Population and genomic lessons from genetic analysis of two Indian populations.

PubMed

Juyal, Garima; Mondal, Mayukh; Luisi, Pierre; Laayouni, Hafid; Sood, Ajit; Midha, Vandana; Heutink, Peter; Bertranpetit, Jaume; Thelma, B K; Casals, Ferran

2014-10-01

Indian demographic history includes special features such as founder effects, interpopulation segregation, complex social structure with a caste system and elevated frequency of consanguineous marriages. It also presents a higher frequency for some rare mendelian disorders and in the last two decades increased prevalence of some complex disorders. Despite the fact that India represents about one-sixth of the human population, deep genetic studies from this terrain have been scarce. In this study, we analyzed high-density genotyping and whole-exome sequencing data of a North and a South Indian population. Indian populations show higher differentiation levels than those reported between populations of other continents. In this work, we have analyzed its consequences, by specifically assessing the transferability of genetic markers from or to Indian populations. We show that there is limited genetic marker portability from available genetic resources such as HapMap or the 1,000 Genomes Project to Indian populations, which also present an excess of private rare variants. Conversely, tagSNPs show a high level of portability between the two Indian populations, in contrast to the common belief that North and South Indian populations are genetically very different. By estimating kinship from mates and consanguinity in our data from trios, we also describe different patterns of assortative mating and inbreeding in the two populations, in agreement with distinct mating preferences and social structures. In addition, this analysis has allowed us to describe genomic regions under recent adaptive selection, indicating differential adaptive histories for North and South Indian populations. Our findings highlight the importance of considering demography for design and analysis of genetic studies, as well as the need for extending human genetic variation catalogs to new populations and particularly to those with particular demographic histories.

Population viability analysis: using a modeling tool to assess the viability of tapir populations in fragmented landscapes.

PubMed

Medici, Emília Patrícia; Desbiez, Arnaud Leonard Jean

2012-12-01

A population viability analysis (PVA) was conducted of the lowland tapir populations in the Atlantic Forest of the Pontal do Paranapanema region, Brazil, including Morro do Diabo State Park (MDSP) and surrounding forest fragments. Results from the model projected that the population of 126 tapirs in MDSP is likely to persist over the next 100 years; however, 200 tapirs would be required to maintain a viable population. Sensitivity analysis showed that sub-adult mortality and adult mortality have the strongest influence on the dynamics of lowland tapir populations. High road-kill has a major impact on the MDSP tapir population and can lead to population extinction. Metapopulation modeling showed that dispersal of tapirs from MDSP to the surrounding fragments can be detrimental to the overall metapopulation, as fragments act as sinks. Nevertheless, the model showed that under certain conditions the maintenance of the metapopulation dynamics might be determinant for the persistence of tapirs in the region, particularly in the smaller fragments. The establishment of corridors connecting MDSP to the forest fragments models resulted in an increase in the stochastic growth rate, making tapirs more resilient to threats and catastrophes, but only if rates of mortality were not increased when using corridors. The PVA showed that the conservation of tapirs in the Pontal region depends on: the effective protection of MDSP; maintenance and, whenever possible, enhancement of the functional connectivity of the landscape, reducing mortality during dispersal and threats in the unprotected forest fragments; and neutralization of all threats affecting tapirs in the smaller forest fragments. © 2012 Wiley Publishing Asia Pty Ltd, ISZS and IOZ/CAS.

Imputation-Based Meta-Analysis of Severe Malaria in Three African Populations

PubMed Central

Band, Gavin; Le, Quang Si; Jostins, Luke; Pirinen, Matti; Kivinen, Katja; Jallow, Muminatou; Sisay-Joof, Fatoumatta; Bojang, Kalifa; Pinder, Margaret; Sirugo, Giorgio; Conway, David J.; Nyirongo, Vysaul; Kachala, David; Molyneux, Malcolm; Taylor, Terrie; Ndila, Carolyne; Peshu, Norbert; Marsh, Kevin; Williams, Thomas N.; Alcock, Daniel; Andrews, Robert; Edkins, Sarah; Gray, Emma; Hubbart, Christina; Jeffreys, Anna; Rowlands, Kate; Schuldt, Kathrin; Clark, Taane G.; Small, Kerrin S.; Teo, Yik Ying; Kwiatkowski, Dominic P.; Rockett, Kirk A.; Barrett, Jeffrey C.; Spencer, Chris C. A.

2013-01-01

Combining data from genome-wide association studies (GWAS) conducted at different locations, using genotype imputation and fixed-effects meta-analysis, has been a powerful approach for dissecting complex disease genetics in populations of European ancestry. Here we investigate the feasibility of applying the same approach in Africa, where genetic diversity, both within and between populations, is far more extensive. We analyse genome-wide data from approximately 5,000 individuals with severe malaria and 7,000 population controls from three different locations in Africa. Our results show that the standard approach is well powered to detect known malaria susceptibility loci when sample sizes are large, and that modern methods for association analysis can control the potential confounding effects of population structure. We show that pattern of association around the haemoglobin S allele differs substantially across populations due to differences in haplotype structure. Motivated by these observations we consider new approaches to association analysis that might prove valuable for multicentre GWAS in Africa: we relax the assumptions of SNP–based fixed effect analysis; we apply Bayesian approaches to allow for heterogeneity in the effect of an allele on risk across studies; and we introduce a region-based test to allow for heterogeneity in the location of causal alleles. PMID:23717212

Region-wide and ecotype-specific differences in demographic histories of threespine stickleback populations, estimated from whole genome sequences.

PubMed

Liu, Shenglin; Hansen, Michael M; Jacobsen, Magnus W

2016-10-01

We analysed 81 whole genome sequences of threespine sticklebacks from Pacific North America, Greenland and Northern Europe, representing 16 populations. Principal component analysis of nuclear SNPs grouped populations according to geographical location, with Pacific populations being more divergent from each other relative to European and Greenlandic populations. Analysis of mitogenome sequences showed Northern European populations to represent a single phylogeographical lineage, whereas Greenlandic and particularly Pacific populations showed admixture between lineages. We estimated demographic history using a genomewide coalescence with recombination approach. The Pacific populations showed gradual population expansion starting >100 Kya, possibly reflecting persistence in cryptic refuges near the present distributional range, although we do not rule out possible influence of ancient admixture. Sharp population declines ca. 14-15 Kya were suggested to reflect founding of freshwater populations by marine ancestors. In Greenland and Northern Europe, demographic expansion started ca. 20-25 Kya coinciding with the end of the Last Glacial Maximum. In both regions, marine and freshwater populations started to show different demographic trajectories ca. 8-9 Kya, suggesting that this was the time of recolonization. In Northern Europe, this estimate was surprisingly late, but found support in subfossil evidence for presence of several freshwater fish species but not sticklebacks 12 Kya. The results demonstrate distinctly different demographic histories across geographical regions with potential consequences for adaptive processes. They also provide empirical support for previous assumptions about freshwater populations being founded independently from large, coherent marine populations, a key element in the Transporter Hypothesis invoked to explain the widespread occurrence of parallel evolution across freshwater stickleback populations. © 2016 John Wiley & Sons Ltd.

Population Structure, Genetic Diversity and Molecular Marker-Trait Association Analysis for High Temperature Stress Tolerance in Rice

PubMed Central

Barik, Saumya Ranjan; Sahoo, Ambika; Mohapatra, Sudipti; Nayak, Deepak Kumar; Mahender, Anumalla; Meher, Jitandriya; Anandan, Annamalai

2016-01-01

Rice exhibits enormous genetic diversity, population structure and molecular marker-traits associated with abiotic stress tolerance to high temperature stress. A set of breeding lines and landraces representing 240 germplasm lines were studied. Based on spikelet fertility percent under high temperature, tolerant genotypes were broadly classified into four classes. Genetic diversity indicated a moderate level of genetic base of the population for the trait studied. Wright’s F statistic estimates showed a deviation of Hardy-Weinberg expectation in the population. The analysis of molecular variance revealed 25 percent variation between population, 61 percent among individuals and 14 percent within individuals in the set. The STRUCTURE analysis categorized the entire population into three sub-populations and suggested that most of the landraces in each sub-population had a common primary ancestor with few admix individuals. The composition of materials in the panel showed the presence of many QTLs representing the entire genome for the expression of tolerance. The strongly associated marker RM547 tagged with spikelet fertility under stress and the markers like RM228, RM205, RM247, RM242, INDEL3 and RM314 indirectly controlling the high temperature stress tolerance were detected through both mixed linear model and general linear model TASSEL analysis. These markers can be deployed as a resource for marker-assisted breeding program of high temperature stress tolerance. PMID:27494320

Population Structure, Genetic Diversity and Molecular Marker-Trait Association Analysis for High Temperature Stress Tolerance in Rice.

PubMed

Pradhan, Sharat Kumar; Barik, Saumya Ranjan; Sahoo, Ambika; Mohapatra, Sudipti; Nayak, Deepak Kumar; Mahender, Anumalla; Meher, Jitandriya; Anandan, Annamalai; Pandit, Elssa

2016-01-01

Rice exhibits enormous genetic diversity, population structure and molecular marker-traits associated with abiotic stress tolerance to high temperature stress. A set of breeding lines and landraces representing 240 germplasm lines were studied. Based on spikelet fertility percent under high temperature, tolerant genotypes were broadly classified into four classes. Genetic diversity indicated a moderate level of genetic base of the population for the trait studied. Wright's F statistic estimates showed a deviation of Hardy-Weinberg expectation in the population. The analysis of molecular variance revealed 25 percent variation between population, 61 percent among individuals and 14 percent within individuals in the set. The STRUCTURE analysis categorized the entire population into three sub-populations and suggested that most of the landraces in each sub-population had a common primary ancestor with few admix individuals. The composition of materials in the panel showed the presence of many QTLs representing the entire genome for the expression of tolerance. The strongly associated marker RM547 tagged with spikelet fertility under stress and the markers like RM228, RM205, RM247, RM242, INDEL3 and RM314 indirectly controlling the high temperature stress tolerance were detected through both mixed linear model and general linear model TASSEL analysis. These markers can be deployed as a resource for marker-assisted breeding program of high temperature stress tolerance.

[Spatial distribution pattern and fractal analysis of Larix chinensis populations in Qinling Mountain].

PubMed

Guo, Hua; Wang, Xiaoan; Xiao, Yaping

2005-02-01

In this paper, the fractal characters of Larix chinensis populations in Qinling Mountain were studied by contiguous grid quadrate sampling method and by boxing-counting dimension and information dimension. The results showed that the high boxing-counting dimension (1.8087) and information dimension (1.7931) reflected a higher spatial occupational degree of L. chinensis populations. Judged by the dispersal index and Morisita's pattern index, L. chinensis populations clumped at three different age stages (0-25, 25-50 and over 50 years). From Greig-Smiths' mean variance analysis, the figure of pattern scale showed that L. chinensis populations clumped in 128 m2 and 512 m2, and the different age groups clumped in different scales. The pattern intensities decreased with increasing age, and tended to reduce with increasing area when detected by Kershaw's PI index. The spatial pattern characters of L. chinensis populations may be their responses to environmental factors.

Genetic Variation of North American Triatomines (Insecta: Hemiptera: Reduviidae): Initial Divergence between Species and Populations of Chagas Disease Vector

PubMed Central

Espinoza, Bertha; Martínez-Ibarra, Jose Alejandro; Villalobos, Guiehdani; De La Torre, Patricia; Laclette, Juan Pedro; Martínez-Hernández, Fernando

2013-01-01

The triatomines vectors of Trypanosoma cruzi are principal factors in acquiring Chagas disease. For this reason, increased knowledge of domestic transmission of T. cruzi and control of its insect vectors is necessary. To contribute to genetic knowledge of North America Triatominae species, we studied genetic variations and conducted phylogenetic analysis of different triatomines species of epidemiologic importance. Our analysis showed high genetic variations between different geographic populations of Triatoma mexicana, Meccus longipennis, M. mazzottii, M. picturatus, and T. dimidiata species, suggested initial divergence, hybridation, or classifications problems. In contrast, T. gerstaeckeri, T. bolivari, and M. pallidipennis populations showed few genetics variations. Analysis using cytochrome B and internal transcribed spacer 2 gene sequences indicated that T. bolivari is closely related to the Rubrofasciata complex and not to T. dimidiata. Triatoma brailovskyi and T. gerstaeckeri showed a close relationship with Dimidiata and Phyllosoma complexes. PMID:23249692

Genetic diversity of Pinus nigra Arn. populations in Southern Spain and Northern Morocco revealed by inter-simple sequence repeat profiles.

PubMed

Rubio-Moraga, Angela; Candel-Perez, David; Lucas-Borja, Manuel E; Tiscar, Pedro A; Viñegla, Benjamin; Linares, Juan C; Gómez-Gómez, Lourdes; Ahrazem, Oussama

2012-01-01

Eight Pinus nigra Arn. populations from Southern Spain and Northern Morocco were examined using inter-simple sequence repeat markers to characterize the genetic variability amongst populations. Pair-wise population genetic distance ranged from 0.031 to 0.283, with a mean of 0.150 between populations. The highest inter-population average distance was between PaCU from Cuenca and YeCA from Cazorla, while the lowest distance was between TaMO from Morocco and MA Sierra Mágina populations. Analysis of molecular variance (AMOVA) and Nei's genetic diversity analyses revealed higher genetic variation within the same population than among different populations. Genetic differentiation (Gst) was 0.233. Cuenca showed the highest Nei's genetic diversity followed by the Moroccan region, Sierra Mágina, and Cazorla region. However, clustering of populations was not in accordance with their geographical locations. Principal component analysis showed the presence of two major groups-Group 1 contained all populations from Cuenca while Group 2 contained populations from Cazorla, Sierra Mágina and Morocco-while Bayesian analysis revealed the presence of three clusters. The low genetic diversity observed in PaCU and YeCA is probably a consequence of inappropriate management since no estimation of genetic variability was performed before the silvicultural treatments. Data indicates that the inter-simple sequence repeat (ISSR) method is sufficiently informative and powerful to assess genetic variability among populations of P. nigra.

