GENETIC STRUCTURE OF TRIATOMA INFESTANS POPULATIONS IN RURAL COMMUNITIES OF SANTIAGO DEL ESTERO, NORTHERN ARGENTINA

PubMed Central

Marcet, PL; Mora, MS; Cutrera, AP; Jones, L; Gürtler, RE; Kitron, U; Dotson, EM

2008-01-01

To gain an understanding of the genetic structure and dispersal dynamics of T. infestans populations, we analyzed the multilocus genotype of 10 microsatellite loci for 352 T. infestans collected in 21 houses of 11 rural communities in October 2002. Genetic structure was analyzed at the community and house compound levels. Analysis revealed that vector control actions affected the genetic structure of T. infestans populations. Bug populations from communities under sustained vector control (core area) were highly structured and genetic differentiation between neighboring house compounds was significant. In contrast, bug populations from communities with sporadic vector control actions were more homogeneous and lacked defined genetic clusters. Genetic differentiation between population pairs did not fit a model of isolation by distance at the microgeographical level. Evidence consistent with flight or walking bug dispersal was detected within and among communities, dispersal was more female-biased in the core area and results suggested that houses received immigrants from more than one source. Putative sources and mechanisms of re-infestation are described. These data may be use to design improved vector control strategies PMID:18773972

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 genetic structure of a California endemic Branchiopod, Branchinecta sandiegonensis

USGS Publications Warehouse

Davies, Cathleen P.; Simovich, Marie A.; Hathaway, Stacie A.

1997-01-01

Branchinecta sandiegonensis (Crustacea: Anostraca) is a narrow range endemic fairy shrimp discontinuously distributed in ephemeral pools on coastal mesas in San Diego County, USA. Ten populations across the range of the species were subjected to allozyme analysis for eleven loci. The species exhibits low variability (P95 =9.1–45.5) and one third of the loci tested did not conform to Hardy-Weinberg equilibrium expectations. The species also exhibited a high degree of genetic differentiation between populations. F ST values (fixation index) for most pairs of populations were above 0.25 (0.036–0.889).Low genetic variability and high genetic structure may result from low gene flow and founder effects due to habitat fragmentation and the lack of potential vectors for cyst dispersal. The unpredictable rainfall of the region also creates potential for variable population sizes which could affect structure and variability.

Anti-LGBT and Anti-immigrant Structural Stigma: An Intersectional Analysis of Sexual Minority Men's HIV Risk When Migrating to or Within Europe.

PubMed

Pachankis, John E; Hatzenbuehler, Mark L; Berg, Rigmor C; Fernández-Dávila, Percy; Mirandola, Massimo; Marcus, Ulrich; Weatherburn, Peter; Schmidt, Axel J

2017-12-01

Gay, bisexual, and other men who have sex with men (MSM) might be particularly likely to migrate to experience freedoms unavailable in their home countries. Structural stigma (eg, laws and policies promoting the unequal treatment of oppressed populations) in MSM migrants' sending and receiving countries represent potential barriers to HIV prevention among this intersectional population. This study represents the first investigation of structural determinants of HIV risk in a large, geographically diverse sample of MSM migrants. The 2010 European MSM Internet Survey (n = 23,371 migrants) was administered across 38 European countries. Structural stigma was assessed using (1) national laws and policies promoting unequal treatment of sexual minorities across 181 countries worldwide and (2) national attitudes against immigrants in the 38 receiving countries. We also assessed linguistic status, time since migrating, and 5 HIV-prevention outcomes. Structural stigma toward sexual minorities (in sending and receiving countries) and toward immigrants (in receiving countries) was associated with a lack of HIV-prevention knowledge, service coverage, and precautionary behaviors among MSM migrants. Linguistic status and time since migrating moderated some associations between structural stigma and lack of HIV prevention. Structural stigma toward MSM and immigrants represents a modifiable structural determinant of the global HIV epidemic.

Structured Medication Review to Improve Pharmacotherapy in People with Intellectual Disability and Behavioural Problems

ERIC Educational Resources Information Center

Scheifes, Arlette; Egberts, Toine C. G.; Stolker, Joost Jan; Nijman, Henk. L. I.; Heerdink, Eibert R.

2016-01-01

Background: Polypharmacy and chronic drug use are common in people with intellectual disability and behavioural problems, although evidence of effectiveness and safety in this population is lacking. This study examined the effects of a structured medication review and aimed to improve pharmacotherapy in inpatients with intellectual disability.…

Tetraploid Wheat Landraces in the Mediterranean Basin: Taxonomy, Evolution and Genetic Diversity

PubMed Central

Oliveira, Hugo R.; Campana, Michael G.; Jones, Huw; Hunt, Harriet V.; Leigh, Fiona; Redhouse, David I.; Lister, Diane L.; Jones, Martin K.

2012-01-01

The geographic distribution of genetic diversity and the population structure of tetraploid wheat landraces in the Mediterranean basin has received relatively little attention. This is complicated by the lack of consensus concerning the taxonomy of tetraploid wheats and by unresolved questions regarding the domestication and spread of naked wheats. These knowledge gaps hinder crop diversity conservation efforts and plant breeding programmes. We investigated genetic diversity and population structure in tetraploid wheats (wild emmer, emmer, rivet and durum) using nuclear and chloroplast simple sequence repeats, functional variations and insertion site-based polymorphisms. Emmer and wild emmer constitute a genetically distinct population from durum and rivet, the latter seeming to share a common gene pool. Our population structure and genetic diversity data suggest a dynamic history of introduction and extinction of genotypes in the Mediterranean fields. PMID:22615891

Genetic population structure in the yellow mongoose, Cynictis penicillata.

PubMed

Van Vuuren, B J; Robinson, T J

1997-12-01

Phylogeographic structure was determined for the yellow mongoose, Cynictis penicillata, using mtDNA RFLPs and control region sequences. The RFLP analysis revealed 13 haplotypes which showed weak geographical patterning consistent with a recent range expansion from a refugial population(s). An analysis of molecular variance (AMOVA) revealed no correspondence between mtDNA phylogeography and subspecies delimitation, nor between matrilines and areas characterized by a high incidence of the viverrid-type rabies, of which the yellow mongoose is the principal vector. The lack of structure was also shown by control region sequences although four of the maternal lineages shared a near-perfect 81 bp repeat. We speculate that regional hot spots of the viverrid rabies biotype reflect population density differences in the yellow mongoose that are not underscored by genetic partitioning, at least at the level of resolution provided by our analyses.

Genetic diversity and structure of wild populations of Carica papaya in Northern Mesoamerica inferred by nuclear microsatellites and chloroplast markers

PubMed Central

Chávez-Pesqueira, Mariana; Núñez-Farfán, Juan

2016-01-01

Background and aims Few studies have evaluated the genetic structure and evolutionary history of wild varieties of important crop species. The wild papaya (Carica papaya) is a key element of early successional tropical and sub-tropical forests in Mexico, and constitutes the genetic reservoir for evolutionary potential of the species. In this study we aimed to determine how diverse and structured is the genetic variability of wild populations of C. papaya in Northern Mesoamerica. Moreover, we assessed if genetic structure and evolutionary history coincide with hypothetized (1) pre-Pleistocene events (Isthmus of Tehuantepec sinking), (2) Pleistocene refugia or (3) recent patterns. Methods We used six nuclear and two chloroplast (cp) DNA markers to assess the genetic diversity and phylogeographical structure of 19 wild populations of C. papaya in its natural distribution in Northern Mesoamerica. Key Results We found high genetic diversity (Ho = 0·681 for nuclear markers, and h = 0·701 for cpDNA markers) and gene flow between populations of C. papaya (migration r up to 420 km). A lack of phylogeographical structure was found with the cpDNA markers (NST < GST), whereas a recent population structure was inferred with the nuclear markers. Evidence indicates that pre-Pleistocene events or refugia did not play an important role in the genetic structuring of wild papaya. Conclusions Because of its life history characteristics and lack of an ancient phylogeographical structure found with the cpDNA markers, we suggest that C. papaya was dispersed throughout the lowland rain forests of Mexico (along the coastal plains and foothills of Sierras). This scenario supports the hypothesis that tropical forests in Northern Mesoamerica did not experience important climate fluctuations during the Pleistocene, and that the life history of C. papaya could have promoted long-distance dispersal and rapid colonization of lowland rainforests. Moreover, the results obtained with the nuclear markers suggest recent human disturbances. The fragmentation of tropical habitats in Northern Mesoamerica appears to be the main driver of genetic structuring, and the major threat to the dispersion and survival of the species in the wild. PMID:27974326

Oceanographic Currents and Local Ecological Knowledge Indicate, and Genetics Does Not Refute, a Contemporary Pattern of Larval Dispersal for The Ornate Spiny Lobster, Panulirus ornatus in the South-East Asian Archipelago

PubMed Central

Dao, Hoc Tan; Smith-Keune, Carolyn; Wolanski, Eric; Jones, Clive M.; Jerry, Dean R.

2015-01-01

Here we utilize a combination of genetic data, oceanographic data, and local ecological knowledge to assess connectivity patterns of the ornate spiny lobster Panulirus ornatus (Fabricius, 1798) in the South-East Asian archipelago from Vietnam to Australia. Partial mitochondrial DNA control region and 10 polymorphic microsatellites did not detect genetic structure of 216 wild P. ornatus samples from Australia, Indonesia and Vietnam. Analyses show no evidence for genetic differentiation among populations (mtDNA control region sequences ΦST = -0.008; microsatellite loci FST = 0.003). A lack of evidence for regional or localized mtDNA haplotype clusters, or geographic clusters of microsatellite genotypes, reveals a pattern of high gene flow in P. ornatus throughout the South-East Asian Archipelago. This lack of genetic structure may be due to the oceanography-driven connectivity of the pelagic lobster larvae between spawning grounds in Papua New Guinea, the Philippines and, possibly, Indonesia. The connectivity cycle necessitates three generations. The lack of genetic structure of P. ornatus population in the South-East Asian archipelago has important implications for the sustainable management of this lobster in that the species within the region needs to be managed as one genetic stock. PMID:25951344

Oceanographic Currents and Local Ecological Knowledge Indicate, and Genetics Does Not Refute, a Contemporary Pattern of Larval Dispersal for The Ornate Spiny Lobster, Panulirus ornatus in the South-East Asian Archipelago.

PubMed

Dao, Hoc Tan; Smith-Keune, Carolyn; Wolanski, Eric; Jones, Clive M; Jerry, Dean R

2015-01-01

Here we utilize a combination of genetic data, oceanographic data, and local ecological knowledge to assess connectivity patterns of the ornate spiny lobster Panulirus ornatus (Fabricius, 1798) in the South-East Asian archipelago from Vietnam to Australia. Partial mitochondrial DNA control region and 10 polymorphic microsatellites did not detect genetic structure of 216 wild P. ornatus samples from Australia, Indonesia and Vietnam. Analyses show no evidence for genetic differentiation among populations (mtDNA control region sequences ΦST = -0.008; microsatellite loci FST = 0.003). A lack of evidence for regional or localized mtDNA haplotype clusters, or geographic clusters of microsatellite genotypes, reveals a pattern of high gene flow in P. ornatus throughout the South-East Asian Archipelago. This lack of genetic structure may be due to the oceanography-driven connectivity of the pelagic lobster larvae between spawning grounds in Papua New Guinea, the Philippines and, possibly, Indonesia. The connectivity cycle necessitates three generations. The lack of genetic structure of P. ornatus population in the South-East Asian archipelago has important implications for the sustainable management of this lobster in that the species within the region needs to be managed as one genetic stock.

European Invasion of North American Pinus strobus at Large and Fine Scales: High Genetic Diversity and Fine-Scale Genetic Clustering over Time in the Adventive Range

PubMed Central

Mandák, Bohumil; Hadincová, Věroslava; Mahelka, Václav; Wildová, Radka

2013-01-01

Background North American Pinus strobus is a highly invasive tree species in Central Europe. Using ten polymorphic microsatellite loci we compared various aspects of the large-scale genetic diversity of individuals from 30 sites in the native distribution range with those from 30 sites in the European adventive distribution range. To investigate the ascertained pattern of genetic diversity of this intercontinental comparison further, we surveyed fine-scale genetic diversity patterns and changes over time within four highly invasive populations in the adventive range. Results Our data show that at the large scale the genetic diversity found within the relatively small adventive range in Central Europe, surprisingly, equals the diversity found within the sampled area in the native range, which is about thirty times larger. Bayesian assignment grouped individuals into two genetic clusters separating North American native populations from the European, non-native populations, without any strong genetic structure shown over either range. In the case of the fine scale, our comparison of genetic diversity parameters among the localities and age classes yielded no evidence of genetic diversity increase over time. We found that SGS differed across age classes within the populations under study. Old trees in general completely lacked any SGS, which increased over time and reached its maximum in the sapling stage. Conclusions Based on (1) the absence of difference in genetic diversity between the native and adventive ranges, together with the lack of structure in the native range, and (2) the lack of any evidence of any temporal increase in genetic diversity at four highly invasive populations in the adventive range, we conclude that population amalgamation probably first happened in the native range, prior to introduction. In such case, there would have been no need for multiple introductions from previously isolated populations, but only several introductions from genetically diverse populations. PMID:23874648

Reduced fine-scale spatial genetic structure in grazed populations of Dianthus carthusianorum

PubMed Central

Rico, Y; Wagner, H H

2016-01-01

Strong spatial genetic structure in plant populations can increase homozygosity, reducing genetic diversity and adaptive potential. The strength of spatial genetic structure largely depends on rates of seed dispersal and pollen flow. Seeds without dispersal adaptations are likely to be dispersed over short distances within the vicinity of the mother plant, resulting in spatial clustering of related genotypes (fine-scale spatial genetic structure, hereafter spatial genetic structure (SGS)). However, primary seed dispersal by zoochory can promote effective dispersal, increasing the mixing of seeds and influencing SGS within plant populations. In this study, we investigated the effects of seed dispersal by rotational sheep grazing on the strength of SGS and genetic diversity using 11 nuclear microsatellites for 49 populations of the calcareous grassland forb Dianthus carthusianorum. Populations connected by rotational sheep grazing showed significantly weaker SGS and higher genetic diversity than populations in ungrazed grasslands. Independent of grazing treatment, small populations showed significantly stronger SGS and lower genetic diversity than larger populations, likely due to genetic drift. A lack of significant differences in the strength of SGS and genetic diversity between populations that were recently colonized and pre-existing populations suggested that populations colonized after the reintroduction of rotational sheep grazing were likely founded by colonists from diverse source populations. We conclude that dispersal by rotational sheep grazing has the potential to considerably reduce SGS within D. carthusianorum populations. Our study highlights the effectiveness of landscape management by rotational sheep grazing to importantly reduce genetic structure at local scales within restored plant populations. PMID:27381322

Reduced fine-scale spatial genetic structure in grazed populations of Dianthus carthusianorum.

PubMed

Rico, Y; Wagner, H H

2016-11-01

Strong spatial genetic structure in plant populations can increase homozygosity, reducing genetic diversity and adaptive potential. The strength of spatial genetic structure largely depends on rates of seed dispersal and pollen flow. Seeds without dispersal adaptations are likely to be dispersed over short distances within the vicinity of the mother plant, resulting in spatial clustering of related genotypes (fine-scale spatial genetic structure, hereafter spatial genetic structure (SGS)). However, primary seed dispersal by zoochory can promote effective dispersal, increasing the mixing of seeds and influencing SGS within plant populations. In this study, we investigated the effects of seed dispersal by rotational sheep grazing on the strength of SGS and genetic diversity using 11 nuclear microsatellites for 49 populations of the calcareous grassland forb Dianthus carthusianorum. Populations connected by rotational sheep grazing showed significantly weaker SGS and higher genetic diversity than populations in ungrazed grasslands. Independent of grazing treatment, small populations showed significantly stronger SGS and lower genetic diversity than larger populations, likely due to genetic drift. A lack of significant differences in the strength of SGS and genetic diversity between populations that were recently colonized and pre-existing populations suggested that populations colonized after the reintroduction of rotational sheep grazing were likely founded by colonists from diverse source populations. We conclude that dispersal by rotational sheep grazing has the potential to considerably reduce SGS within D. carthusianorum populations. Our study highlights the effectiveness of landscape management by rotational sheep grazing to importantly reduce genetic structure at local scales within restored plant populations.

Genetic diversity and population structure of bocachico Prochilodus magdalenae (Pisces, Prochilodontidae) in the Magdalena River basin and its tributaries, Colombia

PubMed Central

Berdugo, Gilberto Orozco; Narváez Barandica, Juan C.

2014-01-01

Prochilodus magdalenae is an endemic freshwater fish that occurs in the Magdalena, Sinú and Atrato hydrographic basins. It has an important economic role and is a food resource for the artisanal fishing communities. Its socioeconomic importance contrasts with the current status of its fisheries, where stocks are being depleted. Considering its importance and lack of information on its genetic structure, we used seven microsatellite markers to assess the genetic structure of wild populations of P. magdalenae. The genetic diversity was assessed and the population genetic structure was estimated through Fst, analysis of molecular variance and Bayesian analysis. A total of 290 alleles were found in all loci throughout all population. The high polymorphism contrasts with the levels of observed heterozygosity (Ho = 0.276), which are the lowest values recorded for the family. We found three populations of bocachico coexisting throughout the studied system, contradicting the hypothesis that freshwater migratory fish form panmictic populations. These results on the genetic structure of P. magdalenae constitute tools for a better understanding of the behavior and biology of this species, contributing to fish management and conservation programs. PMID:24688289

78 FR 56505 - Endangered and Threatened Wildlife and Plants; Designation of Critical Habitat for Georgia Rockcress

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-12

... proposed critical habitat is designed to provide sufficient habitat to maintain self-sustaining populations... as lands covered by water, buildings, pavement, and other structures because such lands lack physical...

The presynaptic ribbon maintains vesicle populations at the hair cell afferent fiber synapse

PubMed Central

Becker, Lars; Schnee, Michael E; Niwa, Mamiko; Sun, Willy; Maxeiner, Stephan; Talaei, Sara; Kachar, Bechara; Rutherford, Mark A

2018-01-01

The ribbon is the structural hallmark of cochlear inner hair cell (IHC) afferent synapses, yet its role in information transfer to spiral ganglion neurons (SGNs) remains unclear. We investigated the ribbon’s contribution to IHC synapse formation and function using KO mice lacking RIBEYE. Despite loss of the entire ribbon structure, synapses retained their spatiotemporal development and KO mice had a mild hearing deficit. IHCs of KO had fewer synaptic vesicles and reduced exocytosis in response to brief depolarization; a high stimulus level rescued exocytosis in KO. SGNs exhibited a lack of sustained excitatory postsynaptic currents (EPSCs). We observed larger postsynaptic glutamate receptor plaques, potentially compensating for the reduced EPSC rate in KO. Surprisingly, large-amplitude EPSCs were maintained in KO, while a small population of low-amplitude slower EPSCs was increased in number. The ribbon facilitates signal transduction at physiological stimulus levels by retaining a larger residency pool of synaptic vesicles. PMID:29328021

Role of evolutionary and ecological factors in the reproductive success and the spatial genetic structure of the temperate gorgonian Paramuricea clavata

PubMed Central

Mokhtar-Jamaï, Kenza; Coma, Rafel; Wang, Jinliang; Zuberer, Frederic; Féral, Jean-Pierre; Aurelle, Didier

2013-01-01

Dispersal and mating features strongly influence the evolutionary dynamics and the spatial genetic structure (SGS) of marine populations. For the first time in a marine invertebrate, we examined individual reproductive success, by conducting larval paternity assignments after a natural spawning event, combined with a small-scale SGS analysis within a population of the gorgonian Paramuricea clavata. Thirty four percent of the larvae were sired by male colonies surrounding the brooding female colonies, revealing that the bulk of the mating was accomplished by males from outside the studied area. Male success increased with male height and decreased with increasing male to female distance. The parentage analyses, with a strong level of self-recruitment (25%), unveiled the occurrence of a complex family structure at a small spatial scale, consistent with the limited larval dispersal of this species. However, no evidence of small scale SGS was revealed despite this family structure. Furthermore, temporal genetic structure was not observed, which appears to be related to the rather large effective population size. The low level of inbreeding found suggests a pattern of random mating in this species, which disagrees with expectations that limited larval dispersal should lead to biparental inbreeding. Surface brooding and investment in sexual reproduction in P. clavata contribute to multiple paternity (on average 6.4 fathers were assigned per brood), which enhance genetic diversity of the brood. Several factors may have contributed to the lack of biparental inbreeding in our study such as (i) the lack of sperm limitation at a small scale, (ii) multiple paternity, and (iii) the large effective population size. Thus, our results indicate that limited larval dispersal and complex family structure do not necessarily lead to biparental inbreeding and SGS. In the framework of conservation purposes, our results suggested that colony size, proximity among colonies and the population size should be taken into consideration for restoration projects. PMID:23789084

Genetic Variation and Population Structure in Native Americans

PubMed Central

Ramachandran, Sohini; Ray, Nicolas; Bedoya, Gabriel; Rojas, Winston; Parra, Maria V; Molina, Julio A; Gallo, Carla; Mazzotti, Guido; Poletti, Giovanni; Hill, Kim; Hurtado, Ana M; Labuda, Damian; Klitz, William; Barrantes, Ramiro; Bortolini, Maria Cátira; Salzano, Francisco M; Petzl-Erler, Maria Luiza; Tsuneto, Luiza T; Llop, Elena; Rothhammer, Francisco; Excoffier, Laurent; Feldman, Marcus W; Rosenberg, Noah A; Ruiz-Linares, Andrés

2007-01-01

We examined genetic diversity and population structure in the American landmass using 678 autosomal microsatellite markers genotyped in 422 individuals representing 24 Native American populations sampled from North, Central, and South America. These data were analyzed jointly with similar data available in 54 other indigenous populations worldwide, including an additional five Native American groups. The Native American populations have lower genetic diversity and greater differentiation than populations from other continental regions. We observe gradients both of decreasing genetic diversity as a function of geographic distance from the Bering Strait and of decreasing genetic similarity to Siberians—signals of the southward dispersal of human populations from the northwestern tip of the Americas. We also observe evidence of: (1) a higher level of diversity and lower level of population structure in western South America compared to eastern South America, (2) a relative lack of differentiation between Mesoamerican and Andean populations, (3) a scenario in which coastal routes were easier for migrating peoples to traverse in comparison with inland routes, and (4) a partial agreement on a local scale between genetic similarity and the linguistic classification of populations. These findings offer new insights into the process of population dispersal and differentiation during the peopling of the Americas. PMID:18039031

Genomic evidence of demographic fluctuations and lack of genetic structure across flyways in a long distance migrant, the European turtle dove.

PubMed

Calderón, Luciano; Campagna, Leonardo; Wilke, Thomas; Lormee, Hervé; Eraud, Cyril; Dunn, Jenny C; Rocha, Gregorio; Zehtindjiev, Pavel; Bakaloudis, Dimitrios E; Metzger, Benjamin; Cecere, Jacopo G; Marx, Melanie; Quillfeldt, Petra

2016-11-07

Understanding how past climatic oscillations have affected organismic evolution will help predict the impact that current climate change has on living organisms. The European turtle dove, Streptopelia turtur, is a warm-temperature adapted species and a long distance migrant that uses multiple flyways to move between Europe and Africa. Despite being abundant, it is categorized as vulnerable because of a long-term demographic decline. We studied the demographic history and population genetic structure of the European turtle dove using genomic data and mitochondrial DNA sequences from individuals sampled across Europe, and performing paleoclimatic niche modelling simulations. Overall our data suggest that this species is panmictic across Europe, and is not genetically structured across flyways. We found the genetic signatures of demographic fluctuations, inferring an effective population size (Ne) expansion that occurred between the late Pleistocene and early Holocene, followed by a decrease in the Ne that started between the mid Holocene and the present. Our niche modelling analyses suggest that the variations in the Ne are coincident with recent changes in the availability of suitable habitat. We argue that the European turtle dove is prone to undergo demographic fluctuations, a trait that makes it sensitive to anthropogenic impacts, especially when its numbers are decreasing. Also, considering the lack of genetic structure, we suggest all populations across Europe are equally relevant for conservation.

Influence of elevation on bark beetle community structure in ponderosa pine stands of northern Arizona

Treesearch

Andrew Miller; Kelly Barton; Joel McMillin; Tom DeGomez; Karen Clancy; John Anhold

2008-01-01

(Please note, this is an abstract only) Bark beetles killed more than 20 million ponderosa pine trees in Arizona during 2002-2004. Historically, bark beetle populations remained endemic and ponderosa pine mortality was limited to localized areas in Arizona. Consequently, there is a lack of information on bark beetle community structure in ponderosa pine stands of...

Genetic structure of the crown-of-thorns seastar in the Pacific Ocean, with focus on Guam.

PubMed

Tusso, Sergio; Morcinek, Kerstin; Vogler, Catherine; Schupp, Peter J; Caballes, Ciemon F; Vargas, Sergio; Wörheide, Gert

2016-01-01

Population outbreaks of the corallivorous crown-of-thorns seastar (COTS), Acanthaster 'planci' L., are among the most important biological disturbances of tropical coral reefs. Over the past 50 years, several devastating outbreaks have been documented around Guam, an island in the western Pacific Ocean. Previous analyses have shown that in the Pacific Ocean, COTS larval dispersal may be geographically restricted to certain regions. Here, we assess the genetic structure of Pacific COTS populations and compared samples from around Guam with a number of distant localities in the Pacific Ocean, and focused on determining the degree of genetic structure among populations previously considered to be isolated. Using microsatellites, we document substantial genetic structure between 14 localities from different geographical regions in the Pacific Ocean. Populations from the 14 locations sampled were found to be structured in three significantly differentiated groups: (1) all locations immediately around Guam, as well as Kingman Reef and Swains Island; (2) Japan, Philippines, GBR and Vanuatu; and (3) Johnston Atoll, which was significantly different from all other localities. The lack of genetic differentiation between Guam and extremely distant populations from Kingman Reef and Swains Island suggests potential long-distance dispersal of COTS in the Pacific.

Global population structure of the tope (Galeorhinus galeus) inferred by mitochondrial control region sequence data.

PubMed

Chabot, C L; Allen, L G

2009-02-01

In order to properly manage and conserve exploited shark species, detailed analyses of their population structure is needed. Global populations of Galeorhinus galeus are in decline due to the exploitation of the fishery over the past 80 years. Currently, the genetic structure of eastern Pacific populations of G. galeus is not known and recent observations in the northeastern Pacific suggest an increase in numbers. To evaluate gene flow among populations of G. galeus, 116 samples were collected and analysed from six geographically dispersed locations: Australia, North America, South Africa, South America (Argentina and Peru), and the UK. Analysis of 968 to 1006 bp of the 1068-bp mitochondrial control region revealed 38 unique haplotypes that were largely restricted to their collecting locality. Significant genetic structure was detected among populations (Phi(ST) = 0.84; P < 0.000001) and migration estimates were low (Nm = 0.05-0.97). Due to an apparent lack of migration, populations of G. galeus appear to be isolated from each other with little to no gene flow occurring among them. As a consequence of this isolation, increasing numbers of G. galeus in the northeastern Pacific can be best explained by local recruitment and not by input from geographically distant populations.

Limits to gene flow in a cosmopolitan marine planktonic diatom.

PubMed

Casteleyn, Griet; Leliaert, Frederik; Backeljau, Thierry; Debeer, Ann-Eline; Kotaki, Yuichi; Rhodes, Lesley; Lundholm, Nina; Sabbe, Koen; Vyverman, Wim

2010-07-20

The role of geographic isolation in marine microbial speciation is hotly debated because of the high dispersal potential and large population sizes of planktonic microorganisms and the apparent lack of strong dispersal barriers in the open sea. Here, we show that gene flow between distant populations of the globally distributed, bloom-forming diatom species Pseudo-nitzschia pungens (clade I) is limited and follows a strong isolation by distance pattern. Furthermore, phylogenetic analysis implies that under appropriate geographic and environmental circumstances, like the pronounced climatic changes in the Pleistocene, population structuring may lead to speciation and hence may play an important role in diversification of marine planktonic microorganisms. A better understanding of the factors that control population structuring is thus essential to reveal the role of allopatric speciation in marine microorganisms.

A general modeling framework for describing spatially structured population dynamics

USGS Publications Warehouse

Sample, Christine; Fryxell, John; Bieri, Joanna; Federico, Paula; Earl, Julia; Wiederholt, Ruscena; Mattsson, Brady; Flockhart, Tyler; Nicol, Sam; Diffendorfer, James E.; Thogmartin, Wayne E.; Erickson, Richard A.; Norris, D. Ryan

2017-01-01

Variation in movement across time and space fundamentally shapes the abundance and distribution of populations. Although a variety of approaches model structured population dynamics, they are limited to specific types of spatially structured populations and lack a unifying framework. Here, we propose a unified network-based framework sufficiently novel in its flexibility to capture a wide variety of spatiotemporal processes including metapopulations and a range of migratory patterns. It can accommodate different kinds of age structures, forms of population growth, dispersal, nomadism and migration, and alternative life-history strategies. Our objective was to link three general elements common to all spatially structured populations (space, time and movement) under a single mathematical framework. To do this, we adopt a network modeling approach. The spatial structure of a population is represented by a weighted and directed network. Each node and each edge has a set of attributes which vary through time. The dynamics of our network-based population is modeled with discrete time steps. Using both theoretical and real-world examples, we show how common elements recur across species with disparate movement strategies and how they can be combined under a unified mathematical framework. We illustrate how metapopulations, various migratory patterns, and nomadism can be represented with this modeling approach. We also apply our network-based framework to four organisms spanning a wide range of life histories, movement patterns, and carrying capacities. General computer code to implement our framework is provided, which can be applied to almost any spatially structured population. This framework contributes to our theoretical understanding of population dynamics and has practical management applications, including understanding the impact of perturbations on population size, distribution, and movement patterns. By working within a common framework, there is less chance that comparative analyses are colored by model details rather than general principles

Molecular Diversity and Population Structure of a Worldwide Collection of Cultivated Tetraploid Alfalfa (Medicago sativa subsp. sativa L.) Germplasm as Revealed by Microsatellite Markers.

PubMed

Qiang, Haiping; Chen, Zhihong; Zhang, Zhengli; Wang, Xuemin; Gao, Hongwen; Wang, Zan

2015-01-01

Information on genetic diversity and population structure of a tetraploid alfalfa collection might be valuable in effective use of the genetic resources. A set of 336 worldwide genotypes of tetraploid alfalfa (Medicago sativa subsp. sativa L.) was genotyped using 85 genome-wide distributed SSR markers to reveal the genetic diversity and population structure in the alfalfa. Genetic diversity analysis identified a total of 1056 alleles across 85 marker loci. The average expected heterozygosity and polymorphism information content values were 0.677 and 0.638, respectively, showing high levels of genetic diversity in the cultivated tetraploid alfalfa germplasm. Comparison of genetic characteristics across chromosomes indicated regions of chromosomes 2 and 3 had the highest genetic diversity. A higher genetic diversity was detected in alfalfa landraces than that of wild materials and cultivars. Two populations were identified by the model-based population structure, principal coordinate and neighbor-joining analyses, corresponding to China and other parts of the world. However, lack of strictly correlation between clustering and geographic origins suggested extensive germplasm exchanges of alfalfa germplasm across diverse geographic regions. The quantitative analysis of the genetic diversity and population structure in this study could be useful for genetic and genomic analysis and utilization of the genetic variation in alfalfa breeding.

Population genetic structure of the point-head flounder, Cleisthenes herzensteini, in the Northwestern Pacific.

PubMed

Xiao, Yongshuang; Zhang, Yan; Yanagimoto, Takashi; Li, Jun; Xiao, Zhizhong; Gao, Tianxiang; Xu, Shihong; Ma, Daoyuan

2011-02-01

Intraspecific phylogenies can provide useful insights into how populations have been shaped by historical and contemporary processes. To determine the population genetic structure and the demographic and colonization history of Cleisthenes herzensteini in the Northwestern Pacific, one hundred and twenty-one individuals were sampled from six localities along the coastal regions of Japan and the Yellow Sea of China. Mitochondrial DNA variation was analyzed using DNA sequence data from the 5' end of control region. High levels of haplotype diversity (>0.96) were found for all populations, indicating a high level of genetic diversity. No pattern of isolation by distance was detected among the population differentiation throughout the examined range. Analyses of molecular variance (AMOVA) and the conventional population statistic Fst revealed no significant population genetic structure among populations. According to the exact test of differentiation among populations, the null hypothesis that C. herzensteini within the examined range constituted a non-differential mtDNA gene pool was accepted. The demographic history of C. herzensteini was examined using neutrality test and mismatch distribution analyses and results indicated Pleistocene population expansion (about 94-376 kya) in the species, which was consistent with the inference result of nested clade phylogeographical analysis (NCPA) showing contiguous range expansion for C. herzensteini. The lack of phylogeographical structure for the species may reflect a recent range expansion after the glacial maximum and insufficient time to attain migration-drift equilibrium.

Population structure and genetic diversity of the giant anteater (Myrmecophaga tridactyla: Myrmecophagidae, Pilosa) in Brazil.

PubMed

Clozato, Camila L; Miranda, Flávia R; Lara-Ruiz, Paula; Collevatti, Rosane G; Santos, Fabrício R

2017-01-01

The giant anteater (Myrmecophaga tridactyla, Pilosa, Linnaeus 1758) belongs to the mammalian order Pilosa and presents a large distribution along South America, occupying a great variety of habitats. It is listed in the IUCN Red List of threatened species as Vulnerable. Despite threatened, there is a lack of studies regarding its genetic variability. The aim of this study was to examine the genetic diversity and patterns of genetic structure within remaining populations. We analyzed 77 individuals from seven different populations distributed in four biomes across Brazil: Cerrado, Pantanal, Atlantic Forest and Amazon Forest. We sequenced two mitochondrial markers (control region and Cyt-b) and two nuclear markers (AMELY and RAG2). We found high genetic diversity within subpopulations from National Parks of Serra da Canastra and Emas, both within the Cerrado biome, with signs of population expansion. Besides, we found a notable population structure between populations from the Cerrado/Pantanal and Amazon Forest biomes. This data is a major contribution to the knowledge of the evolutionary history of the species and to future management actions concerning its conservation.

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

Temporal genetic population structure and interannual variation in migration behavior of Pacific Lamprey Entosphenus tridentatus

USGS Publications Warehouse

Clemens, Benjamin J.; Wyss, Lance A.; McCoun, Rebecca; Courter, Ian; Schwabe, Lawrence; Peery, Christopher; Schreck, Carl B.; Spice, Erin K.; Docker, Margaret F.

2017-01-01

Studies using neutral loci suggest that Pacific lamprey, Entosphenus tridentatus, lack strong spatial genetic population structure. However, it is unknown whether temporal genetic population structure exists. We tested whether adult Pacific lamprey: (1) show temporal genetic population structure; and (2) migrate different distances between years. We non-lethally sampled lamprey for DNA in 2009 and 2010 and used eight microsatellite loci to test for genetic population structure. We used telemetry to record the migration behaviors of these fish. Lamprey were assignable to three moderately differentiated genetic clusters (FST = 0.16–0.24 for all pairwise comparisons): one cluster was composed of individuals from 2009, and the other two contained individuals from 2010. The FST value between years was 0.13 and between genetic clusters within 2010 was 0.20. A total of 372 (72.5%) fish were detected multiple times during their migrations. Most fish (69.9%) remained in the mainstem Willamette River; the remaining 30.1% migrated into tributaries. Eighty-two lamprey exhibited multiple back-and-forth movements among tributaries and the mainstem, which may indicate searching behaviors. All migration distances were significantly greater in 2010, when the amplitude of river discharge was greater. Our data suggest genetic structuring between and within years that may reflect different cohorts.

Genetic diversity and structure of wild populations of Carica papaya in Northern Mesoamerica inferred by nuclear microsatellites and chloroplast markers.

PubMed

Chávez-Pesqueira, Mariana; Núñez-Farfán, Juan

2016-12-01

Few studies have evaluated the genetic structure and evolutionary history of wild varieties of important crop species. The wild papaya (Carica papaya) is a key element of early successional tropical and sub-tropical forests in Mexico, and constitutes the genetic reservoir for evolutionary potential of the species. In this study we aimed to determine how diverse and structured is the genetic variability of wild populations of C. papaya in Northern Mesoamerica. Moreover, we assessed if genetic structure and evolutionary history coincide with hypothetized (1) pre-Pleistocene events (Isthmus of Tehuantepec sinking), (2) Pleistocene refugia or (3) recent patterns. We used six nuclear and two chloroplast (cp) DNA markers to assess the genetic diversity and phylogeographical structure of 19 wild populations of C. papaya in its natural distribution in Northern Mesoamerica. We found high genetic diversity (H o = 0·681 for nuclear markers, and h = 0·701 for cpDNA markers) and gene flow between populations of C. papaya (migration r up to 420 km). A lack of phylogeographical structure was found with the cpDNA markers (NST < GST), whereas a recent population structure was inferred with the nuclear markers. Evidence indicates that pre-Pleistocene events or refugia did not play an important role in the genetic structuring of wild papaya. Because of its life history characteristics and lack of an ancient phylogeographical structure found with the cpDNA markers, we suggest that C. papaya was dispersed throughout the lowland rain forests of Mexico (along the coastal plains and foothills of Sierras). This scenario supports the hypothesis that tropical forests in Northern Mesoamerica did not experience important climate fluctuations during the Pleistocene, and that the life history of C. papaya could have promoted long-distance dispersal and rapid colonization of lowland rainforests. Moreover, the results obtained with the nuclear markers suggest recent human disturbances. The fragmentation of tropical habitats in Northern Mesoamerica appears to be the main driver of genetic structuring, and the major threat to the dispersion and survival of the species in the wild. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Nesting habits influence population genetic structure of a bee living in anthropogenic disturbance.

PubMed

Vickruck, J L; Richards, M H

2017-05-01

While most organisms are negatively affected by anthropogenic disturbance, a few species thrive in landscapes altered by humans. Typically, native bees are negatively impacted by anthropogenic environmental change, including habitat alteration and climate change. Here, we investigate the population structure of the eastern carpenter bee Xylocopa virginica, a generalist pollinator with a broad geographic range spanning eastern North America. Eastern carpenter bees now nest almost exclusively in artificial wooden structures, linking their geographic distribution and population structure to human activities and disturbance. To investigate the population structure of these bees, we sampled females from 16 different populations from across their range. Nine species-specific microsatellite loci showed that almost all populations are genetically distinct, but with high levels of genetic diversity and low levels of inbreeding overall. Broadly speaking, populations clustered into three distinct genetic groups: a northern group, a western group and a core group. The northern group had low effective population sizes, decreased genetic variability and the highest levels of inbreeding in the data set, suggesting that carpenter bees may be expanding their range northward. The western group was genetically distinct, but lacked signals of a recent range expansion. Climatic data showed that summer and winter temperatures explained a significant amount of the genetic differentiation seen among populations, while precipitation did not. Our results indicate that X. virginica may be one of the rare 'anthrophilic' species that thrive in the face of anthropogenic disturbance. © 2017 John Wiley & Sons Ltd.

Genetic Structure of the Han Chinese Population Revealed by Genome-wide SNP Variation

PubMed Central

Chen, Jieming; Zheng, Houfeng; Bei, Jin-Xin; Sun, Liangdan; Jia, Wei-hua; Li, Tao; Zhang, Furen; Seielstad, Mark; Zeng, Yi-Xin; Zhang, Xuejun; Liu, Jianjun

2009-01-01

Population stratification is a potential problem for genome-wide association studies (GWAS), confounding results and causing spurious associations. Hence, understanding how allele frequencies vary across geographic regions or among subpopulations is an important prelude to analyzing GWAS data. Using over 350,000 genome-wide autosomal SNPs in over 6000 Han Chinese samples from ten provinces of China, our study revealed a one-dimensional “north-south” population structure and a close correlation between geography and the genetic structure of the Han Chinese. The north-south population structure is consistent with the historical migration pattern of the Han Chinese population. Metropolitan cities in China were, however, more diffused “outliers,” probably because of the impact of modern migration of peoples. At a very local scale within the Guangdong province, we observed evidence of population structure among dialect groups, probably on account of endogamy within these dialects. Via simulation, we show that empirical levels of population structure observed across modern China can cause spurious associations in GWAS if not properly handled. In the Han Chinese, geographic matching is a good proxy for genetic matching, particularly in validation and candidate-gene studies in which population stratification cannot be directly accessed and accounted for because of the lack of genome-wide data, with the exception of the metropolitan cities, where geographical location is no longer a good indicator of ancestral origin. Our findings are important for designing GWAS in the Chinese population, an activity that is expected to intensify greatly in the near future. PMID:19944401

Inbreeding avoidance under different null models of random mating in the great tit.

PubMed

Szulkin, Marta; Zelazowski, Przemyslaw; Nicholson, George; Sheldon, Ben C

2009-07-01

1. In populations where inbreeding causes a substantial decrease in fitness, selection is expected to favour the evolution of inbreeding avoidance behaviours. Elsewhere we have documented substantial inbreeding depression and the importance of dispersal in avoiding inbreeding in a long-term population study of the great tit Parus major in Wytham (UK). In this study, we ask whether individuals from this population actively avoid mating with kin. 2. We generated four contrasting models of random mate choice that assumed varying levels of mate availability in each year of the data set. This allowed us to compare observed and simulated distributions and frequencies of inbreeding coefficients from 41 years of breeding data. 3. We found no evidence that birds avoid mating with related partners. Our results show that birds breed more often with relatives than expected under null models of mate choice that lack population structure, but not when compared to scenarios where birds were mated with their nearest neighbours. Pedigree-derived F(IS) values were positive for all scenarios of random mating, confirming the lack of inbreeding avoidance in this population. 4. These results imply the existence of spatial genetic structure where related individuals occur closer together than nonrelated individuals while breeding, and suggest that the relatedness between breeding individuals of the opposite sex decreases with distance. Thus, while dispersal from the natal site decreases the number of relatives around an individual, it does not completely homogenize genetic structure. 5. We show that brother-sister pairs are observed more often than under any scenario of random mating, suggesting that not only birds do not avoid mating with kin, but also that the apparently maladaptive choice of mating with a sibling is made more often than expected. 6. Our results provide no evidence to suggest that individuals actively avoid kin. In fact, some types of inbreeding occur more often than expected, despite the substantial fitness costs. The observed lack of inbreeding avoidance is in agreement with other studies of non-cooperatively breeding passerine birds, although the higher than expected frequency of sibling mating remains a puzzling result.

Effects of Large-Scale Releases on the Genetic Structure of Red Sea Bream (Pagrus major, Temminck et Schlegel) Populations in Japan.

PubMed

Blanco Gonzalez, Enrique; Aritaki, Masato; Knutsen, Halvor; Taniguchi, Nobuhiko

2015-01-01

Large-scale hatchery releases are carried out for many marine fish species worldwide; nevertheless, the long-term effects of this practice on the genetic structure of natural populations remains unclear. The lack of knowledge is especially evident when independent stock enhancement programs are conducted simultaneously on the same species at different geographical locations, as occurs with red sea bream (Pagrus major, Temminck et Schlegel) in Japan. In this study, we examined the putative effects of intensive offspring releases on the genetic structure of red sea bream populations along the Japanese archipelago by genotyping 848 fish at fifteen microsatellite loci. Our results suggests weak but consistent patterns of genetic divergence (F(ST) = 0.002, p < 0.001). Red sea bream in Japan appeared spatially structured with several patches of distinct allelic composition, which corresponded to areas receiving an important influx of fish of hatchery origin, either released intentionally or from unintentional escapees from aquaculture operations. In addition to impacts upon local populations inhabiting semi-enclosed embayments, large-scale releases (either intentionally or from unintentional escapes) appeared also to have perturbed genetic structure in open areas. Hence, results of the present study suggest that independent large-scale marine stock enhancement programs conducted simultaneously on one species at different geographical locations may compromise native genetic structure and lead to patchy patterns in population genetic structure.

Population structure and inbreeding from pedigree analysis of purebred dogs.

PubMed

Calboli, Federico C F; Sampson, Jeff; Fretwell, Neale; Balding, David J

2008-05-01

Dogs are of increasing interest as models for human diseases, and many canine population-association studies are beginning to emerge. The choice of breeds for such studies should be informed by a knowledge of factors such as inbreeding, genetic diversity, and population structure, which are likely to depend on breed-specific selective breeding patterns. To address the lack of such studies we have exploited one of the world's most extensive resources for canine population-genetics studies: the United Kingdom (UK) Kennel Club registration database. We chose 10 representative breeds and analyzed their pedigrees since electronic records were established around 1970, corresponding to about eight generations before present. We find extremely inbred dogs in each breed except the greyhound and estimate an inbreeding effective population size between 40 and 80 for all but 2 breeds. For all but 3 breeds, >90% of unique genetic variants are lost over six generations, indicating a dramatic effect of breeding patterns on genetic diversity. We introduce a novel index Psi for measuring population structure directly from the pedigree and use it to identify subpopulations in several breeds. As well as informing the design of canine population genetics studies, our results have implications for breeding practices to enhance canine welfare.

Three-dimensional mapping of microcircuit correlation structure

PubMed Central

Cotton, R. James; Froudarakis, Emmanouil; Storer, Patrick; Saggau, Peter; Tolias, Andreas S.

2013-01-01

Great progress has been made toward understanding the properties of single neurons, yet the principles underlying interactions between neurons remain poorly understood. Given that connectivity in the neocortex is locally dense through both horizontal and vertical connections, it is of particular importance to characterize the activity structure of local populations of neurons arranged in three dimensions. However, techniques for simultaneously measuring microcircuit activity are lacking. We developed an in vivo 3D high-speed, random-access two-photon microscope that is capable of simultaneous 3D motion tracking. This allows imaging from hundreds of neurons at several hundred Hz, while monitoring tissue movement. Given that motion will induce common artifacts across the population, accurate motion tracking is absolutely necessary for studying population activity with random-access based imaging methods. We demonstrate the potential of this imaging technique by measuring the correlation structure of large populations of nearby neurons in the mouse visual cortex, and find that the microcircuit correlation structure is stimulus-dependent. Three-dimensional random access multiphoton imaging with concurrent motion tracking provides a novel, powerful method to characterize the microcircuit activity in vivo. PMID:24133414

Population structure and connectivity of tiger sharks (Galeocerdo cuvier) across the Indo-Pacific Ocean basin

PubMed Central

Williams, Samuel M.; Otway, Nicholas M.; Nielsen, Einar E.; Maher, Safia L.; Bennett, Mike B.; Ovenden, Jennifer R.

2017-01-01

Population genetic structure using nine polymorphic nuclear microsatellite loci was assessed for the tiger shark (Galeocerdo cuvier) at seven locations across the Indo-Pacific, and one location in the southern Atlantic. Genetic analyses revealed considerable genetic structuring (FST > 0.14, p < 0.001) between all Indo-Pacific locations and Brazil. By contrast, no significant genetic differences were observed between locations from within the Pacific or Indian Oceans, identifying an apparent large, single Indo-Pacific population. A lack of differentiation between tiger sharks sampled in Hawaii and other Indo-Pacific locations identified herein is in contrast to an earlier global tiger shark nDNA study. The results of our power analysis provide evidence to suggest that the larger sample sizes used here negated any weak population subdivision observed previously. These results further highlight the need for cross-jurisdictional efforts to manage the sustainable exploitation of large migratory sharks like G. cuvier. PMID:28791159

Population structure and connectivity of tiger sharks (Galeocerdo cuvier) across the Indo-Pacific Ocean basin.

PubMed

Holmes, Bonnie J; Williams, Samuel M; Otway, Nicholas M; Nielsen, Einar E; Maher, Safia L; Bennett, Mike B; Ovenden, Jennifer R

2017-07-01

Population genetic structure using nine polymorphic nuclear microsatellite loci was assessed for the tiger shark ( Galeocerdo cuvier ) at seven locations across the Indo-Pacific, and one location in the southern Atlantic. Genetic analyses revealed considerable genetic structuring ( F ST  > 0.14, p  < 0.001) between all Indo-Pacific locations and Brazil. By contrast, no significant genetic differences were observed between locations from within the Pacific or Indian Oceans, identifying an apparent large, single Indo-Pacific population. A lack of differentiation between tiger sharks sampled in Hawaii and other Indo-Pacific locations identified herein is in contrast to an earlier global tiger shark nDNA study. The results of our power analysis provide evidence to suggest that the larger sample sizes used here negated any weak population subdivision observed previously. These results further highlight the need for cross-jurisdictional efforts to manage the sustainable exploitation of large migratory sharks like G. cuvier .

Inference and Analysis of Population Structure Using Genetic Data and Network Theory

PubMed Central

Greenbaum, Gili; Templeton, Alan R.; Bar-David, Shirli

2016-01-01

Clustering individuals to subpopulations based on genetic data has become commonplace in many genetic studies. Inference about population structure is most often done by applying model-based approaches, aided by visualization using distance-based approaches such as multidimensional scaling. While existing distance-based approaches suffer from a lack of statistical rigor, model-based approaches entail assumptions of prior conditions such as that the subpopulations are at Hardy-Weinberg equilibria. Here we present a distance-based approach for inference about population structure using genetic data by defining population structure using network theory terminology and methods. A network is constructed from a pairwise genetic-similarity matrix of all sampled individuals. The community partition, a partition of a network to dense subgraphs, is equated with population structure, a partition of the population to genetically related groups. Community-detection algorithms are used to partition the network into communities, interpreted as a partition of the population to subpopulations. The statistical significance of the structure can be estimated by using permutation tests to evaluate the significance of the partition’s modularity, a network theory measure indicating the quality of community partitions. To further characterize population structure, a new measure of the strength of association (SA) for an individual to its assigned community is presented. The strength of association distribution (SAD) of the communities is analyzed to provide additional population structure characteristics, such as the relative amount of gene flow experienced by the different subpopulations and identification of hybrid individuals. Human genetic data and simulations are used to demonstrate the applicability of the analyses. The approach presented here provides a novel, computationally efficient model-free method for inference about population structure that does not entail assumption of prior conditions. The method is implemented in the software NetStruct (available at https://giligreenbaum.wordpress.com/software/). PMID:26888080

Inference and Analysis of Population Structure Using Genetic Data and Network Theory.

PubMed

Greenbaum, Gili; Templeton, Alan R; Bar-David, Shirli

2016-04-01

Clustering individuals to subpopulations based on genetic data has become commonplace in many genetic studies. Inference about population structure is most often done by applying model-based approaches, aided by visualization using distance-based approaches such as multidimensional scaling. While existing distance-based approaches suffer from a lack of statistical rigor, model-based approaches entail assumptions of prior conditions such as that the subpopulations are at Hardy-Weinberg equilibria. Here we present a distance-based approach for inference about population structure using genetic data by defining population structure using network theory terminology and methods. A network is constructed from a pairwise genetic-similarity matrix of all sampled individuals. The community partition, a partition of a network to dense subgraphs, is equated with population structure, a partition of the population to genetically related groups. Community-detection algorithms are used to partition the network into communities, interpreted as a partition of the population to subpopulations. The statistical significance of the structure can be estimated by using permutation tests to evaluate the significance of the partition's modularity, a network theory measure indicating the quality of community partitions. To further characterize population structure, a new measure of the strength of association (SA) for an individual to its assigned community is presented. The strength of association distribution (SAD) of the communities is analyzed to provide additional population structure characteristics, such as the relative amount of gene flow experienced by the different subpopulations and identification of hybrid individuals. Human genetic data and simulations are used to demonstrate the applicability of the analyses. The approach presented here provides a novel, computationally efficient model-free method for inference about population structure that does not entail assumption of prior conditions. The method is implemented in the software NetStruct (available at https://giligreenbaum.wordpress.com/software/). Copyright © 2016 by the Genetics Society of America.

New microsatellites revealed strong gene flow among populations of a new outbreak pest, Athetis lepigone (Möschler).

PubMed

Zhu, W-C; Sun, J-T; Dai, J; Huang, J-R; Chen, L; Hong, X-Y

2017-11-27

Athetis lepigone (Möschler) (Lepidoptera: Noctuidae) is a new outbreak pest in China. Consequently, it is unclear whether the emergence and spread of the outbreak of this pest are triggered by rapid in situ population size increases in each outbreak area, or by immigrants from a potential source area in China. In order to explore the outbreak process of this pest through a population genetics approach, we developed ten novel polymorphic expressed sequence tags (EST)-derived microsatellites. These new microsatellites had moderately high levels of polymorphism in the tested population. The number of alleles per locus ranged from 3 to 19, with an average of 8.6, and the expected heterozygosity ranged from 0.269 to 0.783. A preliminary population genetic analysis using these new microsatellites revealed a lack of population genetic structure in natural populations of A. lepigone. The estimates of recent migration rate revealed strong gene flow among populations. In conclusion, our study developed the first set of EST-microsatellite markers and shed a new light on the population genetic structure of this pest in China.

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 structure of the crown-of-thorns seastar in the Pacific Ocean, with focus on Guam

PubMed Central

Tusso, Sergio; Morcinek, Kerstin; Vogler, Catherine; Schupp, Peter J.; Caballes, Ciemon F.; Vargas, Sergio

2016-01-01

Population outbreaks of the corallivorous crown-of-thorns seastar (COTS), Acanthaster ‘planci’ L., are among the most important biological disturbances of tropical coral reefs. Over the past 50 years, several devastating outbreaks have been documented around Guam, an island in the western Pacific Ocean. Previous analyses have shown that in the Pacific Ocean, COTS larval dispersal may be geographically restricted to certain regions. Here, we assess the genetic structure of Pacific COTS populations and compared samples from around Guam with a number of distant localities in the Pacific Ocean, and focused on determining the degree of genetic structure among populations previously considered to be isolated. Using microsatellites, we document substantial genetic structure between 14 localities from different geographical regions in the Pacific Ocean. Populations from the 14 locations sampled were found to be structured in three significantly differentiated groups: (1) all locations immediately around Guam, as well as Kingman Reef and Swains Island; (2) Japan, Philippines, GBR and Vanuatu; and (3) Johnston Atoll, which was significantly different from all other localities. The lack of genetic differentiation between Guam and extremely distant populations from Kingman Reef and Swains Island suggests potential long-distance dispersal of COTS in the Pacific. PMID:27168979

The potential influence of morphology on the evolutionary divergence of an acoustic signal

PubMed Central

Pitchers, W. R.; Klingenberg, C.P.; Tregenza, Tom; Hunt, J.; Dworkin, I.

2014-01-01

The evolution of acoustic behaviour and that of the morphological traits mediating its production are often coupled. Lack of variation in the underlying morphology of signalling traits has the potential to constrain signal evolution. This relationship is particularly likely in field crickets, where males produce acoustic advertisement signals to attract females by stridulating with specialized structures on their forewings. In this study, we characterise the size and geometric shape of the forewings of males from six allopatric populations of the black field cricket (Teleogryllus commodus) known to have divergent advertisement calls. We sample from each of these populations using both wild-caught and common-garden reared cohorts, allowing us to test for multivariate relationships between wing morphology and call structure. We show that the allometry of shape has diverged across populations. However, there was a surprisingly small amount of covariation between wing shape and call structure within populations. Given the importance of male size for sexual selection in crickets, the divergence we observe among populations has the potential to influence the evolution of advertisement calls in this species. PMID:25223712

Microsatellites indicate minimal barriers to mule deer Odocoileus hemionus dispersal across Montana, USA

USGS Publications Warehouse

Powell, John H.; Kalinowski, Steven T.; Higgs, Megan D.; Ebinger, Michael R.; Vu, Ninh V.; Cross, Paul C.

2013-01-01

To better understand the future spread of chronic wasting disease, we conducted a genetic assessment of mule deer Odocoileus hemionus population structure across the state of Montana, USA. Individual based analyses were used to test for population structure in the absence of a priori designations of population membership across the sampling area. Samples from the states of Wyoming, Colorado and Utah were also included in the analysis to provide a geographic context to the levels of population structure observed within Montana. Results showed that mule deer across our entire study region were characterized by weak isolation by distance and a lack of spatial autocorrelation at distances > 10 km. We found evidence for contemporary male bias in dispersal, with female mule deer exhibiting higher mean individual pairwise genetic distance than males. We tested for potential homogenizing effects of past translocations within Montana, but were unable to detect a genetic signature of these events. Our results indicate high levels of connectivity among mule deer populations in Montana and suggest few, if any, detectable barriers to mule deer gene flow or chronic wasting disease transmission.

Individual movement behavior, matrix heterogeneity, and the dynamics of spatially structured populations.

PubMed

Revilla, Eloy; Wiegand, Thorsten

2008-12-09

The dynamics of spatially structured populations is characterized by within- and between-patch processes. The available theory describes the latter with simple distance-dependent functions that depend on landscape properties such as interpatch distance or patch size. Despite its potential role, we lack a good mechanistic understanding of how the movement of individuals between patches affects the dynamics of these populations. We used the theoretical framework provided by movement ecology to make a direct representation of the processes determining how individuals connect local populations in a spatially structured population of Iberian lynx. Interpatch processes depended on the heterogeneity of the matrix where patches are embedded and the parameters defining individual movement behavior. They were also very sensitive to the dynamic demographic variables limiting the time moving, the within-patch dynamics of available settlement sites (both spatiotemporally heterogeneous) and the response of individuals to the perceived risk while moving. These context-dependent dynamic factors are an inherent part of the movement process, producing connectivities and dispersal kernels whose variability is affected by other demographic processes. Mechanistic representations of interpatch movements, such as the one provided by the movement-ecology framework, permit the dynamic interaction of birth-death processes and individual movement behavior, thus improving our understanding of stochastic spatially structured populations.

Molecular Diversity and Population Structure of a Worldwide Collection of Cultivated Tetraploid Alfalfa (Medicago sativa subsp. sativa L.) Germplasm as Revealed by Microsatellite Markers

PubMed Central

Qiang, Haiping; Chen, Zhihong; Zhang, Zhengli; Wang, Xuemin; Gao, Hongwen; Wang, Zan

2015-01-01

Information on genetic diversity and population structure of a tetraploid alfalfa collection might be valuable in effective use of the genetic resources. A set of 336 worldwide genotypes of tetraploid alfalfa (Medicago sativa subsp. sativa L.) was genotyped using 85 genome-wide distributed SSR markers to reveal the genetic diversity and population structure in the alfalfa. Genetic diversity analysis identified a total of 1056 alleles across 85 marker loci. The average expected heterozygosity and polymorphism information content values were 0.677 and 0.638, respectively, showing high levels of genetic diversity in the cultivated tetraploid alfalfa germplasm. Comparison of genetic characteristics across chromosomes indicated regions of chromosomes 2 and 3 had the highest genetic diversity. A higher genetic diversity was detected in alfalfa landraces than that of wild materials and cultivars. Two populations were identified by the model-based population structure, principal coordinate and neighbor-joining analyses, corresponding to China and other parts of the world. However, lack of strictly correlation between clustering and geographic origins suggested extensive germplasm exchanges of alfalfa germplasm across diverse geographic regions. The quantitative analysis of the genetic diversity and population structure in this study could be useful for genetic and genomic analysis and utilization of the genetic variation in alfalfa breeding. PMID:25901573

[An adjustment to the age structure of the Italian population in the 1971 census].

PubMed

Caselli, G; Golini, A; Capocaccia, R

1989-01-01

"Having verified, in the 1971 [Italian] census, the presence of certain anomalous data for cohorts born in 1900, 1911, 1920, 1924, 1930, 1936, 1940, 1948, 1950 and 1960, we assessed the size of the error and estimated the new population total which emerged both by age and year of birth. The method used [is similar] to more classical methods to correct biases in age structure in previous censuses and in those countries where the data available are somewhat lacking. The adjusted values, referring to Italy as a whole, are contained in the text...." (SUMMARY IN ENG AND FRE) excerpt

Preliminary Genetic Analysis Supports Cave Populations as Targets for Conservation in the Endemic Endangered Puerto Rican Boa (Boidae: Epicrates inornatus)

PubMed Central

Revell, Liam J.

2013-01-01

The endemic Puerto Rican boa (Epicrates inornatus) has spent 42 years on the Endangered Species List with little evidence for recovery. One significant impediment to effective conservation planning has been a lack of knowledge of the distribution of genetic variability in the species. It has previously been suggested that boas might best be protected around caves that harbor large populations of bats. Prior study has found Puerto Rican boas at relatively high densities in and around bat caves, which they use both to feed and seek shelter. However, it is unknown whether these behaviorally distinctive populations represent a distinct evolutionary lineage, or (conversely) whether caves harbor representative genetic diversity for the species across the island. We provide the first genetic study of the Puerto Rican boa, and we examine and compare genetic diversity and divergence among two cave populations and two surface populations of boas. We find three haplogroups and an apparent lack of phylogeographic structure across the island. In addition, we find that the two cave populations appear no less diverse than the two surface populations, and harbor multiple mtDNA lineages. We discuss the conservation implications of these findings, including a call for the immediate protection of the remaining cave-associated populations of boas. PMID:23691110

Preliminary genetic analysis supports cave populations as targets for conservation in the endemic endangered Puerto Rican boa (Boidae: Epicrates inornatus).

PubMed

Puente-Rolón, Alberto R; Reynolds, R Graham; Revell, Liam J

2013-01-01

The endemic Puerto Rican boa (Epicrates inornatus) has spent 42 years on the Endangered Species List with little evidence for recovery. One significant impediment to effective conservation planning has been a lack of knowledge of the distribution of genetic variability in the species. It has previously been suggested that boas might best be protected around caves that harbor large populations of bats. Prior study has found Puerto Rican boas at relatively high densities in and around bat caves, which they use both to feed and seek shelter. However, it is unknown whether these behaviorally distinctive populations represent a distinct evolutionary lineage, or (conversely) whether caves harbor representative genetic diversity for the species across the island. We provide the first genetic study of the Puerto Rican boa, and we examine and compare genetic diversity and divergence among two cave populations and two surface populations of boas. We find three haplogroups and an apparent lack of phylogeographic structure across the island. In addition, we find that the two cave populations appear no less diverse than the two surface populations, and harbor multiple mtDNA lineages. We discuss the conservation implications of these findings, including a call for the immediate protection of the remaining cave-associated populations of boas.

An Educational Perspective of Autism: Implications for Curriculum Development and Personnel Development.

ERIC Educational Resources Information Center

Donnellan, Anne M.

The paper addresses the history and current status of educational provisions for autistic students, discusses the requirements for effective education for this population, and analyzes the implications for teacher education practices. A status report cites lack of structure in programs, non-functional and age-inappropriate curricula, largely…

Life History and Production of the Western Gray Whale's Prey, Ampelisca eschrichtii Krøyer, 1842 (Amphipoda, Ampeliscidae).

PubMed

Demchenko, Natalia L; Chapman, John W; Durkina, Valentina B; Fadeev, Valeriy I

2016-01-01

Ampelisca eschrichtii are among the most important prey of the Western North Pacific gray whales, Eschrichtius robustus. The largest and densest known populations of this amphipod occur in the gray whale's Offshore feeding area on the Northeastern Sakhalin Island Shelf. The remote location, ice cover and stormy weather at the Offshore area have prevented winter sampling. The incomplete annual sampling has confounded efforts to resolve life history and production of A. eschrichtii. Expanded comparisons of population size structure and individual reproductive development between late spring and early fall over six sampling years between 2002 and 2013 however, reveal that A. eschrichtii are gonochoristic, iteroparous, mature at body lengths greater than 15 mm and have a two-year life span. The low frequencies of brooding females, the lack of early stage juveniles, the lack of individual or population growth or biomass increases over late spring and summer, all indicate that growth and reproduction occur primarily in winter, when sampling does not occur. Distinct juvenile and adult size cohorts additionally indicate growth and juvenile production occurs in winter through spring under ice cover. Winter growth thus requires that winter detritus or primary production are critical food sources for these ampeliscid populations and yet, the Offshore area and the Eastern Sakhalin Shelf ampeliscid communities may be the most abundant and productive amphipod population in the world. These A. eschrichtii populations are unlikely to be limited by western gray whale predation. Whether benthic community structure can limit access and foraging success of western gray whales is unclear.

Emergent vortices in populations of colloidal rollers

PubMed Central

Bricard, Antoine; Caussin, Jean-Baptiste; Das, Debasish; Savoie, Charles; Chikkadi, Vijayakumar; Shitara, Kyohei; Chepizhko, Oleksandr; Peruani, Fernando; Saintillan, David; Bartolo, Denis

2015-01-01

Coherent vortical motion has been reported in a wide variety of populations including living organisms (bacteria, fishes, human crowds) and synthetic active matter (shaken grains, mixtures of biopolymers), yet a unified description of the formation and structure of this pattern remains lacking. Here we report the self-organization of motile colloids into a macroscopic steadily rotating vortex. Combining physical experiments and numerical simulations, we elucidate this collective behaviour. We demonstrate that the emergent-vortex structure lives on the verge of a phase separation, and single out the very constituents responsible for this state of polar active matter. Building on this observation, we establish a continuum theory and lay out a strong foundation for the description of vortical collective motion in a broad class of motile populations constrained by geometrical boundaries. PMID:26088835

Genetic diversity and population structure of Eleutheronema rhadinum in the East and South China Seas revealed in mitochondrial COI sequences

NASA Astrophysics Data System (ADS)

Sun, Xinxu; Xu, Dongdong; Lou, Bao; Zhang, Tao; Xin, Jian; Guo, Yaoshi; Ma, Shilei

2013-11-01

Eleutheronema rhadinum is a potential commercial fisheries species and is subject to intense exploitation in China. Knowledge on the population structure of E. rhadinum in Chinese coastal waters, which is important for sustainable exploitation and proper resource management, is lacking. In the present study, the genetic diversity and population structure of E. rhadinum were evaluated using a 564-base pair fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene. A total of 76 specimens were collected from three localities around the East (Qidong and Zhoushan) and South China Seas (Zhuhai). Among these individuals, nine polymorphic sites were detected and 11 distinct haplotypes were defined. High levels of haplotype diversity ( h =0.759±0.035) and low levels of nucleotide diversity ( π= 0.001 98±0.003 26) were observed in these populations. Hierarchical analysis of molecular variance (AMOVA) indicated that 96.72% of the genetic variation occurred within the populations, whereas 3.28% occurred among populations. No significant genealogical branches or clusters were recognized on the neighbor-joining tree. Intra-group variation among populations was significant ( φ st=0.032 85, P<0.01). These results suggest that E. rhadinum populations in the East and South China Seas have developed divergent genetic structures. Tests of neutral evolution and mismatch distribution suggest that E. rhadinum may have experienced a population expansion. The present study provides basic information for the conservation and sustainable exploitation of this species.

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.

Residence rule flexibility and descent groups dynamics shape uniparental genetic diversities in South East Asia.

PubMed

Ly, Goki; Alard, Bérénice; Laurent, Romain; Lafosse, Sophie; Toupance, Bruno; Monidarin, Chou; Diffloth, Gérard; Bourdier, Frédéric; Evrard, Olivier; Pavard, Samuel; Chaix, Raphaëlle

2018-03-01

Social organization plays a major role in shaping human population genetic diversity. In particular, matrilocal populations tend to exhibit less mitochondrial diversity than patrilocal populations, and the other way around for Y chromosome diversity. However, several studies have not replicated such findings. The objective of this study is to understand the reasons for such inconsistencies and further evaluate the influence of social organization on genetic diversity. We explored uniparental diversity patterns using mitochondrial HV1 sequences and 17 Y-linked short tandem repeats (STRs) in 12 populations (n = 619) from mainland South-East Asia exhibiting a wide range of social organizations, along with quantitative ethno-demographic information sampled at the individual level. MtDNA diversity was lower in matrilocal than in multilocal and patrilocal populations while Y chromosome diversity was similar among these social organizations. The reasons for such asymmetry at the genetic level were understood by quantifying sex-specific migration rates from our ethno-demographic data: while female migration rates varied between social organizations, male migration rates did not. This unexpected lack of difference in male migrations resulted from a higher flexibility in residence rule in patrilocal than in matrilocal populations. In addition, our data suggested an impact of clan fission process on uniparental genetic patterns. The observed lack of signature of patrilocality on Y chromosome patterns might be attributed to the higher residence flexibility in the studied patrilocal populations, thus providing a potential explanation for the apparent discrepancies between social and genetic structures. Altogether, this study highlights the need to quantify the actual residence and descent patterns to fit social to genetic structures. © 2018 Wiley Periodicals, Inc.

Demographic threats to the sustainability of Brazil nut exploitation.

PubMed

Peres, Carlos A; Baider, Claudia; Zuidema, Pieter A; Wadt, Lúcia H O; Kainer, Karen A; Gomes-Silva, Daisy A P; Salomão, Rafael P; Simões, Luciana L; Franciosi, Eduardo R N; Cornejo Valverde, Fernando; Gribel, Rogério; Shepard, Glenn H; Kanashiro, Milton; Coventry, Peter; Yu, Douglas W; Watkinson, Andrew R; Freckleton, Robert P

2003-12-19

A comparative analysis of 23 populations of the Brazil nut tree (Bertholletia excelsa) across the Brazilian, Peruvian, and Bolivian Amazon shows that the history and intensity of Brazil nut exploitation are major determinants of population size structure. Populations subjected to persistent levels of harvest lack juvenile trees less than 60 centimeters in diameter at breast height; only populations with a history of either light or recent exploitation contain large numbers of juvenile trees. A harvesting model confirms that intensive exploitation levels over the past century are such that juvenile recruitment is insufficient to maintain populations over the long term. Without management, intensively harvested populations will succumb to a process of senescence and demographic collapse, threatening this cornerstone of the Amazonian extractive economy.

The genetic structure of Nautilus pompilius populations surrounding Australia and the Philippines.

PubMed

Williams, Rachel C; Jackson, Benjamin C; Duvaux, Ludovic; Dawson, Deborah A; Burke, Terry; Sinclair, William

2015-07-01

Understanding the distribution of genetic diversity in exploited species is fundamental to successful conservation. Genetic structure and the degree of gene flow among populations must be assessed to design appropriate strategies to prevent the loss of distinct populations. The cephalopod Nautilus pompilius is fished unsustainably in the Philippines for the ornamental shell trade and has limited legislative protection, despite the species' recent dramatic decline in the region. Here, we use 14 microsatellite markers to evaluate the population structure of N. pompilius around Australia and the Philippines. Despite their relative geographical proximity, Great Barrier Reef individuals are genetically isolated from Osprey Reef and Shark Reef in the Coral Sea (FST  = 0.312, 0.229, respectively). Conversely, despite the larger geographical distances between the Philippines and west Australian reefs, samples display a small degree of genetic structure (FST  = 0.015). Demographic scenarios modelled using approximate Bayesian computation analysis indicate that this limited divergence is not due to contemporary gene flow between the Philippines and west Australia. Instead, present-day genetic similarity can be explained by very limited genetic drift that has occurred due to large average effective population sizes that persisted at both locations following their separation. The lack of connectivity among populations suggests that immigrants from west Australia would not facilitate natural recolonization if Philippine populations were fished to extinction. These data help to rectify the paucity of information on the species' biology currently inhibiting their conservation classification. Understanding population structure can allow us to facilitate sustainable harvesting, thereby preserving the diversity of genetically distinct stocks. © 2015 John Wiley & Sons Ltd.

Rapid recovery of genetic diversity of dogwhelk (Nucella lapillus L.) populations after local extinction and recolonization contradicts predictions from life-history characteristics.

PubMed

Colson, I; Hughes, R N

2004-08-01

The dogwhelk Nucella lapillus is a predatory marine gastropod populating North Atlantic rocky shores. As with many other gastropod species, N. lapillus was affected by tributyltin (TBT) pollution during the 1970s and 1980s, when local populations became extinct. After a partial ban on TBT in the United Kingdom in 1987, vacant sites have been recolonized. N. lapillus lacks a planktonic larval stage and is therefore expected to have limited dispersal ability. Relatively fast recolonization of some sites, however, contradicts this assumption. We compared levels of genetic diversity and genetic structuring between recolonized sites and sites that showed continuous population at three localities across the British Isles. No significant genetic effects of extinction/recolonization events were observed in SW Scotland and NE England. In SW England we observed a decrease in genetic diversity and an increase in genetic structure in recolonized populations. This last result could be an artefact, however, due to the superposition of other local factors influencing the genetic structuring of dogwhelk populations. We conclude that recolonization of vacant sites was accomplished by a relatively high number of individuals originating from several source populations (the 'migrant-pool' model of recolonization), implying that movements are more widespread than expected on the basis of development mode alone. Comparison with published data on genetic structure of marine organisms with contrasted larval dispersal supports this hypothesis. Our results also stress the importance of local factors (geographical or ecological) in determining genetic structure of dogwhelk populations. Copyright 2004 Blackwell Publishing Ltd

Use of Restriction Fragment Length Polymorphisms to Investigate Strain Variation Within Neisseria Meningitidis.

NASA Astrophysics Data System (ADS)

Williams, Shelley Diane

Similarity within bacterial populations is difficult to assess due to the limited number of characters available for evaluation and the heterogeneity of bacterial species. Currently, the preferred method used to evaluate the structure of bacterial populations is multilocus enzyme electrophoresis. However, this method is extremely cumbersome and only offers an indirect measure of genetic similarities. The development of a more direct and less cumbersome method for this purpose is warranted. Restriction fragment length polymorphism analysis was evaluated as a tool for use in the study of bacterial population structures and in the epidemiology and surveillance of infectious disease. A collection of Neisseria meningitidis was available for use in the investigation of this technique. Neisseria meningitidis is the causative agent of epidemic cerebrospinal meningitis and septicemia as well as a variety of other clinical manifestations. Each isolate in the collection was defined in terms of serogroup specificity, clinical history, geographic source, and date of isolation. Forty -six strains were chosen for this study. The DNA from each strain was restricted with Pst1 and EcoR1 and electrophoresed on agarose gels. The DNA was transferred to nylon filters and hybridized with P ^{32} labeled DNA probes. Two randomly generated probes and a gene-specific probe were used to estimate the genetic similarities between and among the strains in the study population. A total of 28 different restriction fragment migration types were detected by the probes used. Data obtained from the RFLP analysis was analysed by cluster analysis and multivariate statistical methods. A total of 7 clones groups were detected. Two of these appear to be major clones that comprise 35% of the population. This analysis demonstrates the lack of structure within Neisseria meningitidis due primarily to a heterogenous population and the lack of geographic segregation. The potential utility of this technique as a tool in epidemiologic surveillance is addressed. Further work is needed in the evaluation of RFLP analysis in the taxonomy bacteria.

Atlantic salmon Salmo salar in the chalk streams of England are genetically unique.

PubMed

Ikediashi, C; Paris, J R; King, R A; Beaumont, W R C; Ibbotson, A; Stevens, J R

2018-03-01

Recent research has identified genetic groups of Atlantic salmon Salmo salar that show association with geological and environmental boundaries. This study focuses on one particular subgroup of the species inhabiting the chalk streams of southern England, U.K. These fish are genetically distinct from other British and European S. salar populations and have previously demonstrated markedly low admixture with populations in neighbouring regions. The genetic population structure of S. salar occupying five chalk streams was explored using 16 microsatellite loci. The analysis provides evidence of the genetic distinctiveness of chalk-stream S. salar in southern England, in comparison with populations from non-chalk regions elsewhere in western Europe. Little genetic differentiation exists between the chalk-stream populations and a pattern of isolation by distance was evident. Furthermore, evidence of temporal stability of S. salar populations across the five chalk streams was found. This work provides new insights into the temporal stability and lack of genetic population sub-structuring within a unique component of the species' range of S. salar. © 2018 The Fisheries Society of the British Isles.

Structure and genetic diversity of natural Brazilian pepper populations (Schinus terebinthifolius Raddi).

PubMed

Álvares-Carvalho, S V; Duarte, J F; Santos, T C; Santos, R M; Silva-Mann, R; Carvalho, D

2016-06-17

In the face of a possible loss of genetic diversity in plants due the environmental changes, actions to ensure the genetic variability are an urgent necessity. The extraction of Brazilian pepper fruits is a cause of concern because it results in the lack of seeds in soil, hindering its distribution in space and time. It is important to address this concern and explore the species, used by riparian communities and agro-factories without considering the need for keeping the seeds for natural seed banks and for species sustainability. The objective of this study was to evaluate the structure and the genetic diversity in natural Brazilian pepper populations (Schinus terebinthifolius Raddi). Twenty-two alleles in 223 individuals were identified from eight forest remnants located in the states of Minas Gerais, Espírito Santo, and Sergipe. All populations presented loci in Hardy-Weinberg equilibrium deviation. Four populations presented six combinations of loci in linkage disequilibrium. Six exclusive alleles were detected in four populations. Analysis of molecular variance showed the absence of diversity between regions and that between the populations (GST) was 41%. Genetic diversity was structured in seven clusters (ΔK7). Brazilian pepper populations were not structured in a pattern of isolation by distance and present genetic bottleneck. The populations São Mateus, Canastra, Barbacena, and Ilha das Flores were identified as management units and may support conservation projects, ecological restoration and in implementation of management plans for Brazilian pepper in the State of Sergipe.

Adherence to antiretroviral therapy among a conflict-affected population in Northeastern Uganda: a qualitative study.

PubMed

Olupot-Olupot, Peter; Katawera, Andrew; Cooper, Curtis; Small, Will; Anema, Aranka; Mills, Edward

2008-09-12

We aimed to determine patient and health worker concerns regarding antiretroviral adherence in a conflict-affected population using focus groups (n = 40) and semi-structured interviews (n = 11). Patient concerns include security attending clinics, food security, distance to health centers and access to health providers. During periods of famine and flooding, the lack of food security and only single daily meals makes taking multiple doses impossible. Possible facilitating strategies included mobile teams, increased security and regularity of drug stocks.

Mutation rates among RNA viruses

PubMed Central

Drake, John W.; Holland, John J.

1999-01-01

The rate of spontaneous mutation is a key parameter in modeling the genetic structure and evolution of populations. The impact of the accumulated load of mutations and the consequences of increasing the mutation rate are important in assessing the genetic health of populations. Mutation frequencies are among the more directly measurable population parameters, although the information needed to convert them into mutation rates is often lacking. A previous analysis of mutation rates in RNA viruses (specifically in riboviruses rather than retroviruses) was constrained by the quality and quantity of available measurements and by the lack of a specific theoretical framework for converting mutation frequencies into mutation rates in this group of organisms. Here, we describe a simple relation between ribovirus mutation frequencies and mutation rates, apply it to the best (albeit far from satisfactory) available data, and observe a central value for the mutation rate per genome per replication of μg ≈ 0.76. (The rate per round of cell infection is twice this value or about 1.5.) This value is so large, and ribovirus genomes are so informationally dense, that even a modest increase extinguishes the population. PMID:10570172

Aspiration dynamics in structured population acts as if in a well-mixed one.

PubMed

Du, Jinming; Wu, Bin; Wang, Long

2015-01-26

Understanding the evolution of human interactive behaviors is important. Recent experimental results suggest that human cooperation in spatial structured population is not enhanced as predicted in previous works, when payoff-dependent imitation updating rules are used. This constraint opens up an avenue to shed light on how humans update their strategies in real life. Studies via simulations show that, instead of comparison rules, self-evaluation driven updating rules may explain why spatial structure does not alter the evolutionary outcome. Though inspiring, there is a lack of theoretical result to show the existence of such evolutionary updating rule. Here we study the aspiration dynamics, and show that it does not alter the evolutionary outcome in various population structures. Under weak selection, by analytical approximation, we find that the favored strategy in regular graphs is invariant. Further, we show that this is because the criterion under which a strategy is favored is the same as that of a well-mixed population. By simulation, we show that this holds for random networks. Although how humans update their strategies is an open question to be studied, our results provide a theoretical foundation of the updating rules that may capture the real human updating rules.

Population sub-structuring among Trypanosoma evansi stocks.

