Kunio; Kishida, Osamu

2015-07-01

Although natural populations consist of individuals with different traits, and the degree of phenotypic variation varies among populations, the impact of phenotypic variation on ecological interactions has received little attention, because traditional approaches to community ecology assume homogeneity of individuals within a population. Stage structure, which is a common way of generating size and developmental variation within predator populations, can drive cannibalistic interactions, which can affect the strength of predatory effects on the predator's heterospecific prey. Studies have shown that predator cannibalism weakens predatory effects on heterospecific prey by reducing the size of the predator population and by inducing less feeding activity of noncannibal predators. We predict, however, that predator cannibalism, by promoting rapid growth of the cannibals, can also intensify predation pressure on heterospecific prey, because large predators have large resource requirements and may utilize a wider variety of prey species. To test this hypothesis, we conducted an experiment in which we created carnivorous salamander (Hynobius retardatus) populations with different stage structures by manipulating the salamander's hatch timing (i.e., populations with large or small variation in the timing of hatching), and explored the resultant impacts on the abundance, behavior, morphology, and life history of the salamander's large heterospecific prey, Rana pirica frog tadpoles. Cannibalism was rare in salamander populations having small hatch-timing variation, but was frequent in those having large hatch-timing variation. Thus, giant salamander cannibals occurred only in the latter. We clearly showed that salamander giants exerted strong predation pressure on frog tadpoles, which induced large behavioral and morphological defenses in the tadpoles and caused them to metamorphose late at large size. Hence, predator cannibalism arising from large variation in the timing of hatching can strengthen predatory effects on heterospecific prey and can have impacts on various, traits of both predator and prey. Because animals commonly broaden their diet as they grow, such negative impacts of predator cannibalism on the heterospecific prey may be common in interactions between predators and prey species of similar size.

Re-colonization by common eiders Somateria mollissima in the Aleutian Archipelago following removal of introduced arctic foxes Vulpes lagopus

USGS Publications Warehouse

Petersen, Margaret R.; Sonsthagen, Sarah A.; Sexson, Matthew G.

2015-01-01

Islands provide refuges for populations of many species where they find safety from predators, but the introduction of predators frequently results in elimination or dramatic reductions in island-dwelling organisms. When predators are removed, re-colonization for some species occurs naturally, and inter-island phylogeographic relationships and current movement patterns can illuminate processes of colonization. We studied a case of re-colonization of common eiders Somateria mollissima following removal of introduced arctic foxes Vulpes lagopus in the Aleutian Archipelago, Alaska. We expected common eiders to resume nesting on islands cleared of foxes and to re-colonize from nearby islets, islands, and island groups. We thus expected common eiders to show limited genetic structure indicative of extensive mixing among island populations. Satellite telemetry was used to record current movement patterns of female common eiders from six islands across three island groups. We collected genetic data from these and other nesting common eiders at 14 microsatellite loci and the mitochondrial DNA control region to examine population genetic structure, historical fluctuations in population demography, and gene flow. Our results suggest recent interchange among islands. Analysis of microsatellite data supports satellite telemetry data of increased dispersal of common eiders to nearby areas and little between island groups. Although evidence from mtDNA is suggestive of female dispersal among island groups, gene flow is insufficient to account for recolonization and rapid population growth. Instead, near-by remnant populations of common eiders contributed substantially to population expansion, without which re-colonization would have likely occurred at a much lower rate. Genetic and morphometric data of common eiders within one island group two and three decades after re-colonization suggests reduced movement of eiders among islands and little movement between island groups after populations were re-established. We predict that re-colonization of an island group where all common eiders are extirpated could take decades.

High migration rates shape the postglacial history of amphi-Atlantic bryophytes.

PubMed

Désamoré, Aurélie; Patiño, Jairo; Mardulyn, Patrick; Mcdaniel, Stuart F; Zanatta, Florian; Laenen, Benjamin; Vanderpoorten, Alain

2016-11-01

Paleontological evidence and current patterns of angiosperm species richness suggest that European biota experienced more severe bottlenecks than North American ones during the last glacial maximum. How well this pattern fits other plant species is less clear. Bryophytes offer a unique opportunity to contrast the impact of the last glacial maximum in North America and Europe because about 60% of the European bryoflora is shared with North America. Here, we use population genetic analyses based on approximate Bayesian computation on eight amphi-Atlantic species to test the hypothesis that North American populations were less impacted by the last glacial maximum, exhibiting higher levels of genetic diversity than European ones and ultimately serving as a refugium for the postglacial recolonization of Europe. In contrast with this hypothesis, the best-fit demographic model involved similar patterns of population size contractions, comparable levels of genetic diversity and balanced migration rates between European and North American populations. Our results thus suggest that bryophytes have experienced comparable demographic glacial histories on both sides of the Atlantic. Although a weak, but significant genetic structure was systematically recovered between European and North American populations, evidence for migration from and towards both continents suggests that amphi-Atlantic bryophyte population may function as a metapopulation network. Reconstructing the biogeographic history of either North American or European bryophyte populations therefore requires a large, trans-Atlantic geographic framework. © 2016 John Wiley & Sons Ltd.

Nuclear and mitochondrial DNA reveals isolation of imperilled grey nurse shark populations (Carcharias taurus).

PubMed

Ahonen, H; Harcourt, R G; Stow, A J

2009-11-01

Loss of sharks and other upper-trophic marine predators has sparked worldwide concern for the stability of ocean ecosystems. The grey nurse (ragged-tooth or sand tiger) shark (Carcharias taurus) is Vulnerable on a global scale, Critically Endangered in Australia and presumed extinct in parts of its historical range. We used 193 muscle and fin samples collected from six extant populations to assess global mtDNA and microsatellite diversity and the degree of global population genetic structure. Control region mtDNA diversity was low in every population, and two populations (eastern Australia and Japan) contained only a single mtDNA haplotype. Genetic signatures of recent losses of genetic variation were not yet apparent at microsatellite loci, indicating that this low mtDNA variation is not a result of anthropogenic population declines. Population differentiation was substantial between each population pair except Brazil and South Africa, F(ST) values ranged from 0.050 to 0.699 and 0.100 to 1.00 for microsatellite and mitochondrial data respectively. Bayesian analysis clearly partitioned individuals into five of the populations from which they were sampled. Our data imply a low frequency of immigrant exchange among each of these regions and we suggest that each be recognized as a distinct evolutionary significant unit. In contrast to pelagic species such as whale shark and white shark that may cross ocean basins and where cooperative international efforts are necessary for conservation, grey nurse shark, like many coastal species, need to be managed regionally.

Maternal beliefs and parenting practices regarding their preschool child's TV viewing: An exploration in a sample of low-income Mexican-origin mothers

PubMed Central

Thompson, Darcy A.; Polk, Sarah; Cheah, Charissa S.L.; Vandewater, Elizabeth A.; Johnson, Susan L.; Chrismer, Marilyn Camacho; Tschann, Jeanne M.

2014-01-01

Objective To explore maternal beliefs about TV viewing and related parenting practices in low-income Mexican-origin mothers of preschoolers. Methods Semi-structured interviews were conducted with 21 low-income Mexican-origin mothers of preschoolers. Interviews were audio recorded and analyzed using a theoretically based thematic analytic approach. Results Mothers described strong beliefs about the positive and negative impact of television content. Mothers emphasized the educational value of specific programming. Content restrictions were common. Time restrictions were not clearly defined; however, many mothers preferred short versus long episodes of viewing. Mothers spoke positively about family viewing and the role of TV viewing in enabling mothers to accomplish household tasks. Discussion These findings have implications for intervening in this population. Interventionists should consider the value mothers place on the educational role of TV viewing, the direct benefit to mothers of viewing time, the lack of clear time limits, and the common practice of family co-viewing. PMID:25724994

[Reflections about the efficiency criteria for cancer treatments during marketing authorization application].

PubMed

Jeannin, Noémie; Blois-Da Conceição, Stéphanie; Protière, Christel

2013-03-01

Although clear and validated recommendations exist concerning the evaluation of cancer treatments at the international level, the criteria retained to obtain the marketing authorization (MA) are multiple and heterogeneous. This qualitative survey explores the opinion related to the assessment of cancer treatment among the several concerned population. By the way of semi-structured interviews, our aim was to elicit perceptions toward the criteria which should be retained during the process of MA, by patients, oncologists, members of the pharmaceutical industry, health decision-makers and general population. Our survey emphasizes the variability of the significations associated with the criteria of efficiency of cancer treatments according to the characteristics of the respondents. We also have observed some common expectations from patients and oncologists toward the economic and political aspect, but also from the whole respondents toward the importance of the comfort of the patients. Lastly, the necessity to define specific criteria related to clinical cases emerges.

Computer re-sampling for demographically representative user populations in anthropometry: a case of doorway and clear floor space widths.

PubMed

Paquet, Victor; Joseph, Caroline; D'Souza, Clive

2012-01-01

Anthropometric studies typically require a large number of individuals that are selected in a manner so that demographic characteristics that impact body size and function are proportionally representative of a user population. This sampling approach does not allow for an efficient characterization of the distribution of body sizes and functions of sub-groups within a population and the demographic characteristics of user populations can often change with time, limiting the application of the anthropometric data in design. The objective of this study is to demonstrate how demographically representative user populations can be developed from samples that are not proportionally representative in order to improve the application of anthropometric data in design. An engineering anthropometry problem of door width and clear floor space width is used to illustrate the value of the approach.

Ranking landscape development scenarios affecting natterjack toad (Bufo calamita) population dynamics in Central Poland.

PubMed

Franz, Kamila W; Romanowski, Jerzy; Johst, Karin; Grimm, Volker

2013-01-01

When data are limited it is difficult for conservation managers to assess alternative management scenarios and make decisions. The natterjack toad (Bufo calamita) is declining at the edges of its distribution range in Europe and little is known about its current distribution and abundance in Poland. Although different landscape management plans for central Poland exist, it is unclear to what extent they impact this species. Based on these plans, we investigated how four alternative landscape development scenarios would affect the total carrying capacity and population dynamics of the natterjack toad. To facilitate decision-making, we first ranked the scenarios according to their total carrying capacity. We used the software RAMAS GIS to determine the size and location of habitat patches in the landscape. The estimated carrying capacities were very similar for each scenario, and clear ranking was not possible. Only the reforestation scenario showed a marked loss in carrying capacity. We therefore simulated metapopulation dynamics with RAMAS taking into account dynamical processes such as reproduction and dispersal and ranked the scenarios according to the resulting species abundance. In this case, we could clearly rank the development scenarios. We identified road mortality of adults as a key process governing the dynamics and separating the different scenarios. The renaturalisation scenario clearly ranked highest due to its decreased road mortality. Taken together our results suggest that road infrastructure development might be much more important for natterjack toad conservation than changes in the amount of habitat in the semi-natural river valley. We gained these insights by considering both the resulting metapopulation structure and dynamics in the form of a PVA. We conclude that the consideration of dynamic processes in amphibian conservation management may be indispensable for ranking management scenarios.

Benchmarking novel approaches for modelling species range dynamics

PubMed Central

Zurell, Damaris; Thuiller, Wilfried; Pagel, Jörn; Cabral, Juliano S; Münkemüller, Tamara; Gravel, Dominique; Dullinger, Stefan; Normand, Signe; Schiffers, Katja H.; Moore, Kara A.; Zimmermann, Niklaus E.

2016-01-01

Increasing biodiversity loss due to climate change is one of the most vital challenges of the 21st century. To anticipate and mitigate biodiversity loss, models are needed that reliably project species’ range dynamics and extinction risks. Recently, several new approaches to model range dynamics have been developed to supplement correlative species distribution models (SDMs), but applications clearly lag behind model development. Indeed, no comparative analysis has been performed to evaluate their performance. Here, we build on process-based, simulated data for benchmarking five range (dynamic) models of varying complexity including classical SDMs, SDMs coupled with simple dispersal or more complex population dynamic models (SDM hybrids), and a hierarchical Bayesian process-based dynamic range model (DRM). We specifically test the effects of demographic and community processes on model predictive performance. Under current climate, DRMs performed best, although only marginally. Under climate change, predictive performance varied considerably, with no clear winners. Yet, all range dynamic models improved predictions under climate change substantially compared to purely correlative SDMs, and the population dynamic models also predicted reasonable extinction risks for most scenarios. When benchmarking data were simulated with more complex demographic and community processes, simple SDM hybrids including only dispersal often proved most reliable. Finally, we found that structural decisions during model building can have great impact on model accuracy, but prior system knowledge on important processes can reduce these uncertainties considerably. Our results reassure the clear merit in using dynamic approaches for modelling species’ response to climate change but also emphasise several needs for further model and data improvement. We propose and discuss perspectives for improving range projections through combination of multiple models and for making these approaches operational for large numbers of species. PMID:26872305

Benchmarking novel approaches for modelling species range dynamics.

PubMed

Zurell, Damaris; Thuiller, Wilfried; Pagel, Jörn; Cabral, Juliano S; Münkemüller, Tamara; Gravel, Dominique; Dullinger, Stefan; Normand, Signe; Schiffers, Katja H; Moore, Kara A; Zimmermann, Niklaus E

2016-08-01

Increasing biodiversity loss due to climate change is one of the most vital challenges of the 21st century. To anticipate and mitigate biodiversity loss, models are needed that reliably project species' range dynamics and extinction risks. Recently, several new approaches to model range dynamics have been developed to supplement correlative species distribution models (SDMs), but applications clearly lag behind model development. Indeed, no comparative analysis has been performed to evaluate their performance. Here, we build on process-based, simulated data for benchmarking five range (dynamic) models of varying complexity including classical SDMs, SDMs coupled with simple dispersal or more complex population dynamic models (SDM hybrids), and a hierarchical Bayesian process-based dynamic range model (DRM). We specifically test the effects of demographic and community processes on model predictive performance. Under current climate, DRMs performed best, although only marginally. Under climate change, predictive performance varied considerably, with no clear winners. Yet, all range dynamic models improved predictions under climate change substantially compared to purely correlative SDMs, and the population dynamic models also predicted reasonable extinction risks for most scenarios. When benchmarking data were simulated with more complex demographic and community processes, simple SDM hybrids including only dispersal often proved most reliable. Finally, we found that structural decisions during model building can have great impact on model accuracy, but prior system knowledge on important processes can reduce these uncertainties considerably. Our results reassure the clear merit in using dynamic approaches for modelling species' response to climate change but also emphasize several needs for further model and data improvement. We propose and discuss perspectives for improving range projections through combination of multiple models and for making these approaches operational for large numbers of species. © 2016 John Wiley & Sons Ltd.

Cancer stem-like cells of ovarian clear cell carcinoma are enriched in the ALDH-high population associated with an accelerated scavenging system in reactive oxygen species.

PubMed

Mizuno, T; Suzuki, N; Makino, H; Furui, T; Morii, E; Aoki, H; Kunisada, T; Yano, M; Kuji, S; Hirashima, Y; Arakawa, A; Nishio, S; Ushijima, K; Ito, K; Itani, Y; Morishige, K

2015-05-01

In ovarian cancer cases, recurrence after chemotherapy is frequently observed, suggesting the involvement of ovarian cancer stem-like cells (CSCs). The chemoresistance of ovarian clear cell carcinomas is particularly strong in comparison to other epithelial ovarian cancer subtypes. We investigated the relationship between a CSC marker, aldehyde dehydrogenase 1 (ALDH1), and clinical prognosis using ovarian clear cell carcinoma tissue samples. Furthermore, we investigated the antioxidant mechanism by which CSCs maintain a lower reactive oxygen species (ROS) level, which provides protection from chemotherapeutic agents. Immunohistochemical staining was performed to examine the CSC markers (CD133, CD44, ALDH1) using ovarian clear cell carcinoma tissue samples (n=81). Clear cell carcinoma cell lines (KOC-7C, OVTOKO) are separated into the ALDH-high and ALDH-low populations by ALDEFLUOR assay and fluorescence-activated cell sorting (FACS). We compared the intracellular ROS level, mRNA level of the antioxidant enzymes and Nrf2 expression of the two populations. High ALDH1 expression levels are related to advanced stage in clear cell carcinoma cases. ALDH1 expression significantly reduced progression free survival. Other markers are not related to clinical stage and prognosis. ALDH-high cells contained a lower ROS level than ALDH-low cells. Antioxidant enzymes were upregulated in ALDH-high cells. ALDH-high cells showed increased expression of Nrf2, a key transcriptional factor of the antioxidant system. ALDH-positive CSCs might have increased Nrf2-induced antioxidant scavengers, which lower ROS level relevant to chemoresistance in ovarian clear cell carcinoma. Copyright © 2014 Elsevier Inc. All rights reserved.

Autosomal and X chromosome Alu insertions in Bolivian Aymaras and Quechuas: two languages and one genetic pool.

PubMed

Gayà-Vidal, Magdalena; Dugoujon, Jean-Michel; Esteban, Esther; Athanasiadis, Georgios; Rodríguez, Armando; Villena, Mercedes; Vasquez, René; Moral, Pedro

2010-01-01

Thirty-two polymorphic Alu insertions (18 autosomal and 14 from the X chromosome) were studied in 192 individuals from two Amerindian populations of the Bolivian Altiplano (Aymara and Quechua speakers: the two main Andean linguistic groups), to provide relevant information about their genetic relationships and demographic processes. The main objective was to determine from genetic data whether the expansion of the Quechua language into Bolivia could be associated with demographic (Inca migration of Quechua-speakers from Peru into Bolivia) or cultural (language imposition by the Inca Empire) processes. Allele frequencies were used to assess the genetic relationships between these two linguistic groups. Our results indicated that the two Bolivian samples showed a high genetic similarity for both sets of markers and were clearly differentiated from the two Peruvian Quechua samples available in the literature. Additionally, our data were compared with the available literature to determine the genetic and linguistic structure, and East-West differentiation in South America. The close genetic relationship between the two Bolivian samples and their differentiation from the Quechua-speakers from Peru suggests that the Quechua language expansion in Bolivia took place without any important demographic contribution. Moreover, no clear geographical or linguistic structure was found for the Alu variation among South Amerindians. (c) 2009 Wiley-Liss, Inc.

Species delimitation, genetic diversity and population historical dynamics of Cycas diannanensis (Cycadaceae) occurring sympatrically in the Red River region of China

PubMed Central

Liu, Jian; Zhou, Wei; Gong, Xun

2015-01-01

Delimitating species boundaries could be of critical importance when evaluating the species' evolving process and providing guidelines for conservation genetics. Here, species delimitation was carried out on three endemic and endangered Cycas species with resembling morphology and overlapped distribution range along the Red River (Yuanjiang) in China: Cycas diananensis Z. T. Guan et G. D. Tao, Cycas parvula S. L. Yang and Cycas multiovula D. Y. Wang. A total of 137 individuals from 15 populations were genotyped by using three chloroplastic (psbA-trnH, atpI-atpH, and trnL-rps4) and two single copy nuclear (RPB1 and SmHP) DNA sequences. Basing on the carefully morphological comparison and cladistic haplotype aggregation (CHA) analysis, we propose all the populations as one species, with the rest two incorporated into C. diannanensis. Genetic diversity and structure analysis of the conflated C. diannanensis revealed this species possessed a relative lower genetic diversity than estimates of other Cycas species. The higher genetic diversity among populations and relative lower genetic diversity within populations, as well as obvious genetic differentiation among populations inferred from chloroplastic DNA (cpDNA) suggested a recent genetic loss within this protected species. Additionally, a clear genetic structure of C. diannanensis corresponding with geography was detected based on cpDNA, dividing its population ranges into “Yuanjiang-Nanhun” basin and “Ejia-Jiepai” basin groups. Demographical history analyses based on combined cpDNA and one nuclear DNA (nDNA) SmHP both showed the population size of C. diannanensis began to decrease in Quaternary glaciation with no subsequent expansion, while another nDNA RPB1 revealed a more recent sudden expansion after long-term population size contraction, suggesting its probable bottleneck events in history. Our findings offer grounded views for clarifying species boundaries of C. diannanensis when determining the conservation objectives. For operational guidelines, the downstream populations which occupy high and peculiar haplotypes should be given prior in-situ conservation. In addition, ex-situ conservation and reintroduction measures for decades of generations are supplemented for improving the population size and genetic diversity of the endemic and endangered species. PMID:26442013

Species delimitation, genetic diversity and population historical dynamics of Cycas diannanensis (Cycadaceae) occurring sympatrically in the Red River region of China.

PubMed

Liu, Jian; Zhou, Wei; Gong, Xun

2015-01-01

Delimitating species boundaries could be of critical importance when evaluating the species' evolving process and providing guidelines for conservation genetics. Here, species delimitation was carried out on three endemic and endangered Cycas species with resembling morphology and overlapped distribution range along the Red River (Yuanjiang) in China: Cycas diananensis Z. T. Guan et G. D. Tao, Cycas parvula S. L. Yang and Cycas multiovula D. Y. Wang. A total of 137 individuals from 15 populations were genotyped by using three chloroplastic (psbA-trnH, atpI-atpH, and trnL-rps4) and two single copy nuclear (RPB1 and SmHP) DNA sequences. Basing on the carefully morphological comparison and cladistic haplotype aggregation (CHA) analysis, we propose all the populations as one species, with the rest two incorporated into C. diannanensis. Genetic diversity and structure analysis of the conflated C. diannanensis revealed this species possessed a relative lower genetic diversity than estimates of other Cycas species. The higher genetic diversity among populations and relative lower genetic diversity within populations, as well as obvious genetic differentiation among populations inferred from chloroplastic DNA (cpDNA) suggested a recent genetic loss within this protected species. Additionally, a clear genetic structure of C. diannanensis corresponding with geography was detected based on cpDNA, dividing its population ranges into "Yuanjiang-Nanhun" basin and "Ejia-Jiepai" basin groups. Demographical history analyses based on combined cpDNA and one nuclear DNA (nDNA) SmHP both showed the population size of C. diannanensis began to decrease in Quaternary glaciation with no subsequent expansion, while another nDNA RPB1 revealed a more recent sudden expansion after long-term population size contraction, suggesting its probable bottleneck events in history. Our findings offer grounded views for clarifying species boundaries of C. diannanensis when determining the conservation objectives. For operational guidelines, the downstream populations which occupy high and peculiar haplotypes should be given prior in-situ conservation. In addition, ex-situ conservation and reintroduction measures for decades of generations are supplemented for improving the population size and genetic diversity of the endemic and endangered species.

Design of a 9K illumina BeadChip for polar bears (Ursus maritimus) from RAD and transcriptome sequencing.

PubMed

Malenfant, René M; Coltman, David W; Davis, Corey S

2015-05-01

Single-nucleotide polymorphisms (SNPs) offer numerous advantages over anonymous markers such as microsatellites, including improved estimation of population parameters, finer-scale resolution of population structure and more precise genomic dissection of quantitative traits. However, many SNPs are needed to equal the resolution of a single microsatellite, and reliable large-scale genotyping of SNPs remains a challenge in nonmodel species. Here, we document the creation of a 9K Illumina Infinium BeadChip for polar bears (Ursus maritimus), which will be used to investigate: (i) the fine-scale population structure among Canadian polar bears and (ii) the genomic architecture of phenotypic traits in the Western Hudson Bay subpopulation. To this end, we used restriction-site associated DNA (RAD) sequencing from 38 bears across their circumpolar range, as well as blood/fat transcriptome sequencing of 10 individuals from Western Hudson Bay. Six-thousand RAD SNPs and 3000 transcriptomic SNPs were selected for the chip, based primarily on genomic spacing and gene function respectively. Of the 9000 SNPs ordered from Illumina, 8042 were successfully printed, and - after genotyping 1450 polar bears - 5441 of these SNPs were found to be well clustered and polymorphic. Using this array, we show rapid linkage disequilibrium decay among polar bears, we demonstrate that in a subsample of 78 individuals, our SNPs detect known genetic structure more clearly than 24 microsatellites genotyped for the same individuals and that these results are not driven by the SNP ascertainment scheme. Here, we present one of the first large-scale genotyping resources designed for a threatened species. © 2014 John Wiley & Sons Ltd.

Historical fire and multidecadal drought as context for piñon - Juniper woodland restoration in western Colorado

USGS Publications Warehouse

Shinneman, Douglas J.; Baker, William L.

2009-01-01

Fire is known to structure tree populations, but the role of broad-scale climate variability is less clear. For example, the influence of climatic “teleconnections” (the relationship between oceanic–atmospheric fluctuations and anomalous weather patterns across broad scales) on forest age structure is relatively unexplored. We sampled semiarid piñon–juniper (Pinus edulis–Juniperus osteosperma) woodlands in western Colorado, USA, to test the hypothesis that woodland age structures are shaped by climate, including links to oceanic–atmospheric fluctuations, and by past fires and livestock grazing. Low-severity surface fire was lacking, as fire scars were absent, and did not influence woodland densities, but stand-replacing fires served as long-rotation (>400–600 years), stand-initiating events. Old-growth stands (>300 years old) were found in 75% of plots, consistent with a long fire rotation. Juniper and piñon age structures suggest contrasting responses during the past several centuries to dry and wet episodes linked to the Atlantic Multidecadal Oscillation (AMO) and Pacific Decadal Oscillation (PDO). Juniper density increased slightly during periods of drought, positive (warm) AMO (after ∼10-year lag), and negative (cool) PDO. In contrast, piñon populations may still be recovering from a long, drought-filled period (AD 1620–1820), with pulses of recovery favored during cool AMO, warm PDO, and above-average moisture periods. Analysis of 20th-century tree establishment and instrumental climate data corroborate the long-term relationships between age structure and climate. After Euro–American settlement (AD 1881), livestock grazing reduced understory grasses and forbs, reducing competition with tree seedlings and facilitating climate-induced increases in piñons. Thus tree populations in these woodlands are in flux, affected by drought and wet periods linked to oceanic–atmospheric variability, Euro–American livestock grazing, and long-rotation, high-severity fires. Reductions in livestock grazing levels may aid ecological restoration efforts. However, given long-term fluctuations in tree density and composition, and expected further drought, thinning or burning to reduce tree populations may be misdirected.

Networks and Models with Heterogeneous Population Structure in Epidemiology

NASA Astrophysics Data System (ADS)

Kao, R. R.

Heterogeneous population structure can have a profound effect on infectious disease dynamics, and is particularly important when investigating “tactical” disease control questions. At times, the nature of the network involved in the transmission of the pathogen (bacteria, virus, macro-parasite, etc.) appears to be clear; however, the nature of the network involved is dependent on the scale (e.g. within-host, between-host, or between-population), the nature of the contact, which ranges from the highly specific (e.g. sexual acts or needle sharing at the person-to-person level) to almost completely non-specific (e.g. aerosol transmission, often over long distances as can occur with the highly infectious livestock pathogen foot-and-mouth disease virus—FMDv—at the farm-to-farm level, e.g. Schley et al. in J. R. Soc. Interface 6:455-462, 2008), and the timescale of interest (e.g. at the scale of the individual, the typical infectious period of the host). Theoretical approaches to examining the implications of particular network structures on disease transmission have provided critical insight; however, a greater challenge is the integration of network approaches with data on real population structures. In this chapter, some concepts in disease modelling will be introduced, the relevance of selected network phenomena discussed, and then results from real data and their relationship to network analyses summarised. These include examinations of the patterns of air traffic and its relation to the spread of SARS in 2003 (Colizza et al. in BMC Med., 2007; Hufnagel et al. in Proc. Natl. Acad. Sci. USA 101:15124-15129, 2004), the use of the extensively documented Great Britain livestock movements network (Green et al. in J. Theor. Biol. 239:289-297, 2008; Robinson et al. in J. R. Soc. Interface 4:669-674, 2007; Vernon and Keeling in Proc. R. Soc. Lond. B, Biol. Sci. 276:469-476, 2009) and the growing interest in combining contact structure data with phylogenetics to identify real contact patterns as they directly relate to diseases of interest (Cottam et al. in PLoS Pathogens 4:1000050, 2007; Hughes et al. in PLoS Pathogens 5:1000590, 2009).

Increased frequency of chromosomal aberrations in railroad car painters.

PubMed

Piña-Calva, A; Madrigal-Bujaidar, E; Fuentes, M V; Neria, P; Pérez-Lucio, C; Vélez-Zamora, N M

1991-01-01

The purpose of this study was to determine if exposure to paints and solvents contributes to chromosomal alterations in occupationally exposed individuals. A total of 25 male railroad and underground railroad car painters were studied. This group had a mean age of 32.7 y and a mean exposure time of 5.2 y. The results were compared with those obtained for 25 healthy (unexposed) males. The scoring of structural chromosome aberrations clearly revealed an increase in the number of all types of aberrations considered in the population of painters. This suggests that exposure to a combination of chemicals may increase genotoxicity in industrial workers.

Anti-Stokes Luminescence in High Quality Quantum Wells

NASA Astrophysics Data System (ADS)

Vinattieri, A.; Bogani, F.; Miotto, A.; Ceccherini, S.

1997-11-01

We present a detailed investigation of the anti-Stokes (AS) luminescence which originates from exciton recombination when below gap excitation is used, in a set of high quality quantum well structures. We observe strong excitonic resonances in the AS signal as measured from photoluminescence and photoluminescence excitation spectra. We demonstrate that neither the electromagnetic coupling between the wells nor the morphological disorder can explain this up-conversion effect. Time-resolved luminescence data after ps excitation and fs correlation spectroscopy results provide clear evidence of the occurrence of a two-step absorption which is assisted by the exciton population resonantly excited by the first photon.

On the origin of Iberomaurusians: new data based on ancient mitochondrial DNA and phylogenetic analysis of Afalou and Taforalt populations.

PubMed

Kefi, Rym; Hechmi, Meriem; Naouali, Chokri; Jmel, Haifa; Hsouna, Sana; Bouzaid, Eric; Abdelhak, Sonia; Beraud-Colomb, Eliane; Stevanovitch, Alain

2018-01-01

The Western North African population was characterized by the presence of Iberomaurusian civilization at the Epiplaeolithic period (around 20,000 years before present (YBP) to 10,000 YBP). The origin of this population is still not clear: they may come from Europe, Near East, sub-Saharan Africa or they could have evolved in situ in North Africa. With the aim to contribute to a better knowledge of the settlement of North Africa we analysed the mitochondrial DNA extracted from Iberomaurusian skeletons exhumed from the archaeological site of Afalou (AFA) (15,000-11,000 YBP) in Algeria and from the archaeological site of Taforalt (TAF) (23,000-10,800 YBP) in Morocco. Then, we carried out a phylogenetic analysis relating these Iberomaurusians to 61 current Mediterranean populations. The genetic structure of TAF and AFA specimens contains only North African and Eurasian maternal lineages. These finding demonstrate the presence of these haplotypes in North Africa from at least 20,000 YBP. The very low contribution of a Sub-Saharan African haplotype in the Iberomaurusian samples is confirmed. We also highlighted the existence of genetic flows between Southern and Northern coast of the Mediterranean.