Genetic Diversity of Pinus nigra Arn. Populations in Southern Spain and Northern Morocco Revealed By Inter-Simple Sequence Repeat Profiles †

PubMed Central

Rubio-Moraga, Angela; Candel-Perez, David; Lucas-Borja, Manuel E.; Tiscar, Pedro A.; Viñegla, Benjamin; Linares, Juan C.; Gómez-Gómez, Lourdes; Ahrazem, Oussama

2012-01-01

Eight Pinus nigra Arn. populations from Southern Spain and Northern Morocco were examined using inter-simple sequence repeat markers to characterize the genetic variability amongst populations. Pair-wise population genetic distance ranged from 0.031 to 0.283, with a mean of 0.150 between populations. The highest inter-population average distance was between PaCU from Cuenca and YeCA from Cazorla, while the lowest distance was between TaMO from Morocco and MA Sierra Mágina populations. Analysis of molecular variance (AMOVA) and Nei’s genetic diversity analyses revealed higher genetic variation within the same population than among different populations. Genetic differentiation (Gst) was 0.233. Cuenca showed the highest Nei’s genetic diversity followed by the Moroccan region, Sierra Mágina, and Cazorla region. However, clustering of populations was not in accordance with their geographical locations. Principal component analysis showed the presence of two major groups—Group 1 contained all populations from Cuenca while Group 2 contained populations from Cazorla, Sierra Mágina and Morocco—while Bayesian analysis revealed the presence of three clusters. The low genetic diversity observed in PaCU and YeCA is probably a consequence of inappropriate management since no estimation of genetic variability was performed before the silvicultural treatments. Data indicates that the inter-simple sequence repeat (ISSR) method is sufficiently informative and powerful to assess genetic variability among populations of P. nigra. PMID:22754321

Comparative and Familial Analysis of Handedness in Great Apes

PubMed Central

Hopkins, William D.

2007-01-01

Historically, population-level handedness has been considered a hallmark of human evolution. Whether nonhuman primates exhibit population-level handedness remains a topic of considerable debate. This paper summarizes published data on handedness in great apes. Comparative analysis indicated that chimpanzees and bonobos show population-level right handedness, whereas gorillas and orangutans do not. All ape species showed evidence of population-level handedness when considering specific tasks. Familial analyses in chimpanzees indicated that offspring and maternal (but not paternal) handedness was significantly positively correlated, but this finding was contingent upon the classification criteria used to evaluate hand preference. Overall, the proportion of right handedness is lower in great apes compared with humans, and various methodological and theoretical explanations for this discrepancy are discussed. PMID:16822166

Estimating the age of Hb G-Coushatta [β22(B4)Glu→Ala] mutation by haplotypes of β-globin gene cluster in Denizli, Turkey.

PubMed

Ozturk, Onur; Arikan, Sanem; Atalay, Ayfer; Atalay, Erol O

2018-05-01

Hb G-Coushatta variant was reported from various populations' parts of the world such as Thai, Korea, Algeria, Thailand, China, Japan and Turkey. In our study, we aimed to discuss the possible historical relationships of the Hb G-Coushatta mutation with the possible migration routes of the world. For this purpose, associated haplotypes were determined using polymorphic loci in the beta globin gene cluster of hemoglobin G-Coushatta and normal populations in Denizli, Turkey. We performed statistical analysis such as haplotype analysis, Hardy-Weinberg equilibrium, measurement of genetic diversity and population differentiation parameters, analysis of molecular variance using F-statistics, historical-demographic analyses, mismatch distribution analysis of both populations and applied the test statistics in Arlequin ver. 3.5 software program. The diversity of haplotypes has been shown to indicate different genetic origins for two populations. However, AMOVA results, molecular diversity parameters and population demographic expansion times showed that the Hb G-Coushatta mutation develops on the normal population gene pool. Our estimated τ values showed the average time since the demographic expansion for normal and Hb G-Coushatta populations ranged from approximately 42,000 to 38,000 ybp, respectively. Our data suggest that Hb G-Coushatta population originate in normal population in Denizli, Turkey. These results support the hypothesis that the multiple origin of Hb G-Coushatta and indicate that mutation may have been triggered the formation of new variants on beta globin haplotypes. © 2018 The Authors. Molecular Genetics & Genomic Medicine published by Wiley Periodicals, Inc.

Molecular phylogenetic analysis of Chinese indigenous blue-shelled chickens inferred from whole genomic region of the SLCO1B3 gene.

PubMed

Dalirsefat, Seyed Benyamin; Dong, Xianggui; Deng, Xuemei

2015-08-01

In total, 246 individuals from 8 Chinese indigenous blue- and brown-shelled chicken populations (Yimeng Blue, Wulong Blue, Lindian Blue, Dongxiang Blue, Lushi Blue, Jingmen Blue, Dongxiang Brown, and Lushi Brown) were genotyped for 21 SNP markers from the SLCO1B3 gene to evaluate phylogenetic relationships. As a representative of nonblue-shelled breeds, White Leghorn was included in the study for reference. A high proportion of SNP polymorphism was observed in Chinese chicken populations, ranging from 89% in Jingmen Blue to 100% in most populations, with a mean of 95% across all populations. The White Leghorn breed showed the lowest polymorphism, accounting for 43% of total SNPs. The mean expected heterozygosity varied from 0.11 in Dongxiang Blue to 0.46 in Yimeng Blue. Analysis of molecular variation (AMOVA) for 2 groups of Chinese chickens based on eggshell color type revealed 52% within-group and 43% between-group variations of the total genetic variation. As expected, FST and Reynolds' genetic distance were greatest between White Leghorn and Chinese chicken populations, with average values of 0.40 and 0.55, respectively. The first and second principal coordinates explained approximately 92% of the total variation and supported the clustering of the populations according to their eggshell color type and historical origins. STRUCTURE analysis showed a considerable source of variation among populations for the clustering into blue-shelled and nonblue-shelled chicken populations. The low estimation of genetic differentiation (FST) between Chinese chicken populations is possibly due to a common historical origin and high gene flow. Remarkably similar population classifications were obtained with all methods used in the study. Aligning endogenous avian retroviral (EAV)-HP insertion sequences showed no difference among the blue-shelled chickens. © 2015 Poultry Science Association Inc.

Population subdivision and molecular sequence variation: theory and analysis of Drosophila ananassae data.

PubMed

Vogl, Claus; Das, Aparup; Beaumont, Mark; Mohanty, Sujata; Stephan, Wolfgang

2003-11-01

Population subdivision complicates analysis of molecular variation. Even if neutrality is assumed, three evolutionary forces need to be considered: migration, mutation, and drift. Simplification can be achieved by assuming that the process of migration among and drift within subpopulations is occurring fast compared to mutation and drift in the entire population. This allows a two-step approach in the analysis: (i) analysis of population subdivision and (ii) analysis of molecular variation in the migrant pool. We model population subdivision using an infinite island model, where we allow the migration/drift parameter Theta to vary among populations. Thus, central and peripheral populations can be differentiated. For inference of Theta, we use a coalescence approach, implemented via a Markov chain Monte Carlo (MCMC) integration method that allows estimation of allele frequencies in the migrant pool. The second step of this approach (analysis of molecular variation in the migrant pool) uses the estimated allele frequencies in the migrant pool for the study of molecular variation. We apply this method to a Drosophila ananassae sequence data set. We find little indication of isolation by distance, but large differences in the migration parameter among populations. The population as a whole seems to be expanding. A population from Bogor (Java, Indonesia) shows the highest variation and seems closest to the species center.

Self-fertilization is the main sexual reproduction mechanism in native wine yeast populations.

PubMed

Cubillos, Francisco A; Vásquez, Claudia; Faugeron, Sylvain; Ganga, Angélica; Martínez, Claudio

2009-01-01

Saccharomyces cerevisiae is a model eukaryotic organism for classical genetics and genomics, and yet its ecology is still largely unknown. In this work, a population genetic analysis was performed on five yeast populations isolated from wine-making areas with different enological practices using simple sequence repeats and restriction fragment length polymorphism of mitochondrial DNA as molecular markers on 292 strains. In accordance with other studies, genome size estimation suggests that native S. cerevisiae strains are mainly homothallic and diploids. Analysis of mtDNA data showed that yeast populations from nonindustrial areas have 40% higher genetic diversity than populations isolated from industrial areas, demonstrating that industrial enological practices are likely to affect native yeast populations negatively by reducing its biodiversity. On the other hand, genetic differentiation analysis based on their microsatellite showed no correlation between genetic and geographic distance and a nonsignificant value when a Mantel test was applied. Finally, in the five populations studied, positive inbreeding (F(is)) values from 0.4 to 0.75, a low but significant level of linkage disequilibrium and a high number of multilocus genotypes were detected. These results strongly advocate that sexual reproduction is frequent enough to erase clonal signature in natural populations and that self-fertilization is the main mating system.

Analysis of the population genetic structure of Hb D-Los Angeles [β121 (GH4) Glu→Gln GAA→CAA] in Denizli, Turkey; genetic diversity, historical demography and estimation of the mutation rates based on haplotype variation.

PubMed

Ozturk, Onur; Arikan, Sanem; Atalay, Ayfer; Atalay, Erol O

2016-07-01

Understanding the genetic origin of the Hb D-Los Angeles hemoglobin may elucidate population interactions such as movements, migrations, and environmental effects on mutation mechanisms in human biology throughout history. Our study aimed to understand the genetic origin of Hb D-Los Angeles based on haplotype data, observed in the Denizli province of Turkey. We studied DNA samples from 40 unrelated patients with abnormal hemoglobin Hb D-Los Angeles and 59 unrelated healthy subjects from our DNA bank. Possible associated haplotypes, HWE, genetic diversity and population differentiation, population genetic structure analysis and historical-demographic analysis for the two populations were determined by Arlequin ver. 3.5. Molecular diversity results from the two populations show that both populations are genetically similar as far as development and expansion during the historical period. Historical gene flow results show high gene flow between the two populations. SSD and rg tests failed to reject the null hypothesis of population expansion which is consistent with unimodal distribution. Our estimated τ values show that the average time since the demographic expansion for normal and Hb D-Los Angeles populations ranged from approximately 42,000-38,000 ybp, respectively. Our data suggest that the Hb D-Los Angeles population originated within the normal population in Denizli, Turkey. Our results support the hypothesis that the Hb D-Los Angeles mutation may have originated in the Mediterranean area, independent from other populations such as India and China. The evaluation of such data may contribute valuable information to anthropological, paleoclimatic, archaeological, and phylogeographical approaches to human biology throughout the historical period. Am. J. Hum. Biol. 28:476-483, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Genetic structure in the Sherpa and neighboring Nepalese populations.

PubMed

Cole, Amy M; Cox, Sean; Jeong, Choongwon; Petousi, Nayia; Aryal, Dhana R; Droma, Yunden; Hanaoka, Masayuki; Ota, Masao; Kobayashi, Nobumitsu; Gasparini, Paolo; Montgomery, Hugh; Robbins, Peter; Di Rienzo, Anna; Cavalleri, Gianpiero L

2017-01-19

We set out to describe the fine-scale population structure across the Eastern region of Nepal. To date there is relatively little known about the genetic structure of the Sherpa residing in Nepal and their genetic relationship with the Nepalese. We assembled dense genotype data from a total of 1245 individuals representing Nepal and a variety of different populations resident across the greater Himalayan region including Tibet, China, India, Pakistan, Kazakhstan, Uzbekistan, Tajikistan and Kirghizstan. We performed analysis of principal components, admixture and homozygosity. We identified clear substructure across populations resident in the Himalayan arc, with genetic structure broadly mirroring geographical features of the region. Ethnic subgroups within Nepal show distinct genetic structure, on both admixture and principal component analysis. We detected differential proportions of ancestry from northern Himalayan populations across Nepalese subgroups, with the Nepalese Rai, Magar and Tamang carrying the greatest proportions of Tibetan ancestry. We show that populations dwelling on the Himalayan plateau have had a clear impact on the Northern Indian gene pool. We illustrate how the Sherpa are a remarkably isolated population, with little gene flow from surrounding Nepalese populations.

[Spatial point pattern analysis of main trees and flowering Fargesia qinlingensis in Abies fargesii forests in Mt Taibai of the Qinling Mountains, China].

PubMed

Li, Guo Chun; Song, Hua Dong; Li, Qi; Bu, Shu Hai

2017-11-01

In Abies fargesii forests of the giant panda's habitats in Mt. Taibai, the spatial distribution patterns and interspecific associations of main tree species and their spatial associations with the understory flowering Fargesia qinlingensis were analyzed at multiple scales by univariate and bivaria-te O-ring function in point pattern analysis. The results showed that in the A. fargesii forest, the number of A. fargesii was largest but its population structure was in decline. The population of Betula platyphylla was relatively young, with a stable population structure, while the population of B. albo-sinensis declined. The three populations showed aggregated distributions at small scales and gradually showed random distributions with increasing spatial scales. Spatial associations among tree species were mainly showed at small scales and gradually became not spatially associated with increasing scale. A. fargesii and B. platyphylla were positively associated with flowering F. qinlingensis at large and medium scales, whereas B. albo-sinensis showed negatively associated with flowering F. qinlingensis at large and medium scales. The interaction between trees and F. qinlingensis in the habitats of giant panda promoted the dynamic succession and development of forests, which changed the environment of giant panda's habitats in Qinling.

Comparative and familial analysis of handedness in great apes.

PubMed

Hopkins, William D

2006-07-01

Historically, population-level handedness has been considered a hallmark of human evolution. Whether nonhuman primates exhibit population-level handedness remains a topic of considerable debate. This paper summarizes published data on handedness in great apes. Comparative analysis indicated that chimpanzees and bonobos show population-level right handedness, whereas gorillas and orangutans do not. All ape species showed evidence of population-level handedness when considering specific tasks. Familial analyses in chimpanzees indicated that offspring and maternal (but not paternal) handedness was significantly positively correlated, but this finding was contingent upon the classification criteria used to evaluate hand preference. Overall, the proportion of right handedness is lower in great apes compared with humans, and various methodological and theoretical explanations for this discrepancy are discussed. Copyright (c) 2006 APA, all rights reserved.

The structure of cross-cultural musical diversity.

PubMed

Rzeszutek, Tom; Savage, Patrick E; Brown, Steven

2012-04-22

Human cultural traits, such as languages, musics, rituals and material objects, vary widely across cultures. However, the majority of comparative analyses of human cultural diversity focus on between-culture variation without consideration for within-culture variation. In contrast, biological approaches to genetic diversity, such as the analysis of molecular variance (AMOVA) framework, partition genetic diversity into both within- and between-population components. We attempt here for the first time to quantify both components of cultural diversity by applying the AMOVA model to music. By employing this approach with 421 traditional songs from 16 Austronesian-speaking populations, we show that the vast majority of musical variability is due to differences within populations rather than differences between. This demonstrates a striking parallel to the structure of genetic diversity in humans. A neighbour-net analysis of pairwise population musical divergence shows a large amount of reticulation, indicating the pervasive occurrence of borrowing and/or convergent evolution of musical features across populations.

The structure of cross-cultural musical diversity

PubMed Central

Rzeszutek, Tom; Savage, Patrick E.; Brown, Steven

2012-01-01

Human cultural traits, such as languages, musics, rituals and material objects, vary widely across cultures. However, the majority of comparative analyses of human cultural diversity focus on between-culture variation without consideration for within-culture variation. In contrast, biological approaches to genetic diversity, such as the analysis of molecular variance (AMOVA) framework, partition genetic diversity into both within- and between-population components. We attempt here for the first time to quantify both components of cultural diversity by applying the AMOVA model to music. By employing this approach with 421 traditional songs from 16 Austronesian-speaking populations, we show that the vast majority of musical variability is due to differences within populations rather than differences between. This demonstrates a striking parallel to the structure of genetic diversity in humans. A neighbour-net analysis of pairwise population musical divergence shows a large amount of reticulation, indicating the pervasive occurrence of borrowing and/or convergent evolution of musical features across populations. PMID:22072606

Genetic analysis of Mexican Criollo cattle populations.