PubMed

Njiru, Z K; Constantine, C C

2007-10-01

To investigate the population genetic structure of Trypanosoma evansi from domesticated animals, we have analysed 112 stocks from camels, buffaloes, cattle and horses using the tandemly repeated coding sequence (MORF2) and minisatellite markers 292 and cysteine-rich acidic integral membrane protein (CRAM). We recorded a total of six alleles at the MORF2 locus, seven at 292 and 12 at the CRAM loci. Nei's genetic distance showed reduced allelic diversity between buffaloes and cattle stocks (1.2) as compared to the diversity between camels and buffaloes (3.75) and camels and cattle stock (1.69). The mean index of association (IA=0.92) significantly deviated from zero, and the average number of multilocus genotypes (G/N ratio) was 0.21. Twenty-four multilocus genotypes were defined from the combination of alleles at the three loci. The Kenyan sub-populations showed Fst=0.28 and analysis of molecular variance showed significant divergence (22.7%) between the Laikipia, Kulal and Galana regions. The regional and host distribution of multi-locus genotypes significant population differentiation and high Nei's genetic distances suggest existence of genetic sub-structuring within T. evansi stocks while the few multi-locus genotypes and deviation of association index from zero indicate the lack of recombination. In conclusion, this study reveals that some genetic sub-structuring does occur within T. evansi, which has a clonal population structure.

Lack of genetic differentiation in aggressive and secondary bark beetles (Coleoptera: Curculionidae, Scolytinae) from Arizona

Treesearch

Christopher J. Allender; Karen M. Clancy; Tom E. DeGomez; Joel D. McMillin; Scott A. Woolbright; Paul Keim; David M. Wagner

2008-01-01

Bark beetles (Coleoptera: Curculionidae, Scolytinae) play an important role as disturbance agents in ponderosa pine (Pinus ponderosa Douglas ex Lawson) forests of Arizona. However, from 2001 to 2003, elevated bark beetle activity caused unprecedented levels of ponderosa pine mortality. A better understanding of the population structure of these...

Spatial genetic structure of bristle-thighed curlews (Numenius tahitiensis): breeding area differentiation not reflected on the non-breeding grounds

USGS Publications Warehouse

Sonsthagen, Sarah A.; Tibbitts, T. Lee; Gill, Robert E.; Williams, Ian S.; Talbot, Sandra L.

2015-01-01

Migratory birds occupy geographically and ecologically disparate areas during their annual cycle with conditions on breeding and non-breeding grounds playing separate and important roles in population dynamics. We used data from nuclear microsatellite and mitochondrial DNA control region loci to assess the breeding and non-breeding spatial genetic structure of a transoceanic migrant shorebird, the bristle-thighed curlew. We found spatial variance in the distribution of allelic and haplotypic frequencies between the curlew's two breeding areas in Alaska but did not observe this spatial structure throughout its non-breeding range on low-lying tropical and subtropical islands in the Central Pacific (Oceania). This suggests that the two breeding populations do not spatially segregate during the non-breeding season. Lack of migratory connectivity is likely attributable to the species' behavior, as bristle-thighed curlews exhibit differential timing of migration and some individuals move among islands during non-breeding months. Given the detrimental impact of many past and current human activities on island ecosystems, admixture of breeding populations in Oceania may render the bristle-thighed curlew less vulnerable to perturbations there, as neither breeding population will be disproportionally affected by local habitat losses or by stochastic events. Furthermore, lack of migratory connectivity may enable bristle-thighed curlews to respond to changing island ecosystems by altering their non-breeding distribution. However, availability of suitable non-breeding habitat for curlews in Oceania is increasingly limited on both low-lying and high islands by habitat loss, sea level rise, and invasive mammalian predators that pose a threat to flightless and flight-compromised curlews during the molting period.

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.

Synchronisation and stability in river metapopulation networks.

PubMed

Yeakel, J D; Moore, J W; Guimarães, P R; de Aguiar, M A M

2014-03-01

Spatial structure in landscapes impacts population stability. Two linked components of stability have large consequences for persistence: first, statistical stability as the lack of temporal fluctuations; second, synchronisation as an aspect of dynamic stability, which erodes metapopulation rescue effects. Here, we determine the influence of river network structure on the stability of riverine metapopulations. We introduce an approach that converts river networks to metapopulation networks, and analytically show how fluctuation magnitude is influenced by interaction structure. We show that river metapopulation complexity (in terms of branching prevalence) has nonlinear dampening effects on population fluctuations, and can also buffer against synchronisation. We conclude by showing that river transects generally increase synchronisation, while the spatial scale of interaction has nonlinear effects on synchronised dynamics. Our results indicate that this dual stability - conferred by fluctuation and synchronisation dampening - emerges from interaction structure in rivers, and this may strongly influence the persistence of river metapopulations. © 2013 John Wiley & Sons Ltd/CNRS.

Ecology and biology of paddlefish in North America: historical perspectives, management approaches, and research priorities

USGS Publications Warehouse

Jennings, Cecil A.; Zigler, Stephen J.

2000-01-01

Paddlefish (Polyodon spathula, Polyodontidae) are large, mostly-riverine fish that once were abundant in medium- to large-sized river systems throughout much of the central United States. Concern for paddlefish populations has grown from a regional fisheries issue to one of national importance for the United States. In 1989, the U.S. Fish and Wildlife Service (USFWS) was petitioned to list paddlefish as a federally threatened species under the Endangered Species Act. The petition was not granted, primarily because of a lack of empirical data on paddlefish population size, age structure, growth, or harvest rates across the present 22-state range. Nonetheless, concern for paddlefish populations prompted the USFWS to recommend that paddlefish be protected through the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). The addition of paddlefish to Appendix II of CITES, which was approved in March 1992, provides a mechanism to curtail illegal trade in paddlefish and their parts and supports a variety of conservation plans. Paddlefish populations have been negatively affected by overharvest, river modifications, and pollution, but the paddlefish still occupies much of its historic range and most extant populations seem to be stable. Although many facets of paddlefish biology and ecology are well understood, the lack of information on larval and juvenile ecology, mechanisms that determine recruitment, population size and vital rates, interjurisdictional movements, and the effects of anthropogenic activities present significant obstacles for managing paddlefish populations. Questions about the size and structure of local populations, and how such populations are affected by navigation traffic, dams, and pollution are regarded as medium priority areas for future research. The availability of suitable spawning habitat and overall reproductive success in impounded rivers are unknown and represent critical areas for future research. Research on reproductive and recruitment success in impounded rivers have significant implications for managing paddlefish, as rivers are modified further for human use.

Genetic population structure of the alpine species Rhododendron pseudochrysanthum sensu lato (Ericaceae) inferred from chloroplast and nuclear DNA

PubMed Central

2011-01-01

Background A complex of incipient species with different degrees of morphological or ecological differentiation provides an ideal model for studying species divergence. We examined the phylogeography and the evolutionary history of the Rhododendron pseudochrysanthum s. l. Results Systematic inconsistency was detected between gene genealogies of the cpDNA and nrDNA. Rooted at R. hyperythrum and R. formosana, both trees lacked reciprocal monophyly for all members of the complex. For R. pseudochrysanthum s.l., the spatial distribution of the cpDNA had a noteworthy pattern showing high genetic differentiation (FST = 0.56-0.72) between populations in the Yushan Mountain Range and populations of the other mountain ranges. Conclusion Both incomplete lineage sorting and interspecific hybridization/introgression may have contributed to the lack of monophyly among R. hyperythrum, R. formosana and R. pseudochrysanthum s.l. Independent colonizations, plus low capabilities of seed dispersal in current environments, may have resulted in the genetic differentiation between populations of different mountain ranges. At the population level, the populations of Central, and Sheishan Mountains may have undergone postglacial demographic expansion, while populations of the Yushan Mountain Range are likely to have remained stable ever since the colonization. In contrast, the single population of the Alishan Mountain Range with a fixed cpDNA haplotype may have experienced bottleneck/founder's events. PMID:21501530

Genetic diversity and population structure of Anastrepha striata (Diptera: Tephritidae) in three natural regions of southwestern Colombia using mitochondrial sequences.

PubMed

Gallo-Franco, Jenny Johana; Velasco-Cuervo, Sandra Marcela; Aguirre-Ramirez, Elkin; González Obando, Ranulfo; Carrejo, Nancy Soraya; Toro-Perea, Nelson

2017-02-01

Anastrepha striata is widely distributed across the Americas and is a pest of economically important crops, especially crops of the Myrtaceae family. Insect population structures can be influenced by the presence of physical barriers or characteristics associated with habitat differences. This study evaluated the effect of the Western Andes on the population structure of A. striata. Individuals were collected from Psidium guajava fruits from three natural regions of southwestern Colombia (Pacific Coast, mountainous region and the inter-Andean valley of the Cauca River). Based on a 1318 bp concatenated of the genes Cytochrome Oxidase subunit I (COI) and NADH dehydrogenase subunit 6 (ND6), 14 haplotypes with few changes among them (between 1 and 3) were found. There was only one dominant haplotype in all three regions. No genetic structure associated with the three eco-geographical regions of the study was found. Moreover, the Western Andes are not an effective barrier for the genetic isolation of the populations from the Pacific Coast compared with the inter-Andean valley populations. This genetic homogeneity could be partially due to anthropogenic intervention, which acts as a dispersal agent of infested fruits. Another hypothesis to explain the lack of structure would be the relatively recent arrival of A. striata to the region, as indicated by an analysis of the demographic history, which reveals a process of population expansion. This study represents the first attempt to understand the population genetics of A. striata in Colombia and could contribute to the integral management of this pest.

Harlequin Duck recovery from the Exxon Valdez oil spill: A population genetics perspective

USGS Publications Warehouse

Lanctot, R.; Goatcher, B.; Scribner, K.; Talbot, S.; Pierson, B.; Esler, Daniel N.; Zwiefelhofer, D.

1999-01-01

Concerns about Harlequin Duck (Histrionicus histrionicus) population recovery following the Exxon Valdez oil spill led biologists to ask whether birds located in different molting and wintering areas belong to genetically distinct and, thus, demographically independent populations. Owing to the lack of direct observations of movements among marine areas, three classes of genetic markers that differed in mode of inheritance were used to evaluate the degree of genetic differentiation among wintering areas within Prince William Sound (PWS) and the Alaska Peninsula and Kodiak Archipelago (APKA). We could not reject the null hypothesis that the wintering aggregations within each region are composed of a single genetically panmictic population. Differences in genotype frequencies among wintering locations within PWS and APKA were low and nonsignificant for all three classes of markers. Furthermore, we saw no evidence for deviations in Hardy-Weinberg equilibrium or gametic disequilibrium between loci within a winter collection site as would be expected if these locales were composed of individuals from reproductively isolated (and genetically distinct) breeding locales. Finally, no evidence for significant structuring was noted between PWS and APKA. Lack of spatial genetic structuring could be due to the cumulative effects of low levels of gene flow over long time periods, low levels of gene flow by immature birds moving between marine habitats, or to episodic dispersal caused by habitat alteration (e.g. volcanic eruptions). Harlequin Ducks are likely to recolonize or enhance populations in areas recovering from environmental damage via emigration of birds from non-affected areas. Demographic studies suggest, however, that levels of movements are low, and that population recovery by emigration is a long-term process.

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.

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.

Microsatellite and Wolbachia analysis in Rhagoletis cerasi natural populations: population structuring and multiple infections.

PubMed

Augustinos, Antonios A; Asimakopoulou, Anastasia K; Moraiti, Cleopatra A; Mavragani-Tsipidou, Penelope; Papadopoulos, Nikolaos T; Bourtzis, Kostas

2014-05-01

Rhagoletis cerasi (Diptera: Tephritidae) is a major pest of sweet and sour cherries in Europe and parts of Asia. Despite its economic significance, there is a lack of studies on the genetic structure of R. cerasi populations. Elucidating the genetic structure of insects of economic importance is crucial for developing phenological-predictive models and environmental friendly control methods. All natural populations of R. cerasi have been found to harbor the endosymbiont Wolbachia pipientis, which widely affects multiple biological traits contributing to the evolution of its hosts, and has been suggested as a tool for the biological control of insect pests and disease vectors. In the current study, the analysis of 18 R. cerasi populations collected in Greece, Germany, and Russia using 13 microsatellite markers revealed structuring of R. cerasi natural populations, even at close geographic range. We also analyzed the Wolbachia infection status of these populations using 16S rRNA-, MLST- and wsp-based approaches. All 244 individuals screened were positive for Wolbachia. Our results suggest the fixation of the wCer1 strain in Greece while wCer2, wCer4, wCer5, and probably other uncharacterized strains were also detected in multiply infected individuals. The role of Wolbachia and its potential extended phenotypes needs a thorough investigation in R. cerasi. Our data suggest an involvement of this symbiont in the observed restriction in the gene flow in addition to a number of different ecological factors.

Microsatellite and Wolbachia analysis in Rhagoletis cerasi natural populations: population structuring and multiple infections

PubMed Central

Augustinos, Antonios A; Asimakopoulou, Anastasia K; Moraiti, Cleopatra A; Mavragani-Tsipidou, Penelope; Papadopoulos, Nikolaos T; Bourtzis, Kostas

2014-01-01

Rhagoletis cerasi (Diptera: Tephritidae) is a major pest of sweet and sour cherries in Europe and parts of Asia. Despite its economic significance, there is a lack of studies on the genetic structure of R. cerasi populations. Elucidating the genetic structure of insects of economic importance is crucial for developing phenological-predictive models and environmental friendly control methods. All natural populations of R. cerasi have been found to harbor the endosymbiont Wolbachia pipientis, which widely affects multiple biological traits contributing to the evolution of its hosts, and has been suggested as a tool for the biological control of insect pests and disease vectors. In the current study, the analysis of 18 R. cerasi populations collected in Greece, Germany, and Russia using 13 microsatellite markers revealed structuring of R. cerasi natural populations, even at close geographic range. We also analyzed the Wolbachia infection status of these populations using 16S rRNA-, MLST- and wsp-based approaches. All 244 individuals screened were positive for Wolbachia. Our results suggest the fixation of the wCer1 strain in Greece while wCer2, wCer4, wCer5, and probably other uncharacterized strains were also detected in multiply infected individuals. The role of Wolbachia and its potential extended phenotypes needs a thorough investigation in R. cerasi. Our data suggest an involvement of this symbiont in the observed restriction in the gene flow in addition to a number of different ecological factors. PMID:24963388

Response of a tropical tree to non-timber forest products harvest and reduction in habitat size

PubMed Central

Kouagou, M’Mouyohoun; Natta, Armand K.; Gado, Choukouratou

2017-01-01

Non-timber forest products (NTFPs) are widely harvested by local people for their livelihood. Harvest often takes place in human disturbed ecosystems. However, our understanding of NTFPs harvesting impacts in fragmented habitats is limited. We assessed the impacts of fruit harvest, and reduction in habitat size on the population structures of Pentadesma butyracea Sabine (Clusiaceae) across two contrasting ecological regions (dry vs. moist) in Benin. In each region, we selected three populations for each of the three fruit harvesting intensities (low, medium and high). Harvesting intensities were estimated as the proportion of fruits harvested per population. Pentadesma butyracea is found in gallery forests along rivers and streams. We used the width of gallery forests as a measure of habitat size. We found negative effects of fruit harvest on seedling and adult density but no significant effect on population size class distribution in both ecological regions. The lack of significant effect of fruit harvest on population structure may be explained by the ability of P. butyracea to compensate for the negative effect of fruit harvesting by increasing clonal reproduction. Our results suggest that using tree density and population structure to assess the ecological impacts of harvesting clonal plants should be done with caution. PMID:28850624

Response of a tropical tree to non-timber forest products harvest and reduction in habitat size.

PubMed

Gaoue, Orou G; Kouagou, M'Mouyohoun; Natta, Armand K; Gado, Choukouratou

2017-01-01

Non-timber forest products (NTFPs) are widely harvested by local people for their livelihood. Harvest often takes place in human disturbed ecosystems. However, our understanding of NTFPs harvesting impacts in fragmented habitats is limited. We assessed the impacts of fruit harvest, and reduction in habitat size on the population structures of Pentadesma butyracea Sabine (Clusiaceae) across two contrasting ecological regions (dry vs. moist) in Benin. In each region, we selected three populations for each of the three fruit harvesting intensities (low, medium and high). Harvesting intensities were estimated as the proportion of fruits harvested per population. Pentadesma butyracea is found in gallery forests along rivers and streams. We used the width of gallery forests as a measure of habitat size. We found negative effects of fruit harvest on seedling and adult density but no significant effect on population size class distribution in both ecological regions. The lack of significant effect of fruit harvest on population structure may be explained by the ability of P. butyracea to compensate for the negative effect of fruit harvesting by increasing clonal reproduction. Our results suggest that using tree density and population structure to assess the ecological impacts of harvesting clonal plants should be done with caution.

Mitochondrial D-loop sequences reveal a mixture of endemism and immigration in Egyptian goat populations.

PubMed

Ahmed, Sahar; Grobler, Paul; Madisha, Thabang; Kotze, Antionette

2017-09-01

The mitochondrial D-loop region was used to investigate genetic diversity within and between populations of Egyptian goats, to elucidate processes that explain present patterns of diversity and differentiation and to characterize Egyptian goats relative to international breeds. A total of 120 animals from six populations were sampled. Results confirm the main trend from previous studies of mtDNA diversity in goats, with high levels of diversity within populations, but with a comparative lack of genetic structure supporting geographic distribution. Haplotype diversity varied in a narrow range whereas nucleotide diversity values were more informative in showing differences between populations. The majority of goats analyzed (93.2%) displayed haplotypes that group with Haplogroup A, the most common type found in global goat populations. The remaining animals grouped with the less common Haplogroup G. Population differentiation analysis showed some uniqueness in the Aswan and Sharkawi populations from the South and East of Egypt. Overall, the structure of the Egyptian goat population is characterized by a high degree of homogeneity among populations from the north-western coastal region, the Nile Delta and the upper and middle regions of the Nile valley, but with possible introgression of rarer haplotypes into populations at the southern and eastern extremities of the country.

Genetic population structure of the recently introduced Asian clam, Potamocorbula amurensis, in San Francisco Bay

USGS Publications Warehouse

Duda, T. F.

1994-01-01

The genetic population structure of the recently introduced Asian clam, Potamocorbula amurensis, in San Francisco Bay was described using starch gel electrophoresis at eight presumptive loci. Specimens were taken from five environmentally distinct sites located throughout the bay. The population maintains a high degree of genetic variation, with a mean heterozygosity of 0.295, a mean polymorphism of 0.75, and an average of 3.70 alleles per locus. The population is genetically homogeneous, as evidenced from genetic distance values and F-statistics. However, heterogeneity of populations was indicated from a contingency chi-square test. Significant deviations from Hardy-Weinberg equilibrium and heterozygote deficiencies were found at the Lap-1 locus for all populations and at the Lap-2 locus for a single population. High levels of variability could represent a universal characteristic of invading species, the levels of variability in the source population(s), and/or the dynamics of the introduction. Lack of differentiation between subpopulations may be due to the immaturity of the San Francisco Bay population, the “general purpose” phenotype genetic strategy of the species, high rates of gene flow in the population, and/or the selective neutrality of the loci investigated.

Adaptation to local ultraviolet radiation conditions among neighbouring Daphnia populations

PubMed Central

Miner, Brooks E.; Kerr, Benjamin

2011-01-01

Understanding the historical processes that generated current patterns of phenotypic diversity in nature is particularly challenging in subdivided populations. Populations often exhibit heritable genetic differences that correlate with environmental variables, but the non-independence among neighbouring populations complicates statistical inference of adaptation. To understand the relative influence of adaptive and non-adaptive processes in generating phenotypes requires joint evaluation of genetic and phenotypic divergence in an integrated and statistically appropriate analysis. We investigated phenotypic divergence, population-genetic structure and potential fitness trade-offs in populations of Daphnia melanica inhabiting neighbouring subalpine ponds of widely differing transparency to ultraviolet radiation (UVR). Using a combination of experimental, population-genetic and statistical techniques, we separated the effects of shared population ancestry and environmental variables in predicting phenotypic divergence among populations. We found that native water transparency significantly predicted divergence in phenotypes among populations even after accounting for significant population structure. This result demonstrates that environmental factors such as UVR can at least partially account for phenotypic divergence. However, a lack of evidence for a hypothesized trade-off between UVR tolerance and growth rates in the absence of UVR prevents us from ruling out the possibility that non-adaptive processes are partially responsible for phenotypic differentiation in this system. PMID:20943691

High genetic diversity and connectivity in Colossoma macropomum in the Amazon basin revealed by microsatellite markers.

PubMed

Fazzi-Gomes, Paola; Guerreiro, Sávio; Palheta, Glauber David Almeida; Melo, Nuno Filipe Alves Correa de; Santos, Sidney; Hamoy, Igor

2017-01-01

Colossoma macropomum is the second largest scaled fish of the Amazon. It is economically important for commercial fisheries and for aquaculture, but few studies have examined the diversity and genetic structure of natural populations of this species. The aim of this study was to investigate the levels of genetic variability and connectivity that exist between three natural populations of C. macropomum from the Amazon basin. In total, 247 samples were collected from the municipalities of Tefé, Manaus, and Santarém. The populations were genotyped using a panel of 12 multiplex microsatellite markers. The genetic diversity found in these populations was high and similar to other populations described in the literature. These populations showed a pattern of high gene flow associated with the lack of a genetic structure pattern, indicating that the number of migrants per generation and recent migration rates are high. The values of the FST, RST, and exact test of differentiation were not significant for pairwise comparisons between populations. The Bayesian population clustering analysis indicated a single population. Thus, the data provide evidence for high genetic diversity and high gene flow among C. macropomum populations in the investigated region of the Amazon basin. This information is important for programs aiming at the conservation of natural populations.

High genetic diversity and connectivity in Colossoma macropomum in the Amazon basin revealed by microsatellite markers

PubMed Central

Fazzi-Gomes, Paola; Guerreiro, Sávio; Palheta, Glauber David Almeida; de Melo, Nuno Filipe Alves Correa; Santos, Sidney; Hamoy, Igor

2017-01-01

Abstract Colossoma macropomum is the second largest scaled fish of the Amazon. It is economically important for commercial fisheries and for aquaculture, but few studies have examined the diversity and genetic structure of natural populations of this species. The aim of this study was to investigate the levels of genetic variability and connectivity that exist between three natural populations of C. macropomum from the Amazon basin. In total, 247 samples were collected from the municipalities of Tefé, Manaus, and Santarém. The populations were genotyped using a panel of 12 multiplex microsatellite markers. The genetic diversity found in these populations was high and similar to other populations described in the literature. These populations showed a pattern of high gene flow associated with the lack of a genetic structure pattern, indicating that the number of migrants per generation and recent migration rates are high. The values of the FST, RST, and exact test of differentiation were not significant for pairwise comparisons between populations. The Bayesian population clustering analysis indicated a single population. Thus, the data provide evidence for high genetic diversity and high gene flow among C. macropomum populations in the investigated region of the Amazon basin. This information is important for programs aiming at the conservation of natural populations. PMID:28170026

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.

Chinstrap penguin population genetic structure: one or more populations along the Southern Ocean?

PubMed

Mura-Jornet, Isidora; Pimentel, Carolina; Dantas, Gisele P M; Petry, Maria Virginia; González-Acuña, Daniel; Barbosa, Andrés; Lowther, Andrew D; Kovacs, Kit M; Poulin, Elie; Vianna, Juliana A

2018-06-13

Historical factors, demography, reproduction and dispersal are crucial in determining the genetic structure of seabirds. In the Antarctic marine environment, penguins are a major component of the avian biomass, dominant predators and important bioindicators of ecological change. Populations of chinstrap penguins have decreased in nearly all their breeding sites, and their range is expanding throughout the Antarctic Peninsula. Population genetic structure of this species has been studied in some colonies, but not between breeding colonies in the Antarctic Peninsula or at the species' easternmost breeding colony (Bouvetøya). Connectivity, sex-biased dispersal, diversity, genetic structure and demographic history were studied using 12 microsatellite loci and a mitochondrial DNA region (HVRI) in 12 breeding colonies in the South Shetland Islands (SSI) and the Western Antarctic Peninsula (WAP), and one previously unstudied sub-Antarctic island, 3600 km away from the WAP (Bouvetøya). High genetic diversity, evidence of female bias-dispersal and a sign of population expansion after the last glacial maximum around 10,000 mya were detected. Limited population genetic structure and lack of isolation by distance throughout the region were found, along with no differentiation between the WAP and Bouvetøya (overall microsatellite F ST  = 0.002, p = 0.273; mtDNA F ST  = - 0.004, p = 0.766), indicating long distance dispersal. Therefore, genetic assignment tests could not assign individuals to their population(s) of origin. The most differentiated location was Georges Point, one of the southernmost breeding colonies of this species in the WAP. The subtle differentiation found may be explained by some combination of low natal philopatric behavior, high rates of dispersal and/or generally high mobility among colonies of chinstrap penguins compared to other Pygoscelis species.

The Psychiatric Assessment Schedule for Adult with Developmental Disability (PAS-ADD) Checklist: Reliability and Validity of French Version

ERIC Educational Resources Information Center

Gerber, F.; Carminati, G. Galli

2013-01-01

Background: The lack of psychometric measures of psychopathology especially in intellectual disabilities (ID) population was addressed by creation of the Psychiatric Assessment Schedule for Adult with Developmental Disability (PAS-ADD-10) in Moss et?al. This schedule is a structured interview designed for professionals in psychopathology. The…

Exome genotyping, linkage disequilibrium and population structure in loblolly pine (Pinus taeda L.)

Treesearch

Mengmeng Lu; Konstantin V. Krutovsky; C. Dana Nelson; Tomasz E. Koralewski; Thomas D. Byram; Carol A. Loopstra

2016-01-01

Background: Loblolly pine (Pinus taeda L.) is one of the most widely planted and commercially important foresttree species in the USA and worldwide, and is an object of intense genomic research. However, whole genomeresequencing in loblolly pine is hampered by its large size and complexity and a lack of a good...

Using OER as a Tool for Agribusiness Management Training for Hard-to-Reach Rural Farmer Populations

ERIC Educational Resources Information Center

Muniafu, Maina; Wambalaba, Francis; Wanyama, Walter; Nduati, Gidraph; Ndirangu, Dalton

2013-01-01

Agriculture is the mainstay of Kenya's economy and contributes significantly to the gross domestic product. A great majority of this contribution comes from smallholder farmers who paradoxically face numerous obstacles ranging from a lack of support structures to poor policies and inadequate resources. A major challenge is assisting these farmers…

Lack of phonotactic preferences of female frogs and its consequences for signal evolution.

PubMed

Velásquez, Nelson A; Valdés, Jose Luis; Vásquez, Rodrigo A; Penna, Mario

2015-09-01

Sexual selection is one of the main evolutionary forces that drive signal evolution. In previous studies, we have found out that males of Pleurodema thaul, a frog with an extensive latitudinal distribution in Chile, emits advertisement calls that show remarkable variation among populations. In addition, this variation is related to intense inter-male acoustic competition (intra-sexual selection) occurring within each population. However, the extent to which female preferences contribute to the signal divergence observed is unclear. To study the responsiveness of females in each population, we stimulated females with synthetic calls designed with the acoustic structure of their own population and subsequently responsive females were subjected to a two-choice experiment, where they were stimulated with synthetic calls of their own population versus a call of a foreign population. Females do not show phonotactic preferences for calls of their own or foreign populations as measured with both linear and circular variables. The lack of phonotactic preferences suggests an absence of participation of inter-sexual selection processes in the divergence of the acoustic signals of P. thaul, highlighting the importance of intra-sexual selection for the evolution of these signals. These results concur with studies in other vertebrates emphasizing the relevance of interactions among males for the evolution of acoustic communication systems. Copyright © 2015. Published by Elsevier B.V.

Phylogeography and alpha taxonomy of the common dolphin (Delphinus sp.).

PubMed

Natoli, A; Cañadas, A; Peddemors, V M; Aguilar, A; Vaquero, C; Fernández-Piqueras, P; Hoelzel, A R

2006-05-01

The resolution of taxonomic classifications for delphinid cetaceans has been problematic, especially for species in the genera Delphinus, Tursiops and Stenella. The frequent lack of correspondence between morphological and genetic differentiation in these species raises questions about the mechanisms responsible for their evolution. In this study we focus on the genus Delphinus, and use molecular markers to address questions about speciation and the evolution of population structure. Delphinus species have a worldwide distribution and show a high degree of morphological variation. Two distinct morphotypes, long-beaked and short-beaked, have been considered different species named D. capensis and D. delphis, respectively. However, genetic differentiation between these two forms has only been demonstrated in the Pacific. We analysed samples from eight different geographical regions, including two morphologically defined long-beaked form populations, and compared these with the eastern North Pacific populations. We found high differentiation among the populations described as long-beaked instead of the expected monophyly, suggesting that these populations may have evolved from independent events converging on the same morphotype. We observed low genetic differentiation among the short-beaked populations across a large geographical scale. We interpret these phylogeographical patterns in the context of life history and population structure in related species.

Deep Integration: Letting the Epigenome Out of the Bottle Without Losing Sight of the Structural Origins of Population Health

PubMed Central

2013-01-01

Advances in stress physiology and molecular dynamics can illuminate population health inequality. The “weathering” hypothesis posits that socially structured, repeated stress process activation can accumulate and increase disease vulnerability across the life course in marginalized groups. The developmental origins of health and disease (DOHaD) hypothesis focuses on youthful programming for later life disease via epigenetic modifications to limiting uterine or early environments. Weathering and DOHaD are overlapping biopsychosocial models; yet, their emphases and implications vary. Evidence for the primacy of early development over experiences in young through middle adulthood for explaining population health inequality is lacking. By considering weathering and DOHaD together, we call for biomedical researchers to be more cautious in their claims about the social world and for a broader range of social researchers—including qualitative ones—to collaborate with them. PMID:23927509

Uncertainty, learning, and the optimal management of wildlife

USGS Publications Warehouse

Williams, B.K.

2001-01-01

Wildlife management is limited by uncontrolled and often unrecognized environmental variation, by limited capabilities to observe and control animal populations, and by a lack of understanding about the biological processes driving population dynamics. In this paper I describe a comprehensive framework for management that includes multiple models and likelihood values to account for structural uncertainty, along with stochastic factors to account for environmental variation, random sampling, and partial controllability. Adaptive optimization is developed in terms of the optimal control of incompletely understood populations, with the expected value of perfect information measuring the potential for improving control through learning. The framework for optimal adaptive control is generalized by including partial observability and non-adaptive, sample-based updating of model likelihoods. Passive adaptive management is derived as a special case of constrained adaptive optimization, representing a potentially efficient suboptimal alternative that nonetheless accounts for structural uncertainty.

Whole genome sequences are required to fully resolve the linkage disequilibrium structure of human populations.

PubMed

Pengelly, Reuben J; Tapper, William; Gibson, Jane; Knut, Marcin; Tearle, Rick; Collins, Andrew; Ennis, Sarah

2015-09-03

An understanding of linkage disequilibrium (LD) structures in the human genome underpins much of medical genetics and provides a basis for disease gene mapping and investigating biological mechanisms such as recombination and selection. Whole genome sequencing (WGS) provides the opportunity to determine LD structures at maximal resolution. We compare LD maps constructed from WGS data with LD maps produced from the array-based HapMap dataset, for representative European and African populations. WGS provides up to 5.7-fold greater SNP density than array-based data and achieves much greater resolution of LD structure, allowing for identification of up to 2.8-fold more regions of intense recombination. The absence of ascertainment bias in variant genotyping improves the population representativeness of the WGS maps, and highlights the extent of uncaptured variation using array genotyping methodologies. The complete capture of LD patterns using WGS allows for higher genome-wide association study (GWAS) power compared to array-based GWAS, with WGS also allowing for the analysis of rare variation. The impact of marker ascertainment issues in arrays has been greatest for Sub-Saharan African populations where larger sample sizes and substantially higher marker densities are required to fully resolve the LD structure. WGS provides the best possible resource for LD mapping due to the maximal marker density and lack of ascertainment bias. WGS LD maps provide a rich resource for medical and population genetics studies. The increasing availability of WGS data for large populations will allow for improved research utilising LD, such as GWAS and recombination biology studies.

Development of new microsatellite loci and multiplex reactions for muskellunge (Esox masquinongy)

USGS Publications Warehouse

Sloss, Brian L.; Franckowiak, R.P.; Murphy, E.L.

2008-01-01

The muskellunge (Esox masquinongy) is a valued fisheries species throughout its native range. Numerous studies have documented performance and phenotypic differences among muskellunge populations, but genetic markers for assessment have been lacking. We characterized 14 microsatellite loci and developed five multiplex polymerase chain reactions. Successful amplification of northern pike (Esox lucius) was observed for seven loci. These microsatellites will be useful for analysing population structure, performance characteristics of propagated strains, and helping to develop and monitor hatchery management guidelines for muskellunge. ?? 2008 Blackwell Publishing Ltd.

Genetic structure in the Anaxyrus boreas species group (anura, Bufonidae): an evaluation of the Southern Rocky Mountain population

USGS Publications Warehouse

Switzer, John F.; Johnson, Robin L.; Lubinski, Barbara A.; King, Tim L.

2009-01-01

The Anaxyrus boreas species group is comprised of four species endemic to the western United States: A. boreas, A. canorus, A. exsul, and A. nelsoni. Disjunct populations of the widespread western toad Anaxyrus boreas from Colorado and southern Wyoming, the southern rocky mountain population (SRMP), were previously candidates for listing under the United States Endangered Species Act (ESA) as a distinct population segment (DPS), but were removed due to a lack of significant genetic differentiation in preliminary studies. The purpose of this study was to conduct phylogeographic and population genetic analyses of A. boreas and three related species using mitochondrial DNA sequence data and nuclear microsatellite genotype data. The study is specifically focused on testing the evolutionary significance of the SRMP.

Climate Change and Genetic Structure of Leading Edge and Rear End Populations in a Northwards Shifting Marine Fish Species, the Corkwing Wrasse (Symphodus melops).

PubMed

Knutsen, Halvor; Jorde, Per Erik; Gonzalez, Enrique Blanco; Robalo, Joana; Albretsen, Jon; Almada, Vitor

2013-01-01

One mechanism by which marine organisms may respond to climate shifts is range shifts. The corkwing wrasse (Symphodus melops) is a temperate fish species, inhabiting the coasts of Europe, that show strong indications of current as well as historical (ice-age) range shifts towards the north. Nine neutral microsatellite DNA markers were screened to study genetic signatures and spatial population structure over the entire geographic and thermal gradient of the species from Portugal to Norway. A major genetic break (F ST  = 0.159 average among pairs) was identified between Scandinavian and more southern populations, with a marked reduction (30% or more) in levels of genetic variability in Scandinavia. The break is probably related to bottleneck(s) associated with post-glacial colonization of the Scandinavian coasts, and indicates a lack of present gene flow across the North Sea. The lack of gene flow can most likely be attributed to the species' need for rocky substrate for nesting and a relatively short pelagic larval phase, limiting dispersal by ocean currents. These findings demonstrate that long-distance dispersal may be severely limited in the corkwing wrasse, and that successful range-shifts following present climate change may be problematic for this and other species with limited dispersal abilities, even in the seemingly continuous marine environment.

The proportional lack of archaeal pathogens: Do viruses/phages hold the key?

PubMed Central

Gill, Erin E; Brinkman, Fiona S L

2011-01-01

Although Archaea inhabit the human body and possess some characteristics of pathogens, there is a notable lack of pathogenic archaeal species identified to date. We hypothesize that the scarcity of disease-causing Archaea is due, in part, to mutually-exclusive phage and virus populations infecting Bacteria and Archaea, coupled with an association of bacterial virulence factors with phages or mobile elements. The ability of bacterial phages to infect Bacteria and then use them as a vehicle to infect eukaryotes may be difficult for archaeal viruses to evolve independently. Differences in extracellular structures between Bacteria and Archaea would make adsorption of bacterial phage particles onto Archaea (i.e. horizontal transfer of virulence) exceedingly hard. If phage and virus populations are indeed exclusive to their respective host Domains, this has important implications for both the evolution of pathogens and approaches to infectious disease control. PMID:21328413

The challenge of Parkinson's disease management in Africa.

PubMed

Dotchin, C L; Msuya, O; Walker, R W

2007-03-01

Parkinson's disease (PD) is said to be less common in Africa than elsewhere in the world, but previous studies have been based on small numbers. Also, the differences may be due to the diagnostic criteria used, case finding methods and different population age structures. Developing countries have few facilities for chronic disease management and non-communicable diseases, although on the increase, tend to play second fiddle to malaria and HIV/AIDS. Previous reports suggest that, at least from anecdotal information, under-diagnosis of PD is common and long-term availability of medication, follow-up, patient education and multidisciplinary input is lacking. Published literature is scarce and there is a lack of recent information. We are currently conducting a door-to-door prevalence study in northern Tanzania in a population of 161,162. We have reviewed previous literature on PD in Africa and illustrate our personal experience of PD and its management in Africa with three cases.

Tripartite Governance: Enabling Successful Implementations with Vulnerable Populations.

PubMed

Kennedy, Margaret Ann

2016-01-01

Vulnerable populations are often at a distinct disadvantage when it comes to the implementation of health information systems in an equitable, appropriate, and timely manner. The disadvantages experienced by vulnerable populations are innumerable and include lack of representation, lack of appropriate levels of funding, lack of resources and capacity, and lack of representation. Increasingly, models of representation for complex implementations involve a tripartite project governance model. This tripartite partnership distributes accountability across all partners, and ensures that vulnerable populations have an equitable contribution to the direction of implementation according to their needs. This article shares lessons learned and best practices from complex tripartite partnerships supporting implementations with vulnerable populations in Canada.

The role of river drainages in shaping the genetic structure of capybara populations.

PubMed

Byrne, María Soledad; Quintana, Rubén Darío; Bolkovic, María Luisa; Cassini, Marcelo H; Túnez, Juan Ignacio

2015-12-01

The capybara, Hydrochoerus hydrochaeris, is an herbivorous rodent widely distributed throughout most of South American wetlands that lives closely associated with aquatic environments. In this work, we studied the genetic structure of the capybara throughout part of its geographic range in Argentina using a DNA fragment of the mitochondrial control region. Haplotypes obtained were compared with those available for populations from Paraguay and Venezuela. We found 22 haplotypes in 303 individuals. Hierarchical AMOVAs were performed to evaluate the role of river drainages in shaping the genetic structure of capybara populations at the regional and basin scales. In addition, two landscape genetic models, isolation by distance and isolation by resistance, were used to test whether genetic distance was associated with Euclidean distance (i.e. isolation by distance) or river corridor distance (i.e. isolation by resistance) at the basin scale. At the regional scale, the results of the AMOVA grouping populations by mayor river basins showed significant differences between them. At the basin scale, we also found significant differences between sub-basins in Paraguay, together with a significant correlation between genetic and river corridor distance. For Argentina and Venezuela, results were not significant. These results suggest that in Paraguay, the current genetic structure of capybaras is associated with the lack of dispersion corridors through permanent rivers. In contrast, limited structuring in Argentina and Venezuela is likely the result of periodic flooding facilitating dispersion.

Evolutionary Games of Multiplayer Cooperation on Graphs

PubMed Central

Arranz, Jordi; Traulsen, Arne

2016-01-01

There has been much interest in studying evolutionary games in structured populations, often modeled as graphs. However, most analytical results so far have only been obtained for two-player or linear games, while the study of more complex multiplayer games has been usually tackled by computer simulations. Here we investigate evolutionary multiplayer games on graphs updated with a Moran death-Birth process. For cycles, we obtain an exact analytical condition for cooperation to be favored by natural selection, given in terms of the payoffs of the game and a set of structure coefficients. For regular graphs of degree three and larger, we estimate this condition using a combination of pair approximation and diffusion approximation. For a large class of cooperation games, our approximations suggest that graph-structured populations are stronger promoters of cooperation than populations lacking spatial structure. Computer simulations validate our analytical approximations for random regular graphs and cycles, but show systematic differences for graphs with many loops such as lattices. In particular, our simulation results show that these kinds of graphs can even lead to more stringent conditions for the evolution of cooperation than well-mixed populations. Overall, we provide evidence suggesting that the complexity arising from many-player interactions and spatial structure can be captured by pair approximation in the case of random graphs, but that it need to be handled with care for graphs with high clustering. PMID:27513946

Population structure and genetic diversity of the parasite Trichomonas vaginalis in Bristol, UK.

PubMed

Hawksworth, Joseph; Levy, Max; Smale, Chloe; Cheung, Dean; Whittle, Alice; Longhurst, Denise; Muir, Peter; Gibson, Wendy

2015-08-01

The protozoan parasite Trichomonas vaginalis is the causative agent of trichomoniasis, an extremely common, but non-life-threatening, sexually-transmitted disease throughout the world. Recent population genetics studies of T. vaginalis have detected high genetic diversity and revealed a two-type population structure, associated with phenotypic differences in sensitivity to metronidazole, the drug commonly used for treatment, and presence of T. vaginalis virus. There is currently a lack of data on UK isolates; most isolates examined to date are from the US. Here we used a recently described system for multilocus sequence typing (MLST) of T. vaginalis to study diversity of clinical isolates from Bristol, UK. We used MLST to characterise 23 clinical isolates of T. vaginalis collected from female patients during 2013. Seven housekeeping genes were PCR-amplified for each isolate and sequenced. The concatenated sequences were then compared with data from other MLST-characterised isolates available from http://tvaginalis.mlst.net/ to analyse the population structure and construct phylogenetic trees. Among the 23 isolates from the Bristol population of T. vaginalis, we found 23 polymorphic nucleotide sites, 25 different alleles and 19 sequence types (genotypes). Most isolates had a unique genotype, in agreement with the high levels of heterogeneity observed elsewhere in the world. A two-type population structure was evident from population genetic analysis and phylogenetic reconstruction split the isolates into two major clades. Tests for recombination in the Bristol population of T. vaginalis gave conflicting results, suggesting overall a clonal pattern of reproduction. We conclude that the Bristol population of T. vaginalis parasites conforms to the two-type population structure found in most other regions of the world. We found the MLST scheme to be an efficient genotyping method. The online MLST database provides a useful repository and resource that will prove invaluable in future studies linking the genetics of T. vaginalis with the clinical manifestation of trichomoniasis. Copyright © 2015 Elsevier B.V. All rights reserved.

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.

Genetic variability within and among populations of an invasive, exotic orchid

PubMed Central

Ueno, Sueme; Rodrigues, Jucelene Fernandes; Alves-Pereira, Alessandro; Pansarin, Emerson Ricardo; Veasey, Elizabeth Ann

2015-01-01

Despite the fact that invasive species are of great evolutionary interest because of their success in colonizing and spreading into new areas, the factors underlying this success often remain obscure. In this sense, studies on population genetics and phylogenetic relationships of invasive species could offer insights into mechanisms of invasions. Originally from Africa, the terrestrial orchid Oeceoclades maculata, considered an invasive plant, is the only species of the genus throughout the Americas. Considering the lack of information on population genetics of this species, the aim of this study was to evaluate the genetic diversity and structure of Brazilian populations of O. maculata. We used 13 inter-simple sequence repeat primers to assess the genetic diversity of 152 individuals of O. maculata distributed in five sampled sites from three Brazilian states (São Paulo, Mato Grosso and Paraná). Low diversity was found within samples, with estimates of the Shannon index (H) ranging from 0.0094 to 0.1054 and estimates of Nei's gene diversity (He) ranging from 0.0054 to 0.0668. However, when evaluated together, the sampling locations showed substantially higher diversity estimates (H = 0.3869, He = 0.2556), and most of the genetic diversity was found among populations (ΦST = 0.933). Both clustering and principal coordinate analysis indicate the existence of five distinct groups, corresponding to the sampled localities, and which were also recovered in the Bayesian analysis. A substructure was observed in one of the localities, suggesting a lack of gene flow even between very small distances. The patterns of genetic structure found in this study may be understood considering the interaction of several probable reproductive strategies with its history of colonization involving possible genetic drift, selective pressures and multiple introductions. PMID:26162896

Crossing lines: a multidisciplinary framework for assessing connectivity of hammerhead sharks across jurisdictional boundaries

NASA Astrophysics Data System (ADS)

Chin, A.; Simpfendorfer, C. A.; White, W. T.; Johnson, G. J.; McAuley, R. B.; Heupel, M. R.

2017-04-01

Conservation and management of migratory species can be complex and challenging. International agreements such as the Convention on Migratory Species (CMS) provide policy frameworks, but assessments and management can be hampered by lack of data and tractable mechanisms to integrate disparate datasets. An assessment of scalloped (Sphyrna lewini) and great (Sphyrna mokarran) hammerhead population structure and connectivity across northern Australia, Indonesia and Papua New Guinea (PNG) was conducted to inform management responses to CMS and Convention on International Trade in Endangered Species listings of these species. An Integrated Assessment Framework (IAF) was devised to systematically incorporate data across jurisdictions and create a regional synopsis, and amalgamated a suite of data from the Australasian region. Scalloped hammerhead populations are segregated by sex and size, with Australian populations dominated by juveniles and small adult males, while Indonesian and PNG populations included large adult females. The IAF process introduced genetic and tagging data to produce conceptual models of stock structure and movement. Several hypotheses were produced to explain stock structure and movement patterns, but more data are needed to identify the most likely hypothesis. This study demonstrates a process for assessing migratory species connectivity and highlights priority areas for hammerhead management and research.

Crossing lines: a multidisciplinary framework for assessing connectivity of hammerhead sharks across jurisdictional boundaries.

PubMed

Chin, A; Simpfendorfer, C A; White, W T; Johnson, G J; McAuley, R B; Heupel, M R

2017-04-21

Conservation and management of migratory species can be complex and challenging. International agreements such as the Convention on Migratory Species (CMS) provide policy frameworks, but assessments and management can be hampered by lack of data and tractable mechanisms to integrate disparate datasets. An assessment of scalloped (Sphyrna lewini) and great (Sphyrna mokarran) hammerhead population structure and connectivity across northern Australia, Indonesia and Papua New Guinea (PNG) was conducted to inform management responses to CMS and Convention on International Trade in Endangered Species listings of these species. An Integrated Assessment Framework (IAF) was devised to systematically incorporate data across jurisdictions and create a regional synopsis, and amalgamated a suite of data from the Australasian region. Scalloped hammerhead populations are segregated by sex and size, with Australian populations dominated by juveniles and small adult males, while Indonesian and PNG populations included large adult females. The IAF process introduced genetic and tagging data to produce conceptual models of stock structure and movement. Several hypotheses were produced to explain stock structure and movement patterns, but more data are needed to identify the most likely hypothesis. This study demonstrates a process for assessing migratory species connectivity and highlights priority areas for hammerhead management and research.

Efficient Analysis of Systems Biology Markup Language Models of Cellular Populations Using Arrays.

PubMed

Watanabe, Leandro; Myers, Chris J

2016-08-19

The Systems Biology Markup Language (SBML) has been widely used for modeling biological systems. Although SBML has been successful in representing a wide variety of biochemical models, the core standard lacks the structure for representing large complex regular systems in a standard way, such as whole-cell and cellular population models. These models require a large number of variables to represent certain aspects of these types of models, such as the chromosome in the whole-cell model and the many identical cell models in a cellular population. While SBML core is not designed to handle these types of models efficiently, the proposed SBML arrays package can represent such regular structures more easily. However, in order to take full advantage of the package, analysis needs to be aware of the arrays structure. When expanding the array constructs within a model, some of the advantages of using arrays are lost. This paper describes a more efficient way to simulate arrayed models. To illustrate the proposed method, this paper uses a population of repressilator and genetic toggle switch circuits as examples. Results show that there are memory benefits using this approach with a modest cost in runtime.

Genetic relationships among American donkey populations: insights into the process of colonization.

PubMed

Jordana, J; Ferrando, A; Miró, J; Goyache, F; Loarca, A; Martínez López, O R; Canelón, J L; Stemmer, A; Aguirre, L; Lara, M A C; Álvarez, L A; Llambí, S; Gómez, N; Gama, L T; Nóvoa, M F; Martínez, R D; Pérez, E; Sierra, A; Contreras, M A; Guastella, A M; Marletta, D; Arsenos, G; Curik, I; Landi, V; Martínez, A; Delgado, J V

2016-04-01

This study presents the first insights into the genetic diversity and structure of the American donkey metapopulation. The primary objectives were to detect the main structural features underlying variability among American donkey populations, identify boundaries between differentiated gene pools, and draw the main colonization pathways since the introduction of donkeys into America in the 15th century. A panel of 14 microsatellite markers was applied for genotyping 350 American donkeys from 13 countries. The genetic structure of this metapopulation was analysed using descriptive statistics and Bayesian model-based methods. These populations were then compared to a database containing information on 476 individuals from 11 European breeds to identify the most likely ancestral donor populations. Results showed the presence of two distinct genetic pools, with confluence of the two in Colombia. The southern pool showed a unique genetic signature subsequent to an older founder event, but lacked any significant influence of modern gene flow from Europe. The northern pool, conversely, may have retained more ancestral polymorphisms and/or have experienced modern gene flow from Spanish breeds. The Andalusian and, to a lesser extent, the Catalan breeds have left a more pronounced footprint in some of the American donkey populations analysed. © 2015 Blackwell Verlag GmbH.

DISCUSSION OF PLANNING AND IMPLEMENTATION OF GOVERNMENT AND PRIVATE AGENCY PROGRAMS IN NORTHERN NEW MEXICO.

ERIC Educational Resources Information Center

KNOWLTON, CLARK S.

THE MEXICAN AMERICAN POPULATION IN NORTHERN NEW MEXICO ORIGINALLY HAD LAND GRANTS FROM THE SPANISH CROWN. LACK OF UNDERSTANDING OR ACCEPTANCE OF THE AMERICAN SYSTEM OF INDIVIDUAL OWNERSHIP HAS CAUSED THE MEXICAN AMERICAN TO LOSE MUCH OF THE ORIGINAL GRANT LANDS. THE MEXICAN AMERICAN SOCIAL ORGANIZATION, ORIGINALLY STRUCTURED UPON THE FARM VILLAGE,…

Genetic Evaluation of Natural Populations of the Endangered Conifer Thuja koraiensis Using Microsatellite Markers by Restriction-Associated DNA Sequencing

PubMed Central

Hou, Lu; Cui, Yanhong; Li, Xiang; Chen, Wu; Zhang, Zhiyong; Pang, Xiaoming; Li, Yingyue

2018-01-01

Thuja koraiensis Nakai is an endangered conifer of high economic and ecological value in Jilin Province, China. However, studies on its population structure and conservation genetics have been limited by the lack of genomic data. Here, 37,761 microsatellites (simple sequence repeat, SSR) were detected based on 875,792 de novo-assembled contigs using a restriction-associated DNA (RAD) approach. Among these SSRs, 300 were randomly selected to test for polymorphisms and 96 obtained loci were able to amplify a fragment of expected size. Twelve polymorphic SSR markers were developed to analyze the genetic diversity and population structure of three natural populations. High genetic diversity (mean NA = 5.481, HE = 0.548) and moderate population differentiation (pairwise Fst = 0.048–0.078, Nm = 2.940–4.958) were found in this species. Molecular variance analysis suggested that most of the variation (83%) existed within populations. Combining the results of STRUCTURE, principal coordinate, and neighbor-joining analysis, the 232 individuals were divided into three genetic clusters that generally correlated with their geographical distributions. Finally, appropriate conservation strategies were proposed to protect this species. This study provides genetic information for the natural resource conservation and utilization of T. koraiensis and will facilitate further studies of the evolution and phylogeography of the species. PMID:29673217

Population structure of elephant foot yams (Amorphophallus paeoniifolius (Dennst.) Nicolson) in Asia

PubMed Central

Misra, Raj Shekhar; Boonkorkaew, Patchareeya; Thanomchit, Kanokwan

2017-01-01

The corms and leaves of elephant foot yams (Amorphophallus paeoniifolius (Dennst.) Nicolson) are important foods in the local diet in many Asian regions. The crop has high productivity and wide agroecological adaptation and exhibits suitability for the agroforestry system. Although the plant is assumed to reproduce via panmixia, a comprehensive study on the genetic background across regions to enhance wider consumer palatability is still lacking. Here, ten informative microsatellites were analyzed in 29 populations across regions in India, Indonesia and Thailand to understand the genetic diversity, population structure and distribution to improve breeding and conservation programs. The genetic diversity was high among and within regions. Some populations exhibited excess heterozygosity and bottlenecking. Pairwise FST indicated very high genetic differentiation across regions (FST = 0.274), and the Asian population was unlikely to be panmictic. Phylogenetic tree construction grouped the populations according to country of origin with the exception of the Medan population from Indonesia. The current gene flow was apparent within the regions but was restricted among the regions. The present study revealed that Indonesia and Thailand populations could be alternative centers of the gene pool, together with India. Consequently, regional action should be incorporated in genetic conservation and breeding efforts to develop new varieties with global acceptance. PMID:28658282

Unequal contribution of native South African phylogeographic lineages to the invasion of the African clawed frog, Xenopus laevis, in Europe

PubMed Central

Courant, Julien; Herrel, Anthony; Rebelo, Rui; Rödder, Dennis; Measey, G. John; Backeljau, Thierry

2016-01-01

Due to both deliberate and accidental introductions, invasive African Clawed Frog (Xenopus laevis) populations have become established worldwide. In this study, we investigate the geographic origins of invasive X. laevis populations in France and Portugal using the phylogeographic structure of X. laevis in its native South African range. In total, 80 individuals from the whole area known to be invaded in France and Portugal were analysed for two mitochondrial and three nuclear genes, allowing a comparison with 185 specimens from the native range. Our results show that native phylogeographic lineages have contributed differently to invasive European X. laevis populations. In Portugal, genetic and historical data suggest a single colonization event involving a small number of individuals from the south-western Cape region in South Africa. In contrast, French invasive X. laevis encompass two distinct native phylogeographic lineages, i.e., one from the south-western Cape region and one from the northern regions of South Africa. The French X. laevis population is the first example of a X. laevis invasion involving multiple lineages. Moreover, the lack of population structure based on nuclear DNA suggests a potential role for admixture within the invasive French population. PMID:26855879

Paternal phylogeographic structure of the brown bear (Ursus arctos) in northeastern Asia and the effect of male-mediated gene flow to insular populations.

PubMed

Hirata, Daisuke; Mano, Tsutomu; Abramov, Alexei V; Baryshnikov, Gennady F; Kosintsev, Pavel A; Murata, Koichi; Masuda, Ryuichi

2017-01-01

Sex-biased dispersal is widespread among mammals, including the brown bear ( Ursus arctos ). Previous phylogeographic studies of the brown bear based on maternally inherited mitochondrial DNA have shown intraspecific genetic structuring around the northern hemisphere. The brown bears on Hokkaido Island, northern Japan, comprise three distinct maternal lineages that presumably immigrated to the island from the continent in three different periods. Here, we investigate the paternal genetic structure across northeastern Asia and assess the connectivity among and within intraspecific populations in terms of male-mediated gene flow. We analyzed paternally inherited Y-chromosomal DNA sequence data and Y-linked microsatellite data of 124 brown bears from Hokkaido, the southern Kuril Islands (Kunashiri and Etorofu), Sakhalin, and continental Eurasia (Kamchatka Peninsula, Ural Mountains, European Russia, and Tibet). The Hokkaido brown bear population is paternally differentiated from, and lacked recent genetic connectivity with, the continental Eurasian and North American populations. We detected weak spatial genetic structuring of the paternal lineages on Hokkaido, which may have arisen through male-mediated gene flow among natal populations. In addition, our results suggest that the different dispersal patterns between male and female brown bears, combined with the founder effect and subsequent genetic drift, contributed to the makeup of the Etorofu Island population, in which the maternal and paternal lineages show different origins. Brown bears on Hokkaido and the adjacent southern Kuril Islands experienced different maternal and paternal evolutionary histories. Our results indicate that sex-biased dispersal has played a significant role in the evolutionary history of the brown bear in continental populations and in peripheral insular populations, such as on Hokkaido, the southern Kuril Islands, and Sakhalin.

Long-Range Dispersal and High-Latitude Environments Influence the Population Structure of a “Stress-Tolerant” Dinoflagellate Endosymbiont

PubMed Central

Pettay, D. Tye; LaJeunesse, Todd C.

2013-01-01

The migration and dispersal of stress-tolerant symbiotic dinoflagellates (genus Symbiodinium) may influence the response of symbiotic reef-building corals to a warming climate. We analyzed the genetic structure of the stress-tolerant endosymbiont, Symbiodinium glynni nomen nudum (ITS2 - D1), obtained from Pocillopora colonies that dominate eastern Pacific coral communities. Eleven microsatellite loci identified genotypically diverse populations with minimal genetic subdivision throughout the Eastern Tropical Pacific, encompassing 1000’s of square kilometers from mainland Mexico to the Galapagos Islands. The lack of population differentiation over these distances corresponds with extensive regional host connectivity and indicates that Pocillopora larvae, which maternally inherit their symbionts, aid in the dispersal of this symbiont. In contrast to its host, however, subtropical populations of S. glynni in the Gulf of California (Sea of Cortez) were strongly differentiated from populations in tropical eastern Pacific. Selection pressures related to large seasonal fluctuations in temperature and irradiance likely explain this abrupt genetic discontinuity. We infer that S. glynni genotypes harbored by host larvae arriving from more southern locations are rapidly replaced by genotypes adapted to more temperate environments. The strong population structure of S. glynni corresponds with fluctuating environmental conditions and suggests that these genetically diverse populations have the potential to evolve rapidly to changing environments and reveals the importance of environmental extremes in driving microbial eukaryote (e.g., plankton) speciation in marine ecosystems. PMID:24223906

Clonality, genetic diversity and support for the diversifying selection hypothesis in natural populations of a flower-living yeast.

PubMed

Herrera, C M; Pozo, M I; Bazaga, P

2011-11-01

Vast amounts of effort have been devoted to investigate patterns of genetic diversity and structuring in plants and animals, but similar information is scarce for organisms of other kingdoms. The study of the genetic structure of natural populations of wild yeasts can provide insights into the ecological and genetic correlates of clonality, and into the generality of recent hypotheses postulating that microbial populations lack the potential for genetic divergence and allopatric speciation. Ninety-one isolates of the flower-living yeast Metschnikowia gruessii from southeastern Spain were DNA fingerprinted using amplified fragment length polymorphism (AFLP) markers. Genetic diversity and structuring was investigated with band-based methods and model- and nonmodel-based clustering. Linkage disequilibrium tests were used to assess reproduction mode. Microsite-dependent, diversifying selection was tested by comparing genetic characteristics of isolates from bumble bee vectors and different floral microsites. AFLP polymorphism (91%) and genotypic diversity were very high. Genetic diversity was spatially structured, as shown by amova (Φ(st)  = 0.155) and clustering. The null hypothesis of random mating was rejected, clonality seeming the prevailing reproductive mode in the populations studied. Genetic diversity of isolates declined from bumble bee mouthparts to floral microsites, and frequency of five AFLP markers varied significantly across floral microsites, thus supporting the hypothesis of diversifying selection on clonal lineages. Wild populations of clonal fungal microbes can exhibit levels of genetic diversity and spatial structuring that are not singularly different from those shown by sexually reproducing plants or animals. Microsite-dependent, divergent selection can maintain high local and regional genetic diversity in microbial populations despite extensive clonality. © 2011 Blackwell Publishing Ltd.

Persistency of accuracy of genomic breeding values for different simulated pig breeding programs in developing countries.

PubMed

Akanno, E C; Schenkel, F S; Sargolzaei, M; Friendship, R M; Robinson, J A B

2014-10-01

Genetic improvement of pigs in tropical developing countries has focused on imported exotic populations which have been subjected to intensive selection with attendant high population-wide linkage disequilibrium (LD). Presently, indigenous pig population with limited selection and low LD are being considered for improvement. Given that the infrastructure for genetic improvement using the conventional BLUP selection methods are lacking, a genome-wide selection (GS) program was proposed for developing countries. A simulation study was conducted to evaluate the option of using 60 K SNP panel and observed amount of LD in the exotic and indigenous pig populations. Several scenarios were evaluated including different size and structure of training and validation populations, different selection methods and long-term accuracy of GS in different population/breeding structures and traits. The training set included previously selected exotic population, unselected indigenous population and their crossbreds. Traits studied included number born alive (NBA), average daily gain (ADG) and back fat thickness (BFT). The ridge regression method was used to train the prediction model. The results showed that accuracies of genomic breeding values (GBVs) in the range of 0.30 (NBA) to 0.86 (BFT) in the validation population are expected if high density marker panels are utilized. The GS method improved accuracy of breeding values better than pedigree-based approach for traits with low heritability and in young animals with no performance data. Crossbred training population performed better than purebreds when validation was in populations with similar or a different structure as in the training set. Genome-wide selection holds promise for genetic improvement of pigs in the tropics. © 2014 Blackwell Verlag GmbH.

Extensive genetic diversity, unique population structure and evidence of genetic exchange in the sexually transmitted parasite Trichomonas vaginalis.

PubMed

Conrad, Melissa D; Gorman, Andrew W; Schillinger, Julia A; Fiori, Pier Luigi; Arroyo, Rossana; Malla, Nancy; Dubey, Mohan Lal; Gonzalez, Jorge; Blank, Susan; Secor, William E; Carlton, Jane M

2012-01-01

Trichomonas vaginalis is the causative agent of human trichomoniasis, the most common non-viral sexually transmitted infection world-wide. Despite its prevalence, little is known about the genetic diversity and population structure of this haploid parasite due to the lack of appropriate tools. The development of a panel of microsatellite makers and SNPs from mining the parasite's genome sequence has paved the way to a global analysis of the genetic structure of the pathogen and association with clinical phenotypes. Here we utilize a panel of T. vaginalis-specific genetic markers to genotype 235 isolates from Mexico, Chile, India, Australia, Papua New Guinea, Italy, Africa and the United States, including 19 clinical isolates recently collected from 270 women attending New York City sexually transmitted disease clinics. Using population genetic analysis, we show that T. vaginalis is a genetically diverse parasite with a unique population structure consisting of two types present in equal proportions world-wide. Parasites belonging to the two types (type 1 and type 2) differ significantly in the rate at which they harbor the T. vaginalis virus, a dsRNA virus implicated in parasite pathogenesis, and in their sensitivity to the widely-used drug, metronidazole. We also uncover evidence of genetic exchange, indicating a sexual life-cycle of the parasite despite an absence of morphologically-distinct sexual stages. Our study represents the first robust and comprehensive evaluation of global T. vaginalis genetic diversity and population structure. Our identification of a unique two-type structure, and the clinically relevant phenotypes associated with them, provides a new dimension for understanding T. vaginalis pathogenesis. In addition, our demonstration of the possibility of genetic exchange in the parasite has important implications for genetic research and control of the disease.

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.

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

Mitochondrial phylogeography and subspecific variation in the red panda (Ailurus fulgens): implications for conservation.

PubMed

Li, Ming; Wei, Fuwen; Goossens, Benoît; Feng, Zuojian; Tamate, Hidetoshi B; Bruford, Michael W; Funk, Stephan M

2005-07-01

The red panda (Ailurus fulgens) is an endangered species and its present distribution is restricted to isolated mountain ranges in western China (Sichuan, Yunnan, and Tibet provinces) and the Himalayan Mountains chain of Nepal, India, Bhutan, and Burma. To examine the evolutionary history across its current range, and to assess the genetic divergence among current subspecies and population structure among different geographic locations, we sequenced mitochondrial DNA from the control region (CR) and cytochrome (cyt) b gene for 41 individuals in Sichuan, Yunnan, Tibet of China, and Burma. 25 CR haplotypes (10 for cyt b) were identified from 11 geographic locations. Only three haplotypes were shared among sample localities, including one among current subspecies. Nine haplotypes were shared with the study of Su et al. [Mol. Biol. Evol. 18 (2001) 1070]. CR haplotype diversity was high (0.95+/-0.02) and nucleotide diversity among all haplotypes was relatively low (0.018+/-0.009). Phylogenetic confirmed trees show a shallow pattern with very little structure or statistical robustness. The application of two coalescent-based tests for population growth allowed us to interpret this phylogeny as the result of a recent population expansion. Analysis of molecular variance and nested clade analysis failed to detect significant geographic structure in both data sets. The lack of significant differentiation between subspecies does not indicate the presence of evolutionary significant units. We suggest that the present population structure has resulted from habitat fragmentation and expansion from glacial refugia. Due to its habitat requirements it is likely that the red panda has undergone bottlenecks and population expansions several times in the recent past. The present population may exhibit a pattern reminiscent of a relatively recent population expansion.

Pitfalls in Health Communication: Healthcare Policy, Institution, Structure, & Process

PubMed Central

Calderón, José L; Beltrán, Robert A

2004-01-01

The state of health communication for a given population is a function of several tiers of structure and process: government policy, healthcare directives, healthcare structure and process, and the ethnosocial realities of a multicultural society. Common yet specific to these tiers of health communication is the interpersonal and intergroup use of language in all its forms. Language is the most common behavior exhibited by humankind. Its use at all tiers determines quality of healthcare and quality of life for healthcare consumers: patients and their families. Of note, at the consumer end, mounting evidence demonstrates that barriers to health communication contribute to poorer access to care, quality of care, and health outcomes. The lack of comprehensible and usable written and spoken language is a major barrier to health communication targeting primary and secondary disease prevention and is a major contributor to the misuse of healthcare, patient noncompliance, rising healthcare costs. In this paper, we cursorily examine the relationship among government policy, institutional directives, and healthcare structure and process and its influence on the public health, especially vulnerable populations. We conclude that limited health communication in the context of changing healthcare environments and diverse populations is an important underpinning of rising healthcare costs and sustained health disparities. More research is needed to improve communication about health at all tiers and to develop health communication interventions that are usable by all population groups. PMID:15208522

Challenges to assessing connectivity between massive populations of the Australian plague locust

PubMed Central

Chapuis, Marie-Pierre; Popple, Julie-Anne M.; Berthier, Karine; Simpson, Stephen J.; Deveson, Edward; Spurgin, Peter; Steinbauer, Martin J.; Sword, Gregory A.

2011-01-01

Linking demographic and genetic dispersal measures is of fundamental importance for movement ecology and evolution. However, such integration can be difficult, particularly for highly fecund species that are often the target of management decisions guided by an understanding of population movement. Here, we present an example of how the influence of large population sizes can preclude genetic approaches from assessing demographic population structuring, even at a continental scale. The Australian plague locust, Chortoicetes terminifera, is a significant pest, with populations on the eastern and western sides of Australia having been monitored and managed independently to date. We used microsatellites to assess genetic variation in 12 C. terminifera population samples separated by up to 3000 km. Traditional summary statistics indicated high levels of genetic diversity and a surprising lack of population structure across the entire range. An approximate Bayesian computation treatment indicated that levels of genetic diversity in C. terminifera corresponded to effective population sizes conservatively composed of tens of thousands to several million individuals. We used these estimates and computer simulations to estimate the minimum rate of dispersal, m, that could account for the observed range-wide genetic homogeneity. The rate of dispersal between both sides of the Australian continent could be several orders of magnitude lower than that typically considered as required for the demographic connectivity of populations. PMID:21389030

Sexual networks: measuring sexual selection in structured, polyandrous populations.

PubMed

McDonald, Grant C; James, Richard; Krause, Jens; Pizzari, Tommaso

2013-03-05

Sexual selection is traditionally measured at the population level, assuming that populations lack structure. However, increasing evidence undermines this approach, indicating that intrasexual competition in natural populations often displays complex patterns of spatial and temporal structure. This complexity is due in part to the degree and mechanisms of polyandry within a population, which can influence the intensity and scale of both pre- and post-copulatory sexual competition. Attempts to measure selection at the local and global scale have been made through multi-level selection approaches. However, definitions of local scale are often based on physical proximity, providing a rather coarse measure of local competition, particularly in polyandrous populations where the local scale of pre- and post-copulatory competition may differ drastically from each other. These limitations can be solved by social network analysis, which allows us to define a unique sexual environment for each member of a population: 'local scale' competition, therefore, becomes an emergent property of a sexual network. Here, we first propose a novel quantitative approach to measure pre- and post-copulatory sexual selection, which integrates multi-level selection with information on local scale competition derived as an emergent property of networks of sexual interactions. We then use simple simulations to illustrate the ways in which polyandry can impact estimates of sexual selection. We show that for intermediate levels of polyandry, the proposed network-based approach provides substantially more accurate measures of sexual selection than the more traditional population-level approach. We argue that the increasing availability of fine-grained behavioural datasets provides exciting new opportunities to develop network approaches to study sexual selection in complex societies.

Genetic diversity in Oryza glumaepatula wild rice populations in Costa Rica and possible gene flow from O. sativa.

PubMed

Fuchs, Eric J; Meneses Martínez, Allan; Calvo, Amanda; Muñoz, Melania; Arrieta-Espinoza, Griselda

2016-01-01

Wild crop relatives are an important source of genetic diversity for crop improvement. Diversity estimates are generally lacking for many wild crop relatives. The objective of the present study was to analyze how genetic diversity is distributed within and among populations of the wild rice species Oryza glumaepatula in Costa Rica. We also evaluated the likelihood of gene flow between wild and commercial rice species because the latter is commonly sympatric with wild rice populations. Introgression may change wild species by incorporating alleles from domesticated species, increasing the risk of losing original variation. Specimens from all known O. glumaepatula populations in Costa Rica were analyzed with 444 AFLP markers to characterize genetic diversity and structure. We also compared genetic diversity estimates between O. glumaepatula specimens and O. sativa commercial rice. Our results showed that O. glumaepatula populations in Costa Rica have moderately high levels of genetic diversity, comparable to those found in South American populations. Despite the restricted distribution of this species in Costa Rica, populations are fairly large, reducing the effects of drift on genetic diversity. We found a dismissible but significant structure (θ = 0.02 ± 0.001) among populations. A Bayesian structure analysis suggested that some individuals share a significant proportion of their genomes with O. sativa. These results suggest that gene flow from cultivated O. sativa populations may have occurred in the recent past. These results expose an important biohazard: recurrent hybridization may reduce the genetic diversity of this wild rice species. Introgression may transfer commercial traits into O. glumaepatula, which in turn could alter genetic diversity and increase the likelihood of local extinction. These results have important implications for in situ conservation strategies of the only wild populations of O. glumaepatula in Costa Rica.

Genetic diversity in Oryza glumaepatula wild rice populations in Costa Rica and possible gene flow from O. sativa

PubMed Central

Meneses Martínez, Allan; Calvo, Amanda; Muñoz, Melania

2016-01-01

Wild crop relatives are an important source of genetic diversity for crop improvement. Diversity estimates are generally lacking for many wild crop relatives. The objective of the present study was to analyze how genetic diversity is distributed within and among populations of the wild rice species Oryza glumaepatula in Costa Rica. We also evaluated the likelihood of gene flow between wild and commercial rice species because the latter is commonly sympatric with wild rice populations. Introgression may change wild species by incorporating alleles from domesticated species, increasing the risk of losing original variation. Specimens from all known O. glumaepatula populations in Costa Rica were analyzed with 444 AFLP markers to characterize genetic diversity and structure. We also compared genetic diversity estimates between O. glumaepatula specimens and O. sativa commercial rice. Our results showed that O. glumaepatula populations in Costa Rica have moderately high levels of genetic diversity, comparable to those found in South American populations. Despite the restricted distribution of this species in Costa Rica, populations are fairly large, reducing the effects of drift on genetic diversity. We found a dismissible but significant structure (θ = 0.02 ± 0.001) among populations. A Bayesian structure analysis suggested that some individuals share a significant proportion of their genomes with O. sativa. These results suggest that gene flow from cultivated O. sativa populations may have occurred in the recent past. These results expose an important biohazard: recurrent hybridization may reduce the genetic diversity of this wild rice species. Introgression may transfer commercial traits into O. glumaepatula, which in turn could alter genetic diversity and increase the likelihood of local extinction. These results have important implications for in situ conservation strategies of the only wild populations of O. glumaepatula in Costa Rica. PMID:27077002

Hypernatremia in Dice snakes (Natrix tessellata) from a coastal population: implications for osmoregulation in marine snake prototypes.

PubMed

Brischoux, François; Kornilev, Yurii V

2014-01-01

The widespread relationship between salt excreting structures (e.g., salt glands) and marine life strongly suggests that the ability to regulate salt balance has been crucial during the transition to marine life in tetrapods. Elevated natremia (plasma sodium) recorded in several marine snakes species suggests that the development of a tolerance toward hypernatremia, in addition to salt gland development, has been a critical feature in the evolution of marine snakes. However, data from intermediate stage (species lacking salt glands but occasionally using salty environments) are lacking to draw a comprehensive picture of the evolution of an euryhaline physiology in these organisms. In this study, we assessed natremia of free-ranging Dice snakes (Natrix tessellata, a predominantly fresh water natricine lacking salt glands) from a coastal population in Bulgaria. Our results show that coastal N. tessellata can display hypernatremia (up to 195.5 mmol x l(-1)) without any apparent effect on several physiological and behavioural traits (e.g., hematocrit, body condition, foraging). More generally, a review of natremia in species situated along a continuum of habitat use between fresh- and seawater shows that snake species display a concomitant tolerance toward hypernatremia, even in species lacking salt glands. Collectively, these data suggest that a physiological tolerance toward hypernatremia has been critical during the evolution of an euryhaline physiology, and may well have preceded the evolution of salt glands.

Hypernatremia in Dice Snakes (Natrix tessellata) from a Coastal Population: Implications for Osmoregulation in Marine Snake Prototypes

PubMed Central

Brischoux, François; Kornilev, Yurii V.

2014-01-01

The widespread relationship between salt excreting structures (e.g., salt glands) and marine life strongly suggests that the ability to regulate salt balance has been crucial during the transition to marine life in tetrapods. Elevated natremia (plasma sodium) recorded in several marine snakes species suggests that the development of a tolerance toward hypernatremia, in addition to salt gland development, has been a critical feature in the evolution of marine snakes. However, data from intermediate stage (species lacking salt glands but occasionally using salty environments) are lacking to draw a comprehensive picture of the evolution of an euryhaline physiology in these organisms. In this study, we assessed natremia of free-ranging Dice snakes (Natrix tessellata, a predominantly fresh water natricine lacking salt glands) from a coastal population in Bulgaria. Our results show that coastal N. tessellata can display hypernatremia (up to 195.5 mmol.l−1) without any apparent effect on several physiological and behavioural traits (e.g., hematocrit, body condition, foraging). More generally, a review of natremia in species situated along a continuum of habitat use between fresh- and seawater shows that snake species display a concomitant tolerance toward hypernatremia, even in species lacking salt glands. Collectively, these data suggest that a physiological tolerance toward hypernatremia has been critical during the evolution of an euryhaline physiology, and may well have preceded the evolution of salt glands. PMID:24658047

Geographic structure evidenced in the toxic dinoflagellate Alexandrium pacificum Litaker (A. catenella - group IV (Whedon & Kofoid) Balech) along Japanese and Chinese coastal waters.

PubMed

Genovesi, Benjamin; Berrebi, Patrick; Nagai, Satoshi; Reynaud, Nathalie; Wang, Jinhui; Masseret, Estelle

2015-09-15

The intra-specific diversity and genetic structure within the Alexandrium pacificum Litaker (A. catenella - Group IV) populations along the Temperate Asian coasts, were studied among individuals isolated from Japan to China. The UPGMA dendrogram and FCA revealed the existence of 3 clusters. Assignment analysis suggested the occurrence of gene flows between the Japanese Pacific coast (cluster-1) and the Chinese Zhejiang coast (cluster-2). Human transportations are suspected to explain the lack of genetic difference between several pairs of distant Japanese samples, hardly explained by a natural dispersal mechanism. The genetic isolation of the population established in the Sea of Japan (cluster-3) suggested the existence of a strong ecological and geographical barrier. Along the Pacific coasts, the South-North current allows limited exchanges between Chinese and Japanese populations. The relationships between Temperate Asian and Mediterranean individuals suggested different scenario of large-scale dispersal mechanisms. Copyright © 2015. Published by Elsevier Ltd.

Crossing lines: a multidisciplinary framework for assessing connectivity of hammerhead sharks across jurisdictional boundaries

PubMed Central

Chin, A.; Simpfendorfer, C. A.; White, W. T.; Johnson, G. J.; McAuley, R. B.; Heupel, M. R.

2017-01-01

Conservation and management of migratory species can be complex and challenging. International agreements such as the Convention on Migratory Species (CMS) provide policy frameworks, but assessments and management can be hampered by lack of data and tractable mechanisms to integrate disparate datasets. An assessment of scalloped (Sphyrna lewini) and great (Sphyrna mokarran) hammerhead population structure and connectivity across northern Australia, Indonesia and Papua New Guinea (PNG) was conducted to inform management responses to CMS and Convention on International Trade in Endangered Species listings of these species. An Integrated Assessment Framework (IAF) was devised to systematically incorporate data across jurisdictions and create a regional synopsis, and amalgamated a suite of data from the Australasian region. Scalloped hammerhead populations are segregated by sex and size, with Australian populations dominated by juveniles and small adult males, while Indonesian and PNG populations included large adult females. The IAF process introduced genetic and tagging data to produce conceptual models of stock structure and movement. Several hypotheses were produced to explain stock structure and movement patterns, but more data are needed to identify the most likely hypothesis. This study demonstrates a process for assessing migratory species connectivity and highlights priority areas for hammerhead management and research. PMID:28429742

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.

Fish population genetic structure shaped by hydroelectric power plants in the upper Rhine catchment.

PubMed

Gouskov, Alexandre; Reyes, Marta; Wirthner-Bitterlin, Lisa; Vorburger, Christoph

2016-02-01

The Rhine catchment in Switzerland has been transformed by a chain of hydroelectric power stations. We addressed the impact of fragmentation on the genetic structure of fish populations by focusing on the European chub (Squalius cephalus). This fish species is not stocked and copes well with altered habitats, enabling an assessment of the effects of fragmentation per se. Using microsatellites, we genotyped 2133 chub from 47 sites within the catchment fragmented by 37 hydroelectric power stations, two weirs and the Rhine Falls. The shallow genetic population structure reflected drainage topology and was affected significantly by barriers to migration. The effect of power stations equipped with fishpasses on genetic differentiation was detectable, albeit weaker than that of man-made barriers without fishpasses. The Rhine Falls as the only long-standing natural obstacle (formed 14 000 to 17 000 years ago) also had a strong effect. Man-made barriers also exacerbated the upstream decrease in allelic diversity in the catchment, particularly when lacking fishpasses. Thus, existing fishpasses do have the desired effect of mitigating fragmentation, but barriers still reduce population connectivity in a fish that traverses fishpasses better than many other species. Less mobile species are likely to be affected more severely.