Toward a new history and geography of human genes informed by ancient DNA.

PubMed

Pickrell, Joseph K; Reich, David

2014-09-01

Genetic information contains a record of the history of our species, and technological advances have transformed our ability to access this record. Many studies have used genome-wide data from populations today to learn about the peopling of the globe and subsequent adaptation to local conditions. Implicit in this research is the assumption that the geographic locations of people today are informative about the geographic locations of their ancestors in the distant past. However, it is now clear that long-range migration, admixture, and population replacement subsequent to the initial out-of-Africa expansion have altered the genetic structure of most of the world's human populations. In light of this we argue that it is time to critically reevaluate current models of the peopling of the globe, as well as the importance of natural selection in determining the geographic distribution of phenotypes. We specifically highlight the transformative potential of ancient DNA. By accessing the genetic make-up of populations living at archaeologically known times and places, ancient DNA makes it possible to directly track migrations and responses to natural selection. Copyright © 2014 Elsevier Ltd. All rights reserved.

Increased level of linkage disequilibrium in rural compared with urban communities: a factor to consider in association-study design.

PubMed

Vitart, Veronique; Carothers, Andrew D; Hayward, Caroline; Teague, Peter; Hastie, Nicholas D; Campbell, Harry; Wright, Alan F

2005-05-01

Few studies have investigated genetic differentiation within nonisolate European populations, despite the initiation of large national sample collections such as U.K. Biobank. Here, we used short tandem repeat markers to explore fine-scale genetic structure and to examine the extent of linkage disequilibrium (LD) within national subpopulations. We studied 955 unrelated individuals of local ancestry from nine Scottish rural regions and the urban center of Edinburgh, as well as 96 unrelated individuals from the general U.K. population. Despite little overall differentiation on the basis of allele frequencies, there were clear differences among subpopulations in the extent of pairwise LD, measured between a subset of X-linked markers, that reflected presumed differences in the depths of the underlying genealogies within these subpopulations. Therefore, there are strategic advantages in studying rural subpopulations, in terms of increased power and reduced cost, that are lost by sampling across regions or within urban populations. Similar rural-urban contrasts are likely to exist in many other populations with stable rural subpopulations, which could influence the design of genetic association studies and national biobank data collections.

Hybridization and restricted gene flow between native and introduced stocks of Alpine whitefish (Coregonus sp.) across multiple environments

PubMed Central

Winkler, Kathrin A; Pamminger-Lahnsteiner, Barbara; Wanzenböck, Josef; Weiss, Steven

2011-01-01

Translocations of Baltic whitefish (Coregonus sp.) into Austrian Alpine lakes have created ‘artificial hybrid zones’, threatening the genetic integrity of native lineages. We evaluate the genetic structure of Coregonus in Austrian lakes and characterize hybridization and introgression between native and introduced lineages. Fifteen populations (N= 747) were assessed for allelic variation at eight microsatellite loci and a reduced set (N= 253) for variation across two mtDNA genes (cyt b and NADH-3). Bayesian approaches were used to estimate individual admixture proportions (q-values) and classify genotypes as native, introduced or hybrids. q-value distributions varied among populations highlighting differential hybridization and introgression histories. Many lakes revealed a clear distinction between native and introduced genotypes despite hybridization, whereas some locations revealed hybrid swarms. Genetic structure among lakes was congruent with morphological divergence and novelty raising speculation of multiple taxa, including a population south of the Alps, outside the putative native range of Coregonus. Although statistically congruent with inferences based on nuclear markers, mitochondrial haplotype data was not diagnostic with respect to native and non-native lineages, supporting that the Alpine region was colonized post-glacially by an admixture of mtDNA lineages, which coalesce >1 Ma. Mechanisms promoting or eroding lineage isolation are discussed, as well as a high potential to conserve native Alpine lineages despite the extensive historical use of introduced Baltic stocks. PMID:21199024

Two closely related species differ in their regional genetic differentiation despite admixing

PubMed Central

Fischer, Markus; Oja, Tatjana

2018-01-01

Abstract Regional genetic differentiation within species is often addressed in evolutionary ecology and conservation biology. Here, we address regional differentiation in two closely related hybridizing taxa, the perennial sedges Carex flava and C. viridula and their hybrid C. × subviridula in 37 populations in the north and centre of their distribution range in Europe (Estonia, Lowland (<1000 m a.s.l.) and Highland Switzerland) using 10 putative microsatellite loci. We ask whether regional differentiation was larger in the less common taxon C. viridula or whether, possibly due to hybridization, it was similar between taxa. Our results showed similar, low to moderate genetic diversity for the three studied taxa. In total, we found 12 regional species-specific alleles. Analysis of molecular variance (AMOVA), STRUCTURE and multidimensional scaling analysis showed regional structure in genetic variation, where intraspecific differentiation between regions was lower for C. flava (AMOVA: 6.84 %) than for C. viridula (20.77 %) or C. × subviridula (18.27 %) populations. Hybrids differed from the parental taxa in the two regions where they occurred, i.e. in Estonia and Lowland Switzerland. We conclude that C. flava and C. viridula clearly differ from each other genetically, that there is pronounced regional differentiation and that, despite hybridization, this regional differentiation is more pronounced in the less common taxon, C. viridula. We encourage future studies on hybridizing taxa to work with plant populations from more than one region. PMID:29479408

Psychometric evaluation of dietary self-efficacy and outcome expectation scales in female college freshmen.

PubMed

Kedem, Leia E; Evans, Ellen M; Chapman-Novakofski, Karen

2014-11-01

Lifestyle interventions commonly measure psychosocial beliefs as precursors to positive behavior change, but often overlook questionnaire validation. This can affect measurement accuracy if the survey has been developed for a different population, as differing behavioral influences may affect instrument validity. The present study aimed to explore psychometric properties of self-efficacy and outcome expectation scales-originally developed for younger children-in a population of female college freshmen (N = 268). Exploratory principal component analysis was used to investigate underlying data patterns and assess validity of previously published subscales. Composite scores for reliable subscales (Cronbach's α ≥ .70) were calculated to help characterize self-efficacy and outcome expectation beliefs in this population. The outcome expectation factor structure clearly comprised of positive (α = .81-.90) and negative outcomes (α = .63-.67). The self-efficacy factor structure included themes of motivation and effort (α = .75-.94), but items pertaining to hunger and availability cross-loaded often. Based on cross-loading patterns and low Cronbach's alpha values, respectively, self-efficacy items regarding barriers to healthy eating and negative outcome expectation items should be refined to improve reliability. Composite scores suggested that eating healthfully was associated with positive outcomes, but self-efficacy to do so was lower. Thus, dietary interventions for college students may be more successful by including skill-building activities to enhance self-efficacy and increase the likelihood of behavior change. © The Author(s) 2014.

Population structure of eleven Spanish ovine breeds and detection of selective sweeps with BayeScan and hapFLK

PubMed Central

Manunza, A.; Cardoso, T. F.; Noce, A.; Martínez, A.; Pons, A.; Bermejo, L. A.; Landi, V.; Sànchez, A.; Jordana, J.; Delgado, J. V.; Adán, S.; Capote, J.; Vidal, O.; Ugarte, E.; Arranz, J. J.; Calvo, J. H.; Casellas, J.; Amills, M.

2016-01-01

The goals of the current work were to analyse the population structure of 11 Spanish ovine breeds and to detect genomic regions that may have been targeted by selection. A total of 141 individuals were genotyped with the Infinium 50 K Ovine SNP BeadChip (Illumina). We combined this dataset with Spanish ovine data previously reported by the International Sheep Genomics Consortium (N = 229). Multidimensional scaling and Admixture analyses revealed that Canaria de Pelo and, to a lesser extent, Roja Mallorquina, Latxa and Churra are clearly differentiated populations, while the remaining seven breeds (Ojalada, Castellana, Gallega, Xisqueta, Ripollesa, Rasa Aragonesa and Segureña) share a similar genetic background. Performance of a genome scan with BayeScan and hapFLK allowed us identifying three genomic regions that are consistently detected with both methods i.e. Oar3 (150–154 Mb), Oar6 (4–49 Mb) and Oar13 (68–74 Mb). Neighbor-joining trees based on polymorphisms mapping to these three selective sweeps did not show a clustering of breeds according to their predominant productive specialization (except the local tree based on Oar13 SNPs). Such cryptic signatures of selection have been also found in the bovine genome, posing a considerable challenge to understand the biological consequences of artificial selection. PMID:27272025

Population structure of eleven Spanish ovine breeds and detection of selective sweeps with BayeScan and hapFLK.

PubMed

Manunza, A; Cardoso, T F; Noce, A; Martínez, A; Pons, A; Bermejo, L A; Landi, V; Sànchez, A; Jordana, J; Delgado, J V; Adán, S; Capote, J; Vidal, O; Ugarte, E; Arranz, J J; Calvo, J H; Casellas, J; Amills, M

2016-06-07

The goals of the current work were to analyse the population structure of 11 Spanish ovine breeds and to detect genomic regions that may have been targeted by selection. A total of 141 individuals were genotyped with the Infinium 50 K Ovine SNP BeadChip (Illumina). We combined this dataset with Spanish ovine data previously reported by the International Sheep Genomics Consortium (N = 229). Multidimensional scaling and Admixture analyses revealed that Canaria de Pelo and, to a lesser extent, Roja Mallorquina, Latxa and Churra are clearly differentiated populations, while the remaining seven breeds (Ojalada, Castellana, Gallega, Xisqueta, Ripollesa, Rasa Aragonesa and Segureña) share a similar genetic background. Performance of a genome scan with BayeScan and hapFLK allowed us identifying three genomic regions that are consistently detected with both methods i.e. Oar3 (150-154 Mb), Oar6 (4-49 Mb) and Oar13 (68-74 Mb). Neighbor-joining trees based on polymorphisms mapping to these three selective sweeps did not show a clustering of breeds according to their predominant productive specialization (except the local tree based on Oar13 SNPs). Such cryptic signatures of selection have been also found in the bovine genome, posing a considerable challenge to understand the biological consequences of artificial selection.

Observational constraints to boxy/peanut bulge formation time

NASA Astrophysics Data System (ADS)

Pérez, I.; Martínez-Valpuesta, I.; Ruiz-Lara, T.; de Lorenzo-Caceres, A.; Falcón-Barroso, J.; Florido, E.; González Delgado, R. M.; Lyubenova, M.; Marino, R. A.; Sánchez, S. F.; Sánchez-Blázquez, P.; van de Ven, G.; Zurita, A.

2017-09-01

Boxy/peanut bulges are considered to be part of the same stellar structure as bars and both could be linked through the buckling instability. The Milky Way is our closest example. The goal of this Letter is to determine if the mass assembly of the different components leaves an imprint in their stellar populations allowing the estimation the time of bar formation and its evolution. To this aim, we use integral field spectroscopy to derive the stellar age distributions, SADs, along the bar and disc of NGC 6032. The analysis clearly shows different SADs for the different bar areas. There is an underlying old (≥12 Gyr) stellar population for the whole galaxy. The bulge shows star formation happening at all times. The inner bar structure shows stars of ages older than 6 Gyr with a deficit of younger populations. The outer bar region presents an SAD similar to that of the disc. To interpret our results, we use a generic numerical simulation of a barred galaxy. Thus, we constrain, for the first time, the epoch of bar formation, the buckling instability period and the posterior growth from disc material. We establish that the bar of NGC 6032 is old, formed around 10 Gyr ago while the buckling phase possibly happened around 8 Gyr ago. All these results point towards bars being long-lasting even in the presence of gas.

Are Isolated Indigenous Populations Headed toward Extinction?

PubMed Central

Walker, Robert S.; Kesler, Dylan C.; Hill, Kim R.

2016-01-01

At least 50 indigenous groups spread across lowland South America remain isolated and have only intermittent and mostly hostile interactions with the outside world. Except in emergency situations, the current policy of governments in Brazil, Colombia, and Peru towards isolated tribes is a “leave them alone” strategy, in which isolated groups are left uncontacted. However, these no-contact policies are based on the assumption that isolated populations are healthy and capable of persisting in the face of mounting external threats, and that they can maintain population viability in the long-term. Here, we test this assumption by tracking the sizes and movements of cleared horticultural areas made by 8 isolated groups over the last 10–14 years. We used deforestation data derived from remote sensing Landsat satellite sensors to identify clearings, and those were then validated and assessed with high-resolution imagery. We found only a single example of a relatively large and growing population (c. 50 cleared ha and 400 people), whereas all of the other 7 groups exhibited much smaller villages and gardens with no sizable growth through time. These results indicated that the smaller groups are critically endangered, and it prompts an urgent re-thinking of policies toward isolated populations, including plans for well-organized contacts that may help save lives and rescue isolated indigenous populations from imminent extinction. PMID:26954672

Cross-species amplification of microsatellites reveals incongruence in the molecular variation and taxonomic limits of the Pilosocereus aurisetus group (Cactaceae).

PubMed

Moraes, Evandro M; Perez, Manolo F; Téo, Mariana F; Zappi, Daniela C; Taylor, Nigel P; Machado, Marlon C

2012-09-01

The Pilosocereus aurisetus group contains eight cactus species restricted to xeric habitats in eastern and central Brazil that have an archipelago-like distribution. In this study, 5-11 microsatellite markers previously designed for Pilosocereus machrisii were evaluated for cross-amplification and polymorphisms in ten populations from six species of the P. aurisetus group. The genotypic information was subsequently used to investigate the genetic relationships between the individuals, populations, and species analyzed. Only the Pmac101 locus failed to amplify in all of the six analyzed species, resulting in an 88 % success rate. The number of alleles per polymorphic locus ranged from 2 to 12, and the most successfully amplified loci showed at least one population with a larger number of alleles than were reported in the source species. The population relationships revealed clear genetic clustering in a neighbor-joining tree that was partially incongruent with the taxonomic limits between the P. aurisetus and P. machrisii species, a fact which parallels the problematic taxonomy of the P. aurisetus group. A Bayesian clustering analysis of the individual genotypes confirmed the observed taxonomic incongruence. These microsatellite markers provide a valuable resource for facilitating large-scale genetic studies on population structures, systematics and evolutionary history in this group.

Clear Speech Modifications in Children Aged 6-10

NASA Astrophysics Data System (ADS)

Taylor, Griffin Lijding

Modifications to speech production made by adult talkers in response to instructions to speak clearly have been well documented in the literature. Targeting adult populations has been motivated by efforts to improve speech production for the benefit of the communication partners, however, many adults also have communication partners who are children. Surprisingly, there is limited literature on whether children can change their speech production when cued to speak clearly. Pettinato, Tuomainen, Granlund, and Hazan (2016) showed that by age 12, children exhibited enlarged vowel space areas and reduced articulation rate when prompted to speak clearly, but did not produce any other adult-like clear speech modifications in connected speech. Moreover, Syrett and Kawahara (2013) suggested that preschoolers produced longer and more intense vowels when prompted to speak clearly at the word level. These findings contrasted with adult talkers who show significant temporal and spectral differences between speech produced in control and clear speech conditions. Therefore, it was the purpose of this study to analyze changes in temporal and spectral characteristics of speech production that children aged 6-10 made in these experimental conditions. It is important to elucidate the clear speech profile of this population to better understand which adult-like clear speech modifications they make spontaneously and which modifications are still developing. Understanding these baselines will advance future studies that measure the impact of more explicit instructions and children's abilities to better accommodate their interlocutors, which is a critical component of children's pragmatic and speech-motor development.

Does landscape fragmentation influence sex ratio of dioecious plants? A case study of Pistacia chinensis in the Thousand-Island Lake region of China.

PubMed

Yu, Lin; Lu, Jianbo

2011-01-01

The Thousand-Island Lake region in Zhejiang Province, China is a highly fragmented landscape with a clear point-in-time of fragmentation as a result of flooding to form the reservoir. Islands in the artificial lake were surveyed to examine how population sex ratio of a dioecious plant specie Pistacia chinensis B. was affected by landscape fragmentation. A natural population on the mainland near the lake was also surveyed for comparison. Population size, sex ratio and diameter at breast height (DBH) of individuals were measured over 2 years. More than 1,500 individuals, distributed in 31 populations, were studied. Soil nitrogen in the different populations was measured to identify the relationship between sex ratio and micro-environmental conditions. In accordance with the results of many other reports on biased sex ratio in relation to environmental gradient, we found that poor soil nitrogen areas fostered male-biased populations. In addition, the degree of sex ratio bias increased with decreasing population size and population connectivity. The biased sex ratios were only found in younger individuals (less than 50 years old) in small populations, while a stable 1∶1 sex ratio was found in the large population on the mainland. We concluded that the effects of landscape fragmentation on the dioecious population sex ratio were mainly achieved in relation to changing soil nitrogen conditions in patches and pollen limitation within and among populations. Large populations could maintain a more suitable environment in terms of nutrient conditions and pollen flow, subsequently maintaining a stable sex ratio in dioecious plant populations. Both micro-environmental factors and spatial structure should be considered in fragmented landscape for the conservation of dioecious plant species.

Dental and phylogeographic patterns of variation in gorillas.

PubMed

Pilbrow, Varsha

2010-07-01

Gorilla patterns of variation have great relevance for studies of human evolution. In this study, molar morphometrics were used to evaluate patterns of geographic variation in gorillas. Dental specimens of 323 adult individuals, drawn from the current distribution of gorillas in equatorial Africa were divided into 14 populations. Discriminant analyses and Mahalanobis distances were used to study population structure. Results reveal that: 1) the West and East African gorillas form distinct clusters, 2) the Cross River gorillas are well separated from the rest of the western populations, 3) gorillas from the Virunga mountains and the Bwindi Forest can be differentiated from the lowland gorillas of Utu and Mwenga-Fizi, 4) the Tshiaberimu gorillas are distinct from other eastern gorillas, and the Kahuzi-Biega gorillas are affiliated with them. These findings provide support for a species distinction between Gorilla gorilla and Gorilla beringei, with subspecies G. g. diehli, G. g. gorilla, G. b. graueri, G. b. beringei, and possibly, G. b. rex-pygmaeorum. Clear correspondence between dental and other patterns of taxonomic diversity demonstrates that dental data reveal underlying genetic patterns of differentiation. Dental distances increased predictably with altitude but not with geographic distances, indicating that altitudinal segregation explains gorilla patterns of population divergence better than isolation-by-distance. The phylogeographic pattern of gorilla dental metric variation supports the idea that Plio-Pleistocene climatic fluctuations and local mountain building activity in Africa affected gorilla phylogeography. I propose that West Africa comprised the historic center of gorilla distribution and experienced drift-gene flow equilibrium, whereas Nigeria and East Africa were at the periphery, where climatic instability and altitudinal variation promoted drift and genetic differentiation. This understanding of gorilla population structure has implications for gorilla conservation, and for understanding the distribution of sympatric chimpanzees and Plio-Pleistocene hominins.

A comparative phylogenetic study of genetics and folk music.

PubMed

Pamjav, Horolma; Juhász, Zoltán; Zalán, Andrea; Németh, Endre; Damdin, Bayarlkhagva

2012-04-01

Computer-aided comparison of folk music from different nations is one of the newest research areas. We were intrigued to have identified some important similarities between phylogenetic studies and modern folk music. First of all, both of them use similar concepts and representation tools such as multidimensional scaling for modelling relationship between populations. This gave us the idea to investigate whether these connections are merely accidental or if they mirror population migrations from the past. We raised the question; does the complex structure of musical connections display a clear picture and can this system be interpreted by the genetic analysis? This study is the first to systematically investigate the incidental genetic background of the folk music context between different populations. Paternal (42 populations) and maternal lineages (56 populations) were compared based on Fst genetic distances of the Y chromosomal and mtDNA haplogroup frequencies. To test this hypothesis, the corresponding musical cultures were also compared using an automatic overlap analysis of parallel melody styles for 31 Eurasian nations. We found that close musical relations of populations indicate close genetic distances (<0.05) with a probability of 82%. It was observed that there is a significant correlation between population genetics and folk music; maternal lineages have a more important role in folk music traditions than paternal lineages. Furthermore, the combination of these disciplines establishing a new interdisciplinary research field of "music-genetics" can be an efficient tool to get a more comprehensive picture on the complex behaviour of populations in prehistoric time.

Effectiveness of genomic prediction of maize hybrid performance in different breeding populations and environments.

PubMed

Windhausen, Vanessa S; Atlin, Gary N; Hickey, John M; Crossa, Jose; Jannink, Jean-Luc; Sorrells, Mark E; Raman, Babu; Cairns, Jill E; Tarekegne, Amsal; Semagn, Kassa; Beyene, Yoseph; Grudloyma, Pichet; Technow, Frank; Riedelsheimer, Christian; Melchinger, Albrecht E

2012-11-01

Genomic prediction is expected to considerably increase genetic gains by increasing selection intensity and accelerating the breeding cycle. In this study, marker effects estimated in 255 diverse maize (Zea mays L.) hybrids were used to predict grain yield, anthesis date, and anthesis-silking interval within the diversity panel and testcross progenies of 30 F(2)-derived lines from each of five populations. Although up to 25% of the genetic variance could be explained by cross validation within the diversity panel, the prediction of testcross performance of F(2)-derived lines using marker effects estimated in the diversity panel was on average zero. Hybrids in the diversity panel could be grouped into eight breeding populations differing in mean performance. When performance was predicted separately for each breeding population on the basis of marker effects estimated in the other populations, predictive ability was low (i.e., 0.12 for grain yield). These results suggest that prediction resulted mostly from differences in mean performance of the breeding populations and less from the relationship between the training and validation sets or linkage disequilibrium with causal variants underlying the predicted traits. Potential uses for genomic prediction in maize hybrid breeding are discussed emphasizing the need of (1) a clear definition of the breeding scenario in which genomic prediction should be applied (i.e., prediction among or within populations), (2) a detailed analysis of the population structure before performing cross validation, and (3) larger training sets with strong genetic relationship to the validation set.

A multifactorial obesity model developed from nationwide public health exposome data and modern computational analyses.

PubMed

Gittner, LisaAnn S; Kilbourne, Barbara J; Vadapalli, Ravi; Khan, Hafiz M K; Langston, Michael A

Obesity is both multifactorial and multimodal, making it difficult to identify, unravel and distinguish causative and contributing factors. The lack of a clear model of aetiology hampers the design and evaluation of interventions to prevent and reduce obesity. Using modern graph-theoretical algorithms, we are able to coalesce and analyse thousands of inter-dependent variables and interpret their putative relationships to obesity. Our modelling is different from traditional approaches; we make no a priori assumptions about the population, and model instead based on the actual characteristics of a population. Paracliques, noise-resistant collections of highly-correlated variables, are differentially distilled from data taken over counties associated with low versus high obesity rates. Factor analysis is then applied and a model is developed. Latent variables concentrated around social deprivation, community infrastructure and climate, and especially heat stress were connected to obesity. Infrastructure, environment and community organisation differed in counties with low versus high obesity rates. Clear connections of community infrastructure with obesity in our results lead us to conclude that community level interventions are critical. This effort suggests that it might be useful to study and plan interventions around community organisation and structure, rather than just the individual, to combat the nation's obesity epidemic. Copyright © 2017 Asia Oceania Association for the Study of Obesity. Published by Elsevier Ltd. All rights reserved.

Population structure and genomic inbreeding in nine Swiss dairy cattle populations.

PubMed

Signer-Hasler, Heidi; Burren, Alexander; Neuditschko, Markus; Frischknecht, Mirjam; Garrick, Dorian; Stricker, Christian; Gredler, Birgit; Bapst, Beat; Flury, Christine

2017-11-07

Domestication, breed formation and intensive selection have resulted in divergent cattle breeds that likely exhibit their own genomic signatures. In this study, we used genotypes from 27,612 autosomal single nucleotide polymorphisms to characterize population structure based on 9214 sires representing nine Swiss dairy cattle populations: Brown Swiss (BS), Braunvieh (BV), Original Braunvieh (OB), Holstein (HO), Red Holstein (RH), Swiss Fleckvieh (SF), Simmental (SI), Eringer (ER) and Evolèner (EV). Genomic inbreeding (F ROH ) and signatures of selection were determined by calculating runs of homozygosity (ROH). The results build the basis for a better understanding of the genetic development of Swiss dairy cattle populations and highlight differences between the original populations (i.e. OB, SI, ER and EV) and those that have become more popular in Switzerland as currently reflected by their larger populations (i.e. BS, BV, HO, RH and SF). The levels of genetic diversity were highest and lowest in the SF and BS breeds, respectively. Based on F ST values, we conclude that, among all pairwise comparisons, BS and HO (0.156) differ more than the other pairs of populations. The original Swiss cattle populations OB, SI, ER, and EV are clearly genetically separated from the Swiss cattle populations that are now more common and represented by larger numbers of cows. Mean levels of F ROH ranged from 0.027 (ER) to 0.091 (BS). Three of the original Swiss cattle populations, ER (F ROH : 0.027), OB (F ROH : 0.029), and SI (F ROH : 0.039), showed low levels of genomic inbreeding, whereas it was much higher in EV (F ROH : 0.074). Private signatures of selection for the original Swiss cattle populations are reported for BTA4, 5, 11 and 26. The low levels of genomic inbreeding observed in the original Swiss cattle populations ER, OB and SI compared to the other breeds are explained by a lesser use of artificial insemination and greater use of natural service. Natural service results in more sires having progeny at each generation and thus this breeding practice is likely the major reason for the remarkable levels of genetic diversity retained within these populations. The fact that the EV population is regionally restricted and its small census size of herd-book cows explain its high level of genomic inbreeding.

Large-scale gene flow in the barnacle Jehlius cirratus and contrasts with other broadly-distributed taxa along the Chilean coast

PubMed Central

Guo, Baoying

2017-01-01

We evaluate the population genetic structure of the intertidal barnacle Jehlius cirratus across a broad portion of its geographic distribution using data from the mitochondrial cytochrome oxidase I (COI) gene region. Despite sampling diversity from over 3,000 km of the linear range of this species, there is only slight regional structure indicated, with overall Φ CT of 0.036 (p < 0.001) yet no support for isolation by distance. While these results suggest greater structure than previous studies of J. cirratus had indicated, the pattern of diversity is still far more subtle than in other similarly-distributed species with similar larval and life history traits. We compare these data and results with recent findings in four other intertidal species that have planktotrophic larvae. There are no clear patterns among these taxa that can be associated with intertidal depth or other known life history traits. PMID:28194316

15 CFR 291.3 - Environmental tools and techniques projects.

Code of Federal Regulations, 2010 CFR

2010-01-01

... activity, and “customer satisfaction” measures of performance. (6) Management experience and plans... population must be clearly defined. The proposal must demonstrate that it understands the population's...

The evolution of labile traits in sex- and age-structured populations.

PubMed

Childs, Dylan Z; Sheldon, Ben C; Rees, Mark

2016-03-01

Many quantitative traits are labile (e.g. somatic growth rate, reproductive timing and investment), varying over the life cycle as a result of behavioural adaptation, developmental processes and plastic responses to the environment. At the population level, selection can alter the distribution of such traits across age classes and among generations. Despite a growing body of theoretical research exploring the evolutionary dynamics of labile traits, a data-driven framework for incorporating such traits into demographic models has not yet been developed. Integral projection models (IPMs) are increasingly being used to understand the interplay between changes in labile characters, life histories and population dynamics. One limitation of the IPM approach is that it relies on phenotypic associations between parents and offspring traits to capture inheritance. However, it is well-established that many different processes may drive these associations, and currently, no clear consensus has emerged on how to model micro-evolutionary dynamics in an IPM framework. We show how to embed quantitative genetic models of inheritance of labile traits into age-structured, two-sex models that resemble standard IPMs. Commonly used statistical tools such as GLMs and their mixed model counterparts can then be used for model parameterization. We illustrate the methodology through development of a simple model of egg-laying date evolution, parameterized using data from a population of Great tits (Parus major). We demonstrate how our framework can be used to project the joint dynamics of species' traits and population density. We then develop a simple extension of the age-structured Price equation (ASPE) for two-sex populations, and apply this to examine the age-specific contributions of different processes to change in the mean phenotype and breeding value. The data-driven framework we outline here has the potential to facilitate greater insight into the nature of selection and its consequences in settings where focal traits vary over the lifetime through ontogeny, behavioural adaptation and phenotypic plasticity, as well as providing a potential bridge between theoretical and empirical studies of labile trait variation. © 2016 The Authors Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society.

Geography, Ethnicity or Subsistence-Specific Variations in Human Microbiome Composition and Diversity

PubMed Central

Gupta, Vinod K.; Paul, Sandip; Dutta, Chitra

2017-01-01

One of the fundamental issues in the microbiome research is characterization of the healthy human microbiota. Recent studies have elucidated substantial divergences in the microbiome structure between healthy individuals from different race and ethnicity. This review provides a comprehensive account of such geography, ethnicity or life-style-specific variations in healthy microbiome at five major body habitats—Gut, Oral-cavity, Respiratory Tract, Skin, and Urogenital Tract (UGT). The review focuses on the general trend in the human microbiome evolution—a gradual transition in the gross compositional structure along with a continual decrease in diversity of the microbiome, especially of the gut microbiome, as the human populations passed through three stages of subsistence like foraging, rural farming and industrialized urban western life. In general, gut microbiome of the hunter-gatherer populations is highly abundant with Prevotella, Proteobacteria, Spirochaetes, Clostridiales, Ruminobacter etc., while those of the urban communities are often enriched in Bacteroides, Bifidobacterium, and Firmicutes. The oral and skin microbiome are the next most diverse among different populations, while respiratory tract and UGT microbiome show lesser variations. Higher microbiome diversity is observed for oral-cavity in hunter-gatherer group with higher prevalence of Haemophilus than agricultural group. In case of skin microbiome, rural and urban Chinese populations show variation in abundance of Trabulsiella and Propionibacterium. On the basis of published data, we have characterized the core microbiota—the set of genera commonly found in all populations, irrespective of their geographic locations, ethnicity or mode of subsistence. We have also identified the major factors responsible for geography-based alterations in microbiota; though it is not yet clear which factor plays a dominant role in shaping the microbiome—nature or nurture, host genetics or his environment. Some of the geographical/racial variations in microbiome structure have been attributed to differences in host genetics and innate/adaptive immunity, while in many other cases, cultural/behavioral features like diet, hygiene, parasitic load, environmental exposure etc. overshadow genetics. The ethnicity or population-specific variations in human microbiome composition, as reviewed in this report, question the universality of the microbiome-based therapeutic strategies and recommend for geographically tailored community-scale approaches to microbiome engineering. PMID:28690602

Genetic Diversity of an Imperiled Neotropical Catfish and Recommendations for Its Restoration

PubMed Central

Fonseca, Fernando S.; Domingues, Rodrigo R.; Hallerman, Eric M.; Hilsdorf, Alexandre W. S.