PubMed

Ulloa-Arvizu, R; Gayosso-Vázquez, A; Ramos-Kuri, M; Estrada, F J; Montaño, M; Alonso, R A

2008-10-01

The objective of this study was to evaluate the genetic structure of Mexican Criollo cattle populations using microsatellite genetic markers. DNA samples were collected from 168 animals from four Mexican Criollo cattle populations, geographically isolated in remote areas of Sierra Madre Occidental (West Highlands). Also were included samples from two breeds with Iberian origin: the fighting bull (n = 24) and the milking central American Criollo (n = 24) and one Asiatic breed: Guzerat (n = 32). Genetic analysis consisted of the estimation of the genetic diversity in each population by the allele number and the average expected heterozygosity found in nine microsatellite loci. Furthermore, genetic relationships among the populations were defined by their genetic distances. Our data shows that Mexican cattle populations have a relatively high level of genetic diversity based either on the mean number of alleles (10.2-13.6) and on the expected heterozygosity (0.71-0.85). The degree of observed homozygosity within the Criollo populations was remarkable and probably caused by inbreeding (reduced effective population size) possibly due to reproductive structure within populations. Our data shows that considerable genetic differentiation has been occurred among the Criollo cattle populations in different regions of Mexico.

Large-scale replication and heterogeneity in Parkinson disease genetic loci

PubMed Central

Ioannidis, John P.A.; Aasly, Jan O.; Annesi, Grazia; Brice, Alexis; Van Broeckhoven, Christine; Bertram, Lars; Bozi, Maria; Crosiers, David; Clarke, Carl; Facheris, Maurizio; Farrer, Matthew; Garraux, Gaetan; Gispert, Suzana; Auburger, Georg; Vilariño-Güell, Carles; Hadjigeorgiou, Georgios M.; Hicks, Andrew A.; Hattori, Nobutaka; Jeon, Beom; Lesage, Suzanne; Lill, Christina M.; Lin, Juei-Jueng; Lynch, Timothy; Lichtner, Peter; Lang, Anthony E.; Mok, Vincent; Jasinska-Myga, Barbara; Mellick, George D.; Morrison, Karen E.; Opala, Grzegorz; Pramstaller, Peter P.; Pichler, Irene; Park, Sung Sup; Quattrone, Aldo; Rogaeva, Ekaterina; Ross, Owen A.; Stefanis, Leonidas; Stockton, Joanne D.; Satake, Wataru; Silburn, Peter A.; Theuns, Jessie; Tan, Eng-King; Toda, Tatsushi; Tomiyama, Hiroyuki; Uitti, Ryan J.; Wirdefeldt, Karin; Wszolek, Zbigniew; Xiromerisiou, Georgia; Yueh, Kuo-Chu; Zhao, Yi; Gasser, Thomas; Maraganore, Demetrius; Krüger, Rejko

2012-01-01

Objective: Eleven genetic loci have reached genome-wide significance in a recent meta-analysis of genome-wide association studies in Parkinson disease (PD) based on populations of Caucasian descent. The extent to which these genetic effects are consistent across different populations is unknown. Methods: Investigators from the Genetic Epidemiology of Parkinson's Disease Consortium were invited to participate in the study. A total of 11 SNPs were genotyped in 8,750 cases and 8,955 controls. Fixed as well as random effects models were used to provide the summary risk estimates for these variants. We evaluated between-study heterogeneity and heterogeneity between populations of different ancestry. Results: In the overall analysis, single nucleotide polymorphisms (SNPs) in 9 loci showed significant associations with protective per-allele odds ratios of 0.78–0.87 (LAMP3, BST1, and MAPT) and susceptibility per-allele odds ratios of 1.14–1.43 (STK39, GAK, SNCA, LRRK2, SYT11, and HIP1R). For 5 of the 9 replicated SNPs there was nominally significant between-site heterogeneity in the effect sizes (I2 estimates ranged from 39% to 48%). Subgroup analysis by ethnicity showed significantly stronger effects for the BST1 (rs11724635) in Asian vs Caucasian populations and similar effects for SNCA, LRRK2, LAMP3, HIP1R, and STK39 in Asian and Caucasian populations, while MAPT rs2942168 and SYT11 rs34372695 were monomorphic in the Asian population, highlighting the role of population-specific heterogeneity in PD. Conclusion: Our study allows insight to understand the distribution of newly identified genetic factors contributing to PD and shows that large-scale evaluation in diverse populations is important to understand the role of population-specific heterogeneity. Neurology® 2012;79:659–667 PMID:22786590

Large-scale replication and heterogeneity in Parkinson disease genetic loci.

PubMed

Sharma, Manu; Ioannidis, John P A; Aasly, Jan O; Annesi, Grazia; Brice, Alexis; Van Broeckhoven, Christine; Bertram, Lars; Bozi, Maria; Crosiers, David; Clarke, Carl; Facheris, Maurizio; Farrer, Matthew; Garraux, Gaetan; Gispert, Suzana; Auburger, Georg; Vilariño-Güell, Carles; Hadjigeorgiou, Georgios M; Hicks, Andrew A; Hattori, Nobutaka; Jeon, Beom; Lesage, Suzanne; Lill, Christina M; Lin, Juei-Jueng; Lynch, Timothy; Lichtner, Peter; Lang, Anthony E; Mok, Vincent; Jasinska-Myga, Barbara; Mellick, George D; Morrison, Karen E; Opala, Grzegorz; Pramstaller, Peter P; Pichler, Irene; Park, Sung Sup; Quattrone, Aldo; Rogaeva, Ekaterina; Ross, Owen A; Stefanis, Leonidas; Stockton, Joanne D; Satake, Wataru; Silburn, Peter A; Theuns, Jessie; Tan, Eng-King; Toda, Tatsushi; Tomiyama, Hiroyuki; Uitti, Ryan J; Wirdefeldt, Karin; Wszolek, Zbigniew; Xiromerisiou, Georgia; Yueh, Kuo-Chu; Zhao, Yi; Gasser, Thomas; Maraganore, Demetrius; Krüger, Rejko

2012-08-14

Eleven genetic loci have reached genome-wide significance in a recent meta-analysis of genome-wide association studies in Parkinson disease (PD) based on populations of Caucasian descent. The extent to which these genetic effects are consistent across different populations is unknown. Investigators from the Genetic Epidemiology of Parkinson's Disease Consortium were invited to participate in the study. A total of 11 SNPs were genotyped in 8,750 cases and 8,955 controls. Fixed as well as random effects models were used to provide the summary risk estimates for these variants. We evaluated between-study heterogeneity and heterogeneity between populations of different ancestry. In the overall analysis, single nucleotide polymorphisms (SNPs) in 9 loci showed significant associations with protective per-allele odds ratios of 0.78-0.87 (LAMP3, BST1, and MAPT) and susceptibility per-allele odds ratios of 1.14-1.43 (STK39, GAK, SNCA, LRRK2, SYT11, and HIP1R). For 5 of the 9 replicated SNPs there was nominally significant between-site heterogeneity in the effect sizes (I(2) estimates ranged from 39% to 48%). Subgroup analysis by ethnicity showed significantly stronger effects for the BST1 (rs11724635) in Asian vs Caucasian populations and similar effects for SNCA, LRRK2, LAMP3, HIP1R, and STK39 in Asian and Caucasian populations, while MAPT rs2942168 and SYT11 rs34372695 were monomorphic in the Asian population, highlighting the role of population-specific heterogeneity in PD. Our study allows insight to understand the distribution of newly identified genetic factors contributing to PD and shows that large-scale evaluation in diverse populations is important to understand the role of population-specific heterogeneity.

Estimation of the genetic diversity in tetraploid alfalfa populations based on RAPD markers for breeding purposes.

PubMed

Nagl, Nevena; Taski-Ajdukovic, Ksenija; Barac, Goran; Baburski, Aleksandar; Seccareccia, Ivana; Milic, Dragan; Katic, Slobodan

2011-01-01

Alfalfa is an autotetraploid, allogamous and heterozygous forage legume, whose varieties are synthetic populations. Due to the complex nature of the species, information about genetic diversity of germplasm used in any alfalfa breeding program is most beneficial. The genetic diversity of five alfalfa varieties, involved in progeny tests at Institute of Field and Vegetable Crops, was characterized based on RAPD markers. A total of 60 primers were screened, out of which 17 were selected for the analysis of genetic diversity. A total of 156 polymorphic bands were generated, with 10.6 bands per primer. Number and percentage of polymorphic loci, effective number of alleles, expected heterozygosity and Shannon's information index were used to estimate genetic variation. Variety Zuzana had the highest values for all tested parameters, exhibiting the highest level of variation, whereas variety RSI 20 exhibited the lowest. Analysis of molecular variance (AMOVA) showed that 88.39% of the total genetic variation was attributed to intra-varietal variance. The cluster analysis for individual samples and varieties revealed differences in their population structures: variety Zuzana showed a very high level of genetic variation, Banat and Ghareh were divided in subpopulations, while Pecy and RSI 20 were relatively uniform. Ways of exploiting the investigated germplasm in the breeding programs are suggested in this paper, depending on their population structure and diversity. The RAPD analysis shows potential to be applied in analysis of parental populations in semi-hybrid alfalfa breeding program in both, development of new homogenous germplasm, and identification of promising, complementary germplasm.

Pollen flow in the wildservice tree, Sorbus torminalis (L.) Crantz. I. Evaluating the paternity analysis procedure in continuous populations.

PubMed

Oddou-Muratorio, S; Houot, M-L; Demesure-Musch, B; Austerlitz, F

2003-12-01

The joint development of polymorphic molecular markers and paternity analysis methods provides new approaches to investigate ongoing patterns of pollen flow in natural plant populations. However, paternity studies are hindered by false paternity assignment and the nondetection of true fathers. To gauge the risk of these two types of errors, we performed a simulation study to investigate the impact on paternity analysis of: (i) the assumed values for the size of the breeding male population (NBMP), and (ii) the rate of scoring error in genotype assessment. Our simulations were based on microsatellite data obtained from a natural population of the entomophilous wild service tree, Sorbus torminalis (L.) Crantz. We show that an accurate estimate of NBMP is required to minimize both types of errors, and we assess the reliability of a technique used to estimate NBMP based on parent-offspring genetic data. We then show that scoring errors in genotype assessment only slightly affect the assessment of paternity relationships, and conclude that it is generally better to neglect the scoring error rate in paternity analyses within a nonisolated population.

Transgenerational Adaptation to Pollution Changes Energy Allocation in Populations of Nematodes.

PubMed

Goussen, Benoit; Péry, Alexandre R R; Bonzom, Jean-Marc; Beaudouin, Rémy

2015-10-20

Assessing the evolutionary responses of long-term exposed populations requires multigeneration ecotoxicity tests. However, the analysis of the data from these tests is not straightforward. Mechanistic models allow the in-depth analysis of the variation of physiological traits over many generations, by quantifying the trend of the physiological and toxicological parameters of the model. In the present study, a bioenergetic mechanistic model has been used to assess the evolution of two populations of the nematode Caenorhabditis elegans in control conditions or exposed to uranium. This evolutionary pressure resulted in a brood size reduction of 60%. We showed an adaptation of individuals of both populations to experimental conditions (increase of maximal length, decrease of growth rate, decrease of brood size, and decrease of the elimination rate). In addition, differential evolution was also highlighted between the two populations once the maternal effects had been diminished after several generations. Thus, individuals that were greater in maximal length, but with apparently a greater sensitivity to uranium were selected in the uranium population. In this study, we showed that this bioenergetics mechanistic modeling approach provided a precise, certain, and powerful analysis of the life strategy of C. elegans populations exposed to heavy metals resulting in an evolutionary pressure across successive generations.

Development of Microsatellite Markers and Analysis of Genetic Diversity and Population Structure of Colletotrichum gloeosporioides from Ethiopia

PubMed Central

Moges, Asmare D.; Admassu, Belayneh; Belew, Derbew; Yesuf, Mohammed; Njuguna, Joyce; Kyalo, Martina; Ghimire, Sita R.

2016-01-01

Twenty three polymorphic microsatellite markers were developed for citrus plant pathogenic fungus, Colletotrichum gloeosporioides, and were used to analyze genetic diversity and population structure of 163 isolates from four different geographical regions of Ethiopia. These loci produced a total of 118 alleles with an average of 5.13 alleles per microsatellite marker. The polymorphic information content values ranged from 0.104 to 0.597 with an average of 0.371. The average observed heterozygosity across all loci varied from 0.046 to 0.058. The gene diversity among the loci ranged from 0.106 to 0.664. Unweighted Neighbor-joining and population structure analysis grouped these 163 isolates into three major groups. The clusters were not according to the geographic origin of the isolates. Analysis of molecular variance showed 85% of the total variation within populations and only 5% among populations. There was low genetic differentiation in the total populations (FST = 0.049) as evidenced by high level of gene flow estimate (Nm = 4.8 per generation) among populations. The results show that Ethiopian C. gloeosporioides populations are generally characterized by a low level of genetic diversity. The newly developed microsatellite markers were useful in analyzing the genetic diversity and population structure of the C. gloeosporioides populations. Information obtained from this study could be useful as a base to design strategies for better management of leaf and fruit spot disease of citrus in Ethiopia. PMID:26978654

Genetic Evidence Supports the Multiethnic Character of Teopancazco, a Neighborhood Center of Teotihuacan, Mexico (AD 200-600)

PubMed Central

Álvarez-Sandoval, Brenda A.; Manzanilla, Linda R.; González-Ruiz, Mercedes; Malgosa, Assumpció; Montiel, Rafael

2015-01-01

Multiethnicity in Teopancazco, Teotihuacan, is supported by foreign individuals found in the neighborhood center as well as by the diversity observed in funerary rituals at the site. Studies of both stable and strontium isotopes as well as paleodietary analysis, suggest that the population of Teopancazco was composed by three population groups: people from Teotihuacan, people from nearby sites (Tlaxcala-Hidalgo-Puebla), and people from afar, including the coastal plains. In an attempt to understand the genetic dynamics in Teopancazco we conducted an ancient DNA (aDNA) analysis based on mtDNA. Our results show that the level of genetic diversity is consistent with the multiethnicity phenomenon at the neighborhood center. Levels of genetic diversity at different time periods of Teopancazco’s history show that multiethnicity was evident since the beginning and lasted until the collapse of the neighborhood center. However, a PCA and a Neighbor-Joining tree suggested the presence of a genetically differentiated group (buried at the Transitional phase) compared to the population from the initial phase (Tlamimilolpa) as well as the population from the final phase (Xolalpan) of the history of Teopancazco. Genetic studies showed no differences in genetic diversity between males and females in the adult population of Teopancazco, this data along with ample archaeological evidence, suggest a neolocal post-marital pattern of residence in Teopancazco. Nevertheless, genetic analyses on the infant population showed that the males are significantly more heterogeneous than the females suggesting a possible differential role in cultural practices by sex in the infant sector. Regarding interpopulation analysis, we found similar indices of genetic diversity between Teopancazco and heterogeneous native groups, which support the multiethnic character of Teopancazco. Finally, our data showed a close genetic relationship between Teopancazco and populations from the “Teotihuacan corridor” and from Oaxaca and the Maya region, in agreement with previous archaeological evidence. PMID:26200455

Genetic Evidence Supports the Multiethnic Character of Teopancazco, a Neighborhood Center of Teotihuacan, Mexico (AD 200-600).