Life history and past demography maintain genetic structure, outcrossing rate, contemporary pollen gene flow of an understory herb in a highly fragmented rainforest

PubMed Central

Suárez-Montes, Pilar; Chávez-Pesqueira, Mariana

2016-01-01

Introduction Theory predicts that habitat fragmentation, by reducing population size and increasing isolation among remnant populations, can alter their genetic diversity and structure. A cascade of effects is expected: genetic drift and inbreeding after a population bottleneck, changes in biotic interactions that may affect, as in the case of plants, pollen dynamics, mating system, reproductive success. The detection of the effects of contemporary habitat fragmentation on the genetic structure of populations are conditioned by the magnitude of change, given the few number of generations since the onset of fragmentation, especially for long-lived organisms. However, the present-day genetic structure of populations may bear the signature of past demography events. Here, we examine the effects of rainforest fragmentation on the genetic diversity, population structure, mating system (outcrossing rate), indirect gene flow and contemporary pollen dynamics in the understory herb Aphelandra aurantiaca. Also, we assessed its present-day genetic structure under different past demographic scenarios. Methods Twelve populations of A. aurantiaca were sampled in large (4), medium (3), and small (5) forest fragments in the lowland tropical rainforest at Los Tuxtlas region. Variation at 11 microsatellite loci was assessed in 28–30 reproductive plants per population. In two medium- and two large-size fragments we estimated the density of reproductive plants, and the mating system by analyzing the progeny of different mother plants per population. Results Despite prevailing habitat fragmentation, populations of A. aurantiaca possess high genetic variation (He = 0.61), weak genetic structure (Rst = 0.037), and slight inbreeding in small fragments. Effective population sizes (Ne) were large, but slightly lower in small fragments. Migrants derive mostly from large and medium size fragments. Gene dispersal is highly restricted but long distance gene dispersal events were detected. Aphelandra aurantiaca shows a mixed mating system (tm = 0.81) and the outcrossing rate have not been affected by habitat fragmentation. A strong pollen pool structure was detected due to few effective pollen donors (Nep) and low distance pollen movement, pointing that most plants received pollen from close neighbors. Past demographic fluctuations may have affected the present population genetic structure as Bayesian coalescent analysis revealed the signature of past population expansion, possibly during warmer conditions after the last glacial maximum. Discussion Habitat fragmentation has not increased genetic differentiation or reduced genetic diversity of A. aurantiaca despite dozens of generations since the onset of fragmentation in the region of Los Tuxtlas. Instead, past population expansion is compatible with the lack of observed genetic structure. The predicted negative effects of rainforest fragmentation on genetic diversity and population structure of A. aurantiaca seem to have been buffered owing to its large effective populations and long-distance dispersal events. In particular, its mixed-mating system, mostly of outcrossing, suggests high efficiency of pollinators promoting connectivity and reducing inbreeding. However, some results point that the effects of fragmentation are underway, as two small fragments showed higher membership probabilities to their population of origin, suggesting genetic isolation. Our findings underscore the importance of fragment size to maintain genetic connectivity across the landscape. PMID:28028460

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

A Neolithic expansion, but strong genetic structure, in the independent history of New Guinea

PubMed Central

Bergström, Anders; Oppenheimer, Stephen J; Mentzer, Alexander J; Auckland, Kathryn; Robson, Kathryn; Attenborough, Robert; Alpers, Michael P; Koki, George; Pomat, William; Siba, Peter; Xue, Yali; Sandhu, Manjinder S; Tyler-Smith, Chris

2018-01-01

New Guinea shows human occupation since ~50 thousand years ago (kya), independent adoption of plant cultivation ~10 kya, and great cultural and linguistic diversity today. We performed genome-wide SNP genotyping on 381 individuals from 85 language groups in Papua New Guinea (PNG) and find a sharp divide originating 10-20 kya between lowland and highland groups, and a lack of non-New Guinean admixture in the latter. All highlanders share ancestry within the last 10 kya, with major population growth in the same period, suggesting population structure was reshaped following the Neolithic lifestyle transition. However, genetic differentiation between groups in PNG is much stronger than in comparable regions in Eurasia, demonstrating that such a transition does not necessarily limit the genetic and linguistic diversity of human societies. PMID:28912245

The contrasting nature of woody plant species in different neotropical forest biomes reflects differences in ecological stability.

PubMed

Pennington, R Toby; Lavin, Matt

2016-04-01

A fundamental premise of this review is that distinctive phylogenetic and biogeographic patterns in clades endemic to different major biomes illuminate the evolutionary process. In seasonally dry tropical forests (SDTFs), phylogenies are geographically structured and multiple individuals representing single species coalesce. This pattern of monophyletic species, coupled with their old species stem ages, is indicative of maintenance of small effective population sizes over evolutionary timescales, which suggests that SDTF is difficult to immigrate into because of persistent resident lineages adapted to a stable, seasonally dry ecology. By contrast, lack of coalescence in conspecific accessions of abundant and often widespread species is more frequent in rain forests and is likely to reflect large effective population sizes maintained over huge areas by effective seed and pollen flow. Species nonmonophyly, young species stem ages and lack of geographical structure in rain forest phylogenies may reflect more widespread disturbance by drought and landscape evolution causing resident mortality that opens up greater opportunities for immigration and speciation. We recommend full species sampling and inclusion of multiple accessions representing individual species in phylogenies to highlight nonmonophyletic species, which we predict will be frequent in rain forest and savanna, and which represent excellent case studies of incipient speciation. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

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.

Refining mortality estimates in shark demographic analyses: a Bayesian inverse matrix approach.

PubMed

Smart, Jonathan J; Punt, André E; White, William T; Simpfendorfer, Colin A

2018-01-18

Leslie matrix models are an important analysis tool in conservation biology that are applied to a diversity of taxa. The standard approach estimates the finite rate of population growth (λ) from a set of vital rates. In some instances, an estimate of λ is available, but the vital rates are poorly understood and can be solved for using an inverse matrix approach. However, these approaches are rarely attempted due to prerequisites of information on the structure of age or stage classes. This study addressed this issue by using a combination of Monte Carlo simulations and the sample-importance-resampling (SIR) algorithm to solve the inverse matrix problem without data on population structure. This approach was applied to the grey reef shark (Carcharhinus amblyrhynchos) from the Great Barrier Reef (GBR) in Australia to determine the demography of this population. Additionally, these outputs were applied to another heavily fished population from Papua New Guinea (PNG) that requires estimates of λ for fisheries management. The SIR analysis determined that natural mortality (M) and total mortality (Z) based on indirect methods have previously been overestimated for C. amblyrhynchos, leading to an underestimated λ. The updated Z distributions determined using SIR provided λ estimates that matched an empirical λ for the GBR population and corrected obvious error in the demographic parameters for the PNG population. This approach provides opportunity for the inverse matrix approach to be applied more broadly to situations where information on population structure is lacking. © 2018 by the Ecological Society of America.

Measuring local genetic variability in populations of codling moth (Lepidoptera: Tortricidae) across an unmanaged and commercial orchard interface.

PubMed

Fuentes-Contreras, Eduardo; Basoalto, Esteban; Franck, Pierre; Lavandero, Blas; Knight, Alan L; Ramírez, Claudio C

2014-04-01

The genetic structure of adult codling moth, Cydia pomonella (L.), populations was characterized both inside a managed apple, Malus domestica Borkdhausen, orchard and in surrounding unmanaged hosts and nonhost trees in central Chile during 2006-2007. Adult males were collected using an array of sex pheromone-baited traps. Five microsatellite genetic markers were used to study the population genetic structure across both spatial (1-100 ha) and temporal (generations within a season) gradients. Analysis of molecular variance (AMOVA) found a significant, but weak, association in both the spatial and temporal genetic structures. Discriminant analysis also found significant differentiation between the first and second generation for traps located either inside or outside the managed orchard. The Bayesian assignment test detected three genetic clusters during each of the two generations, which corresponded to different areas within the unmanaged and managed apple orchard interface. The lack of a strong spatial structure at a local scale was hypothesized to be because of active adult movement between the managed and unmanaged hosts and the asymmetry in the insecticide selection pressure inside and outside the managed habitats. These data highlight the importance of developing area-wide management programs that incorporate management tactics effective at the landscape level for successful codling moth control.

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.

Human-Mediated Marine Dispersal Influences the Population Structure of Aedes aegypti in the Philippine Archipelago

PubMed Central

Fonzi, Eugenio; Higa, Yukiko; Bertuso, Arlene G.; Futami, Kyoko; Minakawa, Noboru

2015-01-01

Background Dengue virus (DENV) is an extraordinary health burden on global scale, but still lacks effective vaccine. The Philippines is endemic for dengue fever, but massive employment of insecticides favored the development of resistance mutations in its major vector, Aedes aegypti. Alternative vector control strategies consist in releasing artificially modified mosquitos in the wild, but knowledge on their dispersal ability is necessary for a successful implementation. Despite being documented that Ae. aegypti can be passively transported for long distances, no study to date has been aimed at understanding whether human marine transportation can substantially shape the migration patterns of this mosquito. With thousands of islands connected by a dense network of ships, the Philippines is an ideal environment to fill this knowledge gap. Methodology/principal findings Larvae of Ae. aegypti from 15 seaports in seven major islands of central-western Philippines were collected and genotyped at seven microsatellite loci. Low genetic structure and considerable gene flow was found in the area. Univariate and multivariate regression analyses suggested that anthropic factors (specifically the amount of processed cargo and human population density) can explain the observed population structure, while geographical distance was not correlated. Interestingly, cargo shipments seem to be more efficient than passenger ships in transporting Ae. aegypti. Bayesian clustering confirmed that Ae. aegypti from busy ports are more genetically similar, while populations from idle ports are relatively structured, regardless of the geographical distance that separates them. Conclusions/significance The results confirmed the pivotal role of marine human-mediated long-range dispersal in determining the population structure of Ae. aegypti. Hopefully corroborated by further research, the present findings could assist the design of more effective vector control strategies. PMID:26039311

Health and Social Security Needs of Rickshaw Pullers in Ranchi.

PubMed

Kumar, Anant; Thomas, Joe; Wadhwa, Sonal S; Mishra, Aprajita; Dasgupta, Smita

2016-07-01

A significant number of "marginalized" population groups are denied their health rights, healthcare access, benefits of government health programs, and other health-related social security benefits. These population groups, particularly the rickshaw pullers of India, are vulnerable because of their poor social and economic status, migration history, lack of permanent settlements, lack of social capital, and so on. These reasons, coupled with other social-political reasons, lead to no or limited access to health services and poor health conditions. This study intends to explore and understand the context and health seeking behavior of rickshaw pullers in Ranchi, the capital city of Jharkhand state in India, with special reference to wider social determinants of health such as, access, affordability, and delivery of health services. The data was collected from 1,000 rickshaw pullers from 40 "rickshaw garages" in Ranchi. The findings of the study show that rickshaw pullers can't afford to "attach" much importance to their health due to various reasons and suffer from a variety of occupational and other illnesses. The health conditions of the rickshaw pullers are affected by poverty, negligence, illiteracy, lack of awareness and unavailability of affordable, quality health services. These are only a symptom of the larger structural issues affecting health. The study suggests that rickshaw pullers, being a marginalized and excluded population group, require special health and social security programs that include safe, affordable, and accessible services along with a special focus on health education, behavior change, and promotion of appropriate health-seeking behavior.

CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data.

PubMed

duVerle, David A; Yotsukura, Sohiya; Nomura, Seitaro; Aburatani, Hiroyuki; Tsuda, Koji

2016-09-13

Single-cell RNA sequencing is fast becoming one the standard method for gene expression measurement, providing unique insights into cellular processes. A number of methods, based on general dimensionality reduction techniques, have been suggested to help infer and visualise the underlying structure of cell populations from single-cell expression levels, yet their models generally lack proper biological grounding and struggle at identifying complex differentiation paths. Here we introduce cellTree: an R/Bioconductor package that uses a novel statistical approach, based on document analysis techniques, to produce tree structures outlining the hierarchical relationship between single-cell samples, while identifying latent groups of genes that can provide biological insights. With cellTree, we provide experimentalists with an easy-to-use tool, based on statistically and biologically-sound algorithms, to efficiently explore and visualise single-cell RNA data. The cellTree package is publicly available in the online Bionconductor repository at: http://bioconductor.org/packages/cellTree/ .

Factors associated with stocked cutthroat trout populations in high-mountain lakes

USGS Publications Warehouse

Bailey, Paul E.; Hubert, W.A.

2003-01-01

High-mountain lakes provide important fisheries in the Rocky Mountains; therefore we sought to gain an understanding of the relationships among environmental factors, accessibility to anglers, stocking rates, and features of stocks of cutthroat trout Oncorhynchus clarki in high-mountain lakes of the Bighorn Mountains, Wyoming. We sampled fish with experimental gill nets, measured lake habitat features, and calculated factors affecting angler access among 19 lakes that lacked sufficient natural reproduction to support salmonid fisheries and that were stocked at 1-, 2-, or 4-year intervals with fingerling cutthroat trout. We found that angler accessibility was probably the primary factor affecting stock structure, whereas stocking rates affected the densities of cutthroat trout among lakes. The maximum number of years survived after stocking appeared to have the greatest affect on biomass and population structure. Our findings suggest that control of harvest and manipulation of stocking densities can affect the density, biomass, and structure of cutthroat trout stocks in high-elevation lakes.

Historical and contemporary factors generate unique butterfly communities on islands

NASA Astrophysics Data System (ADS)

Vodă, Raluca; Dapporto, Leonardo; Dincă, Vlad; Shreeve, Tim G.; Khaldi, Mourad; Barech, Ghania; Rebbas, Khellaf; Sammut, Paul; Scalercio, Stefano; Hebert, Paul D. N.; Vila, Roger

2016-06-01

The mechanisms shaping island biotas are not yet well understood mostly because of a lack of studies comparing eco-evolutionary fingerprints over entire taxonomic groups. Here, we linked community structure (richness, frequency and nestedness) and genetic differentiation (based on mitochondrial DNA) in order to compare insular butterfly communities occurring over a key intercontinental area in the Mediterranean (Italy-Sicily-Maghreb). We found that community characteristics and genetic structure were influenced by a combination of contemporary and historical factors, and among the latter, connection during the Pleistocene had an important impact. We showed that species can be divided into two groups with radically different properties: widespread taxa had high dispersal capacity, a nested pattern of occurrence, and displayed little genetic structure, while rare species were mainly characterized by low dispersal, high turnover and genetically differentiated populations. These results offer an unprecedented view of the distinctive butterfly communities and of the main processes determining them on each studied island and highlight the importance of assessing the phylogeographic value of populations for conservation.

Microsatellite and mtDNA analysis of lake trout, Salvelinus namaycush, from Great Bear Lake, Northwest Territories: impacts of historical and contemporary evolutionary forces on Arctic ecosystems

PubMed Central

Harris, Les N; Howland, Kimberly L; Kowalchuk, Matthew W; Bajno, Robert; Lindsay, Melissa M; Taylor, Eric B

2013-01-01

Resolving the genetic population structure of species inhabiting pristine, high latitude ecosystems can provide novel insights into the post-glacial, evolutionary processes shaping the distribution of contemporary genetic variation. In this study, we assayed genetic variation in lake trout (Salvelinus namaycush) from Great Bear Lake (GBL), NT and one population outside of this lake (Sandy Lake, NT) at 11 microsatellite loci and the mtDNA control region (d-loop). Overall, population subdivision was low, but significant (global FST θ = 0.025), and pairwise comparisons indicated that significance was heavily influenced by comparisons between GBL localities and Sandy Lake. Our data indicate that there is no obvious genetic structure among the various basins within GBL (global FST = 0.002) despite the large geographic distances between sampling areas. We found evidence of low levels of contemporary gene flow among arms within GBL, but not between Sandy Lake and GBL. Coalescent analyses suggested that some historical gene flow occurred among arms within GBL and between GBL and Sandy Lake. It appears, therefore, that contemporary (ongoing dispersal and gene flow) and historical (historical gene flow and large founding and present-day effective population sizes) factors contribute to the lack of neutral genetic structure in GBL. Overall, our results illustrate the importance of history (e.g., post-glacial colonization) and contemporary dispersal ecology in shaping genetic population structure of Arctic faunas and provide a better understanding of the evolutionary ecology of long-lived salmonids in pristine, interconnected habitats. PMID:23404390

Microsatellite and mtDNA analysis of lake trout, Salvelinus namaycush, from Great Bear Lake, Northwest Territories: impacts of historical and contemporary evolutionary forces on Arctic ecosystems.

PubMed

Harris, Les N; Howland, Kimberly L; Kowalchuk, Matthew W; Bajno, Robert; Lindsay, Melissa M; Taylor, Eric B

2012-01-01

Resolving the genetic population structure of species inhabiting pristine, high latitude ecosystems can provide novel insights into the post-glacial, evolutionary processes shaping the distribution of contemporary genetic variation. In this study, we assayed genetic variation in lake trout (Salvelinus namaycush) from Great Bear Lake (GBL), NT and one population outside of this lake (Sandy Lake, NT) at 11 microsatellite loci and the mtDNA control region (d-loop). Overall, population subdivision was low, but significant (global F(ST) θ = 0.025), and pairwise comparisons indicated that significance was heavily influenced by comparisons between GBL localities and Sandy Lake. Our data indicate that there is no obvious genetic structure among the various basins within GBL (global F(ST) = 0.002) despite the large geographic distances between sampling areas. We found evidence of low levels of contemporary gene flow among arms within GBL, but not between Sandy Lake and GBL. Coalescent analyses suggested that some historical gene flow occurred among arms within GBL and between GBL and Sandy Lake. It appears, therefore, that contemporary (ongoing dispersal and gene flow) and historical (historical gene flow and large founding and present-day effective population sizes) factors contribute to the lack of neutral genetic structure in GBL. Overall, our results illustrate the importance of history (e.g., post-glacial colonization) and contemporary dispersal ecology in shaping genetic population structure of Arctic faunas and provide a better understanding of the evolutionary ecology of long-lived salmonids in pristine, interconnected habitats.

Evidence for environmental and ecological selection in a microbe with no geographic limits to gene flow.

PubMed

Whittaker, Kerry A; Rynearson, Tatiana A

2017-03-07

The ability for organisms to disperse throughout their environment is thought to strongly influence population structure and thus evolution of diversity within species. A decades-long debate surrounds processes that generate and support high microbial diversity, particularly in the ocean. The debate concerns whether diversification occurs primarily through geographic partitioning (where distance limits gene flow) or through environmental selection, and remains unresolved due to lack of empirical data. Here we show that gene flow in a diatom, an ecologically important eukaryotic microbe, is not limited by global-scale geographic distance. Instead, environmental and ecological selection likely play a more significant role than dispersal in generating and maintaining diversity. We detected significantly diverged populations ( F ST > 0.130) and discovered temporal genetic variability at a single site that was on par with spatial genetic variability observed over distances of 15,000 km. Relatedness among populations was decoupled from geographic distance across the global ocean and instead, correlated significantly with water temperature and whole-community chlorophyll a Correlations with temperature point to the importance of environmental selection in structuring populations. Correlations with whole-community chlorophyll a , a proxy for autotrophic biomass, suggest that ecological selection via interactions with other plankton may generate and maintain population genetic structure in marine microbes despite global-scale dispersal. Here, we provide empirical evidence for global gene flow in a marine eukaryotic microbe, suggesting that everything holds the potential to be everywhere, with environmental and ecological selection rather than geography or dispersal dictating the structure and evolution of diversity over space and time.

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.

Estimation of the real population and its impact on the utilisation of healthcare services in Mediterranean resort regions: an ecological study

PubMed Central

Perea-Milla, Emilio; Pons, Sergi Mari; Rivas-Ruiz, Francisco; Gallofre, Anna; Jurado, Enrique Navarro; Ales, Marco A Navarro; Jimenez-Puente, Alberto; Fernandez-Nieto, Fidel; Cerda, Joan C March; Carrasco, Manuel; Martin, Lydia; Cano, Damian Lopez; Gutierrez, Gonzalo E; Macías, Rafael Cortes; Garcia-Ruiz, Jose A

2007-01-01

Background The demographic structure has a significant influence on the use of healthcare services, as does the size of the population denominators. Very few studies have been published on methods for estimating the real population such as tourist resorts. The lack of information about these problems means there is a corresponding lack of information about the behaviour of populational denominators (the floating population or tourist load) and the effect of this on the use of healthcare services. The objectives of the study were: a) To determine the Municipal Solid Waste (MSW) ratio, per person per day, among populations of known size; b) to estimate, by means of this ratio, the real population in an area where tourist numbers are very significant; and c) to determine the impact on the utilisation of hospital emergency healthcare services of the registered population, in comparison to the non-resident population, in two areas where tourist numbers are very significant. Methods An ecological study design was employed. We analysed the Healthcare Districts of the Costa del Sol and the island of Menorca. Both are Spanish territories in the Mediterranean region. Results In the two areas analysed, the correlation coefficient between the MSW ratio and admissions to hospital emergency departments exceeded 0.9, with p < 0.001. On the basis of MSW generation ratios, obtained for a control zone and also measured in neighbouring countries, we estimated the real population. For the summer months, when tourist activity is greatest and demand for emergency healthcare at hospitals is highest, this value was found to be double that of the registered population. Conclusion The MSW indicator, which is both ecological and indirect, can be used to estimate the real population in areas where population levels vary significantly during the year. This parameter is of interest in planning and dimensioning the provision of healthcare services. PMID:17266744

Estimation of the real population and its impact on the utilisation of healthcare services in Mediterranean resort regions: an ecological study.

PubMed

Perea-Milla, Emilio; Pons, Sergi Mari; Rivas-Ruiz, Francisco; Gallofre, Anna; Jurado, Enrique Navarro; Ales, Marco A Navarro; Jimenez-Puente, Alberto; Fernandez-Nieto, Fidel; Cerda, Joan C March; Carrasco, Manuel; Martin, Lydia; Cano, Damian Lopez; Gutierrez, Gonzalo E; Macías, Rafael Cortes; Garcia-Ruiz, Jose A

2007-01-31

The demographic structure has a significant influence on the use of healthcare services, as does the size of the population denominators. Very few studies have been published on methods for estimating the real population such as tourist resorts. The lack of information about these problems means there is a corresponding lack of information about the behaviour of populational denominators (the floating population or tourist load) and the effect of this on the use of healthcare services. The objectives of the study were: a) To determine the Municipal Solid Waste (MSW) ratio, per person per day, among populations of known size; b) to estimate, by means of this ratio, the real population in an area where tourist numbers are very significant; and c) to determine the impact on the utilisation of hospital emergency healthcare services of the registered population, in comparison to the non-resident population, in two areas where tourist numbers are very significant. An ecological study design was employed. We analysed the Healthcare Districts of the Costa del Sol and the island of Menorca. Both are Spanish territories in the Mediterranean region. In the two areas analysed, the correlation coefficient between the MSW ratio and admissions to hospital emergency departments exceeded 0.9, with p < 0.001. On the basis of MSW generation ratios, obtained for a control zone and also measured in neighbouring countries, we estimated the real population. For the summer months, when tourist activity is greatest and demand for emergency healthcare at hospitals is highest, this value was found to be double that of the registered population. The MSW indicator, which is both ecological and indirect, can be used to estimate the real population in areas where population levels vary significantly during the year. This parameter is of interest in planning and dimensioning the provision of healthcare services.

Life histories predict genetic diversity and population structure within three species of octopus targeted by small-scale fisheries in Northwest Mexico.

PubMed

Domínguez-Contreras, José F; Munguia-Vega, Adrian; Ceballos-Vázquez, Bertha P; Arellano-Martínez, Marcial; García-Rodríguez, Francisco J; Culver, Melanie; Reyes-Bonilla, Hector

2018-01-01

The fishery for octopus in Northwest Mexico has increased to over 2,000 tons annually, but to date the specific composition of the catch has been ignored. With at least three main species targeted by artisanal fisheries in the region with distinct life histories, the lack of basic biological information about the distribution, metapopulation size and structure of each species could impede effective fisheries management to avoid overexploitation. We tested if different life histories of three species of octopus could help predict observed patterns of genetic diversity, population dynamics, structure and connectivity and how this information could be relevant to the sustainable management of the fishery. We sequenced two mitochondrial genes and genotyped seven nuclear microsatellite loci to identify the distribution of each species in 20 locations from the Gulf of California and the west coast of the Baja California peninsula. We tested five hypotheses derived from population genetic theory based on differences in the fecundity and dispersal potential for each species. We discovered that Octopus bimaculoides with low fecundity and direct development (without a planktonic phase) had lower average effective population size and genetic diversity, but higher levels of kinship, population structure, and richness of private alleles, than the other two species. These features indicated limited dispersal and high local recruitment. In contrast, O. bimaculatus and O. hubbsorum with higher fecundity and planktonic phase as paralarvae had higher effective population size and genetic diversity, and overall lower kinship and population structure than O. bimaculoides . These observations supported higher levels of gene flow over a larger geographical scale. O. bimaculatus with the longest planktonic paralarval duration and therefore larger dispersal potential had differences in the calculated parameters possibly associated with increased connectivity. We propose O. bimaculoides is more susceptible to over exploitation of small, isolated populations and could have longer recovery times than the other two species. This species may benefit from distinct fishery management within each local population. O. bimaculatus and O. hubbsorum may benefit from fishery management that takes into account metapopulation structure over larger geographic scales and the directionality and magnitude of larval dispersal driven by ocean currents and population connectivity among individuals of each locality. The distribution of each species and variations in their reproductive phenology is also important to consider when establishing marine reserves or seasonal fishing closures.

Genetic structure of the Common Eider in the western Aleutian Islands prior to fox eradication

USGS Publications Warehouse

Sonsthagen, Sarah A.; Talbot, Sandra L.; Wilson, Robert E.; Petersen, Margaret R.; Williams, Jeffrey C.; Byrd, G. Vernon; McCracken, Kevin G.

2013-01-01

Since the late 18th century bird populations residing in the Aleutian Archipelago have been greatly reduced by introduced arctic foxes (Alopex lagopus). We analyzed data from microsatellite, nuclear intron, and mitochondrial (mtDNA) loci to examine the spatial genetic structure, demography, and gene flow among four Aleutian Island populations of the Common Eider (Somateria mollissima) much reduced by introduced foxes. In mtDNA, we found high levels of genetic structure within and between island groups (ΦST = 0.643), but we found no population subdivision in microsatellites or nuclear introns. Differences in genetic structure between the mitochondrial and nuclear genomes are consistent with the Common Eider's breeding and winter biology, as females are highly philopatric and males disperse. Nevertheless, significant differences between islands in the mtDNA of males and marginal significance (P =0.07) in the Z-linked locus Smo 1 suggest that males may also have some level of fidelity to island groups. Severe reduction of populations by the fox, coupled with females' high philopatry, may have left the genetic signature of a bottleneck effect, resulting in the high levels of genetic differentiation observed in mtDNA (ΦST = 0.460–0.807) between islands only 440 km apart. Reestablishment of the Common Eider following the fox's eradication was likely through recruitment from within the islands and bolstered by dispersal from neighboring islands, as suggested by the lack of genetic structure and asymmetry in gene flow between Attu and the other Near Islands.

Perceptions of severe storms, climate change, ecological structures and resiliency three years post-hurricane Sandy in New Jersey.

PubMed

Burger, Joanna; Gochfeld, Michael

2017-12-01

Global warming is leading to increased frequency and severity of storms that are associated with flooding, increasing the risk to urban, coastal populations. This study examined perceptions of the relationship between severe storms, sea level rise, climate change and ecological barriers by a vulnerable environmental justice population in New Jersey. Patients using New Jersey's Federally Qualified Health Centers were interviewed after Hurricane [Superstorm] Sandy because it is essential to understand the perceptions of uninsured, underinsured, and economically challenged people to better develop a resiliency strategy for the most vulnerable people. Patients ( N = 355) using 6 centers were interviewed using a structured interview form. Patients were interviewed in the order they entered the reception area, in either English or Spanish. Respondents were asked to rate their agreement with environmental statements. Respondents 1) agreed with experts that "severe storms were due to climate change", "storms will come more often", and that "flooding was due to sea level rise", 2) did not agree as strongly that "climate change was due to human activity", 3) were neutral for statements that " Sandy damages were due to loss of dunes or salt marshes". 4) did not differ as a function of ethnic/racial categories, and 5) showed few gender differences. It is imperative that the public understand that climate change and sea level rise are occurring so that they support community programs (and funding) to prepare for increased frequency of storms and coastal flooding. The lack of high ratings for the role of dunes and marshes in preventing flooding indicates a lack of understanding that ecological structures protect coasts, and suggests a lack of support for management actions to restore dunes as part of a coastal preparedness strategy. Perceptions that do not support a public policy of coastal zone management to protect coastlines can lead to increased flooding, extensive property damages, and injuries or loss of life.

Perceptions of severe storms, climate change, ecological structures and resiliency three years post-hurricane Sandy in New Jersey

PubMed Central

Gochfeld, Michael

2017-01-01

Global warming is leading to increased frequency and severity of storms that are associated with flooding, increasing the risk to urban, coastal populations. This study examined perceptions of the relationship between severe storms, sea level rise, climate change and ecological barriers by a vulnerable environmental justice population in New Jersey. Patients using New Jersey’s Federally Qualified Health Centers were interviewed after Hurricane [Superstorm] Sandy because it is essential to understand the perceptions of uninsured, underinsured, and economically challenged people to better develop a resiliency strategy for the most vulnerable people. Patients (N = 355) using 6 centers were interviewed using a structured interview form. Patients were interviewed in the order they entered the reception area, in either English or Spanish. Respondents were asked to rate their agreement with environmental statements. Respondents 1) agreed with experts that “severe storms were due to climate change”, “storms will come more often”, and that “flooding was due to sea level rise”, 2) did not agree as strongly that “climate change was due to human activity”, 3) were neutral for statements that “Sandy damages were due to loss of dunes or salt marshes”. 4) did not differ as a function of ethnic/racial categories, and 5) showed few gender differences. It is imperative that the public understand that climate change and sea level rise are occurring so that they support community programs (and funding) to prepare for increased frequency of storms and coastal flooding. The lack of high ratings for the role of dunes and marshes in preventing flooding indicates a lack of understanding that ecological structures protect coasts, and suggests a lack of support for management actions to restore dunes as part of a coastal preparedness strategy. Perceptions that do not support a public policy of coastal zone management to protect coastlines can lead to increased flooding, extensive property damages, and injuries or loss of life. PMID:29398897

A mutation that eliminates bundle sheath extensions reduces leaf hydraulic conductance, stomatal conductance and assimilation rates in tomato (Solanum lycopersicum).

PubMed

Zsögön, Agustin; Negrini, Ana Clarissa Alves; Peres, Lázaro Eustáquio Pereira; Nguyen, Hoa Thi; Ball, Marilyn C

2015-01-01

Bundle sheath extensions (BSEs) are key features of leaf structure whose distribution differs among species and ecosystems. The genetic control of BSE development is unknown, so BSE physiological function has not yet been studied through mutant analysis. We screened a population of ethyl methanesulfonate (EMS)-induced mutants in the genetic background of the tomato (Solanum lycopersicum) model Micro-Tom and found a mutant lacking BSEs. The leaf phenotype of the mutant strongly resembled the tomato mutant obscuravenosa (obv). We confirmed that obv lacks BSEs and that it is not allelic to our induced mutant, which we named obv-2. Leaves lacking BSEs had lower leaf hydraulic conductance and operated with lower stomatal conductance and correspondingly lower assimilation rates than wild-type leaves. This lower level of function occurred despite similarities in vein density, midvein vessel diameter and number, stomatal density, and leaf area between wild-type and mutant leaves, the implication being that the lack of BSEs hindered water dispersal within mutant leaves. Our results comparing near-isogenic lines within a single species confirm the hypothesised role of BSEs in leaf hydraulic function. They further pave the way for a genetic model-based analysis of a common leaf structure with deep ecological consequences. © 2014 The Authors New Phytologist © 2014 New Phytologist Trust.

Genetic population structure of the malaria vector Anopheles baimaii in north-east India using mitochondrial DNA

PubMed Central

2012-01-01

Background Anopheles baimaii is a primary vector of human malaria in the forest settings of Southeast Asia including the north-eastern region of India. Here, the genetic population structure and the basic population genetic parameters of An. baimaii in north-east India were estimated using DNA sequences of the mitochondrial cytochrome oxidase sub unit II (COII) gene. Methods Anopheles baimaii were collected from 26 geo-referenced locations across the seven north-east Indian states and the COII gene was sequenced from 176 individuals across these sites. Fifty-seven COII sequences of An. baimaii from six locations in Bangladesh, Myanmar and Thailand from a previous study were added to this dataset. Altogether, 233 sequences were grouped into eight population groups, to facilitate analyses of genetic diversity, population structure and population history. Results A star-shaped median joining haplotype network, unimodal mismatch distribution and significantly negative neutrality tests indicated population expansion in An. baimaii with the start of expansion estimated to be ~0.243 million years before present (MYBP) in north-east India. The populations of An. baimaii from north-east India had the highest haplotype and nucleotide diversity with all other populations having a subset of this diversity, likely as the result of range expansion from north-east India. The north-east Indian populations were genetically distinct from those in Bangladesh, Myanmar and Thailand, indicating that mountains, such as the Arakan mountain range between north-east India and Myanmar, are a significant barrier to gene flow. Within north-east India, there was no genetic differentiation among populations with the exception of the Central 2 population in the Barail hills area that was significantly differentiated from other populations. Conclusions The high genetic distinctiveness of the Central 2 population in the Barail hills area of the north-east India should be confirmed and its epidemiological significance further investigated. The lack of genetic population structure in the other north-east Indian populations likely reflects large population sizes of An. baimaii that, historically, were able to disperse through continuous forest habitats in the north-east India. Additional markers and analytical approaches are required to determine if recent deforestation is now preventing ongoing gene flow. Until such information is acquired, An. baimaii in north-east India should be treated as a single unit for the implementation of vector control measures. PMID:22429500

Strong population genetic structuring in an annual fish, Nothobranchius furzeri, suggests multiple savannah refugia in southern Mozambique.

PubMed

Bartáková, Veronika; Reichard, Martin; Janko, Karel; Polačik, Matej; Blažek, Radim; Reichwald, Kathrin; Cellerino, Alessandro; Bryja, Josef

2013-09-12

Intraspecific genetic variation of African fauna has been significantly affected by pronounced climatic fluctuations in Plio-Pleistocene, but, with the exception of large mammals, very limited empirical data on diversity of natural populations are available for savanna-dwelling animals. Nothobranchius furzeri is an annual fish from south-eastern Africa, inhabiting discrete temporary savannah pools outside main river alluvia. Their dispersal is limited and population processes affecting its genetic structure are likely a combination of those affecting terrestrial and aquatic taxa. N. furzeri is a model taxon in ageing research and several populations of known geographical origin are used in laboratory studies. Here, we analysed the genetic structure, diversity, historical demography and temporal patterns of divergence in natural populations of N. furzeri across its entire distribution range. Genetic structure and historical demography of N. furzeri were analysed using a combination of mitochondrial (partial cytochrome b sequences, 687 bp) and nuclear (13 microsatellites) markers in 693 fish from 36 populations. Genetic markers consistently demonstrated strong population structuring and suggested two main genetic groups associated with river basins. The split was dated to the Pliocene (>2 Mya). The northern group inhabits savannah pools across the basin of the intermittent river Chefu in south-western Mozambique and eastern Zimbabwe. The southern group (from southernmost Mozambique) is subdivided, with the River Limpopo forming a barrier (maximum divergence time 1 Mya). A strong habitat fragmentation (isolated temporary pools) is reflected in significant genetic structuring even between adjacent pools, with a major influence of genetic drift and significant isolation-by-distance. Analysis of historical demography revealed that the expansion of both groups is ongoing, supported by frequent founder effects in marginal parts of the range and evidence of secondary contact between Chefu and Limpopo populations. We demonstrated: (1) ancient (pre-Pleistocene) divergence between the two main N. furzeri lineages, their recent secondary contact and lack of reproductive isolation; (2) important genetic structuring attributed to the fragmented nature of their environment and isolation-by-distance, suggesting that dispersal is limited, occurs over short distances and is not directly associated with river routes; (3) an apparent role of the River Limpopo as a barrier to dispersal and gene flow.

Study of genetic direct search algorithms for function optimization

NASA Technical Reports Server (NTRS)

Zeigler, B. P.

1974-01-01

The results are presented of a study to determine the performance of genetic direct search algorithms in solving function optimization problems arising in the optimal and adaptive control areas. The findings indicate that: (1) genetic algorithms can outperform standard algorithms in multimodal and/or noisy optimization situations, but suffer from lack of gradient exploitation facilities when gradient information can be utilized to guide the search. (2) For large populations, or low dimensional function spaces, mutation is a sufficient operator. However for small populations or high dimensional functions, crossover applied in about equal frequency with mutation is an optimum combination. (3) Complexity, in terms of storage space and running time, is significantly increased when population size is increased or the inversion operator, or the second level adaptation routine is added to the basic structure.

Zebra Finch Song Phonology and Syntactical Structure across Populations and Continents-A Computational Comparison.

PubMed

Lachlan, Robert F; van Heijningen, Caroline A A; Ter Haar, Sita M; Ten Cate, Carel

2016-01-01

Learned bird songs are often characterized by a high degree of variation between individuals and sometimes between populations, while at the same time maintaining species specificity. The evolution of such songs depends on the balance between plasticity and constraints. Captive populations provide an opportunity to examine signal variation and differentiation in detail, so we analyzed adult male zebra finch (Taeniopygia guttata) songs recorded from 13 populations across the world, including one sample of songs from wild-caught males in their native Australia. Cluster analysis suggested some, albeit limited, evidence that zebra finch song units belonged to universal, species-wide categories, linked to restrictions in vocal production and non-song parts of the vocal repertoire. Across populations, songs also showed some syntactical structure, although any song unit could be placed anywhere within the song. On the other hand, there was a statistically significant differentiation between populations, but the effect size was very small, and its communicative significance dubious. Our results suggest that variation in zebra finch songs within a population is largely determined by species-wide constraints rather than population-specific features. Although captive zebra finch populations have been sufficiently isolated to allow them to genetically diverge, there does not appear to have been any divergence in the genetically determined constraints that underlie song learning. Perhaps more surprising is the lack of locally diverged cultural traditions. Zebra finches serve as an example of a system where frequent learning errors may rapidly create within-population diversity, within broad phonological and syntactical constraints, and prevent the formation of long-term cultural traditions that allow populations to diverge.

A Neolithic expansion, but strong genetic structure, in the independent history of New Guinea.

PubMed

Bergström, Anders; Oppenheimer, Stephen J; Mentzer, Alexander J; Auckland, Kathryn; Robson, Kathryn; Attenborough, Robert; Alpers, Michael P; Koki, George; Pomat, William; Siba, Peter; Xue, Yali; Sandhu, Manjinder S; Tyler-Smith, Chris

2017-09-15

New Guinea shows human occupation since ~50 thousand years ago (ka), independent adoption of plant cultivation ~10 ka, and great cultural and linguistic diversity today. We performed genome-wide single-nucleotide polymorphism genotyping on 381 individuals from 85 language groups in Papua New Guinea and find a sharp divide originating 10 to 20 ka between lowland and highland groups and a lack of non-New Guinean admixture in the latter. All highlanders share ancestry within the last 10 thousand years, with major population growth in the same period, suggesting population structure was reshaped following the Neolithic lifestyle transition. However, genetic differentiation between groups in Papua New Guinea is much stronger than in comparable regions in Eurasia, demonstrating that such a transition does not necessarily limit the genetic and linguistic diversity of human societies. Copyright © 2017, American Association for the Advancement of Science.

A new fun and robust version of an fMRI localizer for the frontotemporal language system.

PubMed

Scott, Terri L; Gallée, Jeanne; Fedorenko, Evelina

2017-07-01

A set of brain regions in the frontal, temporal, and parietal lobes supports high-level linguistic processing. These regions can be reliably identified in individual subjects using fMRI, by contrasting neural responses to meaningful and structured language stimuli vs. stimuli matched for low-level properties but lacking meaning and/or structure. We here present a novel version of a language 'localizer,' which should be suitable for diverse populations including children and/or clinical populations who may have difficulty with reading or cognitively demanding tasks. In particular, we contrast responses to auditorily presented excerpts from engaging interviews or stories, and acoustically degraded versions of these materials. This language localizer is appealing because it uses (a) naturalistic and engaging linguistic materials, (b) auditory presentation, (c) a passive listening task, and can be easily adapted to new stimulus materials enabling comparisons of language activation in children and speakers of diverse languages.

HOW TO STUDY ADAPTATION (AND WHY TO DO IT THAT WAY).

PubMed

Olson, Mark E; Arroyo-Santos, Alfonso

2015-06-01

Some adaptationist explanations are regarded as maximally solid and others fanciful just-so stories. Just-so stories are explanations based on very little evidence. Lack of evidence leads to circular-sounding reasoning: "this trait was shaped by selection in unseen ancestral populations and this selection must have occurred because the trait is present." Well-supported adaptationist explanations include evidence that is not only abundant but selected from comparative, populational, and optimality perspectives, the three adaptationist subdisciplines. Each subdiscipline obtains its broad relevance in evolutionary biology via assumptions that can only be tested with the methods of the other subdisciplines. However, even in the best-supported explanations, assumptions regarding variation, heritability, and fitness in unseen ancestral populations are always present. These assumptions are accepted given how well they would explain the data if they were true. This means that some degree of "circularity" is present in all evolutionary explanations. Evolutionary explanation corresponds not to a deductive structure, as biologists usually assert, but instead to ones such as abduction or Bayesianism. With these structures in mind, we show the way to a healthier view of "circularity" in evolutionary biology and why integration across the comparative, populational, and optimality approaches is necessary.

Panmixia in a Critically Endangered Fish: The Totoaba (Totoaba macdonaldi) in the Gulf of California.

PubMed

Valenzuela-Quiñonez, Fausto; De-Anda-Montañez, Juan A; Gilbert-Horvath, Elizabeth; Garza, John Carlos; García-De León, Francisco J

2016-11-01

Conservation of the evolutionary legacy of endangered species is a key component for long-term persistence. Totoaba is a long-lived fish endemic to the Gulf of California and is considered critically endangered. There is currently a debate concerning its conservation status and whether it can be used as a fishery resource. Unfortunately, basic information on biological and genetic population structure of the species is lacking. We sampled 313 individuals and employed 16 microsatellite loci and 3 mitochondrial DNA markers (16S, 547 pb; COI, 619 pb; control region, 650 pb) to assess population structure and demography of totoaba in the Gulf of California, with samples from locations that encompass nearly all of its recognized geographic distribution. We could not reject a hypothesis of panmixia for totoaba, using nuclear or mitochondrial markers. Demographic analysis of mtDNA suggests a sudden population expansion model. The results have important implications for totoaba conservation because poaching is a significant conservation challenge and could have additive negative effects over the single population of totoaba in the Gulf of California. © The American Genetic Association 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Conservation genetics of the eastern yellow-bellied racer (Coluber constrictor flaviventris) and bullsnake (Pituophis catenifer sayi): River valleys are critical features for snakes at northern range limits.

PubMed

Somers, Christopher M; Graham, Carly F; Martino, Jessica A; Frasier, Timothy R; Lance, Stacey L; Gardiner, Laura E; Poulin, Ray G

2017-01-01

On the North American Great Plains, several snake species reach their northern range limit where they rely on sparsely distributed hibernacula located in major river valleys. Independent colonization histories for the river valleys and barriers to gene flow caused by the lack of suitable habitat between them may have produced genetically differentiated snake populations. To test this hypothesis, we used 10 microsatellite loci to examine the population structure of two species of conservation concern in Canada: the eastern yellow-bellied racer (Coluber constrictor flaviventris) and bullsnake (Pituophis catenifer sayi) in 3 major river valleys in southern Saskatchewan. Fixation indices (FST) showed that populations in river valleys were significantly differentiated for both species (racers, FST = 0.096, P = 0.001; bullsnakes FST = 0.045-0.157, P = 0.001). Bayesian assignment (STRUCTURE) and ordination (DAPC) strongly supported genetically differentiated groups in the geographically distinct river valleys. Finer-scale subdivision of populations within river valleys was not apparent based on our data, but is a topic that should be investigated further. Our findings highlight the importance of major river valleys for snakes at the northern extent of their ranges, and raise the possibility that populations in each river valley may warrant separate management strategies.

Reforming "developing" health systems: Tanzania, Mexico, and the United States.

PubMed

Chernichovsky, Dov; Martinez, Gabriel; Aguilera, Nelly

2009-01-01

Tanzania, Mexico, and the United States are at vastly different points on the economic development scale. Yet, their health systems can be classified as "developing": they do not live up to their potential, considering the resources available to them. The three, representing many others, share a common structural deficiency: a segregated health care system that cannot achieve its basic goals, the optimal health of its people, and their possible satisfaction with the system. Segregation follows and signifies first and foremost the lack of financial integration in the system that prevents it from serving its goals through the objectives of equity, cost containment and sustainability, efficient production of care and health, and choice. The chapter contrasts the nature of the developing health care system with the common goals', objectives, and principles of the Emerging Paradigm (EP) in developed, integrated--yet decentralized--systems. In this context, the developing health care system is defined by its structural deficiencies, and reform proposals are outlined. In spite of the vast differences amongst the three countries, their health care systems share strikingly similar features. At least 50% of their total funding sources are private. The systems comprise exclusive vertically integrated, yet segregated, "silos" that handle all systemic functions. These reflect and promote wide variations in health insurance coverage and levels of benefits--substantial portions of their populations are without adequate coverage altogether; a considerable lack of income protection from medical spending; an inability to formalize and follow a coherent health policy; a lack of financial discipline that threatens sustainability and overall efficiency; inefficient production of care and health; and an dissatisfied population. These features are often promoted by the state, using tax money, and donors. The situation can be rectified by (a) "centralizing"--at any level of development and resource availability--health system finance around a set package of core medical benefits that is made available to the entire population and (b) "decentralizing" consumption and provision of care. The first serves equity and cost containment and sustainability. The second supports efficiency and client satisfaction. The chapter views commonly discussed problems of the health care system--a lack of insurance coverage and income protection--as symptoms of a large problem: health system segregation.

The Population Origins and Expansion of Feral Cats in Australia

PubMed Central

Yurchenko, Andrey A.; David, Victor A.; Scott, Rachael; Koepfli, Klaus-Peter; Driscoll, Carlos; O’Brien, Stephen J.; Menotti-Raymond, Marilyn

2016-01-01

The historical literature suggests that in Australia, the domestic cat (Felis catus) had a European origin [~200 years before present (ybp)], but it is unclear if cats arrived from across the Asian land bridge contemporaneously with the dingo (4000 ybp), or perhaps immigrated ~40000 ybp in association with Aboriginal settlement from Asia. The origin of cats in Australia is important because the continent has a complex and ancient faunal assemblage that is dominated by endemic rodents and marsupials and lacks the large placental carnivores found on other large continents. Cats are now ubiquitous across the entire Australian continent and have been implicit in the range contraction or extinction of its small to medium sized (<3.5kg) mammals. We analyzed the population structure of 830 cats using 15 short tandem repeat (STR) genomic markers. Their origin appears to come exclusively from European founders. Feral cats in continental Australia exhibit high genetic diversity in comparison with the low diversity found in populations of feral cats living on islands. The genetic structure is consistent with a rapid westerly expansion from eastern Australia and a limited expansion in coastal Western Australia. Australian cats show modest if any population structure and a close genetic alignment with European feral cats as compared to cats from Asia, the Christmas and Cocos (Keeling) Islands (Indian Ocean), and European wildcats (F. silvestris silvestris). PMID:26647063

Extensive Genetic Diversity, Unique Population Structure and Evidence of Genetic Exchange in the Sexually Transmitted Parasite Trichomonas vaginalis

PubMed Central

Conrad, Melissa D.; Gorman, Andrew W.; Schillinger, Julia A.; Fiori, Pier Luigi; Arroyo, Rossana; Malla, Nancy; Dubey, Mohan Lal; Gonzalez, Jorge; Blank, Susan; Secor, William E.; Carlton, Jane M.

2012-01-01

Background Trichomonas vaginalis is the causative agent of human trichomoniasis, the most common non-viral sexually transmitted infection world-wide. Despite its prevalence, little is known about the genetic diversity and population structure of this haploid parasite due to the lack of appropriate tools. The development of a panel of microsatellite makers and SNPs from mining the parasite's genome sequence has paved the way to a global analysis of the genetic structure of the pathogen and association with clinical phenotypes. Methodology/Principal Findings Here we utilize a panel of T. vaginalis-specific genetic markers to genotype 235 isolates from Mexico, Chile, India, Australia, Papua New Guinea, Italy, Africa and the United States, including 19 clinical isolates recently collected from 270 women attending New York City sexually transmitted disease clinics. Using population genetic analysis, we show that T. vaginalis is a genetically diverse parasite with a unique population structure consisting of two types present in equal proportions world-wide. Parasites belonging to the two types (type 1 and type 2) differ significantly in the rate at which they harbor the T. vaginalis virus, a dsRNA virus implicated in parasite pathogenesis, and in their sensitivity to the widely-used drug, metronidazole. We also uncover evidence of genetic exchange, indicating a sexual life-cycle of the parasite despite an absence of morphologically-distinct sexual stages. Conclusions/Significance Our study represents the first robust and comprehensive evaluation of global T. vaginalis genetic diversity and population structure. Our identification of a unique two-type structure, and the clinically relevant phenotypes associated with them, provides a new dimension for understanding T. vaginalis pathogenesis. In addition, our demonstration of the possibility of genetic exchange in the parasite has important implications for genetic research and control of the disease. PMID:22479659

Evaluation of genetic population structure of smallmouth bass in the Susquehanna River basin, Pennsylvania

USGS Publications Warehouse

Schall, Megan K.; Bartron, Meredith L.; Wertz, Timothy; Niles, Jonathan M.; Shaw, Cassidy H.; Wagner, Tyler

2017-01-01

The Smallmouth Bass Micropterus dolomieu was introduced into the Susquehanna River basin, Pennsylvania, nearly 150 years ago. Since introduction, it has become an economically and ecologically important species that supports popular recreational fisheries. It is also one of the most abundant top predators in the system. Currently, there is no information on the level of genetic diversity or genetic structuring that may have occurred since introduction. An understanding of genetic diversity is important for the delineation of management units and investigation of gene flow at various management scales. The goals of this research were to investigate population genetic structure of Smallmouth Bass at sites within the Susquehanna River basin and to assess genetic differentiation relative to Smallmouth Bass at an out-of-basin site (Allegheny River, Pennsylvania) located within the species’ native range. During spring 2015, fin clips (n = 1,034) were collected from adults at 11 river sites and 13 tributary sites in the Susquehanna River basin and at one site on the Allegheny River. Fin clips were genotyped at 12 polymorphic microsatellite loci. Based on our results, adults sampled throughout the Susquehanna River basin did not represent separate genetic populations. There were only subtle differences in genetic diversity among sites (mean pairwise genetic differentiation index FST = 0.012), and there was an overall lack of population differentiation (K = 3 admixed populations). The greatest genetic differentiation was observed between fish collected from the out-of-basin site and those from the Susquehanna River basin sites. Knowledge that separate genetic populations of Smallmouth Bass do not exist in the Susquehanna River basin is valuable information for fisheries management in addition to providing baseline genetic data on an introduced sport fish population.

Lack of sex-biased dispersal promotes fine-scale genetic structure in alpine ungulates

USGS Publications Warehouse

Roffler, Gretchen H.; Talbot, Sandra L.; Luikart, Gordon; Sage, George K.; Pilgrim, Kristy L.; Adams, Layne G.; Schwartz, Michael K.

2014-01-01

Identifying patterns of fine-scale genetic structure in natural populations can advance understanding of critical ecological processes such as dispersal and gene flow across heterogeneous landscapes. Alpine ungulates generally exhibit high levels of genetic structure due to female philopatry and patchy configuration of mountain habitats. We assessed the spatial scale of genetic structure and the amount of gene flow in 301 Dall’s sheep (Ovis dalli dalli) at the landscape level using 15 nuclear microsatellites and 473 base pairs of the mitochondrial (mtDNA) control region. Dall’s sheep exhibited significant genetic structure within contiguous mountain ranges, but mtDNA structure occurred at a broader geographic scale than nuclear DNA within the study area, and mtDNA structure for other North American mountain sheep populations. No evidence of male-mediated gene flow or greater philopatry of females was observed; there was little difference between markers with different modes of inheritance (pairwise nuclear DNA F ST = 0.004–0.325; mtDNA F ST = 0.009–0.544), and males were no more likely than females to be recent immigrants. Historical patterns based on mtDNA indicate separate northern and southern lineages and a pattern of expansion following regional glacial retreat. Boundaries of genetic clusters aligned geographically with prominent mountain ranges, icefields, and major river valleys based on Bayesian and hierarchical modeling of microsatellite and mtDNA data. Our results suggest that fine-scale genetic structure in Dall’s sheep is influenced by limited dispersal, and structure may be weaker in populations occurring near ancestral levels of density and distribution in continuous habitats compared to other alpine ungulates that have experienced declines and marked habitat fragmentation.

Lack of access and continuity of adult health care: a national population-based survey

PubMed Central

Dilélio, Alitéia Santiago; Tomasi, Elaine; Thumé, Elaine; da Silveira, Denise Silva; Siqueira, Fernando Carlos Vinholes; Piccini, Roberto Xavier; Silva, Suele Manjourany; Nunes, Bruno Pereira; Facchini, Luiz Augusto

2015-01-01

OBJECTIVE To describe the lack of access and continuity of health care in adults. METHODS A cross-sectional population-based study was performed on a sample of 12,402 adults aged 20 to 59 years in urban areas of 100 municipalities of 23 states in the five Brazilian geopolitical regions. Barriers to the access and continuity of health care and were investigated based on receiving, needing and seeking health care (hospitalization and accident/emergency care in the last 12 months; care provided by a doctor, by other health professional or home care in the last three months). Based on the results obtained by the description of the sample, a projection is provided for adults living in Brazilian urban areas. RESULTS The highest prevalence of lack of access to health services and to provision of care by health professionals was for hospitalization (3.0%), whilst the lowest prevalence was for care provided by a doctor (1.1%). The lack of access to care provided by other health professionals was 2.0%; to accident and emergency services, 2.1%; and to home care, 2.9%. As for prevalences, the greatest absolute lack of access occurred in emergency care (more than 360,000 adults). The main reasons were structural and organizational problems, such as unavailability of hospital beds, of health professionals, of appointments for the type of care needed and charges made for care. CONCLUSIONS The universal right to health care in Brazil has not yet been achieved. These projections can help health care management in scaling the efforts needed to overcome this problem, such as expanding the infrastructure of health services and the workforce. PMID:26061454

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.

Population genetic analysis and sub-structuring of Theileria parva in the northern and eastern parts of Zambia

PubMed Central

2012-01-01

Background Theileriosis, caused by Theileria parva, is an economically important disease in Africa. It is a major constraint to the development of the livestock industry in some parts of eastern, central and southern Africa. In Zambia, theileriosis causes losses of up to 10,000 cattle annually. Methods Cattle blood samples were collected for genetic analysis of Theileria parva from Isoka and Petauke districts in Zambia. Microsatellite analysis was then performed on all Theileria parva positive samples for PCR using a panel of 9 microsatellite markers. Microsatellite data was analyzed using microsatellite toolkit, GenAlEx ver. 6, Fstat ver. 2.9.3.2, and LIAN computer softwares. Results The combined percentage of positive samples in both districts determined by PCR using the p104 gene primers was 54.9% (95% CI: 46.7 – 63.1%, 78/142), while in each district, it was 44.8% (95% CI: 34.8 – 54.8%) and 76.1% (95% CI = 63.9 – 88.4%) for Isoka and Petauke districts, respectively. We analyzed the population genetic structure of Theileria parva from a total of 61 samples (33 from Isoka and 28 from Petauke) using a panel of 9 microsatellite markers encompassing the 4 chromosomes of Theileria parva. Wright’s F index (FST = 0.178) showed significant differentiation between the Isoka and Petauke populations. Linkage disequilibrium was observed when populations from both districts were treated as a single population. When analyzed separately, linkage disequilibrium was observed in Kanyelele and Kalembe areas in Isoka district, Isoka district overall and in Petauke district. Petauke district had a higher multiplicity of infection than Isoka district. Conclusion Population genetic analyses of Theileria parva from Isoka and Petauke districts showed a low level of genotype exchange between the districts, but a high level of genetic diversity within each district population, implying genetic and geographic sub-structuring between the districts. The sub-structuring observed, along with the lack of panmixia in the populations, could have been due to low transmission levels at the time of sampling. However, the Isoka population was less diverse than the Petauke population. PMID:23146577

The Role of Structural Barriers in Risky Sexual Behavior, Victimization and Readiness to Change HIV/STI-Related Risk Behavior Among Transgender Women.

PubMed

Raiford, Jerris L; Hall, Grace J; Taylor, Raekiela D; Bimbi, David S; Parsons, Jeffrey T

2016-10-01

This study examines the role of structural barriers experienced by a community-based sample of 63 HIV-positive and negative transgender women that may elevate HIV infection and transmission risks. Separate hierarchical linear multiple regression analyses tested the association between structural barriers (e.g., unemployment, lack of food, shelter) and condomless anal sex acts, abuse, and readiness to change risk behavior, while controlling for other related factors. Among this primarily Hispanic and African-American sample, HIV-positive and negative transgender women experienced a similar number of structural barriers and experiencing structural barriers was significantly associated with an increased number of condomless anal sex acts (p = .002), victimization (p = .000) and a decreased readiness to change HIV-related risk behavior (p = .014). Structural-level interventions are needed to address this elevated risk among this underserved and hard-to-reach population.

Structural Interventions in HIV Prevention: A Taxonomy and Descriptive Systematic Review

PubMed Central

Sipe, Theresa Ann; Barham, Terrika L.; Johnson, Wayne; Joseph, Heather; Tungol-Ashmon, Maria Luisa; O’Leary, Ann

2018-01-01

One of the four national HIV prevention goals is to incorporate combinations of effective, evidence-based approaches to prevent HIV infection. In fields of public health, techniques that alter environment and affect choice options are effective. Structural approaches may be effective in preventing HIV infection. Existing frameworks for structural interventions were lacking in breadth and/or depth. We conducted a systematic review and searched CDC’s HIV/AIDS Prevention Research Synthesis Project’s database for relevant interventions during 1988–2013. We used an iterative process to develop the taxonomy. We identified 213 structural interventions: Access (65%), Policy/Procedure (32%), Mass Media (29%), Physical Structure (27%), Capacity Building (24%), Community Mobilization (9%), and Social Determinants of Health (8%). Forty percent targeted high-risk populations (e.g., people who inject drugs [12%]). This paper describes a comprehensive, well-defined taxonomy of structural interventions with 7 categories and 20 subcategories. The taxonomy accommodated all interventions identified. PMID:29159594

Auditing Knowledge toward Leveraging Organizational IQ in Healthcare Organizations.

PubMed

Shahmoradi, Leila; Karami, Mahtab; Farzaneh Nejad, Ahmadreza

2016-04-01

In this study, a knowledge audit was conducted based on organizational intelligence quotient (OIQ) principles of Iran's Ministry of Health and Medical Education (MOHME) to determine levers that can enhance OIQ in healthcare. The mixed method study was conducted within the MOHME. The study population consisted of 15 senior managers and policymakers. A tool based on literature review and panel expert opinions was developed to perform a knowledge audit. The significant results of this auditing revealed the following: lack of defined standard processes for organizing knowledge management (KM), lack of a knowledge map, absence of a trustee to implement KM, absence of specialists to produce a knowledge map, individuals' unwillingness to share knowledge, implicitness of knowledge format, occasional nature of knowledge documentation for repeated use, lack of a mechanism to determine repetitive tasks, lack of a reward system for the formation of communities, groups and networks, non-updatedness of the available knowledge, and absence of commercial knowledge. The analysis of the audit findings revealed that three levers for enhancing OIQ, including structure and process, organizational culture, and information technology must be created or modified.

Auditing Knowledge toward Leveraging Organizational IQ in Healthcare Organizations

PubMed Central

Shahmoradi, Leila; Farzaneh Nejad, Ahmadreza

2016-01-01

Objectives In this study, a knowledge audit was conducted based on organizational intelligence quotient (OIQ) principles of Iran's Ministry of Health and Medical Education (MOHME) to determine levers that can enhance OIQ in healthcare. Methods The mixed method study was conducted within the MOHME. The study population consisted of 15 senior managers and policymakers. A tool based on literature review and panel expert opinions was developed to perform a knowledge audit. Results The significant results of this auditing revealed the following: lack of defined standard processes for organizing knowledge management (KM), lack of a knowledge map, absence of a trustee to implement KM, absence of specialists to produce a knowledge map, individuals' unwillingness to share knowledge, implicitness of knowledge format, occasional nature of knowledge documentation for repeated use, lack of a mechanism to determine repetitive tasks, lack of a reward system for the formation of communities, groups and networks, non-updatedness of the available knowledge, and absence of commercial knowledge. Conclusions The analysis of the audit findings revealed that three levers for enhancing OIQ, including structure and process, organizational culture, and information technology must be created or modified. PMID:27200221

Continent-Wide Decoupling of Y-Chromosomal Genetic Variation from Language and Geography in Native South Americans

PubMed Central

Gusmão, Leonor; Gomes, Veronica; González, Miguel; Corach, Daniel; Sala, Andrea; Alechine, Evguenia; Palha, Teresinha; Santos, Ney; Ribeiro-dos-Santos, Andrea; Geppert, Maria; Willuweit, Sascha; Nagy, Marion; Zweynert, Sarah; Baeta, Miriam; Núñez, Carolina; Martínez-Jarreta, Begoña; González-Andrade, Fabricio; Fagundes de Carvalho, Elizeu; da Silva, Dayse Aparecida; Builes, Juan José; Turbón, Daniel; Lopez Parra, Ana Maria; Arroyo-Pardo, Eduardo; Toscanini, Ulises; Borjas, Lisbeth; Barletta, Claudia; Ewart, Elizabeth; Santos, Sidney; Krawczak, Michael

2013-01-01

Numerous studies of human populations in Europe and Asia have revealed a concordance between their extant genetic structure and the prevailing regional pattern of geography and language. For native South Americans, however, such evidence has been lacking so far. Therefore, we examined the relationship between Y-chromosomal genotype on the one hand, and male geographic origin and linguistic affiliation on the other, in the largest study of South American natives to date in terms of sampled individuals and populations. A total of 1,011 individuals, representing 50 tribal populations from 81 settlements, were genotyped for up to 17 short tandem repeat (STR) markers and 16 single nucleotide polymorphisms (Y-SNPs), the latter resolving phylogenetic lineages Q and C. Virtually no structure became apparent for the extant Y-chromosomal genetic variation of South American males that could sensibly be related to their inter-tribal geographic and linguistic relationships. This continent-wide decoupling is consistent with a rapid peopling of the continent followed by long periods of isolation in small groups. Furthermore, for the first time, we identified a distinct geographical cluster of Y-SNP lineages C-M217 (C3*) in South America. Such haplotypes are virtually absent from North and Central America, but occur at high frequency in Asia. Together with the locally confined Y-STR autocorrelation observed in our study as a whole, the available data therefore suggest a late introduction of C3* into South America no more than 6,000 years ago, perhaps via coastal or trans-Pacific routes. Extensive simulations revealed that the observed lack of haplogroup C3* among extant North and Central American natives is only compatible with low levels of migration between the ancestor populations of C3* carriers and non-carriers. In summary, our data highlight the fact that a pronounced correlation between genetic and geographic/cultural structure can only be expected under very specific conditions, most of which are likely not to have been met by the ancestors of native South Americans. PMID:23593040

Population genetic structure in Sabatieria (Nematoda) reveals intermediary gene flow and admixture between distant cold seeps from the Mediterranean Sea.

PubMed

De Groote, Annelies; Hauquier, Freija; Vanreusel, Ann; Derycke, Sofie

2017-07-01

There is a general lack of information on the dispersal and genetic structuring for populations of small-sized deep-water taxa, including free-living nematodes which inhabit and dominate the seafloor sediments. This is also true for unique and scattered deep-sea habitats such as cold seeps. Given the limited dispersal capacity of marine nematodes, genetic differentiation between such geographically isolated habitat patches is expected to be high. Against this background, we examined genetic variation in both mitochondrial (COI) and nuclear (18S and 28S ribosomal) DNA markers of 333 individuals of the genus Sabatieria, abundantly present in reduced cold-seep sediments. Samples originated from four Eastern Mediterranean cold seeps, separated by hundreds of kilometers, and one seep in the Southeast Atlantic. Individuals from the Mediterranean and Atlantic were divided into two separate but closely-related species clades. Within the Eastern Mediterranean, all specimens belonged to a single species, but with a strong population genetic structure (Φ ST  = 0.149). The haplotype network of COI contained 19 haplotypes with the most abundant haplotype (52% of the specimens) shared between all four seeps. The number of private haplotypes was high (15), but the number of mutations between haplotypes was low (1-8). These results indicate intermediary gene flow among the Mediterranean Sabatieria populations with no evidence of long-term barriers to gene flow. The presence of shared haplotypes and multiple admixture events indicate that Sabatieria populations from disjunct cold seeps are not completely isolated, with gene flow most likely facilitated through water current transportation of individuals and/or eggs. Genetic structure and molecular diversity indices are comparable to those of epiphytic shallow-water marine nematodes, while no evidence of sympatric cryptic species was found for the cold-seep Sabatieria.

Early events in xenograft development from the human embryonic stem cell line HS181--resemblance with an initial multiple epiblast formation.

PubMed

Gertow, Karin; Cedervall, Jessica; Jamil, Seema; Ali, Rouknuddin; Imreh, Marta P; Gulyas, Miklos; Sandstedt, Bengt; Ahrlund-Richter, Lars

2011-01-01

Xenografting is widely used for assessing in vivo pluripotency of human stem cell populations. Here, we report on early to late events in the development of mature experimental teratoma from a well-characterized human embryonic stem cell (HESC) line, HS181. The results show an embryonic process, increasingly chaotic. Active proliferation of the stem cell derived cellular progeny was detected already at day 5, and characterized by the appearance of multiple sites of engraftment, with structures of single or pseudostratified columnar epithelium surrounding small cavities. The striking histological resemblance to developing embryonic ectoderm, and the formation of epiblast-like structures was supported by the expression of the markers OCT4, NANOG, SSEA-4 and KLF4, but a lack of REX1. The early neural marker NESTIN was uniformly expressed, while markers linked to gastrulation, such as BMP-4, NODAL or BRACHYURY were not detected. Thus, observations on day 5 indicated differentiation comparable to the most early transient cell populations in human post implantation development. Confirming and expanding on previous findings from HS181 xenografts, these early events were followed by an increasingly chaotic development, incorporated in the formation of a benign teratoma with complex embryonic components. In the mature HS181 teratomas not all types of organs/tissues were detected, indicating a restricted differentiation, and a lack of adequate spatial developmental cues during the further teratoma formation. Uniquely, a kinetic alignment of rare complex structures was made to human embryos at diagnosed gestation stages, showing minor kinetic deviations between HS181 teratoma and the human counterpart.

Molecular Diversity of Cyanobacteria Inhabiting Coniform Structures and Surrounding Mat in a Yellowstone Hot Spring

NASA Astrophysics Data System (ADS)

Lau, Evan; Nash, Cody Z.; Vogler, Detlev R.; Cullings, K. W.

2005-02-01

Lithified coniform structures are common within cyanobacterial mats in Yellowstone National Park hot springs. It is unknown whether these structures and the mats from which they develop are inhabited by the same cyanobacterial populations. Denaturing gradient gel electrophoresis and sequencing and phylogenetic analysis of 16S rDNA was used to determine whether (1) three different morphological types of lithified coniform structures are inhabited by different cyanobacterial species, (2) these species are partitioned along a vertical gradient of these structures, and (3) lithified and non-lithified sections of mat are inhabited by different cyanobacterial species. Our results, based on multiple samplings, indicate that the cyanobacterial community compositions in the three lithified morphological types were identical and lacked any vertical differentiation. However, lithified and non-lithified portions of the same mat were inhabited by distinct and different populations of cyanobacteria. Cyanobacteria inhabiting lithified structures included at least one undefined Oscillatorialean taxon, which may represent the dominant cyanobacteria genus in lithified coniform stromatolites, Phormidium, three Synechococcus-like species, and two unknown cyanobacterial taxa. In contrast, the surrounding mats contained four closely related Synechococcus-like species. Our results indicate that the distribution of lithified coniform stromatolites may be dependent on the presence of one or more microorganisms, which are phylogenetically different from those inhabiting surrounding non-lithified mats.

Lack of genetic polymorphism among peregrine falcons Falco peregrinus of Fiji

USGS Publications Warehouse

Talbot, Sandra; Palmer, Angela G.; Sage, George K.; Sonsthagen, Sarah A.; Swem, Ted; Brimm, Daniel J.; White, Clayton M

2014-01-01

We compared levels of genetic diversity and isolation among peregrine falcons Falco peregrinus from two South Pacific island complexes (Fiji and Vanuatu: F. p. nesiotes), relative to other island and mainland populations. Fragment data from 12 microsatellite loci and sequence information from the control region of the mitochondrial DNA indicated levels of genetic variation in the South Pacific populations were lower than other island and mainland populations. Indeed, diversity varied from extremely low (Vanuatu) to completely absent (Fiji). We find little support for a hypothesis that populations on Fiji or Vanuatu were colonized via Australia. The complete lack of polymorphism in peregrine falcons of Fiji is remarkable, and to our knowledge has not been observed in a natural avian population. This lack of polymorphism, and the inability to test for decrease in polymorphism using museum samples, precludes testing whether the lack of genetic diversity in the population on Fiji is due to a recent bottleneck, or sustained isolation over evolutionary time. Increased fertility in eggs of Fiji peregrines upon outbreeding with males from other areas is consistent with inbreeding depression within a population typified by heterozygote deficiency.

Limits on reliable information flows through stochastic populations.

PubMed

Boczkowski, Lucas; Natale, Emanuele; Feinerman, Ofer; Korman, Amos

2018-06-06

Biological systems can share and collectively process information to yield emergent effects, despite inherent noise in communication. While man-made systems often employ intricate structural solutions to overcome noise, the structure of many biological systems is more amorphous. It is not well understood how communication noise may affect the computational repertoire of such groups. To approach this question we consider the basic collective task of rumor spreading, in which information from few knowledgeable sources must reliably flow into the rest of the population. We study the effect of communication noise on the ability of groups that lack stable structures to efficiently solve this task. We present an impossibility result which strongly restricts reliable rumor spreading in such groups. Namely, we prove that, in the presence of even moderate levels of noise that affect all facets of the communication, no scheme can significantly outperform the trivial one in which agents have to wait until directly interacting with the sources-a process which requires linear time in the population size. Our results imply that in order to achieve efficient rumor spread a system must exhibit either some degree of structural stability or, alternatively, some facet of the communication which is immune to noise. We then corroborate this claim by providing new analyses of experimental data regarding recruitment in Cataglyphis niger desert ants. Finally, in light of our theoretical results, we discuss strategies to overcome noise in other biological systems.

[Foodstuff as sources of vitamin C in nutrition of the population of the Russian Federation].

PubMed

Kpsheleva, O V; Baturin, A K; Shatniuk, L N

2006-01-01

The estimation of the contribution of foodstuff in security of the population of the Russian Federation by vitamin C in view of volumes of their consumption is lead. It is shown, that the basic sources of vitamin, borrowing in the general structure of consumption of foodstuff about 30%, do not provide sufficient volume its receipt. The real maintenance of vitamin C certain by standard analytical methods in some fruit-and-vegetable cultures, shows significant variability and difference from the given official tables of a chemical compound. The lack of the micronutrient is expedient to compensate by inclusion of biologically active additives to food or enriched foodstuff in a diet.

Eight polymorphic microsatellite loci for the Australian plague locust, Chortoicetes terminifera.

PubMed

Chapuis, Marie-Pierre; Popple, Julie-Anne; Simpson, Stephen J; Estoup, Arnaud; Martin, Jean-François; Steinbauer, Martin; McCulloch, Laurence; Sword, Gregory A

2008-11-01

Few population genetics studies have been carried out on major locust species. In particular, an understanding of the population genetic structure of the Australian plague locust, Chortoicetes terminifera, is lacking. We isolated and characterized eight polymorphic microsatellite loci in C. terminifera, and described experimental conditions for polymerase chain reaction multiplexing and genotyping these loci. The number of alleles per locus ranged from 11 to 29 and the expected heterozygosity ranged from 0.797 to 0.977. One locus was found to be X-linked. Results of cross-taxon amplification tests are reported in four species of the Oedipodinae subfamily. Journal compilation © 2008 Blackwell Publishing Ltd. No claim to original US government works.

Extreme Glacial Legacies: A Synthesis of the Antarctic Springtail Phylogeographic Record

PubMed Central

McGaughran, Angela; Stevens, Mark I.; Hogg, Ian D.; Carapelli, Antonio

2011-01-01

We review current phylogeographic knowledge from across the Antarctic terrestrial landscape with a focus on springtail taxa. We describe consistent patterns of high genetic diversity and structure among populations which have persisted in glacial refugia across Antarctica over both short (<2 Mya) and long (>10 Mya) timescales. Despite a general concordance of results among species, we explain why location is important in determining population genetic patterns within bioregions. We complete our review by drawing attention to the main limitations in the field of Antarctic phylogeography, namely that the scope of geographic focus is often lacking within studies, and that large gaps remain in our phylogeographic knowledge for most terrestrial groups. PMID:26467614

Genetic Diversity of Plasmodium falciparum in Haiti: Insights from Microsatellite Markers

PubMed Central

Carter, Tamar E.; Malloy, Halley; Existe, Alexandre; Memnon, Gladys; St. Victor, Yves; Okech, Bernard A.; Mulligan, Connie J.

2015-01-01

Hispaniola, comprising Haiti and the Dominican Republic, has been identified as a candidate for malaria elimination. However, incomplete surveillance data in Haiti hamper efforts to assess the impact of ongoing malaria control interventions. Characteristics of the genetic diversity of Plasmodium falciparum populations can be used to assess parasite transmission, which is information vital to evaluating malaria elimination efforts. Here we characterize the genetic diversity of P. falciparum samples collected from patients at seven sites in Haiti using 12 microsatellite markers previously employed in population genetic analyses of global P. falciparum populations. We measured multiplicity of infections, level of genetic diversity, degree of population geographic substructure, and linkage disequilibrium (defined as non-random association of alleles from different loci). For low transmission populations like Haiti, we expect to see few multiple infections, low levels of genetic diversity, high degree of population structure, and high linkage disequilibrium. In Haiti, we found low levels of multiple infections (12.9%), moderate to high levels of genetic diversity (mean number of alleles per locus = 4.9, heterozygosity = 0.61), low levels of population structure (highest pairwise Fst = 0.09 and no clustering in principal components analysis), and moderate linkage disequilibrium (ISA = 0.05, P<0.0001). In addition, population bottleneck analysis revealed no evidence for a reduction in the P. falciparum population size in Haiti. We conclude that the high level of genetic diversity and lack of evidence for a population bottleneck may suggest that Haiti’s P. falciparum population has been stable and discuss the implications of our results for understanding the impact of malaria control interventions. We also discuss the relevance of parasite population history and other host and vector factors when assessing transmission intensity from genetic diversity data. PMID:26462203

The Four-Dimensional Symptom Questionnaire (4DSQ) in the general population: scale structure, reliability, measurement invariance and normative data: a cross-sectional survey.

PubMed

Terluin, Berend; Smits, Niels; Brouwers, Evelien P M; de Vet, Henrica C W

2016-09-15

The Four-Dimensional Symptom Questionnaire (4DSQ) is a self-report questionnaire measuring distress, depression, anxiety and somatization with separate scales. The 4DSQ has extensively been validated in clinical samples, especially from primary care settings. Information about measurement properties and normative data in the general population was lacking. In a Dutch general population sample we examined the 4DSQ scales' structure, the scales' reliability and measurement invariance with respect to gender, age and education, the scales' score distributions across demographic categories, and normative data. 4DSQ data were collected in a representative Dutch Internet panel. Confirmatory factor analysis was used to examine the scales' structure. Reliability was examined by Cronbach's alpha, and coefficients omega-total and omega-hierarchical. Differential item functioning (DIF) analysis was used to evaluate measurement invariance across gender, age and education. The total response rate was 82.4 % (n = 5273/6399). The depression scale proved to be unidimensional. The other scales were best represented as bifactor models consisting of a large general factor and one or more smaller specific factors. The general factors accounted for more than 95 % of the reliable variance of the scales. Reliability was high (≥0.85) by all estimates. The distress-, depression- and anxiety scales were invariant across gender, age and education. The somatization scale demonstrated some lack of measurement invariance as a result of decreased thresholds for some of the items in young people (16-24 years) and increased thresholds in elderly people (65+ years). The somatization scale was invariant regarding gender and education. The 4DSQ scores varied significantly across demographic categories, but the explained variance was small (<6 %). Normative data were generated for gender and age categories. Approximately 17 % of the participants scored above average on de distress scale, whereas 12 % scored above average on de somatization scale. Percentages of people scoring high enough on depression or anxiety as to suspect the presence of depressive or anxiety disorder were 4.1 and 2.5 respectively. Evidence supports reliability and measurement invariance of the 4DSQ in the general Dutch population. The normative data provided in this study can be used to compare a subject's 4DSQ scores with a general population reference group.

Gut microbial communities of American pikas (Ochotona princeps): Evidence for phylosymbiosis and adaptations to novel diets.

PubMed

Kohl, Kevin D; Varner, Johanna; Wilkening, Jennifer L; Dearing, M Denise

2018-03-01

Gut microbial communities provide many physiological functions to their hosts, especially in herbivorous animals. We still lack an understanding of how these microbial communities are structured across hosts in nature, especially within a given host species. Studies on laboratory mice have demonstrated that host genetics can influence microbial community structure, but that diet can overwhelm these genetic effects. We aimed to test these ideas in a natural system, the American pika (Ochotona princeps). First, pikas are high-elevation specialists with significant population structure across various mountain ranges in the USA, allowing us to investigate whether similarities in microbial communities match host genetic differences. Additionally, pikas are herbivorous, with some populations exhibiting remarkable dietary plasticity and consuming high levels of moss, which is exceptionally high in fibre and low in protein. This allows us to investigate adaptations to an herbivorous diet, as well as to the especially challenging diet of moss. Here, we inventoried the microbial communities of pika caecal pellets from various populations using 16S rRNA sequencing to investigate structuring of microbial communities across various populations with different natural diets. Microbial communities varied significantly across populations, and differences in microbial community structure were congruent with genetic differences in host population structure, a pattern known as "phylosymbiosis." Several microbial members (Ruminococcus, Prevotella, Oxalobacter and Coprococcus) were detected across all samples, and thus likely represent a "core microbiome." These genera are known to perform a number of services for herbivorous hosts such as fibre fermentation and the degradation of plant defensive compounds, and thus are likely important for herbivory in pikas. Moreover, pikas that feed on moss harboured microbial communities highly enriched in Melainabacteria. This uncultivable candidate phylum has been proposed to ferment fibre for herbivores, and thus may contribute to the ability of some pika populations to consume high amounts of moss. These findings demonstrate that both host genetics and diet can influence the microbial communities of the American pika. These animals may be novel sources of fibre-degrading microbes. Last, we discuss the implications of population-specific microbial communities for conservation efforts in this species. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

High tunnels: protection for rather than from insect pests?

PubMed

Ingwell, Laura L; Thompson, Sarah L; Kaplan, Ian; Foster, Ricky E

2017-12-01

High tunnels are a season extension tool creating a hybrid of field and greenhouse growing conditions. High tunnels have recently increased in the USA and thus research on their management is lacking. One purported advantage of these structures is protection from common field pests, but evidence to support this claim is lacking. We compared insect pest populations in high tunnels with field production over two years for three crops: tomato, broccoli and cucumber. Greenhouse pests (e.g. aphids, whiteflies) were more prevalent in high tunnels, compared to field plots. Hornworms (tobacco (Manduca sexta L.) and tomato (M. quinquemaculata Haworth)), a common field pest on tomato, were also more abundant in high tunnels, requiring chemical control while field populations were low. The crucifer caterpillar complex (imported cabbageworm (Pieris rapae L.), diamondback moth (Plutella xylostella L.) and cabbage looper (Trichoplusia ni Hübner)) was also more abundant in high tunnels in 2010. Cucumber beetle (striped (Acalymma vittatum F.) and spotted (Diabrotica undecimpunctata Mannerheim)) densities were higher in high tunnels in 2010 and field plots in 2011. The common assumption that high tunnels offer protection from field pests was not supported. Instead, high tunnel growing conditions may facilitate higher pest populations. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Population models for passerine birds: structure, parameterization, and analysis

USGS Publications Warehouse

Noon, B.R.; Sauer, J.R.; McCullough, D.R.; Barrett, R.H.