2017-01-01

The long-whiskered catfish Steindachneridion parahybae (Family Pimelodidae) is endemic to the Paraíba do Sul River basin in southeastern Brazil. This species was heavily exploited by artisanal fisheries and faces challenges posed by dams, introduced species, and deterioration of critical habitat. The remaining populations are small and extirpated from some locales, and the species is listed as critically endangered in Brazil. Screening variation at a partial mitochondrial control region sequence (mtCR) and 20 microsatellite loci, we: (i) describe the patterns of genetic diversity along its current distributional range; (ii) test the null hypothesis of panmixia; (iii) investigate the main factors driving its current population structure, and (iv) propose management of broodstock for fostering recovery of wild populations through genetically cognizant restocking. Our microsatellite data for 70 individuals from five collections indicate moderate levels of heterozygosity (HO = 0.45) and low levels of inbreeding (FIS = 0.016). Individual-based cluster analyses showed clear genetic structure, with three clusters of individuals over the collection area with no mis-assigned individuals, suggesting no recent migration among the three clusters. Pairwise DEST values showed moderate and significant genetic differentiation among all populations so identified. The MUR population may have suffered a recent demographic reduction. mtCRs for 70 individuals exhibited 36 haplotypes resulting from 38 polymorphic sites. Overall, mitochondrial haplotype diversity was 0.930 (±0.023) and nucleotide diversity was 0.011 (±0.002). Significant population structure was observed, with ϕST = 0.226. Genetic markers could be used in a hatchery-based restoration program emphasizing breeding of pairs with low kinship values in order to promote retention of genetic diversity and avoid inbreeding. Individual average kinship relationships showed 87.3% advised matings, 11.0% marginal matings, and 1.7% advised against. While these results comprise a contribution toward planning better breeding management and monitoring, parallel actions to be undertaken include surveying healthy riverine habits for reintroduction and continued searching for wild individuals to introduce new variation into the captive broodstock to avoid adaptation to captivity and to minimize inbreeding. PMID:29312433

Genetic Diversity of an Imperiled Neotropical Catfish and Recommendations for Its Restoration.

PubMed

Fonseca, Fernando S; Domingues, Rodrigo R; Hallerman, Eric M; Hilsdorf, Alexandre W S

2017-01-01

The long-whiskered catfish Steindachneridion parahybae (Family Pimelodidae) is endemic to the Paraíba do Sul River basin in southeastern Brazil. This species was heavily exploited by artisanal fisheries and faces challenges posed by dams, introduced species, and deterioration of critical habitat. The remaining populations are small and extirpated from some locales, and the species is listed as critically endangered in Brazil. Screening variation at a partial mitochondrial control region sequence (mtCR) and 20 microsatellite loci, we: (i) describe the patterns of genetic diversity along its current distributional range; (ii) test the null hypothesis of panmixia; (iii) investigate the main factors driving its current population structure, and (iv) propose management of broodstock for fostering recovery of wild populations through genetically cognizant restocking. Our microsatellite data for 70 individuals from five collections indicate moderate levels of heterozygosity ( H O = 0.45) and low levels of inbreeding ( F IS = 0.016). Individual-based cluster analyses showed clear genetic structure, with three clusters of individuals over the collection area with no mis-assigned individuals, suggesting no recent migration among the three clusters. Pairwise D EST values showed moderate and significant genetic differentiation among all populations so identified. The MUR population may have suffered a recent demographic reduction. mtCRs for 70 individuals exhibited 36 haplotypes resulting from 38 polymorphic sites. Overall, mitochondrial haplotype diversity was 0.930 (±0.023) and nucleotide diversity was 0.011 (±0.002). Significant population structure was observed, with ϕ ST = 0.226. Genetic markers could be used in a hatchery-based restoration program emphasizing breeding of pairs with low kinship values in order to promote retention of genetic diversity and avoid inbreeding. Individual average kinship relationships showed 87.3% advised matings, 11.0% marginal matings, and 1.7% advised against. While these results comprise a contribution toward planning better breeding management and monitoring, parallel actions to be undertaken include surveying healthy riverine habits for reintroduction and continued searching for wild individuals to introduce new variation into the captive broodstock to avoid adaptation to captivity and to minimize inbreeding.

Phylogeny and genetic structure of Erophaca (Leguminosae), a East-West Mediterranean disjunct genus from the Tertiary.

PubMed

Casimiro-Soriguer, Ramón; Talavera, María; Balao, Francisco; Terrab, Anass; Herrera, Javier; Talavera, Salvador

2010-07-01

The genus Erophaca comprises a single herbaceous perennial species with two subspecies distributed at opposite ends of the Mediterranean region. We used nrDNA ITS to investigate the phylogeny of the genus, and AFLP markers (9 primers, 20 populations) to establish the genetic relationship between subspecies, and among populations at each side of the Gibraltar Strait. According to nrDNA ITS, Erophaca is monophyletic, old (Miocene), and sister to the Astragalean clade. Life form attributes and molecular clock estimates suggest that Erophaca is one of the many Tertiary relicts that form part of the present Mediterranean flora. Within the occidental subspecies, European plants are clearly derived from North-African populations (Morocco) which, despite being rare on a regional scale, present the highest genetic diversity (as estimated by private and rare fragment numbers). In general, genetic diversity decreased with increasing distance from Morocco. AFLP and nrDNA ITS markers evidenced that the Eastern and the Western subspecies are genetically distinct. Possible causes for their disjunct distribution are discussed. Copyright 2010 Elsevier Inc. All rights reserved.

Asymptomatic bacteriuria: when to screen and when to treat.

PubMed

Nicolle, Lindsay E

2003-06-01

Asymptomatic bacteriuria is common. Populations with structural or functional abnormalities of the genitourinary tract may have an exceedingly high prevalence of bacteriuria, but even healthy individuals frequently have positive urine cultures. Asymptomatic bacteriuria is seldom associated with adverse outcomes. Pregnant women and individuals who are to undergo traumatic genitourinary interventions are at risk for complications of bacteriuria and benefit from screening and treatment programs. Although screening is recommended for renal transplant recipients, the benefits for these patients are less clear. For other populations, including most bacteriuric individuals, negative outcomes attributable to asymptomatic bacteriuria have not been described. Treatment of asymptomatic bacteriuria in these patients is not beneficial and, in fact, may be associated with harmful outcomes, such as increased short-term frequency of symptomatic infection, adverse drug effects, and reinfection with organisms of increased antimicrobial resistance. Screening for asymptomatic bacteriuria and treatment is recommended for only selected groups where benefit has been shown. Many research questions still need to be addressed. Different populations have unique risk factors, and the benefits and risks of different management approaches for asymptomatic bacteriuria must continue to be addressed systematically in appropriate clinical trials.

Coherent driving and freezing of bosonic matter wave in an optical Lieb lattice

PubMed Central

Taie, Shintaro; Ozawa, Hideki; Ichinose, Tomohiro; Nishio, Takuei; Nakajima, Shuta; Takahashi, Yoshiro

2015-01-01

Although kinetic energy of a massive particle generally has quadratic dependence on its momentum, a flat, dispersionless energy band is realized in crystals with specific lattice structures. Such macroscopic degeneracy causes the emergence of localized eigenstates and has been a key concept in the context of itinerant ferromagnetism. We report the realization of a “Lieb lattice” configuration with an optical lattice, which has a flat energy band as the first excited state. Our optical lattice potential has various degrees of freedom in its manipulation, which enables coherent transfer of a Bose-Einstein condensate into the flat band. In addition to measuring lifetime of the flat band population for different tight-binding parameters, we investigate the inter-sublattice dynamics of the system by projecting the sublattice population onto the band population. This measurement clearly shows the formation of the localized state with the specific sublattice decoupled in the flat band, and even detects the presence of flat-band breaking perturbations, resulting in the delocalization. Our results will open up the possibilities of exploring the physics of flat bands with a highly controllable quantum system. PMID:26665167

Epigenetic Differentiation of Natural Populations of Lilium bosniacum Associated with Contrasting Habitat Conditions.

PubMed

Zoldoš, Vlatka; Biruš, Ivan; Muratovic, Edina; Šatovic, Zlatko; Vojta, Aleksandar; Robin, Odile; Pustahija, Fatima; Bogunic, Faruk; Vicic Bockor, Vedrana; Siljak-Yakovlev, Sonja

2018-01-01

Epigenetic variation in natural populations with contrasting habitats might be an important element, in addition to the genetic variation, in plant adaptation to environmental stress. Here, we assessed genetic, epigenetic, and cytogenetic structure of the three Lilium bosniacum populations growing on distinct habitats. One population was growing under habitual ecological conditions for this species and the other two were growing under stress associated with high altitude and serpentine soil. Amplified fragment length polymorphism and methylation-sensitive amplification polymorphism analyses revealed that the three populations did not differentiate genetically, but were clearly separated in three distinct clusters according to DNA methylation profiles. Principal coordinate analysis showed that overall epigenetic variation was closely related to habitat conditions. A new methylation-sensitive amplification polymorphism scoring approach allowed identification of mainly unmethylated (φST = 0.190) and fully CpG methylated (φST = 0.118) subepiloci playing a role in overall population differentiation, in comparison with hemimethylated sites (φST = 0.073). In addition, unusual rDNA repatterning and the presence of B chromosomes bearing 5S rDNA loci were recorded in the population growing on serpentine soil, suggesting dynamic chromosome rearrangements probably linked to global genome demethylation, which might have reactivated some mobile elements. We discuss our results considering our earlier data on morphology and leaf anatomy of several L. bosniacum populations, and suggest a possible role of epigenetics as a key element in population differentiation associated with environmental stress in these particular lily populations. © The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Inferring the Structure of Social Contacts from Demographic Data in the Analysis of Infectious Diseases Spread

PubMed Central

Fumanelli, Laura; Ajelli, Marco; Manfredi, Piero; Vespignani, Alessandro; Merler, Stefano

2012-01-01

Social contact patterns among individuals encode the transmission route of infectious diseases and are a key ingredient in the realistic characterization and modeling of epidemics. Unfortunately, the gathering of high quality experimental data on contact patterns in human populations is a very difficult task even at the coarse level of mixing patterns among age groups. Here we propose an alternative route to the estimation of mixing patterns that relies on the construction of virtual populations parametrized with highly detailed census and demographic data. We present the modeling of the population of 26 European countries and the generation of the corresponding synthetic contact matrices among the population age groups. The method is validated by a detailed comparison with the matrices obtained in six European countries by the most extensive survey study on mixing patterns. The methodology presented here allows a large scale comparison of mixing patterns in Europe, highlighting general common features as well as country-specific differences. We find clear relations between epidemiologically relevant quantities (reproduction number and attack rate) and socio-demographic characteristics of the populations, such as the average age of the population and the duration of primary school cycle. This study provides a numerical approach for the generation of human mixing patterns that can be used to improve the accuracy of mathematical models in the absence of specific experimental data. PMID:23028275

75 FR 63113 - Financial Resources Requirements for Derivatives Clearing Organizations

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-14

... Resources Requirements for Derivatives Clearing Organizations AGENCY: Commodity Futures Trading Commission... regulations establish financial resources requirements for derivatives clearing organizations (DCOs) for the... DCO's organizational structure, i.e., whether or not the DCO is a membership organization. Clearing...

Population Health Measurement: Applying Performance Measurement Concepts in Population Health Settings

PubMed Central

Stoto, Michael A.

2014-01-01

Introduction: Whether the focus of population-health improvement efforts, the measurement of health outcomes, risk factors, and interventions to improve them are central to achieving collective impact in the population health perspective. And because of the importance of a shared measurement system, appropriate measures can help to ensure the accountability of and ultimately integrate the efforts of public health, the health care delivery sector, and other public and private entities in the community to improve population health. Yet despite its importance, population health measurement efforts in the United States are poorly developed and uncoordinated. Collaborative Measurement Development: To achieve the potential of the population health perspective, public health officials, health system leaders, and others must work together to develop sets of population health measures that are suitable for different purposes yet are harmonized so that together they can help to improve a community’s health. This begins with clearly defining the purpose of a set of measures, distinguishing between outcomes for which all share responsibility and actions to improve health for which the health care sector, public health agencies, and others should be held accountable. Framework for Population Health Measurement: Depending on the purpose of the analysis, then, measurement systems should clearly specify what to measure—in particular the population served (the denominator), what the critical health dimensions are in a measurement framework, and how the measures can be used to ensure accountability. Building on a clear understanding of the purpose and dimensions of population health that must be measured, developers can then choose specific measures using existing data or developing new data sources if necessary, with established validity, reliability, and other scientific characteristics. Rather than indiscriminately choosing among the proliferating data streams, this systematic approach to measure development can yield measurement systems that are more appropriate and useful for improving population health. PMID:25995988

Preliminary juvenile Lost River and shortnose sucker investigations in Clear Lake, California--2011 pilot study summary

USGS Publications Warehouse

Burdick, Summer M.; Rasmussen, Josh

2012-01-01

Poor recruitment appears to limit the recovery of Lost River and shortnose sucker populations in Clear Lake Reservoir, California, but the cause is unknown. Adult suckers migrate up Willow Creek and its tributaries to spawn in some years, but low flow in Willow Creek may inhibit spawning migrations in other years. It is unclear whether spawning is successful, larvae survive, or juveniles persist to adulthood. Environmental variables associated with successful spawning or young-of-year survival have not been identified and early life history for these populations is poorly understood. The U.S. Geological Survey in cooperation with the U.S. Fish and Wildlife Service and Ruby Pipeline L.L.C. Corporation (El Paso, Tex.) initiated a study in 2011 to better understand juvenile sucker life history in Clear Lake Reservoir, and to identify constraints in the early life history that may limit recruitment to the adult spawning populations. This is a report on the 2011 pilot study for this project.

Genetic structuring, dispersal and taxonomy of the high-alpine populations of the Geranium arabicum/kilimandscharicum complex in tropical eastern Africa

PubMed Central

Gizaw, Abel; Tusiime, Felly M.; Masao, Catherine A.; Abdi, Ahmed A.; Hou, Yan; Nemomissa, Sileshi; Brochmann, Christian

2017-01-01

The scattered eastern African high mountains harbor a renowned and highly endemic flora, but the taxonomy and phylogeographic history of many plant groups are still insufficiently known. The high-alpine populations of the Geranium arabicum/kilimandscharicum complex present intricate morphological variation and have recently been suggested to comprise two new endemic taxa. Here we aim to contribute to a clarification of the taxonomy of these populations by analyzing genetic (AFLP) variation in range-wide high-alpine samples, and we address whether hybridization has contributed to taxonomic problems. We identified only two genetic groups. One corresponded to G. kilimandscharicum, which has been reported as exclusively high-alpine and confined to the eastern Rift mountains in East Africa. The other corresponded to G. arabicum, reported from lower altitudes on the same mountains as well as from a wide altitudinal span in Ethiopia and on the western Rift mountains in East Africa. The four populations analyzed of a recently described species from the Bale Mts in Ethiopia were admixed, indicating that they result from recent long-distance dispersal of G. kilimandscharicum from East Africa followed by hybridization with local G. arabicum in naturally disturbed habitats. Some admixture between the two genetic groups was also inferred on other mountains, supporting earlier suggestions of introgression based on morphology. We did not find support for recognition of the recently suggested new subspecies of G. arabicum in Ethiopia. Interestingly, the high-alpine G. kilimandscharicum lacked clear geographic structuring, suggesting a recent history of colonization of the different mountains or extensive intermountain gene flow. PMID:28552970

A large, switchable optical clearing skull window for cerebrovascular imaging

PubMed Central

Zhang, Chao; Feng, Wei; Zhao, Yanjie; Yu, Tingting; Li, Pengcheng; Xu, Tonghui; Luo, Qingming; Zhu, Dan

2018-01-01

Rationale: Intravital optical imaging is a significant method for investigating cerebrovascular structure and function. However, its imaging contrast and depth are limited by the turbid skull. Tissue optical clearing has a great potential for solving this problem. Our goal was to develop a transparent skull window, without performing a craniotomy, for use in assessing cerebrovascular structure and function. Methods: Skull optical clearing agents were topically applied to the skulls of mice to create a transparent window within 15 min. The clearing efficacy, repeatability, and safety of the skull window were then investigated. Results: Imaging through the optical clearing skull window enhanced both the contrast and the depth of intravital imaging. The skull window could be used on 2-8-month-old mice and could be expanded from regional to bi-hemispheric. In addition, the window could be repeatedly established without inducing observable inflammation and metabolic toxicity. Conclusion: We successfully developed an easy-to-handle, large, switchable, and safe optical clearing skull window. Combined with various optical imaging techniques, cerebrovascular structure and function can be observed through this optical clearing skull window. Thus, it has the potential for use in basic research on the physiopathologic processes of cortical vessels. PMID:29774069

Secondary successional trajectories of structural and catabolic bacterial communities in oil-polluted soil planted with hybrid poplar.

PubMed

Mukherjee, Shinjini; Sipilä, Timo; Pulkkinen, Pertti; Yrjälä, Kim

2015-02-01

Poplars have widely been used for rhizoremediation of a broad range of organic contaminants for the past two decades. Still, there is a knowledge gap regarding the rhizosphere-associated bacterial communities of poplars and their dynamics during the remediation process. It is envisaged that a detailed understanding of rhizosphere-associated microbial populations will greatly contribute to a better design and implementation of rhizoremediation. To investigate the long-term succession of structural and catabolic bacterial communities in oil-polluted soil planted with hybrid poplar, we carried out a 2-year field study. Hybrid aspen (Populus tremula × Populus tremuloides) seedlings were planted in polluted soil excavated from an accidental oil-spill site. Vegetated and un-vegetated soil samples were collected for microbial community analyses at seven different time points during the course of 2 years and sampling time points were chosen to cover the seasonal variation in the boreal climate zone. Bacterial community structure was accessed by means of 16S rRNA gene amplicon pyrosequencing, whereas catabolic diversity was monitored by pyrosequencing of alkane hydroxylase and extradiol dioxygenase genes. We observed a clear succession of bacterial communities on both structural and functional levels from early to late-phase communities. Sphingomonas type extradiol dioxygenases and alkane hydroxylase homologs of Rhodococcus clearly dominated the early-phase communities. The high-dominance/low-diversity functional gene communities underwent a transition to low-dominance/high-diversity communities in the late phase. These results pointed towards increased catabolic capacities and a change from specialist to generalist strategy of bacterial communities during the course of secondary succession. © 2014 John Wiley & Sons Ltd.

15 CFR 292.2 - Training development and deployment projects.

Code of Federal Regulations, 2010 CFR

2010-01-01

... of the activity, and “customer satisfaction” measures of performance. (6) Management and... clearly defined and the proposal must demonstrate that it understands the population's training needs... implementation mechanisms. The proposal must set forth clearly defined, effective mechanisms for delivery and/or...

Population Education Accessions List. July-December 1978.

ERIC Educational Resources Information Center

United Nations Educational, Scientific, and Cultural Organization, Bangkok (Thailand). Regional Office for Education in Asia and Oceania.

Identified in this pamphlet are 317 resources about population education. Compiled by UNESCO's Population Education Clearing House in Thailand, the list contains references to journal articles, monographs, research reports, teaching guides, and curriculum materials. Most were published in Asian countries and the United States during the period…

Population connectivity and larval dispersal of the exploited mangrove crab Ucides cordatus along the Brazilian coast.

PubMed

Britto, Fábio B; Schmidt, Anders J; Carvalho, Adriana M F; Vasconcelos, Carolina C M P; Farias, Antonia M; Bentzen, Paul; Diniz, Fábio M

2018-01-01

The mangrove crab Ucides cordatus is considered a key species for the ecological balance of mangrove forests and a major source of employment and income for traditional crab collectors in Brazil. Several studies evidenced weak genetic variation among populations due to an efficient larval transport. However, gene flow patterns of the species is poorly understood, with no information about migration rates. The influence of the two main Brazilian currents in larval dispersion is also not clear. In order to provide baseline information for conservation, planning and management of this important fishery resource, the present study aimed to estimate and evaluate spatial distribution of genetic diversity, migration rates and gene flow directivity among populations of U. cordatus in Brazil. Nine microsatellites were used to resolve population structure of 319 crabs collected from six sites located along the Brazilian coast. The degree of geographical differentiation included estimates of genetic diversity, population structure and gene flow models, with spatial analysis of shared alleles (SAShA), isolation by distance tests, AMOVA, discriminant analysis of principal components (DAPC) and Bayesian clustering. We estimated the amount of ongoing gene flow between clusters using the coalescent-based method implemented in Migrate-N. Loci were highly polymorphic (average of 12.4 alleles per locus) evidencing high genetic variability. There was significant differentiation among localities, despite of the low value of F ST (= 0.019; P < 0.001). F ST and Jost's D indexes were also estimated in pairwise comparisons and showed significant differences between most of the surveyed site pairs ( P < 0.05). Structure evidenced a single genetic group among samples, however SAShA pointed to a non-panmictic condition ( P = 0.011). AMOVA detected four statistical significant clusters with low level of differentiation ( F CT = 0.037; P = 0.023). The gene flow model that best described the population connectivity was the island model, with ∼24 crabs being exchanged among localities per generation. The high migration rates found among localities seem to be the main force acting to sustain the distribution of the genetic diversity of U. cordatus . Despite the high gene flow and the weak population structure among samples, the significant genetic differences found suggest that gene flow alone does not bypass the effects of genetic drift, natural selection and/or human exploitation. These findings are vital for the establishment of a database to be used in the development of conservation programs.

Population connectivity and larval dispersal of the exploited mangrove crab Ucides cordatus along the Brazilian coast

PubMed Central

Schmidt, Anders J.; Carvalho, Adriana M.F.; Vasconcelos, Carolina C.M.P.; Farias, Antonia M.; Bentzen, Paul

2018-01-01

Background The mangrove crab Ucides cordatus is considered a key species for the ecological balance of mangrove forests and a major source of employment and income for traditional crab collectors in Brazil. Several studies evidenced weak genetic variation among populations due to an efficient larval transport. However, gene flow patterns of the species is poorly understood, with no information about migration rates. The influence of the two main Brazilian currents in larval dispersion is also not clear. In order to provide baseline information for conservation, planning and management of this important fishery resource, the present study aimed to estimate and evaluate spatial distribution of genetic diversity, migration rates and gene flow directivity among populations of U. cordatus in Brazil. Methods Nine microsatellites were used to resolve population structure of 319 crabs collected from six sites located along the Brazilian coast. The degree of geographical differentiation included estimates of genetic diversity, population structure and gene flow models, with spatial analysis of shared alleles (SAShA), isolation by distance tests, AMOVA, discriminant analysis of principal components (DAPC) and Bayesian clustering. We estimated the amount of ongoing gene flow between clusters using the coalescent-based method implemented in Migrate-N. Results Loci were highly polymorphic (average of 12.4 alleles per locus) evidencing high genetic variability. There was significant differentiation among localities, despite of the low value of FST (= 0.019; P < 0.001). FST and Jost’s D indexes were also estimated in pairwise comparisons and showed significant differences between most of the surveyed site pairs (P < 0.05). Structure evidenced a single genetic group among samples, however SAShA pointed to a non-panmictic condition (P = 0.011). AMOVA detected four statistical significant clusters with low level of differentiation (FCT = 0.037; P = 0.023). The gene flow model that best described the population connectivity was the island model, with ∼24 crabs being exchanged among localities per generation. Discussion The high migration rates found among localities seem to be the main force acting to sustain the distribution of the genetic diversity of U. cordatus. Despite the high gene flow and the weak population structure among samples, the significant genetic differences found suggest that gene flow alone does not bypass the effects of genetic drift, natural selection and/or human exploitation. These findings are vital for the establishment of a database to be used in the development of conservation programs. PMID:29736340

Experimentally observed conformation-dependent geometry and hidden strain in proteins.

PubMed Central

Karplus, P. A.

1996-01-01

A database has been compiled documenting the peptide conformations and geometries from 70 diverse proteins refined at 1.75 A or better. Analysis of the well-ordered residues within the database shows phi, psi-distributions that have more fine structure than is generally observed. Also, clear evidence is presented that the peptide covalent geometry depends on conformation, with the interpeptide N-C alpha-C bond angle varying by nearly +/-5 degrees from its standard value. The observed deviations from standard peptide geometry are greatest near the edges of well-populated regions, consistent with strain occurring in these conformations. Minimization of such hidden strain could be an important factor in thermostability of proteins. These empirical data describing how equilibrium peptide geometry varies as a function of conformation confirm and extend quantum mechanics calculations, and have predictive value that will aid both theoretical and experimental analyses of protein structure. PMID:8819173

Participatory action research in corrections: The HITEC 2 program.

PubMed

Cherniack, Martin; Dussetschleger, Jeffrey; Dugan, Alicia; Farr, Dana; Namazi, Sara; El Ghaziri, Mazen; Henning, Robert

2016-03-01

HITEC 2 (Health Improvement through Employee Control 2) is the follow-up to HITEC, a participatory action research (PAR) program that integrates health and work conditions interventions designed by the workforce. HITEC 2 compares intervention programs between two correctional sites, one using a pure workforce level design team and the other using a more structured and time delineated labor-management kaizen effectiveness team. HITEC 2 utilizes a seven step participatory Intervention Design and Analysis Scorecard (IDEAS) for planning interventions. Consistent with PAR, process and intervention efficacy measures are developed and administered through workforce representation. Participation levels, robustness of participatory structures and sophistication of interventions have increased at each measured interval. Health comparisons between 2008 and 2013 showed increased hypertension, static weight maintenance, and increased 'readiness to change'. The PAR approaches are robust and sustained. Their long-term effectiveness in this population is not yet clear. Copyright © 2015 Elsevier Ltd and The Ergonomics Society. All rights reserved.

Development and characterization of EST-SSR markers for Artocarpus hypargyreus (Moraceae)1

PubMed Central

Liu, Haijun; Tan, Weizheng; Sun, Hongbin; Liu, Yu; Meng, Kaikai; Liao, Wenbo

2016-01-01

Premise of the study: Polymorphic microsatellite markers were developed for Artocarpus hypargyreus (Moraceae), a threatened species endemic to China, to investigate the genetic diversity and structure of the species. Methods and Results: Based on the transcriptome data of A. hypargyreus, 63 primer pairs were preliminarily designed and tested, of which 34 were successfully amplified and 10 displayed clear polymorphisms across the 67 individuals from four populations of A. hypargyreus. The results showed the number of alleles per locus ranged from three to 10, and the observed heterozygosity and expected heterozygosity per locus varied from 0.000 to 0.706 and from 0.328 to 0.807, respectively. Conclusions: These microsatellite markers will be useful in exploring genetic diversity and structure of A. hypargyreus. Furthermore, most loci were successfully cross-amplified in A. nitidus and A. heterophyllus, indicating that they will be of great value for genetic study across this genus. PMID:28101438

Development and characterization of EST-SSR markers for Artocarpus hypargyreus (Moraceae).

PubMed

Liu, Haijun; Tan, Weizheng; Sun, Hongbin; Liu, Yu; Meng, Kaikai; Liao, Wenbo

2016-12-01

Polymorphic microsatellite markers were developed for Artocarpus hypargyreus (Moraceae), a threatened species endemic to China, to investigate the genetic diversity and structure of the species. Based on the transcriptome data of A. hypargyreus , 63 primer pairs were preliminarily designed and tested, of which 34 were successfully amplified and 10 displayed clear polymorphisms across the 67 individuals from four populations of A. hypargyreus . The results showed the number of alleles per locus ranged from three to 10, and the observed heterozygosity and expected heterozygosity per locus varied from 0.000 to 0.706 and from 0.328 to 0.807, respectively. These microsatellite markers will be useful in exploring genetic diversity and structure of A. hypargyreus . Furthermore, most loci were successfully cross-amplified in A. nitidus and A. heterophyllus , indicating that they will be of great value for genetic study across this genus.

The year-class phenomenon and the storage effect in marine fishes

NASA Astrophysics Data System (ADS)

Secor, David H.

2007-02-01

Factors contributing to population growth through strong year-class formation have driven a century of directed research in fisheries science. A central discovery of Hjort's paradigm was that multiple generations overlap and longevity is matched with frequency of strong recruitments. Here, I elaborate on this tenet by examining how intra-population modalities in spawning and early habitat use favour population resiliency. A modern theory that has application is the storage effect [Warner, R.R., Chesson, P.L., 1985. Coexistence mediated by recruitment fluctuations - a field guide to the storage effect. Am. Nat. 125, 769-787], whereby spawning stock biomass accumulates each year so that when early survival conditions are favourable, stored egg production can result in explosive population growth. I review two early life history behaviours that contribute to the storage effect: split cohorts (i.e., seasonal pulses of eggs and larvae) and contingent behaviour (i.e., dispersive and retentive patterns in early dispersal). Episodic and pulsed production of larvae is a common feature for marine fishes, well documented through otolith microstructure and hatch-date analyses. In temperate and boreal fishes, early and late spawned cohorts of larvae and juveniles may have differing fates dependent upon seasonal and inter-annual fluctuations in weather and climate. Often, a coastal fish may spawn for a protracted period, yet only a few days' egg production will result in successful recruitment. In these and other instances, it is clear that diversity in spawning behaviour can confer resilience against temporal variations in early survival conditions. Although many factors contribute to intra-population spawning modalities, size and age structure of adults play an important role. Contingent structure, an idea dating to Hjort (herring contingents) and Gilbert (salmon contingents), has been resurrected to describe the diversity of intra-population modalities observed through otolith microchemical and electronic tagging approaches. Retentive and dispersive behaviours confer resiliency against early survival conditions that vary spatially. Examples of contingent structure are increasingly numerous for diadromous fishes. Here, a nursery habitat associated with a contingent behaviour may make a small contribution in a given year, but over a decade contribute significantly to spawning stock biomass. For flatfish and other marine fishes, contingent structure is probable but not well documented. Proximate factors leading to contingent structure are poorly known, but for diadromous fishes, time of spawning and early life history energetic thresholds is hypothesized to lead to alternative life cycles. Here again time of spawning may lead to the storage effect by hedging against spatial variance in early vital rates. Managing for the storage effect will be promoted by conservation of adult age structure and early habitats upon which both strong and weak year-classes rely.

High molecular diversity in the true service tree (Sorbus domestica) despite rareness: data from Europe with special reference to the Austrian occurrence.