PubMed

Álvarez-Sandoval, Brenda A; Manzanilla, Linda R; González-Ruiz, Mercedes; Malgosa, Assumpció; Montiel, Rafael

2015-01-01

Multiethnicity in Teopancazco, Teotihuacan, is supported by foreign individuals found in the neighborhood center as well as by the diversity observed in funerary rituals at the site. Studies of both stable and strontium isotopes as well as paleodietary analysis, suggest that the population of Teopancazco was composed by three population groups: people from Teotihuacan, people from nearby sites (Tlaxcala-Hidalgo-Puebla), and people from afar, including the coastal plains. In an attempt to understand the genetic dynamics in Teopancazco we conducted an ancient DNA (aDNA) analysis based on mtDNA. Our results show that the level of genetic diversity is consistent with the multiethnicity phenomenon at the neighborhood center. Levels of genetic diversity at different time periods of Teopancazco's history show that multiethnicity was evident since the beginning and lasted until the collapse of the neighborhood center. However, a PCA and a Neighbor-Joining tree suggested the presence of a genetically differentiated group (buried at the Transitional phase) compared to the population from the initial phase (Tlamimilolpa) as well as the population from the final phase (Xolalpan) of the history of Teopancazco. Genetic studies showed no differences in genetic diversity between males and females in the adult population of Teopancazco, this data along with ample archaeological evidence, suggest a neolocal post-marital pattern of residence in Teopancazco. Nevertheless, genetic analyses on the infant population showed that the males are significantly more heterogeneous than the females suggesting a possible differential role in cultural practices by sex in the infant sector. Regarding interpopulation analysis, we found similar indices of genetic diversity between Teopancazco and heterogeneous native groups, which support the multiethnic character of Teopancazco. Finally, our data showed a close genetic relationship between Teopancazco and populations from the "Teotihuacan corridor" and from Oaxaca and the Maya region, in agreement with previous archaeological evidence.

[Frequency of healthy eating habits measured by the 10 Steps to Healthy Eating score proposed by the Ministry of Health: Pelotas, Rio Grande do Sul State, Brazil].

PubMed

Vinholes, Daniele Botelho; Assunção, Maria Cecília Formoso; Neutzling, Marilda Borges

2009-04-01

This study aimed to measure frequency of healthy eating habits and associated factors using the 10 Steps to Healthy Eating score proposed by the Ministry of Health in the adult population in Pelotas, Rio Grande do Sul State, Brazil. A cross-sectional population-based survey was conducted on a cluster sample of 3,136 adult residents in Pelotas. The frequency of each step to healthy eating was collected with a pre-coded questionnaire. Data analysis consisted of descriptive analysis, followed by bivariate analysis using the chi-square test. Only 1.1% of the population followed all the recommended steps. The average number of steps was six. Step four, salt intake, showed the highest frequency, while step nine, physical activity, showed the lowest. Knowledge of the population's eating habits and their distribution according to demographic and socioeconomic variables is important to guide local and national strategies to promote healthy eating habits and thus improve quality of life.

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

PubMed

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

2017-03-17

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

New Insights into the Lake Chad Basin Population Structure Revealed by High-Throughput Genotyping of Mitochondrial DNA Coding SNPs

PubMed Central

Černý, Viktor; Carracedo, Ángel

2011-01-01

Background Located in the Sudan belt, the Chad Basin forms a remarkable ecosystem, where several unique agricultural and pastoral techniques have been developed. Both from an archaeological and a genetic point of view, this region has been interpreted to be the center of a bidirectional corridor connecting West and East Africa, as well as a meeting point for populations coming from North Africa through the Saharan desert. Methodology/Principal Findings Samples from twelve ethnic groups from the Chad Basin (n = 542) have been high-throughput genotyped for 230 coding region mitochondrial DNA (mtDNA) Single Nucleotide Polymorphisms (mtSNPs) using Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight (MALDI-TOF) mass spectrometry. This set of mtSNPs allowed for much better phylogenetic resolution than previous studies of this geographic region, enabling new insights into its population history. Notable haplogroup (hg) heterogeneity has been observed in the Chad Basin mirroring the different demographic histories of these ethnic groups. As estimated using a Bayesian framework, nomadic populations showed negative growth which was not always correlated to their estimated effective population sizes. Nomads also showed lower diversity values than sedentary groups. Conclusions/Significance Compared to sedentary population, nomads showed signals of stronger genetic drift occurring in their ancestral populations. These populations, however, retained more haplotype diversity in their hypervariable segments I (HVS-I), but not their mtSNPs, suggesting a more ancestral ethnogenesis. Whereas the nomadic population showed a higher Mediterranean influence signaled mainly by sub-lineages of M1, R0, U6, and U5, the other populations showed a more consistent sub-Saharan pattern. Although lifestyle may have an influence on diversity patterns and hg composition, analysis of molecular variance has not identified these differences. The present study indicates that analysis of mtSNPs at high resolution could be a fast and extensive approach for screening variation in population studies where labor-intensive techniques such as entire genome sequencing remain unfeasible. PMID:21533064

Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity

PubMed Central

Pope, Welkin H; Bowman, Charles A; Russell, Daniel A; Jacobs-Sera, Deborah; Asai, David J; Cresawn, Steven G; Jacobs, William R; Hendrix, Roger W; Lawrence, Jeffrey G; Hatfull, Graham F; Abbazia, Patrick; Ababio, Amma; Adam, Naazneen

2015-01-01

The bacteriophage population is large, dynamic, ancient, and genetically diverse. Limited genomic information shows that phage genomes are mosaic, and the genetic architecture of phage populations remains ill-defined. To understand the population structure of phages infecting a single host strain, we isolated, sequenced, and compared 627 phages of Mycobacterium smegmatis. Their genetic diversity is considerable, and there are 28 distinct genomic types (clusters) with related nucleotide sequences. However, amino acid sequence comparisons show pervasive genomic mosaicism, and quantification of inter-cluster and intra-cluster relatedness reveals a continuum of genetic diversity, albeit with uneven representation of different phages. Furthermore, rarefaction analysis shows that the mycobacteriophage population is not closed, and there is a constant influx of genes from other sources. Phage isolation and analysis was performed by a large consortium of academic institutions, illustrating the substantial benefits of a disseminated, structured program involving large numbers of freshman undergraduates in scientific discovery. DOI: http://dx.doi.org/10.7554/eLife.06416.001 PMID:25919952

Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity.

PubMed

Pope, Welkin H; Bowman, Charles A; Russell, Daniel A; Jacobs-Sera, Deborah; Asai, David J; Cresawn, Steven G; Jacobs, William R; Hendrix, Roger W; Lawrence, Jeffrey G; Hatfull, Graham F

2015-04-28

The bacteriophage population is large, dynamic, ancient, and genetically diverse. Limited genomic information shows that phage genomes are mosaic, and the genetic architecture of phage populations remains ill-defined. To understand the population structure of phages infecting a single host strain, we isolated, sequenced, and compared 627 phages of Mycobacterium smegmatis. Their genetic diversity is considerable, and there are 28 distinct genomic types (clusters) with related nucleotide sequences. However, amino acid sequence comparisons show pervasive genomic mosaicism, and quantification of inter-cluster and intra-cluster relatedness reveals a continuum of genetic diversity, albeit with uneven representation of different phages. Furthermore, rarefaction analysis shows that the mycobacteriophage population is not closed, and there is a constant influx of genes from other sources. Phage isolation and analysis was performed by a large consortium of academic institutions, illustrating the substantial benefits of a disseminated, structured program involving large numbers of freshman undergraduates in scientific discovery.

Volatility and Growth in Populations of Rural Associations

ERIC Educational Resources Information Center

Wollebaek, Dag

2010-01-01

This article uses unique community-level data aggregated from censuses of associations to analyze growth and volatility in rural populations of grassroots associations. A qualitative comparative analysis (QCA) shows that the two main paths to growth were (1) centralization in polycephalous (multicentered) municipalities and (2) population growth…

Harbor porpoise Phocoena phocoena strandings on the Dutch coast: No genetic structure, but evidence of inbreeding

NASA Astrophysics Data System (ADS)

van der Plas-Duivesteijn, Suzanne J.; Smit, Femmie J. L.; van Alphen, Jacques J. M.; Kraaijeveld, Ken

2015-03-01

Conservation management in the North Sea is often motivated by the population size of marine mammals, like harbor porpoises Phocoena phocoena. In the Dutch part of the North Sea, sighting and stranding data are used to estimate population sizes, but these data give little insight into genetic structuring of the population. In this study we investigated genetic structure among animals stranded at different locations and times of year. We also tested whether there is a link between stranding and necropsy data, and genetic diversity. We made use of both mitochondrial (mtDNA) and microsatellite DNA analysis of samples from dead stranded porpoises along the Dutch coast during 2007. mtDNA analysis showed 6 variable positions in the control region, defining 3 different haplotypes. mtDNA haplotypes were not randomly distributed along the Dutch coastline. However, microsatellite analysis showed that these mtDNA haplotypes did not represent separate groups on a nuclear level. Furthermore, microsatellite analysis revealed no genotypic differences between seasons, locations or genders. The results of this study indicate that the Dutch population is panmictic. In contrast, heterozygosity levels were low, indicating some level of inbreeding in this population. However, this was not corroborated by other indices of inbreeding. This research provided insight into genetic structuring of stranded porpoises in 2007, but data from multiple years should be included to be able to help estimate population sizes.

Forensic and population genetic analysis of Xinjiang Uyghur population on 21 short tandem repeat loci of 6-dye GlobalFiler™ PCR Amplification kit.

PubMed

Zhang, Honghua; Xia, Mingying; Qi, Lijie; Dong, Lei; Song, Shuang; Ma, Teng; Yang, Shuping; Jin, Li; Li, Liming; Li, Shilin

2016-05-01

Estimating the allele frequencies and forensic statistical parameters of commonly used short tandem repeat (STR) loci of the Uyghur population, which is the fifth largest group in China, provides a more precise reference database for forensic investigation. The 6-dye GlobalFiler™ Express PCR Amplification kit incorporates 21 autosomal STRs, which have been proven that could provide reliable DNA typing results and enhance the power of discrimination. Here we analyzed the GlobalFiler STR loci on 1962 unrelated individuals from Chinese Uyghur population of Xinjiang, China. No significant deviations from Hardy-Weinberg equilibrium and linkage disequilibrium were detected within and between the GlobalFiler STR loci. SE33 showed the greatest power of discrimination in Uyghur population, whereas TPOX showed the lowest. The combined power of discrimination was 99.999999999999999999999998746%. No significant difference was observed between Uyghur and the other two Uyghur populations at all tested STRs, as well as Dai and Mongolian. Significant differences were only observed between Uyghur and other Chinese populations at TH01, as well as Central-South Asian at D13S317, East Asian at TH01 and VWA. The phylogenetic analysis showed that Uyghur is genetically close to Chinese populations, as well as East Asian and Central-South Asian. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

The effects of plant extracts on microbial community structure in a rumen-simulating continuous-culture system as revealed by molecular profiling.

PubMed

Ferme, D; Banjac, M; Calsamiglia, S; Busquet, M; Kamel, C; Avgustin, G

2004-01-01

An in vitro study in dual-flow continuous-culture fermentors was conducted with two different concentrations of monensin, cinnamaldehyde or garlic extract added to 1:1 forage-to-concentrate diet in order to determine their effects on selected rumen bacterial populations. Samples were subjected to total DNA extraction, restriction analysis of PCR amplified parts of 16S rRNA genes (ARDRA) and subsequent analysis of the restriction profiles by lab-on-chip technology with the Agilent's Bioanalyser 2100. Eub338-BacPre primer pair was used to select for the bacteria from the genera Bacteroides, Porphyromonas and Prevotella, especially the latter representing the dominant Gram-negative bacterial population in the rumen. Preliminary results of HaeIII restriction analysis show that the effects of monensin, cinnamaldehyde and garlic extract on the BacPre targeted ruminal bacteria are somewhat different in regard to targeted populations and to the nature of the effect. Garlic extract was found to trigger the most intensive changes in the structure of the BacPre targeted population. Comparison of the in silico restriction analysis of BacPre sequences deposited in different DNA databanks and of the results of performed amplified ribosomal DNA restriction analysis showed differences between the predicted and obtained HaeIII restriction profiles, and suggested the presence of novel, still unknown Prevotella populations in studied samples.

Allelic Prevalence of ABO Blood Group Genes in Iranian Azari Population.

PubMed

Nojavan, Mohammad; Shamsasenjan, Karrim; Movassaghpour, Ali Akbar; Akbarzadehlaleh, Parvin; Torabi, Seyd Esmail; Ghojazadeh, Morteza

2012-01-01

ABO blood group system is the most important blood group in transfusion and has been widely used in population studies. Several molecular techniques for ABO allele's detection are widely used for distinguishing various alleles of glycosyl transferase locus on chromosome 9. 744 randomly selected samples from Azari donors of East Azerbaijan province (Iran) were examined using well-adjusted multiplex allele- specific PCR ABO genotyping technique. The results were consistent for all individuals. The ABO blood group genotype of 744 healthy Azari blood donors was: 25.8% AA/AO (2), 7.6% AO (1), 1.6% BB, 11.3% B0 (1), 10% AB, 9.3% 0(1)0(1) and 15.3%0(1)0(2). The highest genotype frequency belonged to O01/O02 genotype (15.3%) and the lowest frequency belonged to A101/A102 genotype (0.4%). The frequencies of ABO alleles didn't show significant differences between East Azerbaijan province population and that of other areas of the country. Meanwhile, statistical analysis of frequencies of A and B alleles between East Azerbaijan province population and neighbor countries showed significant differences whereas the frequency of allele O between them did not show significant difference (P>0.05). The frequencies of ABO alleles didn't show significant differences between East Azerbaijan province population and that of other areas of the country. Meanwhile, statistical analysis of frequencies of A and B alleles between East Azerbaijan province population and neighbor countries showed significant differences whereas the frequency of allele O between them did not show significant difference (P>0.05).

Agriculture, population growth, and statistical analysis of the radiocarbon record.