1992-01-01

Population models have great potential as management tools, as they use infonnation about the life history of a species to summarize estimates of fecundity and survival into a description of population change. Models provide a framework for projecting future populations, determining the effects of management decisions on future population dynamics, evaluating extinction probabilities, and addressing a variety of questions of ecological and evolutionary interest. Even when insufficient information exists to allow complete identification of the model, the modelling procedure is useful because it forces the investigator to consider the life history of the species when determining what parameters should be estimated from field studies and provides a context for evaluating the relative importance of demographic parameters. Models have been little used in the study of the population dynamics of passerine birds because of: (1) widespread misunderstandings of the model structures and parameterizations, (2) a lack of knowledge of life histories of many species, (3) difficulties in obtaining statistically reliable estimates of demographic parameters for most passerine species, and (4) confusion about functional relationships among demographic parameters. As a result, studies of passerine demography are often designed inappropriately and fail to provide essential data. We review appropriate models for passerine bird populations and illustrate their possible uses in evaluating the effects of management or other environmental influences on population dynamics. We identify environmental influences on population dynamics. We identify parameters that must be estimated from field data, briefly review existing statistical methods for obtaining valid estimates, and evaluate the present status of knowledge of these parameters.

Genetic differentiation and phylogeography of Mediterranean-North Eastern Atlantic blue shark (Prionace glauca, L. 1758) using mitochondrial DNA: panmixia or complex stock structure?

PubMed

Leone, Agostino; Urso, Ilenia; Damalas, Dimitrios; Martinsohn, Jann; Zanzi, Antonella; Mariani, Stefano; Sperone, Emilio; Micarelli, Primo; Garibaldi, Fulvio; Megalofonou, Persefoni; Bargelloni, Luca; Franch, Rafaella; Macias, David; Prodöhl, Paulo; Fitzpatrick, Séan; Stagioni, Marco; Tinti, Fausto; Cariani, Alessia

2017-01-01

The blue shark ( Prionace glauca , Linnaeus 1758) is one of the most abundant epipelagic shark inhabiting all the oceans except the poles, including the Mediterranean Sea, but its genetic structure has not been confirmed at basin and interoceanic distances. Past tagging programs in the Atlantic Ocean failed to find evidence of migration of blue sharks between the Mediterranean and the adjacent Atlantic, despite the extreme vagility of the species. Although the high rate of by-catch in the Mediterranean basin, to date no genetic study on Mediterranean blue shark was carried out, which constitutes a significant knowledge gap, considering that this population is classified as "Critically Endangered", unlike its open-ocean counterpart. Blue shark phylogeography and demography in the Mediterranean Sea and North-Eastern Atlantic Ocean were inferred using two mitochondrial genes (Cytb and control region) amplified from 207 and 170 individuals respectively, collected from six localities across the Mediterranean and two from the North-Eastern Atlantic. Although no obvious pattern of geographical differentiation was apparent from the haplotype network, Φst analyses indicated significant genetic structure among four geographical groups. Demographic analyses suggest that these populations have experienced a constant population expansion in the last 0.4-0.1 million of years. The weak, but significant, differences in Mediterranean and adjacent North-eastern Atlantic blue sharks revealed a complex phylogeographic structure, which appears to reject the assumption of panmixia across the study area, but also supports a certain degree of population connectivity across the Strait of Gibraltar, despite the lack of evidence of migratory movements observed by tagging data. Analyses of spatial genetic structure in relation to sex-ratio and size could indicate some level of sex/stage biased migratory behaviour.

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.

No genetic adaptation of the Mediterranean keystone shrub Cistus ladanifer in response to experimental fire and extreme drought.

PubMed

Torres, Iván; Parra, Antonio; Moreno, José M; Durka, Walter

2018-01-01

In Mediterranean ecosystems, climate change is projected to increase fire danger and summer drought, thus reducing post-fire recruitment of obligate seeder species, and possibly affecting the population genetic structure. We performed a genome-wide genetic marker study, using AFLP markers, on individuals from one Central Spain population of the obligate post-fire seeder Cistus ladanifer L. that established after experimental fire and survived during four subsequent years under simulated drought implemented with a rainout shelter system. We explored the effects of the treatments on marker diversity, spatial genetic structure and presence of outlier loci suggestive of selection. We found no effect of fire or drought on any of the genetic diversity metrics. Analysis of Molecular Variance showed very low genetic differentiation among treatments. Neither fire nor drought altered the small-scale spatial genetic structure of the population. Only one locus was significantly associated with the fire treatment, but inconsistently across outlier detection methods. Neither fire nor drought are likely to affect the genetic makeup of emerging C. ladanifer, despite reduced recruitment caused by drought. The lack of genetic change suggests that reduced recruitment is a random, non-selective process with no genome-wide consequences on this keystone, drought- and fire tolerant Mediterranean species.

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.

Land use and management in PR China: problems and strategies.

PubMed

Cai, Y

1990-10-01

The conflict between population and land in China results from high population density, declining availability of arable land, decrease in cropland, overgrazing, inability to afford imported grain, and expansion of land use for urbanization. Unwise decisions have been made. These decisions have resulted in land degradation, soil erosion, deforestation, degradation of grasslands, waste of land for freight storage or waste disposal due to low grain prices, and nonagricultural constructions on croplands. Ineffective land management problems are identified as: 1) the lack of an economic means of guiding land use and land is not valued; the lack of any mechanism to ensure economic land use including public lands which are not accounted for with rent; 2) the lack of integration of departments into the decision making structure and too many departments making decisions about the same land; 3) the lack of choice in land use which results in higher government departments being unaware of local conditions, and the lack of appropriate investment which results in short-term exploitation; and 4) surveys are inadequate for decision making. The strategies suggested for improvement in land use management include low resources expenditure in production and appropriate goods consumption. The goal is to sustain subsistence with gradual improvement through development. Land resources must be conserved and the environment protected. The solutions to depend on food imports or reduce the nutritional level deny the equally plausible solution to generate a higher level of input. The profit motive and scientific agricultural practices could accomplish this end. Reclamation for cropland is possible for 8 million hectares of wasteland in wide areas in Sanjiang Plain and 3.4 million hectares in small pockets in Eastern Monsoon China. Traditional agriculture must be transformed and an optimum scale of land operation established. Land tenure reform is necessary. Regional conditions must prevail as the guiding principles. Several implementation strategies are suggested: controlling population growth and establishing a balance between expenditure and land productivity, expanding and conserving forest areas, increasing agricultural investment, reforming land tenure, adjusting land product prices, strengthening land administration, developing other industries, and reforming economic and political systems.

Molecular simulations and Markov state modeling reveal the structural diversity and dynamics of a theophylline-binding RNA aptamer in its unbound state

PubMed Central

Warfield, Becka M.

2017-01-01

RNA aptamers are oligonucleotides that bind with high specificity and affinity to target ligands. In the absence of bound ligand, secondary structures of RNA aptamers are generally stable, but single-stranded and loop regions, including ligand binding sites, lack defined structures and exist as ensembles of conformations. For example, the well-characterized theophylline-binding aptamer forms a highly stable binding site when bound to theophylline, but the binding site is unstable and disordered when theophylline is absent. Experimental methods have not revealed at atomic resolution the conformations that the theophylline aptamer explores in its unbound state. Consequently, in the present study we applied 21 microseconds of molecular dynamics simulations to structurally characterize the ensemble of conformations that the aptamer adopts in the absence of theophylline. Moreover, we apply Markov state modeling to predict the kinetics of transitions between unbound conformational states. Our simulation results agree with experimental observations that the theophylline binding site is found in many distinct binding-incompetent states and show that these states lack a binding pocket that can accommodate theophylline. The binding-incompetent states interconvert with binding-competent states through structural rearrangement of the binding site on the nanosecond to microsecond timescale. Moreover, we have simulated the complete theophylline binding pathway. Our binding simulations supplement prior experimental observations of slow theophylline binding kinetics by showing that the binding site must undergo a large conformational rearrangement after the aptamer and theophylline form an initial complex, most notably, a major rearrangement of the C27 base from a buried to solvent-exposed orientation. Theophylline appears to bind by a combination of conformational selection and induced fit mechanisms. Finally, our modeling indicates that when Mg2+ ions are present the population of binding-competent aptamer states increases more than twofold. This population change, rather than direct interactions between Mg2+ and theophylline, accounts for altered theophylline binding kinetics. PMID:28437473

A domains-based taxonomy of supported accommodation for people with severe and persistent mental illness.

PubMed

Siskind, Dan; Harris, Meredith; Pirkis, Jane; Whiteford, Harvey

2013-06-01

A lack of definitional clarity in supported accommodation and the absence of a widely accepted system for classifying supported accommodation models creates barriers to service planning and evaluation. We undertook a systematic review of existing supported accommodation classification systems. Using a structured system for qualitative data analysis, we reviewed the stratification features in these classification systems, identified the key elements of supported accommodation and arranged them into domains and dimensions to create a new taxonomy. The existing classification systems were mapped onto the new taxonomy to verify the domains and dimensions. Existing classification systems used either a service-level characteristic or programmatic approach. We proposed a taxonomy based around four domains: duration of tenure; patient characteristics; housing characteristics; and service characteristics. All of the domains in the taxonomy were drawn from the existing classification structures; however, none of the existing classification structures covered all of the domains in the taxonomy. Existing classification systems are regionally based, limited in scope and lack flexibility. A domains-based taxonomy can allow more accurate description of supported accommodation services, aid in identifying the service elements likely to improve outcomes for specific patient populations, and assist in service planning.

Distress and unemployment: the related economic and noneconomic factors in a sample of unemployed adults.

PubMed

Frasquilho, Diana; de Matos, Margarida Gaspar; Marques, Adilson; Gaspar, Tânia; Caldas-de-Almeida, José Miguel

2016-09-01

To examine the associations between economic and noneconomic factors and psychological distress in a group of 748 unemployed adults during economic recession. Data were collected through a questionnaire. Bivariate and logistic regression analyses were used to test the associations between distress and the deprivation of income and latent benefits of employment (time structure, activity, status, collective purpose and social contact). The participants' mean of distress was higher than the national population mean, and 46.5% of the participants scored above that. All economic and noneconomic factors emerged as strong predictors of distress; particularly financial deprivation (OR 1.06; CI 95 % 1.04-1.09) and lack of structured time (OR 1.07; CI 95 % 1.05-1.09). Women (OR 1.40; CI 95 % 1.04-1.86) and people with lower education levels (OR 0.45; CI 95 % 0.34-0.61) were more affected. The unemployed individuals score high on distress, especially those facing financial strain and lack of structured time, and women and individuals with lower education in particular. Given the recessionary context and high unemployment rates, these insights raise awareness for policies and actions targeting the needs of unemployed people.

Life histories predict genetic diversity and population structure within three species of octopus targeted by small-scale fisheries in Northwest Mexico

PubMed Central

Ceballos-Vázquez, Bertha P.; Arellano-Martínez, Marcial; García-Rodríguez, Francisco J.; Culver, Melanie; Reyes-Bonilla, Hector

2018-01-01

The fishery for octopus in Northwest Mexico has increased to over 2,000 tons annually, but to date the specific composition of the catch has been ignored. With at least three main species targeted by artisanal fisheries in the region with distinct life histories, the lack of basic biological information about the distribution, metapopulation size and structure of each species could impede effective fisheries management to avoid overexploitation. We tested if different life histories of three species of octopus could help predict observed patterns of genetic diversity, population dynamics, structure and connectivity and how this information could be relevant to the sustainable management of the fishery. We sequenced two mitochondrial genes and genotyped seven nuclear microsatellite loci to identify the distribution of each species in 20 locations from the Gulf of California and the west coast of the Baja California peninsula. We tested five hypotheses derived from population genetic theory based on differences in the fecundity and dispersal potential for each species. We discovered that Octopus bimaculoides with low fecundity and direct development (without a planktonic phase) had lower average effective population size and genetic diversity, but higher levels of kinship, population structure, and richness of private alleles, than the other two species. These features indicated limited dispersal and high local recruitment. In contrast, O. bimaculatus and O. hubbsorum with higher fecundity and planktonic phase as paralarvae had higher effective population size and genetic diversity, and overall lower kinship and population structure than O. bimaculoides. These observations supported higher levels of gene flow over a larger geographical scale. O. bimaculatus with the longest planktonic paralarval duration and therefore larger dispersal potential had differences in the calculated parameters possibly associated with increased connectivity. We propose O. bimaculoides is more susceptible to over exploitation of small, isolated populations and could have longer recovery times than the other two species. This species may benefit from distinct fishery management within each local population. O. bimaculatus and O. hubbsorum may benefit from fishery management that takes into account metapopulation structure over larger geographic scales and the directionality and magnitude of larval dispersal driven by ocean currents and population connectivity among individuals of each locality. The distribution of each species and variations in their reproductive phenology is also important to consider when establishing marine reserves or seasonal fishing closures. PMID:29472993

The accuracy of matrix population model projections for coniferous trees in the Sierra Nevada, California

USGS Publications Warehouse

van Mantgem, P.J.; Stephenson, N.L.

2005-01-01

1 We assess the use of simple, size-based matrix population models for projecting population trends for six coniferous tree species in the Sierra Nevada, California. We used demographic data from 16 673 trees in 15 permanent plots to create 17 separate time-invariant, density-independent population projection models, and determined differences between trends projected from initial surveys with a 5-year interval and observed data during two subsequent 5-year time steps. 2 We detected departures from the assumptions of the matrix modelling approach in terms of strong growth autocorrelations. We also found evidence of observation errors for measurements of tree growth and, to a more limited degree, recruitment. Loglinear analysis provided evidence of significant temporal variation in demographic rates for only two of the 17 populations. 3 Total population sizes were strongly predicted by model projections, although population dynamics were dominated by carryover from the previous 5-year time step (i.e. there were few cases of recruitment or death). Fractional changes to overall population sizes were less well predicted. Compared with a null model and a simple demographic model lacking size structure, matrix model projections were better able to predict total population sizes, although the differences were not statistically significant. Matrix model projections were also able to predict short-term rates of survival, growth and recruitment. Mortality frequencies were not well predicted. 4 Our results suggest that simple size-structured models can accurately project future short-term changes for some tree populations. However, not all populations were well predicted and these simple models would probably become more inaccurate over longer projection intervals. The predictive ability of these models would also be limited by disturbance or other events that destabilize demographic rates. ?? 2005 British Ecological Society.

Towards sustainable fishery management for skates in South America: The genetic population structure of Zearaja chilensis and Dipturus trachyderma (Chondrichthyes, Rajiformes) in the south-east Pacific Ocean.

PubMed

Vargas-Caro, Carolina; Bustamante, Carlos; Bennett, Michael B; Ovenden, Jennifer R

2017-01-01

The longnose skates (Zearaja chilensis and Dipturus trachyderma) are the main component of the elasmobranch fisheries in the south-east Pacific Ocean. Both species are considered to be a single stock by the fishery management in Chile however, little is known about the level of demographic connectivity within the fishery. In this study, we used a genetic variation (560 bp of the control region of the mitochondrial genome and ten microsatellite loci) to explore population connectivity at five locations along the Chilean coast. Analysis of Z. chilensis populations revealed significant genetic structure among off-shore locations (San Antonio, Valdivia), two locations in the Chiloé Interior Sea (Puerto Montt and Aysén) and Punta Arenas in southern Chile. For example, mtDNA haplotype diversity was similar across off-shore locations and Punta Arenas (h = 0.46-0.50), it was significantly different to those in the Chiloé Interior Sea (h = 0.08). These results raise concerns about the long-term survival of the species within the interior sea, as population resilience will rely almost exclusively on self-recruitment. In contrast, little evidence of genetic structure was found for D. trachyderma. Our results provide evidence for three management units for Z. chilensis, and we recommend that separate management arrangements are required for each of these units. However, there is no evidence to discriminate the extant population of Dipturus trachyderma as separate management units. The lack of genetic population subdivision for D. trachyderma appears to correspond with their higher dispersal ability and more offshore habitat preference.

Collaboration between non-governmental organizations and public services in health - a qualitative case study from rural Ecuador.

PubMed

Biermann, Olivia; Eckhardt, Martin; Carlfjord, Siw; Falk, Magnus; Forsberg, Birger C

2016-01-01

Non-governmental organizations (NGOs) have a key role in improving health in low- and middle-income countries. Their work needs to be synergistic, complementary to public services, and rooted in community mobilization and collective action. The study explores how an NGO and its health services are perceived by the population that it serves, and how it can contribute to reducing barriers to care. A qualitative exploratory study was conducted in remote Ecuador, characterized by its widespread poverty and lack of official governance. An international NGO collaborated closely with the public services to deliver preventative and curative health services. Data were collected using focus group discussions and semistructured interviews with purposively sampled community members, healthcare personnel, and community health workers based on their links to the health services. Conventional qualitative content analysis was used, focusing on manifest content. Emerging themes relate to the public private partnership (PPP), the NGO and its services, and community participation. The population perceives the NGO positively, linking it to healthcare improvements. Their priority is to get services, irrespective of the provider's structure. The presence of an NGO in the operation may contribute to unrealistic expectations of health services, affecting perceptions of the latter negatively. To avoid unrealistic expectations and dissatisfaction, and to increase and sustain the population's trust in the organization, an NGO should operate in a manner that is as integrated as possible within the existing structure. The NGO should work close to the population it serves, with services anchored in the community. PPP parties should develop a common platform with joint messages to the target population on the provider's structure, and regarding partners' roles and responsibilities. Interaction between the population and the providers on service content and their expectations is key to positive outcomes of PPP operations.

Determination of Genetic Structure and Signatures of Selection in Three Strains of Tanzania Shorthorn Zebu, Boran and Friesian Cattle by Genome-Wide SNP Analyses

PubMed Central

Msalya, George; Kim, Eui-Soo; Laisser, Emmanuel L. K.; Kipanyula, Maulilio J.; Karimuribo, Esron D.; Kusiluka, Lughano J. M.; Chenyambuga, Sebastian W.; Rothschild, Max F.

2017-01-01

Background More than 90 percent of cattle in Tanzania belong to the indigenous Tanzania Short Horn Zebu (TSZ) population which has been classified into 12 strains based on historical evidence, morphological characteristics, and geographic distribution. However, specific genetic information of each TSZ population has been lacking and has caused difficulties in designing programs such as selection, crossbreeding, breed improvement or conservation. This study was designed to evaluate the genetic structure, assess genetic relationships, and to identify signatures of selection among cattle of Tanzania with the main goal of understanding genetic relationship, variation and uniqueness among them. Methodology/Principal findings The Illumina Bos indicus SNP 80K BeadChip was used to genotype genome wide SNPs in 168 DNA samples obtained from three strains of TSZ cattle namely Maasai, Tarime and Sukuma as well as two comparative breeds; Boran and Friesian. Population structure and signatures of selection were examined using principal component analysis (PCA), admixture analysis, pairwise distances (FST), integrated haplotype score (iHS), identical by state (IBS) and runs of homozygosity (ROH). There was a low level of inbreeding (F~0.01) in the TSZ population compared to the Boran and Friesian breeds. The analyses of FST, IBS and admixture identified no considerable differentiation between TSZ trains. Importantly, common ancestry in Boran and TSZ were revealed based on admixture and IBD, implying gene flow between two populations. In addition, Friesian ancestry was found in Boran. A few common significant iHS were detected, which may reflect influence of recent selection in each breed or strain. Conclusions Population admixture and selection signatures could be applied to develop conservation plan of TSZ cattle as well as future breeding programs in East African cattle. PMID:28129396

Towards sustainable fishery management for skates in South America: The genetic population structure of Zearaja chilensis and Dipturus trachyderma (Chondrichthyes, Rajiformes) in the south-east Pacific Ocean

PubMed Central

Bustamante, Carlos; Bennett, Michael B.; Ovenden, Jennifer R.

2017-01-01

The longnose skates (Zearaja chilensis and Dipturus trachyderma) are the main component of the elasmobranch fisheries in the south-east Pacific Ocean. Both species are considered to be a single stock by the fishery management in Chile however, little is known about the level of demographic connectivity within the fishery. In this study, we used a genetic variation (560 bp of the control region of the mitochondrial genome and ten microsatellite loci) to explore population connectivity at five locations along the Chilean coast. Analysis of Z. chilensis populations revealed significant genetic structure among off-shore locations (San Antonio, Valdivia), two locations in the Chiloé Interior Sea (Puerto Montt and Aysén) and Punta Arenas in southern Chile. For example, mtDNA haplotype diversity was similar across off-shore locations and Punta Arenas (h = 0.46–0.50), it was significantly different to those in the Chiloé Interior Sea (h = 0.08). These results raise concerns about the long-term survival of the species within the interior sea, as population resilience will rely almost exclusively on self-recruitment. In contrast, little evidence of genetic structure was found for D. trachyderma. Our results provide evidence for three management units for Z. chilensis, and we recommend that separate management arrangements are required for each of these units. However, there is no evidence to discriminate the extant population of Dipturus trachyderma as separate management units. The lack of genetic population subdivision for D. trachyderma appears to correspond with their higher dispersal ability and more offshore habitat preference. PMID:28207832

Population structure of an endemic vulnerable species, the Jamaican boa (Epicrates subflavus).

PubMed

Tzika, Athanasia C; Koenig, Susan; Miller, Ricardo; Garcia, Gerardo; Remy, Christophe; Milinkovitch, Michel C

2008-01-01

The Jamaican boa (Epicrates subflavus; also called Yellow boa) is an endemic species whose natural populations greatly and constantly declined since the late 19th century, mainly because of predation by introduced species, human persecution, and habitat destruction. In-situ conservation of the Jamaican boa is seriously hindered by the lack of information on demographic and ecological parameters as well as by a poor understanding of the population structure and species distribution in the wild. Here, using nine nuclear microsatellite loci and a fragment of the mitochondrial cytochrome b gene from 87 wild-born individuals, we present the first molecular genetic analyses focusing on the diversity and structure of the natural populations of the Jamaican boa. A model-based clustering analysis of multilocus microsatellite genotypes identifies three groups that are also significantly differentiated on the basis of F-statistics. Similarly, haplotypic network reconstruction methods applied on the cytochrome b haplotypes isolated here identify two well-differentiated haplogroups separated by four to six fixed mutations. Bayesian and metaGA analyses of the mitochondrial data set combined with sequences from other Boidae species indicate that rooting of the haplotypic network occurs most likely between the two defined haplogroups. Both analyses (based on nuclear and mitochondrial markers) underline an Eastern vs. (Western + Central) pattern of differentiation in agreement with geological data and patterns of differentiation uncovered in other vertebrate and invertebrate Jamaican species. Our results provide important insights for improving management of ex-situ captive populations and for guiding the development of proper in-situ species survival and habitat management plans for this spectacular, yet poorly known and vulnerable, snake.

Development of novel SSR markers for evaluation of genetic diversity and population structure in Tribulus terrestris L. (Zygophyllaceae).

PubMed

Kaur, Kuljit; Sharma, Vikas; Singh, Vijay; Wani, Mohammad Saleem; Gupta, Raghbir Chand

2016-12-01

Tribulus terrestris L., commonly called puncture vine and gokhru, is an important member of Zygophyllaceae. The species is highly important in context to therapeutic uses and provides important active principles responsible for treatment of various diseases and also used as tonic. It is widely distributed in tropical regions of India and the world. However, status of its genetic diversity remained concealed due to lack of research work in this species. In present study, genetic diversity and structure of different populations of T. terrestris from north India was examined at molecular level using newly developed Simple Sequence Repeat (SSR) markers. In total, 20 primers produced 48 alleles in a size range of 100-500 bp with maximum (4) fragments amplified by TTMS-1, TTMS-25 and TTMS-33. Mean Polymorphism Information Content (PIC) and Marker Index (MI) were 0.368 and 1.01, respectively. Dendrogram showed three groups, one of which was purely containing accessions from Rajasthan while other two groups corresponded to Punjab and Haryana regions with intermixing of few other accessions. Analysis of molecular variance partitioned 76 % genetic variance within populations and 24 % among populations. Bayesian model based STRUCTURE analysis detected two genetic stocks for analyzed germplasm and also detected some admixed individuals. Different geographical populations of this species showed high level of genetic diversity. Results of present study can be useful in identifying diverse accessions and management of this plant resource. Moreover, the novel SSR markers developed can be utilized for various genetic analyses in this species in future.

‘Scared of going to the clinic’: Contextualising healthcare access for men who have sex with men, female sex workers and people who use drugs in two South African cities

PubMed Central

2018-01-01

Background Men who have sex with men (MSM), sex workers (SW) and people who use drugs (PWUD) are at increased risk for HIV because of multiple socio-structural barriers and do not have adequate access to appropriate HIV prevention, diagnosis and treatment services. Objective To examine the context of access to healthcare experienced by these three ‘Key Populations’, we conducted a qualitative study in two South African cities: Bloemfontein in the Free State province and Mafikeng in the North West province. Method We carried out in-depth interviews to explore healthcare workers’ perceptions, beliefs and attitudes towards Key Populations. Focus group discussions were also conducted with members of Key Populations exploring their experiences of accessing healthcare. Results Healthcare workers described their own attitudes towards Key Populations and demonstrated a lack of relevant knowledge, skills and training to manage the particular health needs and vulnerabilities facing Key Populations. Female SW, MSM and PWUD described their experiences of stigmatisation, and of being made to feel guilt, shame and a loss of dignity as a result of the discrimination by healthcare providers and other community. members. Our findings suggest that the uptake and effectiveness of health services amongst Key Populations in South Africa is limited by internalised stigma, reluctance to seek care, unwillingness to disclose risk behaviours to healthcare workers, combined with a lack of knowledge and understanding on the part of the broader community members, including healthcare workers. Conclusion This research highlights the need to address the broader healthcare provision environment, improving alignment of policies and programming in order to strengthen provision of effective health services that people from Key Populations will be able to access. PMID:29568645

The effect of biogeographic and phylogeographic barriers on gene flow in the brown smoothhound shark, Mustelus henlei, in the northeastern Pacific

PubMed Central

Chabot, Chris L; Espinoza, Mario; Mascareñas-Osorio, Ismael; Rocha-Olivares, Axayácatl

2015-01-01

We assessed the effects of the prominent biogeographic (Point Conception and the Peninsula of Baja California) and phylogeographic barriers (Los Angeles Region) of the northeastern Pacific on the population connectivity of the brown smoothhound shark, Mustelus henlei (Triakidae). Data from the mitochondrial control region and six nuclear microsatellite loci revealed significant population structure among three populations: northern (San Francisco), central (Santa Barbara, Santa Catalina, Punta Lobos, and San Felipe), and southern (Costa Rica). Patterns of long-term and contemporary migration were incongruent, with long-term migration being asymmetric and occurring in a north to south direction and a lack of significant contemporary migration observed between localities with the exception of Punta Lobos that contributed migrants to all localities within the central population. Our findings indicate that Point Conception may be restricting gene flow between the northern and central populations whereas barriers to gene flow within the central population would seem to be ineffective; additionally, a contemporary expansion of tropical M. henlei into subtropical and temperate waters may have been observed. PMID:25937903

Maturation of Cerebellar Purkinje Cell Population Activity during Postnatal Refinement of Climbing Fiber Network.

PubMed

Good, Jean-Marc; Mahoney, Michael; Miyazaki, Taisuke; Tanaka, Kenji F; Sakimura, Kenji; Watanabe, Masahiko; Kitamura, Kazuo; Kano, Masanobu

2017-11-21

Neural circuits undergo massive refinements during postnatal development. In the developing cerebellum, the climbing fiber (CF) to Purkinje cell (PC) network is drastically reshaped by eliminating early-formed redundant CF to PC synapses. To investigate the impact of CF network refinement on PC population activity during postnatal development, we monitored spontaneous CF responses in neighboring PCs and the activity of populations of nearby CF terminals using in vivo two-photon calcium imaging. Population activity is highly synchronized in newborn mice, and the degree of synchrony gradually declines during the first postnatal week in PCs and, to a lesser extent, in CF terminals. Knockout mice lacking P/Q-type voltage-gated calcium channel or glutamate receptor δ2, in which CF network refinement is severely impaired, exhibit an abnormally high level of synchrony in PC population activity. These results suggest that CF network refinement is a structural basis for developmental desynchronization and maturation of PC population activity. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Lack of congruence between morphometric evolution and genetic differentiation suggests a recent dispersal and local habitat adaptation of the Madeiran lizard Lacerta dugesii

PubMed Central

Brehm, António; Khadem, Mahnaz; Jesus, José; Andrade, Paula; Vicente, Luis

2001-01-01

Genetic differentiation among nine populations of the endemic lizard Lacerta dugesii Milne-Edwards 1829 (Lacertidae) from four groups of islands constituting the Archipelago of Madeira, was investigated by protein electrophoresis at 23 enzyme loci. Among twenty polymorphic loci, the total genetic diversity was due primarily to intra-population variation. The allele and genotypic frequencies among populations showed some heterogeneity, allowing the species to present a structuring pattern compatible with their geographical clustering. Some evidence suggests that selection acting on some loci in different ecological conditions may be responsible for the clustering of the populations studied. There was no apparent isolation effect expected under an "island" model of population divergence, and no correlation was found between genetic and geographic distances among populations. Morphological variation of the proposed three L. dugesii subspecies is not congruent with the allozyme analysis. This most probably suggests a rapid colonization of the islands followed by a strong effect of selection operating over the morphological characters used to define the subspecies. PMID:11742635

Psychometric Properties of the Bermond-Vorst Alexithymia Questionnaire (BVAQ) in the General Population and a Clinical Population.

PubMed

de Vroege, Lars; Emons, Wilco H M; Sijtsma, Klaas; van der Feltz-Cornelis, Christina M

2018-01-01

The Bermond-Vorst Alexithymia Questionnaire (BVAQ) has been validated in student samples and small clinical samples, but not in the general population; thus, representative general-population norms are lacking. We examined the factor structure of the BVAQ in Longitudinal Internet Studies for the Social Sciences panel data from the Dutch general population ( N  = 974). Factor analyses revealed a first-order five-factor model and a second-order two-factor model. However, in the second-order model, the factor interpreted as analyzing ability loaded on both the affective factor and the cognitive factor. Further analyses showed that the first-order test scores are more reliable than the second-order test scores. External and construct validity were addressed by comparing BVAQ scores with a clinical sample of patients suffering from somatic symptom and related disorder (SSRD) ( N  = 235). BVAQ scores differed significantly between the general population and patients suffering from SSRD, suggesting acceptable construct validity. Age was positively associated with alexithymia. Males showed higher levels of alexithymia. The BVAQ is a reliable alternative measure for measuring alexithymia.

Population genetic characterization of Cyclospora cayetanensis from discrete geographical regions.

PubMed

Guo, Yaqiong; Li, Na; Ortega, Ynes R; Zhang, Longxian; Roellig, Dawn M; Feng, Yaoyu; Xiao, Lihua

2018-01-01

Cyclospora cayetanensis is an emerging pathogen that is endemic in developing countries and responsible for many large foodborne cyclosporiasis outbreaks in North America since 1990s. Because of the lack of typing targets, the genetic diversity and population genetics of C. cayetanensis have not been investigated. In this study, we undertook a population genetic analysis of multilocus sequence typing data we recently collected from 64 C. cayetanensis specimens. Despite the extensive genetic heterogeneity in the overall C. cayetanensis population, there were significant intra- and inter-genic linkage disequilibria (LD). A disappearance of LD was observed when only multilocus genotypes were included in the population genetic analysis, indicative of an epidemic nature of C. cayetanensis. Geographical segregation-associated sub-structuring was observed between specimens from China and those from Peru and the United States. The two subpopulations had reduced LD, indicating the likely occurrence of genetic exchange among isolates in endemic areas. Further analyses of specimens from other geographical regions are necessary to fully understand the population genetics of C. cayetanensis. Copyright © 2017 Elsevier Inc. All rights reserved.

Flying between sky islands: the effect of naturally fragmented habitat on butterfly population structure.

PubMed

Sekar, Sandhya; Karanth, Praveen

2013-01-01

High elevation montane areas are called "sky islands" when they occur as a series of high mountains separated by lowland valleys. Different climatic conditions at high elevations makes sky islands a specialized type of habitat, rendering them naturally fragmented compared to more continuous habitat at lower elevations. Species in sky islands face unsuitable climate in the intervening valleys when moving from one montane area to another. The high elevation shola-grassland mosaic in the Western Ghats of southern India form one such sky island complex. The fragmented patches make this area ideal to study the effect of the spatial orientation of suitable habitat patches on population genetic structure of species found in these areas. Past studies have suggested that sky islands tend to have genetically structured populations, possibly due to reduced gene flow between montane areas. To test this hypothesis, we adopted the comparative approach. Using Amplified Fragment Length Polymorphisms, we compared population genetic structures of two closely related, similar sized butterfly species: Heteropsis oculus, a high elevation shola-grassland specialist restricted to the southern Western Ghats, and Mycalesis patnia, found more continuously distributed in lower elevations. In all analyses, as per expectation the sky island specialist H. oculus exhibited a greater degree of population genetic structure than M. patnia, implying a difference in geneflow. This difference in geneflow in turn appears to be due to the natural fragmentation of the sky island complexes. Detailed analysis of a subset of H. oculus samples from one sky island complex (the Anamalais) showed a surprising genetic break. A possible reason for this break could be unsuitable conditions of higher temperature and lower rainfall in the intervening valley region. Thus, sky island species are not only restricted by lack of habitat continuity between montane areas, but also by the nature of the intervening habitat.

Mobile phone-based interactive voice response as a tool for improving access to healthcare in remote areas in Ghana - an evaluation of user experiences.

PubMed

Brinkel, J; May, J; Krumkamp, R; Lamshöft, M; Kreuels, B; Owusu-Dabo, E; Mohammed, A; Bonacic Marinovic, A; Dako-Gyeke, P; Krämer, A; Fobil, J N

2017-05-01

To investigate and determine the factors that enhanced or constituted barriers to the acceptance of an mHealth system which was piloted in Asante-Akim North District of Ghana to support healthcare of children. Four semi-structured focus group discussions were conducted with a total of 37 mothers. Participants were selected from a study population of mothers who subscribed to a pilot mHealth system which used an interactive voice response (IVR) for its operations. Data were evaluated using qualitative content analysis methods. In addition, a short quantitative questionnaire assessed system's usability (SUS). Results revealed 10 categories of factors that facilitated user acceptance of the IVR system including quality-of-care experience, health education and empowerment of women. The eight categories of factors identified as barriers to user acceptance included the lack of human interaction, lack of update and training on the electronic advices provided and lack of social integration of the system into the community. The usability (SUS median: 79.3; range: 65-97.5) of the system was rated acceptable. The principles of the tested mHealth system could be of interest during infectious disease outbreaks, such as Ebola or Lassa fever, when there might be a special need for disease-specific health information within populations. © 2017 John Wiley & Sons Ltd.

Genetic conservation and management of the Californian endemic, Torrey Pine (Pinus torreyana Parry)

Treesearch

Jill A. Hamilton; Jessica W. Wright; F. Thomas Ledig

2017-01-01

Torrey pine (Pinus torreyana) is one of the rarest pine species in the world. Restricted to one mainland and one island population in California, Torrey pine is a species of conservation concern under threat due to low population sizes, lack of genetic variation, and environmental stochasticity. Previous research points to a lack of within population variation that is...

Population structure and linkage disequilibrium in Lupinus albus L. germplasm and its implication for association mapping.

PubMed

Iqbal, Muhammad Javed; Mamidi, Sujan; Ahsan, Rubina; Kianian, Shahryar F; Coyne, Clarice J; Hamama, Anwar A; Narina, Satya S; Bhardwaj, Harbans L

2012-08-01

White lupin (Lupinus albus L.) has been around since 300 B.C. and is recognized for its ability to grow on poor soils and application as green manure in addition to seed harvest. The seed has very high levels of protein (33-47 %) and oil (6-13 %). It also has many secondary metabolites that are potentially of nutraceutical value to animals and humans. Despite such a great potential, lupins role in modern agriculture began only in the twentieth century. Although a large collection of Lupinus germplasm accessions is available worldwide, rarely have they been genetically characterized. Additionally, scarce genomic resources in terms of recombinant populations and genome information have been generated for L. albus. With the advancement in association mapping methods, the natural populations have the potential to replace the recombinant populations in gene mapping and marker-trait associations. Therefore, we studied the genetic similarity, population structure and marker-trait association in a USDA germplasm collection for their current and future application in this crop improvement. A total of 122 PI (Plant Inventory) lines were screened with 18 AFLP primer pairs that generated 2,277 fragments. A subset of 892 polymorphic markers with MAF >0.05 (minor allele frequency) were used for association mapping. The cluster analysis failed to group accessions on the basis of their passport information, and a weak structure and low linkage disequilibrium (LD) were observed indicating the usefulness of the collection for association mapping. Moreover, we were also able to identify two markers (a p value of 1.53 × 10(-4) and 2.3 × 10(-4)) that explained 22.69 and 20.5 % of seed weight variation determined using R (LR) (2) . The implications of lack of geographic clustering, population structure, low LD and the ability of AFLP to map seed weight trait using association mapping and the usefulness of the PI collections in breeding programs are discussed.

Connectivity, passability and heterogeneity interact to determine fish population persistence in river networks

PubMed Central

Samia, Yasmine; Lutscher, Frithjof; Hastings, Alan

2015-01-01

The movement of fish in watersheds is frequently inhibited by human-made migration barriers such as dams or culverts. The resulting lack of connectivity of spatial subpopulations is often cited as a cause for observed population decline. We formulate a matrix model for a spatially distributed fish population in a watershed, and we investigate how location and other characteristics of a single movement barrier impact the asymptotic growth rate of the population. We find that while population growth rate often decreases with the introduction of a movement obstacle, it may also increase due to a ‘retention effect’. Furthermore, obstacle mortality greatly affects population growth rate. In practice, different connectivity indices are used to predict population effects of migration barriers, but the relation of these indices to population growth rates in demographic models is often unclear. When comparing our results with the dentritic connectivity index, we see that the index captures neither the retention effect nor the influences of obstacle mortality. We argue that structural indices cannot entirely replace more detailed demographic models to understand questions of persistence and extinction. We advocate the development of novel functional indices and characteristics. PMID:26311313

Connectivity, passability and heterogeneity interact to determine fish population persistence in river networks.

PubMed

Samia, Yasmine; Lutscher, Frithjof; Hastings, Alan

2015-09-06

The movement of fish in watersheds is frequently inhibited by human-made migration barriers such as dams or culverts. The resulting lack of connectivity of spatial subpopulations is often cited as a cause for observed population decline. We formulate a matrix model for a spatially distributed fish population in a watershed, and we investigate how location and other characteristics of a single movement barrier impact the asymptotic growth rate of the population. We find that while population growth rate often decreases with the introduction of a movement obstacle, it may also increase due to a 'retention effect'. Furthermore, obstacle mortality greatly affects population growth rate. In practice, different connectivity indices are used to predict population effects of migration barriers, but the relation of these indices to population growth rates in demographic models is often unclear. When comparing our results with the dentritic connectivity index, we see that the index captures neither the retention effect nor the influences of obstacle mortality. We argue that structural indices cannot entirely replace more detailed demographic models to understand questions of persistence and extinction. We advocate the development of novel functional indices and characteristics. © 2015 The Author(s).

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

Prevalence and factors associated with metabolic syndrome in an urban population of adults living with HIV in Nairobi, Kenya.

PubMed

Kiama, Catherine Nduku; Wamicwe, Joyce Njeri; Oyugi, Elvis Omondi; Obonyo, Mark Odhiambo; Mungai, Jane Githuku; Roka, Zeinab Gura; Mwangi, Ann

2018-01-01

Metabolic syndrome affects 20-25% of the adult population globally. It predisposes to cardiovascular disease and Type 2 diabetes. Studies in other countries suggest a high prevalence of metabolic syndrome among HIV-infected patients but no studies have been reported in Kenya. The objective of this study was to assess the prevalence and factors associated with metabolic syndrome in adult HIV-infected patients in an urban population in Nairobi, Kenya. In a cross-sectional study design, conducted at Riruta Health Centre in 2016, 360 adults infected with HIV were recruited. A structured questionnaire was used to collect data on socio-demography. Blood was collected by finger prick for fasting glucose and venous sampling for lipid profile. Using the harmonized Joint Scientific Statement criteria, metabolic syndrome was present in 19.2%. The prevalence was higher among females than males (20.7% vs. 16.0%). Obesity (AOR = 5.37, P < 0.001), lack of formal education (AOR = 5.20, P = 0.002) and family history of hypertension (AOR = 2.06, P = 0.029) were associated with increased odds of metabolic syndrome while physical activity (AOR = 0.28, P = 0.001) was associated with decreased odds. Metabolic syndrome is prevalent in this study population. Obesity, lack of formal education, family history of hypertension, and physical inactivity are associated with metabolic syndrome. Screening for risk factors, promotion of healthy lifestyle, and nutrition counselling should be offered routinely in HIV care and treatment clinics.

Population genetic studies of the polar bear (Ursus maritimus): A summary of available data and interpretation of results

USGS Publications Warehouse

Scribner, Kim T.; Garner, G.W.; Amstrup, Steven C.; Cronin, M.A.; Dizon, Andrew E.; Chivers, Susan J.; Perrin, William F.

1997-01-01

A summary of existing population genetics literature is presented for polar bears (Ursus maritimus) and interpreted in the context of the species' life-history characteristics and regional heterogeneity in environmental regimes and movement patterns. Several nongenetic data sets including morphology, contaminant levels, geographic variation in reproductive characteristics, and the location and distribution of open-water foraging habitat suggest some degree of spatial structuring. Eleven populations are recognized by the IUCN Polar Bear Specialist Group. Few genetics studies exist for polar bears. Interpretation and generalizations of regional variation in intra- and interpopulation levels of genetic variability are confounded by the paucity of data from many regions and by the fact that no single informative genetic marker has been employed in multiple regions. Early allozyme studies revealed comparatively low levels of genetic variability and no compelling evidence of spatial structuring. Studies employing mitochondrial DNA (mtDNA) also found low levels of genetic variation, a lack of phylogenetic structure, and no significant evidence for spatial variation in haplotype frequency. In contrast, microsatellite variable number of tandem repeat (VNTR) loci have revealed significant heterogeneity in allele frequency among populations in the Canadian Arctic. These regions are characterized by archipelgic patterns of sea-ice movements. Further studies using highly polymorphic loci are needed in regions characterized by greater polar bear dependency on pelagic sea-ice movements and in regions for which no data currently exist (i.e., Laptev and Novaya Zemlya/Franz Josef).

The Population Origins and Expansion of Feral Cats in Australia.

PubMed

Spencer, Peter B S; Yurchenko, Andrey A; David, Victor A; Scott, Rachael; Koepfli, Klaus-Peter; Driscoll, Carlos; O'Brien, Stephen J; Menotti-Raymond, Marilyn

2016-03-01

The historical literature suggests that in Australia, the domestic cat (Felis catus) had a European origin [~200 years before present (ybp)], but it is unclear if cats arrived from across the Asian land bridge contemporaneously with the dingo (4000 ybp), or perhaps immigrated ~40000 ybp in association with Aboriginal settlement from Asia. The origin of cats in Australia is important because the continent has a complex and ancient faunal assemblage that is dominated by endemic rodents and marsupials and lacks the large placental carnivores found on other large continents. Cats are now ubiquitous across the entire Australian continent and have been implicit in the range contraction or extinction of its small to medium sized (<3.5kg) mammals. We analyzed the population structure of 830 cats using 15 short tandem repeat (STR) genomic markers. Their origin appears to come exclusively from European founders. Feral cats in continental Australia exhibit high genetic diversity in comparison with the low diversity found in populations of feral cats living on islands. The genetic structure is consistent with a rapid westerly expansion from eastern Australia and a limited expansion in coastal Western Australia. Australian cats show modest if any population structure and a close genetic alignment with European feral cats as compared to cats from Asia, the Christmas and Cocos (Keeling) Islands (Indian Ocean), and European wildcats (F. silvestris silvestris). © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Microsatellite variation reveals weak genetic structure and retention of genetic variability in threatened Chinook salmon (Oncorhynchus tshawytscha) within a Snake River watershed

USGS Publications Warehouse

Neville, Helen; Issacs, Frank B.; Thurow, Russel; Dunham, J.B.; Rieman, B.

2007-01-01

Pacific salmon (Oncorhynchus spp.) have been central to the development of management concepts associated with evolutionarily significant units (ESUs), yet there are still relatively few studies of genetic diversity within threatened and endangered ESUs for salmon or other species. We analyzed genetic variation at 10 microsatellite loci to evaluate spatial population structure and genetic variability in indigenous Chinook salmon (Oncorhynchus tshawytscha) across a large wilderness basin within a Snake River ESU. Despite dramatic 20th century declines in abundance, these populations retained robust levels of genetic variability. No significant genetic bottlenecks were found, although the bottleneck metric (M ratio) was significantly correlated with average population size and variability. Weak but significant genetic structure existed among tributaries despite evidence of high levels of gene flow, with the strongest genetic differentiation mirroring the physical segregation of fish from two sub-basins. Despite the more recent colonization of one sub-basin and differences between sub-basins in the natural level of fragmentation, gene diversity and genetic differentiation were similar between sub-basins. Various factors, such as the (unknown) genetic contribution of precocial males, genetic compensation, lack of hatchery influence, and high levels of current gene flow may have contributed to the persistence of genetic variability in this system in spite of historical declines. This unique study of indigenous Chinook salmon underscores the importance of maintaining natural populations in interconnected and complex habitats to minimize losses of genetic diversity within ESUs.

Low Genetic Diversity in Wide-Spread Eurasian Liver Fluke Opisthorchis felineus Suggests Special Demographic History of This Trematode Species

PubMed Central

Brusentsov, Ilja I.; Katokhin, Alexey V.; Brusentsova, Irina V.; Shekhovtsov, Sergei V.; Borovikov, Sergei N.; Goncharenko, Grigoriy G.; Lider, Lyudmila A.; Romashov, Boris V.; Rusinek, Olga T.; Shibitov, Samat K.; Suleymanov, Marat M.; Yevtushenko, Andrey V.; Mordvinov, Viatcheslav A.

2013-01-01

Opisthorchis felineus or Siberian liver fluke is a trematode parasite (Opisthorchiidae) that infects the hepato-biliary system of humans and other mammals. Despite its public health significance, this wide-spread Eurasian species is one of the most poorly studied human liver flukes and nothing is known about its population genetic structure and demographic history. In this paper, we attempt to fill this gap for the first time and to explore the genetic diversity in O. felineus populations from Eastern Europe (Ukraine, European part of Russia), Northern Asia (Siberia) and Central Asia (Northern Kazakhstan). Analysis of marker DNA fragments from O. felineus mitochondrial cytochrome c oxidase subunit 1 and 3 (cox1, cox3) and nuclear rDNA internal transcribed spacer 1 (ITS1) sequences revealed that genetic diversity is very low across the large geographic range of this species. Microevolutionary processes in populations of trematodes may well be influenced by their peculiar biology. Nevertheless, we suggest that lack of population genetics structure observed in O. felineus can be primarily explained by the Pleistocene glacial events and subsequent sudden population growth from a very limited group of founders. Rapid range expansion of O. felineus through Asian and European territories after severe bottleneck points to a high dispersal potential of this trematode species. PMID:23634228

Bathymetric and geographic population structure in the pan-Atlantic deep-sea bivalve Deminucula atacellana (Schenck, 1939).

PubMed

Zardus, John D; Etter, Ron J; Chase, Michael R; Rex, Michael A; Boyle, Elizabeth E

2006-03-01

The deep-sea soft-sediment environment hosts a diverse and highly endemic fauna of uncertain origin. We know little about how this fauna evolved because geographic patterns of genetic variation, the essential information for inferring patterns of population differentiation and speciation are poorly understood. Using formalin-fixed specimens from archival collections, we quantify patterns of genetic variation in the protobranch bivalve Deminucula atacellana, a species widespread throughout the Atlantic Ocean at bathyal and abyssal depths. Samples were taken from 18 localities in the North American, West European and Argentine basins. A hypervariable region of mitochondrial 16S rDNA was amplified by polymerase chain reaction (PCR) and sequenced from 130 individuals revealing 21 haplotypes. Except for several important exceptions, haplotypes are unique to each basin. Overall gene diversity is high (h = 0.73) with pronounced population structure (Phi(ST) = 0.877) and highly significant geographic associations (P < 0.0001). Sequences cluster into four major clades corresponding to differences in geography and depth. Genetic divergence was much greater among populations at different depths within the same basin, than among those at similar depths but separated by thousands of kilometres. Isolation by distance probably explains much of the interbasin variation. Depth-related divergence may reflect historical patterns of colonization or strong environmental selective gradients. Broadly distributed deep-sea organisms can possess highly genetically divergent populations, despite the lack of any morphological divergence.

Conservation genetics of the eastern yellow-bellied racer (Coluber constrictor flaviventris) and bullsnake (Pituophis catenifer sayi): River valleys are critical features for snakes at northern range limits

PubMed Central

Graham, Carly F.; Martino, Jessica A.; Frasier, Timothy R.; Lance, Stacey L.; Gardiner, Laura E.; Poulin, Ray G.

2017-01-01

On the North American Great Plains, several snake species reach their northern range limit where they rely on sparsely distributed hibernacula located in major river valleys. Independent colonization histories for the river valleys and barriers to gene flow caused by the lack of suitable habitat between them may have produced genetically differentiated snake populations. To test this hypothesis, we used 10 microsatellite loci to examine the population structure of two species of conservation concern in Canada: the eastern yellow-bellied racer (Coluber constrictor flaviventris) and bullsnake (Pituophis catenifer sayi) in 3 major river valleys in southern Saskatchewan. Fixation indices (FST) showed that populations in river valleys were significantly differentiated for both species (racers, FST = 0.096, P = 0.001; bullsnakes FST = 0.045–0.157, P = 0.001). Bayesian assignment (STRUCTURE) and ordination (DAPC) strongly supported genetically differentiated groups in the geographically distinct river valleys. Finer-scale subdivision of populations within river valleys was not apparent based on our data, but is a topic that should be investigated further. Our findings highlight the importance of major river valleys for snakes at the northern extent of their ranges, and raise the possibility that populations in each river valley may warrant separate management strategies. PMID:29095863

Lack of spatial genetic structure among nesting and wintering King Eiders

USGS Publications Warehouse

Pearce, J.M.; Talbot, S.L.; Pierson, Barbara J.; Petersen, M.R.; Scribner, K.T.; Dickson, D.L.; Mosbech, A.

2004-01-01

The King Eider (Somateria spectabilis) has been delineated into two broadly distributed breeding populations in North America (the western and eastern Arctic) on the basis of banding data and their use of widely separated Pacific and Atlantic wintering areas. Little is known about the level of gene flow between these two populations. Also unknown is whether behavioral patterns common among migratory waterfowl, such as site fidelity to wintering areas and pair formation at these sites, have existed for sufficient time to create a population structure defined by philopatry to wintering rather than to nesting locations. We used six nuclear microsatellite DNA loci and cytochrome b mitochondrial DNA sequence data to estimate the extent of spatial genetic differentiation among nesting and wintering areas of King Eiders across North America and adjacent regions. Estimates of interpopulation variance in microsatellite allele and mtDNA haplotype frequency were both low and nonsignificant based on samples from three wintering and four nesting areas. Results from nested clade analysis, mismatch distributions, and coalescent-based analyses suggest historical population growth and gene flow that collectively may have homogenized gene frequencies. The presence of several unique mtDNA haplotypes among birds wintering near Greenland suggests that gene flow may now be more limited between the western and eastern Arctic, which is consistent with banding data.

An example of phenotypic adherence to the island rule? – Anticosti gray jays are heavier but not structurally larger than mainland conspecifics

PubMed Central

Strickland, Dan; Norris, D Ryan

2015-01-01

The island rule refers to the tendency of small vertebrates to become larger when isolated on islands and the frequent dwarfing of large forms. It implies genetic control, and a necessary linkage, of size and body-mass differences between insular and mainland populations. To examine the island rule, we compared body size and mass of gray jays (Perisoreus canadensis) on Anticosti Island, Québec, located in the Gulf of St. Lawrence, with three mainland populations (2 in Québec and 1 in Ontario). Although gray jays on Anticosti Island were ca 10% heavier, they were not structurally larger, than the three mainland populations. This suggests that Anticosti jays are not necessarily genetically distinct from mainland gray jays and that they may have achieved their greater body masses solely through packing more mass onto mainland-sized body frames. As such, they may be the first-known example of a proposed, purely phenotypic initial step in the adherence to the island rule by an insular population. Greater jay body mass is probably advantageous in Anticosti's high-density, intensely competitive social environment that may have resulted from the island's lack of mammalian nest predators. PMID:26380697

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.

A qualitative study into the perceived barriers of accessing healthcare among a vulnerable population involved with a community centre in Romania.

PubMed

George, Siân; Daniels, Katy; Fioratou, Evridiki

2018-04-03

Minority vulnerable communities, such as the European Roma, often face numerous barriers to accessing healthcare services, resulting in negative health outcomes. Both these barriers and outcomes have been reported extensively in the literature. However, reports on barriers faced by European non-Roma native communities are limited. The "Health Care Access Barriers" (HCAB) model identifies pertinent financial, structural and cognitive barriers that can be measured and potentially modified. The present study thus aims to explore the barriers to accessing healthcare for a vulnerable population of mixed ethnicity from a charity community centre in Romania, as perceived by the centre's family users and staff members, and assess whether these reflect the barriers identified from the HCAB model. Eleven community members whose children attend the centre and seven staff members working at the centre participated in face-to-face semi-structured interviews, exploring personal experiences and views on accessing healthcare. The interviews were transcribed and analysed using an initial deductive and secondary inductive approach to identify HCAB themes and other emerging themes and subthemes. Identified themes from both groups aligned with HCAB's themes of financial, structural and cognitive barriers and emergent subthemes important to the specific population were identified. Specifically, financial barriers related mostly to health insurance and bribery issues, structural barriers related mostly to service availability and accessibility, and cognitive barriers related mostly to healthcare professionals' attitudes and discrimination and the vulnerable population's lack of education and health literacy. A unique theme of psychological barriers emerged from both groups with associated subthemes of mistrust, hopelessness, fear and anxiety of this vulnerable population. The current study highlights healthcare access barriers to a vulnerable non-Roma native population involved with a charity community centre in Romania. The "Healthcare Access Barriers for Vulnerable Populations" (HABVP) model is proposed as an adaption to the existing HCAB model to account for the unique perceived barriers to healthcare for this population. Recommendations for future resolution of these identified barriers are proposed.

Sexual recombination is a signature of a persisting malaria epidemic in Peru

PubMed Central

2011-01-01

Background The aim of this study was to consider the impact that multi-clone, complex infections have on a parasite population structure in a low transmission setting. In general, complexity of infection (minimum number of clones within an infection) and the overall population level diversity is expected to be minimal in low transmission settings. Additionally, the parasite population structure is predicted to be clonal, rather than sexual due to infrequent parasite inoculation and lack of recombination between genetically distinct clones. However, in this low transmission of the Peruvian Amazon, complex infections are becoming more frequent, in spite of decreasing infection prevalence. In this study, it was hypothesized that sexual recombination between distinct clonal lineages of Plasmodium falciparum parasites were altering the subpopulation structure and effectively maintaining the population-level diversity. Methods Fourteen microsatellite markers were chosen to describe the genetic diversity in 313 naturally occurring P. falciparum infections from Peruvian Amazon. The population and subpopulation structure was characterized by measuring: clusteredness, expected heterozygosity (He), allelic richness, private allelic richness, and linkage disequilibrium. Next, microsatellite haplotypes and alleles were correlated with P. falciparum merozoite surface protein 1 Block 2 (Pfmsp1-B2) to examine the presence of recombinant microsatellite haplotypes. Results The parasite population structure consists of six genetically diverse subpopulations of clones, called "clusters". Clusters 1, 3, 4, and 6 have unique haplotypes that exceed 70% of the total number of clones within each cluster, while Clusters 2 and 5 have a lower proportion of unique haplotypes, but still exceed 46%. By measuring the He, allelic richness, and private allelic richness within each of the six subpopulations, relatively low levels of genetic diversity within each subpopulation (except Cluster 4) are observed. This indicated that the number of alleles, and not the combination of alleles, are limited. Next, the standard index of association (IAS) was measured, which revealed a significant decay in linkage disequilibrium (LD) associated with Cluster 6, which is indicative of independent assortment of alleles. This decay in LD is a signature of this subpopulation approaching linkage equilibrium by undergoing sexual recombination. To trace possible recombination events, the two most frequent microsatellite haplotypes observed over time (defined by either a K1 or Mad20) were selected as the progenitors and then potential recombinants were identified in within the natural population. Conclusions Contrary to conventional low transmission models, this study provides evidence of a parasite population structure that is superficially defined by a clonal backbone. Sexual recombination does occur and even arguably is responsible for maintaining the substructure of this population. PMID:22039962

Limited genetic differentiation among breeding, molting, and wintering groups of the threatened Steller's eider: The role of historic and contemporary factors

USGS Publications Warehouse

Pearce, J.M.; Talbot, S.L.; Petersen, M.R.; Rearick, J.R.

2005-01-01

Due to declines in the Alaska breeding population, the Steller's eider (Polysticta stelleri) was listed as threatened in North America in 1997. Periodic non-breeding in Russia and Alaska has hampered field-based assessments of behavioral patterns critical to recovery plans, such as levels of breeding site fidelity and movements among three regional populations: Atlantic-Russia, Pacific-Russia and Alaska. Therefore, we analyzed samples from across the species range with seven nuclear microsatellite DNA loci and cytochrome b mitochondrial (mt)DNA sequence data to infer levels of interchange among sampling areas and patterns of site fidelity. Results demonstrated low levels of population differentiation within Atlantic and Pacific nesting areas, with higher levels observed between these regions, but only for mtDNA. Bayesian analysis of microsatellite data from wintering and molting birds showed no signs of sub-population structure, even though band-recovery data suggests multiple breeding areas are present. We observed higher estimates of F-statistics for female mtDNA data versus male data, suggesting female-biased natal site fidelity. Summary statistics for mtDNA were consistent with models of historic population expansion. Lack of spatial structure in Steller's eiders may result largely from insufficient time since historic population expansions for behaviors, such as natal site fidelity, to isolate breeding areas genetically. However, other behaviors such as the periodic non-breeding observed in Steller's eiders may also play a more contemporary role in genetic homogeneity, especially for microsatellite loci. 

Research into health, population and social transitions in rural South Africa: Data and methods of the Agincourt Health and Demographic Surveillance System1

PubMed Central

KAHN, KATHLEEN; TOLLMAN, STEPHEN M.; COLLINSON, MARK A.; CLARK, SAMUEL J.; TWINE, RHIAN; CLARK, BENJAMIN D.; SHABANGU, MILDRED; GÓMEZ-OLIVÉ, FRANCESC XAVIER; MOKOENA, OBED; GARENNE, MICHEL L.

2010-01-01

Rationale for study Vital registration is generally lacking in infrastructurally weak areas where health and development problems are most pressing. Health and demographic surveillance is a response to the lack of a valid information base that can provide high-quality longitudinal data on population dynamics, health, and social change to inform policy and practice. Design and measurement procedures Continuous demographic monitoring of an entire geographically defined population involves a multi-round, prospective community study, with annual recording of all vital events (births, deaths, migrations). Status observations and special modules add value to particular research areas. A verbal autopsy is conducted on every death to determine its probable cause. A geographic surveillance system supports spatial analyses, and strengthens field management. Population and sample size considerations Health and demographic surveillance covers the Agincourt sub-district population, sited in rural north-eastern South Africa, of some 70,000 people (nearly a third are Mozambican immigrants) in 21 villages and 11,700 households. Data enumerated are consistent or more detailed when compared with national sources; strategies to improve incomplete data, such as counts of perinatal deaths, have been introduced with positive effect. Basic characteristics A major health and demographic transition was documented over a 12-year period with marked changes in population structure, escalating mortality, declining fertility, and high levels of temporary migration increasing particularly amongst women. A dual burden of infectious and non-communicable disease exists against a background of dramatically progressing HIV/AIDS. Potential and research questions Health and demographic surveillance sites – fundamental to the INDEPTH Network – generate research questions and hypotheses from empirical data, highlight health, social and population priorities, provide cost-effective support for diverse study designs, and track population change and the impact of interventions over time. PMID:17676498

Is Toxoplasma gondii a threat to the conservation of free-ranging Australian marsupial populations?

PubMed Central

Hillman, Alison E.; Lymbery, Alan J.; Thompson, R.C. Andrew

2015-01-01

It has often been asserted that Australian marsupial species are particularly susceptible to Toxoplasma gondii infection and to clinical toxoplasmosis following infection. This implicates T. gondii as a potential threat to marsupial population viability, and contrasts to what is known of T. gondii in populations of several other host species. We reviewed the literature, and found a lack of scientifically robust evidence addressing the occurrence of T. gondii infection in free-ranging populations of Australian marsupial species, and the impacts of the infection on population health. Key limitations included a lack of studies in free-ranging marsupial populations, study findings susceptible to substantial chance influences, and selection, misclassification and confounding biases. The lack of scientifically robust data available on this topic indicates that assertions that free-ranging populations of Australian marsupials are particularly susceptible to T. gondii infection and to toxoplasmosis are premature. The threat of T. gondii to the viability of free-ranging marsupial populations should therefore be regarded, at this stage, as a hypothesis. PMID:27141439

Latin American immigrants have limited access to health insurance in Japan: a cross sectional study

PubMed Central

2012-01-01

Background Japan provides universal health insurance to all legal residents. Prior research has suggested that immigrants to Japan disproportionately lack health insurance coverage, but no prior study has used rigorous methodology to examine this issue among Latin American immigrants in Japan. The aim of our study, therefore, was to assess the pattern of health insurance coverage and predictors of uninsurance among documented Latin American immigrants in Japan. Methods We used a cross sectional, mixed method approach using a probability proportional to estimated size sampling procedure. Of 1052 eligible Latin American residents mapped through extensive fieldwork in selected clusters, 400 immigrant residents living in Nagahama City, Japan were randomly selected for our study. Data were collected through face-to-face interviews using a structured questionnaire developed from qualitative interviews. Results Our response rate was 70.5% (n = 282). Respondents were mainly from Brazil (69.9%), under 40 years of age (64.5%) and had lived in Japan for 9.45 years (SE 0.44; median, 8.00). We found a high prevalence of uninsurance (19.8%) among our sample compared with the estimated national average of 1.3% in the general population. Among the insured full time workers (n = 209), 55.5% were not covered by the Employee's Health Insurance. Many immigrants cited financial trade-offs as the main reasons for uninsurance. Lacking of knowledge that health insurance is mandatory in Japan, not having a chronic disease, and having one or no children were strong predictors of uninsurance. Conclusions Lack of health insurance for immigrants in Japan is a serious concern for this population as well as for the Japanese health care system. Appropriate measures should be taken to facilitate access to health insurance for this vulnerable population. PMID:22443284

Characteristics and analysis of scientific articles submitted to the European Annals of Otorhinolaryngology, Head and Neck Diseases.

PubMed

Laccourreye, O; Bonfils, P; Denoyelle, F; Garrel, R; Jankowski, R; Karkas, A; Makeieff, M; Righini, C; Vincent, C; Martin, C

2015-09-01

To evaluate characteristics, suggested modifications and reasons for rejection in scientific articles submitted for publication in the European Annals of Otorhinolaryngology, Head and Neck Diseases. A prospective study analyzed the flaws noted by reviewers in 52 scientific articles submitted to the European Annals of Otorhinolaryngology, Head and Neck Diseases between August 31, 2014 and February 28, 2015. Fifteen flaws concerning content and 7 concerning form were identified. In more than 25% of submissions, major flaws were noted: purely descriptive paper; lack of contribution to existing state of knowledge; failure to define a clear study objective and/or analyze the impact of major variables; poorly structured Materials and methods section, lacking description of study population, objective and/or variables; lack of or inappropriate statistical analysis; Introduction verbose and/or misrepresenting the literature; excessively heterogeneous and/or poorly described study population; imprecise discussion, straying from the point, overstating the significance of results and/or introducing new results not mentioned in the Results section; description of the study population placed in the Results section instead of under Materials and methods; serious mistakes of syntax, spelling and/or tense; and failure to follow the Instructions to Authors. After review, 21.1% of articles were published, 65.3% rejected and 13.4% non-resubmitted within 3 months of review. On univariate analysis, the only variable increasing the percentage of articles accepted was the topic not being devoted to head and neck surgery (P=0.03). These results document the excessive flaw rate still to be found in manuscripts and demonstrate the continuing need for authors to master and implement the rules of scientific medical writing. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

A Trunk Support System to Identify Posture Control Mechanisms in Populations Lacking Independent Sitting

PubMed Central

Goodworth, Adam D.; Wu, Yen-Hsun; Felmlee, Duffy; Dunklebarger, Ellis; Saavedra, Sandra

2016-01-01

Populations with moderate-to-severe motor control impairments often exhibit degraded trunk control and/or lack the ability to sit unassisted. These populations need more research, yet their underdeveloped trunk control complicates identification of neural mechanisms behind their movements. The purpose of this study was to overcome this barrier by developing the first multi-articulated trunk support system to identify visual, vestibular, and proprioception contributions to posture in populations lacking independent sitting. The system provided external stability at a user-specific level on the trunk, so that body segments above the level of support required active posture control. The system included a tilting surface (controlled via servomotor) as a stimulus to investigate sensory contributions to postural responses. Frequency response and coherence functions between the surface tilt and trunk support were used to characterize system dynamics and indicated that surface tilts were accurately transmitted up to 5Hz. Feasibility of collecting kinematic data in participants lacking independent sitting was demonstrated in two populations: two typically developing infants, ~2-8 months, in a longitudinal study (8 sessions each) and four children with moderate-to-severe cerebral palsy (GMFCS III-V). Adaptability in the system was assessed by testing 16 adults (ages 18-63). Kinematic responses to continuous pseudorandom surface tilts were evaluated across 0.046–2Hz and qualitative feedback indicated that the trunk support and stimulus were comfortable for all subjects. Concepts underlying the system enable both research for, and rehabilitation in, populations lacking independent sitting. PMID:27046877

Density, distribution, and genetic structure of grizzly bears in the Cabinet-Yaak Ecosystem

USGS Publications Warehouse

Macleod, Amy C.; Boyd, Kristina L.; Boulanger, John; Royle, J. Andrew; Kasworm, Wayne F.; Paetkau, David; Proctor, Michael F.; Annis, Kim; Graves, Tabitha A.

2016-01-01

The conservation status of the 2 threatened grizzly bear (Ursus arctos) populations in the Cabinet-Yaak Ecosystem (CYE) of northern Montana and Idaho had remained unchanged since designation in 1975; however, the current demographic status of these populations was uncertain. No rigorous data on population density and distribution or analysis of recent population genetic structure were available to measure the effectiveness of conservation efforts. We used genetic detection data from hair corral, bear rub, and opportunistic sampling in traditional and spatial capture–recapture models to generate estimates of abundance and density of grizzly bears in the CYE. We calculated mean bear residency on our sampling grid from telemetry data using Huggins and Pledger models to estimate the average number of bears present and to correct our superpopulation estimates for lack of geographic closure. Estimated grizzly bear abundance (all sex and age classes) in the CYE in 2012 was 48–50 bears, approximately half the population recovery goal. Grizzly bear density in the CYE (4.3–4.5 grizzly bears/1,000 km2) was among the lowest of interior North American populations. The sizes of the Cabinet (n = 22–24) and Yaak (n = 18–22) populations were similar. Spatial models produced similar estimates of abundance and density with comparable precision without requiring radio-telemetry data to address assumptions of geographic closure. The 2 populations in the CYE were demographically and reproductively isolated from each other and the Cabinet population was highly inbred. With parentage analysis, we documented natural migrants to the Cabinet and Yaak populations by bears born to parents in the Selkirk and Northern Continental Divide populations. These events supported data from other sources suggesting that the expansion of neighboring populations may eventually help sustain the CYE populations. However, the small size, isolation, and inbreeding documented by this study demonstrate the need for comprehensive management designed to support CYE population growth and increased connectivity and gene flow with other populations.

Genetic differences among Haplorchis taichui populations in Indochina revealed by mitochondrial COX1 sequences.

PubMed

Thaenkham, U; Phuphisut, O; Nuamtanong, S; Yoonuan, T; Sa-Nguankiat, S; Vonghachack, Y; Belizario, V Y; Dung, D T; Dekumyoy, P; Waikagul, J

2017-09-01

Haplorchis taichui is an intestinal heterophyid fluke that is pathogenic to humans. It is widely distributed in Asia, with a particularly high prevalence in Indochina. Previous work revealed that the lack of gene flow between three distinct populations of Vietnamese H. taichui can be attributed to their geographic isolation with no interconnected river basins. To test the hypothesis that interconnected river basins allow gene flow between otherwise isolated populations of H. taichui, as previously demonstrated for another trematode, Opisthorchis viverrini, we compared the genetic structures of seven populations of H. taichui from various localities in the lower Mekong Basin, in Thailand and Laos, with those in Vietnam, using the mitochondrial cytochrome c oxidase subunit 1 (COX1) gene. To determine the gene flow between these H. taichui populations, we calculated their phylogenetic relationships, genetic distances and haplotype diversity. Each population showed very low nucleotide diversity at this locus. However, high levels of genetic differentiation between the populations indicated very little gene flow. A phylogenetic analysis divided the populations into four clusters that correlated with the country of origin. The negligible gene flow between the Thai and Laos populations, despite sharing the Mekong Basin, caused us to reject our hypothesis. Our data suggest that the distribution of H. taichui populations was incidentally associated with national borders.

Genetic variability of natural populations of trematodes of the genus Lecithochirium parasites of eels.

PubMed

Vilas, R; Sanmartín, M L; Paniagua, E

2004-08-01

Allozyme variation within and among populations of 3 species of the genus Lecithochirium (Trematoda: Hemiuridae) was studied by starch gel electrophoresis. In total, 19 loci were analysed in 7 populations. The level of genetic variability was relatively high in all populations. The percentage of polymorphic loci (0.95 criterion) observed per population varied from 21.0% to 55.5%, and expected heterozygosity levels varied from 0.082 to 0.197. All populations showed significant heterozygote deficiencies. In Lecithochirium fusiforme most of the deviations from Hardy-Weinberg proportions were within the populations and this species showed moderate population structuring (F(IS)=0.486, F(ST)=0.142, Nm= 1.51) and accordingly low intraspecific genetic distances (D=0.003 to 0.027). A significant lack of heterozygotes for several polymorphic loci was revealed in Lecithochirium rufoviride and Lecithochirium musculus. The most probable cause of the population genetic subdivision in L. rufoviride is the presence of at least 1 cryptic species in the populations studied. Although the lowest percentage of fixed genetic differences was that between L. fusiforme and L. musculus, two different algorithms for the construction of evolutionary trees on a matrix of genetic distances confirmed that L. fusiforme and L. rufoviride are phenetically the most closely related species.

Inference of biogeographical ancestry across central regions of Eurasia.

PubMed

Bulbul, O; Filoglu, G; Zorlu, T; Altuncul, H; Freire-Aradas, A; Söchtig, J; Ruiz, Y; Klintschar, M; Triki-Fendri, S; Rebai, A; Phillips, C; Lareu, M V; Carracedo, Á; Schneider, P M

2016-01-01

The inference of biogeographical ancestry (BGA) can provide useful information for forensic investigators when there are no suspects to be compared with DNA collected at the crime scene or when no DNA database matches exist. Although public databases are increasing in size and population scope, there is a lack of information regarding genetic variation in Eurasian populations, especially in central regions such as the Middle East. Inhabitants of these regions show a high degree of genetic admixture, characterized by an allele frequency cline running from NW Europe to East Asia. Although a proper differentiation has been established between the cline extremes of western Europe and South Asia, populations geographically located in between, i.e, Middle East and Mediterranean populations, require more detailed study in order to characterize their genetic background as well as to further understand their demographic histories. To initiate these studies, three ancestry informative SNP (AI-SNP) multiplex panels: the SNPforID 34-plex, Eurasiaplex and a novel 33-plex assay were used to describe the ancestry patterns of a total of 24 populations ranging across the longitudinal axis from NW Europe to East Asia. Different ancestry inference approaches, including STRUCTURE, PCA, DAPC and Snipper Bayes analysis, were applied to determine relationships among populations. The structure results show differentiation between continental groups and a NW to SE allele frequency cline running across Eurasian populations. This study adds useful population data that could be used as reference genotypes for future ancestry investigations in forensic cases. The 33-plex assay also includes pigmentation predictive SNPs, but this study primarily focused on Eurasian population differentiation using 33-plex and its combination with the other two AI-SNP sets.

Population Genetics of Overwintering Monarch Butterflies, Danaus plexippus (Linnaeus), from Central Mexico Inferred from Mitochondrial DNA and Microsatellite Markers

PubMed Central

Pfeiler, Edward; Nazario-Yepiz, Nestor O.; Pérez-Gálvez, Fernan; Chávez-Mora, Cristina Alejandra; Laclette, Mariana Ramírez Loustalot; Rendón-Salinas, Eduardo

2017-01-01

Abstract Population genetic variation and demographic history in Danaus plexippus (L.), from Mexico were assessed based on analyses of mitochondrial cytochrome c oxidase subunit I (COI; 658 bp) and subunit II (COII; 503 bp) gene segments and 7 microsatellite loci. The sample of 133 individuals included both migratory monarchs, mainly from 4 overwintering sites within the Monarch Butterfly Biosphere Reserve (MBBR) in central Mexico (states of Michoacán and México), and a nonmigratory population from Irapuato, Guanajuato. Haplotype (h) and nucleotide (π) diversities were relatively low, averaging 0.466 and 0.00073, respectively, for COI, and 0.629 and 0.00245 for COII. Analysis of molecular variance of the COI data set, which included additional GenBank sequences from a nonmigratory Costa Rican population, showed significant population structure between Mexican migratory monarchs and nonmigratory monarchs from both Mexico and Costa Rica, suggesting limited gene flow between the 2 behaviorally distinct groups. Interestingly, while the COI haplotype frequencies of the nonmigratory populations differed from the migratory, they were similar to each other, despite the great physical distance between them. Microsatellite analyses, however, suggested a lack of structure between the 2 groups, possibly owing to the number of significant deviations from Hardy–Weinberg equilibrium resulting from heterzoygote deficiencies found for most of the loci. Estimates of demographic history of the combined migratory MBBR monarch population, based on the mismatch distribution and Bayesian skyline analyses of the concatenated COI and COII data set (n = 89) suggested a population expansion dating to the late Pleistocene (~35000–40000 years before present) followed by a stable effective female population size (Nef) of about 6 million over the last 10000 years. PMID:28003372

Population Genetics of Overwintering Monarch Butterflies, Danaus plexippus (Linnaeus), from Central Mexico Inferred from Mitochondrial DNA and Microsatellite Markers.

PubMed

Pfeiler, Edward; Nazario-Yepiz, Nestor O; Pérez-Gálvez, Fernan; Chávez-Mora, Cristina Alejandra; Laclette, Mariana Ramírez Loustalot; Rendón-Salinas, Eduardo; Markow, Therese Ann

2017-03-01

Population genetic variation and demographic history in Danaus plexippus (L.), from Mexico were assessed based on analyses of mitochondrial cytochrome c oxidase subunit I (COI; 658 bp) and subunit II (COII; 503 bp) gene segments and 7 microsatellite loci. The sample of 133 individuals included both migratory monarchs, mainly from 4 overwintering sites within the Monarch Butterfly Biosphere Reserve (MBBR) in central Mexico (states of Michoacán and México), and a nonmigratory population from Irapuato, Guanajuato. Haplotype (h) and nucleotide (π) diversities were relatively low, averaging 0.466 and 0.00073, respectively, for COI, and 0.629 and 0.00245 for COII. Analysis of molecular variance of the COI data set, which included additional GenBank sequences from a nonmigratory Costa Rican population, showed significant population structure between Mexican migratory monarchs and nonmigratory monarchs from both Mexico and Costa Rica, suggesting limited gene flow between the 2 behaviorally distinct groups. Interestingly, while the COI haplotype frequencies of the nonmigratory populations differed from the migratory, they were similar to each other, despite the great physical distance between them. Microsatellite analyses, however, suggested a lack of structure between the 2 groups, possibly owing to the number of significant deviations from Hardy-Weinberg equilibrium resulting from heterzoygote deficiencies found for most of the loci. Estimates of demographic history of the combined migratory MBBR monarch population, based on the mismatch distribution and Bayesian skyline analyses of the concatenated COI and COII data set (n = 89) suggested a population expansion dating to the late Pleistocene (~35000-40000 years before present) followed by a stable effective female population size (Nef) of about 6 million over the last 10000 years. © The American Genetic Association 2016.

Phylogeographical structure inferred from cpDNA sequence variation of Zygophyllum xanthoxylon across north-west China.

PubMed

Shi, Xiao-Jun; Zhang, Ming-Li

2015-03-01

Zygophyllum xanthoxylon, a desert species, displaying a broad east-west continuous distribution pattern in arid Northwestern China, can be considered as a model species to investigate the biogeographical history of this region. We sequenced two chloroplast DNA spacers (psbK-psbI and rpl32-trnL) in 226 individuals from 31 populations to explore the phylogeographical structure. Median-joining network was constructed and analysis of AMOVA, SMOVA, neutrality tests and distribution analysis were used to examine genetic structure and potential range expansion. Using species distribution modeling, the geographical distribution of Z. xanthoxylon was modeled during the present and at the Last Glacial Maximum (LGM). Among 26 haplotypes, one was widely distributed, but most was restricted to either the eastern or western region. The populations with the highest levels of haplotype diversity were found in the Tianshan Mountains and its surroundings in the west, and the Helan Mountains and Alxa Plateau in the east. AMOVA and SAMOVA showed that over all populations, the species lacks phylogeographical structure, which is speculated to be the result of its specific biology. Neutrality tests and mismatch distribution analysis support past range expansions of the species. Comparing the current distribution to those cold and dry conditions in LGM, Z. xanthoxylon had a shrunken and more fragmented range during LGM. Based on the evidences from phylogeographical patterns, distribution of genetic variability, and paleodistribution modeling, Z. xanthoxylon is speculated most likely to have originated from the east and migrated westward via the Hexi Corridor.

The Symbolic Value and Limitations of Racial Concordance in Minority Research Engagement

PubMed Central

Fryer, Craig S.; Passmore, Susan R.; Maietta, Raymond C.; Petruzzelli, Jeff; Casper, Erica; Brown, Natasha A.; Butler, James; Garza, Mary A.; Thomas, Stephen B.; Quinn, Sandra C.

2015-01-01

The well-documented underrepresentation of racial and ethnic minorities in research demands action. The field of health disparities research, however, lacks scientific consensus about how best to respectfully recruit underrepresented minority populations in research. We explore the investigators’ perspective regarding how their own racial and ethnic background influenced their ability to recruit minorities, including 1) the influence of racial concordance (“race-matching”) in research recruitment, 2) attributes and shared values important in the development of trust with minority communities, and 3) the role self-reflection plays in the development of meaningful research relationships. In 2010, we conducted in-depth, semi-structured, telephone interviews with investigators (N=31) experienced with minority populations. Through the analysis of this coherent narrative, we uncovered both the symbolic and surface level assumptions regarding minority recruitment to expose a deep structure understanding of race, ethnicity, and social context that are critical for bridging the true social difference between researchers and participants. PMID:25769299

Participatory assessment of the health of Latino immigrant men in a community with a growing Latino population.