PubMed

George, Jan-Peter; Konrad, Heino; Collin, Eric; Thevenet, Jean; Ballian, Dalibor; Idzojtic, Marilena; Kamm, Urs; Zhelev, Peter; Geburek, Thomas

2015-06-01

Sorbus domestica (Rosaceae) is one of the rarest deciduous tree species in Europe and is characterized by a scattered distribution. To date, no large-scale geographic studies on population genetics have been carried out. Therefore, the aims of this study were to infer levels of molecular diversity across the major part of the European distribution of S. domestica and to determine its population differentiation and structure. In addition, spatial genetic structure was examined together with the patterns of historic and recent gene flow between two adjacent populations. Leaf or cambium samples were collected from 17 populations covering major parts of the European native range from north-west France to south-east Bulgaria. Seven nuclear microsatellites and one chloroplast minisatellite were examined and analysed using a variety of methods. Allelic richness was unexpectedly high for both markers within populations (mean per locus: 3·868 for nSSR and 1·647 for chloroplast minisatellite). Moreover, there was no evidence of inbreeding (mean Fis = -0·047). The Italian Peninsula was characterized as a geographic region with comparatively high genetic diversity for both genomes. Overall population differentiation was moderate (FST = 0·138) and it was clear that populations formed three groups in Europe, namely France, Mediterranean/Balkan and Austria. Historic gene flow between two local Austrian populations was high and asymmetric, while recent gene flow seemed to be disrupted. It is concluded that molecular mechanisms such as self-incompatibility and high gene flow distances are responsible for the observed level of allelic richness as well as for population differentiation. However, human influence could have contributed to the present genetic pattern, especially in the Mediterranean region. Comparison of historic and recent gene flow may mirror the progress of habitat fragmentation in eastern Austria. © The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

A molecular analysis of the patterns of genetic diversity in local chickens from western Algeria in comparison with commercial lines and wild jungle fowls.

PubMed

Mahammi, F Z; Gaouar, S B S; Laloë, D; Faugeras, R; Tabet-Aoul, N; Rognon, X; Tixier-Boichard, M; Saidi-Mehtar, N

2016-02-01

The objectives of this study were to characterize the genetic variability of village chickens from three agro-ecological regions of western Algeria: coastal (CT), inland plains (IP) and highlands (HL), to reveal any underlying population structure, and to evaluate potential genetic introgression from commercial lines into local populations. A set of 233 chickens was genotyped with a panel of 23 microsatellite markers. Geographical coordinates were individually recorded. Eight reference populations were included in the study to investigate potential gene flow: four highly selected commercial pure lines and four lines of French slow-growing chickens. Two populations of wild red jungle fowls were also genotyped to compare the range of diversity between domestic and wild fowls. A genetic diversity analysis was conducted both within and between populations. Multivariate redundancy analyses were performed to assess the relative influence of geographical location among Algerian ecotypes. The results showed a high genetic variability within the Algerian population, with 184 alleles and a mean number of 8.09 alleles per locus. The values of heterozygosity (He and Ho) ranged from 0.55 to 0.62 in Algerian ecotypes and were smaller than values found in Jungle fowl populations and higher than values found in commercial populations. Although the structuring analysis of genotypes did not reveal clear subpopulations within Algerian ecotypes, the supervised approach using geographical data showed a significant (p < 0.01) differentiation between the three ecotypes which was mainly due to altitude. Thus, the genetic diversity of Algerian ecotypes may be under the influence of two factors with contradictory effects: the geographical location and climatic conditions may induce some differentiation, whereas the high level of exchanges and gene flow may suppress it. Evidence of gene flow between commercial and Algerian local populations was observed, which may be due to unrecorded crossing with commercial chickens. Chicken ecotypes from western Algeria are characterized by a high genetic diversity and must be safeguarded as an important reservoir of genetic diversity. © 2015 Blackwell Verlag GmbH.

Determinants of Refusal of A/H1N1 Pandemic Vaccination in a High Risk Population: A Qualitative Approach

PubMed Central

d'Alessandro, Eugenie; Hubert, Dominique; Launay, Odile; Bassinet, Laurence; Lortholary, Olivier; Jaffre, Yannick; Sermet-Gaudelus, Isabelle

2012-01-01

Background Our study analyses the main determinants of refusal or acceptance of the 2009 A/H1N1 vaccine in patients with cystic fibrosis, a high-risk population for severe flu infection, usually very compliant for seasonal flu vaccine. Methodology/Principal Findings We conducted a qualitative study based on semi-structured interviews in 3 cystic fibrosis referral centres in Paris, France. The study included 42 patients with cystic fibrosis: 24 who refused the vaccine and 18 who were vaccinated. The two groups differed quite substantially in their perceptions of vaccine- and disease-related risks. Those who refused the vaccine were motivated mainly by the fears it aroused and did not explicitly consider the 2009 A/H1N1 flu a potentially severe disease. People who were vaccinated explained their choice, first and foremost, as intended to prevent the flu's potential consequences on respiratory cystic fibrosis disease. Moreover, they considered vaccination to be an indirect collective prevention tool. Patients who refused the vaccine mentioned multiple, contradictory information sources and did not appear to consider the recommendation of their local health care provider as predominant. On the contrary, those who were vaccinated stated that they had based their decision solely on the clear and unequivocal advice of their health care provider. Conclusions/Significance These results of our survey led us to formulate three main recommendations for improving adhesion to new pandemic vaccines. (1) it appears necessary to reinforce patient education about the disease and its specific risks, but also general population information about community immunity. (2) it is essential to disseminate a clear and effective message about the safety of novel vaccines. (3) this message should be conveyed by local health care providers, who should be involved in implementing immunization. PMID:22506011

Population dynamics of plant nematodes in cultivated soil: length of rotation in newly cleared and old agricultural land.

PubMed

Good, J M; Murphy, W S; Brodie, B B

1973-04-01

During a 6-year study of 1-, 2-, and 3-year crop rotations, population densities of Pratylenchus brachyurus, Trichodorus christiei, and Meloidogyne incognita were significantly affected by the choice of crops but not by length of crop rotation. The density of P. brachyurus and T. christiei increased rapidly on milo (Sorghum vulgate). In addition, populations of P. brachyurus increased significantly in cropping systems that involved crotalaria (C. rnucronata), millet (Setaria italica), and sudangrass (Sorghum sudanense). Lowest numbers of P. brachyurus occurred where okra (Hibiscus esculentus) was grown or where land was fallow. The largest increase in populations of T. christiei occurred in cropping systems that involved millet, sudangrass, and okra whereas the smallest increase occurred in cropping systems that involved crotalaria or fallow. A winter cover of rye (Secale cereale) had no distinguishable effect on population densities of P. brachyurus or T. christiei. Meloidogyne incognita was detected during the fourth year in both newly cleared and old agricultural land when okra was included in the cropping system. Detectable populations of M. incognita did not develop in any of the other cropping systems. Yields of tomato transplants were higher on the newly cleared land than on the old land. Highest yields were obtained when crotalaria was included in the cropping system. Lowest yields were obtained when milo, or fallow were included in the cropping system. Length of rotation had no distinguishable effect on yields of tomato transplants.

The Contribution of Genetic Diversity to Subdivide Populations Living in the Silk Road of China

PubMed Central

Gui, Hongsheng; Yuan, Zuyi; Li, Shengbin

2014-01-01

There are several indigenous ethnic populations along the silk road in the Northwest of China that display clear differences in culture and social customs, perhaps as a result of geographic isolation and different linguistic traditions. However, extensive trade and other interactions probably facilitated the admixture of different gene pools between these populations over the last two millennia. To further explore the evolutionary relationships of the 13 ethnic populations residing in Northwest China and to reveal the features of population admixture, the 9 most-commonly employed CODIS loci (D3S1358, TH01, D5S818, D13S317, D7S820, CSF1PO, vWA, TPOX, FGA) were selected for genotyping and further analysis. Phylogenetic tree and principal component analysis revealed clear pattern of population differentiation between 4 populations living in Sinkiang Uighur Autonomous Region and other 9 populations dwelled in the upper regions of Silk Road. R matrix regression showed high-level gene flow and population admixture dose exist among these ethic populations in the Northwest region of China. Furthermore, the Mantel test suggests that larger percent of genetic variance (21.58% versus 2.3%) can be explained by geographic isolation than linguistic barriers, which matched with the contribution of geographic factors to other world populations. PMID:24828511

Genome-wide analysis of signatures of selection in populations of African honey bees (Apis mellifera) using new web-based tools.

PubMed

Fuller, Zachary L; Niño, Elina L; Patch, Harland M; Bedoya-Reina, Oscar C; Baumgarten, Tracey; Muli, Elliud; Mumoki, Fiona; Ratan, Aakrosh; McGraw, John; Frazier, Maryann; Masiga, Daniel; Schuster, Stephen; Grozinger, Christina M; Miller, Webb

2015-07-10

With the development of inexpensive, high-throughput sequencing technologies, it has become feasible to examine questions related to population genetics and molecular evolution of non-model species in their ecological contexts on a genome-wide scale. Here, we employed a newly developed suite of integrated, web-based programs to examine population dynamics and signatures of selection across the genome using several well-established tests, including F ST, pN/pS, and McDonald-Kreitman. We applied these techniques to study populations of honey bees (Apis mellifera) in East Africa. In Kenya, there are several described A. mellifera subspecies, which are thought to be localized to distinct ecological regions. We performed whole genome sequencing of 11 worker honey bees from apiaries distributed throughout Kenya and identified 3.6 million putative single-nucleotide polymorphisms. The dense coverage allowed us to apply several computational procedures to study population structure and the evolutionary relationships among the populations, and to detect signs of adaptive evolution across the genome. While there is considerable gene flow among the sampled populations, there are clear distinctions between populations from the northern desert region and those from the temperate, savannah region. We identified several genes showing population genetic patterns consistent with positive selection within African bee populations, and between these populations and European A. mellifera or Asian Apis florea. These results lay the groundwork for future studies of adaptive ecological evolution in honey bees, and demonstrate the use of new, freely available web-based tools and workflows ( http://usegalaxy.org/r/kenyanbee ) that can be applied to any model system with genomic information.

Population Growth and Economic and Social Development.

ERIC Educational Resources Information Center

Clausen, A. W.

Because evidence is clear that in many developing countries development will be postponed indefinitely unless slower population growth can be achieved soon, the international community must work together in a renewed effort to slow population growth. Assistance can be accomplished in three ways: (1) encouraging dialog aimed at forging…

Genetic structure and early effects of inbreeding in fragmented temperate forests of a self-incompatible tree, Embothrium coccineum.

PubMed

Mathiasen, Paula; Rovere, Adriana E; Premoli, Andrea C

2007-02-01

Deforestation of temperate forests has created landscapes of forest remnants in matrices of intense human use. We studied the genetic effects of fragmentation in southern Chile on Embothrium coccineum J.R. et G. Forster, an early colonizing, bird-pollinated tree. We tested the hypothesis that, because of its self-incompatibility and life-history strategy, E. coccineum is less strongly affected by fragmentation. We studied the effects of reduced population size and increased isolation on population genetic structure and early performance of progeny. Samples were collected from spatially isolated trees and six fragments of differing sizes (small, 1 ha; medium, 20 ha; large, >150 ha). Based on isozyme polymorphisms we estimated parameters of genetic diversity, divergence, and inbreeding for adults and greenhouse-grown progeny. We also measured germination, seedling growth, and outcrossing rates on progeny arrays. Genetic variation of adults did not correlate significantly with population size, as expected, given that fragmentation occurred relatively recently. Weak effects of fragmentation were measured on progeny. Only adults yielded significant inbreeding. Similar total genetic diversity was found in adults and progeny. Low but significant genetic differentiation existed among adult and progeny populations. Seedling growth correlated positively with the effective number of alleles, showing deleterious effects of inbreeding on progeny. Seeds from small fragments had the highest outcrossing rates and germination success, indicating that higher pollinator activity in such fragments reduced selfing, thereby buffering genetic erosion and maintaining adaptive variation. The effects of forest fragmentation were detectable in E. coccineum, but these effects will probably not be detrimental to the viability of remnant populations because small, fragmented populations demonstrated higher levels of gene flow and lower inbreeding than larger stands. Pioneer species that are insensitive to forest clearing may be crucial in recovery plans to facilitate the establishment of species intolerant to such disturbance.

Functional acclimation across microgeographic scales in Dodonaea viscosa

PubMed Central

Baruch, Zdravko; Jones, Alice R; Hill, Kathryn E; McInerney, Francesca A; Blyth, Colette; Caddy-Retalic, Stefan; Christmas, Matthew J; Gellie, Nicholas J C; Lowe, Andrew J; Martin-Fores, Irene; Nielson, Kristine E

2018-01-01

Abstract Intraspecific plant functional trait variation provides mechanistic insight into persistence and can infer population adaptive capacity. However, most studies explore intraspecific trait variation in systems where geographic and environmental distances co-vary. Such a design reduces the certainty of trait–environment associations, and it is imperative for studies that make trait–environment associations be conducted in systems where environmental distance varies independently of geographic distance. Here we explored trait variation in such a system, and aimed to: (i) quantify trait variation of parent and offspring generations, and associate this variation to parental environments; (ii) determine the traits which best explain population differences; (iii) compare parent and offspring trait–trait relationships. We characterized 15 plant functional traits in eight populations of a shrub with a maximum separation ca. 100 km. Populations differed markedly in aridity and elevation, and environmental distance varied independently of geographic distance. We measured traits in parent populations collected in the field, as well as their offspring reared in greenhouse conditions. Parent traits regularly associated with their environment. These associations were largely lost in the offspring generation, indicating considerable phenotypic plasticity. An ordination of parent traits showed clear structure with strong influence of leaf area, specific leaf area, stomatal traits, isotope δ13C and δ15N ratios, and Narea, whereas the offspring ordination was less structured. Parent trait–trait correlations were in line with expectations from the leaf economic spectrum. We show considerable trait plasticity in the woody shrub over microgeographic scales (<100 km), indicating it has the adaptive potential within a generation to functionally acclimate to a range of abiotic conditions. Since our study shrub is commonly used for restoration in southern Australia and local populations do not show strong genetic differentiation in functional traits, the potential risks of transferring seed across the broad environmental conditions are not likely to be a significant issue.

The development of 10 novel polymorphic microsatellite markers through next generation sequencing and a preliminary population genetic analysis for the endangered Glenelg spiny crayfish, Euastacus bispinosus.

PubMed

Miller, Adam D; Van Rooyen, Anthony; Sweeney, Oisín F; Whiterod, Nick S; Weeks, Andrew R

2013-07-01

The Glenelg spiny crayfish, Euastacus bispinosus, is an iconic freshwater invertebrate of south eastern Australia and listed as 'endangered' under the Environment Protection and Biodiversity Conservation Act 1999, and 'vulnerable' under the International Union for Conservation of Nature's Red List. The species has suffered major population declines as a result of over-fishing, low environmental flows, the introduction of invasive fish species and habitat degradation. In order to develop an effective conservation strategy, patterns of gene flow, genetic structure and genetic diversity across the species distribution need to be clearly understood. In this study we develop a suite of polymorphic microsatellite markers by next generation sequencing. A total of 15 polymorphic loci were identified and 10 characterized using 22 individuals from the lower Glenelg River. We observed low to moderate genetic variation across most loci (mean number of alleles per locus = 2.80; mean expected heterozygosity = 0.36) with no evidence of individual loci deviating significantly from Hardy-Weinberg equilibrium. Marker independence was confirmed with tests for linkage disequilibrium, and analyses indicated no evidence of null alleles across loci. Individuals from two additional sites (Crawford River, Victoria; Ewens Ponds Conservation Park, South Australia) were genotyped at all 10 loci and a preliminary investigation of genetic diversity and population structure was undertaken. Analyses indicate high levels of genetic differentiation among sample locations (F ST = 0.49), while the Ewens Ponds population is genetically homogeneous, indicating a likely small founder group and ongoing inbreeding. Management actions will be needed to restore genetic diversity in this and possibly other at risk populations. These markers will provide a valuable resource for future population genetic assessments so that an effective framework can be developed for implementing conservation strategies for E. bispinosus.

Comparison of alternative image reformatting techniques in micro-computed tomography and tooth clearing for detailed canal morphology.

PubMed

Lee, Ki-Wook; Kim, Yeun; Perinpanayagam, Hiran; Lee, Jong-Ki; Yoo, Yeon-Jee; Lim, Sang-Min; Chang, Seok Woo; Ha, Byung-Hyun; Zhu, Qiang; Kum, Kee-Yeon

2014-03-01

Micro-computed tomography (MCT) shows detailed root canal morphology that is not seen with traditional tooth clearing. However, alternative image reformatting techniques in MCT involving 2-dimensional (2D) minimum intensity projection (MinIP) and 3-dimensional (3D) volume-rendering reconstruction have not been directly compared with clearing. The aim was to compare alternative image reformatting techniques in MCT with tooth clearing on the mesiobuccal (MB) root of maxillary first molars. Eighteen maxillary first molar MB roots were scanned, and 2D MinIP and 3D volume-rendered images were reconstructed. Subsequently, the same MB roots were processed by traditional tooth clearing. Images from 2D, 3D, 2D + 3D, and clearing techniques were assessed by 4 endodontists to classify canal configuration and to identify fine anatomic structures such as accessory canals, intercanal communications, and loops. All image reformatting techniques in MCT showed detailed configurations and numerous fine structures, such that none were classified as simple type I or II canals; several were classified as types III and IV according to Weine classification or types IV, V, and VI according to Vertucci; and most were nonclassifiable because of their complexity. The clearing images showed less detail, few fine structures, and numerous type I canals. Classification of canal configuration was in 100% intraobserver agreement for all 18 roots visualized by any of the image reformatting techniques in MCT but for only 4 roots (22.2%) classified according to Weine and 6 (33.3%) classified according to Vertucci, when using the clearing technique. The combination of 2D MinIP and 3D volume-rendered images showed the most detailed canal morphology and fine anatomic structures. Copyright © 2014 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Genetic structure of the date palm (Phoenix dactylifera) in the Old World reveals a strong differentiation between eastern and western populations.

PubMed

Zehdi-Azouzi, Salwa; Cherif, Emira; Moussouni, Souhila; Gros-Balthazard, Muriel; Abbas Naqvi, Summar; Ludeña, Bertha; Castillo, Karina; Chabrillange, Nathalie; Bouguedoura, Nadia; Bennaceur, Malika; Si-Dehbi, Farida; Abdoulkader, Sabira; Daher, Abdourahman; Terral, Jean-Frederic; Santoni, Sylvain; Ballardini, Marco; Mercuri, Antonio; Ben Salah, Mohamed; Kadri, Karim; Othmani, Ahmed; Littardi, Claudio; Salhi-Hannachi, Amel; Pintaud, Jean-Christophe; Aberlenc-Bertossi, Frédérique

2015-07-01

Date palms (Phoenix dactylifera, Arecaceae) are of great economic and ecological value to the oasis agriculture of arid and semi-arid areas. However, despite the availability of a large date palm germplasm spreading from the Atlantic shores to Southern Asia, improvement of the species is being hampered by a lack of information on global genetic diversity and population structure. In order to contribute to the varietal improvement of date palms and to provide new insights on the influence of geographic origins and human activity on the genetic structure of the date palm, this study analysed the diversity of the species. Genetic diversity levels and population genetic structure were investigated through the genotyping of a collection of 295 date palm accessions ranging from Mauritania to Pakistan using a set of 18 simple sequence repeat (SSR) markers and a plastid minisatellite. Using a Bayesian clustering approach, the date palm genotypes can be structured into two different gene pools: the first, termed the Eastern pool, consists of accessions from Asia and Djibouti, whilst the second, termed the Western pool, consists of accessions from Africa. These results confirm the existence of two ancient gene pools that have contributed to the current date palm diversity. The presence of admixed genotypes is also noted, which points at gene flows between eastern and western origins, mostly from east to west, following a human-mediated diffusion of the species. This study assesses the distribution and level of genetic diversity of accessible date palm resources, provides new insights on the geographic origins and genetic history of the cultivated component of this species, and confirms the existence of at least two domestication origins. Furthermore, the strong genetic structure clearly established here is a prerequisite for any breeding programme exploiting the effective polymorphism related to each gene pool. © The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Genetic structure, relationships and admixture with wild relatives in native pig breeds from Iberia and its islands.

PubMed

Gama, Luis T; Martínez, Amparo M; Carolino, Inês; Landi, Vincenzo; Delgado, Juan V; Vicente, Antonio A; Vega-Pla, José L; Cortés, Oscar; Sousa, Conceição O

2013-06-14

Native pig breeds in the Iberian Peninsula are broadly classified as belonging to either the Celtic or the Mediterranean breed groups, but there are other local populations that do not fit into any of these groups. Most of the native pig breeds in Iberia are in danger of extinction, and the assessment of their genetic diversity and population structure, relationships and possible admixture between breeds, and the appraisal of conservation alternatives are crucial to adopt appropriate management strategies. A panel of 24 microsatellite markers was used to genotype 844 animals representing the 17 most important native swine breeds and wild populations existing in Portugal and Spain and various statistical tools were applied to analyze the results. Genetic diversity was high in the breeds studied, with an overall mean of 13.6 alleles per locus and an average expected heterozygosity of 0.80. Signs of genetic bottlenecks were observed in breeds with a small census size, and population substructure was present in some of the breeds with larger census sizes. Variability among breeds accounted for about 20% of the total genetic diversity, and was explained mostly by differences among the Celtic, Mediterranean and Basque breed groups, rather than by differences between domestic and wild pigs. Breeds clustered closely according to group, and proximity was detected between wild pigs and the Mediterranean cluster of breeds. Most breeds had their own structure and identity, with very little evidence of admixture, except for the Retinto and Entrepelado varieties of the Mediterranean group, which are very similar. Genetic influence of the identified breed clusters extends beyond the specific geographical areas across borders throughout the Iberian Peninsula, with a very sharp transition from one breed group to another. Analysis of conservation priorities confirms that the ranking of a breed for conservation depends on the emphasis placed on its contribution to the between- and within-breed components of genetic diversity. Native pig breeds in Iberia reveal high levels of genetic diversity, a solid breed structure and a clear organization in well-defined clusters.

Effectiveness of Genomic Prediction of Maize Hybrid Performance in Different Breeding Populations and Environments

PubMed Central

Windhausen, Vanessa S.; Atlin, Gary N.; Hickey, John M.; Crossa, Jose; Jannink, Jean-Luc; Sorrells, Mark E.; Raman, Babu; Cairns, Jill E.; Tarekegne, Amsal; Semagn, Kassa; Beyene, Yoseph; Grudloyma, Pichet; Technow, Frank; Riedelsheimer, Christian; Melchinger, Albrecht E.

2012-01-01

Genomic prediction is expected to considerably increase genetic gains by increasing selection intensity and accelerating the breeding cycle. In this study, marker effects estimated in 255 diverse maize (Zea mays L.) hybrids were used to predict grain yield, anthesis date, and anthesis-silking interval within the diversity panel and testcross progenies of 30 F2-derived lines from each of five populations. Although up to 25% of the genetic variance could be explained by cross validation within the diversity panel, the prediction of testcross performance of F2-derived lines using marker effects estimated in the diversity panel was on average zero. Hybrids in the diversity panel could be grouped into eight breeding populations differing in mean performance. When performance was predicted separately for each breeding population on the basis of marker effects estimated in the other populations, predictive ability was low (i.e., 0.12 for grain yield). These results suggest that prediction resulted mostly from differences in mean performance of the breeding populations and less from the relationship between the training and validation sets or linkage disequilibrium with causal variants underlying the predicted traits. Potential uses for genomic prediction in maize hybrid breeding are discussed emphasizing the need of (1) a clear definition of the breeding scenario in which genomic prediction should be applied (i.e., prediction among or within populations), (2) a detailed analysis of the population structure before performing cross validation, and (3) larger training sets with strong genetic relationship to the validation set. PMID:23173094

Accountable care organization readiness and academic medical centers.

PubMed

Berkowitz, Scott A; Pahira, Jennifer J

2014-09-01

As academic medical centers (AMCs) consider becoming accountable care organizations (ACOs) under Medicare, they must assess their readiness for this transition. Of the 253 Medicare ACOs prior to 2014, 51 (20%) are AMCs. Three critical components of ACO readiness are institutional and ACO structure, leadership, and governance; robust information technology and analytic systems; and care coordination and management to improve care delivery and health at the population level. All of these must be viewed through the lens of unique AMC mission-driven goals.There is clear benefit to developing and maintaining a centralized internal leadership when it comes to driving change within an ACO, yet there is also the need for broad stakeholder involvement. Other important structural features are an extensive primary care foundation; concomitant operation of a managed care plan or risk-bearing entity; or maintaining a close relationship with post-acute-care or skilled nursing facilities, which provide valuable expertise in coordinating care across the continuum. ACOs also require comprehensive and integrated data and analytic systems that provide meaningful population data to inform care teams in real time, promote quality improvement, and monitor spending trends. AMCs will require proven care coordination and management strategies within a population health framework and deployment of an innovative workforce.AMC core functions of providing high-quality subspecialty and primary care, generating new knowledge, and training future health care leaders can be well aligned with a transition to an ACO model. Further study of results from Medicare-related ACO programs and commercial ACOs will help define best practices.

Genetic structure of eelgrass Zostera marina meadows in an embayment with restricted water flow

USGS Publications Warehouse

Munoz-Salazar, R.; Talbot, S.L.; Sage, G.K.; Ward, D.H.; Cabello-Pasini, Alejandro

2006-01-01

Genetic structure of the seagrass Zostera marina in a coastal lagoon with restricted water flow, and with heterogeneous water residence times and oceanographic characteristics, was assessed using 8 polymorphic microsatellite loci. Analyses of genetic differentiation (??) and Bayesian clustering suggested that the Z. marina population in San Quintin Bay (SQB) is genetically substructured, with at least 4 genetically different groups: (1) West Head, (2) Mouth, (3) East Arm, and (4) East Head. The greatest ?? value was observed between the most distant sites (?? = 0.095). The lowest values were found among sites closest to the mouth of the coastal lagoon (?? = 0.000 to 0.009). The maximum likelihood approach showed that the sites at the mouth have a mixed pattern of gene flow without a unidirectional pattern. In contrast, there was a clear pattern of asymmetrical gene flow from the mouth towards the West Head. These results suggested that the restriction of water flow at the heads, current pattern, and the distance between sites can reduce genetic flow and promote genetic differences within Z. marina meadows in small water embayments such as SQB. Though the population is genetically substructured and a 14 % decline in cover has been detected, this study did not show evidence of a recent genetic bottleneck. In contrast, mouth sites have experienced a recent expansion in their population size, and also perhaps a recent influx of rare alleles from genetically distinct immigrants. ?? Inter-Research 2006.

Structural ensembles reveal intrinsic disorder for the multi-stimuli responsive bio-mimetic protein Rec1-resilin

PubMed Central

Balu, Rajkamal; Knott, Robert; Cowieson, Nathan P.; Elvin, Christopher M.; Hill, Anita J.; Choudhury, Namita R.; Dutta, Naba K.

2015-01-01

Rec1-resilin is the first recombinant resilin-mimetic protein polymer, synthesized from exon-1 of the Drosophila melanogaster gene CG15920 that has demonstrated unusual multi-stimuli responsiveness in aqueous solution. Crosslinked hydrogels of Rec1-resilin have also displayed remarkable mechanical properties including near-perfect rubber-like elasticity. The structural basis of these extraordinary properties is not clearly understood. Here we combine a computational and experimental investigation to examine structural ensembles of Rec1-resilin in aqueous solution. The structure of Rec1-resilin in aqueous solutions is investigated experimentally using circular dichroism (CD) spectroscopy and small angle X-ray scattering (SAXS). Both bench-top and synchrotron SAXS are employed to extract structural data sets of Rec1-resilin and to confirm their validity. Computational approaches have been applied to these experimental data sets in order to extract quantitative information about structural ensembles including radius of gyration, pair-distance distribution function, and the fractal dimension. The present work confirms that Rec1-resilin is an intrinsically disordered protein (IDP) that displays equilibrium structural qualities between those of a structured globular protein and a denatured protein. The ensemble optimization method (EOM) analysis reveals a single conformational population with partial compactness. This work provides new insight into the structural ensembles of Rec1-resilin in solution. PMID:26042819

Structural ensembles reveal intrinsic disorder for the multi-stimuli responsive bio-mimetic protein Rec1-resilin.

PubMed

Balu, Rajkamal; Knott, Robert; Cowieson, Nathan P; Elvin, Christopher M; Hill, Anita J; Choudhury, Namita R; Dutta, Naba K

2015-06-04

Rec1-resilin is the first recombinant resilin-mimetic protein polymer, synthesized from exon-1 of the Drosophila melanogaster gene CG15920 that has demonstrated unusual multi-stimuli responsiveness in aqueous solution. Crosslinked hydrogels of Rec1-resilin have also displayed remarkable mechanical properties including near-perfect rubber-like elasticity. The structural basis of these extraordinary properties is not clearly understood. Here we combine a computational and experimental investigation to examine structural ensembles of Rec1-resilin in aqueous solution. The structure of Rec1-resilin in aqueous solutions is investigated experimentally using circular dichroism (CD) spectroscopy and small angle X-ray scattering (SAXS). Both bench-top and synchrotron SAXS are employed to extract structural data sets of Rec1-resilin and to confirm their validity. Computational approaches have been applied to these experimental data sets in order to extract quantitative information about structural ensembles including radius of gyration, pair-distance distribution function, and the fractal dimension. The present work confirms that Rec1-resilin is an intrinsically disordered protein (IDP) that displays equilibrium structural qualities between those of a structured globular protein and a denatured protein. The ensemble optimization method (EOM) analysis reveals a single conformational population with partial compactness. This work provides new insight into the structural ensembles of Rec1-resilin in solution.

Structural ensembles reveal intrinsic disorder for the multi-stimuli responsive bio-mimetic protein Rec1-resilin

NASA Astrophysics Data System (ADS)

Balu, Rajkamal; Knott, Robert; Cowieson, Nathan P.; Elvin, Christopher M.; Hill, Anita J.; Choudhury, Namita R.; Dutta, Naba K.

2015-06-01

Rec1-resilin is the first recombinant resilin-mimetic protein polymer, synthesized from exon-1 of the Drosophila melanogaster gene CG15920 that has demonstrated unusual multi-stimuli responsiveness in aqueous solution. Crosslinked hydrogels of Rec1-resilin have also displayed remarkable mechanical properties including near-perfect rubber-like elasticity. The structural basis of these extraordinary properties is not clearly understood. Here we combine a computational and experimental investigation to examine structural ensembles of Rec1-resilin in aqueous solution. The structure of Rec1-resilin in aqueous solutions is investigated experimentally using circular dichroism (CD) spectroscopy and small angle X-ray scattering (SAXS). Both bench-top and synchrotron SAXS are employed to extract structural data sets of Rec1-resilin and to confirm their validity. Computational approaches have been applied to these experimental data sets in order to extract quantitative information about structural ensembles including radius of gyration, pair-distance distribution function, and the fractal dimension. The present work confirms that Rec1-resilin is an intrinsically disordered protein (IDP) that displays equilibrium structural qualities between those of a structured globular protein and a denatured protein. The ensemble optimization method (EOM) analysis reveals a single conformational population with partial compactness. This work provides new insight into the structural ensembles of Rec1-resilin in solution.

Do Individual and Neighborhood Characteristics Influence Perceived Air Quality?