PubMed

Zahid, H Jabran; Robinson, Erick; Kelly, Robert L

2016-01-26

The human population has grown significantly since the onset of the Holocene about 12,000 y ago. Despite decades of research, the factors determining prehistoric population growth remain uncertain. Here, we examine measurements of the rate of growth of the prehistoric human population based on statistical analysis of the radiocarbon record. We find that, during most of the Holocene, human populations worldwide grew at a long-term annual rate of 0.04%. Statistical analysis of the radiocarbon record shows that transitioning farming societies experienced the same rate of growth as contemporaneous foraging societies. The same rate of growth measured for populations dwelling in a range of environments and practicing a variety of subsistence strategies suggests that the global climate and/or endogenous biological factors, not adaptability to local environment or subsistence practices, regulated the long-term growth of the human population during most of the Holocene. Our results demonstrate that statistical analyses of large ensembles of radiocarbon dates are robust and valuable for quantitatively investigating the demography of prehistoric human populations worldwide.

Genetic Variation and Population Differentiation in a Medical Herb Houttuynia cordata in China Revealed by Inter-Simple Sequence Repeats (ISSRs)

PubMed Central

Wei, Lin; Wu, Xian-Jin

2012-01-01

Houttuynia cordata is an important traditional Chinese herb with unresolved genetics and taxonomy, which lead to potential problems in the conservation and utilization of the resource. Inter-simple sequence repeat (ISSR) markers were used to assess the level and distribution of genetic diversity in 226 individuals from 15 populations of H. cordata in China. ISSR analysis revealed low genetic variations within populations but high genetic differentiations among populations. This genetic structure probably mainly reflects the historical association among populations. Genetic cluster analysis showed that the basal clade is composed of populations from Southwest China, and the other populations have continuous and eastward distributions. The structure of genetic diversity in H. cordata demonstrated that this species might have survived in Southwest China during the glacial age, and subsequently experienced an eastern postglacial expansion. Based on the results of genetic analysis, it was proposed that as many as possible targeted populations for conservation be included. PMID:22942696

Genetic variation and population differentiation in a medical herb Houttuynia cordata in China revealed by inter-simple sequence repeats (ISSRs).

PubMed

Wei, Lin; Wu, Xian-Jin

2012-01-01

Houttuynia cordata is an important traditional Chinese herb with unresolved genetics and taxonomy, which lead to potential problems in the conservation and utilization of the resource. Inter-simple sequence repeat (ISSR) markers were used to assess the level and distribution of genetic diversity in 226 individuals from 15 populations of H. cordata in China. ISSR analysis revealed low genetic variations within populations but high genetic differentiations among populations. This genetic structure probably mainly reflects the historical association among populations. Genetic cluster analysis showed that the basal clade is composed of populations from Southwest China, and the other populations have continuous and eastward distributions. The structure of genetic diversity in H. cordata demonstrated that this species might have survived in Southwest China during the glacial age, and subsequently experienced an eastern postglacial expansion. Based on the results of genetic analysis, it was proposed that as many as possible targeted populations for conservation be included.

Genome-wide analysis of the diversity and ancestry of Korean dogs.

PubMed

Choi, Bong Hwan; Wijayananda, Hasini I; Lee, Soo Hyun; Lee, Doo Ho; Kim, Jong Seok; Oh, Seok Il; Park, Eung Woo; Lee, Cheul Koo; Lee, Seung Hwan

2017-01-01

There are various hypotheses on dog domestication based on archeological and genetic studies. Although many studies have been conducted on the origin of dogs, the existing literature about the ancestry, diversity, and population structure of Korean dogs is sparse. Therefore, this study is focused on the origin, diversity and population structure of Korean dogs. The study sample comprised four major categories, including non-dogs (coyotes and wolves), ancient, modern and Korean dogs. Selected samples were genotyped using an Illumina CanineHD array containing 173,662 single nucleotide polymorphisms. The genome-wide data were filtered using quality control parameters in PLINK 1.9. Only autosomal chromosomes were used for further analysis. The negative off-diagonal variance of the genetic relationship matrix analysis depicted, the variability of samples in each population. FIS (inbreeding rate within a population) values indicated, a low level of inbreeding within populations, and the patterns were in concordance with the results of Nei's genetic distance analysis. The lowest FST (inbreeding rate between populations) values among Korean and Chinese breeds, using a phylogenetic tree, multi-dimensional scaling, and a TreeMix likelihood tree showed Korean breeds are highly related to Chinese breeds. The Korean breeds possessed a unique and large diversity of admixtures compared with other breeds. The highest and lowest effective population sizes were observed in Korean Jindo Black (485) and Korean Donggyeong White (109), respectively. The historical effective population size of all Korean dogs showed declining trend from the past to present. It is important to take immediate action to protect the Korean dog population while conserving their diversity. Furthermore, this study suggests that Korean dogs have unique diversity and are one of the basal lineages of East Asian dogs, originating from China.

Genome-wide analysis of the diversity and ancestry of Korean dogs

PubMed Central

Lee, Doo Ho; Kim, Jong Seok; Oh, Seok Il; Park, Eung Woo; Lee, Cheul Koo; Lee, Seung Hwan

2017-01-01

There are various hypotheses on dog domestication based on archeological and genetic studies. Although many studies have been conducted on the origin of dogs, the existing literature about the ancestry, diversity, and population structure of Korean dogs is sparse. Therefore, this study is focused on the origin, diversity and population structure of Korean dogs. The study sample comprised four major categories, including non-dogs (coyotes and wolves), ancient, modern and Korean dogs. Selected samples were genotyped using an Illumina CanineHD array containing 173,662 single nucleotide polymorphisms. The genome-wide data were filtered using quality control parameters in PLINK 1.9. Only autosomal chromosomes were used for further analysis. The negative off-diagonal variance of the genetic relationship matrix analysis depicted, the variability of samples in each population. FIS (inbreeding rate within a population) values indicated, a low level of inbreeding within populations, and the patterns were in concordance with the results of Nei’s genetic distance analysis. The lowest FST (inbreeding rate between populations) values among Korean and Chinese breeds, using a phylogenetic tree, multi-dimensional scaling, and a TreeMix likelihood tree showed Korean breeds are highly related to Chinese breeds. The Korean breeds possessed a unique and large diversity of admixtures compared with other breeds. The highest and lowest effective population sizes were observed in Korean Jindo Black (485) and Korean Donggyeong White (109), respectively. The historical effective population size of all Korean dogs showed declining trend from the past to present. It is important to take immediate action to protect the Korean dog population while conserving their diversity. Furthermore, this study suggests that Korean dogs have unique diversity and are one of the basal lineages of East Asian dogs, originating from China. PMID:29182674

The contributions of admixture and genetic drift to diversity among post-contact populations in the Americas.

PubMed

Koehl, Anthony J; Long, Jeffrey C

2018-02-01

We present a model that partitions Nei's minimum genetic distance between admixed populations into components of admixture and genetic drift. We applied this model to 17 admixed populations in the Americas to examine how admixture and drift have contributed to the patterns of genetic diversity. We analyzed 618 short tandem repeat loci in 949 individuals from 49 population samples. Thirty-two samples serve as proxies for continental ancestors. Seventeen samples represent admixed populations: (4) African-American and (13) Latin American. We partition genetic distance, and then calculate fixation indices and principal coordinates to interpret our results. A computer simulation confirms that our method correctly estimates drift and admixture components of genetic distance when the assumptions of the model are met. The partition of genetic distance shows that both admixture and genetic drift contribute to patterns of genetic diversity. The admixture component of genetic distance provides evidence for two distinct axes of continental ancestry. However, the genetic distances show that ancestry contributes to only one axis of genetic differentiation. The genetic distances among the 13 Latin American populations in this analysis show contributions from both differences in ancestry and differences in genetic drift. By contrast, the genetic distances among the four African American populations in this analysis owe mostly to genetic drift because these groups have similar fractions of European and African ancestry. The genetic structure of admixed populations in the Americas reflects more than admixture. We show that the history of serial founder effects constrains the impact of admixture on allele frequencies to a single dimension. Genetic drift in the admixed populations imposed a new level of genetic structure onto that created by admixture. © 2017 Wiley Periodicals, Inc.

Morphometric evaluation of the knee in Chinese population reveals sexual dimorphism and age-related differences.

PubMed

Li, Ke; Cavaignac, Etienne; Xu, Wei; Cheng, Qiang; Telmon, Nobert; Huang, Wei

2018-02-20

Morphologic data of the knee is very important in the design of total knee prostheses. Generally, the designs of the total knee prostheses are based on the knee anatomy of Caucasian population. Moreover, in forensic medicine, a person's age and sex might be estimated by the shape of their knees. The aim of this study is to utilize three-dimensional morphometric analysis of the knee in Chinese population to reveal sexual dimorphism and age-related differences. Sexually dimorphic differences and age-related differences of the distal femur were studied by using geometric morphometric analysis of ten osteometric landmarks on three-dimensional reconstructions of 259 knees in Chinese population. General Procrustes analysis, PCA, and other discriminant analysis such as Mahalanobis and Goodall's F test were conducted for the knee to identify sexually dimorphism and age-related differences of the knee. The shape of distal femur between the male and female is significantly different. A difference between males and females in distal femur shape was identified by PCA; PC1 and PC2 accounted for 61.63% of the variance measured. The correct sex was assigned in 84.9% of cases by CVA, and the cross-validation revealed a 81.1% rate of correct sex estimation. The osteometric analysis also showed significant differences between the three age-related subgroups (< 40, 40-60, > 60 years, p < 0.005). This study showed both sex-related difference and age-related difference in the distal femur in Chinese population by 3D geometric morphometric analysis. Our bone measurements and geometric morphometric analysis suggest that population characteristics should be taken into account and may provide references for design of total knee prostheses in a Chinese population. Moreover, this reliable, accurate method could be used to perform diachronic and interethnic comparisons.

Single cell versus large population analysis: cell variability in elemental intracellular concentration and distribution.

PubMed

Malucelli, Emil; Procopio, Alessandra; Fratini, Michela; Gianoncelli, Alessandra; Notargiacomo, Andrea; Merolle, Lucia; Sargenti, Azzurra; Castiglioni, Sara; Cappadone, Concettina; Farruggia, Giovanna; Lombardo, Marco; Lagomarsino, Stefano; Maier, Jeanette A; Iotti, Stefano

2018-01-01

The quantification of elemental concentration in cells is usually performed by analytical assays on large populations missing peculiar but important rare cells. The present article aims at comparing the elemental quantification in single cells and cell population in three different cell types using a new approach for single cells elemental analysis performed at sub-micrometer scale combining X-ray fluorescence microscopy and atomic force microscopy. The attention is focused on the light element Mg, exploiting the opportunity to compare the single cell quantification to the cell population analysis carried out by a highly Mg-selective fluorescent chemosensor. The results show that the single cell analysis reveals the same Mg differences found in large population of the different cell strains studied. However, in one of the cell strains, single cell analysis reveals two cells with an exceptionally high intracellular Mg content compared with the other cells of the same strain. The single cell analysis allows mapping Mg and other light elements in whole cells at sub-micrometer scale. A detailed intensity correlation analysis on the two cells with the highest Mg content reveals that Mg subcellular localization correlates with oxygen in a different fashion with respect the other sister cells of the same strain. Graphical abstract Single cells or large population analysis this is the question!

Population genomic analysis uncovers environmental stress-driven selection and adaptation of Lentinula edodes population in China.

PubMed

Xiao, Yang; Cheng, Xuanjin; Liu, Jun; Li, Chuang; Nong, Wenyan; Bian, Yinbing; Cheung, Man Kit; Kwan, Hoi Shan

2016-11-10

The elucidation of genome-wide variations could help reveal aspects of divergence, domestication, and adaptation of edible mushrooms. Here, we resequenced the whole genomes of 39 wild and 21 cultivated strains of Chinese Lentinula edodes, the shiitake mushroom. We identified three distinct genetic groups in the Chinese L. edodes population with robust differentiation. Results of phylogenetic and population structure analyses suggest that the cultivated strains and most of the wild trains of L. edodes in China possess different gene pools and two outlier strains show signatures of hybridization between groups. Eighty-four candidate genes contributing to population divergence were detected in outlier analysis, 18 of which are involved in response to environmental stresses. Gene enrichment analysis of group-specific single nucleotide polymorphisms showed that the cultivated strains were genetically diversified in biological processes related to stress response. As the formation of fruiting bodies is a stress-response process, we postulate that environment factors, such as temperature, drove the population divergence of L. edodes in China by natural or artificial selection. We also found phenotypic variations between groups and identified some wild strains that have potential to diversify the genetic pool for improving agricultural traits of L. edodes cultivars in China.

Population genomic analysis uncovers environmental stress-driven selection and adaptation of Lentinula edodes population in China

PubMed Central

Xiao, Yang; Cheng, Xuanjin; Liu, Jun; Li, Chuang; Nong, Wenyan; Bian, Yinbing; Cheung, Man Kit; Kwan, Hoi Shan

2016-01-01

The elucidation of genome-wide variations could help reveal aspects of divergence, domestication, and adaptation of edible mushrooms. Here, we resequenced the whole genomes of 39 wild and 21 cultivated strains of Chinese Lentinula edodes, the shiitake mushroom. We identified three distinct genetic groups in the Chinese L. edodes population with robust differentiation. Results of phylogenetic and population structure analyses suggest that the cultivated strains and most of the wild trains of L. edodes in China possess different gene pools and two outlier strains show signatures of hybridization between groups. Eighty-four candidate genes contributing to population divergence were detected in outlier analysis, 18 of which are involved in response to environmental stresses. Gene enrichment analysis of group-specific single nucleotide polymorphisms showed that the cultivated strains were genetically diversified in biological processes related to stress response. As the formation of fruiting bodies is a stress-response process, we postulate that environment factors, such as temperature, drove the population divergence of L. edodes in China by natural or artificial selection. We also found phenotypic variations between groups and identified some wild strains that have potential to diversify the genetic pool for improving agricultural traits of L. edodes cultivars in China. PMID:27830835

Genetic characterization of an X-STR decaplex system in the State of Mato Grosso, Brazil: distribution, forensic efficiency and population structure.

PubMed

Martins, Joyce A; Martins, Denise P; Oliveira-Brancati, Camila I F; Martinez, Juliana; Cicarelli, Regina M B; Souza, Dorotéia R S

2017-11-01

Studies with X-STR loci show population genetic substructure, which makes necessary the characterization of such markers in the different geographical and/or ethnic populations. Therefore, this study assessed the distribution and forensic efficiency of an X-STR decaplex system in the population of the State of Mato Grosso, as well as analysed the population structure of this State based on the aforementioned system. All X-STR markers were in Hardy-Weinberg equilibrium and linkage equilibrium, and the DXS6809 was the most informative marker. The power of discrimination value in females and males was 0.99999999995 and 0.9999994, respectively. Analysis of molecular variance indicated 1.10% (p < 0.00001) of heterogeneity among Europeans, Africans, Brazilians and other Latin Americans, and in relation to such groups, the population of the State of Mato Grosso showed lower genetic variation when compared with the Brazilian group (-0.10%, p = 0.67327). The genetic distance analysis showed lower values of F ST (0.0004 ≤ F ST  ≤ 0.00331), with non-significant p value (p > 0.00024), between the populations of Mato Grosso and Mato Grosso do Sul, Paraná and the Southeast region of Brazil (except for one sample of Rio de Janeiro). F ST values with significant p values (p ≤ 0.00024) were obtained between the population of Mato Grosso and Iberian, African and some Latin American populations. The X-STR decaplex system proved to be extremely useful in the population of the State of Mato Grosso, and the data obtained does not show the need for a specific forensic database for this State in relation to the Brazilian populations compared in this study, except for population of Rio de Janeiro.