PubMed

Documėt, Patricia I; Kamouyerou, Andrea; Pesantes, Amalia; Macia, Laura; Maldonado, Hernan; Fox, Andrea; Bachurski, Leslie; Morgenstern, Dawn; Gonzalez, Miguel; Boyzo, Roberto; Guadamuz, Thomas

2015-02-01

Latino immigrant men are an understudied population in the US, especially in areas with small yet growing Latino populations. For this community-based participatory health assessment we conducted four focus groups and 66 structured surveys with Latino immigrant men, and 10 openended interviews with service providers. We analyzed transcripts using content analysis and survey data using Pearson Chi-square tests. Overall, 53% of participating men had not completed high school. Our findings suggest that their social circumstances precluded men from behaving in a way they believe would protect their health. Loneliness, fear and lack of connections prompted stress among men, who had difficulty locating healthcare services. Newly immigrated men were significantly more likely to experience depression symptoms. Latino immigrant men face social isolation resulting in negative health consequences, which are amplified by the new growth community context. Men can benefit from interventions aimed at building their social connections.

Immigration as a social determinant of health.

PubMed

Castañeda, Heide; Holmes, Seth M; Madrigal, Daniel S; Young, Maria-Elena DeTrinidad; Beyeler, Naomi; Quesada, James

2015-03-18

Although immigration and immigrant populations have become increasingly important foci in public health research and practice, a social determinants of health approach has seldom been applied in this area. Global patterns of morbidity and mortality follow inequities rooted in societal, political, and economic conditions produced and reproduced by social structures, policies, and institutions. The lack of dialogue between these two profoundly related phenomena-social determinants of health and immigration-has resulted in missed opportunities for public health research, practice, and policy work. In this article, we discuss primary frameworks used in recent public health literature on the health of immigrant populations, note gaps in this literature, and argue for a broader examination of immigration as both socially determined and a social determinant of health. We discuss priorities for future research and policy to understand more fully and respond appropriately to the health of the populations affected by this global phenomenon.

Strong genetic structure corresponds to small-scale geographic breaks in the Australian alpine grasshopper Kosciuscola tristis.

PubMed

Slatyer, Rachel A; Nash, Michael A; Miller, Adam D; Endo, Yoshinori; Umbers, Kate D L; Hoffmann, Ary A

2014-10-02

Mountain landscapes are topographically complex, creating discontinuous 'islands' of alpine and sub-alpine habitat with a dynamic history. Changing climatic conditions drive their expansion and contraction, leaving signatures on the genetic structure of their flora and fauna. Australia's high country covers a small, highly fragmented area. Although the area is thought to have experienced periods of relative continuity during Pleistocene glacial periods, small-scale studies suggest deep lineage divergence across low-elevation gaps. Using both DNA sequence data and microsatellite markers, we tested the hypothesis that genetic partitioning reflects observable geographic structuring across Australia's mainland high country, in the widespread alpine grasshopper Kosciuscola tristis (Sjösted). We found broadly congruent patterns of regional structure between the DNA sequence and microsatellite datasets, corresponding to strong divergence among isolated mountain regions. Small and isolated mountains in the south of the range were particularly distinct, with well-supported divergence corresponding to climate cycles during the late Pliocene and Pleistocene. We found mixed support, however, for divergence among other mountain regions. Interestingly, within areas of largely contiguous alpine and sub-alpine habitat around Mt Kosciuszko, microsatellite data suggested significant population structure, accompanied by a strong signature of isolation-by-distance. Consistent patterns of strong lineage divergence among different molecular datasets indicate genetic breaks between populations inhabiting geographically distinct mountain regions. Three primary phylogeographic groups were evident in the highly fragmented Victorian high country, while within-region structure detected with microsatellites may reflect more recent population isolation. Despite the small area of Australia's alpine and sub-alpine habitats, their low topographic relief and lack of extensive glaciation, divergence among populations was on the same scale as that detected in much more extensive Northern hemisphere mountain systems. The processes driving divergence in the Australian mountains might therefore differ from their Northern hemisphere counterparts.

Lessons Learned in Promoting Evidence-Based Public Health: Perspectives from Managers in State Public Health Departments.

PubMed

Allen, Peg; Jacob, Rebekah R; Lakshman, Meenakshi; Best, Leslie A; Bass, Kathryn; Brownson, Ross C

2018-03-02

Evidence-based public health (EBPH) practice, also called evidence-informed public health, can improve population health and reduce disease burden in populations. Organizational structures and processes can facilitate capacity-building for EBPH in public health agencies. This study involved 51 structured interviews with leaders and program managers in 12 state health department chronic disease prevention units to identify factors that facilitate the implementation of EBPH. Verbatim transcripts of the de-identified interviews were consensus coded in NVIVO qualitative software. Content analyses of coded texts were used to identify themes and illustrative quotes. Facilitator themes included leadership support within the chronic disease prevention unit and division, unit processes to enhance information sharing across program areas and recruitment and retention of qualified personnel, training and technical assistance to build skills, and the ability to provide support to external partners. Chronic disease prevention leaders' role modeling of EBPH processes and expectations for staff to justify proposed plans and approaches were key aspects of leadership support. Leaders protected staff time in order to identify and digest evidence to address the common barrier of lack of time for EBPH. Funding uncertainties or budget cuts, lack of political will for EBPH, and staff turnover remained challenges. In conclusion, leadership support is a key facilitator of EBPH capacity building and practice. Section and division leaders in public health agencies with authority and skills can institute management practices to help staff learn and apply EBPH processes and spread EBPH with partners.

In silico models for predicting vector control chemicals targeting Aedes aegypti

PubMed Central

Devillers, J.; Lagneau, C.; Lattes, A.; Garrigues, J.C.; Clémenté, M.M.; Yébakima, A.

2014-01-01

Human arboviral diseases have emerged or re-emerged in numerous countries worldwide due to a number of factors including the lack of progress in vaccine development, lack of drugs, insecticide resistance in mosquitoes, climate changes, societal behaviours, and economical constraints. Thus, Aedes aegypti is the main vector of the yellow fever and dengue fever flaviviruses and is also responsible for several recent outbreaks of the chikungunya alphavirus. As for the other mosquito species, the A. aegypti control relies heavily on the use of insecticides. However, because of increasing resistance to the different families of insecticides, reduction of Aedes populations is becoming increasingly difficult. Despite the unquestionable utility of insecticides in fighting mosquito populations, there are very few new insecticides developed and commercialized for vector control. This is because the high cost of the discovery of an insecticide is not counterbalanced by the ‘low profitability’ of the vector control market. Fortunately, the use of quantitative structure–activity relationship (QSAR) modelling allows the reduction of time and cost in the discovery of new chemical structures potentially active against mosquitoes. In this context, the goal of the present study was to review all the existing QSAR models on A. aegypti. The homology and pharmacophore models were also reviewed. Specific attention was paid to show the variety of targets investigated in Aedes in relation to the physiology and ecology of the mosquito as well as the diversity of the chemical structures which have been proposed, encompassing man-made and natural substances. PMID:25275884

Long-distance dispersal via ocean currents connects Omani clownfish populations throughout entire species range.

PubMed

Simpson, Stephen D; Harrison, Hugo B; Claereboudt, Michel R; Planes, Serge

2014-01-01

Dispersal is a crucial ecological process, driving population dynamics and defining the structure and persistence of populations. Measuring demographic connectivity between discreet populations remains a long-standing challenge for most marine organisms because it involves tracking the movement of pelagic larvae. Recent studies demonstrate local connectivity of reef fish populations via the dispersal of planktonic larvae, while biogeography indicates some larvae must disperse 100-1000 s kilometres. To date, empirical measures of long-distance dispersal are lacking and the full scale of dispersal is unknown. Here we provide the first measure of long-distance dispersal in a coral reef fish, the Omani clownfish Amphiprion omanensis, throughout its entire species range. Using genetic assignment tests we demonstrate bidirectional exchange of first generation migrants, with subsequent social and reproductive integration, between two populations separated by over 400 km. Immigration was 5.4% and 0.7% in each region, suggesting a biased southward exchange, and matched predictions from a physically-coupled dispersal model. This rare opportunity to measure long-distance dispersal demonstrates connectivity of isolated marine populations over distances of 100 s of kilometres and provides a unique insight into the processes of biogeography, speciation and adaptation.

Long-Distance Dispersal via Ocean Currents Connects Omani Clownfish Populations throughout Entire Species Range

PubMed Central

Claereboudt, Michel R.; Planes, Serge

2014-01-01

Dispersal is a crucial ecological process, driving population dynamics and defining the structure and persistence of populations. Measuring demographic connectivity between discreet populations remains a long-standing challenge for most marine organisms because it involves tracking the movement of pelagic larvae. Recent studies demonstrate local connectivity of reef fish populations via the dispersal of planktonic larvae, while biogeography indicates some larvae must disperse 100–1000 s kilometres. To date, empirical measures of long-distance dispersal are lacking and the full scale of dispersal is unknown. Here we provide the first measure of long-distance dispersal in a coral reef fish, the Omani clownfish Amphiprion omanensis, throughout its entire species range. Using genetic assignment tests we demonstrate bidirectional exchange of first generation migrants, with subsequent social and reproductive integration, between two populations separated by over 400 km. Immigration was 5.4% and 0.7% in each region, suggesting a biased southward exchange, and matched predictions from a physically-coupled dispersal model. This rare opportunity to measure long-distance dispersal demonstrates connectivity of isolated marine populations over distances of 100 s of kilometres and provides a unique insight into the processes of biogeography, speciation and adaptation. PMID:25229550

Ecology driving genetic variation: a comparative phylogeography of jungle cat (Felis chaus) and leopard cat (Prionailurus bengalensis) in India.

PubMed

Mukherjee, Shomita; Krishnan, Anand; Tamma, Krishnapriya; Home, Chandrima; Navya, R; Joseph, Sonia; Das, Arundhati; Ramakrishnan, Uma

2010-10-29

Comparative phylogeography links historical population processes to current/ecological processes through congruent/incongruent patterns of genetic variation among species/lineages. Despite high biodiversity, India lacks a phylogeographic paradigm due to limited comparative studies. We compared the phylogenetic patterns of Indian populations of jungle cat (Felis chaus) and leopard cat (Prionailurus bengalensis). Given similarities in their distribution within India, evolutionary histories, body size and habits, congruent patterns of genetic variation were expected. We collected scats from various biogeographic zones in India and analyzed mtDNA from 55 jungle cats (460 bp NADH5, 141 bp cytochrome b) and 40 leopard cats (362 bp NADH5, 202 bp cytochrome b). Jungle cats revealed high genetic variation, relatively low population structure and demographic expansion around the mid-Pleistocene. In contrast, leopard cats revealed lower genetic variation and high population structure with a F(ST) of 0.86 between North and South Indian populations. Niche-model analyses using two approaches (BIOCLIM and MaxEnt) support absence of leopard cats from Central India, indicating a climate associated barrier. We hypothesize that high summer temperatures limit leopard cat distribution and that a rise in temperature in the peninsular region of India during the LGM caused the split in leopard cat population in India. Our results indicate that ecological variables describing a species range can predict genetic patterns. Our study has also resolved the confusion over the distribution of the leopard cat in India. The reciprocally monophyletic island population in the South mandates conservation attention.

Ecology Driving Genetic Variation: A Comparative Phylogeography of Jungle Cat (Felis chaus) and Leopard Cat (Prionailurus bengalensis) in India

PubMed Central

Mukherjee, Shomita; Krishnan, Anand; Tamma, Krishnapriya; Home, Chandrima; R, Navya; Joseph, Sonia; Das, Arundhati; Ramakrishnan, Uma

2010-01-01

Background Comparative phylogeography links historical population processes to current/ecological processes through congruent/incongruent patterns of genetic variation among species/lineages. Despite high biodiversity, India lacks a phylogeographic paradigm due to limited comparative studies. We compared the phylogenetic patterns of Indian populations of jungle cat (Felis chaus) and leopard cat (Prionailurus bengalensis). Given similarities in their distribution within India, evolutionary histories, body size and habits, congruent patterns of genetic variation were expected. Methodology/Principal Findings We collected scats from various biogeographic zones in India and analyzed mtDNA from 55 jungle cats (460 bp NADH5, 141 bp cytochrome b) and 40 leopard cats (362 bp NADH5, 202 bp cytochrome b). Jungle cats revealed high genetic variation, relatively low population structure and demographic expansion around the mid-Pleistocene. In contrast, leopard cats revealed lower genetic variation and high population structure with a F ST of 0.86 between North and South Indian populations. Niche-model analyses using two approaches (BIOCLIM and MaxEnt) support absence of leopard cats from Central India, indicating a climate associated barrier. We hypothesize that high summer temperatures limit leopard cat distribution and that a rise in temperature in the peninsular region of India during the LGM caused the split in leopard cat population in India. Conclusions/Significance Our results indicate that ecological variables describing a species range can predict genetic patterns. Our study has also resolved the confusion over the distribution of the leopard cat in India. The reciprocally monophyletic island population in the South mandates conservation attention. PMID:21060831

[Size structure as evidence of population establishment of Pterois volitans (Scorpaeniformes: Scorpaenidae) in the South Mexican Caribbean].

PubMed

Sabido-Itzá, Miguel Mateo; Medina-Quej, Alejandro; de Jesús-Navarrete, Alberto; Gómez-Poot, Jorge Manuel; García-Rivas, María del Carmen

2016-03-01

The lionfish (P. volitans) has now invaded all the Mexican Caribbean and Gulf of Mexico, with the potential to cause negative impacts on the reefs. In the South Mexican Caribbean was firstly reported in July 2009, and six years after this report, some control measures such as fish tournament and local marketing have been implemented. However, information on its biology and invasion is still-lacking, so this study analyzed the population structure of 2 164 organisms collected from 2009 to 2012. An increase was observed in sizes for each year averaging Total length (Tl): 118 ± 34.8, 133 ± 56.3, 187 ± 74.8 and 219 ± 72.4 mm, respectively. Lionfish establishment at the study site is shown for the presence of juveniles’ sizes 20 mm TL up to 375 mm TL. When the back-calculation was obtained, we estimated that the larger fish could have recruited in early 2006, three years before the first report was made. A continuous population monitoring and an ecological study, will allow us to clarify the real impact in the ecosystems of the region and so to propose the most effective control actions.

Read count-based method for high-throughput allelic genotyping of transposable elements and structural variants.

PubMed

Kuhn, Alexandre; Ong, Yao Min; Quake, Stephen R; Burkholder, William F

2015-07-08

Like other structural variants, transposable element insertions can be highly polymorphic across individuals. Their functional impact, however, remains poorly understood. Current genome-wide approaches for genotyping insertion-site polymorphisms based on targeted or whole-genome sequencing remain very expensive and can lack accuracy, hence new large-scale genotyping methods are needed. We describe a high-throughput method for genotyping transposable element insertions and other types of structural variants that can be assayed by breakpoint PCR. The method relies on next-generation sequencing of multiplex, site-specific PCR amplification products and read count-based genotype calls. We show that this method is flexible, efficient (it does not require rounds of optimization), cost-effective and highly accurate. This method can benefit a wide range of applications from the routine genotyping of animal and plant populations to the functional study of structural variants in humans.

Energy, ecology and the distribution of microbial life.

PubMed

Macalady, Jennifer L; Hamilton, Trinity L; Grettenberger, Christen L; Jones, Daniel S; Tsao, Leah E; Burgos, William D

2013-07-19

Mechanisms that govern the coexistence of multiple biological species have been studied intensively by ecologists since the turn of the nineteenth century. Microbial ecologists in the meantime have faced many fundamental challenges, such as the lack of an ecologically coherent species definition, lack of adequate methods for evaluating population sizes and community composition in nature, and enormous taxonomic and functional diversity. The accessibility of powerful, culture-independent molecular microbiology methods offers an opportunity to close the gap between microbial science and the main stream of ecological theory, with the promise of new insights and tools needed to meet the grand challenges humans face as planetary engineers and galactic explorers. We focus specifically on resources related to energy metabolism because of their direct links to elemental cycling in the Earth's history, engineering applications and astrobiology. To what extent does the availability of energy resources structure microbial communities in nature? Our recent work on sulfur- and iron-oxidizing autotrophs suggests that apparently subtle variations in the concentration ratios of external electron donors and acceptors select for different microbial populations. We show that quantitative knowledge of microbial energy niches (population-specific patterns of energy resource use) can be used to predict variations in the abundance of specific taxa in microbial communities. Furthermore, we propose that resource ratio theory applied to micro-organisms will provide a useful framework for identifying how environmental communities are organized in space and time.

Energy, ecology and the distribution of microbial life

PubMed Central

Macalady, Jennifer L.; Hamilton, Trinity L.; Grettenberger, Christen L.; Jones, Daniel S.; Tsao, Leah E.; Burgos, William D.

2013-01-01

Mechanisms that govern the coexistence of multiple biological species have been studied intensively by ecologists since the turn of the nineteenth century. Microbial ecologists in the meantime have faced many fundamental challenges, such as the lack of an ecologically coherent species definition, lack of adequate methods for evaluating population sizes and community composition in nature, and enormous taxonomic and functional diversity. The accessibility of powerful, culture-independent molecular microbiology methods offers an opportunity to close the gap between microbial science and the main stream of ecological theory, with the promise of new insights and tools needed to meet the grand challenges humans face as planetary engineers and galactic explorers. We focus specifically on resources related to energy metabolism because of their direct links to elemental cycling in the Earth's history, engineering applications and astrobiology. To what extent does the availability of energy resources structure microbial communities in nature? Our recent work on sulfur- and iron-oxidizing autotrophs suggests that apparently subtle variations in the concentration ratios of external electron donors and acceptors select for different microbial populations. We show that quantitative knowledge of microbial energy niches (population-specific patterns of energy resource use) can be used to predict variations in the abundance of specific taxa in microbial communities. Furthermore, we propose that resource ratio theory applied to micro-organisms will provide a useful framework for identifying how environmental communities are organized in space and time. PMID:23754819

Hydrogen-bonded turns in proteins: The case for a recount

PubMed Central

Panasik, Nick; Fleming, Patrick J.; Rose, George D.

2005-01-01

β-Turns are sites at which proteins change their overall chain direction, and they occur with high frequency in globular proteins. The Protein Data Bank has many instances of conformations that resemble β-turns but lack the characteristic N–H(i) → O=C(i − 3) hydrogen bond of an authentic β-turn. Here, we identify potential hydrogen-bonded β-turns in the coil library, a Web-accessible database utility comprised of all residues not in repetitive secondary structure, neither α-helix nor β-sheet (http://www.roselab.jhu.edu/coil). In particular, candidate turns were identified as four-residue segments satisfying highly relaxed geometric criteria but lacking a strictly defined hydrogen bond. Such candidates were then subjected to a minimization protocol to determine whether slight changes in torsion angles are sufficient to shift the conformation into reference-quality geometry without deviating significantly from the original structure. This approach of applying constrained minimization to known structures reveals a substantial population of previously unidentified, stringently defined, hydrogen-bonded β-turns. In particular, 33% of coil library residues were classified as β-turns prior to minimization. After minimization, 45% of such residues could be classified as β-turns, with another 8% in 310 helixes (which closely resemble type III β-turns). Of the remaining coil library residues, 37% have backbone dihedral angles in left-handed polyproline II structure. PMID:16251367

Hydrogen-bonded turns in proteins: the case for a recount.

PubMed

Panasik, Nick; Fleming, Patrick J; Rose, George D

2005-11-01

Beta-turns are sites at which proteins change their overall chain direction, and they occur with high frequency in globular proteins. The Protein Data Bank has many instances of conformations that resemble beta-turns but lack the characteristic N-H(i) --> O=C(i - 3) hydrogen bond of an authentic beta-turn. Here, we identify potential hydrogen-bonded beta-turns in the coil library, a Web-accessible database utility comprised of all residues not in repetitive secondary structure, neither alpha-helix nor beta-sheet (http://www.roselab.jhu.edu/coil). In particular, candidate turns were identified as four-residue segments satisfying highly relaxed geometric criteria but lacking a strictly defined hydrogen bond. Such candidates were then subjected to a minimization protocol to determine whether slight changes in torsion angles are sufficient to shift the conformation into reference-quality geometry without deviating significantly from the original structure. This approach of applying constrained minimization to known structures reveals a substantial population of previously unidentified, stringently defined, hydrogen-bonded beta-turns. In particular, 33% of coil library residues were classified as beta-turns prior to minimization. After minimization, 45% of such residues could be classified as beta-turns, with another 8% in 3(10) helixes (which closely resemble type III beta-turns). Of the remaining coil library residues, 37% have backbone dihedral angles in left-handed polyproline II structure.

Demography of the Pacific walrus (Odobenus rosmarus divergens): 1974-2006

USGS Publications Warehouse

Taylor, Rebecca L.; Udevitz, Mark S.

2015-01-01

Global climate change may fundamentally alter population dynamics of many species for which baseline population parameter estimates are imprecise or lacking. Historically, the Pacific walrus is thought to have been limited by harvest, but it may become limited by global warming-induced reductions in sea ice. Loss of sea ice, on which walruses rest between foraging bouts, may reduce access to food, thus lowering vital rates. Rigorous walrus survival rate estimates do not exist, and other population parameter estimates are out of date or have well-documented bias and imprecision. To provide useful population parameter estimates we developed a Bayesian, hidden process demographic model of walrus population dynamics from 1974 through 2006 that combined annual age-specific harvest estimates with five population size estimates, six standing age structure estimates, and two reproductive rate estimates. Median density independent natural survival was high for juveniles (0.97) and adults (0.99), and annual density dependent vital rates rose from 0.06 to 0.11 for reproduction, 0.31 to 0.59 for survival of neonatal calves, and 0.39 to 0.85 for survival of older calves, concomitant with a population decline. This integrated population model provides a baseline for estimating changing population dynamics resulting from changing harvests or sea ice.

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

Silicon chemistry in interstellar clouds

NASA Technical Reports Server (NTRS)

Langer, William D.; Glassgold, A. E.

1990-01-01

A new model of interstellar silicon chemistry is presented that explains the lack of SiO detections in cold clouds and contains an exponential temperature dependence for the SiO abundance. A key aspect of the model is the sensitivity of SiO production by neutral silicon reactions to density and temperature, which arises from the dependence of the rate coefficients on the population of the excited fine-structure levels of the silicon atom. As part of the explanation of the lack of SiO detections at low temperatures and densities, the model also emphasizes the small efficiencies of the production routes and the correspondingly long times needed to reach equilibrium. Measurements of the abundance of SiO, in conjunction with theory, can provide information on the physical properties of interstellar clouds such as the abundance of oxygen bearing molecules and the depletion of interstellar silicon.

Tracking the evolutionary history of Cortinarius species in section Calochroi, with transoceanic disjunct distributions.

PubMed

Garnica, Sigisfredo; Spahn, Philipp; Oertel, Bernhard; Ammirati, Joseph; Oberwinkler, Franz

2011-07-19

Cortinarius species in section Calochroi display local, clinal and circumboreal patterns of distribution across the Northern Hemisphere where these ectomycorrhizal fungi occur with host trees throughout their geographical range within a continent, or have disjunct intercontinental distributions, the origins of which are not understood. We inferred evolutionary histories of four species, 1) C. arcuatorum, 2) C. aureofulvus, 3) C. elegantior and 4) C. napus, from populations distributed throughout the Old World, and portions of the New World (Central- and North America) based on genetic variation of 154 haplotype internal transcribed spacer (ITS) sequences from 83 population samples. By describing the population structure of these species across their geographical distribution, we attempt to identify their historical migration and patterns of diversification. Models of population structure from nested clade, demographic and coalescent-based analyses revealed genetically differentiated and geographically structured haplotypes in C. arcuatorum and C. elegantior, while C. aureofulvus showed considerably less population structure and C. napus lacked sufficient genetic differentiation to resolve any population structure. Disjunct populations within C. arcuatorum, C. aureofulvus and C. elegantior show little or no morphological differentiation, whereas in C. napus there is a high level of homoplasy and phenotypic plasticity for veil and lamellae colour. The ITS sequences of the type specimens of C. albobrunnoides and C. albobrunnoides var. violaceovelatus were identical to one another and are treated as one species with a wider range of geographic distribution under C. napus. Our results indicate that each of the Calochroi species has undergone a relatively independent evolutionary history, hypothesised as follows: 1) a widely distributed ancestral population of C. arcuatorum diverged into distinctive sympatric populations in the New World; 2) two divergent lineages in C. elegantior gave rise to the New World and Old World haplotypes, respectively; and 3) the low levels of genetic divergence within C. aureofulvus and C. napus may be the result of more recent demographic population expansions. The scenario of migration via the Bering Land Bridge provides the most probable explanation for contemporaneous disjunct geographic distributions of these species, but it does not offer an explanation for the low degree of genetic divergence between populations of C. aureofulvus and C. napus. Our findings are mostly consistent with the designation of New World allopatric populations as separate species from the European counterpart species C. arcuatorum and C. elegantior. We propose the synonymy of C. albobrunnoides, C. albobrunnoides var. violaceovelatus and C. subpurpureophyllus var. sulphureovelatus with C. napus. The results also reinforce previous observations that linked C. arcuatorum and C. aureofulvus displaying distributions in parts of North America and Europe. Interpretations of the population structure of these fungi suggest that host tree history has heavily influenced their modern distributions; however, the complex issues related to co-migration of these fungi with their tree hosts remain unclear at this time.

Genetic structure of the threatened Dipterocarpus costatus populations in lowland tropical rainforests of southern Vietnam.

PubMed

Duc, N M; Duy, V D; Xuan, B T T; Thang, B V; Ha, N T H; Tam, N M

2016-10-24

Dipterocarpus costatus is an endangered species restricted to the lowland forests of southern Vietnam. Habitat loss and over-exploitation of D. costatus wood are the major threats to this species. We investigated the level of genetic variability within and among populations of D. costatus in order to provide guidelines for the conservation, management, and restoration of this species to the Forest Protection Department, Vietnam. Nine microsatellite markers were used to analyze 114 samples from four populations representing the natural range of D. costatus in southeast Vietnam. We indicated the low allelic diversity (N A = 2.3) and low genetic diversities with an average observed and expected heterozygosity of 0.130 and 0.151, respectively, in the lowland forests of southeast Vietnam. The low genetic diversity might be a consequence of inbreeding within the small and isolated populations of D. costatus owing to its habitat loss and over-exploitation. All populations deviated from Hardy-Weinberg equilibrium showing reduced heterozygosity. Alleles were lost from the populations by genetic drift. Genetic differentiation among populations was high (average pairwise F ST = 0.405), indicating low gene flow (<1) and isolated populations due to its destructed habitat and large geographical distances (P < 0.05) among populations. Heterozygosity excess tests (except of Bu Gia Map only under infinite allele model) were negative. The high genetic variation (62.7%) was found within populations. The STRUCTURE and neighbor joining tree results suggest strong differentiation among D. costatus populations, with the three genetic clusters, Phu Quoc, Tan Phu and Bu Gia Map, and Lo Go-Xa Mat due to habitat fragmentation and isolation. The threatened status of D. costatus was related to a lack of genetic diversity, with all its populations isolated in small forest patches. We recommend the establishment of an ex situ conservation site for D. costatus with a new big population comprising all genetic groups in order to enhance its survival under different environmental stresses.

Multilocus Sequence Typing Analysis of Staphylococcus lugdunensis Implies a Clonal Population Structure

PubMed Central

Chassain, Benoît; Lemée, Ludovic; Didi, Jennifer; Thiberge, Jean-Michel; Brisse, Sylvain; Pons, Jean-Louis

2012-01-01

Staphylococcus lugdunensis is recognized as one of the major pathogenic species within the genus Staphylococcus, even though it belongs to the coagulase-negative group. A multilocus sequence typing (MLST) scheme was developed to study the genetic relationships and population structure of 87 S. lugdunensis isolates from various clinical and geographic sources by DNA sequence analysis of seven housekeeping genes (aroE, dat, ddl, gmk, ldh, recA, and yqiL). The number of alleles ranged from four (gmk and ldh) to nine (yqiL). Allelic profiles allowed the definition of 20 different sequence types (STs) and five clonal complexes. The 20 STs lacked correlation with geographic source. Isolates recovered from hematogenic infections (blood or osteoarticular isolates) or from skin and soft tissue infections did not cluster in separate lineages. Penicillin-resistant isolates clustered mainly in one clonal complex, unlike glycopeptide-tolerant isolates, which did not constitute a distinct subpopulation within S. lugdunensis. Phylogenies from the sequences of the seven individual housekeeping genes were congruent, indicating a predominantly mutational evolution of these genes. Quantitative analysis of the linkages between alleles from the seven loci revealed a significant linkage disequilibrium, thus confirming a clonal population structure for S. lugdunensis. This first MLST scheme for S. lugdunensis provides a new tool for investigating the macroepidemiology and phylogeny of this unusually virulent coagulase-negative Staphylococcus. PMID:22785196

The subtle role of climate change on population genetic structure in Canada lynx.

PubMed

Row, Jeffrey R; Wilson, Paul J; Gomez, Celine; Koen, Erin L; Bowman, Jeff; Thornton, Daniel; Murray, Dennis L

2014-07-01

Anthropogenically driven climatic change is expected to reshape global patterns of species distribution and abundance. Given recent links between genetic variation and environmental patterns, climate change may similarly impact genetic population structure, but we lack information on the spatial and mechanistic underpinnings of genetic-climate associations. Here, we show that current genetic variability of Canada lynx (Lynx canadensis) is strongly correlated with a winter climate gradient (i.e. increasing snow depth and winter precipitation from west-to-east) across the Pacific-North American (PNO) to North Atlantic Oscillation (NAO) climatic systems. This relationship was stronger than isolation by distance and not explained by landscape variables or changes in abundance. Thus, these patterns suggest that individuals restricted dispersal across the climate boundary, likely in the absence of changes in habitat quality. We propose habitat imprinting on snow conditions as one possible explanation for this unusual phenomenon. Coupling historical climate data with future projections, we also found increasingly diverging snow conditions between the two climate systems. Based on genetic simulations using projected climate data (2041-2070), we predicted that this divergence could lead to a threefold increase in genetic differentiation, potentially leading to isolated east-west populations of lynx in North America. Our results imply that subtle genetic structure can be governed by current climate and that substantive genetic differentiation and related ecological divergence may arise from changing climate patterns. © 2014 John Wiley & Sons Ltd.

Protocol and practice in the adaptive management of waterfowl harvests

USGS Publications Warehouse

Johnson, F.; Williams, K.

1999-01-01

Waterfowl harvest management in North America, for all its success, historically has had several shortcomings, including a lack of well-defined objectives, a failure to account for uncertain management outcomes, and inefficient use of harvest regulations to understand the effects of management. To address these and other concerns, the U.S. Fish and Wildlife Service began implementation of adaptive harvest management in 1995. Harvest policies are now developed using a Markov decision process in which there is an explicit accounting for uncontrolled environmental variation, partial controllability of harvest, and structural uncertainty in waterfowl population dynamics. Current policies are passively adaptive, in the sense that any reduction in structural uncertainty is an unplanned by-product of the regulatory process. A generalization of the Markov decision process permits the calculation of optimal actively adaptive policies, but it is not yet clear how state-specific harvest actions differ between passive and active approaches. The Markov decision process also provides managers the ability to explore optimal levels of aggregation or "management scale" for regulating harvests in a system that exhibits high temporal, spatial, and organizational variability. Progress in institutionalizing adaptive harvest management has been remarkable, but some managers still perceive the process as a panacea, while failing to appreciate the challenges presented by this more explicit and methodical approach to harvest regulation. Technical hurdles include the need to develop better linkages between population processes and the dynamics of landscapes, and to model the dynamics of structural uncertainty in a more comprehensive fashion. From an institutional perspective, agreement on how to value and allocate harvests continues to be elusive, and there is some evidence that waterfowl managers have overestimated the importance of achievement-oriented factors in setting hunting regulations. Indeed, it is these unresolved value judgements, and the lack of an effective structure for organizing debate, that present the greatest threat to adaptive harvest management as a viable means for coping with management uncertainty. Copyright ?? 1999 by The Resilience Alliance.

Post-Glacial Expansion and Population Genetic Divergence of Mangrove Species Avicennia germinans (L.) Stearn and Rhizophora mangle L. along the Mexican Coast

PubMed Central

Sandoval-Castro, Eduardo; Dodd, Richard S.; Riosmena-Rodríguez, Rafael; Enríquez-Paredes, Luis Manuel; Tovilla-Hernández, Cristian; López-Vivas, Juan Manuel; Aguilar-May, Bily; Muñiz-Salazar, Raquel

2014-01-01

Mangrove forests in the Gulf of California, Mexico represent the northernmost populations along the Pacific coast and thus they are likely to be source populations for colonization at higher latitudes as climate becomes more favorable. Today, these populations are relatively small and fragmented and prior research has indicated that they are poor in genetic diversity. Here we set out to investigate whether the low diversity in this region was a result of recent colonization, or fragmentation and genetic drift of once more extensive mangroves due to climatic changes in the recent past. By sampling the two major mangrove species, Rhizophora mangle and Avicennia germinans, along the Pacific and Atlantic coasts of Mexico, we set out to test whether concordant genetic signals could elucidate recent evolution of the ecosystem. Genetic diversity of both mangrove species showed a decreasing trend toward northern latitudes along the Pacific coast. The lowest levels of genetic diversity were found at the range limits around the Gulf of California and the outer Baja California peninsula. Lack of a strong spatial genetic structure in this area and recent northern gene flow in A. germinans suggest recent colonization by this species. On the other hand, lack of a signal of recent northern dispersal in R. mangle, despite the higher dispersal capability of this species, indicates a longer presence of populations, at least in the southern Gulf of California. We suggest that the longer history, together with higher genetic diversity of R. mangle at the range limits, likely provides a gene pool better able to colonize northwards under climate change than A. germinans. PMID:24699389

To donate or not donate, that is the question: an analysis of the critical factors of blood donation.

PubMed

Pereira, Jefferson Rodrigues; Sousa, Caissa Veloso E; Matos, Eliane Bragança de; Rezende, Leonardo Benedito Oliveira; Bueno, Natália Xavier; Dias, Álvaro Machado

2016-08-01

Currently, in Brazil, 1.78% of the population area blood donors, a level lower than the ideal one that, according to WHO, should be between 3% and 5% of the population. Following this scenario, the current study has a general goal of identifying and analyzing the main critical factors of the process of blood donation in the city of Belo Horizonte, MG, under the perception of donors, potential donors and non donors. A qualitative research approach was conducted, through twenty-four semi-structured interviews. The results highlight the lack of information in the various stages of the blood donation system. During the stages of donor recruitment and awareness, communication actions convey to society incomplete information about the donation process, discouraging future actions of donation. On the other hand, a lack of appreciation of the donation experience and the construction of social values associated with the donor prevent the multiplication of social behaviors for donation. The results of this study, found from theoretical framework outlined in this study, highlight the causes or critical factors that impede changes in behavior, incremental or radical, proposed by social marketing.

Optimal distribution of medical backpacks and health surveillance assistants in Malawi.

PubMed

Kunkel, Amber G; Van Itallie, Elizabeth S; Wu, Duo

2014-09-01

Despite recent progress, Malawi continues to perform poorly on key health indicators such as child mortality and life expectancy. These problems are exacerbated by a severe lack of access to health care. Health Surveillance Assistants (HSAs) help bridge this gap by providing community-level access to basic health care services. However, the success of these HSAs is limited by a lack of supplies and long distances between HSAs and patients. To address this issue, we used large-scale weighted p-median and capacitated facility location problems to create a scalable, three-tiered plan for optimal allocation of HSAs, HSA designated medical backpacks, and backpack resupply centers. Our analysis uses real data on the location and characteristics of hospitals, health centers, and the general population. In addition to offering specific recommendations for HSA, backpack, and resupply center locations, it provides general insights into the scope of the proposed HSA backpack program scale-up. In particular, it demonstrates the importance of local health centers to the resupply network. The proposed assignments are robust to changes in the underlying population structure, and could significantly improve access to medical supplies for both HSAs and patients.

The willingness to participate in health research studies of individuals with Turkish migration backgrounds: barriers and resources.

PubMed

Dingoyan, D; Schulz, H; Mösko, M

2012-06-01

Lower participation rates of ethnic minorities in health research studies and potential participation barriers are commonly reported. Four semi-structured focus groups of individuals with Turkish migration backgrounds living in Germany were conducted to identify potential participation barriers. Documented statements and superscripted presentation cards by the participants were evaluated with a qualitative content analysis. The following eight potential reasons for the lower participation rates were identified: role of women, lack of knowledge, lack of interest, German-Turkish interactions, mistrust, anxiety, data privacy protection and benefits of the study. Additionally, the following recruitment strategies to enhance participation rates were found: public relations, especially word-of-mouth promotion and contacting Turkish key figures, (non-) tangible incentives and trust building through transparent communication of the project and its conditions. The findings provide a wide range of potential participation barriers and implications that should be considered to enhance the participation rates of minority populations. The willingness to participate in health research studies can be increased through particular efforts, which should be tailored to the recruitment of the underrepresented target population. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

Providers’ Perceptions of and Receptivity toward Evidence-Based HIV Prevention Interventions

PubMed Central

Owczarzak, Jill; Dickson-Gomez, Julia

2014-01-01

Since 1999, the Centers for Disease Control have trained over 10,000 service providers from more than 5,000 agencies to implement evidence-based HIV prevention interventions through its Diffusion of Effective Behavioral Interventions (DEBI) program. Based on in-depth, semi-structured interviews with a convenience sample of 22 HIV prevention service providers from 8 agencies in Wisconsin who participated in DEBI training, this article explores providers’ motivations for attending DEBI training, perceptions of the utility and value of the DEBI program, and criticisms of the program. Providers indicated that they attended training as part of general skill-building efforts, as a way to improve services through the adoption of evidence-based interventions, and to better meet client needs. DEBI training participants were critical of the program's “top down” approach, perceived lack of fit between the DEBI and their target populations, and what they perceived as a lack of evidence that the interventions would work with their particular populations. These results suggest that in order for the DEBI program to be more widely accepted, the experiences and expertise of providers need to be more fully integrated into the processes of developing, disseminating, and adapting evidence-based HIV prevention interventions. PMID:21517660

Vertical and horizontal genetic connectivity in Chromis verater, an endemic damselfish found on shallow and mesophotic reefs in the Hawaiian Archipelago and adjacent Johnston Atoll.

PubMed

Tenggardjaja, Kimberly A; Bowen, Brian W; Bernardi, Giacomo

2014-01-01

Understanding vertical and horizontal connectivity is a major priority in research on mesophotic coral ecosystems (30-150 m). However, horizontal connectivity has been the focus of few studies, and data on vertical connectivity are limited to sessile benthic mesophotic organisms. Here we present patterns of vertical and horizontal connectivity in the Hawaiian Islands-Johnston Atoll endemic threespot damselfish, Chromis verater, based on 319 shallow specimens and 153 deep specimens. The mtDNA markers cytochrome b and control region were sequenced to analyze genetic structure: 1) between shallow (< 30 m) and mesophotic (30-150 m) populations and 2) across the species' geographic range. Additionally, the nuclear markers rhodopsin and internal transcribed spacer 2 of ribosomal DNA were sequenced to assess connectivity between shallow and mesophotic populations. There was no significant genetic differentiation by depth, indicating high levels of vertical connectivity between shallow and deep aggregates of C. verater. Consequently, shallow and deep samples were combined by location for analyses of horizontal connectivity. We detected low but significant population structure across the Hawaiian Archipelago (overall cytochrome b: ΦST = 0.009, P = 0.020; control region: ΦST = 0.012, P = 0.009) and a larger break between the archipelago and Johnston Atoll (cytochrome b: ΦST = 0.068, P < 0.001; control region: ΦST = 0.116, P < 0.001). The population structure within the archipelago was driven by samples from the island of Hawaii at the southeast end of the chain and Lisianski in the middle of the archipelago. The lack of vertical genetic structure supports the refugia hypothesis that deep reefs may constitute a population reservoir for species depleted in shallow reef habitats. These findings represent the first connectivity study on a mobile organism that spans shallow and mesophotic depths and provide a reference point for future connectivity studies on mesophotic fishes.

Vertical and Horizontal Genetic Connectivity in Chromis verater, an Endemic Damselfish Found on Shallow and Mesophotic Reefs in the Hawaiian Archipelago and Adjacent Johnston Atoll

PubMed Central

Tenggardjaja, Kimberly A.; Bowen, Brian W.; Bernardi, Giacomo

2014-01-01

Understanding vertical and horizontal connectivity is a major priority in research on mesophotic coral ecosystems (30–150 m). However, horizontal connectivity has been the focus of few studies, and data on vertical connectivity are limited to sessile benthic mesophotic organisms. Here we present patterns of vertical and horizontal connectivity in the Hawaiian Islands-Johnston Atoll endemic threespot damselfish, Chromis verater, based on 319 shallow specimens and 153 deep specimens. The mtDNA markers cytochrome b and control region were sequenced to analyze genetic structure: 1) between shallow (<30 m) and mesophotic (30–150 m) populations and 2) across the species' geographic range. Additionally, the nuclear markers rhodopsin and internal transcribed spacer 2 of ribosomal DNA were sequenced to assess connectivity between shallow and mesophotic populations. There was no significant genetic differentiation by depth, indicating high levels of vertical connectivity between shallow and deep aggregates of C. verater. Consequently, shallow and deep samples were combined by location for analyses of horizontal connectivity. We detected low but significant population structure across the Hawaiian Archipelago (overall cytochrome b: ΦST = 0.009, P = 0.020; control region: ΦST = 0.012, P = 0.009) and a larger break between the archipelago and Johnston Atoll (cytochrome b: ΦST = 0.068, P<0.001; control region: ΦST = 0.116, P<0.001). The population structure within the archipelago was driven by samples from the island of Hawaii at the southeast end of the chain and Lisianski in the middle of the archipelago. The lack of vertical genetic structure supports the refugia hypothesis that deep reefs may constitute a population reservoir for species depleted in shallow reef habitats. These findings represent the first connectivity study on a mobile organism that spans shallow and mesophotic depths and provide a reference point for future connectivity studies on mesophotic fishes. PMID:25517964

Genetic Diversity and Population Structure of Rice Varieties Cultivated in Temperate Regions.

PubMed

Reig-Valiente, Juan L; Viruel, Juan; Sales, Ester; Marqués, Luis; Terol, Javier; Gut, Marta; Derdak, Sophia; Talón, Manuel; Domingo, Concha

2016-12-01

After its domestication, rice cultivation expanded from tropical regions towards northern latitudes with temperate climate in a progressive process to overcome limiting photoperiod and temperature conditions. This process has originated a wide range of diversity that can be regarded as a valuable resource for crop improvement. In general, current rice breeding programs have to deal with a lack of both germplasm accessions specifically adapted to local agro-environmental conditions and adapted donors carrying desired agronomical traits. Comprehensive maps of genome variability and population structure would facilitate genome-wide association studies of complex traits, functional gene investigations and the selection of appropriate donors for breeding purposes. A collection of 217 rice varieties mainly cultivated in temperate regions was generated. The collection encompasses modern elite and old cultivars, as well as traditional landraces covering a wide genetic diversity available for rice breeders. Whole Genome Sequencing was performed on 14 cultivars representative of the collection and the genomic profiles of all cultivars were constructed using a panel of 2697 SNPs with wide coverage throughout the rice genome, obtained from the sequencing data. The population structure and genetic relationship analyses showed a strong substructure in the temperate rice population, predominantly based on grain type and the origin of the cultivars. Dendrogram also agrees population structure results. Based on SNP markers, we have elucidated the genetic relationship and the degree of genetic diversity among a collection of 217 temperate rice varieties possessing an enormous variety of agromorphological and physiological characters. Taken together, the data indicated the occurrence of relatively high gene flow and elevated rates of admixture between cultivars grown in remote regions, probably favoured by local breeding activities. The results of this study significantly expand the current genetic resources available for temperate varieties of rice, providing a valuable tool for future association mapping studies.

Population genetics at three spatial scales of a rare sponge living in fragmented habitats

PubMed Central

2010-01-01

Background Rare species have seldom been studied in marine habitats, mainly because it is difficult to formally assess the status of rare species, especially in patchy benthic organisms, for which samplings are often assumed to be incomplete and, thus, inappropriate for establishing the real abundance of the species. However, many marine benthic invertebrates can be considered rare, due to the fragmentation and rarity of suitable habitats. Consequently, studies on the genetic connectivity of rare species in fragmented habitats are basic for assessing their risk of extinction, especially in the context of increased habitat fragmentation by human activities. Sponges are suitable models for studying the intra- and inter-population genetic variation of rare invertebrates, as they produce lecitotrophic larvae and are often found in fragmented habitats. Results We investigated the genetic structure of a Mediterranean sponge, Scopalina lophyropoda (Schmidt), using the allelic size variation of seven specific microsatellite loci. The species can be classified as "rare" because of its strict habitat requirements, the low number of individuals per population, and the relatively small size of its distribution range. It also presents a strong patchy distribution, philopatric larval dispersal, and both sexual and asexual reproduction. Classical genetic-variance-based methods (AMOVA) and differentiation statistics revealed that the genetic diversity of S. lophyropoda was structured at the three spatial scales studied: within populations, between populations of a geographic region, and between isolated geographic regions, although some stochastic gene flow might occur among populations within a region. The genetic structure followed an isolation-by-distance pattern according to the Mantel test. However, despite philopatric larval dispersal and fission events in the species, no single population showed inbreeding, and the contribution of clonality to the population makeup was minor (only ca. 4%). Conclusions The structure of the S. lophyropoda populations at all spatial scales examined confirms the philopatric larval dispersal that has been reported. Asexual reproduction does not seem to play a relevant role in the populations. The heterozygote excess and the lack of inbreeding could be interpreted as a hitherto unknown outcrossing strategy of the species. The envisaged causes for this strategy are sperm dispersal, a strong selection against the mating of genetically related individuals to avoid inbreeding depression or high longevity of genets combined with stochastic recruitment events by larvae from other populations. It should be investigated whether this strategy could also explain the genetic diversity of many other patchy marine invertebrates whose populations remain healthy over time, despite their apparent rarity. PMID:20074333

The structure of a bottlenose dolphin society is coupled to a unique foraging cooperation with artisanal fishermen.

PubMed

Daura-Jorge, F G; Cantor, M; Ingram, S N; Lusseau, D; Simões-Lopes, P C

2012-10-23

Diverse and localized foraging behaviours have been reported in isolated populations of many animal species around the world. In Laguna, southern Brazil, a subset of resident bottlenose dolphins (Tursiops truncatus) uses a foraging tactic involving cooperative interactions with local, beach-casting fishermen. We used individual photo-identification data to assess whether cooperative and non-cooperative dolphins were socially segregated. The social structure of the population was found to be a fission-fusion system with few non-random associations, typical for this species. However, association values were greater among cooperative dolphins than among non-cooperative dolphins or between dolphins from different foraging classes. Furthermore, the dolphin social network was divided into three modules, clustering individuals that shared or lacked the cooperative foraging tactic. Space-use patterns were not sufficient to explain this partitioning, indicating a behavioural factor. The segregation of dolphins using different foraging tactics could result from foraging behaviour driving social structure, while the closer association between dolphins engaged in the cooperation could facilitate the transmission and learning of this behavioural trait from conspecifics. This unique case of a dolphin-human interaction represents a valuable opportunity to explore hypotheses on the role of social learning in wild cetaceans.

Spatial genetic structure and regional demography in the southern torrent salamander: Implications for conservation and management

USGS Publications Warehouse

Miller, Mark P.; Haig, Susan M.; Wagner, R.S.

2006-01-01

The Southern torrent salamander (Rhyacotriton variegatus) was recently found not warranted for listing under the US Endangered Species Act due to lack of information regarding population fragmentation and gene flow. Found in small-order streams associated with late-successional coniferous forests of the US Pacific Northwest, threats to their persistence include disturbance related to timber harvest activities. We conducted a study of genetic diversity throughout this species' range to 1) identify major phylogenetic lineages and phylogeographic barriers and 2) elucidate regional patterns of population genetic and spatial phylogeographic structure. Cytochrome b sequence variation was examined for 189 individuals from 72 localities. We identified 3 major lineages corresponding to nonoverlapping geographic regions: a northern California clade, a central Oregon clade, and a northern Oregon clade. The Yaquina River may be a phylogeographic barrier between the northern Oregon and central Oregon clades, whereas the Smith River in northern California appears to correspond to the discontinuity between the central Oregon and northern California clades. Spatial analyses of genetic variation within regions encompassing major clades indicated that the extent of genetic structure is comparable among regions. We discuss our results in the context of conservation efforts for Southern torrent salamanders.

Occupational chronic obstructive pulmonary disease: a systematic literature review.

PubMed

Omland, Oyvind; Würtz, Else Toft; Aasen, Tor Brøvig; Blanc, Paul; Brisman, Jonas Brisman; Miller, Martin Reginald; Pedersen, Ole Find; Schlünssen, Vivi; Sigsgaard, Torben; Ulrik, Charlotte Suppli; Viskum, Sven

2014-01-01

Occupational-attributable chronic obstructive pulmonary disease (COPD) presents a substantial health challenge. Focusing on spirometric criteria for airflow obstruction, this review of occupational COPD includes both population-wide and industry-specific exposures. We used PubMed and Embase to identify relevant original epidemiological peer-reviewed articles, supplemented with citations identified from references in key review articles. This yielded 4528 citations. Articles were excluded for lack of lung function measurement, insufficient occupational exposure classification, lack of either external or internal referents, non-accounting of age or smoking effect, or major analytic inadequacies preventing interpretation of findings. A structured data extraction sheet was used for the remaining 147 articles. Final inclusion was based on a positive qualitative Scottish Intercollegiate Guidelines Network (SIGN) score (≥2+) for study quality, yielding 25 population-wide and 34 industry/occupation-specific studies, 15 on inorganic and 19 on organic dust exposure, respectively. There was a consistent and predominantly significant association between occupational exposures and COPD in 22 of 25 population-based studies, 12 of 15 studies with an inorganic/mineral dust exposure, and 17 of 19 studies on organic exposure, even though the studies varied in design, populations, and the use of measures of exposure and outcome. A nearly uniform pattern of a dose-response relationship between various exposures and COPD was found, adding to the evidence that occupational exposures from vapors, gas, dust, and fumes are risk factors for COPD. There is strong and consistent evidence to support a causal association between multiple categories of occupational exposure and COPD, both within and across industry groups.

Genetic diversity and structure of Megabalanus azoricus in the Azores: Implications for aquaculture management

NASA Astrophysics Data System (ADS)

De Girolamo, Mirko; Torboli, Valentina; Pallavicini, Alberto; Isidro, Eduardo

2017-11-01

Megabalanus azoricus giant barnacles are the most traditional seafood of the Azores archipelago (NE Atlantic). This valuable commercial species has been highly exploited in the past and it is considered one of the key species for the development of aquaculture in the region. Despite the importance for conservation and aquaculture there is still a lack of basic information about M. azoricus genetic diversity and population structure. Here we used seven microsatellites markers to analyse 300 samples collected at six out of nine islands of the Azores archipelago, including also different locations from a single island, to provide information on the scale of genetic diversity and population structure of this species. Parameters like heterozygosity, allelic richness and effective number of alleles indicated a high genetic diversity and variability among islands. Pairwise comparisons and PCoA analysis on FST and Jost's DEST showed significant and evident differentiation among sampling locations. Additionally, AMOVA allocates a small (6.02%) but statistically significant portion of the variance to the among Island level revealing also a weak resolution (1.87%) at finer scale. Additionally Monte Carlo resampling methods indicated the most likely sources of the recruits were the local or adjacent populations. Genetic risks associated with the giant barnacle potential production scheme should be taken into account in a future management plan delimiting, as precautionary measure, this culture at a single island or at groups of islands here identified. Moreover a monitoring strategy should be implemented with the aim to evaluate possible changes in genetic parameters of native populations.

Low genetic differentiation in a sedentary bird: house sparrow population genetics in a contiguous landscape

PubMed Central

Kekkonen, J; Seppä, P; Hanski, I K; Jensen, H; Väisänen, R A; Brommer, J E

2011-01-01

The house sparrow Passer domesticus has been declining in abundance in many localities, including Finland. We studied the genetic diversity and differentiation of the house sparrow populations across Finland in the 1980s, at the onset of the species' decline in abundance. We genotyped 472 adult males (the less dispersive sex) from 13 locations in Finland (covering a range of 400 × 800 km) and one in Sweden (Stockholm) for 13 polymorphic microsatellite markers. Our analysis of Finnish ringing records showed that natal dispersal distances are limited (90% <16 km), which confirmed earlier finding from other countries. The Finnish populations were panmictic, and genetically very homogeneous and the limited dispersal was sufficiently large to maintain their connectivity. However, all Finnish populations differed significantly from the Stockholm population, even though direct geographical distance to it was often smaller than among Finnish populations. Hence, the open sea between Finland and Sweden appears to form a dispersal barrier for this species, whereas dispersal is much less constrained across the Finnish mainland (which lacks geographical barriers). Our findings provide a benchmark for conservation biologists and emphasize the influence of landscape structure on gene flow. PMID:20372181

Dissecting maize diversity in lowland South America: genetic structure and geographic distribution models.

PubMed

Bracco, Mariana; Cascales, Jimena; Hernández, Julián Cámara; Poggio, Lidia; Gottlieb, Alexandra M; Lia, Verónica V

2016-08-26

Maize landraces from South America have traditionally been assigned to two main categories: Andean and Tropical Lowland germplasm. However, the genetic structure and affiliations of the lowland gene pools have been difficult to assess due to limited sampling and the lack of comparative analysis. Here, we examined SSR and Adh2 sequence variation in a diverse sample of maize landraces from lowland middle South America, and performed a comprehensive integrative analysis of population structure and diversity including already published data of archaeological and extant specimens from the Americas. Geographic distribution models were used to explore the relationship between environmental factors and the observed genetic structure. Bayesian and multivariate analyses of population structure showed the existence of two previously overlooked lowland gene pools associated with Guaraní indigenous communities of middle South America. The singularity of this germplasm was also evidenced by the frequency distribution of microsatellite repeat motifs of the Adh2 locus and the distinct spatial pattern inferred from geographic distribution models. Our results challenge the prevailing view that lowland middle South America is just a contact zone between Andean and Tropical Lowland germplasm and highlight the occurrence of a unique, locally adapted gene pool. This information is relevant for the conservation and utilization of maize genetic resources, as well as for a better understanding of environment-genotype associations.

Population Pharmacokinetic Model of Doxycycline Plasma Concentrations Using Pooled Study Data

PubMed Central

Wojciechowski, Jessica; Mudge, Stuart; Upton, Richard N.; Foster, David J. R.

2017-01-01

ABSTRACT The literature presently lacks a population pharmacokinetic analysis of doxycycline. This study aimed to develop a population pharmacokinetic model of doxycycline plasma concentrations that could be used to assess the power of bioequivalence between Doryx delayed-release tablets and Doryx MPC. Doxycycline pharmacokinetic data were available from eight phase 1 clinical trials following single/multiple doses of conventional-release doxycycline capsules, Doryx delayed-release tablets, and Doryx MPC under fed and fasted conditions. A population pharmacokinetic model was developed in a stepwise manner using NONMEM, version 7.3. The final covariate model was developed according to a forward inclusion (P < 0.01) and then backward deletion (P < 0.001) procedure. The final model was a two-compartment model with two-transit absorption compartments. Structural covariates in the base model included formulation effects on relative bioavailability (F), absorption lag (ALAG), and the transit absorption rate (KTR) under the fed status. An absorption delay (lag) for the fed status (FTLAG2 = 0.203 h) was also included in the model as a structural covariate. The fed status was observed to decrease F by 10.5%, and the effect of female sex was a 14.4% increase in clearance. The manuscript presents the first population pharmacokinetic model of doxycycline plasma concentrations following oral doxycycline administration. The model was used to assess the power of bioequivalence between Doryx delayed-release tablets and Doryx MPC, and it could potentially be used to critically examine and optimize doxycycline dose regimens. PMID:28052851

Population Pharmacokinetic Model of Doxycycline Plasma Concentrations Using Pooled Study Data.

PubMed

Hopkins, Ashley M; Wojciechowski, Jessica; Abuhelwa, Ahmad Y; Mudge, Stuart; Upton, Richard N; Foster, David J R

2017-03-01

The literature presently lacks a population pharmacokinetic analysis of doxycycline. This study aimed to develop a population pharmacokinetic model of doxycycline plasma concentrations that could be used to assess the power of bioequivalence between Doryx delayed-release tablets and Doryx MPC. Doxycycline pharmacokinetic data were available from eight phase 1 clinical trials following single/multiple doses of conventional-release doxycycline capsules, Doryx delayed-release tablets, and Doryx MPC under fed and fasted conditions. A population pharmacokinetic model was developed in a stepwise manner using NONMEM, version 7.3. The final covariate model was developed according to a forward inclusion ( P < 0.01) and then backward deletion ( P < 0.001) procedure. The final model was a two-compartment model with two-transit absorption compartments. Structural covariates in the base model included formulation effects on relative bioavailability ( F ), absorption lag (ALAG), and the transit absorption rate (KTR) under the fed status. An absorption delay (lag) for the fed status (FTLAG2 = 0.203 h) was also included in the model as a structural covariate. The fed status was observed to decrease F by 10.5%, and the effect of female sex was a 14.4% increase in clearance. The manuscript presents the first population pharmacokinetic model of doxycycline plasma concentrations following oral doxycycline administration. The model was used to assess the power of bioequivalence between Doryx delayed-release tablets and Doryx MPC, and it could potentially be used to critically examine and optimize doxycycline dose regimens. Copyright © 2017 American Society for Microbiology.

A successful strategy for the recovering of active P21, an insoluble recombinant protein of Trypanosoma cruzi

NASA Astrophysics Data System (ADS)

Santos, Marlus Alves Dos; Teixeira, Francesco Brugnera; Moreira, Heline Hellen Teixeira; Rodrigues, Adele Aud; Machado, Fabrício Castro; Clemente, Tatiana Mordente; Brigido, Paula Cristina; Silva, Rebecca Tavares E.; Purcino, Cecílio; Gomes, Rafael Gonçalves Barbosa; Bahia, Diana; Mortara, Renato Arruda; Munte, Claudia Elisabeth; Horjales, Eduardo; da Silva, Claudio Vieira

2014-03-01

Structural studies of proteins normally require large quantities of pure material that can only be obtained through heterologous expression systems and recombinant technique. In these procedures, large amounts of expressed protein are often found in the insoluble fraction, making protein purification from the soluble fraction inefficient, laborious, and costly. Usually, protein refolding is avoided due to a lack of experimental assays that can validate correct folding and that can compare the conformational population to that of the soluble fraction. Herein, we propose a validation method using simple and rapid 1D 1H nuclear magnetic resonance (NMR) spectra that can efficiently compare protein samples, including individual information of the environment of each proton in the structure.

A Pilot Study of Deaf Trauma Survivors’ Experiences: Early Traumas Unique to Being Deaf in a Hearing World

PubMed Central

Wolf Craig, Kelly S.; Hall, Wyatte C.; Ziedonis, Douglas M.

2016-01-01

Conducting semi-structured American Sign Language interviews with 17 Deaf trauma survivors, this pilot study explored Deaf individuals’ trauma experiences and whether these experiences generally align with trauma in the hearing population. Most commonly reported traumas were physical assault, sudden unexpected deaths, and “other” very stressful events. Although some “other” events overlap with traumas in the general population, many are unique to Deaf people (e.g., corporal punishment at oral/aural school if caught using sign language, utter lack of communication with hearing parents). These findings suggest that Deaf individuals may experience developmental traumas distinct to being raised in a hearing world. Such traumas are not captured by available trauma assessments, nor are they considered in evidence-based trauma treatments. PMID:28138351

A Pilot Study of Deaf Trauma Survivors' Experiences: Early Traumas Unique to Being Deaf in a Hearing World.

PubMed

Anderson, Melissa L; Wolf Craig, Kelly S; Hall, Wyatte C; Ziedonis, Douglas M

2016-12-01

Conducting semi-structured American Sign Language interviews with 17 Deaf trauma survivors, this pilot study explored Deaf individuals' trauma experiences and whether these experiences generally align with trauma in the hearing population. Most commonly reported traumas were physical assault, sudden unexpected deaths, and "other" very stressful events. Although some "other" events overlap with traumas in the general population, many are unique to Deaf people (e.g., corporal punishment at oral/aural school if caught using sign language, utter lack of communication with hearing parents). These findings suggest that Deaf individuals may experience developmental traumas distinct to being raised in a hearing world. Such traumas are not captured by available trauma assessments, nor are they considered in evidence-based trauma treatments.

[The singularity of population policies in Latin America and the Caribbean in the late 20th century].

PubMed

Sojo, A

1993-06-01

This work questions the assumption that population policies in Latin America and the Caribbean are closely related to population growth, identifies common obstacles to population policies, and recommends actions to increase the efficacy of population policies. The demographic transition has occurred in Latin American countries with widely varying levels of economic development, cultural traditions, and family planning programs. The governments of the region that regard their rates of population growth and fertility as satisfactory seldom intervene to modify them. The demographic transition is well underway in all these countries except Guatemala and Paraguay. A diverse array of strategies has been used by the countries that have achieved significant fertility reductions, ranging from family planning services provided through the national health system in Mexico to key roles by the private and commercial sectors and intensive use of the mass media in Brazil. Governments adopting population policies defined various institutional forms for them, ranging from small technical units at a high level to interministerial councils. Institutionalization of population policies created high hopes for integration of population concerns into development strategies, but performance has largely failed to meet expectations, both because of the fragility and inferior status in the government bureaucracy of policy structures, and because of their inability to develop effective programs integrating population and development. The economic crisis of the 1980s lowered the priority of population themes. Political instability, lack of adequate human resources and financing, limited decision making capacity, and failure to establish strong interinstitutional ties have all been factors in the disappointing results of population policies. The difficulty of pinpointing exactly what constitutes the population policy and the tendency to equate population policy and family planning have been other factors hindering their full implementation. The effectiveness of population policies appears to have been compromised by their lack of specificity among government policies. To increase their efficacy it will be necessary to define their uniqueness with respect to other social policies. Population policies, their institutional framework, and the actors called upon to support then must be redefined. A national population policy should orient interventions in three areas: establishment of consensus regarding population goals, channeling funds to the implementing agencies, and providing follow-up and evaluation of demographic effects. Implementation of population policies and programs should be decentralized and should be achieved through insertion of population parameters in the activities of the health, education, and other social sectors.

Genetic differentiation and phylogeography of Mediterranean-North Eastern Atlantic blue shark (Prionace glauca, L. 1758) using mitochondrial DNA: panmixia or complex stock structure?

PubMed Central

Damalas, Dimitrios; Martinsohn, Jann; Zanzi, Antonella; Mariani, Stefano; Sperone, Emilio; Micarelli, Primo; Garibaldi, Fulvio; Megalofonou, Persefoni; Bargelloni, Luca; Franch, Rafaella; Macias, David; Prodöhl, Paulo; Fitzpatrick, Séan; Stagioni, Marco; Tinti, Fausto; Cariani, Alessia

2017-01-01

Background The blue shark (Prionace glauca, Linnaeus 1758) is one of the most abundant epipelagic shark inhabiting all the oceans except the poles, including the Mediterranean Sea, but its genetic structure has not been confirmed at basin and interoceanic distances. Past tagging programs in the Atlantic Ocean failed to find evidence of migration of blue sharks between the Mediterranean and the adjacent Atlantic, despite the extreme vagility of the species. Although the high rate of by-catch in the Mediterranean basin, to date no genetic study on Mediterranean blue shark was carried out, which constitutes a significant knowledge gap, considering that this population is classified as “Critically Endangered”, unlike its open-ocean counterpart. Methods Blue shark phylogeography and demography in the Mediterranean Sea and North-Eastern Atlantic Ocean were inferred using two mitochondrial genes (Cytb and control region) amplified from 207 and 170 individuals respectively, collected from six localities across the Mediterranean and two from the North-Eastern Atlantic. Results Although no obvious pattern of geographical differentiation was apparent from the haplotype network, Φst analyses indicated significant genetic structure among four geographical groups. Demographic analyses suggest that these populations have experienced a constant population expansion in the last 0.4–0.1 million of years. Discussion The weak, but significant, differences in Mediterranean and adjacent North-eastern Atlantic blue sharks revealed a complex phylogeographic structure, which appears to reject the assumption of panmixia across the study area, but also supports a certain degree of population connectivity across the Strait of Gibraltar, despite the lack of evidence of migratory movements observed by tagging data. Analyses of spatial genetic structure in relation to sex-ratio and size could indicate some level of sex/stage biased migratory behaviour. PMID:29230359

Low but significant genetic differentiation underlies biologically meaningful phenotypic divergence in a large Atlantic salmon population.

PubMed

Aykanat, Tutku; Johnston, Susan E; Orell, Panu; Niemelä, Eero; Erkinaro, Jaakko; Primmer, Craig R

2015-10-01

Despite decades of research assessing the genetic structure of natural populations, the biological meaning of low yet significant genetic divergence often remains unclear due to a lack of associated phenotypic and ecological information. At the same time, structured populations with low genetic divergence and overlapping boundaries can potentially provide excellent models to study adaptation and reproductive isolation in cases where high-resolution genetic markers and relevant phenotypic and life history information are available. Here, we combined single nucleotide polymorphism (SNP)-based population inference with extensive phenotypic and life history data to identify potential biological mechanisms driving fine-scale subpopulation differentiation in Atlantic salmon (Salmo salar) from the Teno River, a major salmon river in Europe. Two sympatrically occurring subpopulations had low but significant genetic differentiation (FST  = 0.018) and displayed marked differences in the distribution of life history strategies, including variation in juvenile growth rate, age at maturity and size within age classes. Large, late-maturing individuals were virtually absent from one of the two subpopulations, and there were significant differences in juvenile growth rates and size at age after oceanic migration between individuals in the respective subpopulations. Our findings suggest that different evolutionary processes affect each subpopulation and that hybridization and subsequent selection may maintain low genetic differentiation without hindering adaptive divergence. © 2015 John Wiley & Sons Ltd.

Early modern human diversity suggests subdivided population structure and a complex out-of-Africa scenario

PubMed Central

Gunz, Philipp; Bookstein, Fred L.; Mitteroecker, Philipp; Stadlmayr, Andrea; Seidler, Horst; Weber, Gerhard W.

2009-01-01

The interpretation of genetic evidence regarding modern human origins depends, among other things, on assessments of the structure and the variation of ancient populations. Because we lack genetic data from the time when the first anatomically modern humans appeared, between 200,000 and 60,000 years ago, instead we exploit the phenotype of neurocranial geometry to compare the variation in early modern human fossils with that in other groups of fossil Homo and recent modern humans. Variation is assessed as the mean-squared Procrustes distance from the group average shape in a representation based on several hundred neurocranial landmarks and semilandmarks. We find that the early modern group has more shape variation than any other group in our sample, which covers 1.8 million years, and that they are morphologically similar to recent modern humans of diverse geographically dispersed populations but not to archaic groups. Of the currently competing models of modern human origins, some are inconsistent with these findings. Rather than a single out-of-Africa dispersal scenario, we suggest that early modern humans were already divided into different populations in Pleistocene Africa, after which there followed a complex migration pattern. Our conclusions bear implications for the inference of ancient human demography from genetic models and emphasize the importance of focusing research on those early modern humans, in particular, in Africa. PMID:19307568

Population genetic structure and connectivity in the widespread coral-reef fish Abudefduf saxatilis: the role of historic and contemporary factors

NASA Astrophysics Data System (ADS)

Piñeros, Victor Julio; Gutiérrez-Rodríguez, Carla

2017-09-01

We assessed geographic patterns of genetic variation and connectivity in the widely distributed coral-reef fish Abudefduf saxatilis at different temporal scales. We sequenced two mitochondrial regions (cytochrome b and control region) and genotyped 12 microsatellite loci in a total of 296 individuals collected from 14 reefs in two biogeographic provinces in the tropical western Atlantic Ocean and from three provinces within the Caribbean Sea. We used phylogeography, population genetics and coalescent methods to assess the potential effects of climatic oscillations in the Pleistocene and contemporary oceanographic barriers on the population genetic structure and connectivity of the species. Sequence analyses indicated high genetic diversity and a lack of genetic differentiation throughout the Caribbean and between the two biogeographic provinces. Different lines of evidence depicted demographic expansions of A. saxatilis populations dated to the Pleistocene. The microsatellites exhibited high genetic diversity, and no genetic differentiation was detected within the Caribbean; however, these markers identified a genetic discontinuity between the two western Atlantic biogeographic provinces. Migration estimates revealed gene flow across the Amazon-Orinoco Plume, suggesting that genetic divergence may be promoted by differential environmental conditions on either side of the barrier. The climatic oscillations of the Pleistocene, together with oceanographic barriers and the dispersal potential of the species, constitute important factors determining the geographic patterns of genetic variation in A. saxatilis.

Genetic monogamy despite social promiscuity in the pot-bellied seahorse (Hippocampus abdominalis).

PubMed

Wilson, A B; Martin-Smith, K M

2007-06-01

Sexual selection theory predicts a positive correlation between relative parental investment and mate choice. In syngnathid fishes (seahorses and pipefish), males brood offspring in specialized brooding structures. While female-female mating competition has been demonstrated in some pipefishes, all seahorses (genus Hippocampus) studied to date have been found to have conventional sex roles with greater male-male competition for access to mates despite possessing the most complex brood structures in the family. Although multiple mating is common in pipefish, seahorses are again exceptional, exhibiting strict genetic monogamy. Both demographic and behavioural explanations have been offered to explain the lack of multiple mating in seahorse species, but these hypotheses have not yet been explicitly addressed. We investigated mating systems and brood parentage of the pot-bellied seahorse, Hippocampus abdominalis, a temperate-water species that is socially promiscuous with conventional sex roles in laboratory populations. We observed promiscuous courtship behaviour and sex-role reversal in high density, female-biased field populations of H. abdominalis. We hypothesize that sex roles are plastic in H. abdominalis, depending on local population density and sex ratio. Despite promiscuous courtship behaviour, all assayed male seahorses were genetically monogamous in both laboratory and wild populations. Physiological limitations associated with embryo incubation may explain the absence of multiple mating in seahorses and may have played an important role in the development of the unique reproductive behaviour typical in these species.

Lack of genetic structure among ecologically adapted populations of an Australian rainforest Drosophila species as indicated by microsatellite markers and mitochondrial DNA sequences.

PubMed

Schiffer, Michele; Kennington, W J; Hoffmann, A A; Blacket, M J

2007-04-01

Although fragmented rainforest environments represent hotspots for invertebrate biodiversity, few genetic studies have been conducted on rainforest invertebrates. Thus, it is not known if invertebrate species in rainforests are highly genetically fragmented, with the potential for populations to show divergent selection responses, or if there are low levels of gene flow sufficient to maintain genetic homogeneity among fragmented populations. Here we use microsatellite markers and DNA sequences from the mitochondrial ND5 locus to investigate genetic differences among Drosophila birchii populations from tropical rainforests in Queensland, Australia. As found in a previous study, mitochondrial DNA diversity was low with no evidence for population differentiation among rainforest fragments. The pattern of mitochondrial haplotype variation was consistent with D. birchii having undergone substantial past population growth. Levels of nuclear genetic variation were high in all populations while F(ST) values were very low, even for flies from geographically isolated areas of rainforest. No significant differentiation was observed between populations on either side of the Burdekin Gap (a long-term dry corridor), although there was evidence for higher gene diversity in low-latitude populations. Spatial autocorrelation coefficients were low and did not differ significantly from random, except for one locus which revealed a clinal-like pattern. Comparisons of microsatellite differentiation contrasted with previously established clinal patterns in quantitative traits in D. birchii, and indicate that the patterns in quantitative traits are likely to be due to selection. These results suggest moderate gene flow in D. birchii over large distances. Limited population structure in this species appears to be due to recent range expansions or cycles of local extinctions followed by recolonizations/expansions. Nevertheless, patterns of local adaptation have developed in D. birchii that may result in populations showing different selection responses when faced with environmental change.

Population declines lead to replicate patterns of internal range structure at the tips of the distribution of the California red-legged frog (Rana draytonii)

USGS Publications Warehouse

Richmond, Jonathan Q.; Backlin, Adam R.; Tatarian, Patricia J.; Solvesky, Ben G.; Fisher, Robert N.

2014-01-01

Demographic declines and increased isolation of peripheral populations of the threatened California red-legged frog (Rana draytonii) have led to the formation of internal range boundaries at opposite ends of the species’ distribution. While the population genetics of the southern internal boundary has been studied in some detail, similar information is lacking for the northern part of the range. In this study, we used microsatellite and mtDNA data to examine the genetic structuring and diversity of some of the last remaining R. draytonii populations in the northern Sierra Nevada, which collectively form the northern external range boundary. We compared these data to coastal populations in the San Francisco Bay Area, where the species is notably more abundant and still exists throughout much of its historic range. We show that ‘external’ Sierra Nevada populations have lower genetic diversity and are more differentiated from one another than their ‘internal’ Bay Area counterparts. This same pattern was mirrored across the distribution in California, where Sierra Nevada and Bay Area populations had lower allelic variability compared to those previously studied in coastal southern California. This genetic signature of northward range expansion was mirrored in the phylogeography of mtDNA haplotypes; northern Sierra Nevada haplotypes showed greater similarity to haplotypes from the south Coast Ranges than to the more geographically proximate populations in the Bay Area. These data cast new light on the geographic origins of Sierra Nevada R. draytonii populations and highlight the importance of distinguishing the genetic effects of contemporary demographic declines from underlying signatures of historic range expansion when addressing the most immediate threats to population persistence. Because there is no evidence of contemporary gene flow between any of the Sierra Nevada R. draytonii populations, we suggest that management activities should focus on maintaining and creating additional ponds to support breeding within typical dispersal distances of occupied habitat.

Effects of seed bank disturbance on the fine-scale genetic structure of populations of the rare shrub Grevillea macleayana.

PubMed

England, P R; Whelan, R J; Ayre, D J

2003-11-01

Dispersal in most plants is mediated by the movement of seeds and pollen, which move genes across the landscape differently. Grevillea macleayana is a rare, fire-dependent Australian shrub with large seeds lacking adaptations for dispersal; yet it produces inflorescences adapted to pollination by highly mobile vertebrates (eg birds). Interpreting fine-scale genetic structure in the light of these two processes is confounded by the recent imposition of anthropogenic disturbances with potentially contrasting genetic consequences: (1) the unusual foraging behaviour of exotic honeybees and 2. widespread disturbance of the soil-stored seedbank by road building and quarrying. To test for evidence of fine-scale genetic structure within G. macleayana populations and to test the prediction that such structure might be masked by disturbance of the seed bank, we sampled two sites in undisturbed habitat and compared their genetic structure with two sites that had been strongly affected by road building using a test for spatial autocorrelation of genotypes. High selfing levels inferred from genotypes at all four sites implies that pollen dispersal is limited. Consistent with this, we observed substantial spatial clustering of genes at 10 m or less in the two undisturbed populations and argue that this reflects the predicted effects of both high selfing levels and limited seed dispersal. In contrast, at the two sites disturbed by road building, spatial autocorrelation was weak. This suggests there has been mixing of the seed bank, counteracting the naturally low dispersal and elevated selfing due to honeybees. Pollination between near neighbours with reduced relatedness potentially has fitness consequences for G. macleayana in disturbed sites.

Conservation genetics of extremely isolated urban populations of the northern dusky salamander (Desmognathus fuscus) in New York City

PubMed Central

Zak, Yana; Pehek, Ellen

2013-01-01

Urbanization is a major cause of amphibian decline. Stream-dwelling plethodontid salamanders are particularly susceptible to urbanization due to declining water quality and hydrological changes, but few studies have examined these taxa in cities. The northern dusky salamander (Desmognathus fuscus) was once common in the New York City metropolitan area, but has substantially declined throughout the region in recent decades. We used five tetranucleotide microsatellite loci to examine population differentiation, genetic variation, and bottlenecks among five remnant urban populations of dusky salamanders in NYC. These genetic measures provide information on isolation, prevalence of inbreeding, long-term prospects for population persistence, and potential for evolutionary responses to future environmental change. All populations were genetically differentiated from each other, and the most isolated populations in Manhattan have maintained very little genetic variation (i.e. <20% heterozygosity). A majority of the populations also exhibited evidence of genetic bottlenecks. These findings contrast with published estimates of high genetic variation within and lack of structure between populations of other desmognathine salamanders sampled over similar or larger spatial scales. Declines in genetic variation likely resulted from population extirpations and the degradation of stream and terrestrial paths for dispersal in NYC. Loss of genetic variability in populations isolated by human development may be an underappreciated cause and/or consequence of the decline of this species in urbanized areas of the northeast USA. PMID:23646283

Microgeographic Population Structuring of Culex quinquefasciatus (Diptera: Culicidae) From São Paulo, Brazil.

PubMed

Wilke, André Barretto Bruno; de Carvalho, Gabriela Cristina; Marrelli, Mauro Toledo

2017-11-07

The continuing worldwide increase in urbanization can potentially have a major impact on the epidemiology of vector-borne diseases, as anthropogenic changes to the environment are known to favor a few species of mosquitoes that can thrive in urban environments. Culex quinquefasciatus Say (Diptera: Culicidae) is found extensively in urban habitats, where it lives in degraded, polluted areas and is often the only species of mosquito capable to surviving under such conditions. Traditional mosquito control strategies no longer have the desired effect due to the several factors such as insecticide resistance, abundance of breeding sites, lack of proper sewage and sanitation, and absence of natural predator, leading Cx. quinquefasciatus populations to increase its numbers in cities. In this study, five Cx. quinquefasciatus populations were analyzed using 12 microsatellite markers to investigate whether the dynamics of these populations are being modulated by urbanization and how they are structured in the city of São Paulo, Brazil. Our results indicate that only one of the study populations (the population from Anhanguera Park) exhibited evidence of expansion. The populations from Ibirapuera Park and Piqueri Park, the most urbanized regions of the areas studied, did not show signs of expansion. A better understanding of the mechanisms involved in the dispersal of Cx. quinquefasciatus and its colonization of new areas, as well as the species' demographic patterns and how these are associated with urbanization, particularly in areas undergoing a rural-to-urban transformation, such as Anhanguera Park, is of great importance for mosquito control. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

3-D habitat suitability of jack mackerel Trachurus murphyi in the Southeastern Pacific, a comprehensive study

NASA Astrophysics Data System (ADS)

Bertrand, Arnaud; Habasque, Jérémie; Hattab, Tarek; Hintzen, Niels T.; Oliveros-Ramos, Ricardo; Gutiérrez, Mariano; Demarcq, Hervé; Gerlotto, François

2016-08-01

South Pacific jack mackerel, Trachurus murphyi, has an ocean-scale distribution, from the South American coastline to New Zealand and Tasmania. This fish, captured by Humans since the Holocene, is nowadays heavily exploited and its population has decreased substantially since the mid-1990s. The uncertainty associated to jack mackerel population structure currently hampers management. Several hypotheses have been proposed from a single population up to several discrete populations. Still no definitive answer was given. Determining how environmental conditions drive jack mackerel distribution can provide insights on its population structure. To do so, here we performed in three steps. First, we used satellite data to develop a statistical model of jack mackerel horizontal habitat suitability. Model predictions based on interaction between temperature and chlorophyll-a match the observed jack mackerel distribution, even during extreme El Niño event. Second, we studied the impact of oxygen and show that jack mackerel distribution and abundance is correlated to oxygen over a wide variety of scales and avoid low oxygen areas and periods. Third, on the basis of the above we built a conceptual 3D model of jack mackerel habitat in the Southeastern Pacific. We reveal the presence of a low suitable habitat along the Chilean and Peruvian coast, figuratively presenting a closed door caused by a gap in the horizontal habitat at ∼19-22°S and a shallow oxycline off south-centre Peru. This kind of situation likely occurs on a seasonal basis, in austral summer but also at longer temporal scales. A lack of exchanges at some periods/seasons partially isolate jack mackerel distributed off Peru. On the other hand the continuity in the habitat during most of the year explains why exchanges occur. We conclude that the more likely population structure for jack mackerel is a pelagic metapopulation.