PubMed Central

Deguen, Séverine; Padilla, Manon; Kihal-Talantikite, Wahida

2017-01-01

Background: Despite improvements, air pollution still remains a major public health issue. Numerous epidemiological studies have demonstrated the adverse health effects of air pollution exposure based on modeled measures, but only a few have considered the health impact of perceived air quality. Improving our knowledge of individual perceptions is crucial to defining targeted actions and promoting appropriate intervention measures. Our objective is to investigate the relationship between subjective and objective measures of air pollution and to focus on how individual characteristics combined with the neighborhood socioeconomic deprivation index, measured at a fine spatial scale, may or may not alter this relationship. Materials and Methods: The subjective measures of air quality reported by a sample of Lyon residents were collected via an individual questionnaire. The objective measures of air pollution were modeled by the local air quality monitoring network of the Rhône-Alpes region at census block level. We used a socioeconomic deprivation index to capture the different socioeconomic dimensions at census block level. The statistical analysis was structured in two steps: (1) identification of individual determinants of the subjective measures of air quality using multiple correspondence analysis followed by hierarchical clustering; (2) identification of individual and contextual characteristics that may alter the relationship between the objective and subjective measures of air pollution. Results: Among the youngest and the middle aged population (ages 30 to 59), consistent results between level of satisfaction, perceived air quality and objective measures of air pollution were found whatever the individual characteristics of the population. It is less clear among the oldest population: globally no significant difference between the NO2 concentrations and the level of satisfaction was observed. Conclusions: We found a significant relationship between the subjective and objective measures of air pollution in many population sub-groups with different combinations of individual characteristics. The relationship is less clear among the oldest population, which confirms previous findings. Our finding highlights that age combined with low level of education and unemployment, or women or health problems as well as the neighborhood deprivation index influence the level of air quality satisfaction. PMID:29231899

Do Individual and Neighborhood Characteristics Influence Perceived Air Quality?

PubMed

Deguen, Séverine; Padilla, Manon; Padilla, Cindy; Kihal-Talantikite, Wahida

2017-12-12

Background : Despite improvements, air pollution still remains a major public health issue. Numerous epidemiological studies have demonstrated the adverse health effects of air pollution exposure based on modeled measures, but only a few have considered the health impact of perceived air quality. Improving our knowledge of individual perceptions is crucial to defining targeted actions and promoting appropriate intervention measures. Our objective is to investigate the relationship between subjective and objective measures of air pollution and to focus on how individual characteristics combined with the neighborhood socioeconomic deprivation index, measured at a fine spatial scale, may or may not alter this relationship. Materials and Methods : The subjective measures of air quality reported by a sample of Lyon residents were collected via an individual questionnaire. The objective measures of air pollution were modeled by the local air quality monitoring network of the Rhône-Alpes region at census block level. We used a socioeconomic deprivation index to capture the different socioeconomic dimensions at census block level. The statistical analysis was structured in two steps: (1) identification of individual determinants of the subjective measures of air quality using multiple correspondence analysis followed by hierarchical clustering; (2) identification of individual and contextual characteristics that may alter the relationship between the objective and subjective measures of air pollution. Results : Among the youngest and the middle aged population (ages 30 to 59), consistent results between level of satisfaction, perceived air quality and objective measures of air pollution were found whatever the individual characteristics of the population. It is less clear among the oldest population: globally no significant difference between the NO₂ concentrations and the level of satisfaction was observed. Conclusion s : We found a significant relationship between the subjective and objective measures of air pollution in many population sub-groups with different combinations of individual characteristics. The relationship is less clear among the oldest population, which confirms previous findings. Our finding highlights that age combined with low level of education and unemployment, or women or health problems as well as the neighborhood deprivation index influence the level of air quality satisfaction.

Chemical evolution and stellar populations in the Sagittarius dwarf Spheroidal Galaxy

NASA Astrophysics Data System (ADS)

Sbordone, L.; Bonifacio, P.; Giuffrida, G.; Marconi, G.; Monaco, L.; Zaggia, S.

2007-05-01

The closest neighbour of the Milky Way (MW), the Sagittarius dwarf Spheroidal Galaxy (Sgr dSph) is being tidally destroyed by the interaction with our Galaxy, losing its stellar content along a huge stream clearly detectable within the Halo. This makes the Sgr dSph an ideal laboratory to study at the same time the chemical evolution of dwarf galaxies and their role in building bigger structures such as the MW. Since some years we are studying the stellar populations of the Sgr main body and stream, with particular attention to their detailed chemical composition. We collected detailed abundances (up to 22 elements, O to Eu) for 27 stars in the Sgr dSph main body, 5 in the associated globular cluster Terzan 7, and 12 more in the trailing Sgr tidal arm (UVES@VLT and SARG@TNG data). We are also conducting a large FLAMES@VLT chemical and dynamical analysis aimed at obtaining metallicities, alpha-elements content and radial velocities from automated analysis of the spectra. Finally, we just completed the first large scale photometric and spectroscopic survey of the stellar populations across all the dSph main body extension with VIMOS@VLT, aimed at exploring the variations in stellar populations and at deriving radial velocity memberships for future high resolution spectroscopic analysis. The picture emerging from all these studies portraits a large and extremely complex object, with signs of a long and still unclear evolution. Metallicity varies across three orders of magnitude ([Fe/H] from -3 to 0), CMDs change surprisingly from the core to the outskirts of the galaxy, and the chemical composition of the most metal rich objects show a very characteristic signature, with underabundant alpha elements, deficient Na, underabundant Fe-peak Mn, Co, Ni, Cu and Zn, and strongly enhanced n-capture elements La and Nd. This highly peculiar "signature" can also be effectively used to recognized stripped populations lost by Sgr in favour of the MW system, as clearly showed by the globular Palomar 12, which shows the same chemical anomalies detected in Sgr dSph.

Bonding in Heavier Group 14 Zero-Valent Complexes-A Combined Maximum Probability Domain and Valence Bond Theory Approach.

PubMed

Turek, Jan; Braïda, Benoît; De Proft, Frank

2017-10-17

The bonding in heavier Group 14 zero-valent complexes of a general formula L 2 E (E=Si-Pb; L=phosphine, N-heterocyclic and acyclic carbene, cyclic tetrylene and carbon monoxide) is probed by combining valence bond (VB) theory and maximum probability domain (MPD) approaches. All studied complexes are initially evaluated on the basis of the structural parameters and the shape of frontier orbitals revealing a bent structural motif and the presence of two lone pairs at the central E atom. For the VB calculations three resonance structures are suggested, representing the "ylidone", "ylidene" and "bent allene" structures, respectively. The influence of both ligands and central atoms on the bonding situation is clearly expressed in different weights of the resonance structures for the particular complexes. In general, the bonding in the studied E 0 compounds, the tetrylones, is best described as a resonating combination of "ylidone" and "ylidene" structures with a minor contribution of the "bent allene" structure. Moreover, the VB calculations allow for a straightforward assessment of the π-backbonding (E→L) stabilization energy. The validity of the suggested resonance model is further confirmed by the complementary MPD calculations focusing on the E lone pair region as well as the E-L bonding region. Likewise, the MPD method reveals a strong influence of the σ-donating and π-accepting properties of the ligand. In particular, either one single domain or two symmetrical domains are found in the lone pair region of the central atom, supporting the predominance of either the "ylidene" or "ylidone" structures having one or two lone pairs at the central atom, respectively. Furthermore, the calculated average populations in the lone pair MPDs correlate very well with the natural bond orbital (NBO) populations, and can be related to the average number of electrons that is backdonated to the ligands. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Genetic structure of duckweed population of Spirodela, Landoltia and Lemna from Lake Tai, China.

PubMed

Tang, Jie; Zhang, Fei; Cui, Weihua; Ma, Jiong

2014-06-01

Duckweed is widely used in environmental biotechnology and has recently emerged as a potential feedstock for biofuels due to its high growth rate and starch content. The genetic diversity and composition of a natural duckweed population in genera Spirodela, Landoltia and Lemna from Lake Tai, China, were investigated using probabilistic analysis of multilocus sequence typing (MLST). The 78 strains were categorized into five lineages, among which strains representing L. aequinoctialis and S. polyrhiza were predominant. Among the five lineages, interlineage transfers of markers were infrequent and no recombination was statistically detected. Tajima's D tests determined that all loci are subject to population bottlenecks, which is likely one of the main reasons for the low genetic diversity observed within the lineages. Interestingly, strains of L. turionifera are found to contain small admixture from L. minor, providing rare evidence of transfer of genetic materials in duckweed. This was discussed with respect to the hypothesis that a cross of these two gave rise to L. japonica. Moreover, the conventional maximum-likelihood phylogenetic analysis clearly recognized all the species in the three genera with high bootstrap supports. In conclusion, this work offers a basic framework for using MLST to characterize Spirodela, Landoltia and in particular Lemna strains at the species level, and to study population genetics and evolution history of natural duckweed populations.

A genetically diverse but distinct North American population of Sarcocystis neurona includes an overrepresented clone described by 12 microsatellite alleles.

PubMed

Asmundsson, Ingrid M; Dubey, J P; Rosenthal, Benjamin M

2006-09-01

The population genetics and systematics of most coccidians remain poorly defined despite their impact on human and veterinary health. Non-recombinant parasite clones characterized by distinct transmission and pathogenesis traits persist in the coccidian Toxoplasma gondii despite opportunities for sexual recombination. In order to determine whether this may be generally true for tissue-cyst forming coccidia, and to address evolutionary and taxonomic problems within the genus Sarcocystis, we characterized polymorphic microsatellite markers in Sarcocystis neurona, the major causative agent of equine protozoal myeloencephalitis (EPM). Bayesian statistical modeling, phylogenetic reconstruction based on genotypic chord distances, and analyses of linkage disequilibrium were employed to examine the population structure within S. neurona and closely related Sarcocystis falcatula isolates from North and South America. North American S. neurona were clearly differentiated from those of South America and also from isolates of S. falcatula. Although S. neurona is characterized by substantial allelic and genotypic diversity typical of interbreeding populations, one genotype occurs with significantly excessive frequency; thus, some degree of asexual propagation of S. neurona clones may naturally occur. Finally, S. neurona isolated from disparate North American localities and diverse hosts (opossums, a Southern sea otter, and horses) comprise a single genetic population. Isolates associated with clinical neurological disease bear no obvious distinction as measured by these presumably neutral genetic markers.

Extensive population genetic structure in the giraffe

PubMed Central

Brown, David M; Brenneman, Rick A; Koepfli, Klaus-Peter; Pollinger, John P; Milá, Borja; Georgiadis, Nicholas J; Louis, Edward E; Grether, Gregory F; Jacobs, David K; Wayne, Robert K

2007-01-01

Background A central question in the evolutionary diversification of large, widespread, mobile mammals is how substantial differentiation can arise, particularly in the absence of topographic or habitat barriers to dispersal. All extant giraffes (Giraffa camelopardalis) are currently considered to represent a single species classified into multiple subspecies. However, geographic variation in traits such as pelage pattern is clearly evident across the range in sub-Saharan Africa and abrupt transition zones between different pelage types are typically not associated with extrinsic barriers to gene flow, suggesting reproductive isolation. Results By analyzing mitochondrial DNA sequences and nuclear microsatellite loci, we show that there are at least six genealogically distinct lineages of giraffe in Africa, with little evidence of interbreeding between them. Some of these lineages appear to be maintained in the absence of contemporary barriers to gene flow, possibly by differences in reproductive timing or pelage-based assortative mating, suggesting that populations usually recognized as subspecies have a long history of reproductive isolation. Further, five of the six putative lineages also contain genetically discrete populations, yielding at least 11 genetically distinct populations. Conclusion Such extreme genetic subdivision within a large vertebrate with high dispersal capabilities is unprecedented and exceeds that of any other large African mammal. Our results have significant implications for giraffe conservation, and imply separate in situ and ex situ management, not only of pelage morphs, but also of local populations. PMID:18154651

Extensive population genetic structure in the giraffe.

PubMed

Brown, David M; Brenneman, Rick A; Koepfli, Klaus-Peter; Pollinger, John P; Milá, Borja; Georgiadis, Nicholas J; Louis, Edward E; Grether, Gregory F; Jacobs, David K; Wayne, Robert K

2007-12-21

A central question in the evolutionary diversification of large, widespread, mobile mammals is how substantial differentiation can arise, particularly in the absence of topographic or habitat barriers to dispersal. All extant giraffes (Giraffa camelopardalis) are currently considered to represent a single species classified into multiple subspecies. However, geographic variation in traits such as pelage pattern is clearly evident across the range in sub-Saharan Africa and abrupt transition zones between different pelage types are typically not associated with extrinsic barriers to gene flow, suggesting reproductive isolation. By analyzing mitochondrial DNA sequences and nuclear microsatellite loci, we show that there are at least six genealogically distinct lineages of giraffe in Africa, with little evidence of interbreeding between them. Some of these lineages appear to be maintained in the absence of contemporary barriers to gene flow, possibly by differences in reproductive timing or pelage-based assortative mating, suggesting that populations usually recognized as subspecies have a long history of reproductive isolation. Further, five of the six putative lineages also contain genetically discrete populations, yielding at least 11 genetically distinct populations. Such extreme genetic subdivision within a large vertebrate with high dispersal capabilities is unprecedented and exceeds that of any other large African mammal. Our results have significant implications for giraffe conservation, and imply separate in situ and ex situ management, not only of pelage morphs, but also of local populations.

Is proximity to land-based sources of coral stressors an appropriate measure of risk to coral reefs? An example from the Florida Reef Tract.

PubMed

Lirman, Diego; Fong, Peggy

2007-06-01

Localized declines in coral condition are commonly linked to land-based sources of stressors that influence gradients of water quality, and the distance to sources of stressors is commonly used as a proxy for predicting the vulnerability and future status of reef resources. In this study, we evaluated explicitly whether proximity to shore and connections to coastal bays, two measures of potential land-based sources of disturbance, influence coral community and population structure, and the abundance, distribution, and condition of corals within patch reefs of the Florida Reef Tract. In the Florida Keys, long-term monitoring has documented significant differences in water quality along a cross-shelf gradient. Inshore habitats exhibit higher levels of nutrients (DIN and TP), TOC, turbidity, and light attenuation, and these levels decrease with increasing distance from shore and connections to tidal bays. In clear contrast to these patterns of water quality, corals on inshore patch reefs exhibited significantly higher coral cover, higher growth rates, and lower partial mortality rates than those documented in similar offshore habitats. Coral recruitment rates did not differ between inshore and offshore habitats. Corals on patch reefs closest to shore had well-spread population structures numerically dominated by intermediate to large colonies, while offshore populations showed narrower size-distributions that become increasingly positively skewed. Differences in size-structure of coral populations were attributed to faster growth and lower rates of partial mortality at inshore habitats. While the underlying causes for the favorable condition of inshore coral communities are not yet known, we hypothesize that the ability of corals to shift their trophic mode under adverse environmental conditions may be partly responsible for the observed patterns, as shown in other reef systems. This study, based on data collected from a uniform reef habitat type and coral species with diverse life-history and stress-response patterns from a heavily exploited reef system, showed that proximity to potential sources of stressors may not always prove an adequate proxy for assigning potential risks to reef health, and that hypothesized patterns of coral cover, population size-structure, growth, and mortality are not always directly related to water quality gradients.

Zonal hierarchy of differentiation markers and nestin expression during oval cell mediated rat liver regeneration.

PubMed

Koenig, Sarah; Probst, Irmelin; Becker, Heinz; Krause, Petra

2006-12-01

Oval cells constitute a heterogeneous population of proliferating progenitors found in rat livers following carcinogenic treatment (2-acetylaminofluorene and 70% hepatectomy). The aim of this study was to investigate the cellular pattern of various differentiation and cell type markers in this model of liver regeneration. Immunophenotypic characterisation revealed at least two subtypes emerging from the portal field. First, a population of oval cells formed duct-like structures and expressed bile duct (CD49f) as well as hepatocytic markers (alpha-foetoprotein, CD26). Second, a population of non-ductular oval cells was detected between and distally from the ductules expressing the neural marker nestin and the haematopoietic marker Thy1. Following oval cell isolation, a subset of the nestin-positive cells was shown to co-express hepatocytic and epithelial markers (albumin, CD26, pancytokeratin) and could be clearly distinguished from anti-desmin reactive hepatic stellate cells. The gene expression profiles (RT-PCR) of isolated oval cells and oval cell liver tissue were found to be similar to foetal liver (ED14). The present results suggest that the two oval cell populations are organised in a zonal hierarchy with a marker gradient from the inner (displaying hepatocytic and biliary markers) to the outer zone (showing hepatocytic and extrahepatic progenitor markers) of the proliferating progeny clusters.

Porcine colonization of the Americas: a 60k SNP story

PubMed Central

Burgos-Paz, W; Souza, C A; Megens, H J; Ramayo-Caldas, Y; Melo, M; Lemús-Flores, C; Caal, E; Soto, H W; Martínez, R; Álvarez, L A; Aguirre, L; Iñiguez, V; Revidatti, M A; Martínez-López, O R; Llambi, S; Esteve-Codina, A; Rodríguez, M C; Crooijmans, R P M A; Paiva, S R; Schook, L B; Groenen, M A M; Pérez-Enciso, M

2013-01-01

The pig, Sus scrofa, is a foreign species to the American continent. Although pigs originally introduced in the Americas should be related to those from the Iberian Peninsula and Canary islands, the phylogeny of current creole pigs that now populate the continent is likely to be very complex. Because of the extreme climates that America harbors, these populations also provide a unique example of a fast evolutionary phenomenon of adaptation. Here, we provide a genome wide study of these issues by genotyping, with a 60k SNP chip, 206 village pigs sampled across 14 countries and 183 pigs from outgroup breeds that are potential founders of the American populations, including wild boar, Iberian, international and Chinese breeds. Results show that American village pigs are primarily of European ancestry, although the observed genetic landscape is that of a complex conglomerate. There was no correlation between genetic and geographical distances, neither continent wide nor when analyzing specific areas. Most populations showed a clear admixed structure where the Iberian pig was not necessarily the main component, illustrating how international breeds, but also Chinese pigs, have contributed to extant genetic composition of American village pigs. We also observe that many genes related to the cardiovascular system show an increased differentiation between altiplano and genetically related pigs living near sea level. PMID:23250008

The Latin American Social Medicine database

PubMed Central

Eldredge, Jonathan D; Waitzkin, Howard; Buchanan, Holly S; Teal, Janis; Iriart, Celia; Wiley, Kevin; Tregear, Jonathan

2004-01-01

Background Public health practitioners and researchers for many years have been attempting to understand more clearly the links between social conditions and the health of populations. Until recently, most public health professionals in English-speaking countries were unaware that their colleagues in Latin America had developed an entire field of inquiry and practice devoted to making these links more clearly understood. The Latin American Social Medicine (LASM) database finally bridges this previous gap. Description This public health informatics case study describes the key features of a unique information resource intended to improve access to LASM literature and to augment understanding about the social determinants of health. This case study includes both quantitative and qualitative evaluation data. Currently the LASM database at The University of New Mexico brings important information, originally known mostly within professional networks located in Latin American countries to public health professionals worldwide via the Internet. The LASM database uses Spanish, Portuguese, and English language trilingual, structured abstracts to summarize classic and contemporary works. Conclusion This database provides helpful information for public health professionals on the social determinants of health and expands access to LASM. PMID:15627401

A systematic review of economic models used to assess the cost-effectiveness of strategies for identifying latent tuberculosis in high-risk groups.

PubMed

Auguste, Peter; Tsertsvadze, Alexander; Court, Rachel; Pink, Joshua

2016-07-01

Timely diagnosis and treatment of latent tuberculosis infection (LTBI) through screening remains a key public health priority. Although globally it is recommended to screen people at high risk of developing TB, the economic evidence underpinning these recommendations is limited. This review critically appraised studies that had used a decision-analytical modelling framework to estimate the cost-effectiveness of interferon gamma release assays (IGRAs) compared to tuberculin skin test (TST) for detecting LTBI in high risk populations. A comprehensive search of MEDLINE, EMBASE, NHS-EED was undertaken from 2009 up to June 2015. Studies were screened and extracted by independent reviewers. The study quality was assessed using the Consolidated Health Economic Evaluation Reporting Standards (CHEERS) and the Philips' checklist, respectively. A narrative synthesis of the included studies was undertaken. Ten studies were included in this review. Two economic evaluations were conducted in a child population, six in an immunocompromised population and two in a recently arrived population from a country with a high incidence of TB. Most studies (n = 7) used a decision tree structure with Markov nodes. In general, all models were clearly described in terms of reporting quality, but were subject to limitations to structure and model inputs. Models have not elaborated on their setting or the perspective of the studies was not consistent with their analyses. Other concerns were related to derivation of prevalence, test accuracy and transition probabilities. Current methods available highlight limitations in the clinical effectiveness literature, model structures and assumptions, which impact on the robustness of the cost-effectiveness results. These models available are useful, but limited on the information that can be used to inform on future cost-effectiveness analysis. Until consideration is given on deriving the performance of tests used to identify LTBI that progresses to active TB, and the development of more comprehensive models, the economic benefit of LTBI testing with TST/IGRAs in high risk populations will remain unanswered. Copyright © 2016 Elsevier Ltd. All rights reserved.

Colombia a Source of Cacao Genetic Diversity As Revealed by the Population Structure Analysis of Germplasm Bank of Theobroma cacao L.

PubMed

Osorio-Guarín, Jaime A; Berdugo-Cely, Jhon; Coronado, Roberto Antonio; Zapata, Yeny Patricia; Quintero, Constanza; Gallego-Sánchez, Gerardo; Yockteng, Roxana

2017-01-01

Beans of the species Theobroma cacao L., also known as cacao, are the raw material to produce chocolate. Colombian cacao has been classified as a fine flavor cacao that represents the 5% of cacao world's production. Colombian genetic resources from this species are conserved in ex situ and in-field germplasm banks, since T. cacao has recalcitrant seeds to desication and long-term storage. Currently, the collection of T. cacao of the Colombian Corporation of Agricultural Research (CORPOICA) has approximately 700 germplasm accessions. We conducted a molecular analysis of Corpoica's cacao collection and a morphological characterization of some accessions with the goal to study its genetic diversity and population structure and, to select interesting accessions for the cacao's breeding program. Phenotypic evaluation was performed based on 18 morphological traits and 4 biochemical traits. PCA analysis of morphological traits explained 60.6% of the total variation in seven components and 100% of the total variation of biochemical traits in four components, grouping the collection in 4 clusters for both variables. We explored 565 accessions from Corpoica's germplasm and 252 accessions from reference populations using 96 single nucleotide polymorphism (SNP) molecular markers. Molecular patterns of cacao Corpoica's collection were obtained amplifying specific alleles in a Fluidigm platform that used integrated circuits of fluids. Corpoica's collection showed highest genetic diversity [Expected Heterozygosity ( H E = 0.314), Observed Heterozygosity ( H O = 0.353)] that is reduced when reference populations were included in the dataset ( H E = 0.294, H O = 0.261). The collection was divided into four clusters based on population structure analysis. Cacao accessions from distinct groups showed some taxonomic concordance and reflected their geographic origins. For instance, accessions classified as Criollo were clearly differentiated in one group and we identified two new Colombian genetic groups. Using a number of allelic variations based on 87 SNP markers and 22 different morphological/biochemical traits, a core collection with a total of 232 accessions was selected as a primary genetic resource for cacao breeders.

Colombia a Source of Cacao Genetic Diversity As Revealed by the Population Structure Analysis of Germplasm Bank of Theobroma cacao L.

PubMed Central

Osorio-Guarín, Jaime A.; Berdugo-Cely, Jhon; Coronado, Roberto Antonio; Zapata, Yeny Patricia; Quintero, Constanza; Gallego-Sánchez, Gerardo; Yockteng, Roxana

2017-01-01

Beans of the species Theobroma cacao L., also known as cacao, are the raw material to produce chocolate. Colombian cacao has been classified as a fine flavor cacao that represents the 5% of cacao world’s production. Colombian genetic resources from this species are conserved in ex situ and in-field germplasm banks, since T. cacao has recalcitrant seeds to desication and long-term storage. Currently, the collection of T. cacao of the Colombian Corporation of Agricultural Research (CORPOICA) has approximately 700 germplasm accessions. We conducted a molecular analysis of Corpoica’s cacao collection and a morphological characterization of some accessions with the goal to study its genetic diversity and population structure and, to select interesting accessions for the cacao’s breeding program. Phenotypic evaluation was performed based on 18 morphological traits and 4 biochemical traits. PCA analysis of morphological traits explained 60.6% of the total variation in seven components and 100% of the total variation of biochemical traits in four components, grouping the collection in 4 clusters for both variables. We explored 565 accessions from Corpoica’s germplasm and 252 accessions from reference populations using 96 single nucleotide polymorphism (SNP) molecular markers. Molecular patterns of cacao Corpoica’s collection were obtained amplifying specific alleles in a Fluidigm platform that used integrated circuits of fluids. Corpoica’s collection showed highest genetic diversity [Expected Heterozygosity (HE = 0.314), Observed Heterozygosity (HO = 0.353)] that is reduced when reference populations were included in the dataset (HE = 0.294, HO = 0.261). The collection was divided into four clusters based on population structure analysis. Cacao accessions from distinct groups showed some taxonomic concordance and reflected their geographic origins. For instance, accessions classified as Criollo were clearly differentiated in one group and we identified two new Colombian genetic groups. Using a number of allelic variations based on 87 SNP markers and 22 different morphological/biochemical traits, a core collection with a total of 232 accessions was selected as a primary genetic resource for cacao breeders. PMID:29209353

Using Population Data to Address the Human Dimensions of Environmental Change

Treesearch

D.M. Mageean; J.G. Bartlett

1999-01-01

In recent years researchers and policy makers have identified population-environment interactions as crucial to issues of ecology, economic development, and human welfare. It seems clear that human populations and demands on the environment are driving ecological change in such areas as global warming, ozone depletion, deforestation, biodiversity loss, land degradation...

Biological objectives for bird populations

Treesearch

Jonathan Bart; Mark Koneff; Steve Wendt

2005-01-01

This paper explores the development of population based objectives for birds. The concept of population based objectives for bird conservation lies at the core of planning in the North American Bird Conservation Initiative. Clear objectives are needed as a basis for partnership, and a basis for program evaluation in an adaptive context. In the case of waterfowl,...

Diversity and evolution of Lactobacillus casei group isolated from fermented dairy products in Tibet.

PubMed

Feng, Jing; Jiang, Yujun; Li, Mingyu; Zhao, Siyu; Zhang, Yanming; Li, Xuesong; Wang, Hui; Lin, Guangen; Wang, Hao; Li, Tiejing; Man, Chaoxin

2018-05-25

Bacteria in Lactobacillus casei group, including Lactobacillus casei (L. casei), Lactobacillus paracasei (L. paracasei), and Lactobacillus rhamnosus (L. rhamnosus) are important lactic acid bacteria in the production of fermented dairy products and are faced with the controversial nomenclatural status due to their close phylogenetic similarity. To probe the evolution and phylogeny of L. casei group, 100 isolates of lactic acid bacteria originated from naturally fermented dairy products in Tibet of China were subjected to multilocus sequence typing (MLST). The MLST scheme, based on analysis of the housekeeping genes fusA, ileS, lepA, leuS, pyrG, recA and recG, revealed that all the isolates belonged to a group containing the L. paracasei reference strains and were clearly different from the strains of L. casei and L. rhamnosus. Although nucleotide diversity (π) was low for the seven genes (ranging from 0.00341 for fusA to 0.01307 for recG), high genetic diversity represented by 83 sequence types (STs) with a discriminatory index of 0.98 was detected. A network-like structure based on split decomposition analysis, and the high values of the relative effect of recombination and mutation in the diversification of the lineages (r/m = 4.76) and the relative frequency of occurrence of recombination and mutation (ρ/θ = 2.62) indicated that intra-species recombination occurred frequently and homologous recombination played a key role in generating genotypic diversity amongst L. paracasei strains in Tibet. The discovery of 51 new STs and the results of STRUCTURE analysis suggested that the L. casei group in Tibet had an individual and particular population structure in comparison to European isolates. Overall, this research might be the first report about genetic diversity and population structure of Lactobacillus populations isolated from naturally fermented dairy products in Tibet based on MLST scheme.

Seasonal, spatial, and maternal effects on gut microbiome in wild red squirrels.

PubMed

Ren, Tiantian; Boutin, Stan; Humphries, Murray M; Dantzer, Ben; Gorrell, Jamieson C; Coltman, David W; McAdam, Andrew G; Wu, Martin

2017-12-21

Our understanding of gut microbiota has been limited primarily to findings from human and laboratory animals, but what shapes the gut microbiota in nature remains largely unknown. To fill this gap, we conducted a comprehensive study of gut microbiota of a well-studied North American red squirrel (Tamiasciurus hudsonicus) population. Red squirrels are territorial, solitary, and live in a highly seasonal environment and therefore represent a very attractive system to study factors that drive the temporal and spatial dynamics of gut microbiota. For the first time, this study revealed significant spatial patterns of gut microbiota within a host population, suggesting limited dispersal could play a role in shaping and maintaining the structure of gut microbial communities. We also found a remarkable seasonal rhythm in red squirrel's gut microbial composition manifested by a tradeoff between relative abundance of two genera Oscillospira and Corpococcus and clearly associated with seasonal variation in diet availability. Our results show that in nature, environmental factors exert a much stronger influence on gut microbiota than host-associated factors including age and sex. Despite strong environmental effects, we found clear evidence of individuality and maternal effects, but host genetics did not seem to be a significant driver of the gut microbial communities in red squirrels. Taken together, the results of this study emphasize the importance of external ecological factors rather than host attributes in driving temporal and spatial patterns of gut microbiota in natural environment.

'Between one and three million': towards the demographic reconstruction of a decade of Cambodian history (1970-79).

PubMed

Heuveline, P

1998-03-01

Estimates of mortality in Camabodia during the Khmer Rouge regime (1975-79) range from 20,000 deaths according to former Khmer Rouge sources, to over three million victims according to Vietnamese government sources. This paper uses an unusual data source - the 1992 electoral lists registered by the United Nations - to estimate the population size after the Khmer Rouge regime and the extent of "excess" mortality in the 1970s. These data also provide the first breakdown of population by single year of age, which allows analysis of the age structure of "excess" mortality and inference of the relative importance of violence as a cause of death in that period. The estimates derived here are more comparable with the higher estimates made in the past. In addition, the analysis of likely causes of death that could have generated the age pattern of "excess" mortality clearly shows a larger contribution of direct or violent mortality than has been previously recognized.

Genetic diversity of the captive Asian tapir population in Thailand, based on mitochondrial control region sequence data and the comparison of its nucleotide structure with Brazilian tapir.