Controversial opinion: evaluation of EGR1 and LAMA2 loci for high myopia in Chinese populations.

PubMed

Lin, Fang-yu; Huang, Zhu; Lu, Ning; Chen, Wei; Fang, Hui; Han, Wei

2016-03-01

Functional studies have suggested the important role of early growth response 1 (EGR1) and Laminin α2-chain (LAMA2) in human eye development. Genetic studies have reported a significant association of the single nucleotide polymorphism (SNP) in the LAMA2 gene with myopia. This study aimed to evaluate the association of the tagging SNPs (tSNPs) in the EGR1 and LAMA2 genes with high myopia in two independent Han Chinese populations. Four tSNPs (rs11743810 in the EGR1 gene; rs2571575, rs9321170, and rs1889891 in the LAMA2 gene) were selected, according to the HapMap database (http://hapmap.ncbi.nlm.nih.gov), and were genotyped using the ligase detection reaction (LDR) approach for 167 Han Chinese nuclear families with extremely highly myopic offspring (<-10.0 diopters) and an independent group with 485 extremely highly myopic cases (<-10.0 diopters) and 499 controls. Direct sequencing was used to confirm the LDR results in twenty randomly selected subjects. Family-based association analysis was performed using the family-based association test (FBAT) software package (Version 1.5.5). Population-based association analysis was performed using the Chi-square test. The association analysis power was estimated using online software (http://design.cs.ucla.edu). The FBAT demonstrated that all four tSNPs tested did not show association with high myopia (P>0.05). Haplotype analysis of tSNPs in the LAMA2 genes also did not show a significant association (P>0.05). Meanwhile, population-based association analysis also showed no significant association results with high myopia (P>0.05). On the basis of our family- and population-based analyses for the Han Chinese population, we did not find positive association signals of the four SNPs in the LAMA2 and EGR1 genes with high myopia.

Restricted Gene Flow among Hospital Subpopulations of Enterococcus faecium

PubMed Central

Willems, Rob J. L.; Top, Janetta; van Schaik, Willem; Leavis, Helen; Bonten, Marc; Sirén, Jukka; Hanage, William P.; Corander, Jukka

2012-01-01

ABSTRACT Enterococcus faecium has recently emerged as an important multiresistant nosocomial pathogen. Defining population structure in this species is required to provide insight into the existence, distribution, and dynamics of specific multiresistant or pathogenic lineages in particular environments, like the hospital. Here, we probe the population structure of E. faecium using Bayesian-based population genetic modeling implemented in Bayesian Analysis of Population Structure (BAPS) software. The analysis involved 1,720 isolates belonging to 519 sequence types (STs) (491 for E. faecium and 28 for Enterococcus faecalis). E. faecium isolates grouped into 13 BAPS (sub)groups, but the large majority (80%) of nosocomial isolates clustered in two subgroups (2-1 and 3-3). Phylogenetic and eBURST analysis of BAPS groups 2 and 3 confirmed the existence of three separate hospital lineages (17, 18, and 78), highlighting different evolutionary trajectories for BAPS 2-1 (lineage 78) and 3-3 (lineage 17 and lineage 18) isolates. Phylogenomic analysis of 29 E. faecium isolates showed agreement between BAPS assignment of STs and their relative positions in the phylogenetic tree. Odds ratio calculation confirmed the significant association between hospital isolates with BAPS 3-3 and lineages 17, 18, and 78. Admixture analysis showed a scarce number of recombination events between the different BAPS groups. For the E. faecium hospital population, we propose an evolutionary model in which strains with a high propensity to colonize and infect hospitalized patients arise through horizontal gene transfer. Once adapted to the distinct hospital niche, this subpopulation becomes isolated, and recombination with other populations declines. PMID:22807567

Genetic Variation of Beet Armyworm (Lepidoptera: Noctuidae) Populations Detected Using Microsatellite Markers in Iran.

PubMed

Golikhajeh, Neshat; Naseri, Bahram; Razmjou, Jabraeil; Hosseini, Reza; Aghbolaghi, Marzieh Asadi

2018-05-28

In order to understand the population genetic diversity and structure of Spodoptera exigua (Hübner) (Lepidoptera: Noctuidae), a serious pest of sugar beet in Iran and the world, we genotyped 133 individuals from seven regions in Iran using four microsatellite loci. Significant difference was seen between the observed and expected heterozygosity in all loci. A lower observed heterozygosity than expected heterozygosity indicated a low heterozygosity in these populations. The value of F showed a high genetic differentiation, so that the mean of Fst was 0.21. Molecular analysis variance showed significant differences within and among populations with group variance accounted for 71 and 21%, respectively. No correlation was found between pair-wise Fst and geographic distance by Mantel test. Bayesian clustering analysis grouped all regions to two clusters. These data suggested that a combination of different factors, such as geographic distance, environmental condition, and physiological behavior in addition to genetic factors, could play an important role in forming variation within and between S. exigua populations.

How memory of direct animal interactions can lead to territorial pattern formation.

PubMed

Potts, Jonathan R; Lewis, Mark A

2016-05-01

Mechanistic home range analysis (MHRA) is a highly effective tool for understanding spacing patterns of animal populations. It has hitherto focused on populations where animals defend their territories by communicating indirectly, e.g. via scent marks. However, many animal populations defend their territories using direct interactions, such as ritualized aggression. To enable application of MHRA to such populations, we construct a model of direct territorial interactions, using linear stability analysis and energy methods to understand when territorial patterns may form. We show that spatial memory of past interactions is vital for pattern formation, as is memory of 'safe' places, where the animal has visited but not suffered recent territorial encounters. Additionally, the spatial range over which animals make decisions to move is key to understanding the size and shape of their resulting territories. Analysis using energy methods, on a simplified version of our system, shows that stability in the nonlinear system corresponds well to predictions of linear analysis. We also uncover a hysteresis in the process of territory formation, so that formation may depend crucially on initial space-use. Our analysis, in one dimension and two dimensions, provides mathematical groundwork required for extending MHRA to situations where territories are defended by direct encounters. © 2016 The Author(s).

Geostatistics and spatial analysis in biological anthropology.

PubMed

Relethford, John H

2008-05-01

A variety of methods have been used to make evolutionary inferences based on the spatial distribution of biological data, including reconstructing population history and detection of the geographic pattern of natural selection. This article provides an examination of geostatistical analysis, a method used widely in geology but which has not often been applied in biological anthropology. Geostatistical analysis begins with the examination of a variogram, a plot showing the relationship between a biological distance measure and the geographic distance between data points and which provides information on the extent and pattern of spatial correlation. The results of variogram analysis are used for interpolating values of unknown data points in order to construct a contour map, a process known as kriging. The methods of geostatistical analysis and discussion of potential problems are applied to a large data set of anthropometric measures for 197 populations in Ireland. The geostatistical analysis reveals two major sources of spatial variation. One pattern, seen for overall body and craniofacial size, shows an east-west cline most likely reflecting the combined effects of past population dispersal and settlement. The second pattern is seen for craniofacial height and shows an isolation by distance pattern reflecting rapid spatial changes in the midlands region of Ireland, perhaps attributable to the genetic impact of the Vikings. The correspondence of these results with other analyses of these data and the additional insights generated from variogram analysis and kriging illustrate the potential utility of geostatistical analysis in biological anthropology. (c) 2008 Wiley-Liss, Inc.

Comparison of diagnostic capability of macular ganglion cell complex and retinal nerve fiber layer among primary open angle glaucoma, ocular hypertension, and normal population using Fourier-domain optical coherence tomography and determining their functional correlation in Indian population

PubMed Central

Barua, Nabanita; Sitaraman, Chitra; Goel, Sonu; Chakraborti, Chandana; Mukherjee, Sonai; Parashar, Hemandra

2016-01-01

Context: Analysis of diagnostic ability of macular ganglionic cell complex and retinal nerve fiber layer (RNFL) in glaucoma. Aim: To correlate functional and structural parameters and comparing predictive value of each of the structural parameters using Fourier-domain (FD) optical coherence tomography (OCT) among primary open angle glaucoma (POAG) and ocular hypertension (OHT) versus normal population. Setting and Design: Single centric, cross-sectional study done in 234 eyes. Materials and Methods: Patients were enrolled in three groups: POAG, ocular hypertensive and normal (40 patients in each group). After comprehensive ophthalmological examination, patients underwent standard automated perimetry and FD-OCT scan in optic nerve head and ganglion cell mode. The relationship was assessed by correlating ganglion cell complex (GCC) parameters with mean deviation. Results were compared with RNFL parameters. Statistical Analysis: Data were analyzed with SPSS, analysis of variance, t-test, Pearson's coefficient, and receiver operating curve. Results: All parameters showed strong correlation with visual field (P < 0.001). Inferior GCC had highest area under curve (AUC) for detecting glaucoma (0.827) in POAG from normal population. However, the difference was not statistically significant (P > 0.5) when compared with other parameters. None of the parameters showed significant diagnostic capability to detect OHT from normal population. In diagnosing early glaucoma from OHT and normal population, only inferior GCC had statistically significant AUC value (0.715). Conclusion: In this study, GCC and RNFL parameters showed equal predictive capability in perimetric versus normal group. In early stage, inferior GCC was the best parameter. In OHT population, single day cross-sectional imaging was not valuable. PMID:27221682

The clinical effect of nicorandil on perioperative myocardial protection in patients undergoing elective PCI: A Systematic Review and Meta-Analysis.

PubMed

Ye, Ziliang; Su, Qiang; Li, Lang

2017-03-21

Many scholars have studied the effect of nicorandil on perioperative myocardial protection in patients undergoing elective percutaneous coronary intervention (PCI), but results are inconsistent. Therefore, we performed this meta-analysis. Finally, 16 articles, including 1616 patients, were included into this meta-analysis. Meta-analysis results showed that: (1) Nicorandil can reduce the level of CK-MB after PCI, including at 6 hours, 12 hours, 18 hours and 24 hours. (2) Nicorandil can reduce the level of TnT after PCI, including at 6 hours, 12 hours, 18 hours and 24 hours. (3) Nicorandil can reduce the incidence of adverse reactions after PCI. (4) Nicorandil cannot reduce the level of MVP after PCI, including at 12 hours and 24 hours. (5) Subgroup analysis showed that nicorandil can reduce CK-MB and TnT level at 24 hours after PCI for Chinese's population (P < 0.05), but can not reduce CK-MB and TnT level at 24 hours after PCI for non Chinese's population (P > 0.05). Our meta-analysis indicate that nicorandil can reduce myocardial injury and reduce the incidence of adverse reaction caused by PCI for Chinese's population, but is not obvious for non Chinese's population. However, this conclusion still needs to be confirmed in the future.

Phylogeography of the sandy beach amphipod Haustorioides japonicus along the Sea of Japan: Paleogeographical signatures of cryptic regional divergences

NASA Astrophysics Data System (ADS)

Takada, Yoshitake; Sakuma, Kay; Fujii, Tetsuo; Kojima, Shigeaki

2018-01-01

Recent findings of genetic breaks within apparently continuous marine populations challenge the traditional vicariance paradigm in population genetics. Such "invisible" boundaries are sometimes associated with potential geographic barriers that have forced divergence of an ancestral population, habitat discontinuities, biogeographic disjunctions due to environmental gradients, or a combination of these factors. To explore the factors that influence the genetic population structure of apparently continuous populations along the Sea of Japan, the sandy beach amphipod Haustorioides japonicus was examined. We sampled a total of 300 individuals of H. japonicus from the coast of Japan, and obtained partial sequences of the mitochondrial COI gene. The sequences from 19 local populations were clustered into five groups (Northwestern Pacific, Northern, Central, Southern Sea of Japan, and East China Sea) based on a spatial genetic mixture analysis and a minimum-spanning network. AMOVA and pairwise Fst tests further supported the significant divergence of the five groups. Phylogenetic analysis revealed the relationship among the haplotypes of H. japonicus and outgroups, which inferred the northward range expansion of the species. A relaxed molecular-clock Bayesian analysis inferred the early-to middle-Pleistocene divergence of the populations. Among the five clusters, the Central Sea of Japan showed the highest values for genetic diversity indices indicating the existence of a relatively stable and large population there. The hypothesis is also supported by Bayesian Skyline Plots that showed sudden population expansion for all the clusters except for Central Sea of Japan. The present study shows genetic boundaries between the Sea of Japan and the neighboring seas, probably due to geographic isolation during the Pleistocene glacial periods. We further found divergence between the populations along the apparently continuous coast of the Sea of Japan. Historical changes in the geographic range of H. japonicus in relation to sandy beach habitat availability, account for the genetic breaks among the three populations in the Sea of Japan. The present results infer that the past geographic events influenced the population formation of H. japonicus.

Allelic Prevalence of ABO Blood Group Genes in Iranian Azari Population

PubMed Central

Nojavan, Mohammad; Shamsasenjan, Karrim; Movassaghpour, Ali Akbar; Akbarzadehlaleh, Parvin; Torabi, Seyd Esmail; Ghojazadeh, Morteza

2012-01-01

Introduction ABO blood group system is the most important blood group in transfusion and has been widely used in population studies. Several molecular techniques for ABO allele’s detection are widely used for distinguishing various alleles of glycosyl transferase locus on chromosome 9. Methods 744 randomly selected samples from Azari donors of East Azerbaijan province (Iran) were examined using well-adjusted multiplex allele- specific PCR ABO genotyping technique. Results The results were consistent for all individuals. The ABO blood group genotype of 744 healthy Azari blood donors was: 25.8% AA/AO (2), 7.6% AO (1), 1.6% BB, 11.3% B0 (1), 10% AB, 9.3% 0(1)0(1) and 15.3%0(1)0(2). The highest genotype frequency belonged to O01/O02 genotype (15.3%) and the lowest frequency belonged to A101/A102 genotype (0.4%). Conclusions: The frequencies of ABO alleles didn’t show significant differences between East Azerbaijan province population and that of other areas of the country. Meanwhile, statistical analysis of frequencies of A and B alleles between East Azerbaijan province population and neighbor countries showed significant differences whereas the frequency of allele O between them did not show significant difference (P>0.05). Conclusions The frequencies of ABO alleles didn’t show significant differences between East Azerbaijan province population and that of other areas of the country. Meanwhile, statistical analysis of frequencies of A and B alleles between East Azerbaijan province population and neighbor countries showed significant differences whereas the frequency of allele O between them did not show significant difference (P>0.05). PMID:23678461

Genetic identification of Theobroma cacao L. trees with high Criollo ancestry in Soconusco, Chiapas, Mexico.