Collaboration between non-governmental organizations and public services in health – a qualitative case study from rural Ecuador

PubMed Central

Biermann, Olivia; Eckhardt, Martin; Carlfjord, Siw; Falk, Magnus; Forsberg, Birger C.

2016-01-01

Background Non-governmental organizations (NGOs) have a key role in improving health in low- and middle-income countries. Their work needs to be synergistic, complementary to public services, and rooted in community mobilization and collective action. The study explores how an NGO and its health services are perceived by the population that it serves, and how it can contribute to reducing barriers to care. Design A qualitative exploratory study was conducted in remote Ecuador, characterized by its widespread poverty and lack of official governance. An international NGO collaborated closely with the public services to deliver preventative and curative health services. Data were collected using focus group discussions and semistructured interviews with purposively sampled community members, healthcare personnel, and community health workers based on their links to the health services. Conventional qualitative content analysis was used, focusing on manifest content. Results Emerging themes relate to the public private partnership (PPP), the NGO and its services, and community participation. The population perceives the NGO positively, linking it to healthcare improvements. Their priority is to get services, irrespective of the provider's structure. The presence of an NGO in the operation may contribute to unrealistic expectations of health services, affecting perceptions of the latter negatively. Conclusions To avoid unrealistic expectations and dissatisfaction, and to increase and sustain the population's trust in the organization, an NGO should operate in a manner that is as integrated as possible within the existing structure. The NGO should work close to the population it serves, with services anchored in the community. PPP parties should develop a common platform with joint messages to the target population on the provider's structure, and regarding partners’ roles and responsibilities. Interaction between the population and the providers on service content and their expectations is key to positive outcomes of PPP operations. PMID:27852423

Genetic differentiation of spring-spawning and fall-spawning male Atlantic sturgeon in the James River, Virginia

PubMed Central

Balazik, Matthew T.; Farrae, Daniel J.; Darden, Tanya L.; Garman, Greg C.

2017-01-01

Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus, Acipenseridae) populations are currently at severely depleted levels due to historic overfishing, habitat loss, and pollution. The importance of biologically correct stock structure for effective conservation and management efforts is well known. Recent improvements in our understanding of Atlantic sturgeon migrations, movement, and the occurrence of putative dual spawning groups leads to questions regarding the true stock structure of this endangered species. In the James River, VA specifically, captures of spawning Atlantic sturgeon and accompanying telemetry data suggest there are two discrete spawning groups of Atlantic sturgeon. The two putative spawning groups were genetically evaluated using a powerful microsatellite marker suite to determine if they are genetically distinct. Specifically, this study evaluates the genetic structure, characterizes the genetic diversity, estimates effective population size, and measures inbreeding of Atlantic sturgeon in the James River. The results indicate that fall and spring spawning James River Atlantic sturgeon groups are genetically distinct (overall FST = 0.048, F’ST = 0.181) with little admixture between the groups. The observed levels of genetic diversity and effective population sizes along with the lack of detected inbreeding all indicated that the James River has two genetically healthy populations of Atlantic sturgeon. The study also demonstrates that samples from adult Atlantic sturgeon, with proper sample selection criteria, can be informative when creating reference population databases. The presence of two genetically-distinct spawning groups of Atlantic sturgeon within the James River raises concerns about the current genetic assignment used by managers. Other nearby rivers may also have dual spawning groups that either are not accounted for or are pooled in reference databases. Our results represent the second documentation of genetically distinct dual spawning groups of Atlantic sturgeon in river systems along the U.S. Atlantic coast, suggesting that current reference population database should be updated to incorporate both new samples and our increased understanding of Atlantic sturgeon life history. PMID:28686610

Phylogeographic and population insights of the Asian common toad (Bufo gargarizans) in Korea and China: population isolation and expansions as response to the ice ages

PubMed Central

Santos, Joana L.; Sánchez-RamÍrez, Santiago; Bae, Yoonhyuk; Jang, Yikweon

2017-01-01

The effects of ice ages on speciation have been well documented for many European and North American taxa. In contrast, very few studies have addressed the consequences of such environmental and topographical changes in North East Asian species. More precisely, the Korean Peninsula offers a unique model to assess patterns and processes of speciation as it hosts the northern- and eastern-most distribution limit of some widespread Asian taxa. Despite this, studies addressing phylogeographic patterns and population genetics in the peninsula and surrounding countries are few and studies for most families are lacking. Here we inferred the phylogenetic relationships of the common toad (Bufo gargarizans) from South Korea and their North East Asian counterpart populations, based on mitochondrial data. Korean B. gargarizans GenBank BLASTs matched few individuals from nearby China, but the presence of a Korean clade suggests isolation on the Korean Peninsula, previous to the last glacial maximum, linked to sea level resurgence. Molecular clock calibrations within this group were used to date the divergence between clades and their relationship to paleo-climatic events in the area. Lack of genetic structure among South Korean populations and strong homogeneity between the Korean and some Chinese localities suggest weak isolation and recent expansion. Geographical projection of continuous coalescent maximum-clade-credibility trees shows an original Chinese expansion towards the Korean Peninsula through the Yellow Sea circa two million years ago with colonisation events dating circa 800 thousand years ago (K. y. a.). Following this colonisation, the data point to outgoing Korean Peninsula dispersal events throughout different periods, towards the North through land, and West through land bridge formations over the Yellow Sea during sea level falls. In accordance, demographic analyses revealed a population expansion in the Koran Peninsula circa 300 K. y. a., likely attributed to glacial cycle fluctuations. PMID:29201561

Corporatization of pain medicine: implications for widening pain care disparities.

PubMed

Meghani, Salimah H

2011-04-01

The current health care system in the United States is structured in a way that ensures that more opportunity and resources flow to the wealthy and socially advantaged. The values intrinsic to the current profit-oriented culture are directly antithetical to the idea of equitable access. A large body of literature points to disparities in pain treatment and pain outcomes among vulnerable groups. These disparities range from the presence of disproportionately higher numbers and magnitude of risk factors for developing disabling pain, lack of access to primary care providers, analgesics and interventions, lack of referral to pain specialists, longer wait times to receive care, receipt of poor quality of pain care, and lack of geographical access to pharmacies that carry opioids. This article examines the manner in which the profit-oriented culture in medicine has directly and indirectly structured access to pain care, thereby widening pain treatment disparities among vulnerable groups. Specifically, the author argues that the corporatization of pain medicine amplifies disparities in pain outcomes in two ways: 1) directly through driving up the cost of pain care, rendering it inaccessible to the financially vulnerable; and 2) indirectly through an interface with corporate loss-aversion/risk management culture that draws upon irrelevant social characteristics, thus worsening disparities for certain populations. Thus, while financial vulnerability is the core reason for lack of access, it does not fully explain the implications of corporate microculture regarding access. The effect of corporatization on pain medicine must be conceptualized in terms of overt access to facilities, providers, pharmaceuticals, specialty services, and interventions, but also in terms of the indirect or covert effect of corporate culture in shaping clinical interactions and outcomes. Wiley Periodicals, Inc.

Larval Population Density Alters Adult Sleep in Wild-Type Drosophila melanogaster but Not in Amnesiac Mutant Flies

PubMed Central

Chi, Michael W.; Griffith, Leslie C.; Vecsey, Christopher G.

2014-01-01

Sleep has many important biological functions, but how sleep is regulated remains poorly understood. In humans, social isolation and other stressors early in life can disrupt adult sleep. In fruit flies housed at different population densities during early adulthood, social enrichment was shown to increase subsequent sleep, but it is unknown if population density during early development can also influence adult sleep. To answer this question, we maintained Drosophila larvae at a range of population densities throughout larval development, kept them isolated during early adulthood, and then tested their sleep patterns. Our findings reveal that flies that had been isolated as larvae had more fragmented sleep than those that had been raised at higher population densities. This effect was more prominent in females than in males. Larval population density did not affect sleep in female flies that were mutant for amnesiac, which has been shown to be required for normal memory consolidation, adult sleep regulation, and brain development. In contrast, larval population density effects on sleep persisted in female flies lacking the olfactory receptor or83b, suggesting that olfactory signals are not required for the effects of larval population density on adult sleep. These findings show that population density during early development can alter sleep behavior in adulthood, suggesting that genetic and/or structural changes are induced by this developmental manipulation that persist through metamorphosis. PMID:25116571

Larval Population Density Alters Adult Sleep in Wild-Type Drosophila melanogaster but Not in Amnesiac Mutant Flies.

PubMed

Chi, Michael W; Griffith, Leslie C; Vecsey, Christopher G

2014-08-11

Sleep has many important biological functions, but how sleep is regulated remains poorly understood. In humans, social isolation and other stressors early in life can disrupt adult sleep. In fruit flies housed at different population densities during early adulthood, social enrichment was shown to increase subsequent sleep, but it is unknown if population density during early development can also influence adult sleep. To answer this question, we maintained Drosophila larvae at a range of population densities throughout larval development, kept them isolated during early adulthood, and then tested their sleep patterns. Our findings reveal that flies that had been isolated as larvae had more fragmented sleep than those that had been raised at higher population densities. This effect was more prominent in females than in males. Larval population density did not affect sleep in female flies that were mutant for amnesiac, which has been shown to be required for normal memory consolidation, adult sleep regulation, and brain development. In contrast, larval population density effects on sleep persisted in female flies lacking the olfactory receptor or83b, suggesting that olfactory signals are not required for the effects of larval population density on adult sleep. These findings show that population density during early development can alter sleep behavior in adulthood, suggesting that genetic and/or structural changes are induced by this developmental manipulation that persist through metamorphosis.

Genetic diversity of the golden potato cyst nematode Globodera rostochiensis and determination of the origin of populations in Quebec, Canada.

PubMed

Boucher, Annie Christine; Mimee, Benjamin; Montarry, Josselin; Bardou-Valette, Sylvie; Bélair, Guy; Moffett, Peter; Grenier, Eric

2013-10-01

The golden cyst nematode (Globodera rostochiensis), native to South America, has been introduced in many parts of the world, including Europe and North America. Recently, it was found for the first time in the province of Quebec, Canada in the locality of St. Amable near Montreal. To date, very few studies have examined the population genetics of this pest. Consequently, there is a lack of knowledge about the genetic structure and evolution of this nematode. In this study, twelve new microsatellite markers were developed in order to explore these questions. These markers were used to genotype fifteen populations originating from different regions of the world, including five from Canada. Within populations, the highest genetic diversity was consistently observed in the populations from Bolivia, the postulated region of origin of the golden nematode, and the lowest in populations from British Columbia (Canada) and New York (USA). The two Quebec populations were very similar to each other and to the population found in Newfoundland, but surprisingly, they were significantly different from three other North American populations including those from New York and British Columbia. Based on our results, we conclude that the golden cyst nematode has been introduced in North America at least twice from distinct regions of the world. Crown Copyright © 2013. Published by Elsevier Inc. All rights reserved.

The impact of grazing on plant fractal architecture and fitness of a mediterranean shrub (Anthyllis cytisoidesL.)

USGS Publications Warehouse

Escos, J.; Alados, C.L.; Emlen, J.M.

1997-01-01

1. We examined natural grazing by livestock (sheep and goats) on Albaida Anthyllis cytisoides L. with the aim of determining whether variation in the allometric relationships between plant parts provides a sensitive indicator of the impact of grazing.2. The intra-individual variation in translatory symmetry with scale and increased complexity of fractal structures reflect environmental disturbance under heavy grazing pressure and lack of grazing.3. Fitness consequences of grazing were also investigated. Grazing promotes growth and adult survival, and a drop in seed production as a consequence of consumption. In spite of that, total inclusive fitness (population rate of change) tends to increase with grazing.4. Moderate grazing, while promoting growth, also enhances stability of vegetative structures. The favourable effect of moderate levels of herbivory on A. cytisoides is reflected in the homeostatic maintenance of its translatory symmetry and in the increased complexity of its fractal structures.

A Systematic Review of Behavioral Interventions to Reduce Condomless Sex and Increase HIV Testing for Latino MSM.

PubMed

Pérez, Ashley; Santamaria, E Karina; Operario, Don

2017-12-15

Latino men who have sex with men (MSM) in the United States are disproportionately affected by HIV, and there have been calls to improve availability of culturally sensitive HIV prevention programs for this population. This article provides a systematic review of intervention programs to reduce condomless sex and/or increase HIV testing among Latino MSM. We searched four electronic databases using a systematic review protocol, screened 1777 unique records, and identified ten interventions analyzing data from 2871 Latino MSM. Four studies reported reductions in condomless anal intercourse, and one reported reductions in number of sexual partners. All studies incorporated surface structure cultural features such as bilingual study recruitment, but the incorporation of deep structure cultural features, such as machismo and sexual silence, was lacking. There is a need for rigorously designed interventions that incorporate deep structure cultural features in order to reduce HIV among Latino MSM.

Analysis of the supply chain and conservation status of sharks (Elasmobranchii: Superorder Selachimorpha) based on fisher knowledge.

PubMed

Martins, Ana Paula Barbosa; Feitosa, Leonardo Manir; Lessa, Rosangela Paula; Almeida, Zafira Silva; Heupel, Michelle; Silva, Wagner Macedo; Tchaicka, Ligia; Nunes, Jorge Luiz Silva

2018-01-01

Increasing fishing effort has caused declines in shark populations worldwide. Understanding biological and ecological characteristics of sharks is essential to effectively implement management measures, but to fully understand drivers of fishing pressure social factors must be considered through multidisciplinary and integrated approaches. The present study aimed to use fisher and trader knowledge to describe the shark catch and product supply chain in Northeastern Brazil, and evaluate perceptions regarding the regional conservation status of shark species. Non-systematic observations and structured individual interviews were conducted with experienced fishers and traders. The demand and economic value of shark fins has reportedly decreased over the last 10 years while the shark meat trade has increased slightly, including a small increase in the average price per kilogram of meat. Several threatened shark species were reportedly often captured off shore and traded at local markets. This reported and observed harvest breaches current Brazilian environmental laws. Fishing communities are aware of population declines of several shark species, but rarely take action to avoid capture of sharks. The continuing capture of sharks is mainly due to a lack of knowledge of environmental laws, lack of enforcement by responsible authorities, and difficulties encountered by fishers in finding alternative income streams. National and regional conservation measures are immediately required to reduce overfishing on shark populations in Northeastern Brazil. Social and economic improvements for poor fishing communities must also be implemented to achieve sustainable fisheries.

Analysis of the supply chain and conservation status of sharks (Elasmobranchii: Superorder Selachimorpha) based on fisher knowledge

PubMed Central

Almeida, Zafira Silva; Heupel, Michelle; Silva, Wagner Macedo; Tchaicka, Ligia

2018-01-01

Increasing fishing effort has caused declines in shark populations worldwide. Understanding biological and ecological characteristics of sharks is essential to effectively implement management measures, but to fully understand drivers of fishing pressure social factors must be considered through multidisciplinary and integrated approaches. The present study aimed to use fisher and trader knowledge to describe the shark catch and product supply chain in Northeastern Brazil, and evaluate perceptions regarding the regional conservation status of shark species. Non-systematic observations and structured individual interviews were conducted with experienced fishers and traders. The demand and economic value of shark fins has reportedly decreased over the last 10 years while the shark meat trade has increased slightly, including a small increase in the average price per kilogram of meat. Several threatened shark species were reportedly often captured off shore and traded at local markets. This reported and observed harvest breaches current Brazilian environmental laws. Fishing communities are aware of population declines of several shark species, but rarely take action to avoid capture of sharks. The continuing capture of sharks is mainly due to a lack of knowledge of environmental laws, lack of enforcement by responsible authorities, and difficulties encountered by fishers in finding alternative income streams. National and regional conservation measures are immediately required to reduce overfishing on shark populations in Northeastern Brazil. Social and economic improvements for poor fishing communities must also be implemented to achieve sustainable fisheries. PMID:29534100

Clinical use of the Kessler psychological distress scales with culturally diverse groups.

PubMed

Stolk, Yvonne; Kaplan, Ida; Szwarc, Josef

2014-06-01

The Kessler 10 (K10) and embedded Kessler 6 (K6) was developed to screen for non-specific psychological distress and serious mental illness in mental health surveys of English-speaking populations, but has been adopted in Western and non-Western countries as a screening and outcome measure in primary care and mental health settings. This review examines whether the original K6/K10's validity for culturally diverse populations was established, and whether the cultural equivalence, and sensitivity to change of translated or culturally adapted K6/K10s, has been demonstrated with culturally diverse client groups. Evidence for the original K6/K10's validity for culturally diverse populations is limited. Questions about the conceptual and linguistic equivalence of translated/adapted K6/K10s arise from reports of changes in item connotation and differential item functioning. Evidence for structural equivalence is inconsistent, as is support for criterion equivalence, with the majority of studies compromising on accuracy in case prediction. Research demonstrating sensitivity to change with culturally diverse groups is lacking. Inconsistent evidence for the K6/K10's cultural appropriateness in clinical settings, and a lack of clinical norms for either majority or culturally diverse groups, indicate the importance of further research into the psychological distress construct with culturally diverse clients, and the need for caution in interpreting K6/K10 scores. Copyright © 2014 John Wiley & Sons, Ltd.

The lived experiences of the Sikh population of South East England when caring for a dying relative at home.

PubMed

Cowan, Margaret Mary

2014-04-01

Few ethnic minorities access specialist palliative care (SPC) services when caring for a dying relative at home. This project aimed to explore and understand the experiences of the Sikh population of south east England when caring for a dying relative at home without support from SPC. Six semi-structured interviews were conducted with carers in Punjabi or English and the transcripts were analysed using interpretative phenomenology. Five super-ordinate themes were identified: factors leading to the caring role, emotional effects of caring on the carer, impact of caring on the wider family, influence of health-care services, and religious and cultural influence. The most common emergent theme was lack of support from health professionals, which emerged from a lack of awareness of services. A sense of duty and hard work was apparent throughout, and appeared to sustain the family. There seemed to be a sense of duty to care for the relative at home. Financial concerns were expressed frequently. The decision to adopt the caring role appeared to be made by the entire family. The Sikh faith seemed to give strength to carers. There appeared to be heightened awareness of what other community members think of carers' actions. There is a need for health professionals to reach out to this population to increase awareness of and trust in the services that are available to support care at the end of life. However, an unwillingness to accept assistance may persist in some cases.

THE STELLAR SPHEROID, THE DISK, AND THE DYNAMICS OF THE COSMIC WEB

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

Domínguez-Tenreiro, R.; Obreja, A.; Brook, C. B.

Models of the advanced stages of gravitational instability predict that baryons that form the stellar populations of current galaxies at z = 0 displayed a web-like structure at high z, as part of the cosmic web (CW). We explore details of these predictions using cosmological hydrodynamical simulations. When the stellar populations of the spheroid and disk components of simulated late-type galaxies are traced back separately to high zs we found CW-like structures where spheroid progenitors are more evolved than disk progenitors. The distinction between the corresponding stellar populations, as driven by their specific angular momentum content j, can be explainedmore » in terms of the CW evolution, extended to two processes occurring at lower z. First, the spheroid progenitors strongly lose j at collapse, which contrasts with the insignificant j loss of the disk progenitors. The second is related to the lack of alignment, at assembly, between the spheroid-to-be material and the already settled proto-disk, in contrast to the alignment of disk-to-be material, in some cases resulting from circumgalactic, disk-induced gravitational torques. The different final outcomes of these low-z processes have their origins in the different initial conditions driven by the CW dynamics.« less

A portrait of a sucker using landscape genetics: how colonization and life history undermine the idealized dendritic metapopulation.

PubMed

Salisbury, Sarah J; McCracken, Gregory R; Keefe, Donald; Perry, Robert; Ruzzante, Daniel E

2016-09-01

Dendritic metapopulations have been attributed unique properties by in silico studies, including an elevated genetic diversity relative to a panmictic population of equal total size. These predictions have not been rigorously tested in nature, nor has there been full consideration of the interacting effects among contemporary landscape features, colonization history and life history traits of the target species. We tested for the effects of dendritic structure as well as the relative importance of life history, environmental barriers and historical colonization on the neutral genetic structure of a longnose sucker (Catostomus catostomus) metapopulation in the Kogaluk watershed of northern Labrador, Canada. Samples were collected from eight lakes, genotyped with 17 microsatellites, and aged using opercula. Lakes varied in differentiation, historical and contemporary connectivity, and life history traits. Isolation by distance was detected only by removing two highly genetically differentiated lakes, suggesting a lack of migration-drift equilibrium and the lingering influence of historical factors on genetic structure. Bayesian analyses supported colonization via the Kogaluk's headwaters. The historical concentration of genetic diversity in headwaters inferred by this result was supported by high historical and contemporary effective sizes of the headwater lake, T-Bone. Alternatively, reduced allelic richness in headwaters confirmed the dendritic structure's influence on gene flow, but this did not translate to an elevated metapopulation effective size. A lack of equilibrium and upstream migration may have dampened the effects of dendritic structure. We suggest that interacting historical and contemporary factors prevent the achievement of the idealized traits of a dendritic metapopulation in nature. © 2016 John Wiley & Sons Ltd.

[Poverty and mental disability in the criminal law: The invisibles].

PubMed

Mercurio, Ezequiel N

2016-05-01

In recent decades neuroscience research show the negative consequences of poverty in cognitive development. Environmental factors, such as material deprivation, exposure to stressful situations, violence, nutritional deprivation, environmental toxins may shape the developing brain. The changes of the structure and function of the brain since prenatal stages and their consequences can remain stable throughout the life cycle except early interventions are made. Research investigating have found significant link between child poverty and function and structural brain focusing on prefrontal cortex (i.e., executive functions), hippocampus (learning and memory), amygdala (i.e., fear and emotional processing) and Left Occipitotemporal and Perisylvian Regions (Language and Reading) In recent years, international studies show a growing population with intellectual disabilities in prisons. However, in criminal justice, people with mild intellectual disabilities suffer a normalization process. A lack of access to adequate diagnosis operate as an omission this vulnerable group, as a result the State deprive access to support systems guaranteed in international declarations of Human Rights. Furthermore neglect, discrimination, lack of access to comprehensive health and appropriate social interventions deepen in prison. It is for this reason that from a current human rights perspective a person with disability in jail becomes a doubly vulnerable subject.

Lack of genetic structure in the jellyfish Pelagia noctiluca (Cnidaria: Scyphozoa: Semaeostomeae) across European seas.

PubMed

Stopar, Katja; Ramsak, Andreja; Trontelj, Peter; Malej, Alenka

2010-10-01

The genetic structure of the holopelagic scyphozoan Pelagia noctiluca was inferred based on the study of 144 adult medusae. The areas of study were five geographic regions in two European seas (Eastern Atlantic and Mediterranean Sea). A 655-bp sequence of mitochondrial cytochrome c oxidase subunit I (COI), and a 645-bp sequence of two nuclear internal transcribed spacers (ITS1 and ITS2) were analyzed. The protein coding COI gene showed a higher level of divergence than the combined nuclear ITS fragment (haplotype diversity 0.962 vs. 0.723, nucleotide diversity 1.16% vs. 0.31%). Phylogeographic analysis on COI gene revealed two clades, the larger consisting of specimens from all sampling sites, and the smaller mostly formed of specimens from the Mediterranean Sea. Haplotype diversity was very high throughout the sampled area, and within sample diversity was higher than diversity among geographical regions. No strongly supported genetically or geographically distinct groups of P. noctiluca were found. The results - long distance dispersal, insignificant F(ST) values, lack of isolation by distance - pointed toward an admixture among Mediterranean and East Atlantic populations. Copyright 2010 Elsevier Inc. All rights reserved.

Basic Geriatrics Knowledge Among Internal Medicine Trainees in a Teaching Hospital in Saudi Arabia.

PubMed

Al-Aama, Tareef

2016-06-01

To assess the basic knowledge of medical trainees, in the absence of a structured geriatrics curriculum, around a variety of geriatric medicine components that are considered essential for the care of the rapidly increasing elderly population. Eighty-three trainees at different levels of training in internal medicine were asked about a variety of common geriatric conditions. Those included: delirium, falls, geriatric syndromes, pain, cognitive impairment, and medications. The trainees' knowledge about common geriatric condition was overall poor. The most pronounced deficits included: the lack of familiarity in diagnosing geriatric syndromes (63 %) or managing them (67 %), the underestimation of the prevalence of delirium (49 %), and the tendency to undertreat pain (64 %). Poor familiarity with polypharmacy and its impact, as well as inappropriate prescription practices in the elderly were also observed. In the absence of a structured geriatric medicine curriculum, internal medicine trainees' knowledge about important geriatric conditions is poor, even if their internal medicine knowledge is overall adequate. This would translate into suboptimal care for this vulnerable and rapidly expanding segment of the population.

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.

Evidence of discrete yellowfin tuna (Thunnus albacares) populations demands rethink of management for this globally important resource.

PubMed

Grewe, P M; Feutry, P; Hill, P L; Gunasekera, R M; Schaefer, K M; Itano, D G; Fuller, D W; Foster, S D; Davies, C R

2015-11-23

Tropical tuna fisheries are central to food security and economic development of many regions of the world. Contemporary population assessment and management generally assume these fisheries exploit a single mixed spawning population, within ocean basins. To date population genetics has lacked the required power to conclusively test this assumption. Here we demonstrate heterogeneous population structure among yellowfin tuna sampled at three locations across the Pacific Ocean (western, central, and eastern) via analysis of double digest restriction-site associated DNA using Next Generation Sequencing technology. The differences among locations are such that individuals sampled from one of the three regions examined can be assigned with close to 100% accuracy demonstrating the power of this approach for providing practical markers for fishery independent verification of catch provenance in a way not achieved by previous techniques. Given these results, an extended pan-tropical survey of yellowfin tuna using this approach will not only help combat the largest threat to sustainable fisheries (i.e. illegal, unreported, and unregulated fishing) but will also provide a basis to transform current monitoring, assessment, and management approaches for this globally significant species.

Evidence of discrete yellowfin tuna (Thunnus albacares) populations demands rethink of management for this globally important resource

PubMed Central

Grewe, P. M.; Feutry, P.; Hill, P. L.; Gunasekera, R. M.; Schaefer, K. M.; Itano, D. G.; Fuller, D. W.; Foster, S. D.; Davies, C. R.

2015-01-01

Tropical tuna fisheries are central to food security and economic development of many regions of the world. Contemporary population assessment and management generally assume these fisheries exploit a single mixed spawning population, within ocean basins. To date population genetics has lacked the required power to conclusively test this assumption. Here we demonstrate heterogeneous population structure among yellowfin tuna sampled at three locations across the Pacific Ocean (western, central, and eastern) via analysis of double digest restriction-site associated DNA using Next Generation Sequencing technology. The differences among locations are such that individuals sampled from one of the three regions examined can be assigned with close to 100% accuracy demonstrating the power of this approach for providing practical markers for fishery independent verification of catch provenance in a way not achieved by previous techniques. Given these results, an extended pan-tropical survey of yellowfin tuna using this approach will not only help combat the largest threat to sustainable fisheries (i.e. illegal, unreported, and unregulated fishing) but will also provide a basis to transform current monitoring, assessment, and management approaches for this globally significant species. PMID:26593698

The correlates and treatment of obesity in military populations: a systematic review.

PubMed

Sanderson, Paul W; Clemes, Stacy A; Biddle, Stuart J H

2011-01-01

The emergence of obesity as a distinct disease could have far reaching consequences for an organisation where optimum health and physical fitness are required for personnel to perform their occupational roles effectively. The objectives of this paper are to systematically review the literature concerning correlates and treatment of obesity in military populations. Through computerised searches of English language studies, 17 papers were identified (treatment (13), correlates (4)). Successful treatment interventions incorporated exercise, healthy eating information, behavioural modification, self-monitoring, relapse prevention, and structured follow-up and were supported by trained personnel. Efficacy due to physical activity was underreported. Reduction in body fat rather than body weight was the most significant outcome. The major significant correlates of obesity were being enlisted personnel, male, ≥35 years of age, African-American/Hispanic ethnicity, and married (with spouse present). This systematic review highlights the deficit in knowledge concerning treatment and the lack of engagement in relation to the specific correlates of obesity in military populations. Copyright © 2011 S. Karger AG, Basel.

Present-day central African forest is a legacy of the 19th century human history.

PubMed

Morin-Rivat, Julie; Fayolle, Adeline; Favier, Charly; Bremond, Laurent; Gourlet-Fleury, Sylvie; Bayol, Nicolas; Lejeune, Philippe; Beeckman, Hans; Doucet, Jean-Louis

2017-01-17

The populations of light-demanding trees that dominate the canopy of central African forests are now aging. Here, we show that the lack of regeneration of these populations began ca. 165 ya (around 1850) after major anthropogenic disturbances ceased. Since 1885, less itinerancy and disturbance in the forest has occurred because the colonial administrations concentrated people and villages along the primary communication axes. Local populations formerly gardened the forest by creating scattered openings, which were sufficiently large for the establishment of light-demanding trees. Currently, common logging operations do not create suitable openings for the regeneration of these species, whereas deforestation degrades landscapes. Using an interdisciplinary approach, which included paleoecological, archaeological, historical, and dendrological data, we highlight the long-term history of human activities across central African forests and assess the contribution of these activities to present-day forest structure and composition. The conclusions of this sobering analysis present challenges to current silvicultural practices and to those of the future.

Using the Depression Anxiety Stress Scale 21 (DASS-21) across cultures.

PubMed

Oei, Tian P S; Sawang, Sukanlaya; Goh, Yong Wah; Mukhtar, Firdaus

2013-01-01

The DASS-21 is a well-established instrument for measuring depression, anxiety, and stress with good reliability and validity reported from Hispanic American, British, and Australian adults. However, the lack of appropriate validation among Asian populations continues to pose concerns over the use of DASS-21 in Asian samples. Cultural variation may influence the individual's experience and emotional expression. Thus, when researchers and practitioners employ Western-based assessments with Asian populations by directly translating them without an appropriate validation, the process can be challenging. We conducted a series of rigorous statistical tests and minimized any potential confounds from the demographic information. Following factor analyses, we performed multigroup analysis across six nations to demonstrate consistency of our findings. The advantages of this revised DASS-18 stress scale are twofold. First, it possesses fewer items, which results in a cleaner factorial structure. Second, it has a smaller interfactor correlation. With these justifications, the revised DASS-18 stress scale is potentially more suitable for Asian populations. Nonetheless, given limitations, findings should be considered preliminary.

White Matter Correlates of Musical Anhedonia: Implications for Evolution of Music.

PubMed

Loui, Psyche; Patterson, Sean; Sachs, Matthew E; Leung, Yvonne; Zeng, Tima; Przysinda, Emily

2017-01-01

Recent theoretical advances in the evolution of music posit that affective communication is an evolutionary function of music through which the mind and brain are transformed. A rigorous test of this view should entail examining the neuroanatomical mechanisms for affective communication of music, specifically by comparing individual differences in the general population with a special population who lacks specific affective responses to music. Here we compare white matter connectivity in BW, a case with severe musical anhedonia, with a large sample of control subjects who exhibit normal variability in reward sensitivity to music. We show for the first time that structural connectivity within the reward system can predict individual differences in musical reward in a large population, but specific patterns in connectivity between auditory and reward systems are special in an extreme case of specific musical anhedonia. Results support and extend the Mixed Origins of Music theory by identifying multiple neural pathways through which music might operate as an affective signaling system.

White Matter Correlates of Musical Anhedonia: Implications for Evolution of Music

PubMed Central

Loui, Psyche; Patterson, Sean; Sachs, Matthew E.; Leung, Yvonne; Zeng, Tima; Przysinda, Emily

2017-01-01

Recent theoretical advances in the evolution of music posit that affective communication is an evolutionary function of music through which the mind and brain are transformed. A rigorous test of this view should entail examining the neuroanatomical mechanisms for affective communication of music, specifically by comparing individual differences in the general population with a special population who lacks specific affective responses to music. Here we compare white matter connectivity in BW, a case with severe musical anhedonia, with a large sample of control subjects who exhibit normal variability in reward sensitivity to music. We show for the first time that structural connectivity within the reward system can predict individual differences in musical reward in a large population, but specific patterns in connectivity between auditory and reward systems are special in an extreme case of specific musical anhedonia. Results support and extend the Mixed Origins of Music theory by identifying multiple neural pathways through which music might operate as an affective signaling system. PMID:28993748

[Implementation of the Mobile Emergency Medical Service in Brazil: action strategies and structural dimension].

PubMed

O'Dwyer, Gisele; Konder, Mariana Teixeira; Reciputti, Luciano Pereira; Macedo, Cesar; Lopes, Monica Guimarães Macau

2017-08-07

The Mobile Emergency Medical Service (SAMU) was the first component of the National Policy for Emergency Care implemented in Brazil in the early 2000. The article analyzed the implementation of mobile pre-hospital emergency care in Brazil. The methods included document analysis, interviews with state emergency care coordinators, and an expert panel. The theoretical reference was the strategic conduct analysis from Giddens' Structuration Theory. The results showed uneven implementation of the SAMU between states and regions of Brazil, identifying six patterns of implementation, considering the states' capacity to expand the population coverage and regionalize the service. Structural difficulties included physician retention, poorly equipped dispatch centers, and shortage of ambulances. The North and Northeast were the country's most heavily affected regions. SAMU is formatted as a structuring strategy in the emergency care network, but its performance suffered the impact of limited participation by primary care in the emergency network and especially the lack of hospital beds.

Structured Medication Review to Improve Pharmacotherapy in People with Intellectual Disability and Behavioural Problems.

PubMed

Scheifes, Arlette; Egberts, Toine C G; Stolker, Joost Jan; Nijman, Henk L I; Heerdink, Eibert R

2016-07-01

Polypharmacy and chronic drug use are common in people with intellectual disability and behavioural problems, although evidence of effectiveness and safety in this population is lacking. This study examined the effects of a structured medication review and aimed to improve pharmacotherapy in inpatients with intellectual disability. In a treatment facility for people with mild to borderline intellectual disability and severe behavioural problems, a structured medication review was performed. Prevalence and type of drug-related problems (DRPs) and of the recommended and executed actions were calculated. In a total of 55 patients with intellectual disability and behavioural problems, 284 medications were prescribed, in which a DRP was seen in 106 (34%). No indication/unclear indication was the most prevalent DRP (70). Almost 60% of the recommended actions were also executed. This high prevalence of DRPs is worrying. The structured medication review is a valuable instrument to optimize pharmacotherapy and to support psychiatrists in adequate prescribing of both psychotropic and somatic drugs. © 2015 John Wiley & Sons Ltd.

Structured populations of Sulfolobus acidocaldarius with susceptibility to mobile genetic elements

USGS Publications Warehouse

Anderson, Rika E.; Kouris, Angela; Seward, Christopher H.; Campbell, Kate M.; Whitaker, Rachel J.

2017-01-01

The impact of a structured environment on genome evolution can be determined through comparative population genomics of species that live in the same habitat. Recent work comparing three genome sequences of Sulfolobus acidocaldarius suggested that highly structured, extreme, hot spring environments do not limit dispersal of this thermoacidophile, in contrast to other co-occurring Sulfolobus species. Instead, a high level of conservation among these three S. acidocaldarius genomes was hypothesized to result from rapid, global-scale dispersal promoted by low susceptibility to viruses that sets S. acidocaldarius apart from its sister Sulfolobus species. To test this hypothesis, we conducted a comparative analysis of 47 genomes of S. acidocaldarius from spatial and temporal sampling of two hot springs in Yellowstone National Park. While we confirm the low diversity in the core genome, we observe differentiation among S. acidocaldarius populations, likely resulting from low migration among hot spring “islands” in Yellowstone National Park. Patterns of genomic variation indicate that differing geological contexts result in the elimination or preservation of diversity among differentiated populations. We observe multiple deletions associated with a large genomic island rich in glycosyltransferases, differential integrations of the Sulfolobus turreted icosahedral virus, as well as two different plasmid elements. These data demonstrate that neither rapid dispersal nor lack of mobile genetic elements result in low diversity in the S. acidocaldariusgenomes. We suggest instead that significant differences in the recent evolutionary history, or the intrinsic evolutionary rates, of sister Sulfolobusspecies result in the relatively low diversity of the S. acidocaldarius genome.

A case against an X-shaped structure in the Milky Way young bulge

NASA Astrophysics Data System (ADS)

López-Corredoira, Martín

2016-09-01

Context. A number of recent papers have claimed the discovery of an X-shape structure in the bulge of our Galaxy in the population of the red clumps. Aims: We endeavor to analyze the stellar density of bulge stars in the same regions using a different stellar population that is characteristic of the young bulge (≲ 5 Gyr). Particularly, we use F0-F5 main-sequence stars with distances derived through photometric parallax. Methods: We extract these stars from extinction-corrected color-magnitude diagrams in the near-infrared of VISTA-VVV data in some bulge regions and calculate the densities along the line of sight. We take the uncertaintity in the photometric parallax and the contamination of other sources into account, and we see that these errors do not avoid the detection of a possible double peak along some lines of sight as expected for a X-shape bulge if it existed. Results: Only a single peak in the density distribution along the line of sight is observed, so apparently there is no X-shape structure for this population of stars. Nonetheless, the effects of the dispersion of absolute magnitudes in the selected population might be an alternative explanation, although in principle these effects are insufficient to explain this lack of double peak according to our calculations. Conclusions: The results of the present paper do not demonstrate that previous claims of X-shaped bulge using only red clump stars are incorrect, but there are apparently some puzzling questions if we want to maintain the validity of both the red-clump results and the results of this paper.

Is the Hospital Anxiety and Depression Scale (HADS) a valid measure in a general population 65-80 years old? A psychometric evaluation study.

PubMed

Djukanovic, Ingrid; Carlsson, Jörg; Årestedt, Kristofer

2017-10-04

The HADS (Hospital Anxiety and Depression Scale) aims to measure symptoms of anxiety (HADS Anxiety) and depression (HADS Depression). The HADS is widely used but has shown ambiguous results both regarding the factor structure and sex differences in the prevalence of depressive symptoms. There is also a lack of psychometric evaluations of the HADS in non-clinical samples of older people. The aim of the study was to evaluate the factor structure of the HADS in a general population 65-80 years old and to exam possible presence of differential item functioning (DIF) with respect to sex. This study was based on data from a Swedish sample, randomized from the total population in the age group 65-80 years (n = 6659). Confirmatory factor analyses (CFA) were performed to examine the factor structure. Ordinal regression analyses were conducted to detect DIF for sex. Reliability was examined by both ordinal as well as traditional Cronbach's alpha. The CFA showed a two-factor model with cross-loadings for two items (7 and 8) had excellent model fit. Internal consistency was good in both subscales, measured with ordinal and traditional alpha. Floor effects were presented for all items. No indication for meaningful DIF regarding sex was found for any of the subscales. HADS Anxiety and HADS Depression are unidimensional measures with acceptable internal consistency and are invariant with regard to sex. Despite pronounced ceiling effects and cross-loadings for item 7 and 8, the hypothesized two-factor model of HADS can be recommended to assess psychological distress among a general population 65-80 years old.

Origins of contrasting copper coordination geometries in crystalline copper sulfate pentahydrate.

PubMed

Ruggiero, Michael T; Erba, Alessandro; Orlando, Roberto; Korter, Timothy M

2015-12-14

Metal-aqua ion ([M(H2O)n](X+)) formation is a fundamental step in mechanisms that are central to enzymatic and industrial catalysis. Past investigations of such ions have yielded a wealth of information regarding their properties, however questions still exist involving the exact structures of these complexes. A prominent example of this is hexaaqua copper(II) ([Cu(H2O)6](2+)), with the solution versus gas-phase configurations under debate. The differences are often attributed to the intermolecular interactions between the bulk solvent and the aquated complex, resulting in structures stabilized by extended hydrogen-bonding networks. Yet solution phase systems are difficult to study due to the lack of atomic-level positional details. Crystalline solids are ideal models for comparative study, as they contain fixed structures that can be fully characterized using diffraction techniques. Here, crystalline copper sulfate pentahydrate (CuSO4·5H2O), which contains two unique copper-water geometries, was studied in order to elucidate the origin of these contrasting hydrated metal envrionments. A combination of solid-state density functional theory and low-temperature X-ray diffraction was used to probe the electronic origins of this phenomenon. This was accomplished through implementation of crystal orbital overlap population and crystal orbital Hamiltonian population analyses into a developmental version of the CRYSTAL14 software. These new computational methods help highlight the delicate interplay between electronic structure and metal-water geometries.

Medical Decision-Making for Adults Who Lack Decision-Making Capacity and a Surrogate: State of the Science.

PubMed

Kim, Hyejin; Song, Mi-Kyung

2018-01-01

Adults who lack decision-making capacity and a surrogate ("unbefriended" adults) are a vulnerable, voiceless population in health care. But little is known about this population, including how medical decisions are made for these individuals. This integrative review was to examine what is known about unbefriended adults and identify gaps in the literature. Six electronic databases were searched using 4 keywords: "unbefriended," "unrepresented patients," "adult orphans," and "incapacitated patients without surrogates." After screening, the final sample included 10 data-based articles for synthesis. Main findings include the following: (1) various terms were used to refer to adults who lack decision-making capacity and a surrogate; (2) the number of unbefriended adults was sizable and likely to grow; (3) approaches to medical decision-making for this population in health-care settings varied; and (4) professional guidelines and laws to address the issues related to this population were inconsistent. There have been no studies regarding the quality of medical decision-making and its outcomes for this population or societal impact. Extremely limited empirical data exist on unbefriended adults to develop strategies to improve how medical decisions are made for this population. There is an urgent need for research to examine the quality of medical decision-making and its outcomes for this vulnerable population.

Persistence of historical population structure in an endangered species despite near-complete biome conversion in California's San Joaquin Desert

USGS Publications Warehouse

Richmond, Jonathan Q.; Wood, Dustin A.; Westphal, Michael F.; Vandergast, Amy; Leache, Adam D.; Saslaw, Lawrence; Butterfield, H. Scott; Fisher, Robert N.

2017-01-01

Genomic responses to habitat conversion can be rapid, providing wildlife managers with time-limited opportunities to enact recovery efforts that use population connectivity information that reflects predisturbance landscapes. Despite near-complete biome conversion, such opportunities may still exist for the endemic fauna and flora of California's San Joaquin Desert, but comprehensive genetic data sets are lacking for nearly all species in the region. To fill this knowledge gap, we studied the rangewide population structure of the endangered blunt-nosed leopard lizard Gambelia sila, a San Joaquin Desert endemic, using restriction site-associated DNA (RAD), microsatellite and mtDNA data to test whether admixture patterns and estimates of effective migration surfaces (EEMS) can identify land areas with high population connectivity prior to the conversion of native xeric habitats. Clustering and phylogenetic analyses indicate a recent shared history between numerous isolated populations and EEMS reveals latent signals of corridors and barriers to gene flow over areas now replaced by agriculture and urbanization. Conflicting histories between the mtDNA and nuclear genomes are consistent with hybridization with the sister species G. wislizenii, raising important questions about where legal protection should end at the southern range limit of G. sila. Comparative analysis of different data sets also adds to a growing list of advantages in using RAD loci for genetic studies of rare species. We demonstrate how the results of this work can serve as an evolutionary guidance tool for managing endemic, arid-adapted taxa in one of the world's most compromised landscapes.

Ghosts of Yellowstone: Multi-Decadal Histories of Wildlife Populations Captured by Bones on a Modern Landscape

PubMed Central

Miller, Joshua H.

2011-01-01

Natural accumulations of skeletal material (death assemblages) have the potential to provide historical data on species diversity and population structure for regions lacking decades of wildlife monitoring, thereby contributing valuable baseline data for conservation and management strategies. Previous studies of the ecological and temporal resolutions of death assemblages from terrestrial large-mammal communities, however, have largely focused on broad patterns of community composition in tropical settings. Here, I expand the environmental sampling of large-mammal death assemblages into a temperate biome and explore more demanding assessments of ecological fidelity by testing their capacity to record past population fluctuations of individual species in the well-studied ungulate community of Yellowstone National Park (Yellowstone). Despite dramatic ecological changes following the 1988 wildfires and 1995 wolf re-introduction, the Yellowstone death assemblage is highly faithful to the living community in species richness and community structure. These results agree with studies of tropical death assemblages and establish the broad capability of vertebrate remains to provide high-quality ecological data from disparate ecosystems and biomes. Importantly, the Yellowstone death assemblage also correctly identifies species that changed significantly in abundance over the last 20 to ∼80 years and the directions of those shifts (including local invasions and extinctions). The relative frequency of fresh versus weathered bones for individual species is also consistent with documented trends in living population sizes. Radiocarbon dating verifies the historical source of bones from Equus caballus (horse): a functionally extinct species. Bone surveys are a broadly valuable tool for obtaining population trends and baseline shifts over decadal-to-centennial timescales. PMID:21464921

Interagency Coordination Structures in Stabilization and Reconstruction Operations

DTIC Science & Technology

2010-06-11

poor interagency coordination and lack of unity as significant problems that compromise USG efforts in Afghanistan. This lack of interagency...objectives into consolidated tactical level goals and initiatives. Lack of interagency coordination structures at this level causes a variety of...Iraqi Reconstruction noticed a similar series of issues in an audit of civil police training in Afghanistan and Iraq. The lack of coordination

Improving menstrual hygiene management in emergency contexts: literature review of current perspectives.

PubMed

VanLeeuwen, Crystal; Torondel, Belen

2018-01-01

Management of menstruation in contexts of humanitarian emergencies can be challenging. A lack of empirical research about effective interventions which improve menstrual hygiene management (MHM) among female populations in humanitarian emergencies and a lack of clarity about which sectors within a humanitarian response should deliver MHM interventions can both be attributable to the lack of clear guidance on design and delivery of culturally appropriate MHM intervention in settings of humanitarian emergencies. The objective of this review was to collate, summarize, and appraise existing peer-reviewed and gray literature that describes the current scenario of MHM in emergency contexts in order to describe the breadth and depth of current policies, guidelines, empirical research, and humanitarian aid activities addressing populations' menstrual needs. A structured-search strategy was conducted for peer-reviewed and gray literature to identify studies, published reports, guidelines, and policy papers related to menstrual response in emergency humanitarian contexts. Of the 51 articles included in the review, 16 were peer-reviewed papers and 35 were gray literature. Most of the literature agreed that hardware interventions should focus on the supply of adequate material (not only absorbent material but also other supportive material) and adequate sanitation facilities, with access to water and private space for washing, changing, drying, and disposing menstrual materials. Software interventions should focus on education in the usage of materials to manage menstruation hygienically and education about the female body's biological processes. There was clear agreement that the needs of the target population should be assessed before designing any intervention. Although there is insight about which factors should be included in an effective menstrual hygiene intervention, there is insufficient empirical evidence to establish which interventions are most effective in humanitarian emergencies and which sectors should be responsible for the coordination and implementation of such. Increased monitoring and evaluation studies of interventions should be completed and publicly shared, in order to feed evidence-based guidelines in the humanitarian sector.

Addressing the Lack of Measurement Invariance for the Measure of Acceptance of the Theory of Evolution

NASA Astrophysics Data System (ADS)

Wagler, Amy; Wagler, Ron

2013-09-01

The Measure of Acceptance of the Theory of Evolution (MATE) was constructed to be a single-factor instrument that assesses an individual's overall acceptance of evolutionary theory. The MATE was validated and the scores resulting from the MATE were found to be reliable for the population of inservice high school biology teachers. However, many studies have utilized the MATE for different populations, such as university students enrolled in a biology or genetics course, high school students, and preservice teachers. This is problematic because the dimensionality and reliability of the MATE may not be consistent across populations. It is not uncommon in science education research to find examples where scales are applied to novel populations without proper assessment of the validity and reliability. In order to illustrate this issue, a case study is presented where the dimensionality of the MATE is evaluated for a population of non-science major preservice elementary teachers. With this objective in mind, factor analytic and item response models are fit to the observed data to provide evidence for or against a one-dimensional latent structure and to detect which items do not conform to the theoretical construct for this population. The results of this study call into question any findings and conclusions made using the MATE for a Hispanic population of preservice teachers and point out the error of assuming invariance across substantively different populations.

Analysis of genetic diversity in Bolivian llama populations using microsatellites.

PubMed

Barreta, J; Gutiérrez-Gil, B; Iñiguez, V; Romero, F; Saavedra, V; Chiri, R; Rodríguez, T; Arranz, J J

2013-08-01

South American camelids (SACs) have a major role in the maintenance and potential future of rural Andean human populations. More than 60% of the 3.7 million llamas living worldwide are found in Bolivia. Due to the lack of studies focusing on genetic diversity in Bolivian llamas, this analysis investigates both the genetic diversity and structure of 12 regional groups of llamas that span the greater part of the range of distribution for this species in Bolivia. The analysis of 42 microsatellite markers in the considered regional groups showed that, in general, there were high levels of polymorphism (a total of 506 detected alleles; average PIC across per marker: 0.66), which are comparable with those reported for other populations of domestic SACs. The estimated diversity parameters indicated that there was high intrapopulational genetic variation (average number of alleles and average expected heterozygosity per marker: 12.04 and 0.68, respectively) and weak genetic differentiation among populations (FST range: 0.003-0.052). In agreement with these estimates, Bolivian llamas showed a weak genetic structure and an intense gene flow between all the studied regional groups, which is due to the exchange of reproductive males between the different flocks. Interestingly, the groups for which the largest pairwise FST estimates were observed, Sud Lípez and Nor Lípez, showed a certain level of genetic differentiation that is probably due to the pattern of geographic isolation and limited communication infrastructures of these southern localities. Overall, the population parameters reported here may serve as a reference when establishing conservation policies that address Bolivian llama populations. © 2012 Blackwell Verlag GmbH.

Host association drives genetic divergence in the bed bug, Cimex lectularius.

PubMed

Booth, Warren; Balvín, Ondřej; Vargo, Edward L; Vilímová, Jitka; Schal, Coby

2015-03-01

Genetic differentiation may exist among sympatric populations of a species due to long-term associations with alternative hosts (i.e. host-associated differentiation). While host-associated differentiation has been documented in several phytophagus insects, there are far fewer cases known in animal parasites. The bed bug, Cimex lectularius, a wingless insect, represents a potential model organism for elucidating the processes involved in host-associated differentiation in animal parasites with relatively limited mobility. In conjunction with the expansion of modern humans from Africa into Eurasia, it has been speculated that bed bugs extended their host range from bats to humans in their shared cave domiciles throughout Eurasia. C. lectularius that associate with humans have a cosmopolitan distribution, whereas those associated with bats occur across Europe, often in human-built structures. We assessed genetic structure and gene flow within and among populations collected in association with each host using mtDNA, microsatellite loci and knock-down resistance gene variants. Both nuclear and mitochondrial data support a lack of significant contemporary gene flow between host-specific populations. Within locations human-associated bed bug populations exhibit limited genetic diversity and elevated levels of inbreeding, likely due to human-mediated movement, infrequent additional introduction events per infestation, and pest control. In contrast, populations within bat roosts exhibit higher genetic diversity and lower levels of relatedness, suggesting populations are stable with temporal fluctuations due to host dispersal and bug mortality. In concert with previously published evidence of morphological and behavioural differentiation, the genetic data presented here suggest C. lectularius is currently undergoing lineage divergence through host association. © 2015 John Wiley & Sons Ltd.

Differences in the population structure of invasive Streptococcus suis strains isolated from pigs and from humans in The Netherlands.

PubMed

Schultsz, Constance; Jansen, Ewout; Keijzers, Wendy; Rothkamp, Anja; Duim, Birgitta; Wagenaar, Jaap A; van der Ende, Arie

2012-01-01

Streptococcus suis serotype 2 is the main cause of zoonotic S. suis infection despite the fact that other serotypes are frequently isolated from diseased pigs. Studies comparing concurrent invasive human and pig isolates from a single geographical location are lacking. We compared the population structures of invasive S. suis strains isolated between 1986 and 2008 from human patients (N = 24) and from pigs with invasive disease (N = 124) in The Netherlands by serotyping and multi locus sequence typing (MLST). Fifty-six percent of pig isolates were of serotype 9 belonging to 15 clonal complexes (CCs) or singleton sequence types (ST). In contrast, all human isolates were of serotype 2 and belonged to two non-overlapping clonal complexes CC1 (58%) and CC20 (42%). The proportion of serotype 2 isolates among S. suis strains isolated from humans was significantly higher than among strains isolated from pigs (24/24 vs. 29/124; P<0.0001). This difference remained significant when only strains within CC1 and CC20 were considered (24/24 vs. 27/37,P = 0.004). The Simpson diversity index of the S. suis population isolated from humans (0.598) was smaller than of the population isolated from pigs (0.765, P = 0.05) indicating that the S. suis population isolated from infected pigs was more diverse than the S. suis population isolated from human patients. S. suis serotype 2 strains of CC20 were all negative in a PCR for detection of genes encoding extracellular protein factor (EF) variants. These data indicate that the polysaccharide capsule is an important correlate of human S. suis infection, irrespective of the ST and EF encoding gene type of S. suis strains.

Comparison of the Live Attenuated Yellow Fever Vaccine 17D-204 Strain to Its Virulent Parental Strain Asibi by Deep Sequencing

PubMed Central

Beck, Andrew; Tesh, Robert B.; Wood, Thomas G.; Widen, Steven G.; Ryman, Kate D.; Barrett, Alan D. T.

2014-01-01

Background. The first comparison of a live RNA viral vaccine strain to its wild-type parental strain by deep sequencing is presented using as a model the yellow fever virus (YFV) live vaccine strain 17D-204 and its wild-type parental strain, Asibi. Methods. The YFV 17D-204 vaccine genome was compared to that of the parental strain Asibi by massively parallel methods. Variability was compared on multiple scales of the viral genomes. A modeled exploration of small-frequency variants was performed to reconstruct plausible regions of mutational plasticity. Results. Overt quasispecies diversity is a feature of the parental strain, whereas the live vaccine strain lacks diversity according to multiple independent measurements. A lack of attenuating mutations in the Asibi population relative to that of 17D-204 was observed, demonstrating that the vaccine strain was derived by discrete mutation of Asibi and not by selection of genomes in the wild-type population. Conclusions. Relative quasispecies structure is a plausible correlate of attenuation for live viral vaccines. Analyses such as these of attenuated viruses improve our understanding of the molecular basis of vaccine attenuation and provide critical information on the stability of live vaccines and the risk of reversion to virulence. PMID:24141982

Comparison of the live attenuated yellow fever vaccine 17D-204 strain to its virulent parental strain Asibi by deep sequencing.

PubMed

Beck, Andrew; Tesh, Robert B; Wood, Thomas G; Widen, Steven G; Ryman, Kate D; Barrett, Alan D T

2014-02-01

The first comparison of a live RNA viral vaccine strain to its wild-type parental strain by deep sequencing is presented using as a model the yellow fever virus (YFV) live vaccine strain 17D-204 and its wild-type parental strain, Asibi. The YFV 17D-204 vaccine genome was compared to that of the parental strain Asibi by massively parallel methods. Variability was compared on multiple scales of the viral genomes. A modeled exploration of small-frequency variants was performed to reconstruct plausible regions of mutational plasticity. Overt quasispecies diversity is a feature of the parental strain, whereas the live vaccine strain lacks diversity according to multiple independent measurements. A lack of attenuating mutations in the Asibi population relative to that of 17D-204 was observed, demonstrating that the vaccine strain was derived by discrete mutation of Asibi and not by selection of genomes in the wild-type population. Relative quasispecies structure is a plausible correlate of attenuation for live viral vaccines. Analyses such as these of attenuated viruses improve our understanding of the molecular basis of vaccine attenuation and provide critical information on the stability of live vaccines and the risk of reversion to virulence.

Attitudes and barriers towards HIV screening: A qualitative study of people living with HIV/AIDS (PLWHA) in Malaysia.

PubMed

Ahmed, Syed Imran; Syed Sulaiman, Syed Azhar; Hassali, Mohamed Azmi; Thiruchelvam, Kaeshaelya; Hasan, Syed Shahzad; Lee, Christopher Kc

2017-09-01

Understanding patients' perspective towards HIV screening in Malaysia is pivotal to explore challenges faced by these individuals. This would be beneficial for developing local plans to improve the health-seeking behaviours among population at risk of HIV/AIDS. A qualitative research methodology was adopted to explore HIV/AIDS patients' views about disease screening. A semi-structured interview guide was used for in-depth patient interviews. All interviews were audio-recorded and were subjected to a standard content analysis framework for data analysis. Most patients were positive about screening and the value of knowing about their status early. However, fear of social stigma, discrimination, lack of support system and lack of public understanding were identified as major concerns affecting their willingness to be screened. They were concerned about mandatory screening being implemented without improvement in support system and public education. Reluctance to seek HIV screening is an important factor contributing to transmission in developing countries. In the Malaysian context, efforts should be made to strengthen screening strategies especially in the most-at-risk populations to monitor the epidemic and target prevention strategies. In a multicultural context, HIV preventive strategies must include disease awareness, including measure to tackle barriers towards screening.

Marketing and population problems.

PubMed

Farley, J U; Leavitt, H J

1971-07-01

There are many elements in population programs that are more familiar to marketing men than to some population experts. Advertising is essential to reach the target population, and advertising evaluation techniques (e.g., surrogate indexes or audience measures) might be useful for evaluating both population information activities and the import of the entire program. Fundamental research on basid demand for fertility control is needed and a marketer's experience with planning and evaluating test markets can be useful in assessing potential selling targets and evaluating alternative promotional and distributional strategies. Special family planning clinics have certain disadvantages: expensive and scarce personnel are needed; red tape may be present; the network is based on the assumption that the client is willing to travel relatively great distances repeatedly; and clinics lack anonymity which may scare potential acceptors away. Most developing cultures have an intensively functioning distribution structure which delivers basic commodities to the most remote areas, providing relatively anonymous outlets that are physically close to the customs. Materials requiring a prescription might be distributed in exchange for script issued at and ultimately redeemed by clinics, this requiring only an occasional visit to a clinic. Mail-order service can be used to supplement a clinic's distribution of some contraceptives. It should be remembered that population administrators often have an antipathetic view toward business and marketing and "suspect" the profit motive.

Detecting Selection on Temporal and Spatial Scales: A Genomic Time-Series Assessment of Selective Responses to Devil Facial Tumor Disease

PubMed Central

Brüniche-Olsen, Anna; Austin, Jeremy J.; Jones, Menna E.; Holland, Barbara R.; Burridge, Christopher P.

2016-01-01

Detecting loci under selection is an important task in evolutionary biology. In conservation genetics detecting selection is key to investigating adaptation to the spread of infectious disease. Loci under selection can be detected on a spatial scale, accounting for differences in demographic history among populations, or on a temporal scale, tracing changes in allele frequencies over time. Here we use these two approaches to investigate selective responses to the spread of an infectious cancer—devil facial tumor disease (DFTD)—that since 1996 has ravaged the Tasmanian devil (Sarcophilus harrisii). Using time-series ‘restriction site associated DNA’ (RAD) markers from populations pre- and post DFTD arrival, and DFTD free populations, we infer loci under selection due to DFTD and investigate signatures of selection that are incongruent among methods, populations, and times. The lack of congruence among populations influenced by DFTD with respect to inferred loci under selection, and the direction of that selection, fail to implicate a consistent selective role for DFTD. Instead genetic drift is more likely driving the observed allele frequency changes over time. Our study illustrates the importance of applying methods with different performance optima e.g. accounting for population structure and background selection, and assessing congruence of the results. PMID:26930198

Genetic variations in two seahorse species (Hippocampus mohnikei and Hippocampus trimaculatus): evidence for middle Pleistocene population expansion.

PubMed

Zhang, Yanhong; Pham, Nancy Kim; Zhang, Huixian; Lin, Junda; Lin, Qiang

2014-01-01

Population genetic of seahorses is confidently influenced by their species-specific ecological requirements and life-history traits. In the present study, partial sequences of mitochondrial cytochrome b (cytb) and control region (CR) were obtained from 50 Hippocampus mohnikei and 92 H. trimaculatus from four zoogeographical zones. A total of 780 base pairs of cytb gene were sequenced to characterize mitochondrial DNA (mtDNA) diversity. The mtDNA marker revealed high haplotype diversity, low nucleotide diversity, and a lack of population structure across both populations of H. mohnikei and H. trimaculatus. A neighbour-joining (NJ) tree of cytb gene sequences showed that H. mohnikei haplotypes formed one cluster. A maximum likelihood (ML) tree of cytb gene sequences showed that H. trimaculatus belonged to one lineage. The star-like pattern median-joining network of cytb and CR markers indicated a previous demographic expansion of H. mohnikei and H. trimaculatus. The cytb and CR data sets exhibited a unimodal mismatch distribution, which may have resulted from population expansion. Mismatch analysis suggested that the expansion was initiated about 276,000 years ago for H. mohnikei and about 230,000 years ago for H. trimaculatus during the middle Pleistocene period. This study indicates a possible signature of genetic variation and population expansion in two seahorses under complex marine environments.

Epidemiological research on the incidence and prevalence of arterial hypertension in the Portuguese population: a scoping review.

PubMed

Sousa Uva, Mafalda; Victorino, Paulo; Roquette, Rita; Machado, Ausenda; Matias Dias, Carlos

2014-01-01

The Portuguese population is reported to have among the highest levels of mean blood pressure. The aim of the present study is to conduct a structured literature review describing the scope (quantity, focus and nature) of published epidemiological research on the prevalence and incidence of hypertension in the Portuguese population. The scoping review was conducted during June 2013, using two information sources, B-on and PubMed, to search for published studies on the prevalence and incidence of hypertension with data collected between 2005-2013 and 1995-2013, respectively. We identified 527 publications: 14 on the prevalence and two on the incidence of hypertension. The results show more studies on populations in the North region of Portugal; an apparent lack of published studies specifically targeting the Alentejo and Algarve populations; long delays between data collection and publication of results (up to nine years); considerable variability in measurement methods; and infrequent data stratification by gender and age. Differences in blood pressure measurement methods, not specified in most studies, the infrequency of stratification of results by gender and age, and the geographic asymmetry in coverage of the Portuguese population, hinder monitoring of the incidence and prevalence of hypertension in Portugal. Copyright © 2013 Sociedade Portuguesa de Cardiologia. Published by Elsevier España. All rights reserved.

Connectivity of the habitat-forming kelp, Ecklonia radiata within and among estuaries and open coast.

PubMed

Coleman, Melinda A

2013-01-01

With marine protected areas being established worldwide there is a pressing need to understand how the physical setting in which these areas are placed influences patterns of dispersal and connectivity of important marine organisms. This is particularly critical for dynamic and complex nearshore marine environments where patterns of genetic structure of organisms are often chaotic and uncoupled from broad scale physical processes. This study determines the influence of habitat heterogeneity (presence of estuaries) on patterns of genetic structure and connectivity of the common kelp, Ecklonia radiata. There was no genetic differentiation of kelp between estuaries and the open coast and the presence of estuaries did not increase genetic differentiation among open coast populations. Similarly, there were no differences in level of inbreeding or genetic diversity between estuarine and open coast populations. The presence of large estuaries along rocky coastlines does not appear to influence genetic structure of this kelp and factors other than physical heterogeneity of habitat are likely more important determinants of regional connectivity. Marine reserves are currently lacking in this bioregion and may be designated in the future. Knowledge of the factors that influence important habitat forming organisms such as kelp contribute to informed and effective marine protected area design and conservation initiatives to maintain resilience of important marine habitats.

Phylogeography and population structure of the biologically invasive phytopathogen Erwinia amylovora inferred using minisatellites.

PubMed

Bühlmann, Andreas; Dreo, Tanja; Rezzonico, Fabio; Pothier, Joël F; Smits, Theo H M; Ravnikar, Maja; Frey, Jürg E; Duffy, Brion

2014-07-01

Erwinia amylovora causes a major disease of pome fruit trees worldwide, and is regulated as a quarantine organism in many countries. While some diversity of isolates has been observed, molecular epidemiology of this bacterium is hindered by a lack of simple molecular typing techniques with sufficiently high resolution. We report a molecular typing system of E. amylovora based on variable number of tandem repeats (VNTR) analysis. Repeats in the E. amylovora genome were identified with comparative genomic tools, and VNTR markers were developed and validated. A Multiple-Locus VNTR Analysis (MLVA) was applied to E. amylovora isolates from bacterial collections representing global and regional distribution of the pathogen. Based on six repeats, MLVA allowed the distinction of 227 haplotypes among a collection of 833 isolates of worldwide origin. Three geographically separated groups were recognized among global isolates using Bayesian clustering methods. Analysis of regional outbreaks confirmed presence of diverse haplotypes but also high representation of certain haplotypes during outbreaks. MLVA analysis is a practical method for epidemiological studies of E. amylovora, identifying previously unresolved population structure within outbreaks. Knowledge of such structure can increase our understanding on how plant diseases emerge and spread over a given geographical region. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Phylogeography and spatial genetic structure of the Southern torrent salamander: Implications for conservation and management

USGS Publications Warehouse

Miller, M.P.; Haig, S.M.; Wagner, R.S.

2006-01-01

The Southern torrent salamander (Rhyacotriton variegatus) was recently found not warranted for listing under the US Endangered Species Act due to lack of information regarding population fragmentation and gene flow. Found in small-order streams associated with late-successional coniferous forests of the US Pacific Northwest, threats to their persistence include disturbance related to timber harvest activities. We conducted a study of genetic diversity throughout this species' range to 1) identify major phylogenetic lineages and phylogeographic barriers and 2) elucidate regional patterns of population genetic and spatial phylogeographic structure. Cytochrome b sequence variation was examined for 189 individuals from 72 localities. We identified 3 major lineages corresponding to nonoverlapping geographic regions: a northern California clade, a central Oregon clade, and a northern Oregon clade. The Yaquina River may be a phylogeographic barrier between the northern Oregon and central Oregon clades, whereas the Smith River in northern California appears to correspond to the discontinuity between the central Oregon and northern California clades. Spatial analyses of genetic variation within regions encompassing major clades indicated that the extent of genetic structure is comparable among regions. We discuss our results in the context of conservation efforts for Southern torrent salamanders. ?? The American Genetic Association. 2006. All rights reserved.

Effects of yoga on brain waves and structural activation: A review.

PubMed

Desai, Radhika; Tailor, Anisha; Bhatt, Tanvi

2015-05-01

Previous research has shown the vast mental and physical health benefits associated with yoga. Yoga practice can be divided into subcategories that include posture-holding exercise (asana), breathing (pranayama, Kriya), and meditation (Sahaj) practice. Studies measuring mental health outcomes have shown decreases in anxiety, and increases in cognitive performance after yoga interventions. Similar studies have also shown cognitive advantages amongst yoga practitioners versus non-practitioners. The mental health and cognitive benefits of yoga are evident, but the physiological and structural changes in the brain that lead to this remain a topic that lacks consensus. Therefore, the purpose of this study was to examine and review existing literature on the effects of yoga on brain waves and structural changes and activation. After a narrowed search through a set of specific inclusion and exclusion criteria, 15 articles were used in this review. It was concluded that breathing, meditation, and posture-based yoga increased overall brain wave activity. Increases in graygray matter along with increases in amygdala and frontal cortex activation were evident after a yoga intervention. Yoga practice may be an effective adjunctive treatment for a clinical and healthy aging population. Further research can examine the effects of specific branches of yoga on a designated clinical population. Copyright © 2015 Elsevier Ltd. 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 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

New insights into the phylogenetics and population structure of the prairie falcon (Falco mexicanus)

USGS Publications Warehouse

Doyle, Jacqueline M.; Bell, Douglas A.; Bloom, Peter H.; Emmons, Gavin; Fesnock, Amy; Katzner, Todd; LePre, Larry; Leonard, Kolbe; SanMiguel, Phillip; Westerman, Rick; DeWoody, J. Andrew

2018-01-01

BackgroundManagement requires a robust understanding of between- and within-species genetic variability, however such data are still lacking in many species. For example, although multiple population genetics studies of the peregrine falcon (Falco peregrinus) have been conducted, no similar studies have been done of the closely-related prairie falcon (F. mexicanus) and it is unclear how much genetic variation and population structure exists across the species’ range. Furthermore, the phylogenetic relationship of F. mexicanus relative to other falcon species is contested. We utilized a genomics approach (i.e., genome sequencing and assembly followed by single nucleotide polymorphism genotyping) to rapidly address these gaps in knowledge.ResultsWe sequenced the genome of a single female prairie falcon and generated a 1.17 Gb (gigabases) draft genome assembly. We generated maximum likelihood phylogenetic trees using complete mitochondrial genomes as well as nuclear protein-coding genes. This process provided evidence that F. mexicanus is an outgroup to the clade that includes the peregrine falcon and members of the subgenus Hierofalco. We annotated > 16,000 genes and almost 600,000 high-quality single nucleotide polymorphisms (SNPs) in the nuclear genome, providing the raw material for a SNP assay design featuring > 140 gene-associated markers and a molecular-sexing marker. We subsequently genotyped ~ 100 individuals from California (including the San Francisco East Bay Area, Pinnacles National Park and the Mojave Desert) and Idaho (Snake River Birds of Prey National Conservation Area). We tested for population structure and found evidence that individuals sampled in California and Idaho represent a single panmictic population.ConclusionsOur study illustrates how genomic resources can rapidly shed light on genetic variability in understudied species and resolve phylogenetic relationships. Furthermore, we found evidence of a single, randomly mating population of prairie falcons across our sampling locations. Prairie falcons are highly mobile and relatively rare long-distance dispersal events may promote gene flow throughout the range. As such, California’s prairie falcons might be managed as a single population, indicating that management actions undertaken to benefit the species at the local level have the potential to influence the species as a whole.

Analagous Population Structures for Two Alphabaculoviruses Highlight a Functional Role for Deletion Mutants

PubMed Central

Serrano, Amaya; Williams, Trevor; Simón, Oihane; López-Ferber, Miguel; Caballero, Primitivo

2013-01-01

A natural Spodoptera exigua multiple nucleopolyhedrovirus (SeMNPV) isolate from Florida shares a strikingly similar genotypic composition to that of a natural Spodoptera frugiperda MNPV (SfMNPV) isolate from Nicaragua. Both isolates comprise a high proportion of large-deletion genotypes that lack genes that are essential for viral replication or transmission. To determine the likely origins of such genotypically similar population structures, we performed genomic and functional analyses of these genotypes. The homology of nucleotides in the deleted regions was as high as 79%, similar to those of other colinear genomic regions, although some SfMNPV genes were not present in SeMNPV. In addition, no potential consensus sequences were shared between the deletion flanking sequences. These results indicate an evolutionary mechanism that independently generates and sustains deletion mutants within each virus population. Functional analyses using different proportions of complete and deletion genotypes were performed with the two viruses in mixtures of occlusion bodies (OBs) or co-occluded virions. Ratios greater than 3:1 of complete/deletion genotypes resulted in reduced pathogenicity (expressed as median lethal dose), but there were no significant changes in the speed of kill. In contrast, OB yields increased only in the 1:1 mixture. The three phenotypic traits analyzed provide a broader picture of the functional significance of the most extensively deleted SeMNPV genotype and contribute toward the elucidation of the role of such mutants in baculovirus populations. PMID:23204420

Isolation and Characterization of Novel Polymorphic Microsatellite Markers for Cimex hemipterus F. (Hemiptera: Cimicidae).

PubMed

Seri Masran, Siti Nor Ain; Ab Majid, Abdul Hafiz

2018-05-04

Due to the growing public health and tourism awareness, Cimex hemipterus Fabricius (Hemiptera: Cimicidae) has gained a great interest in increasing reported infestation cases in tropical regions of the world, including Malaysia. Since the information on the molecular ecology and population biology of this species are tremendously lacking, the isolation and development of molecular markers can be used to determine its genetic structure. In this study, novel microsatellite primers isolated from enriched genomic libraries of C. hemipterus were developed using 454 Roche shotgun sequencing. Seven validated polymorphic microsatellite primers were consistently amplified and characterized from 70 tropical bed bugs collected from seven locations throughout Malaysia. The number of alleles per locus identified ranged from 6 to 14. Comparison of loci for overall and between population were done with mean observed and expected heterozygosity were determined at 0.320 and 0.814, 0.320 and 0.727, respectively. Polymorphic information criteria (PIC) valued the markers as highly informative as PIC >0.5. Overall population, they are possibly in Hardy-Weinberg equilibrium with loci Ch_09ttn, Ch_01dn, and Ch_13dn showing signs of a null allele. There were no scoring errors caused by stutter peaks, no large allele dropout was detected for all loci and showed no evidence of linkage disequilibrium. In conclusion, all seven molecular microsatellite markers identified can be beneficially used to gain more information on the population genetic structure and breeding patterns of C. hemipterus as well as the relationship of dispersal and infestation.

Pharmacokinetics of Cannabis in Cancer Cachexia-Anorexia Syndrome.

PubMed

Reuter, Stephanie E; Martin, Jennifer H

2016-07-01

Anorexia can affect up to 90 % of people with advanced cancer. It is a complex symptom associated with changes in taste, lack of hunger at mealtimes and lack of food enjoyment. Associated weight loss is part of the physical decline that occurs as cancer worsens. Weight loss can also occur from cachexia, the increased metabolism of energy due to raised inflammatory cytokines, liver metastases and other factors seen in several advanced cancers. Independent of anorexia, although frequently associated (where it is referred to as the cachexia-anorexia syndrome), it accounts for a significant amount of morbidity and deaths in people with cancer. In particular, quality of life for the patient and the family is significantly affected with this syndrome as it causes anxiety and distress. Therefore, it is important that research into therapies is undertaken, particularly focusing on an understanding of the pharmacokinetic properties of compounds in this cachexic population. Cannabinoids are one such group of therapies that have received a large amount of media focus recently. However, there appears to be a lack on rigorous pharmacokinetic data of these complex and varied compounds in the cachexic population. Similarly, there is a lack of pharmacokinetic data in any population group for the non- tetrahydrocannabinol (THC) and cannabidiol (CBD) cannabinoids (often due to the lack of analytical standards for quantification). This review will thus examine the pharmacokinetics of major cannabinoids i.e. THC and CBD in a cancer population. Overall, based on the current literature, evidence for the use of cannabinoids for the treatment of cancer-related cachexia-anorexia syndrome remains equivocal. A high-quality, rigorous, phase I/II study to elicit pharmacokinetic dose-concentration and concentration-response data, with a clinically acceptable mode of delivery to reduce intrapatient variability and enable more consistent bioavailability is needed in this population.

Population divergence and gene flow in an endangered and highly mobile seabird

PubMed Central

Welch, A J; Fleischer, R C; James, H F; Wiley, A E; Ostrom, P H; Adams, J; Duvall, F; Holmes, N; Hu, D; Penniman, J; Swindle, K A

2012-01-01

Seabirds are highly vagile and can disperse up to thousands of kilometers, making it difficult to identify the factors that promote isolation between populations. The endemic Hawaiian petrel (Pterodroma sandwichensis) is one such species. Today it is endangered, and known to breed only on the islands of Hawaii, Maui, Lanai and Kauai. Historical records indicate that a large population formerly bred on Molokai as well, but this population has recently been extirpated. Given the great dispersal potential of these petrels, it remains unclear if populations are genetically distinct and which factors may contribute to isolation between them. We sampled petrels from across their range, including individuals from the presumably extirpated Molokai population. We sequenced 524 bp of mitochondrial DNA, 741 bp from three nuclear introns, and genotyped 18 microsatellite loci in order to examine the patterns of divergence in this species and to investigate the potential underlying mechanisms. Both mitochondrial and nuclear data sets indicated significant genetic differentiation among all modern populations, but no differentiation was found between historic samples from Molokai and modern birds from Lanai. Population-specific nonbreeding distribution and strong natal philopatry may reduce gene flow between populations. However, the lack of population structure between extirpated Molokai birds and modern birds on Lanai indicates that there was substantial gene flow between these populations and that petrels may be able to overcome barriers to dispersal prior to complete extirpation. Hawaiian petrel populations could be considered distinct management units, however, the dwindling population on Hawaii may require translocation to prevent extirpation in the near future. PMID:22434012

Population divergence and gene flow in an endangered and highly mobile seabird

USGS Publications Warehouse

Welch, A. J.; Fleischer, R. C.; James, H. F.; Wiley, A. E.; Ostrom, P. H.; Adams, J.; Duvall, F.; Holmes, N.; Hu, D.; Penniman, J.; Swindle, K. A.

2012-01-01

Seabirds are highly vagile and can disperse up to thousands of kilometers, making it difficult to identify the factors that promote isolation between populations. The endemic Hawaiian petrel (Pterodroma sandwichensis) is one such species. Today it is endangered, and known to breed only on the islands of Hawaii, Maui, Lanai and Kauai. Historical records indicate that a large population formerly bred on Molokai as well, but this population has recently been extirpated. Given the great dispersal potential of these petrels, it remains unclear if populations are genetically distinct and which factors may contribute to isolation between them. We sampled petrels from across their range, including individuals from the presumably extirpated Molokai population. We sequenced 524 bp of mitochondrial DNA, 741 bp from three nuclear introns, and genotyped 18 microsatellite loci in order to examine the patterns of divergence in this species and to investigate the potential underlying mechanisms. Both mitochondrial and nuclear data sets indicated significant genetic differentiation among all modern populations, but no differentiation was found between historic samples from Molokai and modern birds from Lanai. Population-specific nonbreeding distribution and strong natal philopatry may reduce gene flow between populations. However, the lack of population structure between extirpated Molokai birds and modern birds on Lanai indicates that there was substantial gene flow between these populations and that petrels may be able to overcome barriers to dispersal prior to complete extirpation. Hawaiian petrel populations could be considered distinct management units, however, the dwindling population on Hawaii may require translocation to prevent extirpation in the near future.

Bridging the gap: the role of Physiatrists in caring for adults with cerebral palsy.

PubMed

Cassidy, Caitlin; Campbell, Nerissa; Madady, Mona; Payne, Michael

2016-01-01

Individuals with cerebral palsy (CP) experience a significant gap in care as they move from interdisciplinary pediatric programs to limited or non-existent care in the adult sector. A lack of knowledgeable adult care providers has repeatedly been identified as a challenge in transitioning those with CP from pediatric to adult care. The objective of this study was to determine the extent to which Physiatrists provide care to adults with CP and to identify barriers to their engagement with this population. A survey was distributed to Physiatrists across Canada. Results were analyzed descriptively using SPSS software. Most Physiatrists provide care to very few adults with CP (10 or less), but over 80% feel that Physiatry is the most appropriate specialty to provide disability-related care to adults with CP following their pediatric discharge. Among the most frequently identified barriers to caring for this population were lack of accessible resources (i.e. social work, funded therapy, equipment) and lack of referrals. Physiatrists are willing and appropriate partners in transitioning patients with CP to adult care. Barriers to Physiatrists' engagement with this population appear to be amenable to change. A lack of knowledgeable and interested adult practitioners has repeatedly been identified as a challenge in transition planning for young adults with cerebral palsy (the vast majority of whom survive into adulthood). Physiatrists are ideally suited to manage adults with cerebral palsy, yet in this survey-based study, a majority of Canadian Physiatrists report caring for less than five adults with cerebral palsy on a regular basis. Barriers to further physiatric involvement in this population were reported to include lack of accessible resources and lack of referrals.

Middle East assessment.