PubMed

Muangkram, Yuttamol; Amano, Akira; Wajjwalku, Worawidh; Pinyopummintr, Tanu; Thongtip, Nikorn; Kaolim, Nongnid; Sukmak, Manakorn; Kamolnorranath, Sumate; Siriaroonrat, Boripat; Tipkantha, Wanlaya; Maikaew, Umaporn; Thomas, Warisara; Polsrila, Kanda; Dongsaard, Kwanreaun; Sanannu, Saowaphang; Wattananorrasate, Anuwat

2017-07-01

The Asian tapir (Tapirus indicus) has been classified as Endangered on the IUCN Red List of Threatened Species (2008). Genetic diversity data provide important information for the management of captive breeding and conservation of this species. We analyzed mitochondrial control region (CR) sequences from 37 captive Asian tapirs in Thailand. Multiple alignments of the full-length CR sequences sized 1268 bp comprised three domains as described in other mammal species. Analysis of 16 parsimony-informative variable sites revealed 11 haplotypes. Furthermore, the phylogenetic analysis using median-joining network clearly showed three clades correlated with our earlier cytochrome b gene study in this endangered species. The repetitive motif is located between first and second conserved sequence blocks, similar to the Brazilian tapir. The highest polymorphic site was located in the extended termination associated sequences domain. The results could be applied for future genetic management based in captivity and wild that shows stable populations.

Afterglow Population Studies from Swift Follow-Up Observations of Fermi LAT GRBs

NASA Technical Reports Server (NTRS)

Racusin, Judith L.; Oates, S. R.; McEnery, J.; Vasileiou, V.; Troja, E.; Gehrels, N.

2010-01-01

The small population of Fermi LAT detected GRBs discovered over the last year has been providing interesting and unexpected clues into GRB prompt and afterglow emission mechanisms. Over the last 5 years, it has been Swift that has provided the robust data set of UV/optical and X-ray afterglow observations that opened many windows into other components of GRB emission structure. We explore the new ability to utilize both of these observatories to study the same GRBs over 10 orders of magnitude in energy, although not always concurrently. Almost all LAT GRBs that have been followed-up by Swift within 1-day have been clearly detected and carefully observed. We will present the context of the lower-energy afterglows of this special subset of GRBs that has > 100 MeV emission compared to the hundreds in the Swift database that may or may not have been observed by LAT, and theorize upon the relationship between these properties and the origin of the high energy gamma-ray emission.

Odour dialects among wild mammals.

PubMed

Kean, Eleanor Freya; Bruford, Michael William; Russo, Isa-Rita M; Müller, Carsten Theodor; Chadwick, Elizabeth Anna

2017-10-19

Across multiple taxa, population structure and dynamics depend on effective signalling between individuals. Among mammals, chemical communication is arguably the most important sense, underpinning mate choice, parental care, territoriality and even disease transmission. There is a growing body of evidence that odours signal genetic information that may confer considerable benefits including inbreeding avoidance and nepotism. To date, however, there has been no clear evidence that odours encode population-level information in wild mammals. Here we demonstrate for the first time the existence of 'odour dialects' in genetically distinct mammalian subpopulations across a large geographical scale. We found that otters, Lutra lutra, from across the United Kingdom possess sex and biogeography-specific odours. Subpopulations with the most distinctive odour profiles are also the most genetically diverse but not the most genetically differentiated. Furthermore, geographic distance between individuals does not explain regional odour differences, refuting other potential explanations such as group odour sharing behaviour. Differences in the language of odours between subpopulations have the potential to affect individual interactions, which could impact reproduction and gene-flow.

Detecting Positive Selection of Korean Native Goat Populations Using Next-Generation Sequencing

PubMed Central

Lee, Wonseok; Ahn, Sojin; Taye, Mengistie; Sung, Samsun; Lee, Hyun-Jeong; Cho, Seoae; Kim, Heebal

2016-01-01

Goats (Capra hircus) are one of the oldest species of domesticated animals. Native Korean goats are a particularly interesting group, as they are indigenous to the area and were raised in the Korean peninsula almost 2,000 years ago. Although they have a small body size and produce low volumes of milk and meat, they are quite resistant to lumbar paralysis. Our study aimed to reveal the distinct genetic features and patterns of selection in native Korean goats by comparing the genomes of native Korean goat and crossbred goat populations. We sequenced the whole genome of 15 native Korean goats and 11 crossbred goats using next-generation sequencing (Illumina platform) to compare the genomes of the two populations. We found decreased nucleotide diversity in the native Korean goats compared to the crossbred goats. Genetic structural analysis demonstrated that the native Korean goat and crossbred goat populations shared a common ancestry, but were clearly distinct. Finally, to reveal the native Korean goat’s selective sweep region, selective sweep signals were identified in the native Korean goat genome using cross-population extended haplotype homozygosity (XP-EHH) and a cross-population composite likelihood ratio test (XP-CLR). As a result, we were able to identify candidate genes for recent selection, such as the CCR3 gene, which is related to lumbar paralysis resistance. Combined with future studies and recent goat genome information, this study will contribute to a thorough understanding of the native Korean goat genome. PMID:27989103

Detecting Positive Selection of Korean Native Goat Populations Using Next-Generation Sequencing.

PubMed

Lee, Wonseok; Ahn, Sojin; Taye, Mengistie; Sung, Samsun; Lee, Hyun-Jeong; Cho, Seoae; Kim, Heebal

2016-12-01

Goats ( Capra hircus ) are one of the oldest species of domesticated animals. Native Korean goats are a particularly interesting group, as they are indigenous to the area and were raised in the Korean peninsula almost 2,000 years ago. Although they have a small body size and produce low volumes of milk and meat, they are quite resistant to lumbar paralysis. Our study aimed to reveal the distinct genetic features and patterns of selection in native Korean goats by comparing the genomes of native Korean goat and crossbred goat populations. We sequenced the whole genome of 15 native Korean goats and 11 crossbred goats using next-generation sequencing (Illumina platform) to compare the genomes of the two populations. We found decreased nucleotide diversity in the native Korean goats compared to the crossbred goats. Genetic structural analysis demonstrated that the native Korean goat and crossbred goat populations shared a common ancestry, but were clearly distinct. Finally, to reveal the native Korean goat's selective sweep region, selective sweep signals were identified in the native Korean goat genome using cross-population extended haplotype homozygosity (XP-EHH) and a cross-population composite likelihood ratio test (XP-CLR). As a result, we were able to identify candidate genes for recent selection, such as the CCR3 gene, which is related to lumbar paralysis resistance. Combined with future studies and recent goat genome information, this study will contribute to a thorough understanding of the native Korean goat genome.

Spatiotemporal variation in survival rates: implications for population dynamics of yellow-bellied marmots.

PubMed

Ozgul, Arpat; Armitage, Kenneth B; Blumstein, Daniel T; Oli, Madan K

2006-04-01

Spatiotemporal variation in age-specific survival rates can profoundly influence population dynamics, but few studies of vertebrates have thoroughly investigated both spatial and temporal variability in age-specific survival rates. We used 28 years (1976-2003) of capture-mark-recapture (CMR) data from 17 locations to parameterize an age-structured Cormack-Jolly-Seber model, and investigated spatial and temporal variation in age-specific annual survival rates of yellow-bellied marmots (Marmota flaviventris). Survival rates varied both spatially and temporally, with survival of younger animals exhibiting the highest degree of variation. Juvenile survival rates varied from 0.52 +/- 0.05 to 0.78 +/- 0.10 among sites and from 0.15 +/- 0.14 to 0.89 +/- 0.06 over time. Adult survival rates varied from 0.62 +/- 0.09 to 0.80 +/- 0.03 among sites, but did not vary significantly over time. We used reverse-time CMR models to estimate the realized population growth rate (lamda), and to investigate the influence of the observed variation in age-specific survival rates on lamda. The realized growth rate of the population closely covaried with, and was significantly influenced by, spatiotemporal variation in juvenile survival rate. High variability in juvenile survival rates over space and time clearly influenced the dynamics of our study population and is also likely to be an important determinant of the spatiotemporal variation in the population dynamics of other mammals with similar life history characteristics.

International study of temperature, heat and urban mortality: the 'ISOTHURM' project.

PubMed

McMichael, Anthony J; Wilkinson, Paul; Kovats, R Sari; Pattenden, Sam; Hajat, Shakoor; Armstrong, Ben; Vajanapoom, Nitaya; Niciu, Emilia M; Mahomed, Hassan; Kingkeow, Chamnong; Kosnik, Mitja; O'Neill, Marie S; Romieu, Isabelle; Ramirez-Aguilar, Matiana; Barreto, Mauricio L; Gouveia, Nelson; Nikiforov, Bojidar

2008-10-01

This study describes heat- and cold-related mortality in 12 urban populations in low- and middle-income countries, thereby extending knowledge of how diverse populations, in non-OECD countries, respond to temperature extremes. The cities were: Delhi, Monterrey, Mexico City, Chiang Mai, Bangkok, Salvador, São Paulo, Santiago, Cape Town, Ljubljana, Bucharest and Sofia. For each city, daily mortality was examined in relation to ambient temperature using autoregressive Poisson models (2- to 5-year series) adjusted for season, relative humidity, air pollution, day of week and public holidays. Most cities showed a U-shaped temperature-mortality relationship, with clear evidence of increasing death rates at colder temperatures in all cities except Ljubljana, Salvador and Delhi and with increasing heat in all cities except Chiang Mai and Cape Town. Estimates of the temperature threshold below which cold-related mortality began to increase ranged from 15 degrees C to 29 degrees C; the threshold for heat-related deaths ranged from 16 degrees C to 31 degrees C. Heat thresholds were generally higher in cities with warmer climates, while cold thresholds were unrelated to climate. Urban populations, in diverse geographic settings, experience increases in mortality due to both high and low temperatures. The effects of heat and cold vary depending on climate and non-climate factors such as the population disease profile and age structure. Although such populations will undergo some adaptation to increasing temperatures, many are likely to have substantial vulnerability to climate change. Additional research is needed to elucidate vulnerability within populations.

Genetics of the peloponnesean populations and the theory of extinction of the medieval peloponnesean Greeks

PubMed Central

Stamatoyannopoulos, George; Bose, Aritra; Teodosiadis, Athanasios; Tsetsos, Fotis; Plantinga, Anna; Psatha, Nikoletta; Zogas, Nikos; Yannaki, Evangelia; Zalloua, Pierre; Kidd, Kenneth K; Browning, Brian L; Stamatoyannopoulos, John; Paschou, Peristera; Drineas, Petros

2017-01-01

Peloponnese has been one of the cradles of the Classical European civilization and an important contributor to the ancient European history. It has also been the subject of a controversy about the ancestry of its population. In a theory hotly debated by scholars for over 170 years, the German historian Jacob Philipp Fallmerayer proposed that the medieval Peloponneseans were totally extinguished by Slavic and Avar invaders and replaced by Slavic settlers during the 6th century CE. Here we use 2.5 million single-nucleotide polymorphisms to investigate the genetic structure of Peloponnesean populations in a sample of 241 individuals originating from all districts of the peninsula and to examine predictions of the theory of replacement of the medieval Peloponneseans by Slavs. We find considerable heterogeneity of Peloponnesean populations exemplified by genetically distinct subpopulations and by gene flow gradients within Peloponnese. By principal component analysis (PCA) and ADMIXTURE analysis the Peloponneseans are clearly distinguishable from the populations of the Slavic homeland and are very similar to Sicilians and Italians. Using a novel method of quantitative analysis of ADMIXTURE output we find that the Slavic ancestry of Peloponnesean subpopulations ranges from 0.2 to 14.4%. Subpopulations considered by Fallmerayer to be Slavic tribes or to have Near Eastern origin, have no significant ancestry of either. This study rejects the theory of extinction of medieval Peloponneseans and illustrates how genetics can clarify important aspects of the history of a human population. PMID:28272534

An Ideal Remedial Reading Program.

ERIC Educational Resources Information Center

Boettcher, Judith A.

An ideal secondary level remedial reading program would be based on the philosophy that both freedom and structure are required, that learning demands involvement and feedback, and that success breeds success. Such programs should be structured (i.e., based on clearly defined content and a clearly designated mode of presentation). There are many…

Population structure and reproductive biology of Atlantoscia floridana (van Name, 1940) (Crustacea, Isopoda, Oniscidea) in southern Brazil

NASA Astrophysics Data System (ADS)

Araujo, Paula Beatriz; Bond-Buckup, Georgina

2005-11-01

Data were obtained on the population structure and reproduction of Atlantoscia floridana, one of the most common species of terrestrial isopods in the restinga (coastal dune) forests of the state of Rio Grande do Sul, southern Brazil. During a 19-month period, a total of 7833 individuals were sampled: 2792 males, 3400 females and 1691 mancas. There was a significant difference between the size of both males and females collected in 2000 and 2001: the mean size was smaller in the second year when individuals in the larger size classes were lacking. Population density varied with season. The minimum population was 131 ind per m 2 individuals, the maximum 1040 ind per m 2 and the mean 450 per m 2. While the overall sex ratio was clearly female biased, the operational sex ratio favored males, and showed no changes with season. Because both ovigerous and post-ovigerous females were present throughout the year, reproduction is considered continuous; however, reproduction peaked during autumn and spring. Ovigerous females were measured (CW = cephalothorax width) and the number of eggs was counted. Fecundity (F) varied from 5 to 23 eggs ( x¯ = 11.18 ± 4) per female, and was expressed by the regression F = -18.48 + 22.59 CW, with the female cephalothorax width varying from 1.04 to 1.68 mm. Marsupial mortality was only 0.9%. Egg production was 588 eggs per m 2 in spring and 660 eggs per m 2 in autumn. Recruitment occurred in all months, and eggs, embryos and marsupial mancas were also present year-round. A. floridana is the dominant species of terrestrial isopod in the study area. Its most remarkable characteristic is its high reproductive investment.

Genetic and morphological contrasts between wild and anthropogenic populations of Agave parryi var. huachucensis in south-eastern Arizona.

PubMed

Parker, Kathleen C; Trapnell, Dorset W; Hamrick, J L; Hodgson, Wendy C

2014-05-01

At least seven species of Agave, including A. parryi, were cultivated prehistorically in Arizona, serving as important sources of food and fibre. Many relict populations from ancient cultivation remain in the modern landscape, offering a unique opportunity to study pre-Columbian plant manipulation practices. This study examined genetic and morphological variation in six A. p. var. huachucensis populations of unknown origin to compare them with previous work on A. parryi populations of known origin, to infer their cultivation history and to determine whether artificial selection is evident in populations potentially managed by early agriculturalists. Six A. p. var. huachucensis and 17 A. parryi populations were sampled, and morphometric, allozyme and microsatellite data were used to compare morphology and genetic structure in purportedly anthropogenic and wild populations, as well as in the two taxa. Analysis of molecular variance and Bayesian clustering were performed to partition variation associated with taxonomic identity and hypothesized evolutionary history, to highlight patterns of similarity among populations and to identify potential wild sources for the planting stock. A p. var. huachucensis and A. parryi populations differed significantly both morphologically and genetically. Like A. parryi, wild A. p. var. huachucensis populations were more genetically diverse than the inferred anthropogenic populations, with greater expected heterozygosity, percentage of polymorphic loci and number of alleles. Inferred anthropogenic populations exhibited many traits indicative of past active cultivation: greater morphological uniformity, fixed heterozygosity for several loci (non-existent in wild populations), fewer multilocus genotypes and strong differentiation among populations. Where archaeological information is lacking, the genetic signature of many Agave populations in Arizona can be used to infer their evolutionary history and to identify potentially fruitful sites for archaeological investigation of ancient settlements and cultivation practices. The same approach can clearly be adopted for other species in similar situations.

Genetic and morphological contrasts between wild and anthropogenic populations of Agave parryi var. huachucensis in south-eastern Arizona

PubMed Central

Parker, Kathleen C.; Trapnell, Dorset W.; Hamrick, J. L.; Hodgson, Wendy C.

2014-01-01

Background and Aims At least seven species of Agave, including A. parryi, were cultivated prehistorically in Arizona, serving as important sources of food and fibre. Many relict populations from ancient cultivation remain in the modern landscape, offering a unique opportunity to study pre-Columbian plant manipulation practices. This study examined genetic and morphological variation in six A. p. var. huachucensis populations of unknown origin to compare them with previous work on A. parryi populations of known origin, to infer their cultivation history and to determine whether artificial selection is evident in populations potentially managed by early agriculturalists. Methods Six A. p. var. huachucensis and 17 A. parryi populations were sampled, and morphometric, allozyme and microsatellite data were used to compare morphology and genetic structure in purportedly anthropogenic and wild populations, as well as in the two taxa. Analysis of molecular variance and Bayesian clustering were performed to partition variation associated with taxonomic identity and hypothesized evolutionary history, to highlight patterns of similarity among populations and to identify potential wild sources for the planting stock. Key Results A p. var. huachucensis and A. parryi populations differed significantly both morphologically and genetically. Like A. parryi, wild A. p. var. huachucensis populations were more genetically diverse than the inferred anthropogenic populations, with greater expected heterozygosity, percentage of polymorphic loci and number of alleles. Inferred anthropogenic populations exhibited many traits indicative of past active cultivation: greater morphological uniformity, fixed heterozygosity for several loci (non-existent in wild populations), fewer multilocus genotypes and strong differentiation among populations. Conclusions Where archaeological information is lacking, the genetic signature of many Agave populations in Arizona can be used to infer their evolutionary history and to identify potentially fruitful sites for archaeological investigation of ancient settlements and cultivation practices. The same approach can clearly be adopted for other species in similar situations. PMID:24638822

Pronounced fixation, strong population differentiation and complex population history in the Canary Islands blue tit subspecies complex.

PubMed

Hansson, Bengt; Ljungqvist, Marcus; Illera, Juan-Carlos; Kvist, Laura

2014-01-01

Evolutionary molecular studies of island radiations may lead to insights in the role of vicariance, founder events, population size and drift in the processes of population differentiation. We evaluate the degree of population genetic differentiation and fixation of the Canary Islands blue tit subspecies complex using microsatellite markers and aim to get insights in the population history using coalescence based methods. The Canary Island populations were strongly genetically differentiated and had reduced diversity with pronounced fixation including many private alleles. In population structure models, the relationship between the central island populations (La Gomera, Tenerife and Gran Canaria) and El Hierro was difficult to disentangle whereas the two European populations showed consistent clustering, the two eastern islands (Fuerteventura and Lanzarote) and Morocco weak clustering, and La Palma a consistent unique lineage. Coalescence based models suggested that the European mainland forms an outgroup to the Afrocanarian population, a split between the western island group (La Palma and El Hierro) and the central island group, and recent splits between the three central islands, and between the two eastern islands and Morocco, respectively. It is clear that strong genetic drift and low level of concurrent gene flow among populations have shaped complex allelic patterns of fixation and skewed frequencies over the archipelago. However, understanding the population history remains challenging; in particular, the pattern of extreme divergence with low genetic diversity and yet unique genetic material in the Canary Island system requires an explanation. A potential scenario is population contractions of a historically large and genetically variable Afrocanarian population, with vicariance and drift following in the wake. The suggestion from sequence-based analyses of a Pleistocene extinction of a substantial part of North Africa and a Pleistocene/Holocene eastward re-colonisation of western North Africa from the Canaries remains possible.

Pronounced Fixation, Strong Population Differentiation and Complex Population History in the Canary Islands Blue Tit Subspecies Complex

PubMed Central

Hansson, Bengt; Ljungqvist, Marcus; Illera, Juan-Carlos; Kvist, Laura

2014-01-01

Evolutionary molecular studies of island radiations may lead to insights in the role of vicariance, founder events, population size and drift in the processes of population differentiation. We evaluate the degree of population genetic differentiation and fixation of the Canary Islands blue tit subspecies complex using microsatellite markers and aim to get insights in the population history using coalescence based methods. The Canary Island populations were strongly genetically differentiated and had reduced diversity with pronounced fixation including many private alleles. In population structure models, the relationship between the central island populations (La Gomera, Tenerife and Gran Canaria) and El Hierro was difficult to disentangle whereas the two European populations showed consistent clustering, the two eastern islands (Fuerteventura and Lanzarote) and Morocco weak clustering, and La Palma a consistent unique lineage. Coalescence based models suggested that the European mainland forms an outgroup to the Afrocanarian population, a split between the western island group (La Palma and El Hierro) and the central island group, and recent splits between the three central islands, and between the two eastern islands and Morocco, respectively. It is clear that strong genetic drift and low level of concurrent gene flow among populations have shaped complex allelic patterns of fixation and skewed frequencies over the archipelago. However, understanding the population history remains challenging; in particular, the pattern of extreme divergence with low genetic diversity and yet unique genetic material in the Canary Island system requires an explanation. A potential scenario is population contractions of a historically large and genetically variable Afrocanarian population, with vicariance and drift following in the wake. The suggestion from sequence-based analyses of a Pleistocene extinction of a substantial part of North Africa and a Pleistocene/Holocene eastward re-colonisation of western North Africa from the Canaries remains possible. PMID:24587269

Japanese Structure Survey of Radiation Oncology in 2005 Based on Institutional Stratification of Patterns of Care Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Teshima, Teruki; Numasaki, Hodaka; Shibuya, Hitoshi

2008-09-01

Purpose: To evaluate the structure of radiation oncology in Japan in terms of equipment, personnel, patient load, and geographic distribution to identify and improve any deficiencies. Methods and Materials: A questionnaire-based national structure survey was conducted between March 2006 and February 2007 by the Japanese Society of Therapeutic Radiology and Oncology. These data were analyzed in terms of the institutional stratification of the Patterns of Care Study. Results: The total numbers of new cancer patients and total cancer patients (new and repeat) treated with radiotherapy in 2005 were estimated at approximately 162,000 and 198,000, respectively. In actual use were 765more » linear accelerators, 11 telecobalt machines, 48 GammaKnife machines, 64 {sup 60}Co remote-controlled after-loading systems, and 119 {sup 192}Ir remote-controlled after-loading systems. The linear accelerator systems used dual-energy function in 498 systems (65%), three-dimensional conformal radiotherapy in 462 (60%), and intensity-modulated radiotherapy in 170 (22%). There were 426 Japanese Society of Therapeutic Radiology and Oncology-certified radiation oncologists, 774 full-time equivalent radiation oncologists, 117 medical physicists, and 1,635 radiation therapists. Geographically, a significant variation was found in the use of radiotherapy, from 0.9 to 2.1 patients/1,000 population. The annual patient load/FTE radiation oncologist was 247, exceeding the Blue Book guidelines level. Patterns of Care Study stratification can clearly discriminate the maturity of structures according to their academic nature and caseload. Conclusions: The Japanese structure has clearly improved during the past 15 years in terms of equipment and its use, although the shortage of manpower and variations in maturity disclosed by this Patterns of Care Study stratification remain problematic. These constitute the targets for nationwide improvement in quality assurance and quality control.« less

Impacts of urban wastewater discharge on seagrass meadows ( Zostera noltii)

NASA Astrophysics Data System (ADS)

Cabaço, Susana; Machás, Raquel; Vieira, Vasco; Santos, Rui

2008-06-01

The abiotic disturbance of urban wastewater discharge and its effects in the population structure, plant morphology, leaf nutrient content, epiphyte load and macroalgae abundance of Zostera noltii meadows were investigated in Ria Formosa coastal lagoon, southern Portugal using both univariate and multivariate analysis. Four sites were assessed, on a seasonal basis, along a gradient from a major Waste Water Treatment Works (WWTW) discharge to a main navigation channel. The wastewater discharge caused an evident environmental disturbance through the nutrient enrichment of the water and sediment, particularly of ammonium. Zostera noltii of the sites closest to the nutrient source showed higher leaf N content, clearly reflecting the nitrogen load. The anthropogenic nutrient enrichment resulted in higher biomass, and higher leaf and internode length, except for the meadow closest to the wastewater discharge (270 m). The high ammonium concentration (158-663 μM) in the water at this site resulted in the decrease of biomass, and both the leaf and internode length, suggesting a toxic effect on Z. noltii. The higher abundance of macroalgae and epiphytes found in the meadow closest to the nutrient source may also affect the species negatively. Shoot density was higher at the nutrient-undisturbed site. Two of the three abiotic processes revealed by Principal Component Analysis were clearly related to the WWTW discharge, a contrast between water column salinity and nutrient concentration and a sediment contrast between both porewater nutrients and temperature and redox potential. A multiple regression analysis showed that these abiotic processes had a significant effect on the biomass-density dynamics of meadows and on the overall size of Z. noltii plants, respectively. Results show that the wastewater discharge is an important source of environmental disturbance and nutrients availability in Ria Formosa lagoon affecting the population structure, morphology and N content of Z. noltii. This impact is spatially restricted to areas up to 600 m distant from the WWTW discharge, probably due to the high water renewal of the lagoon.

Induction of sexual reproduction and genetic diversity in the cheese fungus Penicillium roqueforti

PubMed Central

Ropars, Jeanne; López-Villavicencio, Manuela; Dupont, Joëlle; Snirc, Alodie; Gillot, Guillaume; Coton, Monika; Jany, Jean-Luc; Coton, Emmanuel; Giraud, Tatiana

2014-01-01

The emblematic fungus Penicillium roqueforti is used throughout the world as a starter culture in the production of blue-veined cheeses. Like other industrial filamentous fungi, P. roqueforti was thought to lack a sexual cycle. However, an ability to induce recombination is of great economic and fundamental importance, as it would make it possible to transform and improve industrial strains, promoting the creation of novel phenotypes and eliminating the deleterious mutations that accumulate during clonal propagation. We report here, for the first time, the induction of the sexual structures of P. roqueforti — ascogonia, cleistothecia and ascospores. The progeny of the sexual cycle displayed clear evidence of recombination. We also used the recently published genome sequence for this species to develop microsatellite markers for investigating the footprints of recombination and population structure in a large collection of isolates from around the world and from different environments. Indeed, P. roqueforti also occurs in silage, wood and human-related environments other than cheese. We found tremendous genetic diversity within P. roqueforti, even within cheese strains and identified six highly differentiated clusters that probably predate the use of this species for cheese production. Screening for phenotypic and metabolic differences between these populations could guide future development strategies. PMID:24822078

Patterns of Protein Food Intake Are Associated with Nutrient Adequacy in the General French Adult Population.

PubMed

Gavelle, Erwan de; Huneau, Jean-François; Mariotti, François

2018-02-17

Protein food intake appears to partially structure dietary patterns, as most current emergent diets (e.g., vegetarian and flexitarian) can be described according to their levels of specific protein sources. However, few data are available on dietary protein patterns in the general population and their association with nutrient adequacy. Based on protein food intake data concerning 1678 adults from a representative French national dietary survey, and non-negative-matrix factorization followed by cluster analysis, we were able to identify distinctive dietary protein patterns and compare their nutrient adequacy (using PANDiet probabilistic scoring). The findings revealed eight patterns that clearly discriminate protein intakes and were characterized by the intakes of one or more specific protein foods: 'Processed meat', 'Poultry', 'Pork', 'Traditional', 'Milk', 'Take-away', 'Beef' and 'Fish'. 'Fish eaters' and 'Milk drinkers' had the highest overall nutrient adequacy, whereas that of 'Pork' and 'Take-away eaters' was the lowest. Nutrient adequacy could often be accounted for by the characteristics of the food contributing to protein intake: 'Meat eaters' had high probability of adequacy for iron and zinc, for example. We concluded that protein patterns constitute strong elements in the background structure of the dietary intake and are associated with the nutrient profile that they convey.

Genetic structure and isolation by altitude in rice landraces of Yunnan, China revealed by nucleotide and microsatellite marker polymorphisms

PubMed Central

A, Xinxiang; Yu, Tengqiong; Ma, Xiaoding; Zhang, Enlai; Wang, Yanjie; Cao, Guilan; Xu, Furong; Dai, Luyuan; Han, Longzhi

2017-01-01

Rice landraces, a genetic reservoir for varietal improvement, are developed by farmers through artificial selection during the long-term domestication process. To efficiently conserve, manage, and use such germplasm resources, an understanding of the genetic structure and differentiation of local rice landraces is required. In this study, we analyzed 188 accessions of rice landraces collected from localities across an altitudinal gradient from 425 to 2, 274 m above sea level in Yunnan Province, China using ten target genes and 48 SSR markers. We detected clear differentiation of the rice landraces into indica and japonica groups and further separation of the accessions in each group into two subgroups according to altitude, including a lower altitude subgroup and higher altitude subgroup. The AMOVA results showed significant genetic differentiation among altitude zones at SSRs and most genes, except Os1977 and STS22. We further determined that differentiation among landrace populations followed a model of isolation by altitude, in which gene flow was higher among populations at similar altitude levels than across different altitude levels. Our findings demonstrated that both adaptation to altitude and altitude-dependent gene flow played key roles in the genetic differentiation of rice landraces in Yunnan, China. PMID:28423046

Genetic structure and isolation by altitude in rice landraces of Yunnan, China revealed by nucleotide and microsatellite marker polymorphisms.

PubMed

Cui, Di; Tang, Cuifeng; Li, Jinmei; A, Xinxiang; Yu, Tengqiong; Ma, Xiaoding; Zhang, Enlai; Wang, Yanjie; Cao, Guilan; Xu, Furong; Dai, Luyuan; Han, Longzhi; Koh, Hee-Jong

2017-01-01

Rice landraces, a genetic reservoir for varietal improvement, are developed by farmers through artificial selection during the long-term domestication process. To efficiently conserve, manage, and use such germplasm resources, an understanding of the genetic structure and differentiation of local rice landraces is required. In this study, we analyzed 188 accessions of rice landraces collected from localities across an altitudinal gradient from 425 to 2, 274 m above sea level in Yunnan Province, China using ten target genes and 48 SSR markers. We detected clear differentiation of the rice landraces into indica and japonica groups and further separation of the accessions in each group into two subgroups according to altitude, including a lower altitude subgroup and higher altitude subgroup. The AMOVA results showed significant genetic differentiation among altitude zones at SSRs and most genes, except Os1977 and STS22. We further determined that differentiation among landrace populations followed a model of isolation by altitude, in which gene flow was higher among populations at similar altitude levels than across different altitude levels. Our findings demonstrated that both adaptation to altitude and altitude-dependent gene flow played key roles in the genetic differentiation of rice landraces in Yunnan, China.

Population genetic analysis among five Indian population groups using six microsatellite markers.

PubMed

Ghosh, Anu; Das, Birajalaxmi; Seshadri, M

2003-04-01

Genetic variation at six tetranucleotide microsatellites (HUMTHO1, HUMVWA, F13A01, D3S1359, D12S66, and D12S67) has heen determined in five endogamous ethnic population groups of India belonging to two major linguistic families. The populations analyzed were Konkanastha Brahmins and Marathas (Maharashtra state) from the Indo-Aryan linguistic family and Nairs, Ezhavas, and Muslims (Kerala state) from the Dravidian family. All six loci show high gene diversity, ranging from 0.63 +/- 0.04 to 0.84 +/- 0.02. The average GST value observed was 1.7%, indicating that the differences between the populations account for less than 2% of the diversity, while the genetic variation is high within the five population groups studied (>98%). The phylogenetic tree fails to show any clear cluster. The absence of any cluster along with low average GST is suggestive of substantial genetic similarity among the studied populations, in spite of clear geographical, linguistic, and cultural barriers. This similarity indicates either a greater gene flow between these groups or, alternatively, may reflect a recent evolution for them, considering that the Indian caste system evolved only about 3000 years ago.