PubMed

Vázquez-Ovando, J A; Molina-Freaner, F; Nuñez-Farfán, J; Ovando-Medina, I; Salvador-Figueroa, M

2014-12-12

Criollo-type cacao trees are an important pool of genes with potential to be used in cacao breeding and selection programs. For that reason, we assessed the diversity and population structure of Criollo-type trees (108 cultivars with Criollo phenotypic characteristics and 10 Criollo references) using 12 simple sequence repeat (SSR) markers. Cultivars were selected from 7 demes in the Soconusco region of southern Mexico. SSRs amplified 74 alleles with an average of 3.6 alleles per population. The overall populations showed an average observed heterozygosity of 0.28, indicating heterozygote deficiency (average fixation index F = 0.50). However, moderate allelic diversity was found within populations (Shannon index for all populations I = 0.97). Bayesian method analysis determined 2 genetic clusters (K = 2) within individuals. In concordance, an assignment test grouped 37 multilocus genotypes (including 10 references) into a first cluster (Criollo), 54 into a second (presumably Amelonado), and 27 admixed individuals unassigned at the 90% threshold likely corresponding to the Trinitario genotype. This classification was supported by the principal coordinate analysis and analysis of molecular variance, which showed 12% of variation among populations (FST = 0.123, P < 0.0001). Sampled demes sites (1- 7) in the Soconusco region did not show any evidence of clustering by geographic location, and this was supported by the Mantel test (Rxy = 0.54, P = 0.120). Individuals with high Criollo lineage planted in Soconusco farms could be an important reservoir of genes for future breeding programs searching for fine, taste, flavor, and aroma cocoa.

Geographical structuring of Trypanosoma cruzi populations from Chilean Triatoma infestans triatomines and their genetic relationship with other Latino American counterparts

PubMed Central

Venegas, J; Rojas, T; DÍaz, F; Miranda, S; Jercic, M I; González, C; Coñoepán, W; Pichuantes, S; RodrÍguez, J; Gajardo, M; Sánchez, G

2011-01-01

In order to obtain more information about the population structure of Chilean Trypanosoma cruzi, and their genetic relationship with other Latino American counterparts, we performed the study of T. cruzi samples detected in the midgut content of Triatoma infestans insects from three endemic regions of Chile. The genetic characteristics of these samples were analysed using microsatellite markers and PCR conditions that allow the detection of predominant T. cruzi clones directly in triatomine midgut content. Population genetic analyses using the Fisher’s exact method, analysis of molecular variance (AMOVA) and the determination of FST showed that the northern T. cruzi population sample was genetically differentiated from the two southern population counterparts. Further analysis showed that the cause of this genetic differentiation was the asymmetrical distribution of TcIII T. cruzi predominant clones. Considering all triatomines from the three regions, the most frequent predominant lineages were TcIII (38%), followed by TcI (34%) and hybrid (8%). No TcII lineage was observed along the predominant T. cruzi clones. The best phylogenetic reconstruction using the shared allelic genetic distance was concordant with the population genetic analysis and tree topology previously described studying foreign samples. The correlation studies showed that the lineage TcIII from the III region was genetically differentiated from the other two, and this differentiation was correlated with geographical distance including Chilean and mainly Brazilian samples. It will be interesting to investigate whether this geographical structure may be related with different clinical manifestation of Chagas disease. PMID:22325822

[Position of Betula ermanii population ecotone in Changbai Mountains].

PubMed

Zou, Chunjing; Wang, Xiaochun; Han, Shijie

2004-12-01

The vegetation on the northern slope of Changbai Mountains forms a vertical zone due to the vertical differentiation of moisture and heat conditions. Ecotones are obviously existed between different vegetation zones, but it is difficult to decide their positions. In the area from 1400 m to 2200 m elevation, we adopted the methods of gradient sampling, fractal analysis, population pattern analysis, and interspecific competition index analysis to describe Betula ermanii population ecotone. The results showed that there was a forest ecotone between Betula ermanii and Picea-Abies forest near elevation 1650 m, and there was a forest line ecotone between Betula ermanii and alpine tundra near elevation 2080 m.

Genetic diversity in natural populations of mangaba in Sergipe, the largest producer State in Brazil.

PubMed

Soares, A N R; Vitória, M F; Nascimento, A L S; Ledo, A S; Rabbani, A R C; Silva, A V C

2016-08-19

Mangaba (Hancornia speciosa Gomes) is found in areas of coastal tablelands in the Brazilian Northeast and Cerrado regions. This species has been subjected to habitat fragmentation that is mainly due to human activity, and requires conservation strategies. The aim of this study was to analyze the structure and inter- and intrapopulation genetic diversity of natural populations of H. speciosa Gomes using inter-simple sequence repeat (ISSR) molecular markers. A total of 155 individuals were sampled in 10 natural populations (ITA, PAC, IND, EST, BC, PIR, JAP, BG, NEO, and SANT) in the State of Sergipe, Brazil. Fifteen primers were used to generate 162 fragments with 100% polymorphism. Genetic analysis showed that the variability between populations (77%) was higher than within populations (23%). It was possible to identify five different groups by the unweighted pair group method with arithmetic mean and principal coordinate analysis, and only one individual (E10) remained isolated. Using ISSR markers it was possible to obtain a molecular profile of the populations evaluated, showing that these markers were effective and exhibited sufficient polymorphism to estimate the genetic variability of natural populations of H. speciosa Gomes.

New Methods for Analysis of Spatial Distribution and Coaggregation of Microbial Populations in Complex Biofilms

PubMed Central

Almstrand, Robert; Daims, Holger; Persson, Frank; Sörensson, Fred

2013-01-01

In biofilms, microbial activities form gradients of substrates and electron acceptors, creating a complex landscape of microhabitats, often resulting in structured localization of the microbial populations present. To understand the dynamic interplay between and within these populations, quantitative measurements and statistical analysis of their localization patterns within the biofilms are necessary, and adequate automated tools for such analyses are needed. We have designed and applied new methods for fluorescence in situ hybridization (FISH) and digital image analysis of directionally dependent (anisotropic) multispecies biofilms. A sequential-FISH approach allowed multiple populations to be detected in a biofilm sample. This was combined with an automated tool for vertical-distribution analysis by generating in silico biofilm slices and the recently developed Inflate algorithm for coaggregation analysis of microbial populations in anisotropic biofilms. As a proof of principle, we show distinct stratification patterns of the ammonia oxidizers Nitrosomonas oligotropha subclusters I and II and the nitrite oxidizer Nitrospira sublineage I in three different types of wastewater biofilms, suggesting niche differentiation between the N. oligotropha subclusters, which could explain their coexistence in the same biofilms. Coaggregation analysis showed that N. oligotropha subcluster II aggregated closer to Nitrospira than did N. oligotropha subcluster I in a pilot plant nitrifying trickling filter (NTF) and a moving-bed biofilm reactor (MBBR), but not in a full-scale NTF, indicating important ecophysiological differences between these phylogenetically closely related subclusters. By using high-resolution quantitative methods applicable to any multispecies biofilm in general, the ecological interactions of these complex ecosystems can be understood in more detail. PMID:23892743

Morphological and genetic divergence in Swedish postglacial stickleback (Pungitius pungitius) populations

PubMed Central

2011-01-01

Background An important objective of evolutionary biology is to understand the processes that govern phenotypic variation in natural populations. We assessed patterns of morphological and genetic divergence among coastal and inland lake populations of nine-spined stickleback in northern Sweden. Coastal populations are either from the Baltic coast (n = 5) or from nearby coastal lakes (n = 3) that became isolated from the Baltic Sea (< 100 years before present, ybp). Inland populations are from freshwater lakes that became isolated from the Baltic approximately 10,000 ybp; either single species lakes without predators (n = 5), or lakes with a recent history of predation (n = 5) from stocking of salmonid predators (~50 ybp). Results Coastal populations showed little variation in 11 morphological traits and had longer spines per unit of body length than inland populations. Inland populations were larger, on average, and showed greater morphological variation than coastal populations. A principal component analysis (PCA) across all populations revealed two major morphological axes related to spine length (PC1, 47.7% variation) and body size (PC2, 32.9% variation). Analysis of PCA scores showed marked similarity in coastal (Baltic coast and coastal lake) populations. PCA scores indicate that inland populations with predators have higher within-group variance in spine length and lower within-group variance in body size than inland populations without predators. Estimates of within-group PST (a proxy for QST) from PCA scores are similar to estimates of FST for coastal lake populations but PST >FST for Baltic coast populations. PST >FST for PC1 and PC2 for inland predator and inland no predator populations, with the exception that PST

Spatial accessibility of the population to urban health centres in Kermanshah, Islamic Republic of Iran: a geographic information systems analysis.

PubMed

Reshadat, S; Saedi, S; Zangeneh, A; Ghasemi, S R; Gilan, N R; Karbasi, A; Bavandpoor, E

2015-09-08

Geographic information systems (GIS) analysis has not been widely used in underdeveloped countries to ensure that vulnerable populations have accessibility to primary health-care services. This study applied GIS methods to analyse the spatial accessibility to urban primary-care centres of the population in Kermanshah city, Islamic Republic of Iran, by age and sex groups. In a descriptive-analytical study over 3 time periods, network analysis, mean centre and standard distance methods were applied using ArcGIS 9.3. The analysis was based on a standard radius of 750 m distance from health centres, walking speed of 1 m/s and desired access time to health centres of 12.5 mins. The proportion of the population with inadequate geographical access to health centres rose from 47.3% in 1997 to 58.4% in 2012. The mean centre and standard distance mapping showed that the spatial distribution of health centres in Kermanshah needed to be adjusted to changes in population distribution.

Spatial and temporal dynamics of fucoid populations (Ascophyllum nodosum and Fucus serratus): a comparison between central and range edge populations.

PubMed

Araújo, Rita M; Serrão, Ester A; Sousa-Pinto, Isabel; Åberg, Per

2014-01-01

Persistence of populations at range edges relies on local population dynamics and fitness, in the case of geographically isolated populations of species with low dispersal potential. Focusing on spatial variations in demography helps to predict the long-term capability for persistence of populations across the geographical range of species' distribution. The demography of two ecological and phylogenetically close macroalgal species with different life history characteristics was investigated by using stochastic, stage-based matrix models. Populations of Ascophyllum nodosum and Fucus serratus were sampled for up to 4 years at central locations in France and at their southern range limits in Portugal. The stochastic population growth rate (λ(s)) of A. nodosum was lower and more variable in central than in southern sites whilst for F. serratus this trend was reversed with λ(s) much lower and more variable in southern than in central populations. Individuals were larger in central than in southern populations for both species, which was reflected in the lower transition probabilities of individuals to larger size classes and higher probability of shrinkage in the southern populations. In both central and southern populations elasticity analysis (proportional sensitivity) of population growth rate showed that fertility elements had a small contribution to λ(s) that was more sensitive to changes in matrix transitions corresponding to survival. The highest elasticities were found for loop transitions in A. nodosum and for growth to larger size classes in F. serratus. Sensitivity analysis showed high selective pressure on individual growth for both species at both locations. The results of this study highlight the deterministic role of species-specific life-history traits in population demography across the geographical range of species. Additionally, this study demonstrates that individuals' life-transitions differ in vulnerability to environmental variability and shows the importance of vegetative compared to reproductive stages for the long-term persistence of populations.

Lack of genetic association between TREM2 and Alzheimer's disease in East Asian population: a systematic review and meta-analysis.

PubMed

Huang, Man; Wang, Dejun; Xu, Zhijun; Xu, Yongshan; Xu, Xiaoping; Ma, Yuefeng; Xia, Zheng

2015-09-01

Large-scale genome-wide association studies have identified TREM2 variants to be significantly associated with Alzheimer's disease (AD) in caucasian population. The goal of this systematic study and meta-analysis was to assess the association between Triggering receptor expressed on myeloid cells 2 (TREM2) variants and AD in East Asian population. In this study, literatures were searched in PubMed, MEDLINE, EMBASE, and the Cochrane library to screen citations from January 1990 to June 2014. Data analysis was done by using the Stata 12 software. Twelve studies were considered for analysis. A total of 13 535 patients with AD and 22 976 healthy controls were studied. The results showed that rs75932628 variant was significantly associated with AD in caucasian population (P < .001, odds ratio ¼ 3.17, 95% confidence interval 2.45-4.09). However, the association was not found in East Asian population. In our study, we found that TREM2 variant is likely not associated with AD in East Asian population.

Nonmetric tooth crown traits in a Sri Lankan aboriginal Vedda population.

PubMed

Peiris, H R D; Arambawatta, A K S; Hewapathirana, T N; Nanayakkara, C D; Chandrasekara, M; Wickramanayake, E

2011-12-01

This study was conducted to determine the frequencies of non-metric tooth crown traits of Vedda of Sri Lanka and to investigate the affinities of these morphological variations with those of other world populations. Fifty dental plaster casts were observed. The Arizona State University dental anthropology system was adopted for classification of the 16 traits observed. We used 13 traits to compare the Vedda and other world populations. Using the frequencies of 13 traits, Smith Mean Measure of Divergence was calculated to determine inter-population distances. Affinities among the Vedda and other world populations were expressed in two dimensions of the principal coordinate analysis. Cusp number in mandibular second molar and hypocone absence in maxillary second molar had the highest frequency at 95.9% and 93.8%, respectively. Shovelling, double shovelling in the maxillary central incisor and deflecting wrinkle in the mandibular first molar had the lowest frequency at 0%. The principal coordinate analysis showed that Sino American and Western Eurasian populations were separated in negative and positive directions in the first principal coordinate axis. Vedda located with the Western Eurasian population groups. Sahul and Sunda Pacific populations located in the intermediate position between Sino American and Western Eurasian populations. The dental phenotype of Vedda has close affinities with those of early south Asian populations. They are far different from Sino American and Sunda pacific populations. Vedda shows closer affinities to Sahul Pacific and South African (Bantu) populations. Copyright © 2011 Elsevier GmbH. All rights reserved.

Genetic structure of Onchidium "struma" (Mollusca: Gastropoda: Eupulmonata) from the coastal area of China based on mtCO I.

PubMed

Zhou, Na; Shen, Heding; Chen, Cheng; Sun, Bianna; Zheng, Pei; Wang, Chengnuan

2016-01-01

The genetic diversity and population genetic structure of Onchidium "struma" were investigated using mitochondrial cytochrome c oxidase subunit I (CO I) gene sequences. A total of 240 individuals representing 10 collection sites from across a large portion of its known range were included in the analysis. Overall, 42 haplotypes were defined and 97 polymorphic sites were observed. The O. "struma" populations had high haplotype diversity (0.9280) and nucleotide diversity (0.0404). We inferred that the early maturity and extensive survival habitat led to high genetic diversity of O. "struma" populations in China. Bayesian analysis and SAMOVA analysis showed significant genetic differentiation among populations and all populations were divided into two groups, (HK and HN) versus (GY, DF, CX, CN, ND and XM). The Mantel test revealed no significant correlation between geographic distance and genetic distance (r = 0.251; p = 0.058). Restricted gene flow caused by a shorter term pelagic veliger stage and limited dispersal potential were inferred to result in genetic differentiation among populations based on nested analysis. HK population might be an invasive species by artificial transplantation.