PubMed

Mahran, M

1984-06-01

All governments of the Arab world are aware of the population issue, and there has been increasing interest in policies designed to bring about a lower rate of natural increase and older population age structure. Overpopulation is believed to be a major obstacle to economic development. The population activities of the Arab countries can be divided into 3 categories: national policy to reduce population growth; nongovernmental efforts to reduce population growth; and countries with pronatalist policies. The countries with a national policy to reduce population growth include Egypt, Tunisia, and Morocco. All suffer severe problems of high density, young age structure, and lack of balance between the population and the economy. In these countries an active national family planning program operates alongside many active nongovernmental family planning associations. Reduction of the growth rate is regarded as urgent, and emigration is encouraged. In egypt contraceptives are readily available through commerical outlets, and village level social and economic activities are promoted in conjunction with family planning services. Tunisia is the only country to offer voluntary sterilization and 1st trimester abortion on request. Morocco includes family planning in its health and welfare services and there is an active voluntary family planning association. Countries in the group who have made nongovernmental efforts to reduce population growth include Algeria, Bahrain, Iarq, Jordan, Lebanon, Sudan, Syria, and Democratic Yemen. all have major population problems and generally support reduced growth rated but as yet have no national family planning. In this group the highest rate of population increase is in Syria, 3.8% a year; the highest total fertility rate is in Bahrain with almost 8 children per women. Saudi Arabia, Kewait, Qwatar, Libya, and Oman have pronatalist policies. Methods of contraception are available in the private sector. The outstanding feature of these oil rich countries is their high per capita gross national product. A 1981 estimate showed Qatar's at US$27,790, to be the highest in the world. Generally, all the governments of the Arab world have become aware of population issues and of the population pressures within their own borders.

Structure of Penaeus stylirostris Densovirus, a Shrimp Pathogen

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

Kaufmann, Bärbel; Bowman, Valorie D.; Li, Yi

Penaeus stylirostris densovirus (PstDNV), a pathogen of penaeid shrimp, causes significant damage to farmed and wild shrimp populations. In contrast to other parvoviruses, PstDNV probably has only one type of capsid protein that lacks the phospholipase A2 activity that has been implicated as a requirement during parvoviral host cell infection. The structure of recombinant virus-like particles, composed of 60 copies of the 37.5-kDa coat protein, the smallest parvoviral capsid protein reported thus far, was determined to 2.5-{angstrom} resolution by X-ray crystallography. The structure represents the first near-atomic resolution structure within the genus Brevidensovirus. The capsid protein has a {beta}-barrel 'jellymore » roll' motif similar to that found in many icosahedral viruses, including other parvoviruses. The N-terminal portion of the PstDNV coat protein adopts a 'domain-swapped' conformation relative to its twofold-related neighbor similar to the insect parvovirus Galleria mellonella densovirus (GmDNV) but in stark contrast to vertebrate parvoviruses. However, most of the surface loops have little structural resemblance to any of the known parvoviral capsid proteins.« less

Understanding Referral Patterns for Bone Mineral Density Testing among Family Physicians: A Qualitative Descriptive Study.

PubMed

Munce, Sarah E P; Allin, Sonya; Carlin, Leslie; Sale, Joanna; Hawker, Gillian; Kim, Sandra; Butt, Debra A; Polidoulis, Irene; Tu, Karen; Jaglal, Susan B

2016-01-01

Introduction. Evidence of inappropriate bone mineral density (BMD) testing has been identified in terms of overtesting in low risk women and undertesting among patients at high risk. In light of these phenomena, the objective of this study was to understand the referral patterns for BMD testing among Ontario's family physicians (FPs). Methods. A qualitative descriptive approach was adopted. Twenty-two FPs took part in a semi-structured interview lasting approximately 30 minutes. An inductive thematic analysis was performed on the transcribed data in order to understand the referral patterns for BMD testing. Results. We identified a lack of clarity about screening for osteoporosis with a tendency for baseline BMD testing in healthy, postmenopausal women and a lack of clarity on the appropriate age for screening for men in particular. A lack of clarity on appropriate intervals for follow-up testing was also described. Conclusions. These findings lend support to what has been documented at the population level suggesting a tendency among FPs to refer menopausal women (at low risk). Emphasis on referral of high-risk groups as well as men and further clarification and education on the appropriate intervals for follow-up testing is warranted.

Perceived barriers to implementing screening and brief intervention for alcohol consumption by adolescents in hospital emergency department in Spain.

PubMed

Falcón, María; Navarro-Zaragoza, Javier; García-Rodríguez, Rosa María; Nova-López, Daniel; González-Navarro, María Dulce; Mercadal, María; García-Algar, Oscar; Luna Ruiz-Cabello, Aurelio

2017-07-14

Screening for alcohol consumption in adolescents is widely justified in the health care field because of the particular vulnerability of this population, which starts drinking alcohol at a very early age and frequently consumes high levels of the same. Hospital emergency departments (ED) could be a good venue to manage early detection and carry out brief intervention (BI) programmes. The aim of this study was to identify perceived barriers for medical staff of three hospitals in Spain to successfully implement a protocol for alcohol detection and BI for minors in the ED. Exploratory qualitative analysis using focus groups with semi-structured, flexible and open-ended questions to explore beliefs, attitudes, and barriers perceived by professionals to screening alcohol consumption and implementing BI in adolescents attended at the ED. The main perceived barriers by health professionals were lack of time, work overload, mistrust, lack of validated and simple screening tools, lack of training/awareness and legal concerns about informed consent and confidentiality. Barriers to screening and intervention in ED are similar to those described previously. It is necessary to improve organization of time allocated for medical consultations, avoid limiting ED resources, motivate staff and provide appropriate training.

Genetic structure in the southernmost populations of black-and-gold howler monkeys (Alouatta caraya) and its conservation implications

PubMed Central

Miño, Carolina Isabel; Fernández, Gabriela; Caputo, Mariela; Corach, Daniel

2017-01-01

Black-and-gold howler monkeys Alouatta caraya, are arboreal primates, inhabitants of Neotropical forests, highly susceptible to the yellow fever virus, considered early 'sentinels' of outbreaks, and thus, of major epidemiological importance. Currently, anthropogenic habitat loss and modifications threatens their survival. Habitat modification can prevent, reduce or change dispersal behavior, which, in turn, may influence patterns of gene flow. We explored past and contemporary levels of genetic diversity, elucidated genetic structure and identified its possible drivers, in ten populations (n = 138) located in the southernmost distribution range of the species in South America, in Argentina and Paraguay. Overall, genetic variability was moderate (ten microsatellites: 3.16 ± 0.18 alleles per locus, allelic richness of 2.93 ± 0.81, 0.443±0.025 unbiased expected heterozygosity; 22 haplotypes of 491-bp mitochondrial Control Region, haplotypic diversity of 0.930 ± 0.11, and nucleotide diversity of0.01± 0.007). Significant evidence of inbreeding was found in a population that was, later, decimated by yellow fever. Population-based gene flow measures (FST = 0.13; θST = 018), hierarchical analysis of molecular variance and Bayesian clustering methods revealed significant genetic structure, grouping individuals into four clusters. Shared haplotypes and lack of mitochondrial differentiation (non-significant θST) among some populations seem to support the hypothesis of historical dispersal via riparian forests. Current resistance analyses revealed a significant role of landscape features in modeling contemporary gene flow: continuous forest and riparian forests could promote genetic exchange, whereas disturbed forests or crop/grassland fields may restrict it. Estimates of effective population size allow anticipating that the studied populations will lose 75% of heterozygosity in less than 50 generations. Our findings suggest that anthropogenic modifications on native forests, increasingly ongoing in Northeastern Argentina, Southern Paraguay and Southeastern Brazil, might prevent the dispersal of howlers, leading to population isolation. To ensure long-term viability and maintain genetic connectivity of A. caraya remnant populations, we recommend preserving and restoring habitat continuity. To conserve the species genetic pool, as well, the four genetic clusters identified here should be considered separate Management Units and given high conservation priority. In light of our findings and considering complementary non-genetic information, we suggest upgrading the international conservation status of A. caraya to “Vulnerable”. PMID:28968440

Using an isolated population boom to explore barriers to recovery in the keystone Caribbean coral reef herbivore Diadema antillarum

NASA Astrophysics Data System (ADS)

Bodmer, Max D. V.; Rogers, Alex D.; Speight, Martin R.; Lubbock, Natalie; Exton, Dan A.

2015-12-01

Recovery of the keystone herbivore Diadema antillarum after the 1983-1984 mass mortality event poses one of the greatest challenges to Caribbean coral reef conservation, yet our understanding of the problem remains severely limited. Whilst some recovery has been observed, this has been restricted to the shallows (≤5 m). We report a newly discovered, isolated population recovery on Banco Capiro, Honduras, representing the largest recorded post-mortality densities beyond the shallowest environments (0.74-2.27 individuals m-2 at depths ≥10 m) alongside an unusually high mean percentage scleractinian coral cover of 49-62 %, likely no coincidence. On the nearby island of Utila, we report D. antillarum densities of 0.003-0.012 individuals m-2 and scleractinian coral cover of 12 % at depths ≥10 m, "typical" for a contemporary Caribbean coral reef. The three order of magnitude disparity in population density between sites separated by <60 km presents a unique opportunity to investigate barriers preventing their region-wide recovery by simultaneously addressing a range of previously proposed hypotheses. Despite concerns over the impacts of asynchronous spawning in low-density populations, we find that recruitment is occurring on Utila. This suggests that, whilst Allee effects are likely to be a contributing factor, the major barriers suppressing recovery are instead impacting juvenile survival into adulthood. Similarly, variations in heterospecific echinoids, interspecific competitors, and nutrient availability fail to account for population differences. Instead, we highlight a lack of structural complexity on contemporary Caribbean reefs as the most likely explanation for the limited recovery through a lack of provision of juvenile predation refugia, representing a further consequence of the recent ubiquitous phase shifts throughout the region. Using these findings, we propose future management strategies to stimulate recovery and, consequently, reef health throughout the Caribbean.

Assessment of Compliance to Treatment of Diabetes and Hypertension amongst Previously Diagnosed Patients from Rural Community of Raigad District of Maharashtra.

PubMed

Kakumani, Kiranmayi Venkata; Waingankar, Prasad

2016-12-01

Substantial burden of diabetes and hypertension is on rise in India, leading to a twin epidemic. India, being a rural country, has unique problems regarding the treatment compliance which is a serious risk for morbidity and mortality. To assess the compliance to treatment of hypertension and diabetes amongst the diagnosed patients from rural area and to study reasons of non-compliance and knowledge and attitude. Community based, cross sectional, observational study conducted in the rural communities of Tara and Barapada villages of Raigad district of Maharashtra. Survey was conducted covering population of 2115 across 360 families, 250 at Barapada and 110 at Tara. All the cases of diabetes and hypertension diagnosed for more than one year were included. A structured and pre-tested questionnaire was administered including details on demography, medical documentation, treatment details and factors assessing the compliance, knowledge and attitude towards the diseases. When reviewed the treatment adherence pattern based on documentary evidence and interview of the patient, on history of taking medication strictly since the detection illness, it was found that more than 70% of the Diabetics and more than 75% of the Hypertensive have discontinued the treatment in between. The most common reasons of non-compliance is the lack of sufficient motivation for treatment adherence as many mentioned (61.4% diabetics, 55.8% hypertensives) difficulty to remember to take daily medication due to work or forgetfulness. This is followed by lack of money (50%diabetics, 55.8% hypertensives) and living far away from doctor in city (43% diabetics and 46% hypertensives). The study findings are only tip of iceberg and the non-adherence to the treatment of diabetes and hypertension in rural population is at alarmingly high. Illiteracy, lack of faith in treatment and motivation, unawareness and self-neglect as well as financial constraints and lack of specialist care in rural area is playing important role.

Lack of Host Specialization on Winter Annual Grasses in the Fungal Seed Bank Pathogen Pyrenophora semeniperda

PubMed Central

Beckstead, Julie; Meyer, Susan E.; Ishizuka, Toby S.; McEvoy, Kelsey M.; Coleman, Craig E.

2016-01-01

Generalist plant pathogens may have wide host ranges, but many exhibit varying degrees of host specialization, with multiple pathogen races that have narrower host ranges. These races are often genetically distinct, with each race causing highest disease incidence on its host of origin. We examined host specialization in the seed pathogen Pyrenophora semeniperda by reciprocally inoculating pathogen strains from Bromus tectorum and from four other winter annual grass weeds (Bromus diandrus, Bromus rubens, Bromus arvensis and Taeniatherum caput-medusae) onto dormant seeds of B. tectorum and each alternate host. We found that host species varied in resistance and pathogen strains varied in aggressiveness, but there was no evidence for host specialization. Most variation in aggressiveness was among strains within populations and was expressed similarly on both hosts, resulting in a positive correlation between strain-level disease incidence on B. tectorum and on the alternate host. In spite of this lack of host specialization, we detected weak but significant population genetic structure as a function of host species using two neutral marker systems that yielded similar results. This genetic structure is most likely due to founder effects, as the pathogen is known to be dispersed with host seeds. All host species were highly susceptible to their own pathogen races. Tolerance to infection (i.e., the ability to germinate even when infected and thereby avoid seed mortality) increased as a function of seed germination rate, which in turn increased as dormancy was lost. Pyrenophora semeniperda apparently does not require host specialization to fully exploit these winter annual grass species, which share many life history features that make them ideal hosts for this pathogen. PMID:26950931

Phylogeography of Eomecon chionantha in subtropical China: the dual roles of the Nanling Mountains as a glacial refugium and a dispersal corridor.

PubMed

Tian, Shuang; Kou, Yixuan; Zhang, Zhirong; Yuan, Lin; Li, Derong; López-Pujol, Jordi; Fan, Dengmei; Zhang, Zhiyong

2018-02-09

Mountains have not only provided refuge for species, but also offered dispersal corridors during the Neogene and Quaternary global climate changes. Compared with a plethora of studies on the refuge role of China's mountain ranges, their dispersal corridor role has received little attention in plant phylogeographic studies. Using phylogeographic data of Eomecon chionantha Hance (Papaveraceae), this study explicitly tested whether the Nanling Mountains, which spans from west to east for more than 1000 km in subtropical China, could have functioned as a dispersal corridor during the late Quaternary in addition to a glacial refugium. Our analyses revealed a range-wide lack of phylogeographic structure in E. chionantha across three kinds of molecular markers [two chloroplast intergenic spacers, nuclear ribosomal internal transcribed spacer (nrITS), and six nuclear microsatellite loci]. Demographic inferences based on chloroplast and nrITS sequences indicated that E. chionantha could have experienced a strong postglacial range expansion between 6000 and 1000 years ago. Species distribution modelling showed that the Nanling Mountains and the eastern Yungui Plateau were the glacial refugia of E. chionantha. Reconstruction of dispersal corridors indicated that the Nanling Mountains also have acted as a corridor of population connectivity for E. chionantha during the late Quaternary. Our results suggest that the Nanling Mountains may acted dual roles as a dispersal corridor in east-west direction and as a glacial refugium in subtropical China during the late Quaternary. The population connectivity mediated by the mountain range and a strong postglacial range expansion are the most likely reasons for the lack of phylogeographic structure in E. chionantha. The hypothesis of dual roles of the mountain range presented here sheds new insights into the phylogeographic patterns of organisms in subtropical China.

A protocol for better design, application, and communication of population viability analyses.

PubMed

Pe'er, Guy; Matsinos, Yiannis G; Johst, Karin; Franz, Kamila W; Turlure, Camille; Radchuk, Viktoriia; Malinowska, Agnieszka H; Curtis, Janelle M R; Naujokaitis-Lewis, Ilona; Wintle, Brendan A; Henle, Klaus

2013-08-01

Population viability analyses (PVAs) contribute to conservation theory, policy, and management. Most PVAs focus on single species within a given landscape and address a specific problem. This specificity often is reflected in the organization of published PVA descriptions. Many lack structure, making them difficult to understand, assess, repeat, or use for drawing generalizations across PVA studies. In an assessment comparing published PVAs and existing guidelines, we found that model selection was rarely justified; important parameters remained neglected or their implementation was described vaguely; limited details were given on parameter ranges, sensitivity analysis, and scenarios; and results were often reported too inconsistently to enable repeatability and comparability. Although many guidelines exist on how to design and implement reliable PVAs and standards exist for documenting and communicating ecological models in general, there is a lack of organized guidelines for designing, applying, and communicating PVAs that account for their diversity of structures and contents. To fill this gap, we integrated published guidelines and recommendations for PVA design and application, protocols for documenting ecological models in general and individual-based models in particular, and our collective experience in developing, applying, and reviewing PVAs. We devised a comprehensive protocol for the design, application, and communication of PVAs (DAC-PVA), which has 3 primary elements. The first defines what a useful PVA is; the second element provides a workflow for the design and application of a useful PVA and highlights important aspects that need to be considered during these processes; and the third element focuses on communication of PVAs to ensure clarity, comprehensiveness, repeatability, and comparability. Thereby, DAC-PVA should strengthen the credibility and relevance of PVAs for policy and management, and improve the capacity to generalize PVA findings across studies. © 2013 Society for Conservation Biology.

Organising women for Panchayati Raj.

PubMed

Kaushik, S

1993-08-01

The recently passed 73rd Constitution Amendment Act in India focused on political structures and processes of rural India and vulnerable populations. Participation of women in Panchayati Raj Institutions was questioned in terms of the substance and effectiveness of representation. Rural women were particularly vulnerable as a group because of strong traditional values maintained in rural areas, patriarchal families, lack of women's education and access to information, poor exposure to the "outside" world, and lack of power. Local committees insufficiently represented women. Women were rarely heads of Panchayats and needed the lower positions to advance within the system. State acts have been passed to assure women's representation in Andhra Pradesh. The National Perspective Plan of 1988 provided for over 33% of seats for women and minorities as members and chairpersons of Panches and Sarpanches, based on proportional representation in the total population. Greater participation of women in politics was viewed as dependent not just on fulfilling the law but on assuring principles, democratic, and meaningful administration of government. Effort were equally necessary to address attitudinal, social, and structural barricades. Women needed to know where and how to direct their concerns so that solutions were found to the problems women faced. Women members of Panchayats needed to be educated and informed about politics: their rights, the nature of Indian democracy, policies and programs for women and the underprivileged, and voting rights. Women needed financial support for running for office. Women must view themselves as representatives of all people. Women's centers and other organizations can serve as catalysts to mobilize women and help solve political dilemmas. A combination of Constitutional provisions, government policies, social action, and self awareness among rural women will eventually result in Indian women becoming part of the mainstream political power sharing and decision making.

Genetic Status and Timing of a Weevil Introduction to Santa Cruz Island, Galápagos

PubMed Central

2014-01-01

Successful invasive species can overcome or circumvent the potential genetic loss caused by an introduction bottleneck through a rapid population expansion and admixture from multiple introductions. We explore the genetic makeup and the timing of a species introduction to Santa Cruz Island in the Galápagos archipelago. We investigate the presence of processes that can maintain genetic diversity in populations of the broad-nosed weevil Galapaganus howdenae howdenae. Analyses of combined genotypes for 8 microsatellite loci showed evidence of past population size reductions through moment and likelihood-based estimators. No evidence of admixture through multiple introductions was found, but substantial current population sizes (N0 298, 95% credible limits 50–2300), genetic diversity comparable with long-established endemics (Mean number of alleles = 3.875), and lack of genetic structure across the introduced range (F ST = 0.01359) could suggest that foundations are in place for populations to rapidly recover any loss of genetic variability. The time estimates for the introduction into Santa Cruz support an accidental transfer during the colonization period (1832–1959) predating the spurt in human population growth. Our evaluation of the genetic status of G. h. howdenae suggests potential for population growth in addition to our field observations of a concurrent expansion in range and feeding preferences towards protected areas and endemic host plants. PMID:24399746

Gender equality in university sportspeople's drinking.

PubMed

O'Brien, Kerry S; Hunter, Jackie; Kypri, Kypros; Ali, Ajmol

2008-11-01

In large population-based alcohol studies males are shown consistently to drink more, and more hazardously, than females. However, research from some countries suggests that gender differences in drinking are converging, with females drinking more than in the past. Large population-based research may miss gender-based changes in drinking behaviours that occur in sub-populations most at risk of hazardous drinking. We examine gender differences in a sub-population where hazardous drinking is common and endorsed, namely university sportspeople. The Alcohol Use Disorders Identification Test (AUDIT) and a drinking motives measure were used to assess hazardous drinking behaviours and drinking motives in 631 university sportspeople (females = 331, 52%). There were no gender differences in AUDIT scores. However, drinking motives differed between genders, with coping motives being a significant predictor of hazardous drinking in females but not males. Hazardous drinking, including binge drinking (46.3%) and frequent binge drinking (35%), in New Zealand university sportspeople is high for both males and females. New Zealand university sportspeople are one population where gender differences in drinking are not apparent and run counter to European population based research and research in US sporting populations. Gender role equality in the university systems, and endorsement of drinking in sporting culture, may account for the lack of gender differences in this New Zealand sporting population. Future research on gender differences in drinking should examine sub-populations where gender role differentiation is low, and socio-cultural/structural factors supporting gender equality are high.

Dementia Research: Populations, Progress, Problems, and Predictions.

PubMed

Hunter, Sally; Smailagic, Nadja; Brayne, Carol

2018-05-16

Alzheimer's disease (AD) is a clinicopathologically defined syndrome leading to cognitive impairment. Following the recent failures of amyloid-based randomized controlled trials to change the course of AD, there are growing calls for a re-evaluation of basic AD research. Epidemiology offers one approach to integrating the available evidence. Here we examine relationships between evidence from population-based, clinicopathological studies of brain aging and a range of hypotheses from all areas of AD research. We identify various problems, including a lack of systematic approach to measurement of clinical and neuropathological factors associated with dementia in experimental and clinical settings, poor understanding of the strengths and weaknesses of different observational and experimental designs, a lack of clarity in relation to disease definitions from the clinical, neuropathological, and molecular perspectives, inadequate characterization of brain aging in the human population, difficulties in translation between laboratory-based and population-based evidence bases, and a lack of communication between different sections of the dementia research community. Population studies highlight complexity and predict that therapeutic approaches based on single disease features will not be successful. Better characterization of brain aging in the human population is urgently required to select biomarkers and therapeutic targets that are meaningful to human disease. The generation of detailed and reliable evidence must be addressed before progress toward therapeutic interventions can be made.

Inferring Population Genetic Structure in Widely and Continuously Distributed Carnivores: The Stone Marten (Martes foina) as a Case Study

PubMed Central

Vergara, María; Basto, Mafalda P.; Madeira, María José; Gómez-Moliner, Benjamín J.; Santos-Reis, Margarida; Fernandes, Carlos; Ruiz-González, Aritz

2015-01-01

The stone marten is a widely distributed mustelid in the Palaearctic region that exhibits variable habitat preferences in different parts of its range. The species is a Holocene immigrant from southwest Asia which, according to fossil remains, followed the expansion of the Neolithic farming cultures into Europe and possibly colonized the Iberian Peninsula during the Early Neolithic (ca. 7,000 years BP). However, the population genetic structure and historical biogeography of this generalist carnivore remains essentially unknown. In this study we have combined mitochondrial DNA (mtDNA) sequencing (621 bp) and microsatellite genotyping (23 polymorphic markers) to infer the population genetic structure of the stone marten within the Iberian Peninsula. The mtDNA data revealed low haplotype and nucleotide diversities and a lack of phylogeographic structure, most likely due to a recent colonization of the Iberian Peninsula by a few mtDNA lineages during the Early Neolithic. The microsatellite data set was analysed with a) spatial and non-spatial Bayesian individual-based clustering (IBC) approaches (STRUCTURE, TESS, BAPS and GENELAND), and b) multivariate methods [discriminant analysis of principal components (DAPC) and spatial principal component analysis (sPCA)]. Additionally, because isolation by distance (IBD) is a common spatial genetic pattern in mobile and continuously distributed species and it may represent a challenge to the performance of the above methods, the microsatellite data set was tested for its presence. Overall, the genetic structure of the stone marten in the Iberian Peninsula was characterized by a NE-SW spatial pattern of IBD, and this may explain the observed disagreement between clustering solutions obtained by the different IBC methods. However, there was significant indication for contemporary genetic structuring, albeit weak, into at least three different subpopulations. The detected subdivision could be attributed to the influence of the rivers Ebro, Tagus and Guadiana, suggesting that main watercourses in the Iberian Peninsula may act as semi-permeable barriers to gene flow in stone martens. To our knowledge, this is the first phylogeographic and population genetic study of the species at a broad regional scale. We also wanted to make the case for the importance and benefits of using and comparing multiple different clustering and multivariate methods in spatial genetic analyses of mobile and continuously distributed species. PMID:26222680

Inferring Population Genetic Structure in Widely and Continuously Distributed Carnivores: The Stone Marten (Martes foina) as a Case Study.

PubMed

Vergara, María; Basto, Mafalda P; Madeira, María José; Gómez-Moliner, Benjamín J; Santos-Reis, Margarida; Fernandes, Carlos; Ruiz-González, Aritz

2015-01-01

The stone marten is a widely distributed mustelid in the Palaearctic region that exhibits variable habitat preferences in different parts of its range. The species is a Holocene immigrant from southwest Asia which, according to fossil remains, followed the expansion of the Neolithic farming cultures into Europe and possibly colonized the Iberian Peninsula during the Early Neolithic (ca. 7,000 years BP). However, the population genetic structure and historical biogeography of this generalist carnivore remains essentially unknown. In this study we have combined mitochondrial DNA (mtDNA) sequencing (621 bp) and microsatellite genotyping (23 polymorphic markers) to infer the population genetic structure of the stone marten within the Iberian Peninsula. The mtDNA data revealed low haplotype and nucleotide diversities and a lack of phylogeographic structure, most likely due to a recent colonization of the Iberian Peninsula by a few mtDNA lineages during the Early Neolithic. The microsatellite data set was analysed with a) spatial and non-spatial Bayesian individual-based clustering (IBC) approaches (STRUCTURE, TESS, BAPS and GENELAND), and b) multivariate methods [discriminant analysis of principal components (DAPC) and spatial principal component analysis (sPCA)]. Additionally, because isolation by distance (IBD) is a common spatial genetic pattern in mobile and continuously distributed species and it may represent a challenge to the performance of the above methods, the microsatellite data set was tested for its presence. Overall, the genetic structure of the stone marten in the Iberian Peninsula was characterized by a NE-SW spatial pattern of IBD, and this may explain the observed disagreement between clustering solutions obtained by the different IBC methods. However, there was significant indication for contemporary genetic structuring, albeit weak, into at least three different subpopulations. The detected subdivision could be attributed to the influence of the rivers Ebro, Tagus and Guadiana, suggesting that main watercourses in the Iberian Peninsula may act as semi-permeable barriers to gene flow in stone martens. To our knowledge, this is the first phylogeographic and population genetic study of the species at a broad regional scale. We also wanted to make the case for the importance and benefits of using and comparing multiple different clustering and multivariate methods in spatial genetic analyses of mobile and continuously distributed species.

[Public policy, structures of the State and the advocacy of the right to health protection].

PubMed

Ruelas-Barajas, Enrique; Gay-Molina, Juan Gabriel

2008-01-01

Not always public policies for the advocacy of citizen rights meet their goal, among other things, because between their formulation and their implementation there is a lack of appropriate structures to generate, articulate and execute these policies. This has been the case of Mexico regarding the advocacy of the rights of non smokers. Very few has been achieved in this matter in the past. This article lists some of the potential causes of the lack of implementation of public policies. At the same time, explores the highly dynamic nature of the health care system at the present and towards the future. The magnitude of the challenges faced by the health care system requires concerted actions of many actors, not only from the very health care system but also from outside. Thus, public policies have to be considered not just at the governmental level but at the state level. Therefore, the main argument of this paper is that given the need to respond to complex challenges to protect the health of the population and their rights in a very complex context, there is a need to formulate and implement state policies that require the intervention of the appropriate state structures to make sure that the design and execution leads to the expected achievements. One such structure at the state level, among others, is the General Health Council, an organization established in 1841, that was incorporated within the Mexican Constitution in 1917, depending directly from the President of Mexico as Head of State. This Council has been reinforced to improve its assigned role to better participate, along other state structures, in the formulation and implementation of public policies such as those for the advocacy of citizen rights.

Variability of the Structural Coloration in Two Butterfly Species with Different Prezygotic Mating Strategies

PubMed Central

Kertész, Krisztián; Bálint, Zsolt; Biró, László Péter

2016-01-01

Structural coloration variability was investigated in two Blue butterfly species that are common in Hungary. The males of Polyommatus icarus (Common Blue) and Plebejus argus (Silver-studded Blue) use their blue wing coloration for conspecific recognition. Despite living in the same type of habitat, these two species display differences in prezygotic mating strategy: the males of P. icarus are patrolling, while P. argus males have sedentary behavior. Therefore, the species-specific photonic nanoarchitecture, which is the source of the structural coloration, may have been subjected to different evolutionary effects. Despite the increasing interest in photonic nanoarchitectures of biological origin, there is a lack of studies focused on the biological variability of structural coloration that examine a statistically relevant number of individuals from the same species. To investigate possible structural color variation within the same species in populations separated by large geographical distances, climatic differences, or applied experimental conditions, one has to be able to compare these variations to the normal biological variability within a single population. The structural coloration of the four wings of 25 male individuals (100 samples for each species) was measured and compared using different light-collecting setups: perpendicular and with an integrating sphere. Significant differences were found in the near UV wavelength region that are perceptible by these polyommatine butterflies but are invisible to human observers. The differences are attributed to the differences in the photonic nanoarchitecture in the scales of these butterflies. Differences in the intensity of structural coloration were also observed and were tentatively attributed to the different prezygotic mating strategies of these insects. Despite the optical complexity of the scale covered butterfly wings, for sufficiently large sample batches, the averaged normal incidence measurements and the averaged measurements using an integrating sphere are in agreement. PMID:27832120

Variability of the Structural Coloration in Two Butterfly Species with Different Prezygotic Mating Strategies.

PubMed

Piszter, Gábor; Kertész, Krisztián; Bálint, Zsolt; Biró, László Péter

2016-01-01

Structural coloration variability was investigated in two Blue butterfly species that are common in Hungary. The males of Polyommatus icarus (Common Blue) and Plebejus argus (Silver-studded Blue) use their blue wing coloration for conspecific recognition. Despite living in the same type of habitat, these two species display differences in prezygotic mating strategy: the males of P. icarus are patrolling, while P. argus males have sedentary behavior. Therefore, the species-specific photonic nanoarchitecture, which is the source of the structural coloration, may have been subjected to different evolutionary effects. Despite the increasing interest in photonic nanoarchitectures of biological origin, there is a lack of studies focused on the biological variability of structural coloration that examine a statistically relevant number of individuals from the same species. To investigate possible structural color variation within the same species in populations separated by large geographical distances, climatic differences, or applied experimental conditions, one has to be able to compare these variations to the normal biological variability within a single population. The structural coloration of the four wings of 25 male individuals (100 samples for each species) was measured and compared using different light-collecting setups: perpendicular and with an integrating sphere. Significant differences were found in the near UV wavelength region that are perceptible by these polyommatine butterflies but are invisible to human observers. The differences are attributed to the differences in the photonic nanoarchitecture in the scales of these butterflies. Differences in the intensity of structural coloration were also observed and were tentatively attributed to the different prezygotic mating strategies of these insects. Despite the optical complexity of the scale covered butterfly wings, for sufficiently large sample batches, the averaged normal incidence measurements and the averaged measurements using an integrating sphere are in agreement.

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.

An analysis of actions to promote health in underprivileged urban areas: a case in Brazil

PubMed Central

2013-01-01

Background Two policies stood out in the 2000s geared towards changing the care model adopted in Brazil: The National Policy on Primary Health Care, based on a family health care model, and the National Policy on Health Promotion. The aim of this study was to analyze health promotion actions developed by family health care teams in the municipality of Belford Roxo. This town was chosen by virtue of its “below average” level of primary health care services offered in relation to other municipalities in Rio de Janeiro state. Methods The following methodological strategies were employed: analysis of health systems, document analysis (2010 Annual Health Schedule and 2010 Annual Management Report), participant observation and interviews with nine health care professionals in the region of study, namely: the manager of the Regional Health Polyclinic (responsible for health care actions in the region), and nurses belonging to the eight family health teams. Giddens’ Theory of Structuration was used for analysis of the results. Results Varying levels of health care activity were found, indicating that the managers have been either unable or lacked the commitment to perform the proposed actions. From a structural point of view, 87.5% of the teams were incomplete. Also of particular note was the lack of any physicians in the teams, which, despite its detrimental effect, was regarded by the interviewees as “natural”. Strong political party influence in the area hindered relations between the team and the local population. Health education, especially through lectures was the main health promotion activity picked up in this study. No cross-sectorial or public participation actions were identified. Connections between the teams for sharing responsibilities were found to be very weak. Conclusion In addition to political factors, there are also structural limitations such as a lack of human resources that overburdens the teams’ daily activities. From this point of view, the political context and lack of professionals were restrictive factors for health promotion. Belford Roxo is not necessarily representative of other experiences in Brazil. However, problems such as patronage, political manipulation, poverty and incipient cross-sectorial actions are common to other Brazilian towns and cities. PMID:23758615

Who donates? Cross-country and periodical variation in blood donor demographics in Europe between 1994 and 2014.

PubMed

Wittock, Nathan; Hustinx, Lesley; Bracke, Piet; Buffel, Veerle

2017-11-01

Ageing European populations put pressure on national blood supplies, increasing the need for blood and donor base rejuvenation. Therefore, we investigate how European countries' blood donor populations differ and how they have evolved over the last 2 decades. Previous comparative research, based on 1994 Eurobarometer data, indicate that the typical donor is an educated, middle-aged, white, married male. Other sociodemographic and socioeconomic correlates, such as employment status and type of community, are less clear. Multilevel analyses are performed on repeated cross-level data from the Eurobarometer (waves 1994, 2002, 2009, and 2014) to compare information on "ever having donated" across sociodemographic categories, countries, and periods. There are consistent but moderate country and period differences. The donor population rose to become largest in most countries by 2009, and stabilized thereafter. Over the studied period, donors were more likely to be higher educated, married men. Nevertheless, changes across time in donor profiles within countries did occur. Women were less likely to donate blood, especially in Southern and Eastern Europe, but this gender gap has declined. Furthermore, educational attainment seems more relevant for women, although, more recently, to a lesser extent. Although there is a promising trend in which women, young people, and students are increasingly likely to donate, more attention is needed to reach the unemployed and the low to medium educated. Because the unemployed may lack structural opportunities to donate, and the low to medium educated may lack relevant knowledge on blood donation necessity, we recommend providing practical opportunities and information on the necessity of blood donation. © 2017 AABB.

Microhabitat Types Promote the Genetic Structure of a Micro-Endemic and Critically Endangered Mole Salamander (Ambystoma leorae) of Central Mexico

PubMed Central

Sunny, Armando; Monroy-Vilchis, Octavio; Reyna-Valencia, Carlos; Zarco-González, Martha M.

2014-01-01

The reduced immigration and emigration rates resulting from the lack of landscape connectivity of patches and the hospitality of the intervening matrix could favor the loss of alleles through genetic drift and an increased chance of inbreeding. In order for isolated populations to maintain sufficient levels of genetic diversity and adapt to environmental changes, one important conservation goal must be to preserve or reestablish connectivity among patches in a fragmented landscape. We studied the last known population of Ambystoma leorae, an endemic and critically threatened species. The aims of this study were: (1) to assess the demographic parameters of A. leorae and to distinguish and characterize the microhabitats in the river, (2) to determine the number of existing genetic groups or demes of A. leorae and to describe possible relationships between microhabitats types and demes, (3) to determine gene flow between demes, and (4) to search for geographic locations of genetic discontinuities that limit gene flow between demes. We found three types of microhabitats and three genetically differentiated subpopulations with a significant level of genetic structure. In addition, we found slight genetic barriers. Our results suggest that mole salamander’s species are very sensitive to microhabitat features and relatively narrow obstacles in their path. The estimates of bidirectional gene flow are consistent with the pattern of a stepping stone model between demes, where migration occurs between adjacent demes, but there is low gene flow between distant demes. We can also conclude that there is a positive correlation between microhabitats and genetic structure in this population. PMID:25076052

3D characterization of EMT cell density in developing cardiac cushions using optical coherence tomography (Conference Presentation)

NASA Astrophysics Data System (ADS)

Yu, Siyao; Gu, Shi; Zhao, Xiaowei; Liu, Yehe; Jenkins, Michael W.; Watanabe, Michiko; Rollins, Andrew M.

2017-02-01

Congenital heart defects (CHDs) are the most common birth defect, affecting between 4 and 75 per 1,000 live births depending on the inclusion criteria. Many of these defects can be traced to defects of cardiac cushions, critical structures during development that serve as precursors to many structures in the mature heart, including the atrial and ventricular septa, and all four sets of cardiac valves. Epithelial-mesenchymal transition (EMT) is the process through which cardiac cushions become populated with cells. Altered cushion size or altered cushion cell density has been linked to many forms of CHDs, however, quantitation of cell density in the complex 3D cushion structure poses a significant challenge to conventional histology. Optical coherence tomography (OCT) is a technique capable of 3D imaging of the developing heart, but typically lacks the resolution to differentiate individual cells. Our goal is to develop an algorithm to quantitatively characterize the density of cells in the developing cushion using 3D OCT imaging. First, in a heart volume, the atrioventricular (AV) cushions were manually segmented. Next, all voxel values in the region of interest were pooled together to generate a histogram. Finally, two populations of voxels were classified using either K-means classification, or a Gaussian mixture model (GMM). The voxel population with higher values represents cells in the cushion. To test the algorithm, we imaged and evaluated avian embryonic hearts at looping stages. As expected, our result suggested that the cell density increases with developmental stages. We validated the technique against scoring by expert readers.

Multiple-locus variable-number tandem-repeat analysis of the swine dysentery pathogen, Brachyspira hyodysenteriae.

PubMed

Hidalgo, Alvaro; Carvajal, Ana; La, Tom; Naharro, Germán; Rubio, Pedro; Phillips, Nyree D; Hampson, David J

2010-08-01

The spirochete Brachyspira hyodysenteriae is the causative agent of swine dysentery, a severe colonic infection of pigs that has a considerable economic impact in many swine-producing countries. In spite of its importance, knowledge about the global epidemiology and population structure of B. hyodysenteriae is limited. Progress in this area has been hampered by the lack of a low-cost, portable, and discriminatory method for strain typing. The aim of the current study was to develop and test a multiple-locus variable-number tandem-repeat analysis (MLVA) method that could be used in basic veterinary diagnostic microbiology laboratories equipped with PCR technology or in more advanced laboratories with access to capillary electrophoresis. Based on eight loci, and when performed on isolates from different farms in different countries, as well as type and reference strains, the MLVA technique developed was highly discriminatory (Hunter and Gaston discriminatory index, 0.938 [95% confidence interval, 0.9175 to 0.9584]) while retaining a high phylogenetic value. Using the technique, the species was shown to be diverse (44 MLVA types from 172 isolates and strains), although isolates were stable in herds over time. The population structure appeared to be clonal. The finding of B. hyodysenteriae MLVA type 3 in piggeries in three European countries, as well as other, related, strains in different countries, suggests that spreading of the pathogen via carrier pigs is likely. MLVA overcame drawbacks associated with previous typing techniques for B. hyodysenteriae and was a powerful method for epidemiologic and population structure studies on this important pathogenic spirochete.

The impacts of mobile fishing gear on seafloor habitats in the Gulf of Maine (Northwest Atlantic): implications for conservation of fish populations

USGS Publications Warehouse

Auster, Peter J.; Malatesta, Richard J.; Langton, Richard W.; Watting, Les; Valentine, Page C.; Donaldson, Carol Lee S.; Langton, Elizabeth W.; Shepard, Andrew N.; Babb, War G.

1997-01-01

Fishing gear alters seafloor habitats, but the extent of these alterations, and their effects, have not been quantified extensively in the northwest Atlantic. Understanding the extent of these impacts, and their effects on populations of living marine resources, is needed to properly manage current and future levels of fishing effort and fishing power. For example, the entire U.S. side of the Gulf of Maine was impacted annually by mobile fishing gear between 1984 and 1990, based on calculations of area swept by trawl and dredge gear. Georges Bank was imparted three to nearly four times annually during the same period. Studies at three sites in the Gulf of Maine (off Swans Island, Jeffreys Bank, and Stellwagen Bank) showed that mobile fishing gear altered the physical structure (=complexity) of benthic habitats. Complexity was reduced by direct removal of biogenic (e.g., sponges, hydrozoans, bryozoans, amphipod tubes, holothurians, shell aggregates) and‐ sedimentary (e.g., sand waves, depressions) structures. Also, removal of organisms that create.structures (e.g., crabs, scallops) indirectly reduced complexity. Reductions in habitat complexity may lead to increased predation on juveniles of harvested species and ultimately recruitment to the harvestable stock. Because of a lack of reference sites, where use of mobile fishing is prohibited, no empirical studies have yet been conducted on a scale that could demonstrate population level effects of habitat‐management options. If marine fisheries management is to evolve toward an ecosystem or habitat management approach, experiments are required on the effects of habitat change, both anthropogenic and natural.

The impacts of mobile fishing gear on seafloor habitats in the gulf of maine (Northwest Atlantic): Implications for conservation of fish populations

USGS Publications Warehouse

Auster, P.J.; Malatesta, R.J.; Langton, R.W.; Watling, Les; Valentine, P.C.; Donaldson, C.L.S.; Langton, E.W.; Shepard, A.N.; Babb, Ivar G.

1996-01-01

Fishing gear alters seafloor habitats, but the extent of these alterations, and their effects, have not been quantified extensively in the northwest Atlantic. Understanding the extent of these impacts, and their effects on populations of living marine resources, is needed to properly manage current and future levels of fishing effort and fishing power. For example, the entire U.S. side of the Gulf of Maine was impacted annually by mobile fishing gear between 1984 and 1990, based on calculations of area swept by trawl and dredge gear. Georges Bank was impacted three to nearly four times annually during the same period. Studies at three sites in the Gulf of Maine (off Swans Island, Jeffreys Bank, and Stellwagen Bank) showed that mobile fishing gear altered the physical structure (=complexity) of benthic habitats. Complexity was reduced by direct removal of biogenic (e.g., sponges, hydrozoans, bryozoans, amphipod tubes, holothurians, shell aggregates) and sedimentary (e.g., sand waves, depressions) structures. Also, removal of organisms that create structures (e.g., crabs, scallops) indirectly reduced complexity. Reductions in habitat complexity may lead to increased predation on juveniles of harvested species and ultimately recruitment to the harvestable stock. Because of a lack of reference sites, where use of mobile fishing is prohibited, no empirical studies have yet been conducted on a scale that could demonstrate population level effects of habitat-management options. If marine fisheries management is to evolve toward an ecosystem or habitat management approach, experiments are required on the effects of habitat change, both anthropogenic and natural.

Complex small pelagic fish population patterns arising from individual behavioral responses to their environment

NASA Astrophysics Data System (ADS)

Brochier, Timothée; Auger, Pierre-Amaël; Pecquerie, Laure; Machu, Eric; Capet, Xavier; Thiaw, Modou; Mbaye, Baye Cheikh; Braham, Cheikh-Baye; Ettahiri, Omar; Charouki, Najib; Sène, Ousseynou Ndaw; Werner, Francisco; Brehmer, Patrice

2018-05-01

Small pelagic fish (SPF) species are heavily exploited in eastern boundary upwelling systems (EBUS) as their transformation products are increasingly used in the world's food chain. Management relies on regular monitoring, but there is a lack of robust theories for the emergence of the populations' traits and their evolution in highly variable environments. This work aims to address existing knowledge gaps by combining physical and biogeochemical modelling with an individual life-cycle based model applied to round sardinella (Sardinella aurita) off northwest Africa, a key species for regional food security. Our approach focused on the processes responsible for seasonal migrations, spatio-temporal size-structure, and interannual biomass fluctuations. Emergence of preferred habitat resulted from interactions between natal homing behavior and environmental variability that impacts early life stages. Exploration of the environment by the fishes was determined by swimming capabilities, mesoscale to regional habitat structure, and horizontal currents. Fish spatio-temporal abundance variability emerged from a complex combination of distinct life-history traits. An alongshore gradient in fish size distributions is reported and validated by in situ measurements. New insights into population structure are provided, within an area where the species is abundant year-round (Mauritania) and with latitudinal migrations of variable (300-1200 km) amplitude. Interannual biomass fluctuations were linked to modulations of fish recruitment over the Sahara Bank driven by variability in alongshore current intensity. The identified processes constitute an analytical framework that can be implemented in other EBUS and used to explore impacts of regional climate change on SPF.

Health-Needs Assessment for West African Immigrants in Greater Providence, RI.

PubMed

Adu-Boahene, Akosua Boadiwaa; Laws, Michael Barton; Dapaah-Afriyie, Kwame

2017-01-06

African immigrants in the United States may experience barriers to health-care access and effectiveness. This mixed-methods study used paper-based surveys of people (N=101) in the target population from Nigeria, Ghana, and Liberia, recruited through convenience and snowball sampling. Semi-structured interviews were conducted with 3 clergy members who pastor churches with large Nigerian, Ghanaian, and Liberian populations, respectively; and five physicians and a clinical pharmacist who serve African immigrants. Length of stay in the United States was associated with the health status of refugee children. Undocumented immigration status was associated with lack of health insurance. Cardiovascular diseases, uterine fibroids and stress-related disorders were the most prevalent reported conditions. Regardless of English fluency, many immigrants are unfamiliar with medical terminology. African immigrants in the state of Rhode Island need more health education and resources to navigate the US health-care system. [Full article available at http://rimed.org/rimedicaljournal-2017-01.asp].

The potential of disease management for neuromuscular hereditary disorders.

PubMed

Chouinard, Maud-Christine; Gagnon, Cynthia; Laberge, Luc; Tremblay, Carmen; Côté, Charlotte; Leclerc, Nadine; Mathieu, Jean

2009-01-01

Neuromuscular hereditary disorders require long-term multidisciplinary rehabilitation management. Although the need for coordinated healthcare management has long been recognized, most neuromuscular disorders are still lacking clinical guidelines about their long-term management and structured evaluation plan with associated services. One of the most prevalent adult-onset neuromuscular disorders, myotonic dystrophy type 1, generally presents several comorbidities and a variable clinical picture, making management a constant challenge. This article presents a healthcare follow-up plan and proposes a nursing case management within a disease management program as an innovative and promising approach. This disease management program and model consists of eight components including population identification processes, evidence-based practice guidelines, collaborative practice, patient self-management education, and process outcomes evaluation (Disease Management Association of America, 2004). It is believed to have the potential to significantly improve healthcare management for neuromuscular hereditary disorders and will prove useful to nurses delivering and organizing services for this population.

[Professional opinion about hospitalising Latin-American immigrant children in Andalucía, Spain].

PubMed

Fernández-Castillo, Antonio; Vílchez-Lara, María J

2009-01-01

There has been an increase in paediatric hospital attention being provided for Latin-American immigrant patients in Spain during the recent years. This work was aimed at ascertaining professionals' opinion regarding this population's specific and differential needs concerning Latin-American immigrant children being hospitalised. The study consisted of a qualitative, phenomenological type of investigation, based on semi-structured interviews of key informers in Andalusia (Spain). The subjects of the study were professionals from paediatric services in hospital centres in Andalusia. One of the most prominent (positive) results revealed that the Latin-American immigrant population presented less difficulties regarding hospital functioning when compared to other immigrant groups. The psychological aspects which had most impact on paediatric hospitalisation would be emotional alterations, such as the presence of anxiety and stress, or other aspects, like a lack of trust when being hospitalised.

Population structure, genetic diversity and downy mildew resistance among Ocimum species germplasm.

PubMed

Pyne, Robert M; Honig, Josh A; Vaiciunas, Jennifer; Wyenandt, Christian A; Simon, James E

2018-04-23

The basil (Ocimum spp.) genus maintains a rich diversity of phenotypes and aromatic volatiles through natural and artificial outcrossing. Characterization of population structure and genetic diversity among a representative sample of this genus is severely lacking. Absence of such information has slowed breeding efforts and the development of sweet basil (Ocimum basilicum L.) with resistance to the worldwide downy mildew epidemic, caused by the obligate oomycete Peronospora belbahrii. In an effort to improve classification of relationships 20 EST-SSR markers with species-level transferability were developed and used to resolve relationships among a diverse panel of 180 Ocimum spp. accessions with varying response to downy mildew. Results obtained from nested Bayesian model-based clustering, analysis of molecular variance and unweighted pair group method using arithmetic average (UPGMA) analyses were synergized to provide an updated phylogeny of the Ocimum genus. Three (major) and seven (sub) population (cluster) models were identified and well-supported (P < 0.001) by PhiPT (Φ PT ) values of 0.433 and 0.344, respectively. Allelic frequency among clusters supported previously developed hypotheses of allopolyploid genome structure. Evidence of cryptic population structure was demonstrated for the k1 O. basilicum cluster suggesting prevalence of gene flow. UPGMA analysis provided best resolution for the 36-accession, DM resistant k3 cluster with consistently strong bootstrap support. Although the k3 cluster is a rich source of DM resistance introgression of resistance into the commercially important k1 accessions is impeded by reproductive barriers as demonstrated by multiple sterile F1 hybrids. The k2 cluster located between k1 and k3, represents a source of transferrable tolerance evidenced by fertile backcross progeny. The 90-accession k1 cluster was largely susceptible to downy mildew with accession 'MRI' representing the only source of DM resistance. High levels of genetic diversity support the observed phenotypic diversity among Ocimum spp. accessions. EST-SSRs provided a robust evaluation of molecular diversity and can be used for additional studies to increase resolution of genetic relationships in the Ocimum genus. Elucidation of population structure and genetic relationships among Ocimum spp. germplasm provide the foundation for improved DM resistance breeding strategies and more rapid response to future disease outbreaks.

Social capital and lack of belief in the possibility to influence one's own health: a population-based study.

PubMed

Lindström, Martin

2006-01-01

To study the impact of social capital (social participation and trust) on lack of belief in possibility to influence health. The Scania 2000 public-health survey is a cross-sectional, postal questionnaire study including 13,604 persons aged 18-80 years which was conducted in 2000 by the regional healthcare authorities in Region Skåne, southern Sweden, to investigate health-related risk factors in the population. A logistic regression model was used to investigate the association between social capital and lack of belief in possibility to influence health. The multivariate analyses analysed the importance of confounders on the differences in lack of belief in possibility to influence health according to the social capital variables. In total, 31.0% of all men and 33.5% of all women lack belief in the possibility to influence their own health. Lack of belief in possibility to influence health was positively associated with both low social participation and low trust, although stronger for social participation than for trust. Low levels of social capital, particularly low social participation, is positively associated with lack of belief in the possibility to influence one's own health.

Factors influencing the intention of students to work with individuals with intellectual disabilities.

PubMed

Werner, Shirli; Grayzman, Alina

2011-01-01

Providing adequate care to individuals with intellectual disability (ID) requires the willingness of students in various health and social professions to care for this population upon completion of their studies. The aim of the current study was to examine the factors associated with the intentions of students from various fields to work with individuals with ID, using the framework of the Theory of Planned Behavior. A structured self-administered questionnaire was completed by 512 social work, occupational therapy, speech and language therapy, special education, and nursing students. The questionnaire measured students' attitudes toward individuals with ID and toward working with this population, as well as their perceptions of subjective norms, controllability, self-efficacy, prior acquaintance with individuals with ID, and subjective knowledge about ID. Structural equation modeling showed that the students' intentions to work with individuals with ID were predicted by their attitudes and perceptions of subjective norms. Field of study and subjective knowledge were also found to be predictive of behavioral intention. The TPB proved to be a useful framework for examining students' intentions to work with persons with ID. Given the lack of education in the field of ID, as well as the prevailing stigmatic attitudes toward this population, university departments should develop programs aimed at increasing knowledge, promoting positive contact, and reducing the fear attached to working with persons with intellectual disability. Copyright © 2011 Elsevier Ltd. All rights reserved.

Population Structure of mtDNA Variation due to Pleistocene Fluctuations in the South American Maned Wolf (Chrysocyon brachyurus, Illiger, 1815): Management Units for Conservation.

PubMed

González, Susana; Cosse, Mariana; Franco, María del Rosario; Emmons, Louise; Vynne, Carly; Duarte, José Maurício Barbanti; Beccacesi, Marcelo D; Maldonado, Jesús E

2015-01-01

The maned wolf (Chrysocyon brachyurus) is one of the largest South American canids, and conservation across this charismatic carnivore's large range is presently hampered by a lack of knowledge about possible natural subdivisions which could influence the population's viability. To elucidate the phylogeographic patterns and demographic history of the species, we used 2 mtDNA markers (D-loop and cytochrome b) from 87 individuals collected throughout their range, in Argentina, Bolivia, Brazil, and Uruguay. We found moderate levels of haplotype and nucleotide diversity, and the 14 D-loop haplotypes were closely related. Genetic structure results revealed 4 groups, and when coupled with model inferences from a coalescent analysis, suggested that maned wolves have undergone demographic fluctuations due to changes in climate and habitat during the Pleistocene glaciation period approximately 24000 years before present (YBP). This genetic signature points to an event that occurred within the timing estimated for the start of the contraction of the Cerrado around 50000 YBP. Our results reveal a genetic signature of population size expansion followed by contraction during Pleistocene interglaciations, which had similar impacts on other South American mammals. The 4 groups should for now be considered management units, within which future monitoring efforts should be conducted independently. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Development and application of a density dependent matrix ...

EPA Pesticide Factsheets

Ranging along the Atlantic coast from US Florida to the Maritime Provinces of Canada, the Atlantic killifish (Fundulus heteroclitus) is an important and well-studied model organism for understanding the effects of pollutants and other stressors in estuarine and marine ecosystems. Matrix population models are useful tools for ecological risk assessment because they integrate effects across the life cycle, provide a linkage between endpoints observed in the individual and ecological risk to the population as a whole, and project outcomes for many generations in the future. We developed a density dependent matrix population model for Atlantic killifish by modifying a model developed for fathead minnow (Pimephales promelas) that has proved to be extremely useful, e.g. to incorporate data from laboratory studies and project effects of endocrine disrupting chemicals. We developed a size-structured model (as opposed to one that is based upon developmental stages or age class structure) so that we could readily incorporate output from a Dynamic Energy Budget (DEB) model, currently under development. Due to a lack of sufficient data to accurately define killifish responses to density dependence, we tested a number of scenarios realistic for other fish species in order to demonstrate the outcome of including this ecologically important factor. We applied the model using published data for killifish exposed to dioxin-like compounds, and compared our results to those using

Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil)

PubMed Central

Miller, Webb; Hayes, Vanessa M.; Ratan, Aakrosh; Petersen, Desiree C.; Wittekindt, Nicola E.; Miller, Jason; Walenz, Brian; Knight, James; Qi, Ji; Zhao, Fangqing; Wang, Qingyu; Bedoya-Reina, Oscar C.; Katiyar, Neerja; Tomsho, Lynn P.; Kasson, Lindsay McClellan; Hardie, Rae-Anne; Woodbridge, Paula; Tindall, Elizabeth A.; Bertelsen, Mads Frost; Dixon, Dale; Pyecroft, Stephen; Helgen, Kristofer M.; Lesk, Arthur M.; Pringle, Thomas H.; Patterson, Nick; Zhang, Yu; Kreiss, Alexandre; Woods, Gregory M.; Jones, Menna E.; Schuster, Stephan C.

2011-01-01

The Tasmanian devil (Sarcophilus harrisii) is threatened with extinction because of a contagious cancer known as Devil Facial Tumor Disease. The inability to mount an immune response and to reject these tumors might be caused by a lack of genetic diversity within a dwindling population. Here we report a whole-genome analysis of two animals originating from extreme northwest and southeast Tasmania, the maximal geographic spread, together with the genome from a tumor taken from one of them. A 3.3-Gb de novo assembly of the sequence data from two complementary next-generation sequencing platforms was used to identify 1 million polymorphic genomic positions, roughly one-quarter of the number observed between two genetically distant human genomes. Analysis of 14 complete mitochondrial genomes from current and museum specimens, as well as mitochondrial and nuclear SNP markers in 175 animals, suggests that the observed low genetic diversity in today's population preceded the Devil Facial Tumor Disease disease outbreak by at least 100 y. Using a genetically characterized breeding stock based on the genome sequence will enable preservation of the extant genetic diversity in future Tasmanian devil populations. PMID:21709235

Impacts of changing rainfall regime on the demography of tropical birds

NASA Astrophysics Data System (ADS)

Brawn, Jeffrey D.; Benson, Thomas J.; Stager, Maria; Sly, Nicholas D.; Tarwater, Corey E.

2017-02-01

Biodiversity in tropical regions is particularly high and may be highly sensitive to climate change. Unfortunately, a lack of long-term data hampers understanding of how tropical species, especially animals, may react to projected environmental changes. The amount and timing of rainfall is key to the function of tropical ecosystems and, although specific model predictions differ, there is general agreement that rainfall regimes will change over large areas of the tropics. Here, we estimate associations between dry season length (DSL) and the population biology of 20 bird species sampled in central Panama over a 33-year period. Longer dry seasons decreased the population growth rates and viability of nearly one-third of the species sampled. Simulations with modest increases in DSL suggest that consistently longer dry seasons will change the structure of tropical bird communities. Such change may occur even without direct loss of habitat--a finding with fundamental implications for conservation planning. Systematic changes in rainfall regime may threaten some populations and communities of tropical animals even in large tracts of protected habitat. These findings suggest the need for collaboration between climate scientists and conservation biologists to identify areas where rainfall regimes will be able to plausibly maintain wildlife populations.

Beyond Population Distribution: Enhancing Sociocultural Resolution from Remote Sensing

NASA Astrophysics Data System (ADS)

Bhaduri, B. L.; Rose, A.

2017-12-01

At Oak Ridge National Laboratory, since late 1990s, we have focused on developing high resolution population distribution and dynamics data from local to global scales. Increasing resolutions of geographic data has been mirrored by population data sets developed across the community. However, attempts to increase temporal and sociocultural resolutions have been limited given the lack of high resolution data on human settlements and activities. While recent advancements in moderate to high resolution earth observation have led to better physiographic data, the approach of exploiting very high resolution (sub-meter resolution) imagery has also proven useful for generating accurate human settlement maps. It allows potential (social and vulnerability) characterization of population from settlement structures by exploiting image texture and spectral features. Our recent research utilizing machine learning and geocomputation has not only validated "poverty mapping from imagery" hypothesis, but has delineated a new paradigm of rapid analysis of high resolution imagery to enhance such "neighborhood" mapping techniques. Such progress in GIScience is allowing us to move towards the goal of creating a global foundation level database for impervious surfaces and "neighborhoods," and holds tremendous promise for key applications focusing on sustainable development including many social science applications.

Quantum structures: An attempt to explain the origin of their appearance in nature

NASA Astrophysics Data System (ADS)

Aerts, Diederik

1995-08-01

We explain quantum structure as due to two effects: (a) a real change of state of the entity under the influence of the measurement and (b) a lack of knowledge about a deeper deterministic reality of the measurement process. We present a quantum machine, with which we can illustrate in a simple way how the quantum structure arises as a consequence of the two mentioned effects. We introduce a parameter ɛ that measures the size of the lack of knowledge of the measurement process, and by varying this parameter, we describe a continuous evolution from a quantum structure (maximal lack of knowledge) to a classical structure (zero lack of knowledge). We show that for intermediate values of ɛ we find a new type of structure that is neither quantum nor classical. We apply the model to situations of lack of knowledge about the measurement process appearing in other aspects of reality. Specifically, we investigate the quantumlike structures that appear in the situation of psychological decision processes, where the subject is influenced during the testing and forms some opinions during the testing process. Our conclusion is that in the light of this explanation, the quantum probabilities are epistemic and not ontological, which means that quantum mechanics is compatible with a determinism of the whole.

What are community nurses experiences of assessing frailty and assisting in planning subsequent interventions?

PubMed

Britton, Hannah

2017-09-02

With an ageing population and increasing focus on community care, this study aimed to explore the experiences of community nurses in assessing frailty and planning interventions around frailty. Six community nurses were recruited for face-to-face semi-structured interviews as part of this qualitative study which was underpinned by a competence framework ( Royal College of Nursing, 2009 ). Thematic analysis was used and frailty was identified as an emerging topic within practice. Participants discussed several aspects associated with frailty; however, some uncertainty around the concept of frailty and its definition was noted, particularly for staff who had received limited frailty training. Participants had a growing awareness of frailty in practice, but challenges-including time constraints and staffing within some roles, a perception of limited services to support older people, and for some a lack of confidence and training-presented barriers to frailty assessment. The Rockwood frailty scale was used by participants within practice, but evidence suggested it was felt to lack validity within the community setting.

Infants Infected with Respiratory Syncytial Virus Generate Potent Neutralizing Antibodies that Lack Somatic Hypermutation

PubMed Central

Goodwin, Eileen; Gilman, Morgan S. A.; Wrapp, Daniel; Chen, Man; Ngwuta, Joan O.; Moin, Syed M.; Bai, Patricia; Sivasubramanian, Arvind; Connor, Ruth I.; Wright, Peter F.; Graham, Barney S.; McLellan, Jason S.; Walker, Laura M.

2018-01-01

SUMMARY Respiratory syncytial virus (RSV) is a leading cause of infant mortality, and there are currently no licensed vaccines to protect this vulnerable population. A comprehensive understanding of infant antibody responses to natural RSV infection would facilitate vaccine development. Here, we isolated over 450 RSV fusion glycoprotein (F)-specific antibodies from seven RSV-infected infants and found that half of the antibodies recognized only two antigenic sites. Antibodies targeting both sites showed convergent sequence features, and structural studies revealed the molecular basis for their recognition of RSV F. A subset of antibodies targeting one of these sites displayed potent neutralizing activity despite lacking somatic mutations, and similar antibodies were detected in RSV-naïve B cell repertoires, suggesting that expansion of these B cells in infants may be possible with suitably designed vaccine antigens. Collectively, our results provide fundamental insights into infant antibody responses and a framework for the rational design of age-specific RSV vaccines. PMID:29396163

Persistence of historical population structure in an endangered species despite near-complete biome conversion in California's San Joaquin Desert.

PubMed

Richmond, Jonathan Q; Wood, Dustin A; Westphal, Michael F; Vandergast, Amy G; Leaché, Adam D; Saslaw, Lawrence R; Butterfield, H Scott; Fisher, Robert N

2017-07-01

Genomic responses to habitat conversion can be rapid, providing wildlife managers with time-limited opportunities to enact recovery efforts that use population connectivity information that reflects predisturbance landscapes. Despite near-complete biome conversion, such opportunities may still exist for the endemic fauna and flora of California's San Joaquin Desert, but comprehensive genetic data sets are lacking for nearly all species in the region. To fill this knowledge gap, we studied the rangewide population structure of the endangered blunt-nosed leopard lizard Gambelia sila, a San Joaquin Desert endemic, using restriction site-associated DNA (RAD), microsatellite and mtDNA data to test whether admixture patterns and estimates of effective migration surfaces (EEMS) can identify land areas with high population connectivity prior to the conversion of native xeric habitats. Clustering and phylogenetic analyses indicate a recent shared history between numerous isolated populations and EEMS reveals latent signals of corridors and barriers to gene flow over areas now replaced by agriculture and urbanization. Conflicting histories between the mtDNA and nuclear genomes are consistent with hybridization with the sister species G. wislizenii, raising important questions about where legal protection should end at the southern range limit of G. sila. Comparative analysis of different data sets also adds to a growing list of advantages in using RAD loci for genetic studies of rare species. We demonstrate how the results of this work can serve as an evolutionary guidance tool for managing endemic, arid-adapted taxa in one of the world's most compromised landscapes. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.

Population-Level Metrics of Trophic Structure Based on Stable Isotopes and Their Application to Invasion Ecology

PubMed Central

Jackson, Michelle C.; Donohue, Ian; Jackson, Andrew L.; Britton, J. Robert; Harper, David M.; Grey, Jonathan

2012-01-01

Biological invasions are a significant driver of human-induced global change and many ecosystems sustain sympatric invaders. Interactions occurring among these invaders have important implications for ecosystem structure and functioning, yet they are poorly understood. Here we apply newly developed metrics derived from stable isotope data to provide quantitative measures of trophic diversity within populations or species. We then use these to test the hypothesis that sympatric invaders belonging to the same functional feeding group occupy a smaller isotopic niche than their allopatric counterparts. Two introduced, globally important, benthic omnivores, Louisiana swamp crayfish (Procambarus clarkii) and carp (Cyprinus carpio), are sympatric in Lake Naivasha, Kenya. We applied our metrics to an 8-year data set encompassing the establishment of carp in the lake. We found a strong asymmetric interaction between the two invasive populations, as indicated by inverse correlations between carp abundance and measures of crayfish trophic diversity. Lack of isotopic niche overlap between carp and crayfish in the majority of years indicated a predominantly indirect interaction. We suggest that carp-induced habitat alteration reduced the diversity of crayfish prey, resulting in a reduction in the dietary niche of crayfish. Stable isotopes provide an integrated signal of diet over space and time, offering an appropriate scale for the study of population niches, but few isotope studies have retained the often insightful information revealed by variability among individuals in isotope values. Our population metrics incorporate such variation, are robust to the vagaries of sample size and are a useful additional tool to reveal subtle dietary interactions among species. Although we have demonstrated their applicability specifically using a detailed temporal dataset of species invasion in a lake, they have a wide array of potential ecological applications. PMID:22363724

Population-level metrics of trophic structure based on stable isotopes and their application to invasion ecology.

PubMed

Jackson, Michelle C; Donohue, Ian; Jackson, Andrew L; Britton, J Robert; Harper, David M; Grey, Jonathan

2012-01-01

Biological invasions are a significant driver of human-induced global change and many ecosystems sustain sympatric invaders. Interactions occurring among these invaders have important implications for ecosystem structure and functioning, yet they are poorly understood. Here we apply newly developed metrics derived from stable isotope data to provide quantitative measures of trophic diversity within populations or species. We then use these to test the hypothesis that sympatric invaders belonging to the same functional feeding group occupy a smaller isotopic niche than their allopatric counterparts. Two introduced, globally important, benthic omnivores, Louisiana swamp crayfish (Procambarus clarkii) and carp (Cyprinus carpio), are sympatric in Lake Naivasha, Kenya. We applied our metrics to an 8-year data set encompassing the establishment of carp in the lake. We found a strong asymmetric interaction between the two invasive populations, as indicated by inverse correlations between carp abundance and measures of crayfish trophic diversity. Lack of isotopic niche overlap between carp and crayfish in the majority of years indicated a predominantly indirect interaction. We suggest that carp-induced habitat alteration reduced the diversity of crayfish prey, resulting in a reduction in the dietary niche of crayfish. Stable isotopes provide an integrated signal of diet over space and time, offering an appropriate scale for the study of population niches, but few isotope studies have retained the often insightful information revealed by variability among individuals in isotope values. Our population metrics incorporate such variation, are robust to the vagaries of sample size and are a useful additional tool to reveal subtle dietary interactions among species. Although we have demonstrated their applicability specifically using a detailed temporal dataset of species invasion in a lake, they have a wide array of potential ecological applications.

Development of a site fidelity index based on population capture-recapture data

PubMed Central

Ferrari, Mariano A.; Crespo, Enrique A.; Coscarella, Mariano A.

2018-01-01

Background Site fidelity is considered as an animal’s tendency to return to a previously occupied place; this is a component of animal behaviour that allows us to understand movement patterns and aspects related to the animal’s life history. Although there are many site fidelity metrics, the lack of standardisation presents a considerable challenge in terms of comparability among studies. Methods This investigation focused on the theoretical development of a standardised composite site fidelity index and its statistical distribution in order to obtain reliable population-level site fidelity comparisons. The arithmetic and harmonic means were used as mathematical structures in order to create different indexes by combining the most commonly used indicators for site fidelity such as Occurrence, Permanence and Periodicity. The index performance was then evaluated in simulated populations and one real population of Commerson’s dolphins (Cephalorhynchus commersonii (Lacépède 1804)). In the first case, the indexes were evaluated based on how they were affected by different probability values such as the occurrence of the individual within the study area (φ) and capture probability (p). As a precision measure for the comparison of the indexes, the Wald confidence interval (CI) and the mean square error were applied. Given that there was no previous data concerning the distribution parameters of this population, bootstrap CIs were applied for the study case. Results Eight alternative indexes were developed. The indexes with an arithmetic mean structure, in general, had a consistently inferior performance than those with a harmonic mean structure. The index IH4, in particular, achieved the best results in all of the scenarios and in the study case. Additionally, this index presented a normal distribution. As such, it was proposed as a standardised measure for site fidelity (Standardised Site Fidelity Index—SSFI). Discussion The SSFI is the first standardised metric that quantifies site fidelity at a populational level. It is an estimator that varies between zero and one and works in situations where detection is not perfect and effort can be constant or not. Moreover, it has an associated CI that allows users to make comparisons. PMID:29761064

Development of a site fidelity index based on population capture-recapture data.

PubMed

Tschopp, Ayelen; Ferrari, Mariano A; Crespo, Enrique A; Coscarella, Mariano A

2018-01-01

Site fidelity is considered as an animal's tendency to return to a previously occupied place; this is a component of animal behaviour that allows us to understand movement patterns and aspects related to the animal's life history. Although there are many site fidelity metrics, the lack of standardisation presents a considerable challenge in terms of comparability among studies. This investigation focused on the theoretical development of a standardised composite site fidelity index and its statistical distribution in order to obtain reliable population-level site fidelity comparisons. The arithmetic and harmonic means were used as mathematical structures in order to create different indexes by combining the most commonly used indicators for site fidelity such as Occurrence, Permanence and Periodicity. The index performance was then evaluated in simulated populations and one real population of Commerson's dolphins ( Cephalorhynchus commersonii (Lacépède 1804)). In the first case, the indexes were evaluated based on how they were affected by different probability values such as the occurrence of the individual within the study area (φ) and capture probability ( p ). As a precision measure for the comparison of the indexes, the Wald confidence interval (CI) and the mean square error were applied. Given that there was no previous data concerning the distribution parameters of this population, bootstrap CIs were applied for the study case. Eight alternative indexes were developed. The indexes with an arithmetic mean structure, in general, had a consistently inferior performance than those with a harmonic mean structure. The index IH4, in particular, achieved the best results in all of the scenarios and in the study case. Additionally, this index presented a normal distribution. As such, it was proposed as a standardised measure for site fidelity (Standardised Site Fidelity Index-SSFI). The SSFI is the first standardised metric that quantifies site fidelity at a populational level. It is an estimator that varies between zero and one and works in situations where detection is not perfect and effort can be constant or not. Moreover, it has an associated CI that allows users to make comparisons.

Flying with the birds? Recent large-area dispersal of four Australian Limnadopsis species (Crustacea: Branchiopoda: Spinicaudata)

PubMed Central

Schwentner, Martin; Timms, Brian V; Richter, Stefan

2012-01-01

Temporary water bodies are important freshwater habitats in the arid zone of Australia. They harbor a distinct fauna and provide important feeding and breeding grounds for water birds. This paper assesses, on the basis of haplotype networks, analyses of molecular variation and relaxed molecular clock divergence time estimates, the phylogeographic history, and population structure of four common temporary water species of the Australian endemic clam shrimp taxon Limnadopsis in eastern and central Australia (an area of >1,350,000 km2). Mitochondrial cytochrome c oxidase subunit I sequences of 413 individuals and a subset of 63 nuclear internal transcribed spacer 2 sequences were analyzed. Genetic differentiation was observed between populations inhabiting southeastern and central Australia and those inhabiting the northern Lake Eyre Basin and Western Australia. However, over large parts of the study area and across river drainage systems in southeastern and central Australia (the Murray–Darling Basin, Bulloo River, and southern Lake Eyre Basin), no evidence of population subdivision was observed in any of the four Limnadopsis species. This indicates recent gene flow across an area of ∼800,000 km2. This finding contrasts with patterns observed in other Australian arid zone taxa, particularly freshwater species, whose populations are often structured according to drainage systems. The lack of genetic differentiation within the area in question may be linked to the huge number of highly nomadic water birds that potentially disperse the resting eggs of Limnadopsis among temporary water bodies. Genetically undifferentiated populations on a large geographic scale contrast starkly with findings for many other large branchiopods in other parts of the world, where pronounced genetic structure is often observed even in populations inhabiting pools separated by a few kilometers. Due to its divergent genetic lineages (up to 5.6% uncorrected p-distance) and the relaxed molecular clock divergence time estimates obtained, Limnadopsis parvispinus is assumed to have inhabited the Murray–Darling Basin continuously since the mid-Pliocene (∼4 million years ago). This means that suitable temporary water bodies would have existed in this area throughout the wet–dry cycles of the Pleistocene. PMID:22957166

Impaired esophageal motor function in eosinophilic esophagitis.

PubMed

Santander, Cecilio; Chavarría-Herbozo, Carlos M; Becerro-González, Irene; Burgos-Santamaría, Diego

2015-10-01

Eosinophilic esophagitis is a chronic immunoallergic inflammatory disease of the esophagus that represents a major cause of digestive morbidity among the pediatric and young adult populations. Despite the fact that key symptoms in adults include dysphagia and food impaction, many patients lack structural changes in the esophagus to account for their complaints, which suggests the presence of underlying motor disorders and esophageal distensibility impairment. In the last few years the esophageal motility of these patients has been studied using various approaches, most particularly high-resolution manometry, ambulatory manometry, and impedance planimetry. This review focuses on the most relevant findings and scientific evidence regarding esophageal motor disorders in eosinophilic esophagitis.

'Lonely within the mother': An exploratory study of first-time mothers' experiences of loneliness.

PubMed

Lee, Katharine; Vasileiou, Konstantina; Barnett, Julie

2017-08-01

Loneliness is associated with life transitions such as new motherhood, yet there are few studies investigating the issue in this population. Using data from semi-structured interviews and an interpretative phenomenological analysis, this exploratory study sought to understand seven new mothers' experiences of loneliness. Experiences were organised around three themes, reflecting loneliness arising from making unfavourable self-comparisons with perceived mothering 'norms', from reduced social contact and relationships lacking in empathy. Accounts were homogeneous and point to potential solutions to ameliorate loneliness in new mothers; encouraging empathy in new mothers' partners and countering prevalent unrealistic representations of motherhood with more pragmatic accounts.

Understanding the working alliance with clients diagnosed with anorexia nervosa.

PubMed

Oyer, Laura; O'Halloran, Mary Sean; Christoe-Frazier, Liesel

2016-01-01

The therapeutic working alliance is a vital ingredient of psychotherapy, specifically for clients diagnosed with anorexia nervosa, as progress is often slow and treatment difficult. This qualitative phenomenological study investigated the experiences of eight clients with anorexia nervosa and seven therapists who work with this population, regarding which therapist factors aided in and challenged the working alliance formation in individual psychotherapy. Data was gathered through semi-structured interviews. Some helpful therapist factors included collaboration, appropriate self-disclosure, providing a warm and safe environment, and willingness to be contacted outside of a session. Unhelpful factors included lack of attunement and objectivity and failure to individualize treatment.

One Chance in a Million: Altruism and the Bone Marrow Registry.

PubMed

Bergstrom, Theodore C; Garratt, Rodney J; Sheehan-Connor, Damien

2009-09-01

Stem cell transplants save lives of many patients with blood diseases. Donation is painful, but rarely has lasting adverse effects. Patients can accept transplants only from donors with compatible immune systems. Those lacking a sibling match must seek donations from the general population. The probability that two unrelated persons are compatible is less than 1/10,000. Health authorities maintain a registry of several million genetically tested potential donors who agree to donate if asked. We find that the benefits of adding registrants of every race exceed costs. We also explore the peculiar structure of voluntary public good provision that faces potential donors.

Socioeconomic correlations and stratification in social-communication networks.

PubMed

Leo, Yannick; Fleury, Eric; Alvarez-Hamelin, J Ignacio; Sarraute, Carlos; Karsai, Márton

2016-12-01

The uneven distribution of wealth and individual economic capacities are among the main forces, which shape modern societies and arguably bias the emerging social structures. However, the study of correlations between the social network and economic status of individuals is difficult due to the lack of large-scale multimodal data disclosing both the social ties and economic indicators of the same population. Here, we close this gap through the analysis of coupled datasets recording the mobile phone communications and bank transaction history of one million anonymized individuals living in a Latin American country. We show that wealth and debt are unevenly distributed among people in agreement with the Pareto principle; the observed social structure is strongly stratified, with people being better connected to others of their own socioeconomic class rather than to others of different classes; the social network appears to have assortative socioeconomic correlations and tightly connected 'rich clubs'; and that individuals from the same class live closer to each other but commute further if they are wealthier. These results are based on a representative, society-large population, and empirically demonstrate some long-lasting hypotheses on socioeconomic correlations, which potentially lay behind social segregation, and induce differences in human mobility. © 2016 The Author(s).

Time scale matters: genetic analysis does not support adaptation-by-time as the mechanism for adaptive seasonal declines in kokanee reproductive life span

PubMed Central

Morbey, Yolanda E; Jensen, Evelyn L; Russello, Michael A

2014-01-01

Seasonal declines of fitness-related traits are often attributed to environmental effects or individual-level decisions about reproductive timing and effort, but genetic variation may also play a role. In populations of Pacific salmon (Oncorhynchus spp.), seasonal declines in reproductive life span have been attributed to adaptation-by-time, in which divergent selection for different traits occurs among reproductively isolated temporal components of a population. We evaluated this hypothesis in kokanee (freshwater obligate Oncorhynchus nerka) by testing for temporal genetic structure in neutral and circadian-linked loci. We detected no genetic differences in presumably neutral loci among kokanee with different arrival and maturation dates within a spawning season. Similarly, we detected no temporal genetic structure in OtsClock1b, Omy1009uw, or OmyFbxw11, candidate loci associated with circadian function. The genetic evidence from this study and others indicates a lack of support for adaptation-by-time as an important evolutionary mechanism underlying seasonal declines in reproductive life span and a need for greater consideration of other mechanisms such as time-dependent, adaptive adjustment of reproductive effort. PMID:25478160

Psychometric Properties of the Catastrophic Cognitions Questionnaire-Modified (CCQ-Modified) Among Community Samples in Malaysia.

PubMed

Abdul Khaiyom, Jamilah Hanum; Mukhtar, Firdaus; Ibrahim, Normala; Mohd Sidik, Sherina; Oei, Tian Po Sumantri

2016-12-01

The Catastrophic Cognitions Questionnaire-Modified (CCQ-M) is a common instrument for measuring catastrophic thoughts. In some countries, however, CCQ-M still poses concerns following the lack of appropriate validation among their populations. The current study aimed to examine the factor structure of the CCQ-M, the reliability, and the validity in community samples in Malaysia. The Malay version of CCQ-M and additional measures assessing the symptoms and cognitions relevant to anxiety disorders were completed by 682 university students and general community. Exploratory factor analysis revealed a two-factor structure accounting for 62.2% of the total variance. Confirmatory factor analysis confirmed the two-factor model by deleting four items. The Cronbach's alpha coefficients for the total and the two subscales were .94, .90, and .92, respectively. Test-retest reliability analysis was conducted on 82 university students in the interval period of 14 days, and the result was r = .58. Evidence supported the concurrent, convergent, and discriminant validity. In conclusion, the 17-item CCQ-M-Malaysia is a valid and reliable instrument for assessing catastrophic cognitions among Malaysian populations. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

The transition to hospital consultant and the influence of preparedness, social support, and perception: A structural equation modelling approach.