Population Genetics of the Aquatic Fungus Tetracladium marchalianum over Space and Time

PubMed Central

Anderson, Jennifer L.; Shearer, Carol A.

2011-01-01

Aquatic hyphomycete fungi are fundamental mediators of energy flow and nutrient spiraling in rivers. These microscopic fungi are primarily dispersed in river currents, undergo substantial annual fluctuations in abundance, and reproduce either predominantly or exclusively asexually. These aspects of aquatic hyphomycete biology are expected to influence levels and distributions of genetic diversity over both spatial and temporal scales. In this study, we investigated the spatiotemporal distribution of genotypic diversity in the representative aquatic hyphomycete Tetracladium marchalianum. We sampled populations of this fungus from seven sites, three sites each in two rivers in Illinois, USA, and one site in a Wisconsin river, USA, and repeatedly sampled one population over two years to track population genetic parameters through two seasonal cycles. The resulting fungal isolates (N = 391) were genotyped at eight polymorphic microsatellite loci. In spite of seasonal reductions in the abundance of this species, genotypic diversity was consistently very high and allele frequencies remarkably stable over time. Likewise, genotypic diversity was very high at all sites. Genetic differentiation was only observed between the most distant rivers (∼450 km). Clear evidence that T. marchalianum reproduces sexually in nature was not observed. Additionally, we used phylogenetic analysis of partial β-tubulin gene sequences to confirm that the fungal isolates studied here represent a single species. These results suggest that populations of T. marchalianum may be very large and highly connected at local scales. We speculate that large population sizes and colonization of alternate substrates in both terrestrial and aquatic environments may effectively buffer the aquatic populations from in-stream population fluctuations and facilitate stability in allele frequencies over time. These data also suggest that overland dispersal is more important for structuring populations of T. marchalianum over geographic scales than expected. PMID:21264239

Changes in DNA methylation fingerprint of Quercus ilex trees in response to experimental field drought simulating projected climate change.

PubMed

Rico, L; Ogaya, R; Barbeta, A; Peñuelas, J

2014-03-01

Rapid genetic changes in plants have been reported in response to current climate change. We assessed the capacity of trees in a natural forest to produce rapid acclimation responses based on epigenetic modifications. We analysed natural populations of Quercus ilex, the dominant tree species of Mediterranean forests, using the methylation-sensitive amplified polymorphism (MSAP) technique to assess patterns and levels of methylation in individuals from unstressed forest plots and from plots experimentally exposed to drought for 12 years at levels projected for the coming decades. The percentage of hypermethylated loci increased, and the percentage of fully methylated loci clearly decreased in plants exposed to drought. Multivariate analyses exploring the status of methylation at MSAP loci also showed clear differentiation depending on stress. The PCA scores for the MSAP profiles clearly separated the genetic from the epigenetic structure, and also significantly separated the samples within each group in response to drought. Changes in DNA methylation highlight the large capacity of plants to rapidly acclimate to changing environmental conditions, including trees with long life spans, and our results demonstrate those changes. These changes, although unable to prevent the decreased growth and higher mortality associated with this experimental drought, occurred together with a dampening in such decreases as the long-term treatment progressed. © 2013 German Botanical Society and The Royal Botanical Society of the Netherlands.

Rapid biological speciation driven by tectonic evolution in New Zealand

NASA Astrophysics Data System (ADS)

Craw, Dave; Upton, Phaedra; Burridge, Christopher P.; Wallis, Graham P.; Waters, Jonathan M.

2016-02-01

Collisions between tectonic plates lead to the rise of new mountain ranges that can separate biological populations and ultimately result in new species. However, the identification of links between tectonic mountain-building and biological speciation is confounded by environmental and ecological factors. Thus, there are surprisingly few well-documented examples of direct tectonic controls on terrestrial biological speciation. Here we present examples from New Zealand, where the rapid evolution of 18 species of freshwater fishes has resulted from parallel tectonic landscape evolution. We use numerical models to reconstruct changes in the deep crustal structure and surface drainage catchments of the southern island of New Zealand over the past 25 million years. We show that the island and mountain topography evolved in six principal tectonic zones, which have distinct drainage catchments that separated fish populations. We use new and existing phylogenetic analyses of freshwater fish populations, based on over 1,000 specimens from more than 400 localities, to show that fish genomes can retain evidence of this tectonic landscape development, with a clear correlation between geologic age and extent of DNA sequence divergence. We conclude that landscape evolution has controlled on-going biological diversification over the past 25 million years.

Interspecific social networks promote information transmission in wild songbirds.

PubMed

Farine, Damien R; Aplin, Lucy M; Sheldon, Ben C; Hoppitt, William

2015-03-22

Understanding the functional links between social structure and population processes is a central aim of evolutionary ecology. Multiple types of interactions can be represented by networks drawn for the same population, such as kinship, dominance or affiliative networks, but the relative importance of alternative networks in modulating population processes may not be clear. We illustrate this problem, and a solution, by developing a framework for testing the importance of different types of association in facilitating the transmission of information. We apply this framework to experimental data from wild songbirds that form mixed-species flocks, recording the arrival (patch discovery) of individuals to novel foraging sites. We tested whether intraspecific and interspecific social networks predicted the spread of information about novel food sites, and found that both contributed to transmission. The likelihood of acquiring information per unit of connection to knowledgeable individuals increased 22-fold for conspecifics, and 12-fold for heterospecifics. We also found that species varied in how much information they produced, suggesting that some species play a keystone role in winter foraging flocks. More generally, these analyses demonstrate that this method provides a powerful approach, using social networks to quantify the relative transmission rates across different social relationships.

On the physical nature of globular cluster candidates in the Milky Way bulge

NASA Astrophysics Data System (ADS)

Piatti, Andrés E.

2018-06-01

We present results from 2MASS JKs photometry on the physical reality of recently reported globular cluster (GC) candidates in the Milky Way (MW) bulge. We relied our analysis on photometric membership probabilities that allowed us to distinguish real stellar aggregates from the composite field star population. When building colour-magnitude diagrams and stellar density maps for stars at different membership probability levels, the genuine GC candidate populations are clearly highlighted. We then used the tip of the red giant branch (RGB) as distance estimator, resulting in heliocentric distances that place many of the objects in regions near the MW bulge, where no GC had been previously recognized. Some few GC candidates resulted to be MW halo/disc objects. Metallicities estimated from the standard RGB method are in agreement with the values expected according to the position of the GC candidates in the Galaxy. Finally, we derived, for the first time, their structural parameters. We found that the studied objects have core, half-light, and tidal radii in the ranges spanned by the population of known MW GCs. Their internal dynamical evolutionary stages will be described properly when their masses are estimated.

Mass mortalities in bivalve populations: A review of the edible cockle Cerastoderma edule (L.)

NASA Astrophysics Data System (ADS)

Burdon, Daryl; Callaway, Ruth; Elliott, Michael; Smith, Tim; Wither, Andrew

2014-10-01

Mass mortalities in bivalve populations have long been of particular concern, especially when the species supports a commercial fishery or is of conservation interest. Here we consider the evidence of mass mortalities of the edible cockle, Cerastoderma edule (L.). Through the construction of a conceptual model eight potential factors (or groups of factors) which may cause mass mortalities are identified and reviewed. These include: food limitation; density; oxygen depletion and organic loadings; temperature and salinity; parasites, pathogens and commensals; toxicants and other persistent pollutants; predation, and changes in sediment, suspended solids, topography and bathymetry. The interplay between factors in recognized and discussed based on evidence mainly from the published literature relating to temperate edible cockle beds. Anecdotal evidence is also reported from a structured survey of site-specific evidence provided by fisheries managers in England and Wales. Case studies from the UK and Europe indicate that there is often no single, clear generic cause of mass mortalities in cockle populations. The importance of linked site-specific scientific investigations and laboratory-based experiments to fill the gaps in our current understanding of mass mortalities in bivalve species is highlighted as necessary to take account of both local extrinsic and intrinsic factors.

Evolution of the landscape along the Clear Creek Corridor, Colorado; urbanization, aggregate mining and reclamation

USGS Publications Warehouse

Arbogast, Belinda; Knepper, Daniel H.; Melick, Roger A.; Hickman, John

2002-01-01

Prime agricultural land along the Clear Creek floodplain, Colorado, attracted settlement in the 1850's but the demand for sand and gravel for 1900's construction initiated a sequence of events that exceeded previous interests and created the modified landscape and urban ecosystem that exists today. The Clear Creek valley corridor offers a landscape filled with a persistent visible and hidden reminder of it's past use. The map sheets illustrate the Clear Creek landscape as a series of compositions, both at the macro view (in the spatial context of urban structure and highways from aerial photographs) and micro view (from the civic scale where landscape features like trees, buildings, and sidewalks are included). The large-scale topographic features, such as mountains and terraces, appear 'changeless' (they do change over geologic time), while Clear Creek has changed from a wide braided stream to a narrow confined stream. Transportation networks (streets and highways) and spiraling population growth in adjacent cities (from approximately 38,000 people in 1880 to over a million in 1999) form two dominant landscape patterns. Mining and wetland/riparian occupy the smallest amount of land use acres compared to urban, transportation, or water reservoir activities in the Clear Creek aggregate reserve study area. Four types of reclaimed pits along Clear Creek were determined: water storage facilities, wildlife/greenbelt space, multiple-purpose reservoirs, and 'hidden scenery.' The latter involves infilling gravel pits (with earth backfill, concrete rubble, or sanitary landfill) and covering the site with light industry or residential housing making the landform hard to detect as a past mine site. Easier to recognize are the strong-edged, rectilinear water reservoirs, reclaimed from off-channel sand and gravel pits that reflect the land survey grid and property boundaries. The general public may not realize softly contoured linear wildlife corridors connecting urban, industrial, and natural space were once mine sites too. Multiple-use water projects from exhausted pits appear to be the new millennium parks, providing water storage, passive recreation, and habitat restoration for the Denver metropolitan area. The public objects to mining yet enjoys the reclaimed mine sites as recreation and wildlife space.

The benefits of analysing complete mitochondrial genomes: Deep insights into the phylogeny and population structure of Echinococcus granulosus sensu lato genotypes G6 and G7.

PubMed

Laurimäe, Teivi; Kinkar, Liina; Romig, Thomas; Omer, Rihab A; Casulli, Adriano; Umhang, Gérald; Gasser, Robin B; Jabbar, Abdul; Sharbatkhori, Mitra; Mirhendi, Hossein; Ponce-Gordo, Francisco; Lazzarini, Lorena E; Soriano, Silvia V; Varcasia, Antonio; Nejad, Mohammad Rostami; Andresiuk, Vanessa; Maravilla, Pablo; González, Luis Miguel; Dybicz, Monika; Gawor, Jakub; Šarkūnas, Mindaugas; Šnábel, Viliam; Kuzmina, Tetiana; Saarma, Urmas

2018-06-12

Cystic echinococcosis (CE) is a zoonotic disease caused by the larval stage of the species complex Echinococcus granulosus sensu lato. Within this complex, genotypes G6 and G7 have been frequently associated with human CE worldwide. Previous studies exploring the genetic variability and phylogeography of genotypes G6 and G7 have been based on relatively short mtDNA sequences, and the resolution of these studies has often been low. Moreover, using short sequences, the distinction between G6 and G7 has in some cases remained challenging. The aim here was to sequence complete mitochondrial genomes (mitogenomes) to obtain deeper insight into the genetic diversity, phylogeny and population structure of genotypes G6 and G7. We sequenced complete mitogenomes of 94 samples collected from 15 different countries worldwide. The results demonstrated that (i) genotypes G6 and G7 can be clearly distinguished when mitogenome sequences are used; (ii) G7 is represented by two major haplogroups, G7a and G7b, the latter being specific to islands of Corsica and Sardinia; (iii) intensive animal trade, but also geographical isolation, have likely had the largest impact on shaping the genetic structure and distribution of genotypes G6 and G7. In addition, we found phylogenetically highly divergent haplotype from Mongolia (Gmon), which had a higher affinity to G6. Copyright © 2017. Published by Elsevier B.V.

Soil moisture in relation to geologic structure and lithology, northern California

NASA Technical Reports Server (NTRS)

Rich, E. I. (Principal Investigator)

1980-01-01

The author has identified the following significant results. Structural features in the Norther California Coast Ranges are clearly discernable on Nite-IR images and some of the structural linears may results in an extension of known faults within the region. The Late Mesozoic marine sedimentary rocks along the western margin of the Sacramento Valley are clearly defined on the Nite-IR images and in a gross way individual layers of sandstone can be differentiated from shale. Late Pleistocene alluvial fans are clearly differentiated from second generation Holocene fans on the basis of tonal characteristics. Although the tonal characteristics change with the seasons, the differentiation of the two sets of fans is still possible.

The possible physical barrier and coastal dispersal strategy for Japanese grenadier anchovy, Coilia nasus in the East China Sea and Yellow Sea: evidence from AFLP markers.

PubMed

Han, Zhi-Qiang; Han, Gang; Wang, Zhi-Yong; Gao, Tian-Xiang

2015-02-03

In order to ascertain the taxonomic status of the Ariake Sea population of Japanese grenadier anchovy, Coilia nasus, and assess the contemporary possible genetic barrier between the west and east coastal waters of the East China Sea, we used amplified fragment length polymorphism (AFLP) markers to detect the genetic structure of C. nasus, in the East China Sea and Yellow Sea. Eighty-one individuals of C. nasus were collected from five locations and 12 individuals of Coilia mystus were sampled from the Yangtze River Estuary. A total of 371 loci were detected by five primer combinations, 310 of which were polymorphic (83.56%). Analysis of molecular variation (AMOVA) and pairwise fixation index (FST) revealed significant genetic differentiation among five samples, indicating limited gene flow among populations. The dendrogram for populations by neighbor-joining (NJ) cluster analysis provided evidence of a clear relationship between genetic and geographic patterns, supporting significant genetic differentiation between China coastal populations and Ariake Sea populations. Compared to the genetic divergence between C. nasus and C. mystus, the level of genetic differentiation between China and the Ariake Sea populations of C. nasus is obvious below the species level, indicating isolated populations of C. nasus in the Ariake Sea. Isolation by distance analysis revealed that direct ocean distance with deep-water at the continental slope and high salinity between west and east coastal waters of the East China Sea served as major physical barrier to C. nasus, supporting the coastal dispersal pattern in this estuarine species, and rejecting offshore dispersal strategy.

Evolutionary dynamics of methicillin-resistant Staphylococcus aureus within a healthcare system.

PubMed

Hsu, Li-Yang; Harris, Simon R; Chlebowicz, Monika A; Lindsay, Jodi A; Koh, Tse-Hsien; Krishnan, Prabha; Tan, Thean-Yen; Hon, Pei-Yun; Grubb, Warren B; Bentley, Stephen D; Parkhill, Julian; Peacock, Sharon J; Holden, Matthew T G

2015-04-23

In the past decade, several countries have seen gradual replacement of endemic multi-resistant healthcare-associated methicillin-resistant Staphylococcus aureus (MRSA) with clones that are more susceptible to antibiotic treatment. One example is Singapore, where MRSA ST239, the dominant clone since molecular profiling of MRSA began in the mid-1980s, has been replaced by ST22 isolates belonging to EMRSA-15, a recently emerged pandemic lineage originating from Europe. We investigated the population structure of MRSA in Singaporean hospitals spanning three decades, using whole genome sequencing. Applying Bayesian phylogenetic methods we report that prior to the introduction of ST22, the ST239 MRSA population in Singapore originated from multiple introductions from the surrounding region; it was frequently transferred within the healthcare system resulting in a heterogeneous hospital population. Following the introduction of ST22 around the beginning of the millennium, this clone spread rapidly through Singaporean hospitals, supplanting the endemic ST239 population. Coalescent analysis revealed that although the genetic diversity of ST239 initially decreased as ST22 became more dominant, from 2007 onwards the genetic diversity of ST239 began to increase once more, which was not associated with the emergence of a sub-clone of ST239. Comparative genomic analysis of the accessory genome of the extant ST239 population identified that the Arginine Catabolic Mobile Element arose multiple times, thereby introducing genes associated with enhanced skin colonization into this population. Our results clearly demonstrate that, alongside clinical practice and antibiotic usage, competition between clones also has an important role in driving the evolution of nosocomial pathogen populations.

Population genomics reveals seahorses (Hippocampus erectus) of the western mid-Atlantic coast to be residents rather than vagrants.

PubMed

Boehm, J T; Waldman, John; Robinson, John D; Hickerson, Michael J

2015-01-01

Understanding population structure and areas of demographic persistence and transients is critical for effective species management. However, direct observational evidence to address the geographic scale and delineation of ephemeral or persistent populations for many marine fishes is limited. The Lined seahorse (Hippocampus erectus) can be commonly found in three western Atlantic zoogeographic provinces, though inhabitants of the temperate northern Virginia Province are often considered tropical vagrants that only arrive during warm seasons from the southern provinces and perish as temperatures decline. Although genetics can locate regions of historical population persistence and isolation, previous evidence of Virginia Province persistence is only provisional due to limited genetic sampling (i.e., mitochondrial DNA and five nuclear loci). To test alternative hypotheses of historical persistence versus the ephemerality of a northern Virginia Province population we used a RADseq generated dataset consisting of 11,708 single nucleotide polymorphisms (SNP) sampled from individuals collected from the eastern Gulf of Mexico to Long Island, NY. Concordant results from genomic analyses all infer three genetically divergent subpopulations, and strongly support Virginia Province inhabitants as a genetically diverged and a historically persistent ancestral gene pool. These results suggest that individuals that emerge in coastal areas during the warm season can be considered "local" and supports offshore migration during the colder months. This research demonstrates how a large number of genes sampled across a geographical range can capture the diversity of coalescent histories (across loci) while inferring population history. Moreover, these results clearly demonstrate the utility of population genomic data to infer peripheral subpopulation persistence in difficult-to-observe species.

Mixing times towards demographic equilibrium in insect populations with temperature variable age structures.

PubMed

Damos, Petros

2015-08-01

In this study, we use entropy related mixing rate modules to measure the effects of temperature on insect population stability and demographic breakdown. The uncertainty in the age of the mother of a randomly chosen newborn, and how it is moved after a finite act of time steps, is modeled using a stochastic transformation of the Leslie matrix. Age classes are represented as a cycle graph and its transitions towards the stable age distribution are brought forth as an exact Markov chain. The dynamics of divergence, from a non equilibrium state towards equilibrium, are evaluated using the Kolmogorov-Sinai entropy. Moreover, Kullback-Leibler distance is applied as information-theoretic measure to estimate exact mixing times of age transitions probabilities towards equilibrium. Using empirically data, we show that on the initial conditions and simulated projection's trough time, that population entropy can effectively be applied to detect demographic variability towards equilibrium under different temperature conditions. Changes in entropy are correlated with the fluctuations of the insect population decay rates (i.e. demographic stability towards equilibrium). Moreover, shorter mixing times are directly linked to lower entropy rates and vice versa. This may be linked to the properties of the insect model system, which in contrast to warm blooded animals has the ability to greatly change its metabolic and demographic rates. Moreover, population entropy and the related distance measures that are applied, provide a means to measure these rates. The current results and model projections provide clear biological evidence why dynamic population entropy may be useful to measure population stability. Copyright © 2015 Elsevier Inc. All rights reserved.

Atomic structure and dynamics properties of Cu50Zr50 films

NASA Astrophysics Data System (ADS)

Chen, Heng; Qu, Bingyan; Li, Dongdong; Zhou, Rulong; Zhang, Bo

2018-01-01

In this paper, the structural and dynamic properties of Cu50Zr50 films are investigated by molecular dynamics simulations. Our results show that the dynamics of the surface atoms are much faster than those of the bulk. Especially, the diffusion coefficient of the surface atoms is about forty times larger than that of the bulk at 600 K, which qualitatively agrees with the experimental results. Meanwhile, we find that the population of the icosahedral (-like) clusters in the surface region is obviously higher than that of the bulk, which prevents the surface from crystallization. A new method to determine the string-like collective atomic motion is introduced in the paper, and it suggests a possible connection between the glass formation ability and collective atomic motion. By using the method, the effects of surface on collective motion are illustrated. Our results show that the string-like collective atomic motion of surface atoms is weakened while that of the interior atoms is strengthened. The studies clearly explain the effects of surface on the structural and dynamic properties of Cu50Zr50 films from the atomic scale.

A passive mutualistic interaction promotes the evolution of spatial structure within microbial populations.

PubMed

Marchal, Marie; Goldschmidt, Felix; Derksen-Müller, Selina N; Panke, Sven; Ackermann, Martin; Johnson, David R

2017-04-24

While mutualistic interactions between different genotypes are pervasive in nature, their evolutionary origin is not clear. The dilemma is that, for mutualistic interactions to emerge and persist, an investment into the partner genotype must pay off: individuals of a first genotype that invest resources to promote the growth of a second genotype must receive a benefit that is not equally accessible to individuals that do not invest. One way for exclusive benefits to emerge is through spatial structure (i.e., physical barriers to the movement of individuals and resources). Here we propose that organisms can evolve their own spatial structure based on physical attachment between individuals, and we hypothesize that attachment evolves when spatial proximity to members of another species is advantageous. We tested this hypothesis using experimental evolution with combinations of E. coli strains that depend on each other to grow. We found that attachment between cells repeatedly evolved within 8 weeks of evolution and observed that many different types of mutations potentially contributed to increased attachment. We postulate a general principle by which passive beneficial interactions between organisms select for attachment, and attachment then provides spatial structure that could be conducive for the evolution of active mutualistic interactions.

Effects of habitat loss and fragmentation on amphibians: A review and prospectus

Treesearch

Samuel A. Cushman

2006-01-01

Habitat loss and fragmentation are among the largest threats to amphibian populations. However, most studies have not provided clear insights into their population-level implications. There is a critical need to investigate the mechanisms that underlie patterns of distribution and abundance. In order to understand the population- and species-level implications of...

Clear-air radar observations of the atmospheric boundary layer

NASA Astrophysics Data System (ADS)

Ince, Turker

2001-10-01

This dissertation presents the design and operation of a high-resolution frequency-modulated continuous-wave (FM- CW) radar system to study the structure and dynamics of clear-air turbulence in the atmospheric boundary layer (ABL). This sensitive radar can image the vertical structure of the ABL with both high spatial and temporal resolutions, and provide both qualitative information about the morphology of clear-air structures and quantitative information on the intensity of fluctuations in refractive-index of air. The principles of operation and the hardware and data acquisition characteristics of the radar are described in the dissertation. In October 1999, the radar participated in the Cooperative Atmosphere-Surface Exchange Study (CASES'99) Experiment to characterize the temporal structure and evolution of the boundary-layer features in both convective and stable conditions. The observed structures include clear-air convection, boundary layer evolution, gravity waves, Kelvin-Helmholtz instabilities, stably stratified layers, and clear-air turbulence. Many of the S-band radar images also show high- reflectivity returns from Rayleigh scatterers such as insects. An adaptive median filtering technique based on local statistics has, therefore, been developed to discriminate between Bragg and Rayleigh scattering in clear-air radar observations. The filter is tested on radar observations of clear air convection with comparison to two commonly used image processing techniques. The dissertation also examines the statistical mean of the radar-measured C2n for clear-air convection, and compares it with the theoretical predictions. The study also shows that the inversion height, local thickness of the inversion layer, and the height of the elevated atmospheric layers can be estimated from the radar reflectivity measurements. In addition, comparisons to the radiosonde-based height estimates are made. To examine the temporal and spatial structure of C2n , the dissertation presents two case studies with the measurements of remote (the FM-CW radar and Doppler lidar) and in-situ (research aircraft, kite, and radiosonde) sensors from the stable nighttime boundary layer. It also presents a unique observation of evolution of the convective and nocturnal boundary layers by the S-band radar, and provides description of the observed boundary layer characteristics with the aid of in-situ measurements by the 55m instrumented tower and radiosonde.

76 FR 64403 - Self-Regulatory Organizations; The Fixed Income Clearing Corporation; Notice of Filing and...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-18

... Schedule of Timeframes, and Fee Structure in the GSD Rules. II. Self-Regulatory Organization's Statement of...-Regulatory Organizations; The Fixed Income Clearing Corporation; Notice of Filing and Immediate Effectiveness... Timeframes, and Fee Structure in the GSD Rules October 12, 2011. Pursuant to Section 19(b)(1) of the...

Development of population structure and spatial distribution patterns of a restored forest during 17-year succession (1993-2010) in Pingshuo opencast mine spoil, China.

PubMed

Zhao, Zhongqiu; Wang, Lianhua; Bai, Zhongke; Pan, Ziguan; Wang, Yun

2015-07-01

Afforestation of native tree species is often recommended for ecological restoration in mining areas, but the understanding of the ecological processes of restored vegetation is quite limited. In order to provide insight of the ecological processes of restored vegetation, in this study, we investigate the development of the population structure and spatial distribution patterns of restored Robinia pseudoacacia (ROPS) and Pinus tabuliformis (PITA) mixed forests during the 17 years of the mine spoil period of the Pingshuo opencast mine, Shanxi Province, China. After a 17-year succession, apart from the two planted species, Ulmus pumila (ULPU), as an invasive species, settled in the plot along with a large number of small diameter at breast height (DBH) size. In total, there are 10,062 living individual plants, much more than that at the plantation (5105), and ROPS had become the dominant species with a section area with a breast height of 9.40 m(2) hm(-2) and a mean DBH of 6.72 cm, much higher than both PITA and ULPU. The DBH size classes of all the total species showed inverted J-shaped distributions, which may have been a result of the large number of small regenerated ULPU trees. The DBH size classes of both ROPS and PITA showed peak-type structures with individuals mainly gathering in the moderate DBH size class, indicating a relatively healthy DBH size class structure. Meanwhile, invasive ULPU were distributed in a clear L shape, concentrating on the small DBH size class, indicating a relatively low survival rate for adult trees. Both ROPS and PITA species survival in the plantation showed uniform and aggregated distribution at small scales and random with scales increasing. ULPU showed a strong aggregation at small scales as well as random with scales increasing. Both the population structure and spatial distribution indicated that ROPS dominates and will continue to dominate the community in the future succession, which should be continuously monitored.

Resource heterogeneity can facilitate cooperation.

PubMed

Kun, Ádám; Dieckmann, Ulf

2013-01-01

Although social structure is known to promote cooperation, by locally exposing selfish agents to their own deeds, studies to date assumed that all agents have access to the same level of resources. This is clearly unrealistic. Here we find that cooperation can be maintained when some agents have access to more resources than others. Cooperation can then emerge even in populations in which the temptation to defect is so strong that players would act fully selfishly if their resources were distributed uniformly. Resource heterogeneity can thus be crucial for the emergence and maintenance of cooperation. We also show that resource heterogeneity can hinder cooperation once the temptation to defect is significantly lowered. In all cases, the level of cooperation can be maximized by managing resource heterogeneity.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Dong, E-mail: wang.dong.539@m.kyushu-u.ac.jp; Maekura, Takayuki; Kamezawa, Sho

We demonstrated direct band gap (DBG) electroluminescence (EL) at room temperature from n-type bulk germanium (Ge) using a fin type asymmetric lateral metal/Ge/metal structure with TiN/Ge and HfGe/Ge contacts, which was fabricated using a low temperature (<400 °C) process. Small electron and hole barrier heights were obtained for TiN/Ge and HfGe/Ge contacts, respectively. DBG EL spectrum peaked at 1.55 μm was clearly observed even at a small current density of 2.2 μA/μm. Superlinear increase in EL intensity was also observed with increasing current density, due to superlinear increase in population of elections in direct conduction band. The efficiency of hole injection was alsomore » clarified.« less

Bilingual School Psychology: Challenges and Opportunities

ERIC Educational Resources Information Center

Olvera, Pedro; Olvera, Veronica I.

2015-01-01

National demographics clearly demonstrate that children from culturally and linguistically diverse (CLD) backgrounds are on the rise. Many regions in the United States are experiencing unprecedented growth in English language learner (ELL) populations without adequately trained personnel to serve this unique population. Unfortunately, the…

Alternative glacial-interglacial refugia demographic hypotheses tested on Cephalocereus columna-trajani (Cactaceae) in the intertropical Mexican drylands

PubMed Central

Cornejo-Romero, Amelia; Aguilar-Martínez, Gustavo F.; Medina-Sánchez, Javier; Rendón-Aguilar, Beatriz; Valverde, Pedro Luis; Zavala-Hurtado, Jose Alejandro; Serrato, Alejandra; Rivas-Arancibia, Sombra; Pérez-Hernández, Marco Aurelio; López-Ortega, Gerardo; Jiménez-Sierra, Cecilia

2017-01-01

Historic demography changes of plant species adapted to New World arid environments could be consistent with either the Glacial Refugium Hypothesis (GRH), which posits that populations contracted to refuges during the cold-dry glacial and expanded in warm-humid interglacial periods, or with the Interglacial Refugium Hypothesis (IRH), which suggests that populations contracted during interglacials and expanded in glacial times. These contrasting hypotheses are developed in the present study for the giant columnar cactus Cephalocereus columna-trajani in the intertropical Mexican drylands where the effects of Late Quaternary climatic changes on phylogeography of cacti remain largely unknown. In order to determine if the historic demography and phylogeographic structure of the species are consistent with either hypothesis, sequences of the chloroplast regions psbA-trnH and trnT-trnL from 110 individuals from 10 populations comprising the full distribution range of this species were analysed. Standard estimators of genetic diversity and structure were calculated. The historic demography was analysed using a Bayesian approach and the palaeodistribution was derived from ecological niche modelling to determine if, in the arid environments of south-central Mexico, glacial-interglacial cycles drove the genetic divergence and diversification of this species. Results reveal low but statistically significant population differentiation (FST = 0.124, P < 0.001), although very clear geographic clusters are not formed. Genetic diversity, haplotype network and Approximate Bayesian Computation (ABC) demographic analyses suggest a population expansion estimated to have taken place in the Last Interglacial (123.04 kya, 95% CI 115.3–130.03). The species palaeodistribution is consistent with the ABC analyses and indicates that the potential area of palaedistribution and climatic suitability were larger during the Last Interglacial and Holocene than in the Last Glacial Maximum. Overall, these results suggest that C. columna-trajani experienced an expansion following the warm conditions of interglacials, in accordance with the GRH. PMID:28426818

Alternative glacial-interglacial refugia demographic hypotheses tested on Cephalocereus columna-trajani (Cactaceae) in the intertropical Mexican drylands.