PubMed

Westerman, Michiel; Teunissen, Pim W; Fokkema, Joanne P I; van der Vleuten, Cees P M; Scherpbier, Albert J J A; Siegert, Carl E H; Scheele, Fedde

2013-04-01

Insight into the transition from specialist registrar to hospital consultant is needed to better align specialty training with starting as a consultant and to facilitate this transition. This study investigates whether preparedness regarding medical and generic competencies, perceived intensity, and social support are associated with burnout among new consultants. A population-based study among all 2643 new consultants in the Netherlands (all specialties) was conducted in June 2010. A questionnaire covering preparedness for practice, intensity of the transition, social support, and burnout was used. Structural equation modelling was used for statistical analysis. Data from a third of the population were available (32% n = 840) (43% male/57% female). Preparation in generic competencies received lower ratings than in medical competencies. A total of 10% met the criteria for burnout and 18% scored high on the emotional exhaustion subscale. Perceived lack of preparation in generic competencies correlated with burnout (r = 0.15, p < 0.001). No such relation was found for medical competencies. Furthermore, social support protected against burnout. These findings illustrate the relevance of generic competencies for new hospital consultants. Furthermore, social support facilitates this intense and stressful stage within the medical career.

Socioeconomic correlations and stratification in social-communication networks

PubMed Central

Leo, Yannick; Fleury, Eric; Sarraute, Carlos

2016-01-01

The uneven distribution of wealth and individual economic capacities are among the main forces, which shape modern societies and arguably bias the emerging social structures. However, the study of correlations between the social network and economic status of individuals is difficult due to the lack of large-scale multimodal data disclosing both the social ties and economic indicators of the same population. Here, we close this gap through the analysis of coupled datasets recording the mobile phone communications and bank transaction history of one million anonymized individuals living in a Latin American country. We show that wealth and debt are unevenly distributed among people in agreement with the Pareto principle; the observed social structure is strongly stratified, with people being better connected to others of their own socioeconomic class rather than to others of different classes; the social network appears to have assortative socioeconomic correlations and tightly connected ‘rich clubs’; and that individuals from the same class live closer to each other but commute further if they are wealthier. These results are based on a representative, society-large population, and empirically demonstrate some long-lasting hypotheses on socioeconomic correlations, which potentially lay behind social segregation, and induce differences in human mobility. PMID:27974571

Reconstructing population histories from single nucleotide polymorphism data.

PubMed

Sirén, Jukka; Marttinen, Pekka; Corander, Jukka

2011-01-01

Population genetics encompasses a strong theoretical and applied research tradition on the multiple demographic processes that shape genetic variation present within a species. When several distinct populations exist in the current generation, it is often natural to consider the pattern of their divergence from a single ancestral population in terms of a binary tree structure. Inference about such population histories based on molecular data has been an intensive research topic in the recent years. The most common approach uses coalescent theory to model genealogies of individuals sampled from the current populations. Such methods are able to compare several different evolutionary scenarios and to estimate demographic parameters. However, their major limitation is the enormous computational complexity associated with the indirect modeling of the demographies, which limits the application to small data sets. Here, we propose a novel Bayesian method for inferring population histories from unlinked single nucleotide polymorphisms, which is applicable also to data sets harboring large numbers of individuals from distinct populations. We use an approximation to the neutral Wright-Fisher diffusion to model random fluctuations in allele frequencies. The population histories are modeled as binary rooted trees that represent the historical order of divergence of the different populations. A combination of analytical, numerical, and Monte Carlo integration techniques are utilized for the inferences. A particularly important feature of our approach is that it provides intuitive measures of statistical uncertainty related with the estimates computed, which may be entirely lacking for the alternative methods in this context. The potential of our approach is illustrated by analyses of both simulated and real data sets.

Mitochondrial DNA markers reveal high genetic diversity and strong genetic differentiation in populations of Dendrolimus kikuchii Matsumura (Lepidoptera: Lasiocampidae).

PubMed

Men, Qiulei; Xue, Guoxi; Mu, Dan; Hu, Qingling; Huang, Minyi

2017-01-01

Dendrolimus kikuchii Matsumura, 1927 is a serious forest pest causing great damage to coniferous trees in China. Despite its economic importance, the population genetics of this pest are poorly known. We used three mitochondrial genes (COI, COII and Cytb) to investigate the genetic diversity and genetic differentiation of 15 populations collected from the main distribution regions of D. kikuchii in China. Populations show high haplotype and nucleotide diversity. Haplotype network and phylogenetic analysis divides the populations into three major clades, the central and southeastern China (CC+SEC) clade, the eastern China (EC) clade, and the southwestern China (SWC) clade. Populations collected from adjacent localities share the same clade, which is consistent with the strong relationship of isolation by distance (r = 0.74824, P = 0.00001). AMOVA analysis indicated that the major portion of this molecular genetic variation is found among the three groups of CC+SEC, EC and SWC (61.26%). Of 105 pairwise FST comparisons, 93 show high genetic differentiation. Populations of Puer (PE), Yangshuo (YS) and Leishan (LS) are separated from other populations by a larger genetic distance. Distributions of pairwise differences obtained with single and combined gene data from the overall populations are multimodal, suggesting these populations had no prior population expansion in southern China. The nonsignificant neutral test on the basis of Tajima' D and Fu's Fs, and the lack of a star-shaped haplotype network together with the multiple haplotypes support this hypothesis. Pleistocene climatic fluctuations, combined with the host specificity to Pinus species, made these regions of south China into a refuge for D. kikuchii. The high level of population genetic structuring is related to their weak flight capacity, their variations of life history and the geographic distance among populations.

Kinship and the evolution of social behaviours in the sea

PubMed Central

Kamel, Stephanie J.; Grosberg, Richard K.

2013-01-01

Until recently, little attention has been paid to the existence of kin structure in the sea, despite the fact that many marine organisms are sessile or sedentary. This lack of attention to kin structure, and its impacts on social evolution, historically stems from the pervasive assumption that the dispersal of gametes and larvae is almost always sufficient to prevent any persistent associations of closely related offspring or adults. However, growing evidence, both theoretical and empirical, casts doubt on the generality of this assumption, not only in species with limited dispersal, but also in species with long dispersive phases. Moreover, many marine organisms either internally brood their progeny or package them in nurseries, both of which provide ample opportunities for kinship to influence the nature and outcomes of social interactions among family members. As the evidence for kin structure within marine populations mounts, it follows that kin selection may play a far greater role in the evolution of both behaviours and life histories of marine organisms than is presently appreciated. PMID:24132095

Kinship and the evolution of social behaviours in the sea.

PubMed

Kamel, Stephanie J; Grosberg, Richard K

2013-01-01

Until recently, little attention has been paid to the existence of kin structure in the sea, despite the fact that many marine organisms are sessile or sedentary. This lack of attention to kin structure, and its impacts on social evolution, historically stems from the pervasive assumption that the dispersal of gametes and larvae is almost always sufficient to prevent any persistent associations of closely related offspring or adults. However, growing evidence, both theoretical and empirical, casts doubt on the generality of this assumption, not only in species with limited dispersal, but also in species with long dispersive phases. Moreover, many marine organisms either internally brood their progeny or package them in nurseries, both of which provide ample opportunities for kinship to influence the nature and outcomes of social interactions among family members. As the evidence for kin structure within marine populations mounts, it follows that kin selection may play a far greater role in the evolution of both behaviours and life histories of marine organisms than is presently appreciated.

Genetic analysis of Aedes albopictus (Diptera, Culicidae) reveals a deep divergence in the original regions.

PubMed

Ruiling, Zhang; Tongkai, Liu; Zhendong, Huang; Guifen, Zhuang; Dezhen, Ma; Zhong, Zhang

2018-05-02

Aedes albopictus has been described as one of the 100 worst invasive species in the world. This mosquito originated from southeastern Asia and currently has a widespread presence in every continent except Antarctica. The rapid global expansion of Ae. albopictus has increased public health concerns about arbovirus-related disease threats. Adaptation, adaption to novel areas is a biological challenge for invasive species, and the underlying processes can be studied at the molecular level. In this study, genetic analysis was performed using mitochondrial gene NADH dehydrogenase subunit 5 (ND5), based on both native and invasive populations. Altogether, 38 haplotypes were detected with H1 being the dominant and widely distributed in 21 countries. Both phylogenetic and network analyses supported the existence of five clades, with only clade I being involved in the subsequent global spread of Asian tiger mosquito. The other four clades (II, III, IV and V) were restricted to their original regions, which could be ancestral populations that had diverged from clade I in the early stages of evolution. Neutrality tests suggested that most of the populations had experienced recent expansion. Analysis of molecular variance and the population-pair statistic F ST revealed that most populations lacked genetic structure, while high variability was detected within populations. Multiple and independent human-mediated introductions may explain the present results. Copyright © 2018 Elsevier B.V. All rights reserved.

Genetic Variations in Two Seahorse Species (Hippocampus mohnikei and Hippocampus trimaculatus): Evidence for Middle Pleistocene Population Expansion

PubMed Central

Zhang, Yanhong; Pham, Nancy Kim; Zhang, Huixian; Lin, Junda; Lin, Qiang

2014-01-01

Population genetic of seahorses is confidently influenced by their species-specific ecological requirements and life-history traits. In the present study, partial sequences of mitochondrial cytochrome b (cytb) and control region (CR) were obtained from 50 Hippocampus mohnikei and 92 H. trimaculatus from four zoogeographical zones. A total of 780 base pairs of cytb gene were sequenced to characterize mitochondrial DNA (mtDNA) diversity. The mtDNA marker revealed high haplotype diversity, low nucleotide diversity, and a lack of population structure across both populations of H. mohnikei and H. trimaculatus. A neighbour-joining (NJ) tree of cytb gene sequences showed that H. mohnikei haplotypes formed one cluster. A maximum likelihood (ML) tree of cytb gene sequences showed that H. trimaculatus belonged to one lineage. The star-like pattern median-joining network of cytb and CR markers indicated a previous demographic expansion of H. mohnikei and H. trimaculatus. The cytb and CR data sets exhibited a unimodal mismatch distribution, which may have resulted from population expansion. Mismatch analysis suggested that the expansion was initiated about 276,000 years ago for H. mohnikei and about 230,000 years ago for H. trimaculatus during the middle Pleistocene period. This study indicates a possible signature of genetic variation and population expansion in two seahorses under complex marine environments. PMID:25144384

Translating crustacean biological responses from CO2 ...

EPA Pesticide Factsheets

Many studies of animal responses to ocean acidification focus on uniformly conditioned age cohorts that lack complexities typically found in wild populations. These studies have become the primary data source for predicting higher level ecological effects, but the roles of intraspecific interactions in re-shaping biological, demographic and evolutionary responses are not commonly considered. To explore this problem, I assessed responses in the mysid Americamysis bahia to bubbling of CO2-enriched and un-enriched air into the seawater supply in flow-through aquariums. I conducted one experiment using isolated age cohorts and a separate experiment using intact populations. The seawater supply was continuously input from Narragansett Bay (Rhode Island, USA). The 28-day cohort study was maintained without resource or spatial limitations, whereas the 5-month population study consisted of stage-structured populations that were allowed to self-regulate. These differences are common features of experiments and were intentionally retained to demonstrate the effect of methodological approaches on perceptions of effect mechanisms. The CO2 treatment reduced neonate abundance in the cohort experiment (24% reduction due to a mean pH difference of −0.27) but not in the population experiment, where effects were small and were strongest for adult and stage 1 survival (3% change due to a mean pH difference of −0.25). I also found evidence of competition in the population exper

Genetics and evolution of triatomines: from phylogeny to vector control

PubMed Central

Gourbière, S; Dorn, P; Tripet, F; Dumonteil, E

2012-01-01

Triatomines are hemipteran bugs acting as vectors of the protozoan parasite Trypanosoma cruzi. This parasite causes Chagas disease, one of the major parasitic diseases in the Americas. Studies of triatomine genetics and evolution have been particularly useful in the design of rational vector control strategies, and are reviewed here. The phylogeography of several triatomine species is now slowly emerging, and the struggle to reconcile the phenotypic, phylogenetic, ecological and epidemiological species concepts makes for a very dynamic field. Population genetic studies using different markers indicate a wide range of population structures, depending on the triatomine species, ranging from highly fragmented to mobile, interbreeding populations. Triatomines transmit T. cruzi in the context of complex interactions between the insect vectors, their bacterial symbionts and the parasites; however, an integrated view of the significance of these interactions in triatomine biology, evolution and in disease transmission is still lacking. The development of novel genetic markers, together with the ongoing sequencing of the Rhodnius prolixus genome and more integrative studies, will provide key tools to expanding our understanding of these important insect vectors and allow the design of improved vector control strategies. PMID:21897436

"In rape cases we can use this pill": a multimethods assessment of emergency contraception knowledge, access, and needs on the Thailand-Burma border.

PubMed

Hobstetter, Margaret; Sietstra, Cari; Walsh, Meredith; Leigh, Jennifer; Foster, Angel M

2015-08-01

To evaluate availability, service delivery, and barriers to access to emergency contraceptive pills (ECPs) along the Thailand-Burma border. From June 2010 to May 2011 we undertook a multimethods qualitative assessment among cross-border populations, migrants, and refugees. We conducted 46 key informant interviews with representatives from 25 organizations, 18 focus group discussions with migrant adults, migrant adolescents, and healthcare workers, and a service mapping exercise with 22 stakeholders. We found low use of ECPs among the target populations. Structural barriers and lack of evidence-based reproductive health protocols, education, and information restrict access to the limited family planning resources available in this region. Misinformation about ECPs was widespread among health workers and organizational policies were often non-evidence based. Potential policy and program interventions to improve access to ECPs along the Thailand-Burma border include integrating evidence-based practices into community efforts, expanding training opportunities for health workers, and improving communication and coordination among organizations serving populations on both sides of the border. Copyright © 2015. Published by Elsevier Ireland Ltd.

Present-day central African forest is a legacy of the 19th century human history

PubMed Central

Morin-Rivat, Julie; Fayolle, Adeline; Favier, Charly; Bremond, Laurent; Gourlet-Fleury, Sylvie; Bayol, Nicolas; Lejeune, Philippe; Beeckman, Hans; Doucet, Jean-Louis

2017-01-01

The populations of light-demanding trees that dominate the canopy of central African forests are now aging. Here, we show that the lack of regeneration of these populations began ca. 165 ya (around 1850) after major anthropogenic disturbances ceased. Since 1885, less itinerancy and disturbance in the forest has occurred because the colonial administrations concentrated people and villages along the primary communication axes. Local populations formerly gardened the forest by creating scattered openings, which were sufficiently large for the establishment of light-demanding trees. Currently, common logging operations do not create suitable openings for the regeneration of these species, whereas deforestation degrades landscapes. Using an interdisciplinary approach, which included paleoecological, archaeological, historical, and dendrological data, we highlight the long-term history of human activities across central African forests and assess the contribution of these activities to present-day forest structure and composition. The conclusions of this sobering analysis present challenges to current silvicultural practices and to those of the future. DOI: http://dx.doi.org/10.7554/eLife.20343.001 PMID:28093097

Public policy and medical tourism: ethical implications for the Egyptian health care system.

PubMed

Haley, Bob

2011-01-01

Egypt's medical tourism industry has been experiencing tremendous growth. However, Egypt continues to lack the necessary investment in its public health system to effectively care for its population. Current policy and the emergence of medical tourism have led to unequal health care access, resulting in high a prevalence of infectious diseases and lack of resources for its most vulnerable populations. As a new Egyptian government emerges, it is important for policymakers to understand the critical issues and ethical concerns of existing health policy. This understanding may be used to propose new policy that more effectively allocates to care for Egypt's population.

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

Nonequilibrium Conditions Explain Spatial Variability in Genetic Structuring of Little Penguin (Eudyptula minor)

PubMed Central

Peucker, Amanda J.; Valautham, Sureen K.; Styan, Craig A.; Dann, Peter

2015-01-01

Factors responsible for spatial structuring of population genetic variation are varied, and in many instances there may be no obvious explanations for genetic structuring observed, or those invoked may reflect spurious correlations. A study of little penguins (Eudyptula minor) in southeast Australia documented low spatial structuring of genetic variation with the exception of colonies at the western limit of sampling, and this distinction was attributed to an intervening oceanographic feature (Bonney Upwelling), differences in breeding phenology, or sea level change. Here, we conducted sampling across the entire Australian range, employing additional markers (12 microsatellites and mitochondrial DNA, 697 individuals, 17 colonies). The zone of elevated genetic structuring previously observed actually represents the eastern half of a genetic cline, within which structuring exists over much shorter spatial scales than elsewhere. Colonies separated by as little as 27 km in the zone are genetically distinguishable, while outside the zone, homogeneity cannot be rejected at scales of up to 1400 km. Given a lack of additional physical or environmental barriers to gene flow, the zone of elevated genetic structuring may reflect secondary contact of lineages (with or without selection against interbreeding), or recent colonization and expansion from this region. This study highlights the importance of sampling scale to reveal the cause of genetic structuring. PMID:25833231

Using the socio-ecological framework to determine breastfeeding obstacles in a low-income population in Tijuana, Mexico: healthcare services.

PubMed

Bueno-Gutierrez, Diana; Chantry, Caroline

2015-03-01

In Mexico, breastfeeding rates are one of the lowest of Latin America, with 14.4% of infants under 6 months being exclusively breastfed. Previous studies indicate that lack of support from healthcare services is a serious obstacle to breastfeeding mothers in Mexico. Our objective was to identify the main obstacles to breastfeeding presented by the healthcare services in a low-income population in Tijuana, Mexico. We used a socio-ecological framework to determine factors affecting breastfeeding practices. In four low-income communities in Tijuana we conducted focus groups and interviews with mothers, fathers, grandparents, and key informants. Interview notes and focus group transcripts were then studied in-depth independently by three researchers. The primary analytic technique was constant comparison. One hundred twenty-nine subjects participated in this study: six focus groups (n=53) and 51 interviews among mothers, fathers, and grandparents, as well as 25 interviews among key informants. Main healthcare service obstacles to breastfeeding were erroneous information, lack of training and supervision, negative attitudes, miscommunication between healthcare providers (HCPs) and patients, detrimental medical practices such as giving free formula at hospitals, and the conflict of interest between the infant food industry and the HCPs. This study showed that women in low-income communities in Tijuana face multiple obstacles to breastfeeding presented by healthcare services. In order to increase breastfeeding rates, institutional and structural changes are required.

Socio-demographic and behavioral variation in barriers to leisure-time physical activity.

PubMed

Borodulin, Katja; Sipilä, Noora; Rahkonen, Ossi; Leino-Arjas, Päivi; Kestilä, Laura; Jousilahti, Pekka; Prättälä, Ritva

2016-02-01

We examined the socio-demographic and behavioral determinants of perceived barriers to leisure-time physical activity (LTPA) in a population-based sample of working-aged adults. Data comprised the National FINRISK 2002 Study, a population-based health examination study. Analyses were restricted to those aged 25-64 years and who perceived that their amount of LTPA did not reach sufficient levels. They reported barriers to LTPA, defined as a lack of time, motivation and lack of companionship to be active with, as well as high expenses. Age, education, household income, employment status, family type, physical activity, smoking and body mass index (BMI) were included as explanatory variables. Lack of time was the most frequent barrier. Each barrier was explained by a different set of factors that also varied between genders. The strongest and most systematic associations with the barriers were found for age, employment status and family type. Lack of time was less often reported as a barrier among the unemployed, singles without children and older people. Lacking motivation as a barrier was most common among singles without children. High expenses as a barrier was more often reported by the unemployed, and less often reported in the highest income group. When considering actions to promote LTPA, there is not one single solution, because the perceived barriers vary by population subgroups. © 2015 the Nordic Societies of Public Health.

Baseline Risk Factors that Predict the Development of Open-angle Glaucoma in a Population: The Los Angeles Latino Eye Study

PubMed Central

Jiang, Xuejuan; Varma, Rohit; Wu, Shuang; Torres, Mina; Azen, Stanley P; Francis, Brian A.; Chopra, Vikas; Nguyen, Betsy Bao-Thu

2012-01-01

Objective To determine which baseline socio-demographic, lifestyle, anthropometric, clinical, and ocular risk factors predict the development of open-angle glaucoma (OAG) in an adult population. Design A population-based, prospective cohort study. Participants A total of 3,772 self-identified Latinos aged 40 years and older from Los Angeles, California who were free of OAG at baseline. Methods Participants from the Los Angeles Latino Eye Study had standardized study visits at baseline and 4-year follow-up with structured interviews and a comprehensive ophthalmologic examination. OAG was defined as the presence of an open angle and a glaucomatous visual field abnormality and/or evidence of glaucomatous optic nerve damage in at least one eye. Multivariate logistic regression with stepwise selection was performed to determine which potential baseline risk factors independently predict the development of OAG. Main Outcome Measure Odds ratios for various risk factors. Results Over the 4-year follow-up, 87 participants developed OAG. The baseline risk factors that predict the development of OAG include: older age (odds ratio [OR] per decade, 2.19; 95% confidence intervals [CI], 1.74-2.75; P<0.001), higher intraocular pressure (OR per mmHg, 1.18; 95% CI, 1.10-1.26; P<0.001), longer axial length (OR per mm, 1.48; 95% CI, 1.22-1.80; P<0.001), thinner central cornea (OR per 40 μm thinner, 1.30; 95% CI, 1.00-1.70; P=0.050) higher waist to hip ratio (OR per 0.05 higher, 1.21; 95% CI, 1.05-1.39; P=0.007) and lack of vision insurance (OR, 2.08; 95% CI, 1.26-3.41; P=0.004). Conclusions Despite a mean baseline IOP of 14 mmHg in Latinos, higher intraocular pressure is an important risk factor for developing OAG. Biometric measures suggestive of less structural support such as longer axial length and thin CCT were identified as important risk factors. Lack of health insurance reduces access to eye care and increases the burden of OAG by reducing the likelihood of early detection and treatment of OAG. PMID:22796305

The missing lynx of Eurasia at its Southern edge: a connection to the critically endangered Balkan lynx.

PubMed

Cömert, Numan; Carlı, Oya; Dinçtürk, H Benan

2018-03-08

The populations of Eurasian lynx in Anatolia are as fragmented as the European populations. Although the origins of and the connections between the European lynx populations have been elucidated, there have been no genetic studies on the lynx populations in Turkey. The lack of genetic and evolutionary information about lynx in Anatolia, which is considered to be a biodiversity hotspot, makes it difficult to track the migration routes during the Quaternary. In this study, we present the genetic characteristics of two isolated lynx populations in Southwest Taurus Mountains and the Turkish Caucasus as well as two individuals from Erzincan area. DNA purified from the ecological scat samples collected from Çığlıkara Nature Reserve in Elmalı-Antalya and Allahuekber Mountains in Sarıkamış-Kars, as well as two roadkill samples from Erzincan, has been analysed for phylogenetic markers such as the mitochondrial DNA control region and cytochrome b. The DNA sequences were compared with haplotypes previously detected in populations from Europe and the Caucasus in order to determine the evolutionary relationships of the populations. This study compares the current genetic structure of some of the Turkish lynx populations to the other lynx genetic data, mostly carried out with museum samples around the world. Three haplotypes were found in three different regions of Anatolia. The Northeast and Southwest populations harbour genetically distinct haplotypes, the latter one, a new haplotype: H13-TR is the only phylogenetic connection to the critically endangered Balkan lynx yet to be described.

A Spatial Statistical Model for Landscape Genetics

PubMed Central

Guillot, Gilles; Estoup, Arnaud; Mortier, Frédéric; Cosson, Jean François

2005-01-01

Landscape genetics is a new discipline that aims to provide information on how landscape and environmental features influence population genetic structure. The first key step of landscape genetics is the spatial detection and location of genetic discontinuities between populations. However, efficient methods for achieving this task are lacking. In this article, we first clarify what is conceptually involved in the spatial modeling of genetic data. Then we describe a Bayesian model implemented in a Markov chain Monte Carlo scheme that allows inference of the location of such genetic discontinuities from individual geo-referenced multilocus genotypes, without a priori knowledge on populational units and limits. In this method, the global set of sampled individuals is modeled as a spatial mixture of panmictic populations, and the spatial organization of populations is modeled through the colored Voronoi tessellation. In addition to spatially locating genetic discontinuities, the method quantifies the amount of spatial dependence in the data set, estimates the number of populations in the studied area, assigns individuals to their population of origin, and detects individual migrants between populations, while taking into account uncertainty on the location of sampled individuals. The performance of the method is evaluated through the analysis of simulated data sets. Results show good performances for standard data sets (e.g., 100 individuals genotyped at 10 loci with 10 alleles per locus), with high but also low levels of population differentiation (e.g., FST < 0.05). The method is then applied to a set of 88 individuals of wolverines (Gulo gulo) sampled in the northwestern United States and genotyped at 10 microsatellites. PMID:15520263

Research gaps for three main tropical diseases in the People’s Republic of China

PubMed Central

2013-01-01

This scoping review analyzes the research gaps of three diseases: schistosomiasis japonica, malaria and echinococcosis. Based on available data in the P.R. China, we highlight the gaps between control capacity and prevalence levels, and between diagnostic/drug development and population need for treatment at different stages of the national control programme. After reviewing the literature from 848 original studies and consultations with experts in the field, the gaps were identified as follows. Firstly, the malaria research gaps include (i) deficiency of active testing in the public community and no appropriate technique to evaluate elimination, (ii) lack of sensitive diagnostic tools for asymptomatic patients, (iii) lack of safe drugs for mass administration. Secondly, gaps in research of schistosomiasis include (i) incongruent policy in the implementation of integrated control strategy for schistosomiasis, (ii) lack of effective tools for Oncomelania sp. snail control, (iii) lack of a more sensitive and cheaper diagnostic test for large population samples, (iv) lack of new drugs in addition to praziquantel. Thirdly, gaps in research of echinococcosis include (i) low capacity in field epidemiology studies, (ii) lack of sanitation improvement studies in epidemic areas, (iii) lack of a sensitivity test for early diagnosis, (iv) lack of more effective drugs for short-term treatment. We believe these three diseases can eventually be eliminated in mainland China if all the research gaps are abridged in a short period of time. PMID:23895635

The Population Problem as Economic Disarticulation.

ERIC Educational Resources Information Center

Yapa, Lakshman S.

1985-01-01

Overpopulation exists when people lack the basic means of subsistence, or when there is massive and permanent unemployment. Population problems of developing countries are examined, and causes of high rates of fertility are discussed. The utilization of productive resources in solving population problems is also examined. (RM)

The Use of Surrogate Data in Demographic Population Viability Analysis: A Case Study of California Sea Lions

PubMed Central

2015-01-01

Reliable data necessary to parameterize population models are seldom available for imperiled species. As an alternative, data from populations of the same species or from ecologically similar species have been used to construct models. In this study, we evaluated the use of demographic data collected at one California sea lion colony (Los Islotes) to predict the population dynamics of the same species from two other colonies (San Jorge and Granito) in the Gulf of California, Mexico, for which demographic data are lacking. To do so, we developed a stochastic demographic age-structured matrix model and conducted a population viability analysis for each colony. For the Los Islotes colony we used site-specific pup, juvenile, and adult survival probabilities, as well as birth rates for older females. For the other colonies, we used site-specific pup and juvenile survival probabilities, but used surrogate data from Los Islotes for adult survival probabilities and birth rates. We assessed these models by comparing simulated retrospective population trajectories to observed population trends based on count data. The projected population trajectories approximated the observed trends when surrogate data were used for one colony but failed to match for a second colony. Our results indicate that species-specific and even region-specific surrogate data may lead to erroneous conservation decisions. These results highlight the importance of using population-specific demographic data in assessing extinction risk. When vital rates are not available and immediate management actions must be taken, in particular for imperiled species, we recommend the use of surrogate data only when the populations appear to have similar population trends. PMID:26413746

Microbial mutualism at a distance: The role of geometry in diffusive exchanges

NASA Astrophysics Data System (ADS)

Peaudecerf, François J.; Bunbury, Freddy; Bhardwaj, Vaibhav; Bees, Martin A.; Smith, Alison G.; Goldstein, Raymond E.; Croze, Ottavio A.

2018-02-01

The exchange of diffusive metabolites is known to control the spatial patterns formed by microbial populations, as revealed by recent studies in the laboratory. However, the matrices used, such as agarose pads, lack the structured geometry of many natural microbial habitats, including in the soil or on the surfaces of plants or animals. Here we address the important question of how such geometry may control diffusive exchanges and microbial interaction. We model mathematically mutualistic interactions within a minimal unit of structure: two growing reservoirs linked by a diffusive channel through which metabolites are exchanged. The model is applied to study a synthetic mutualism, experimentally parametrized on a model algal-bacterial co-culture. Analytical and numerical solutions of the model predict conditions for the successful establishment of remote mutualisms, and how this depends, often counterintuitively, on diffusion geometry. We connect our findings to understanding complex behavior in synthetic and naturally occurring microbial communities.

[Lack of assertiveness in patients with eating disorders].

PubMed

Behar A, Rosa; Manzo G, Rodrigo; Casanova Z, Dunny

2006-03-01

Low self-assertion has been noted as an important feature among patients with eating disorders. To verify, in a female population, if assertiveness is related or has a predictive capacity for the development of eating disorders. An structured clinical interview, the Eating Attitudes Test (EAT-40) and the Rathus Assertiveness Scale (RAS) were administered to 62 patients that fulfilled the DSM-IV diagnostic criteria for eating disorders and to 120 female students without eating problems. Patients with eating disorders ranked significantly higher on the EAT-40 and its factors (p <0.001) and showed a lower level of assertiveness on the RAS (p <0.001). Assertiveness measured by RAS and its factors was inversely related to EAT-40 and its items (r= -0.21). The predictive capability of the lack of self-assertion in the development of an eating disorder reached 53%, when patients with eating disorders and subjects at risk were considered together and compared to students without such disorder. Lack of assertiveness is a significant trait in patients with eating disorders; it may worsen its outcome and even perpetuate symptoms. Low self-assertion may be considered a predictive factor in the development of an eating disorder and must be managed from a preventive or therapeutic point of view.

Facilitating smallholder tree farming in fragmented tropical landscapes: Challenges and potentials for sustainable land management.

PubMed

Rahman, Syed Ajijur; Sunderland, Terry; Roshetko, James M; Healey, John Robert

2017-08-01

Under changing land use in tropical Asia, there is evidence of forest product diversification through implementation of tree-based farming by smallholders. This paper assesses in two locations, West Java, Indonesia and eastern Bangladesh, current land use conditions from the perspective of smallholder farmers, the factors that facilitate their adoption of tree farming, and the potential of landscape-scale approaches to foster sustainable land management. Data were collected through rapid rural appraisals, focus group discussions, field observations, semi-structured interviews of farm households and key informant interviews of state agricultural officers. Land at both study sites is typically fragmented due to conversion of forest to agriculture and community settlement. Local land use challenges are associated with pressures of population increase, poverty, deforestation, shortage of forest products, lack of community-scale management, weak tenure, underdeveloped markets, government decision-making with insufficient involvement of local people, and poor extension services. Despite these challenges, smallholder tree farming is found to be successful from farmers' perspectives. However, constraints of local food crop cultivation traditions, insecure land tenure, lack of capital, lack of knowledge, lack of technical assistance, and perceived risk of investing in land due to local conflict (in Bangladesh) limit farmers' willingness to adopt this land use alternative. Overcoming these barriers to adoption will require management at a landscape scale, including elements of both segregation and integration of land uses, supported by competent government policies and local communities having sufficiently high social capital. Copyright © 2017 Elsevier Ltd. All rights reserved.

Impacts of structuring nursing records: a systematic review.

PubMed

Saranto, Kaija; Kinnunen, Ulla-Mari; Kivekäs, Eija; Lappalainen, Anna-Mari; Liljamo, Pia; Rajalahti, Elina; Hyppönen, Hannele

2014-12-01

The study aims to describe the impacts of different data structuring methods used in nursing records or care plans. This systematic review examines what kinds of structuring methods have been evaluated and the effects of data structures on healthcare input, processes and outcomes in previous studies. Retrieval from 15 databases yielded 143 papers. Based on Population (Participants), Intervention, Comparators, Outcomes elements and exclusion and inclusion criteria, the search produced 61 studies. A data extraction tool and analysis for empirical articles were used to classify the data referring to the study aim. Thirty-eight studies were included in the final analysis. The study design most often used was a single measurement without any control. The studies were conducted mostly in secondary or tertiary care in institutional care contexts. The standards used in documentation were nursing classifications or the nursing process model in clinical use. The use of standardised nursing language (SNL) increased descriptions of nursing interventions and outcomes supporting daily care, and improving patient safety and information reuse. The nursing process model and classifications are used internationally as nursing data structures in nursing records and care plans. The use of SNL revealed various positive impacts. Unexpected outcomes were most often related to lack of resources. Indexing of SNL studies has not been consistent. That might cause bias in database retrieval, and important articles may be lacking. The study design of the studies analysed varied widely. Further, the time frame of papers was quite long, causing confusion in descriptions of nursing data structures. The value of SNL is proven by its support of daily workflow, delivery of nursing care and data reuse. This facilitates continuity of care, thus contributing to patient safety. Nurses need more education and managerial support in order to be able to benefit from SNL. © 2013 The Authors. Scandinavian Journal of Caring Sciences published by John Wiley & Sons Ltd on behalf of Nordic College of Caring Science.

Opportunities for healthier child feeding. Does ethnic position matter? - self-reported evaluation of family diet and impediments to change among parents with majority and minority status in Denmark.

PubMed

Nielsen, Annemette; Krasnik, Allan; Vassard, Ditte; Holm, Lotte

2014-07-01

Health inequality between ethnic groups is expressed in differences in the prevalence of diet related diseases. The aim of the study was to investigate and compare barriers toward eating healthier among ethnic majority and minority parents in Denmark. A postal survey was carried out among 2511 parents with either Danish or non-western ethnic minority descendant background, investigating barriers on cultural, structural, social, individual, and practical levels. The results showed that compared with parents of Danish origin, ethnic minority parents were more likely to evaluate their own diets negatively (OR 3.0, CI 1.7-5.3), and to evaluate their children's diets negatively (OR 4.6, CI 2.5-8.4). In addition, ethnic minority parents to a higher degree experienced barriers to eating healthier than Danish parents did. Most salient was ethnic minority parents' expression of a lack of control over their own food intake and the food given to their children in everyday life. Such a lack of control was identified on practical, social, structural and individual levels. Young age of the parents was found to explain some of the differences between ethnic groups. It is concluded that dietary interventions directed at parents of small children should address not only cultural background but also barriers operating on practical, social, structural, and individual levels, as some of these influence ethnic minorities and the majority population differently. Further exploration of the importance of young age and the interplay between structural and cultural factors in the lives of ethnic minority families is needed. Copyright © 2014. Published by Elsevier Ltd.

[The use of anthropologic methods for studying the causes of lack of vaccination. The case of Nativitas, Xochimilco].

PubMed

Nigenda-López, G; Orozco-Núñez, E

1990-01-01

The relationship between the socio-cultural characteristics of a population and their participation in immunization programs is described in this paper. An anthropological approach was utilized to study the reasons why certain population groups do not participate in the immunization programs or do so inadequately. The study was undertaken in a community south of Mexico City. The paper contains the description of the community's contextual elements, the organization of the medical care services and the participation of the population in the immunization programs. It was found that a wide millieu of socio-cultural factors are related with people's behavior toward vaccination, such as: lack of information about diseases and vaccines, lack of trust on modern health services, and the strong influence of traditional medicine. Clear implications can be derived from the analysis with regards to the need for revision and modification of strategies of the health education programs, in order to promote a wider participation in immunization programs.

Development of microalgae communities in the Phytotelmata of allochthonous populations of Sarracenia purpurea (Sarraceniaceae).

PubMed

Gebühr, C; Pohlon, E; Schmidt, A R; Küsel, K

2006-11-01

The phytotelmata of the North American pitcher plant Sarracenia purpurea are colonised by a great variety of aquatic organisms and, thus, provide an ideal model to study trophic interactions in small freshwater ecosystems. Although algae are discussed as a potential food source for predators, little is known about the structure of algae coenoses in pitchers of S. purpurea. This study aims to elucidate temporal shifts in the algae community structure in pitchers of an allochthonous population of S. purpurea in Saxony, Germany. A total of 78 algae taxa was found in the pitchers. Mean algae abundances in new and old pitchers were similar (2.6 x 10(5) and 2.3 x 10(5) algae ml(-1), respectively). Taxa from the orders Chlamydomonadales, Chlorococcales, and Ochromonadales were the primary colonisers. With increasing age of the pitchers the filamentous green algae from the order Klebsormidiales became more abundant. In contrast, pennate diatoms dominated the algae coenoses in the fen. Algae community structure in vase-shaped 50 ml Greiner tubes was similar to those of natural pitchers. Differences in the temporal patterns of algae coenoses in individual pitchers suggested a colonisation of the pitchers by algae via trapped insects, air and rain water rather than via the surrounding fen. Biomass of algae approximated 0.3 mg C ml(-1), which corresponds to 82.8 % of the living biomass (bacteria, heterotrophic nanoflagellates, algae, protozoans and rotifers). Rotifers were abundant in new pitchers; nematodes and mites were seldom found in all pitchers. A similar qualitative and quantitative composition of the aquatic biocoenoses was observed in pitchers of another allochthonous S. purpurea population growing in Blekinge, Sweden. Biomass of algae represented nearly one quarter of the total organic matter content in the pitchers. Thus, nitrogen and phosphorus compounds present in the algae biomass might be used by the carnivorous S. purpurea plant as additional food source in allochthonous populations in Europe lacking top predators.

Detecting the Population Structure and Scanning for Signatures of Selection in Horses (Equus caballus) From Whole-Genome Sequencing Data

PubMed Central

Zhang, Cheng; Ni, Pan; Ahmad, Hafiz Ishfaq; Gemingguli, M; Baizilaitibei, A; Gulibaheti, D; Fang, Yaping; Wang, Haiyang; Asif, Akhtar Rasool; Xiao, Changyi; Chen, Jianhai; Ma, Yunlong; Liu, Xiangdong; Du, Xiaoyong; Zhao, Shuhong

2018-01-01

Animal domestication gives rise to gradual changes at the genomic level through selection in populations. Selective sweeps have been traced in the genomes of many animal species, including humans, cattle, and dogs. However, little is known regarding positional candidate genes and genomic regions that exhibit signatures of selection in domestic horses. In addition, an understanding of the genetic processes underlying horse domestication, especially the origin of Chinese native populations, is still lacking. In our study, we generated whole genome sequences from 4 Chinese native horses and combined them with 48 publicly available full genome sequences, from which 15 341 213 high-quality unique single-nucleotide polymorphism variants were identified. Kazakh and Lichuan horses are 2 typical Asian native breeds that were formed in Kazakh or Northwest China and South China, respectively. We detected 1390 loss-of-function (LoF) variants in protein-coding genes, and gene ontology (GO) enrichment analysis revealed that some LoF-affected genes were overrepresented in GO terms related to the immune response. Bayesian clustering, distance analysis, and principal component analysis demonstrated that the population structure of these breeds largely reflected weak geographic patterns. Kazakh and Lichuan horses were assigned to the same lineage with other Asian native breeds, in agreement with previous studies on the genetic origin of Chinese domestic horses. We applied the composite likelihood ratio method to scan for genomic regions showing signals of recent selection in the horse genome. A total of 1052 genomic windows of 10 kB, corresponding to 933 distinct core regions, significantly exceeded neutral simulations. The GO enrichment analysis revealed that the genes under selective sweeps were overrepresented with GO terms, including “negative regulation of canonical Wnt signaling pathway,” “muscle contraction,” and “axon guidance.” Frequent exercise training in domestic horses may have resulted in changes in the expression of genes related to metabolism, muscle structure, and the nervous system.

Magnetic Reconnection Dynamics in the Presence of Low-energy Ion Component: PIC Simulations of Hidden Particle Population

NASA Astrophysics Data System (ADS)

Khotyaintsev, Y. V.; Divin, A. V.; Toledo Redondo, S.; Andre, M.; Vaivads, A.; Markidis, S.; Lapenta, G.

2015-12-01

Magnetospheric and astrophysical plasmas are rarely in the state of thermal equilibrium. Plasma distribution functions may contain beams, supra-thermal tails, multiple ion and electron populations which are not thermalized over long time scales due to the lack of collisions between particles. In particular, the equatorial region of the dayside Earth's magnetosphere is often populated by plasma containing hot and cold ion components of comparable densities [Andre and Cully, 2012], and such ion distribution alters properties of the magnetic reconnection regions at the magnetopause [Toledo-Redondo et. al., 2015]. Motivated by these recent findings and also by fact that this region is one of the targets of the recently launched MMS mission, we performed 2D PIC simulations of magnetic reconnection in collisionless plasma with hot and cold ion components. We used a standard Harris current sheet, to which a uniform cold ion background is added. We found that introduction of the cold component modifies the structure of reconnection diffusion region. Diffusion region displays three-scale structure, with the cold Ion Diffusion Region (cIDR) scale appearing in-between the Electron Diffusion Region (EDR) and Ion Diffusion Region (IDR) scales. Structure and strength of the Hall magnetic field depends weakly on cold ion temperature or density, and is rather controlled by the conditions (B, n) upstream the reconnection region. The cold ions are accelerated predominantly transverse to the magnetic field by the Hall electric fields inside the IDR, leading to a large ion pressure anisotropy, which is unstable to ion Weibel-type or mirror-type mode. On the opposite, acceleration of cold ions is mostly field-aligned at the reconnection jet fronts downstream the X-line, producing intense ion phase-space holes there. Despite comparable reconnection rates produced , we find that the overall evolution of reconnection in presence of cold ion population is more dynamic compared to the case with a single hot ion component.

The effects of drought on population structure, activity, and orientation of toads Bufo quercicus and B. terrestris at a temporary pond

USGS Publications Warehouse

Dodd, C.K.

1994-01-01

From 1985 through 1990, I monitored the populations of two species of toads, Bufo quercicus and B. terrestris, at a temporary pond in the xeric uplands of north-central Florida. A drift fence with pitfall traps completely encircled the pond basin; the fence was monitored 5 days per week throughout the year. The 5-year study coincided with a severe regional drought that resulted in generally short hydroperiods at unpredictable times of the year. More than 800 toads were captured. Successful metamorphosis never occurred at the pond although toads continued to visit it throughout the study. The sex ratio was male biased in B. quercicus but not in B. terrestris, although significant variation was observed from one year to the next. Likewise, the size-class structure and length-weight patterns varied among species, sexes, and years. Although fewer toads entered the pond basin as the study progressed, toads may have gone elsewhere to breed or they may have remained in refugia. Thus, decreased capture does not necessarily indicate that a drought-related population decline occurred. Drought may have disrupted normal arrival patterns and length of stay within the pond basin. Drought also could be responsible for variation in annual size-class structure of captured toads. The uncertainty of the hydroperiod both spatially and temporally in adjacent breeding sites, the ability of toads to move long distances with the potential for migration between breeding sites, and the lack of specificity in the choice of breeding sites (i.e. permanent versus different types of temporary wetlands) may lead to the formation of metapopulations in the xeric upland habitats of north-central Florida. Long-term monitoring under a variety of climatic conditions is needed to assess the effects of drought and other types of environmental stresses on toad populations.

Non-native fishes in Florida freshwaters: a literature review and synthesis

USGS Publications Warehouse

Schofield, Pamela J.; Loftus, William F.

2015-01-01

Non-native fishes have been known from freshwater ecosystems of Florida since the 1950s, and dozens of species have established self-sustaining populations. Nonetheless, no synthesis of data collected on those species in Florida has been published until now. We searched the literature for peer-reviewed publications reporting original data for 42 species of non-native fishes in Florida that are currently established, were established in the past, or are sustained by human intervention. Since the 1950s, the number of non-native fish species increased steadily at a rate of roughly six new species per decade. Studies documented (in decreasing abundance): geographic location/range expansion, life- and natural-history characteristics (e.g., diet, habitat use), ecophysiology, community composition, population structure, behaviour, aquatic-plant management, and fisheries/aquaculture. Although there is a great deal of taxonomic uncertainty and confusion associated with many taxa, very few studies focused on clarifying taxonomic ambiguities of non-native fishes in the State. Most studies were descriptive; only 15 % were manipulative. Risk assessments, population-control studies and evaluations of effects of non-native fishes were rare topics for research, although they are highly valued by natural-resource managers. Though some authors equated lack of data with lack of effects, research is needed to confirm or deny conclusions. Much more is known regarding the effects of lionfish (Pterois spp.) on native fauna, despite its much shorter establishment time. Natural-resource managers need biological and ecological information to make policy decisions regarding non-native fishes. Given the near-absence of empirical data on effects of Florida non-native fishes, and the lengthy time-frames usually needed to collect such information, we provide suggestions for data collection in a manner that may be useful in the evaluation and prediction of non-native fish effects.

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.

Perspectives on Providing And Receiving Preventive Health Care From Primary Care Providers and Their Patients With Mental Illnesses.

PubMed

Stumbo, Scott P; Yarborough, Bobbi Jo H; Yarborough, Micah T; Green, Carla A

2018-01-01

Individuals with mental illnesses have higher morbidity rates and reduced life expectancy compared to the general population. Understanding how patients and providers perceive the need for prevention, as well as the barriers and beliefs that may contribute to insufficient care, are important for improving service delivery tailored to this population. Cross-sectional; mixed methods. An integrated health system and a network of federally qualified health centers and safety net clinics. Interviews (n = 30) and surveys (n = 249) with primary care providers. Interviews (n = 158) and surveys (n = 160) with patients diagnosed with schizophrenia, bipolar, anxiety, or major depressive disorders. Semi-structured interviews and surveys. Thematic analysis for qualitative data; frequencies for quantitative data. More than half (n = 131, 53%) of clinicians believed patients with mental illnesses care less about preventive care than the general population, yet 88% (n = 139) of patients reported interest in improving health. Most providers (n = 216, 88%) lacked confidence that patients with mental illnesses would follow preventive recommendations; 82% (n = 129) of patients reported they would try to change lifestyles if their doctor recommended. Clinicians explained that their perception of patients' chaotic lives and lack of interest in preventive care contributed to their fatalistic attitudes on care delivery to this population. Clinicians and patients agreed on substantial need for additional support for behavior changes. Clinicians reported providing informational support by keeping messages simple; patients reported a desire for more detailed information on reasons to complete preventive care. Patients also detailed the need for assistive and tangible support to manage behavioral health changes. Our results suggest a few clinical changes could help patients complete preventive care recommendations and improve health behaviors: improving clinician-patient collaboration on realistic goal setting, increasing visit time or utilizing behavioral health consultants that bridge primary and specialty mental health care, and increasing educational and tangible patient support services.

Relationships between forest songbird populations and managed forests in Idaho

Treesearch

Diane M. Evans; Deborah M. Finch

1994-01-01

Many species of songbirds have experienced population declines. In the eastern U.S. in recent years, but conclusive data on population trends and factors affecting populations in the West are lacking. Few studies have evaluated the importance of surrounding land configuration to songbird abundances. In 1992, we initiated a study in mixed conifer forest in west-central...

Divide and conquer: intermediate levels of population fragmentation maximize cultural accumulation.

PubMed

Derex, Maxime; Perreault, Charles; Boyd, Robert

2018-04-05

Identifying the determinants of cumulative cultural evolution is a key issue in the interdisciplinary field of cultural evolution. A widely held view is that large and well-connected social networks facilitate cumulative cultural evolution because they promote the spread of useful cultural traits and prevent the loss of cultural knowledge through factors such as drift. This view stems from models that focus on the transmission of cultural information, without considering how new cultural traits actually arise. In this paper, we review the literature from various fields that suggest that, under some circumstances, increased connectedness can decrease cultural diversity and reduce innovation rates. Incorporating this idea into an agent-based model, we explore the effect of population fragmentation on cumulative culture and show that, for a given population size, there exists an intermediate level of population fragmentation that maximizes the rate of cumulative cultural evolution. This result is explained by the fact that fully connected, non-fragmented populations are able to maintain complex cultural traits but produce insufficient variation and so lack the cultural diversity required to produce highly complex cultural traits. Conversely, highly fragmented populations produce a variety of cultural traits but cannot maintain complex ones. In populations with intermediate levels of fragmentation, cultural loss and cultural diversity are balanced in a way that maximizes cultural complexity. Our results suggest that population structure needs to be taken into account when investigating the relationship between demography and cumulative culture.This article is part of the theme issue 'Bridging cultural gaps: interdisciplinary studies in human cultural evolution'. © 2018 The Author(s).

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.

Bay Area Student Involvement in the Environmental and Food Justice Movements: A Narrative of Motivations, Experiences, and Community Impact

ERIC Educational Resources Information Center

Solof, Laura E.

2014-01-01

Many California public school students lack exposure to any formal, academic curriculum that emphasizes environmental awareness and activism. This may result in a population of adults who believe they know more about the environment than they actually do, lack the skills to compete in an expanding green job market, lack creativity and the ability…

Contrasting Patterns of Genetic Differentiation among Blackcaps (Sylvia atricapilla) with Divergent Migratory Orientations in Europe

PubMed Central

Mettler, Raeann; Schaefer, H. Martin; Chernetsov, Nikita; Fiedler, Wolfgang; Hobson, Keith A.; Ilieva, Mihaela; Imhof, Elisabeth; Johnsen, Arild; Renner, Swen C.; Rolshausen, Gregor; Serrano, David; Wesołowski, Tomasz; Segelbacher, Gernot

2013-01-01

Migratory divides are thought to facilitate behavioral, ecological, and genetic divergence among populations with different migratory routes. However, it is currently contentious how much genetic divergence is needed to maintain distinct migratory behavior across migratory divides. Here we investigate patterns of neutral genetic differentiation among Blackcap (Sylvia atricapilla) populations with different migratory strategies across Europe. We compare the level of genetic divergence of populations migrating to southwestern (SW) or southeastern (SE) wintering areas with birds wintering in the British Isles following a recently established northwesterly (NW) migration route. The migratory divide between SW and SE wintering areas can be interpreted as a result of a re-colonization process after the last glaciation. Thus we predicted greater levels of genetic differentiation among the SW/SE populations. However, a lack of genetic differentiation was found between SW and SE populations, suggesting that interbreeding likely occurs among Blackcaps with different migratory orientations across a large area; therefore the SW/SE migratory divide can be seen as diffuse, broad band and is, at best, a weak isolating barrier. Conversely, weak, albeit significant genetic differentiation was evident between NW and SW migrants breeding sympatrically in southern Germany, suggesting a stronger isolating mechanism may be acting in this population. Populations located within/near the SW/SE contact zone were the least genetically divergent from NW migrants, confirming NW migrants likely originated from within the contact zone. Significant isolation-by-distance was found among eastern Blackcap populations (i.e. SE migrants), but not among western populations (i.e. NW and SW migrants), revealing different patterns of genetic divergence among Blackcap populations in Europe. We discuss possible explanations for the genetic structure of European Blackcaps and how gene flow influences the persistence of divergent migratory behaviors. PMID:24278428

The influence of habitats on female mobility in Central and Western Africa inferred from human mitochondrial variation

PubMed Central

2013-01-01

Background When studying the genetic structure of human populations, the role of cultural factors may be difficult to ascertain due to a lack of formal models. Linguistic diversity is a typical example of such a situation. Patrilocality, on the other hand, can be integrated into a biological framework, allowing the formulation of explicit working hypotheses. The present study is based on the assumption that patrilocal traditions make the hypervariable region I of the mtDNA a valuable tool for the exploration of migratory dynamics, offering the opportunity to explore the relationships between genetic and linguistic diversity. We studied 85 Niger-Congo-speaking patrilocal populations that cover regions from Senegal to Central African Republic. A total of 4175 individuals were included in the study. Results By combining a multivariate analysis aimed at investigating the population genetic structure, with a Bayesian approach used to test models and extent of migration, we were able to detect a stepping-stone migration model as the best descriptor of gene flow across the region, with the main discontinuities corresponding to forested areas. Conclusions Our analyses highlight an aspect of the influence of habitat variation on human genetic diversity that has yet to be understood. Rather than depending simply on geographic linear distances, patterns of female genetic variation vary substantially between savannah and rainforest environments. Our findings may be explained by the effects of recent gene flow constrained by environmental factors, which superimposes on a background shaped by pre-agricultural peopling. PMID:23360301

Promoting Utilization of Saccharum spp. Genetic Resources through Genetic Diversity Analysis and Core Collection Construction

PubMed Central

Pathak, Bhuvan; Ayala-Silva, Tomas; Yang, Xiping; Todd, James; Glynn, Neil C.; Kuhn, David N.; Glaz, Barry; Gilbert, Robert A.; Comstock, Jack C.; Wang, Jianping

2014-01-01

Sugarcane (Saccharum spp.) and other members of Saccharum spp. are attractive biofuel feedstocks. One of the two World Collections of Sugarcane and Related Grasses (WCSRG) is in Miami, FL. This WCSRG has 1002 accessions, presumably with valuable alleles for biomass, other important agronomic traits, and stress resistance. However, the WCSRG has not been fully exploited by breeders due to its lack of characterization and unmanageable population. In order to optimize the use of this genetic resource, we aim to 1) genotypically evaluate all the 1002 accessions to understand its genetic diversity and population structure and 2) form a core collection, which captures most of the genetic diversity in the WCSRG. We screened 36 microsatellite markers on 1002 genotypes and recorded 209 alleles. Genetic diversity of the WCSRG ranged from 0 to 0.5 with an average of 0.304. The population structure analysis and principal coordinate analysis revealed three clusters with all S. spontaneum in one cluster, S. officinarum and S. hybrids in the second cluster and mostly non-Saccharum spp. in the third cluster. A core collection of 300 accessions was identified which captured the maximum genetic diversity of the entire WCSRG which can be further exploited for sugarcane and energy cane breeding. Sugarcane and energy cane breeders can effectively utilize this core collection for cultivar improvement. Further, the core collection can provide resources for forming an association panel to evaluate the traits of agronomic and commercial importance. PMID:25333358

Diverse realities: sexually transmitted infections and HIV in India.

PubMed

Hawkes, S; Santhya, K G

2002-04-01

There are many features that make India a vulnerable country as far as a sexually transmitted infection (STI)/HIV epidemic is concerned. These include the lack of a strong evidence base on which to formulate decision making, a pluralistic and often unregulated health sector, and a highly vulnerable population. Nonetheless, India has shown strong commitment to other areas of a comprehensive reproductive health care programme, and may be able to do so in the field of STI/HIV control. Vast numbers of people in India are severely disadvantaged in terms of income, education, power structures, and gender. Addressing these basic issues of human rights lies at the core of achieving better health outcomes.

[The agribusiness industry in northwestern Mexico and the health of female farmworkers: a proposal for study].

PubMed

Aranda, Patricia; Castro Vásquez, María Del Carmen

2016-03-01

This article seeks to outline the structure of the export-oriented agribusiness industry in northwestern Mexico, so as to analyze the conditions of vulnerability of female farmworkers in terms of their access to health services and the medical attention they receive. Using a qualitative approach, focus groups and interviews were carried out with farmworkers and subject experts pertaining to academia and civil society. Their narratives were then analyzed using Pierre Bourdieu's concept of field. The primary results demonstrate a lack of access to health services and social security, and describe the main actors and their positions with respect to the vulnerability of this population.

[The health system of Peru].

PubMed

Alcalde-Rabanal, Jacqueline Elizabeth; Lazo-González, Oswaldo; Nigenda, Gustavo

2011-01-01

This paper describes the health conditions in Peru and, with greater detail, the Peruvian health system, including its structure and coverage, its financial sources, its physical, material and human resources, and its stewardship functions. It also discusses the activities developed in the information and research areas, as well as the participation of citizens in the operation and evaluation of the health system. The article concludes with a discussion of the most recent innovations, including the Comprehensive Health Insurance, the Health Care Enterprises system, the decentralization process and the Local Committees for Health Administration. The main challenge confronted by the Peruvian health system is the extension of coverage to more than I0% of the population presently lacking access to basic health care.

Genetic and epigenetic variation in Spartina alterniflora following the Deepwater Horizon oil spill.

PubMed

Robertson, Marta; Schrey, Aaron; Shayter, Ashley; Moss, Christina J; Richards, Christina

2017-09-01

Catastrophic events offer unique opportunities to study rapid population response to stress in natural settings. In concert with genetic variation, epigenetic mechanisms may allow populations to persist through severe environmental challenges. In 2010, the Deepwater Horizon oil spill devastated large portions of the coastline along the Gulf of Mexico. However, the foundational salt marsh grass, Spartina alterniflora , showed high resilience to this strong environmental disturbance. Following the spill, we simultaneously examined the genetic and epigenetic structure of recovering populations of S. alterniflora to oil exposure. We quantified genetic and DNA methylation variation using amplified fragment length polymorphism and methylation sensitive fragment length polymorphism (MS-AFLP) to test the hypothesis that response to oil exposure in S. alterniflora resulted in genetically and epigenetically based population differentiation. We found high genetic and epigenetic variation within and among sites and found significant genetic differentiation between contaminated and uncontaminated sites, which may reflect nonrandom mortality in response to oil exposure. Additionally, despite a lack of genomewide patterns in DNA methylation between contaminated and uncontaminated sites, we found five MS-AFLP loci (12% of polymorphic MS-AFLP loci) that were correlated with oil exposure. Overall, our findings support genetically based differentiation correlated with exposure to the oil spill in this system, but also suggest a potential role for epigenetic mechanisms in population differentiation.

Population displacements as a risk factor for the emergence of epidemics.

PubMed

Tabbaa, Darem; Seimenis, Aristarco

2013-01-01

Wars and civil conflicts have been terrible experiences since ancient times but, regretfully, they are always present even in the 21st century. Their catastrophic effects are still lived by many populations displaced from their native areas. Conflicts, particularly the civil ones, create disruption in most aspects of national structures and populations, which are forced to move to more or less safer or even distant areas, survive under downgraded conditions. They are usually housed in temporary shelters in overcrowded camps and contaminated environment. Water and food are neither safe nor sufficient. Malnutrition, lack or weak sanitary care and long-term stress lead these populations to being vulnerable to severe infections. Under such conditions there are high rates of morbidity and mortality, with elders and children being the main victims. Public health, animal health, municipalities and other inter-related sectors should work on preparedness plans well in advance in order to provide ways and means to face emergencies. Zoonotic and other communicable disease outbreaks should not be left uncontrolled, as their impact would be an additional burden for the country under unrest. Guidance should be provided on how to best articulate an emergency management plan from the early detection of outbreaks up to their control. These aspects are briefly exposed together with the imperative request for alleviation of suffering and of the multitude of hazards conflict-affected populations have to face.

Genome-wide characterization of genetic diversity and population structure in Secale

PubMed Central

2014-01-01

Background Numerous rye accessions are stored in ex situ genebanks worldwide. Little is known about the extent of genetic diversity contained in any of them and its relation to contemporary varieties, since to date rye genetic diversity studies had a very limited scope, analyzing few loci and/ or few accessions. Development of high throughput genotyping methods for rye opened the possibility for genome wide characterizations of large accessions sets. In this study we used 1054 Diversity Array Technology (DArT) markers with defined chromosomal location to characterize genetic diversity and population structure in a collection of 379 rye accessions including wild species, landraces, cultivated materials, historical and contemporary rye varieties. Results Average genetic similarity (GS) coefficients and average polymorphic information content (PIC) values varied among chromosomes. Comparison of chromosome specific average GS within and between germplasm sub-groups indicated regions of chromosomes 1R and 4R as being targeted by selection in current breeding programs. Bayesian clustering, principal coordinate analysis and Neighbor Joining clustering demonstrated that source and improvement status contributed significantly to the structure observed in the analyzed set of Secale germplasm. We revealed a relatively limited diversity in improved rye accessions, both historical and contemporary, as well as lack of correlation between clustering of improved accessions and geographic origin, suggesting common genetic background of rye accessions from diverse geographic regions and extensive germplasm exchange. Moreover, contemporary varieties were distinct from the remaining accessions. Conclusions Our results point to an influence of reproduction methods on the observed diversity patterns and indicate potential of ex situ collections for broadening the genetic diversity in rye breeding programs. Obtained data show that DArT markers provide a realistic picture of the genetic diversity and population structure present in the collection of 379 rye accessions and are an effective platform for rye germplasm characterization and association mapping studies. PMID:25085433

The role of the Ord Arid Intrusion in the historical and contemporary genetic division of long-tailed finch subspecies in northern Australia

PubMed Central

Rollins, Lee Ann; Svedin, Nina; Pryke, Sarah R; Griffith, Simon C

2012-01-01

The effect of separation by biogeographic features followed by secondary contact can blur taxonomic boundaries and produce complex genetic signatures. We analyzed population structure and gene flow across the range of the long-tailed finch (Poephila acuticauda) in northern Australia (1) to test the hypothesis that Ord Arid Intrusion acted as the causative barrier that led to divergence of P. acuticauda subspecies, (2) to determine whether genetic data support the presence of a gradual cline across the range or a sudden shift, both of which have been suggested based on morphological data, and (3) to estimate levels of contemporary gene flow within this species complex. We collected samples from 302 individuals from 10 localities. Analyses of 12 microsatellite loci and sequence data from 333 base pairs of the mitochondrial control region were used to estimate population structure and gene flow, using analysis of molecular variance (AMOVA), haplotype network analysis, frequency statistics, and clustering methods. Mitochondrial sequence data indicated the presence of three genetic groups (regions) across the range of P. acuticauda. Genetic diversity was highest in the east and lowest in the west. The Ord Arid Intrusion appears to have functioned as a biogeographic barrier in the past, according to mtDNA evidence presented here and evidence from previous studies. The absence of isolation by distance between adjacent regions and the lack of population genetic structure of mtDNA within regions indicates that genetic changes across the range of P. acuticauda subspecies are characterized by discrete breaks between regions. While microsatellite data indicate a complete absence of genetic structure across this species’ range, it appears unlikely that this results from high levels of gene flow. Mitochondrial data do not support the presence of contemporary gene flow across the range of this species. PMID:22833795

Spatial Heterogeneity as a Genetic Mixing Mechanism in Highly Philopatric Colonial Seabirds

PubMed Central

Cristofari, Robin; Trucchi, Emiliano; Whittington, Jason D.; Vigetta, Stéphanie; Gachot-Neveu, Hélène; Stenseth, Nils Christian; Le Maho, Yvon; Le Bohec, Céline

2015-01-01

How genetic diversity is maintained in philopatric colonial systems remains unclear, and understanding the dynamic balance of philopatry and dispersal at all spatial scales is essential to the study of the evolution of coloniality. In the King penguin, Aptenodytes patagonicus, return rates of post-fledging chicks to their natal sub-colony are remarkably high. Empirical studies have shown that adults return year after year to their previous breeding territories within a radius of a few meters. Yet, little reliable data are available on intra- and inter-colonial dispersal in this species. Here, we present the first fine-scale study of the genetic structure in a king penguin colony in the Crozet Archipelago. Samples were collected from individual chicks and analysed at 8 microsatellite loci. Precise geolocation data of hatching sites and selective pressures associated with habitat features were recorded for all sampling locations. We found that despite strong natal and breeding site fidelity, king penguins retain a high degree of panmixia and genetic diversity. Yet, genetic structure appears markedly heterogeneous across the colony, with higher-than-expected inbreeding levels, and local inbreeding and relatedness hotspots that overlap predicted higher-quality nesting locations. This points towards heterogeneous population structure at the sub-colony level, in which fine-scale environmental features drive local philopatric behaviour, while lower-quality patches may act as genetic mixing mechanisms at the colony level. These findings show how a lack of global genetic structuring can emerge from small-scale heterogeneity in ecological parameters, as opposed to the classical model of homogeneous dispersal. Our results also emphasize the importance of sampling design for estimation of population parameters in colonial seabirds, as at high spatial resolution, basic genetic features are shown to be location-dependent. Finally, this study stresses the importance of understanding intra-colonial dispersal and genetic mixing mechanisms in order to better estimate species-wide gene flows and population dynamics. PMID:25680103

Spatial heterogeneity as a genetic mixing mechanism in highly philopatric colonial seabirds.

PubMed

Cristofari, Robin; Trucchi, Emiliano; Whittington, Jason D; Vigetta, Stéphanie; Gachot-Neveu, Hélène; Stenseth, Nils Christian; Le Maho, Yvon; Le Bohec, Céline

2015-01-01

How genetic diversity is maintained in philopatric colonial systems remains unclear, and understanding the dynamic balance of philopatry and dispersal at all spatial scales is essential to the study of the evolution of coloniality. In the King penguin, Aptenodytes patagonicus, return rates of post-fledging chicks to their natal sub-colony are remarkably high. Empirical studies have shown that adults return year after year to their previous breeding territories within a radius of a few meters. Yet, little reliable data are available on intra- and inter-colonial dispersal in this species. Here, we present the first fine-scale study of the genetic structure in a king penguin colony in the Crozet Archipelago. Samples were collected from individual chicks and analysed at 8 microsatellite loci. Precise geolocation data of hatching sites and selective pressures associated with habitat features were recorded for all sampling locations. We found that despite strong natal and breeding site fidelity, king penguins retain a high degree of panmixia and genetic diversity. Yet, genetic structure appears markedly heterogeneous across the colony, with higher-than-expected inbreeding levels, and local inbreeding and relatedness hotspots that overlap predicted higher-quality nesting locations. This points towards heterogeneous population structure at the sub-colony level, in which fine-scale environmental features drive local philopatric behaviour, while lower-quality patches may act as genetic mixing mechanisms at the colony level. These findings show how a lack of global genetic structuring can emerge from small-scale heterogeneity in ecological parameters, as opposed to the classical model of homogeneous dispersal. Our results also emphasize the importance of sampling design for estimation of population parameters in colonial seabirds, as at high spatial resolution, basic genetic features are shown to be location-dependent. Finally, this study stresses the importance of understanding intra-colonial dispersal and genetic mixing mechanisms in order to better estimate species-wide gene flows and population dynamics.

The Relationship between Maternal Nutrition during Pregnancy and Offspring Kidney Structure and Function in Humans: A Systematic Review

PubMed Central

Lee, Yu Qi; Collins, Clare E.; Gordon, Adrienne; Rae, Kym M.; Pringle, Kirsty G.

2018-01-01

The intrauterine environment is critical for fetal growth and organ development. Evidence from animal models indicates that the developing kidney is vulnerable to suboptimal maternal nutrition and changes in health status. However, evidence from human studies are yet to be synthesised. Therefore, the aim of the current study was to systematically review current research on the relationship between maternal nutrition during pregnancy and offspring kidney structure and function in humans. A search of five databases identified 9501 articles, of which three experimental and seven observational studies met the inclusion criteria. Nutrients reviewed to date included vitamin A (n = 3), folate and vitamin B12 (n = 2), iron (n = 1), vitamin D (n = 1), total energy (n = 2) and protein (n = 1). Seven studies were assessed as being of “positive” and three of “neutral” quality. A variety of populations were studied, with limited studies investigating maternal nutrition during pregnancy, while measurements of offspring kidney outcomes were diverse across studies. There was a lack of consistency in the timing of follow-up for offspring kidney structure and/or function assessments, thus limiting comparability between studies. Deficiencies in maternal folate, vitamin A, and total energy during pregnancy were associated with detrimental impacts on kidney structure and function, measured by kidney volume, proteinuria, eGFRcystC and mean creatinine clearance in the offspring. Additional experimental and longitudinal prospective studies are warranted to confirm this relationship, especially in Indigenous populations where the risk of renal disease is greater. PMID:29466283

Selfish evolution of cytonuclear hybrid incompatibility in Mimulus

PubMed Central

Finseth, Findley R.; Barr, Camille M.; Fishman, Lila

2016-01-01

Intraspecific coevolution between selfish elements and suppressors may promote interspecific hybrid incompatibility, but evidence of this process is rare. Here, we use genomic data to test alternative models for the evolution of cytonuclear hybrid male sterility in Mimulus. In hybrids between Iron Mountain (IM) Mimulus guttatus × Mimulus nasutus, two tightly linked M. guttatus alleles (Rf1/Rf2) each restore male fertility by suppressing a local mitochondrial male-sterility gene (IM-CMS). Unlike neutral models for the evolution of hybrid incompatibility loci, selfish evolution predicts that the Rf alleles experienced strong selection in the presence of IM-CMS. Using whole-genome sequences, we compared patterns of population-genetic variation in Rf at IM to a neighbouring population that lacks IM-CMS. Consistent with local selection in the presence of IM-CMS, the Rf region shows elevated FST, high local linkage disequilibrium and a distinct haplotype structure at IM, but not at Cone Peak (CP), suggesting a recent sweep in the presence of IM-CMS. In both populations, Rf2 exhibited lower polymorphism than other regions, but the low-diversity outliers were different between CP and IM. Our results confirm theoretical predictions of ubiquitous cytonuclear conflict in plants and provide a population-genetic mechanism for the evolution of a common form of hybrid incompatibility. PMID:27629037

Pro-natalist population policies in Czechoslovakia.

PubMed

Heitlinger, A

1976-03-01

Summary Given the high rate of women's employment and the lack of labour reserves, other than the natural replacement of the population, pro-natalist population policy in Czechoslovakia should be seen as a response to an anticipated shortage of labour. The rapid post-war decline in the birth rate has been caused by the greatly increased opportunity structure for women in education and employment, and by other policies favouring lower natality - rapid urbanization, inadequate provision of housing, insufficient investment in consumers' goods and services, low wages and relatively free availability of abortion. To reverse this undesirable population trend, the Czechoslovak government has adopted a more restrictive attitude towards abortion, lengthened paid maternity leave, increased family allowances and single grants given at childbirth and introduced the so-called maternity allowance, which is a direct monthly payment given by the state to mothers who wish to stay at home to raise a second or subsequent child, until the child is two years old. The time so spent counts towards the mother's retirement pension and other kinds of seniority, and her job is held open for her. These measures have contributed to the recent increase in the Czechoslovak birth rate, but more time is needed for the assessment of the long-term effectiveness of these measures.

Selfish evolution of cytonuclear hybrid incompatibility in Mimulus.

PubMed

Case, Andrea L; Finseth, Findley R; Barr, Camille M; Fishman, Lila

2016-09-14

Intraspecific coevolution between selfish elements and suppressors may promote interspecific hybrid incompatibility, but evidence of this process is rare. Here, we use genomic data to test alternative models for the evolution of cytonuclear hybrid male sterility in Mimulus In hybrids between Iron Mountain (IM) Mimulus guttatus × Mimulus nasutus, two tightly linked M. guttatus alleles (Rf1/Rf2) each restore male fertility by suppressing a local mitochondrial male-sterility gene (IM-CMS). Unlike neutral models for the evolution of hybrid incompatibility loci, selfish evolution predicts that the Rf alleles experienced strong selection in the presence of IM-CMS. Using whole-genome sequences, we compared patterns of population-genetic variation in Rf at IM to a neighbouring population that lacks IM-CMS. Consistent with local selection in the presence of IM-CMS, the Rf region shows elevated FST, high local linkage disequilibrium and a distinct haplotype structure at IM, but not at Cone Peak (CP), suggesting a recent sweep in the presence of IM-CMS. In both populations, Rf2 exhibited lower polymorphism than other regions, but the low-diversity outliers were different between CP and IM. Our results confirm theoretical predictions of ubiquitous cytonuclear conflict in plants and provide a population-genetic mechanism for the evolution of a common form of hybrid incompatibility. © 2016 The Author(s).

Population-based dietary approaches for the prevention of noncommunicable diseases.

PubMed

Somasundaram, Noel P; Kalupahana, Nishan Sudheera

2016-04-01

As the incidence of noncommunicable diseases such as diabetes continues to rise at an alarming rate in South-East Asia, it is imperative that urgent and population-wide strategies are adopted. The most important contributors to the rise in noncommunicable disease are a rise in mean caloric intake and a decrease in physical activity. The evidence for population-based dietary approaches to counter these factors is reviewed. Several structural and cohesive interdepartmental coordination efforts are required for effective implementation of prevention strategies. Since low- and middle-income countries may lack the frameworks for effective and integrated multi-stakeholder intervention, implementation of population-based dietary and physical-activity approaches may be delayed and may be too late for effective prevention in current at-risk cohorts. Evidence-based strategies to decrease energy intake and increase physical activity are now well established and their urgent adoption by Member States of the World Health Organization South-East Asia Region is essential. In the context of Sri Lanka, for example, it is recommended that the most effective and easy-to-implement interventions would be media campaigns, restrictions on advertisement of unhealthy foods, taxation of unhealthy foods, subsidies for production of healthy foods, and laws on nutrition labelling that introduce colour coding of packaged foods.

Bird on the wire: Landscape planning considering costs and benefits for bird populations coexisting with power lines.

PubMed

D'Amico, Marcello; Catry, Inês; Martins, Ricardo C; Ascensão, Fernando; Barrientos, Rafael; Moreira, Francisco

2018-02-24

Power-line grids are increasingly expanding worldwide, as well as their negative impacts on avifauna, namely the direct mortality through collision and electrocution, the reduction of breeding performance, and the barrier effect. On the other hand, some bird species can apparently benefit from the presence of power lines, for example perching for hunting purposes or nesting on electricity towers. In this perspective essay, we reviewed the scientific literature on both costs and benefits for avifauna coexisting with power lines. Overall, we detected a generalized lack of studies focusing on these costs or benefits at a population level. We suggest that a switch in research approach to a larger spatio-temporal scale would greatly improve our knowledge about the actual effects of power lines on bird populations. This research approach would facilitate suitable landscape planning encompassing both mitigation of costs and promotion of benefits for bird populations coexisting with power lines. For example, the strategic route planning of electricity infrastructures would limit collision risk or barrier effects for threatened bird populations. Concurrently, this strategic route planning would promote the range expansion of threatened populations of other bird species, by providing nesting structures in treeless but potentially suitable landscapes. We suggest establishing a collaborative dialogue among the scientific community, governments, and electricity companies, with the aim to produce a win-win scenario in which both biodiversity conservation and infrastructure development are integrated in a common strategy.

Estimation of the size of the female sex worker population in Rwanda using three different methods

PubMed Central

Kayitesi, Catherine; Gwiza, Aimé; Ruton, Hinda; Koleros, Andrew; Gupta, Neil; Balisanga, Helene; Riedel, David J; Nsanzimana, Sabin

2014-01-01

HIV prevalence is disproportionately high among female sex workers compared to the general population. Many African countries lack useful data on the size of female sex worker populations to inform national HIV programmes. A female sex worker size estimation exercise using three different venue-based methodologies was conducted among female sex workers in all provinces of Rwanda in August 2010. The female sex worker national population size was estimated using capture–recapture and enumeration methods, and the multiplier method was used to estimate the size of the female sex worker population in Kigali. A structured questionnaire was also used to supplement the data. The estimated number of female sex workers by the capture–recapture method was 3205 (95% confidence interval: 2998–3412). The female sex worker size was estimated at 3348 using the enumeration method. In Kigali, the female sex worker size was estimated at 2253 (95% confidence interval: 1916–2524) using the multiplier method. Nearly 80% of all female sex workers in Rwanda were found to be based in the capital, Kigali. This study provided a first-time estimate of the female sex worker population size in Rwanda using capture–recapture, enumeration, and multiplier methods. The capture–recapture and enumeration methods provided similar estimates of female sex worker in Rwanda. Combination of such size estimation methods is feasible and productive in low-resource settings and should be considered vital to inform national HIV programmes. PMID:25336306

Estimation of the size of the female sex worker population in Rwanda using three different methods.

PubMed

Mutagoma, Mwumvaneza; Kayitesi, Catherine; Gwiza, Aimé; Ruton, Hinda; Koleros, Andrew; Gupta, Neil; Balisanga, Helene; Riedel, David J; Nsanzimana, Sabin

2015-10-01

HIV prevalence is disproportionately high among female sex workers compared to the general population. Many African countries lack useful data on the size of female sex worker populations to inform national HIV programmes. A female sex worker size estimation exercise using three different venue-based methodologies was conducted among female sex workers in all provinces of Rwanda in August 2010. The female sex worker national population size was estimated using capture-recapture and enumeration methods, and the multiplier method was used to estimate the size of the female sex worker population in Kigali. A structured questionnaire was also used to supplement the data. The estimated number of female sex workers by the capture-recapture method was 3205 (95% confidence interval: 2998-3412). The female sex worker size was estimated at 3348 using the enumeration method. In Kigali, the female sex worker size was estimated at 2253 (95% confidence interval: 1916-2524) using the multiplier method. Nearly 80% of all female sex workers in Rwanda were found to be based in the capital, Kigali. This study provided a first-time estimate of the female sex worker population size in Rwanda using capture-recapture, enumeration, and multiplier methods. The capture-recapture and enumeration methods provided similar estimates of female sex worker in Rwanda. Combination of such size estimation methods is feasible and productive in low-resource settings and should be considered vital to inform national HIV programmes. © The Author(s) 2015.

Ancient Mitochondrial Capture as Factor Promoting Mitonuclear Discordance in Freshwater Fishes: A Case Study in the Genus Squalius (Actinopterygii, Cyprinidae) in Greece

PubMed Central

Vukić, Jasna; Šanda, Radek; Doadrio, Ignacio

2016-01-01

Hybridization and incomplete lineage sorting are common confounding factors in phylogeny and speciation resulting in mitonuclear disparity. Mitochondrial introgression, a particular case of hybridization, may, in extreme cases, lead to replacement of the mitochondrial genome of one species with that of another (mitochondrial capture). We investigated mitochondrial introgression involving two species of the cyprinid genus Squalius in the western Peloponnese region of Greece using molecular and morphological data. We found evidence of complete mitochondrial introgression of Squalius keadicus into two populations recognized as Squalius peloponensis from the Miras and Pamissos River basins and a divergence of mitochondrial genomes of S. keadicus from the Evrotas basin from that of the introgressed populations dating from the Pleistocene. Secondary contact among basins is a possible factor in connection of the species and the introgression event. Morphological analyses support the hypothesis of mitochondrial introgression, as S. keadicus was different from the other three populations recognized as S. peloponensis, although significant differences were found among the four populations. Isolation by geographical barriers arose during Pleistocene in the western Peloponnese were the source of the evolution of the two reciprocally monophyletic subclades found in the S. keadicus mitochondrial clade, and the morphological differences found among the four populations. Along with the lack of structure in the nuclear genome in the three populations ascribed to S. peloponensis, this suggests an incipient speciation process occurring in these Squalius species in the western Peloponnese. PMID:27906993

Survival in the Rockies of an endangered hybrid swarm from diverged caribou (Rangifer tarandus) lineages.

PubMed

McDevitt, Allan D; Mariani, Stefano; Hebblewhite, Mark; Decesare, Nicholas J; Morgantini, Luigi; Seip, Dale; Weckworth, Byron V; Musiani, Marco

2009-02-01

In North America, caribou (Rangifer tarandus) experienced diversification in separate refugia before the last glacial maximum. Geographical isolation produced the barren-ground caribou (Rangifer tarandus groenlandicus) with its distinctive migratory habits, and the woodland caribou (Rangifer tarandus caribou), which has sedentary behaviour and is now in danger of extinction. Herein we report on the phylogenetics, population structure, and migratory habits of caribou in the Canadian Rockies, utilizing molecular and spatial data for 223 individuals. Mitochondrial DNA analyses show the occurrence of two highly diverged lineages; the Beringian-Eurasian and North American lineages, while microsatellite data reveal that present-day Rockies' caribou populations have resulted from interbreeding between these diverged lineages. An ice-free corridor at the end of the last glaciation likely allowed, for the first time, for barren-ground caribou to migrate from the North and overlap with woodland caribou expanding from the South. The lack of correlation between nuclear and mitochondrial data may indicate that different environmental forces, which might also include human-caused habitat loss and fragmentation, are currently reshaping the population structure of this postglacial hybrid swarm. Furthermore, spatial ecological data show evidence of pronounced migratory behaviour within the study area, and suggest that the probability of being migratory may be higher in individual caribou carrying a Beringian-Eurasian haplotype which is mainly associated with the barren-ground subspecies. Overall, our analyses reveal an intriguing example of postglacial mixing of diverged lineages. In a landscape that is changing due to climatic and human-mediated factors, an understanding of these dynamics, both past and present, is essential for management and conservation of these populations.