PubMed

Cornejo-Romero, Amelia; Vargas-Mendoza, Carlos Fabián; Aguilar-Martínez, Gustavo F; Medina-Sánchez, Javier; Rendón-Aguilar, Beatriz; Valverde, Pedro Luis; Zavala-Hurtado, Jose Alejandro; Serrato, Alejandra; Rivas-Arancibia, Sombra; Pérez-Hernández, Marco Aurelio; López-Ortega, Gerardo; Jiménez-Sierra, Cecilia

2017-01-01

Historic demography changes of plant species adapted to New World arid environments could be consistent with either the Glacial Refugium Hypothesis (GRH), which posits that populations contracted to refuges during the cold-dry glacial and expanded in warm-humid interglacial periods, or with the Interglacial Refugium Hypothesis (IRH), which suggests that populations contracted during interglacials and expanded in glacial times. These contrasting hypotheses are developed in the present study for the giant columnar cactus Cephalocereus columna-trajani in the intertropical Mexican drylands where the effects of Late Quaternary climatic changes on phylogeography of cacti remain largely unknown. In order to determine if the historic demography and phylogeographic structure of the species are consistent with either hypothesis, sequences of the chloroplast regions psbA-trnH and trnT-trnL from 110 individuals from 10 populations comprising the full distribution range of this species were analysed. Standard estimators of genetic diversity and structure were calculated. The historic demography was analysed using a Bayesian approach and the palaeodistribution was derived from ecological niche modelling to determine if, in the arid environments of south-central Mexico, glacial-interglacial cycles drove the genetic divergence and diversification of this species. Results reveal low but statistically significant population differentiation (FST = 0.124, P < 0.001), although very clear geographic clusters are not formed. Genetic diversity, haplotype network and Approximate Bayesian Computation (ABC) demographic analyses suggest a population expansion estimated to have taken place in the Last Interglacial (123.04 kya, 95% CI 115.3-130.03). The species palaeodistribution is consistent with the ABC analyses and indicates that the potential area of palaedistribution and climatic suitability were larger during the Last Interglacial and Holocene than in the Last Glacial Maximum. Overall, these results suggest that C. columna-trajani experienced an expansion following the warm conditions of interglacials, in accordance with the GRH.

Population genetics of Cryptosporidium meleagridis in humans and birds: evidence for cross-species transmission.

PubMed

Wang, Yuanfei; Yang, Wenli; Cama, Vitaliano; Wang, Lin; Cabrera, Lilia; Ortega, Ynes; Bern, Caryn; Feng, Yaoyu; Gilman, Robert; Xiao, Lihua

2014-07-01

Population genetic studies have been used to understand the transmission of pathogens in humans and animals, especially the role of zoonotic infections and evolution and dispersal of virulent subtypes. In this study, we analysed the genetic diversity and population structure of Cryptosporidium meleagridis, the only known Cryptosporidium species that infects both avian and mammalian hosts and is responsible for approximately 10% of human cryptosporidiosis in some areas. A total of 62 C. meleagridis specimens from children, AIDS patients, and birds in Lima, Peru were characterised by sequence analysis of the ssrRNA gene and five minisatellite, microsatellite and polymorphic markers in chromosome 6, including the 60 kDa glycoprotein (gp60), 47 kDa glycoprotein (CP47), a serine repeat antigen (MSC6-5), retinitis pigmentosa GTPase regulator (RPGR) and thrombospondin protein 8 (TSP8). The multilocus sequence analysis identified concurrent infections with Cryptosporidium hominis in four AIDS patients and three children. Unique subtypes of C. meleagridis ranged from eight at the gp60 locus (gene diversity -Hd=0.651), three at the RPGR (Hd=0.556), three at the MSC6-5 locus (Hd=0.242), two at TSP8 (Hd=0.198), to one at CP47 (monomorphic), much lower than that of C. hominis in the same area. Intragenic linkage disequilibrium was strong and complete at all gene loci. Intergenic linkage disequilibrium was highly significant (P<0.001) for all pairs of polymorphic loci. Two major groups of subtypes were seen, with most subtypes belonging to group 1. Within group 1, there was no clear population segregation, and two of the 14 multilocus subtypes of C. meleagridis were found in both AIDS patients and birds. We believe that these results provide the first evidence of a clonal population structure of C. meleagridis and the likely occurrence of cross-species transmission of C. meleagridis between birds and humans. Published by Elsevier Ltd.

Distribution and Differentiation of Wild, Feral, and Cultivated Populations of Perennial Upland Cotton (Gossypium hirsutum L.) in Mesoamerica and the Caribbean

PubMed Central

Coppens d'Eeckenbrugge, Geo; Lacape, Jean-Marc

2014-01-01

Perennial forms of Gossypium hirsutum are classified under seven races. Five Mesoamerican races would have been derived from the wild race ‘yucatanense’ from northern Yucatán. ‘Marie-Galante’, the main race in the Caribbean, would have developed from introgression with G. barbadense. The racial status of coastal populations from the Caribbean has not been clearly defined. We combined Ecological Niche Modeling with an analysis of SSR marker diversity, to elucidate the relationships among cultivated, feral and wild populations of perennial cottons. Out of 954 records of occurrence in Mesoamerica and the Caribbean, 630 were classified into four categories cultivated, feral (disturbed and secondary habitats), wild/feral (protected habitats), and truly wild cotton (TWC) populations. The widely distributed three first categories cannot be differentiated on ecological grounds, indicating they mostly belong to the domesticated pool. In contrast, TWC are restricted to the driest and hottest littoral habitats, in northern Yucatán and in the Caribbean (from Venezuela to Florida), as confirmed by their climatic envelope in the factorial analysis. Extrapolating this TWC climatic model to South America and the Pacific Ocean points towards places where other wild representatives of tetraploid Gossypium species have been encountered. The genetic analysis sample comprised 42 TWC accessions from 12 sites and 68 feral accessions from 18 sites; at nine sites, wild and feral accessions were collected in close vicinity. Principal coordinate analysis, neighbor joining, and STRUCTURE consistently showed a primary divergence between TWC and feral cottons, and a secondary divergence separating ‘Marie-Galante’ from all other feral accessions. This strong genetic structure contrasts strikingly with the absence of geographic differentiation. Our results show that TWC populations of Mesoamerica and the Caribbean constitute a homogenous gene pool. Furthermore, the relatively low genetic divergence between the Mesoamerican and Caribbean domesticated pools supports the hypothesis of domestication of G. hirsutum in northern Yucatán. PMID:25198534

Phenotypic variations in chondrocyte subpopulations and their response to in vitro culture and external stimuli.

PubMed

Coates, Emily E; Fisher, John P

2010-11-01

Articular cartilage defects have limited capacity to self-repair, and cost society up to 60 billion dollars annually in both medical treatments and loss of working days. Recent developments in cartilage tissue engineering have resulted in many new products coming to market or entering clinical trials. However, there is a distinct lack of treatments which aim to recreate the complex zonal organization of articular cartilage. Cartilage tissue withstands repetitive strains throughout an individual's lifetime and provides frictionless movement between joints. The structure and composition of its intricately organized extracellular matrix varies with tissue depth to provide optimal resistance to loading, ensure ease of movement, and integrate with the subchondral bone. Each tissue zone is specially designed to resist the load it experiences, and maximize the tissue properties needed for its location. It is unlikely that a homogenous solution to tissue repair will be able to optimally restore the function of such a heterogeneous tissue. For zonal engineering of articular cartilage to become practical, maintenance of phenotypically stable zonal cell populations must be achieved. The chondrocyte phenotype varies considerably by zone, and it is the activity of these cells that help achieve the structural organization of the tissue. This review provides an examination of literature which has studied variations in cellular phenotype between cartilage zones. By doing so, we have identified critical differences between cell populations and highlighted areas of research which show potential in the field. Current research has made the morphological and metabolic variations between these cell populations clear, but an ideal way of maintaining these differences in vitro culture is yet to be established. Combinations of delivered growth factors, mechanical loading, and layered three-dimensional culture systems all show potential for achieving this goal. Furthermore, differentiation of progenitor cell populations into chondrocyte subpopulations may also hold promise for achieving large numbers of zonal chondrocytes. Success of the field lies in establishing methods of retaining phenotypically stable cell populations for in vitro culture.

Geographic proximity not a prerequisite for invasion: Hawaii not the source of California invasion by light brown apple moth (Epiphyas postvittana).

PubMed

Rubinoff, Daniel; Holland, Brenden S; San Jose, Michael; Powell, Jerry A

2011-01-27

The light brown apple moth (LBAM), Epiphyas postvittana (Walker), is native to Australia but invaded England, New Zealand, and Hawaii more than 100 years ago. In temperate climates, LBAM can be a major agricultural pest. In 2006 LBAM was discovered in California, instigating eradication efforts and quarantine against Hawaiian agriculture, the assumption being that Hawaii was the source of the California infestation. Genetic relationships among populations in Hawaii, California, and New Zealand are crucial to understanding LBAM invasion dynamics across the Pacific. We sequenced mitochondrial DNA (mtDNA) from 1293 LBAM individuals from California (695), Hawaii (448), New Zealand (147), and Australia (3) to examine haplotype diversity and structure among introduced populations, and evaluate the null hypothesis that invasive populations are from a single panmictic source. However, invasive populations in California and New Zealand harbor deep genetic diversity, whereas Hawaii shows low level, shallow diversity. LBAM recently has established itself in California, but was in Hawaii and New Zealand for hundreds of generations, yet California and New Zealand show similar levels of genetic diversity relative to Hawaii. Thus, there is no clear relationship between duration of invasion and genetic structure. Demographic statistics suggest rapid expansion occurring in California and past expansions in New Zealand; multiple introductions of diverse, genetically fragmented lineages could contribute to these patterns. Hawaii and California share no haplotypes, therefore, Hawaii is not the source of the California introduction. Paradoxically, Hawaii and California share multiple haplotypes with New Zealand. New Zealand may be the source for the California and Hawaii infestations, but the introductions were independent, and Hawaii was invaded only once. This has significant implications for quarantine, and suggests that probability of invasion is not directly related to geographic distance. Surprisingly, Hawaiian LBAM populations have much lower genetic diversity than California, despite being older.

Geographic Proximity Not a Prerequisite for Invasion: Hawaii Not the Source of California Invasion by Light Brown Apple Moth (Epiphyas postvittana)

PubMed Central

Rubinoff, Daniel; Holland, Brenden S.; San Jose, Michael; Powell, Jerry A.

2011-01-01

Background The light brown apple moth (LBAM), Epiphyas postvittana (Walker), is native to Australia but invaded England, New Zealand, and Hawaii more than 100 years ago. In temperate climates, LBAM can be a major agricultural pest. In 2006 LBAM was discovered in California, instigating eradication efforts and quarantine against Hawaiian agriculture, the assumption being that Hawaii was the source of the California infestation. Genetic relationships among populations in Hawaii, California, and New Zealand are crucial to understanding LBAM invasion dynamics across the Pacific. Methodology/Principal Findings We sequenced mitochondrial DNA (mtDNA) from 1293 LBAM individuals from California (695), Hawaii (448), New Zealand (147), and Australia (3) to examine haplotype diversity and structure among introduced populations, and evaluate the null hypothesis that invasive populations are from a single panmictic source. However, invasive populations in California and New Zealand harbor deep genetic diversity, whereas Hawaii shows low level, shallow diversity. Conclusions/Significance LBAM recently has established itself in California, but was in Hawaii and New Zealand for hundreds of generations, yet California and New Zealand show similar levels of genetic diversity relative to Hawaii. Thus, there is no clear relationship between duration of invasion and genetic structure. Demographic statistics suggest rapid expansion occurring in California and past expansions in New Zealand; multiple introductions of diverse, genetically fragmented lineages could contribute to these patterns. Hawaii and California share no haplotypes, therefore, Hawaii is not the source of the California introduction. Paradoxically, Hawaii and California share multiple haplotypes with New Zealand. New Zealand may be the source for the California and Hawaii infestations, but the introductions were independent, and Hawaii was invaded only once. This has significant implications for quarantine, and suggests that probability of invasion is not directly related to geographic distance. Surprisingly, Hawaiian LBAM populations have much lower genetic diversity than California, despite being older. PMID:21298019

Population genetics and phylogeography of sea turtles.

PubMed

Bowen, B W; Karl, S A

2007-12-01

The seven species of sea turtles occupy a diversity of niches, and have a history tracing back over 100 million years, yet all share basic life-history features, including exceptional navigation skills and periodic migrations from feeding to breeding habitats. Here, we review the biogeographic, behavioural, and ecological factors that shape the distribution of genetic diversity in sea turtles. Natal homing, wherein turtles return to their region of origin for mating and nesting, has been demonstrated with mtDNA sequences. These maternally inherited markers show strong population structure among nesting colonies while nuclear loci reveal a contrasting pattern of male-mediated gene flow, a phenomenon termed 'complex population structure'. Mixed-stock analyses indicate that multiple nesting colonies can contribute to feeding aggregates, such that exploitation of turtles in these habitats can reduce breeding populations across the region. The mtDNA data also demonstrate migrations across entire ocean basins, some of the longest movements of marine vertebrates. Multiple paternity occurs at reported rates of 0-100%, and can vary by as much as 9-100% within species. Hybridization in almost every combination among members of the Cheloniidae has been documented but the frequency and ultimate ramifications of hybridization are not clear. The global phylogeography of sea turtles reveals a gradient based on habitat preference and thermal regime. The cold-tolerant leatherback turtle (Dermochelys coriacea) shows no evolutionary partitions between Indo-Pacific and Atlantic populations, while the tropical green (Chelonia mydas), hawksbill (Eretmochelys imbricata), and ridleys (Lepidochelys olivacea vs. L. kempi) have ancient separations between oceans. Ridleys and loggerhead (Caretta caretta) also show more recent colonization between ocean basins, probably mediated by warm-water gyres that occasionally traverse the frigid upwelling zone in southern Africa. These rare events may be sufficient to prevent allopatric speciation under contemporary geographic and climatic conditions. Genetic studies have advanced our understanding of marine turtle biology and evolution, but significant gaps persist and provide challenges for the next generation of sea turtle geneticists.

Comparison of mandibular first molar mesial root canal morphology using micro-computed tomography and clearing technique.

PubMed

Kim, Yeun; Perinpanayagam, Hiran; Lee, Jong-Ki; Yoo, Yeon-Jee; Oh, Soram; Gu, Yu; Lee, Seung-Pyo; Chang, Seok Woo; Lee, Woocheol; Baek, Seung-Ho; Zhu, Qiang; Kum, Kee-Yeon

2015-08-01

Micro-computed tomography (MCT) with alternative image reformatting techniques shows complex and detailed root canal anatomy. This study compared two-dimensional (2D) and 3D MCT image reformatting with standard tooth clearing for studying mandibular first molar mesial root canal morphology. Extracted human mandibular first molar mesial roots (n=31) were scanned by MCT (Skyscan 1172). 2D thin-slab minimum intensity projection (TS-MinIP) and 3D volume rendered images were constructed. The same teeth were then processed by clearing and staining. For each root, images obtained from clearing, 2D, 3D and combined 2D and 3D techniques were examined independently by four endodontists and categorized according to Vertucci's classification. Fine anatomical structures such as accessory canals, intercanal communications and loops were also identified. Agreement among the four techniques for Vertucci's classification was 45.2% (14/31). The most frequent were Vertucci's type IV and then type II, although many had complex configurations that were non-classifiable. Generally, complex canal systems were more clearly visible in MCT images than with standard clearing and staining. Fine anatomical structures such as intercanal communications, accessory canals and loops were mostly detected with a combination of 2D TS-MinIP and 3D volume-rendering MCT images. Canal configurations and fine anatomic structures were more clearly observed in the combined 2D and 3D MCT images than the clearing technique. The frequency of non-classifiable configurations demonstrated the complexity of mandibular first molar mesial root canal anatomy.

Temperature-associated population diversity in salmon confers benefits to mobile consumers

USGS Publications Warehouse

Ruff, Casey P.; Schindle, Daniel E.; Armstrong, Jonathan B.; Bentle, Kale T.; Brooks, Gabriel T.; Holtgrieve, Gordon W.; McGlauflin, Molly T.; Torgersen, Christian E.; Seeb, James E.

2011-01-01

Habitat heterogeneity can generate intraspecific diversity through local adaptation of populations. While it is becoming increasingly clear that population diversity can increase stability in species abundance, less is known about how population diversity can benefit consumers that can integrate across population diversity in their prey. Here we demonstrate cascading effects of thermal heterogeneity on trout–salmon interactions in streams where rainbow trout rely heavily on the seasonal availability of anadromous salmon eggs. Water temperature in an Alaskan stream varied spatially from 5°C to 17.5°C, and spawning sockeye salmon showed population differentiation associated with this thermal heterogeneity. Individuals that spawned early in cool regions of the 5 km long stream were genetically differentiated from those spawning in warmer regions later in the season. Sockeye salmon spawning generates a pulsed resource subsidy that supports the majority of seasonal growth in stream-dwelling rainbow trout. The spatial and temporal structuring of sockeye salmon spawn timing in our focal stream extended the duration of the pulsed subsidy compared to a thermally homogeneous stream with a single population of salmon. Further, rainbow trout adopted movement strategies that exploited the multiple pulses of egg subsidies in the thermally heterogeneous stream. Fish that moved to track the resource pulse grew at rates about 2.5 times higher than those that remained stationary or trout in the reference stream with a single seasonal pulse of eggs. Our results demonstrate that habitat heterogeneity can have important effects on the population diversity of dominant species, and in turn, influence their value to species that prey upon them. Therefore, habitat homogenization may have farther-reaching ecological effects than previously considered.

Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects.

PubMed

Zhang, De-Xing; Hewitt, Godfrey M

2003-03-01

Population-genetic studies have been remarkably productive and successful in the last decade following the invention of PCR technology and the introduction of mitochondrial and microsatellite DNA markers. While mitochondrial DNA has proven powerful for genealogical and evolutionary studies of animal populations, and microsatellite sequences are the most revealing DNA markers available so far for inferring population structure and dynamics, they both have important and unavoidable limitations. To obtain a fuller picture of the history and evolutionary potential of populations, genealogical data from nuclear loci are essential, and the inclusion of other nuclear markers, i.e. single copy nuclear polymorphic (scnp) sequences, is clearly needed. Four major uncertainties for nuclear DNA analyses of populations have been facing us, i.e. the availability of scnp markers for carrying out such analysis, technical laboratory hurdles for resolving haplotypes, difficulty in data analysis because of recombination, low divergence levels and intraspecific multifurcation evolution, and the utility of scnp markers for addressing population-genetic questions. In this review, we discuss the availability of highly polymorphic single copy DNA in the nuclear genome, describe patterns and rate of evolution of nuclear sequences, summarize past empirical and theoretical efforts to recover and analyse data from scnp markers, and examine the difficulties, challenges and opportunities faced in such studies. We show that although challenges still exist, the above-mentioned obstacles are now being removed. Recent advances in technology and increases in statistical power provide the prospect of nuclear DNA analyses becoming routine practice, allowing allele-discriminating characterization of scnp loci and microsatellite loci. This certainly will increase our ability to address more complex questions, and thereby the sophistication of genetic analyses of populations.

Future Estimation of Convenience Living Facilities Withdrawal due to Population Decline all Over Japan from 2010 TO 2040 - Focus on Supermarkets, Convenience Stores and Drugstores

NASA Astrophysics Data System (ADS)

Nishimoto, Yuka; Akiyama, Yuki; Shibasaki, Ryosuke

2016-06-01

Population explosion is considered to be one of the most crucial problems in the world. However, in Japan, the opposite problem: population decline has become serious now. Japanese population is estimated to decrease by twenty millions in 2040. This negative situation will cause to increase areas where many residents cannot make a daily living all over Japan because many convenience living facilities such as supermarkets, convenience stores and drugstores will be difficult to maintain their market area population due to future population decline. In our research, we used point data of convenience living facilities developed by address geocoding of digital telephone directory and point data of future population projection developed by distribution of Japanese official population projection data proportionally among the building volume of digital residential map, which can monitor building volumes all over Japan. In conclusion, we estimated that various convenience living facilities in Japan will shrink and close by population decline in near future. In particular, it is cleared that approximately 14.7% of supermarkets will be possible to withdraw all over Japan by 2040. In addition, it is cleared that over 40% of supermarkets in some countryside prefectures will be possible to withdraw by 2040. Thus, we estimated future distributions of convenience living facilities that cannot maintain their market area population due to future population decline. Moreover, we estimated the number of people that they will become inconvenience in buying fresh foods.

Genecological approaches to predicting the effects of climate change on plant populations

Treesearch

Francis F. Kilkenny

2015-01-01

Climate change threatens native plant populations and plant communities globally. It is critical that land managers have a clear understanding of climate change impacts on plant species and populations so that restoration efforts can be adjusted accordingly. This paper reviews the develop.ment and use of seed transfer guidelines for restoration in the face of global...

Sponge epibionts on ecosystem-engineering ascidians: The case of Microcosmus sabatieri

NASA Astrophysics Data System (ADS)

Voultsiadou, Eleni; Kyrodimou, Marianthi; Antoniadou, Chryssanthi; Vafidis, Dimitris

2010-03-01

The study of epibionts on habitat engineering ascidians is of increasing interest because changes in the population structure of the latter may affect associated communities, especially in the case of commercially exploited species. The solitary ascidian Microcosmus sabatieri lives on rocky cliffs in the Eastern Mediterranean and is harvested in certain Aegean areas. Its hard, wrinkled tunic is usually fouled by various epibionts both sessile and motile. Sponges are an important component of this complex and their biomass may be higher than that of the ascidian itself, strongly affecting diversity and abundance of the motile epifauna. The aim of this study was to examine in detail the structure of the epibiotic sponge assemblage on ascidians collected from their main fishing grounds in the South Aegean Sea. A rich (41 species) and taxonomically diverse sponge assemblage was found, while only eight species contributed 80% of the total sponge cover. Most of the epibiotic sponges commonly grow on the surrounding sublittoral cliffs. The encrusting sponge growth form prevailed in cover of the ascidian tunic, while two massive species dominated in terms of frequency of appearance and abundance. Ascidian dimensions, weight and volume were significantly correlated with sponge diversity, abundance and cover area, thus structuring the epibiotic sponge assemblage. Spatial patterns in sponge cover were not clear, but a general declining NW to SE trend in sponge richness, abundance and cover appeared in accordance with previous records. Sponge distribution on the ascidian tunic presented a clear pattern related with characteristic features of the ascidian: the posterior zone supported the richest and most expansive sponge fauna. The ecosystem-engineering process performed by the ascidian is enhanced by the diverse epibiotic sponge assemblage, thus further increasing habitat complexity in this space-limited, temperate, sublittoral, rocky environment.

Predator-induced demographic shifts in coral reef fish assemblages

USGS Publications Warehouse

Ruttenberg, B.I.; Hamilton, S.L.; Walsh, S.M.; Donovan, M.K.; Friedlander, A.; DeMartini, E.; Sala, E.; Sandin, S.A.

2011-01-01

In recent years, it has become apparent that human impacts have altered community structure in coastal and marine ecosystems worldwide. Of these, fishing is one of the most pervasive, and a growing body of work suggests that fishing can have strong effects on the ecology of target species, especially top predators. However, the effects of removing top predators on lower trophic groups of prey fishes are less clear, particularly in highly diverse and trophically complex coral reef ecosystems. We examined patterns of abundance, size structure, and age-based demography through surveys and collection-based studies of five fish species from a variety of trophic levels at Kiritimati and Palmyra, two nearby atolls in the Northern Line Islands. These islands have similar biogeography and oceanography, and yet Kiritimati has ~10,000 people with extensive local fishing while Palmyra is a US National Wildlife Refuge with no permanent human population, no fishing, and an intact predator fauna. Surveys indicated that top predators were relatively larger and more abundant at unfished Palmyra, while prey functional groups were relatively smaller but showed no clear trends in abundance as would be expected from classic trophic cascades. Through detailed analyses of focal species, we found that size and longevity of a top predator were lower at fished Kiritimati than at unfished Palmyra. Demographic patterns also shifted dramatically for 4 of 5 fish species in lower trophic groups, opposite in direction to the top predator, including decreases in average size and longevity at Palmyra relative to Kiritimati. Overall, these results suggest that fishing may alter community structure in complex and non-intuitive ways, and that indirect demographic effects should be considered more broadly in ecosystem-based management. ?? 2011 Ruttenberg et al.

Predator-Induced Demographic Shifts in Coral Reef Fish Assemblages

PubMed Central

Ruttenberg, Benjamin I.; Hamilton, Scott L.; Walsh, Sheila M.; Donovan, Mary K.; Friedlander, Alan; DeMartini, Edward; Sala, Enric; Sandin, Stuart A.

2011-01-01

In recent years, it has become apparent that human impacts have altered community structure in coastal and marine ecosystems worldwide. Of these, fishing is one of the most pervasive, and a growing body of work suggests that fishing can have strong effects on the ecology of target species, especially top predators. However, the effects of removing top predators on lower trophic groups of prey fishes are less clear, particularly in highly diverse and trophically complex coral reef ecosystems. We examined patterns of abundance, size structure, and age-based demography through surveys and collection-based studies of five fish species from a variety of trophic levels at Kiritimati and Palmyra, two nearby atolls in the Northern Line Islands. These islands have similar biogeography and oceanography, and yet Kiritimati has ∼10,000 people with extensive local fishing while Palmyra is a US National Wildlife Refuge with no permanent human population, no fishing, and an intact predator fauna. Surveys indicated that top predators were relatively larger and more abundant at unfished Palmyra, while prey functional groups were relatively smaller but showed no clear trends in abundance as would be expected from classic trophic cascades. Through detailed analyses of focal species, we found that size and longevity of a top predator were lower at fished Kiritimati than at unfished Palmyra. Demographic patterns also shifted dramatically for 4 of 5 fish species in lower trophic groups, opposite in direction to the top predator, including decreases in average size and longevity at Palmyra relative to Kiritimati. Overall, these results suggest that fishing may alter community structure in complex and non-intuitive ways, and that indirect demographic effects should be considered more broadly in ecosystem-based management. PMID:21698165

Second Amman Declaration on Population and Development in the Arab World.

PubMed

1992-01-01

Many demographic changes have occurred in the Arab region. Population increased from 132 million in 1974 to 237 million in 1992. In preparation for the International Conference on Population and Development in 1994, the Arab Population Conference was held in April 1993. This document summarizes the Arab conference proceedings: preamble, general principles, objectives, and recommendations for human development, the environment, population distribution and urbanization, international migration, women in development, maternal and child health and family planning, IEC, nongovernmental development programs, special topics, structural adjustment and population policies, research, and international cooperation. Arab countries were convinced that clear, comprehensive population policies were needed and should be integrated into development programs. Population policies must be based on the achievement of a satisfactory quality of life and integrity for the family as the basic unit of society. Women should be enabled to perform their full role as citizens. Children have a right to a happy, healthy, and secure life. Population is interconnected with development and should not be treated in isolation. The population problems of those in Israeli occupied territory should be addressed with consideration for the demographic pressure from occupational authorities. Arab states should provide family planning services as a basic human right of couples. Environmental concerns must be considered within development strategies. Reforms need to be made to correct imbalances between economic and social conditions and population problems. Arab countries must be involved in restructuring the world economy with the aim of balancing North and South trade. Rescheduling of debt servicing must be achieved. The industrialized countries must "curb excessive consumerism and reduce huge expenditures on armaments." Individual country population policy should be constructed within a pan-Arab framework and an integrated development policy. There should be respect for individual human dignity and rights and the promotion of democracy, collective activity, and individual initiative.

Hand anthropometry survey of rural farm workers in south-eastern Nigeria.

PubMed

Obi, Okey Francis

2016-04-01

The importance of hand anthropometry as it relates to design of hand tools particularly for farm workers have been established; however, anthropometric data for this group of agricultural workers have continued to remain scarce. A survey of hand anthropometry relevant in design of agricultural hand tools was carried out on 200 male and 100 female adult farm workers in south-eastern Nigeria. Comparison of the male and female data obtained showed that male dimensions were higher than that recorded for the females. The hand anthropometric data of the male and female farm workers were compared with that of other populations but no clear distinction was observed. It was however clear that the following hand dimensions, 2nd Joint to root digit 3 and width at tip digit 3 recorded for Nigerian farm workers were highest and lowest, respectively, compared to other populations. Practitioner Summary: Hand anthropometric data relevant in design of hand tools have continued to remain scarce particularly for farm workers. Hand anthropometry survey of farm workers carried out in south-eastern Nigeria revealed higher dimensions for males than females; however, no clear distinction was observed in comparison with other populations.

Population dynamics of intertidal oribatid mites (Acari: Cryptostigmata) from the subtropical archipelago of Bermuda.

PubMed

Pfingstl, Tobias

2013-10-01

The population dynamics of the three intertidal oribatid species, Alismobates inexpectatus, Fortuynia atlantica and Carinozetes bermudensis, have been studied on the archipelago of Bermuda over the course of a year. All three species are univoltine, showing a clear seasonal demographic pattern, with reproduction from spring to late autumn and a complete standstill of egg production in winter. A seasonal shift in sex ratio could also be observed in all three species and is supposed to be based on sex-dependent mortality. The subtropical climate of Bermuda allows longer reproductive periods than shown in other intertidal or edaphic temperate species and temperature is supposed to be the main factor influencing the demography of these intertidal dwelling mites. Although all three Bermudian species exhibit the same basic seasonal demographic pattern, there are slight temporal shifts in population dynamics, presumably caused by local microclimatic differences among the populations. Larviparity, shown in other littoral oribatid mites, is clearly absent in the present species.

Unexpected absence of genetic separation of a highly diverse population of hookworms from geographically isolated hosts.

PubMed

Haynes, Benjamin T; Marcus, Alan D; Higgins, Damien P; Gongora, Jaime; Gray, Rachael; Šlapeta, Jan

2014-12-01

The high natal site fidelity of endangered Australian sea lions (Neophoca cinerea) along the southern Australian coast suggests that their maternally transmitted parasitic species, such as hookworms, will have restricted potential for dispersal. If this is the case, we would expect to find a hookworm haplotype structure corresponding to that of the host mtDNA haplotype structure; that is, restricted among geographically separated colonies. In this study, we used a fragment of the cytochrome c oxidase I mitochondrial DNA (mtDNA) gene to investigate the diversity of hookworms (Uncinaria sanguinis) in N. cinerea to assess the importance of host distribution and ecology on the evolutionary history of the parasite. High haplotype (h=0.986) and nucleotide diversity (π=0.013) were seen, with 45 unique hookworm mtDNA haplotypes across N. cinerea colonies; with most of the variation (78%) arising from variability within hookworms from individual colonies. This is supported by the low genetic differentiation co-efficient (GST=0.007) and a high gene flow (Nm=35.25) indicating a high migration rate between the populations of hookworms. The haplotype network demonstrated no clear distribution and delineation of haplotypes according to geographical location. Our data rejects the vicariance hypothesis; that female host natal site fidelity and the transmammary route of infection restrict hookworm gene flow between N. cinerea populations and highlights the value of studies of parasite diversity and dispersal to challenge our understanding of parasite and host ecology. Copyright © 2014 Elsevier B.V. All rights reserved.