Spatial Analysis of Tuberculosis Cases in Migrants and Permanent Residents, Beijing, 2000–2006

PubMed Central

Jia, Zhong-Wei; Jia, Xiao-Wei; Dye, Christopher; Chen, Feng; Chen, Chang-Sheng; Zhang, Wen-Yi; Li, Xiao-Wen

2008-01-01

To determine the role of the migrant population in the transmission of tuberculosis (TB), we investigated the distribution and magnitude of TB in permanent residents and migrant populations of Beijing, People’s Republic of China, from 2000 through 2006. An exploratory spatial data analysis was applied to detect the “hot spots” of TB among the 2 populations. Results, using the data obtained from 2004–2006, showed that people who migrated from the western, middle, and eastern zones of China had a significantly higher risk of having TB than did permanent residents. These findings indicate that population fluctuations have affected the rate of TB prevalence in Beijing, and interventions to control TB should include the migrant population. PMID:18760008

Population, Migration, and Arctic Community Change

NASA Astrophysics Data System (ADS)

Hamilton, L.; Wirsing, J.

2017-12-01

North American Arctic communities commonly show decadal trends in population growth, driven by natural increase but variably offset by net migration with year-to-year volatility. Migration rates themselves can be a social indicator, integrating a range of push and pull factors. Population and population change of Arctic communities are basic scale properties affecting the resources needed to achieve sustainability, and the adaptations that may be required for climate change (such as relocation from flood-threatened locations). We examine interannual changes 1990-2016 in population and net migration of 43 Alaska Arctic communities, some facing serious threats of flooding. Our Alaska analysis updates previous work with additional years of data. We also extend this demographic analysis for the first time to 25 towns and villages of Nunavut, Canada.

Detecting population-environmental interactions with mismatched time series data.

PubMed

Ferguson, Jake M; Reichert, Brian E; Fletcher, Robert J; Jager, Henriëtte I

2017-11-01

Time series analysis is an essential method for decomposing the influences of density and exogenous factors such as weather and climate on population regulation. However, there has been little work focused on understanding how well commonly collected data can reconstruct the effects of environmental factors on population dynamics. We show that, analogous to similar scale issues in spatial data analysis, coarsely sampled temporal data can fail to detect covariate effects when interactions occur on timescales that are fast relative to the survey period. We propose a method for modeling mismatched time series data that couples high-resolution environmental data to low-resolution abundance data. We illustrate our approach with simulations and by applying it to Florida's southern Snail kite population. Our simulation results show that our method can reliably detect linear environmental effects and that detecting nonlinear effects requires high-resolution covariate data even when the population turnover rate is slow. In the Snail kite analysis, our approach performed among the best in a suite of previously used environmental covariates explaining Snail kite dynamics and was able to detect a potential phenological shift in the environmental dependence of Snail kites. Our work provides a statistical framework for reliably detecting population-environment interactions from coarsely surveyed time series. An important implication of this work is that the low predictability of animal population growth by weather variables found in previous studies may be due, in part, to how these data are utilized as covariates. © 2017 by the Ecological Society of America.

Genetic Variability and Population Structure of Disanthus cercidifolius subsp. longipes (Hamamelidaceae) Based on AFLP Analysis

PubMed Central

Yu, Yi; Fan, Qiang; Shen, Rujiang; Guo, Wei; Jin, Jianhua; Cui, Dafang; Liao, Wenbo

2014-01-01

Disanthus cercidifolius subsp. longipes is an endangered species in China. Genetic diversity and structure analysis of this species was investigated using amplified fragments length polymorphism (AFLP) fingerprinting. Nei's gene diversity ranged from 0.1290 to 0.1394. The AMOVA indicated that 75.06% of variation was distributed within populations, while the between-group component 5.04% was smaller than the between populations-within-group component 19.90%. Significant genetic differentiation was detected between populations. Genetic and geographical distances were not correlated. PCA and genetic structure analysis showed that populations from East China were together with those of the Nanling Range. These patterns of genetic diversity and levels of genetic variation may be the result of D. c. subsp. longipes restricted to several isolated habitats and “excess flowers production, but little fruit set”. It is necessary to protect all existing populations of D. c. subsp. longipes in order to preserve as much genetic variation as possible. PMID:25250583

Copy-number analysis and inference of subclonal populations in cancer genomes using Sclust.

PubMed

Cun, Yupeng; Yang, Tsun-Po; Achter, Viktor; Lang, Ulrich; Peifer, Martin

2018-06-01

The genomes of cancer cells constantly change during pathogenesis. This evolutionary process can lead to the emergence of drug-resistant mutations in subclonal populations, which can hinder therapeutic intervention in patients. Data derived from massively parallel sequencing can be used to infer these subclonal populations using tumor-specific point mutations. The accurate determination of copy-number changes and tumor impurity is necessary to reliably infer subclonal populations by mutational clustering. This protocol describes how to use Sclust, a copy-number analysis method with a recently developed mutational clustering approach. In a series of simulations and comparisons with alternative methods, we have previously shown that Sclust accurately determines copy-number states and subclonal populations. Performance tests show that the method is computationally efficient, with copy-number analysis and mutational clustering taking <10 min. Sclust is designed such that even non-experts in computational biology or bioinformatics with basic knowledge of the Linux/Unix command-line syntax should be able to carry out analyses of subclonal populations.

Genetic diversity analysis of Capparis spinosa L. populations by using ISSR markers.

PubMed

Liu, C; Xue, G P; Cheng, B; Wang, X; He, J; Liu, G H; Yang, W J

2015-12-09

Capparis spinosa L. is an important medicinal species in the Xinjiang Province of China. Ten natural populations of C. spinosa from 3 locations in North, Central, and South Xinjiang were studied using morphological trait inter simple sequence repeat (ISSR) molecular markers to assess the genetic diversity and population structure. In this study, the 10 ISSR primers produced 313 amplified DNA fragments, with 52% of fragments being polymorphic. Unweighted pair-group method with arithmetic average (UPGMA) cluster analysis indicated that 10 C. spinosa populations were clustered into 3 geographically distinct groups. The Nei gene of C. spinosa populations in different regions had Diversity and Shannon's information index ranges of 0.1312-0.2001 and 0.1004-0.1875, respectively. The 362 markers were used to construct the dendrogram based on the UPGMA cluster analysis. The dendrogram indicated that 10 populations of C. spinosa were clustered into 3 geographically distinct groups. The results showed these genotypes have high genetic diversity, and can be used for an alternative breeding program.

Strong population structure of Schizopygopsis chengi and the origin of S. chengi baoxingensis revealed by mtDNA and microsatellite markers.

PubMed

Liu, Dongqi; Hou, Feixia; Liu, Qin; Zhang, Xiuyue; Yan, Taiming; Song, Zhaobin

2015-02-01

The Tibetan Plateau underwent dramatic geological and climatic changes, which had important implications for genetic divergence and population dynamics of freshwater fish populations. Fluctuations of the ecogeographical environment and major hydrographic formations might have promoted the formation of new subspecies or species. In order to understand the impact of plateau uplift on freshwater fish evolutionary history, we estimated the genetic diversity and population structure in two subspecies of Schizopygopsis chengi (S. c. chengi and S. c. baoxingensis) in upper Yangtze River in Tibetan Plateau area using mitochondrial DNA control region and eight microsatellite markers, which suggested that there was a close genetic relationship. S. chengi showed some significant genetic structure that did not correlate with geographic distance. Bayesian assignment tests indicated that S. chengi samples in the study could be divided into four populations: upstream population, midstream population, tributary population and S. c. baoxingensis population. S. c. chengi and S. c. baoxingensis showed significant genetic divergence. However, phylogenetic analysis, population structure analysis and historical gene flow estimation suggested that there was close genetic relationship between S. c. baoxingensis and the Dawei population which belongs to populations of S. c. chengi. The time that Dawei population suffered from a bottleneck and S. c. baoxingensis underwent population expansion was congruent with the last glacial period on the Tibetan Plateau. The results confirmed the hypothesis that the Dawei River and Baoxing River were once connected, and the Dawei and Baoxing populations originated from a single population, but were isolated into separate populations because of crustal movements and the Baoxing population evolved as S. c. baoxingensis.

Strategic conservation of orchard germplasm based on indigenous knowledge and genetic diversity: a case study of sour orange populations in China.

PubMed

Ming, Feng; Liu, Qi-Kun; Shi, Jin-Lei; Wang, Wei; Lu, Bao-Rong

2009-01-01

To effectively conserve sour orange (Citrus aurantium L.) germplasm on two islands at the estuary of the Yangtze River in China, we estimated genetic variation and relationships of the known parental trees and their proposed descendents (young trees) using the fingerprints of random amplified polymorphic DNA (RAPD). Results based on RAPD analyses showed considerable genetic diversity in the parental populations (H(e)=0.202). The overall populations including the parental and young trees showed slightly higher genetic diversity (H(e)=0.298) than the parents, with about 10% variation between populations. An unweighted pair group method with arithmetic mean analysis dendrogram based on cluster analysis of the Jaccard similarity among individuals demonstrated a more complicated relationship of the parental and young trees from the two islands, although the young trees showed a clear association with parental trees. This indicates a significant contribution of parental trees in establishing the sour orange populations on the two islands. According to farmers' knowledge, conservation of only one or two parental trees would be sufficient because they believed that the whole populations were generated from a single mother tree. However, this study suggests that preserving most parental trees and some selected young trees with distant genetic relationships should be an effective conservation strategy for sour orange germplasm on the two islands.

Phylogeography of the dark fruit-eating bat Artibeus obscurus in the Brazilian Amazon.

PubMed

Ferreira, Wallax Augusto Silva; Borges, Bárbara do Nascimento; Rodrigues-Antunes, Symara; de Andrade, Fernanda Atanaena Gonçalves; Aguiar, Gilberto Ferreira de Souza; de Sousa e Silva-Junior, José; Marques-Aguiar, Suely Aparecida; Harada, Maria Lúcia

2014-01-01

Artibeus obscurus (Mammalia: Chiroptera) is endemic to South America, being found in at least 18 Brazilian states. Recent studies revealed that different populations of this genus present distinct phylogeographic patterns; however, very little is known on the population genetics structure of A. obscurus in the Amazon rainforest. Here, using a fragment (1010bp) of the mitochondrial gene cytochrome b from 87 samples, we investigated patterns of genetic divergence among populations of A. obscurus from different locations in the Brazilian Amazon rainforest and compared them with other Brazilian and South American regions. Analysis of molecular variance (AMOVA), fixation index (Fst) analysis, and phylogeographic patterns showed divergence between two major monophyletic groups, each one corresponding to a geographic region associated with the Atlantic and Amazon forest biomes. The Atlantic forest clusters formed a monophyletic group with a high bootstrap support and a fragmented distribution that follows the pattern predicted by the Refuge Theory. On the other hand, a different scenario was observed for the Amazon forest, where no fragmentation was identified. The AMOVA results revealed a significant geographic heterogeneity in the distribution of genetic variation, with 70% found within populations across the studied populations (Fst values ranging from 0.05864 to 0.09673; φST = 0.55). The intrapopulational analysis revealed that one population (Bragança) showed significant evidence of population expansion, with the formation of 2 distinct phylogroups, suggesting the occurrence of a subspecies or at least a different population in this region. These results also suggest considerable heterogeneity for A. obscurus in the Amazon region.

Host Plant-Associated Population Variation in the Carob Moth Ectomyelois ceratoniae in Iran: A Geometric Morphometric Analysis Suggests a Nutritional Basis.

PubMed Central

Mozaffarian, Fariba; Sarafrazi, Alimorad; Ganbalani, Gadir Nouri

2007-01-01

The carob moth, Ectomyelois ceratoniae (Zeller, 1839) (Lepidoptera: Pyralidae), is the most important pest of pomegranate in Iran. As it has been rarely recorded on other host plants, control methods have mostly been focused on its populations on pomegranate. In this study, shapes and sizes of wings were compared in populations on 4 host plants (pomegranate, fig, pistachio and walnut) using a landmark-based geometric morphometric method, and analysis of partial warp scores and centroid sizes. The results showed significantly smaller wing size in populations on pomegranate and a significant host plant-associated shape difference among populations as a consequence of allometric growth. This suggests that the wing size and shape differences among test populations may not have a genetic basis and could happen because of differences in the nutritional content of host plants. The results of the analysis suggest that the female carob moth lays her eggs on host plants that provide suitable conditions for hatching. The larger size of moths on hosts other than pomegranate showed that some host plants such as fig, pistachio and walnut can provide for increased stored nutritional reserves by larvae that may result in more successful over-wintering and higher fecundity in adults. This suggests that in spite of the more extensive activity of carob moth on pomegranate in Iran, populations on other host plants can have an important effect on expanding pest population sizes in following years which should be considered in control methods. PMID:20337550

Cultural hitchhiking and competition between patrilineal kin groups explain the post-Neolithic Y-chromosome bottleneck.

PubMed

Zeng, Tian Chen; Aw, Alan J; Feldman, Marcus W

2018-05-25

In human populations, changes in genetic variation are driven not only by genetic processes, but can also arise from cultural or social changes. An abrupt population bottleneck specific to human males has been inferred across several Old World (Africa, Europe, Asia) populations 5000-7000 BP. Here, bringing together anthropological theory, recent population genomic studies and mathematical models, we propose a sociocultural hypothesis, involving the formation of patrilineal kin groups and intergroup competition among these groups. Our analysis shows that this sociocultural hypothesis can explain the inference of a population bottleneck. We also show that our hypothesis is consistent with current findings from the archaeogenetics of Old World Eurasia, and is important for conceptions of cultural and social evolution in prehistory.

Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers.

PubMed

Zong, Jian-Wei; Zhao, Tian-Tian; Ma, Qing-Hua; Liang, Li-Song; Wang, Gui-Xi

2015-01-01

Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR) markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777). According to the coefficient of genetic differentiation (Fst = 0.1215), genetic variation within the populations (87.85%) were remarkably higher than among populations (12.15%). The average gene flow (Nm = 1.8080) significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080) among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages) dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei's genetic distance and geographic distance (km) among populations (r = 0.419, P = 0.005), suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic distance. These data provide comprehensive information for the development of conservation strategies of these valuable hazelnut resources.

Genetic variations in the Dravidian population of South West coast of India: Implications in designing case-control studies.

PubMed

D'Cunha, Anitha; Pandit, Lekha; Malli, Chaithra

2017-06-01

Indian data have been largely missing from genome-wide databases that provide information on genetic variations in different populations. This hinders association studies for complex disorders in India. This study was aimed to determine whether the complex genetic structure and endogamy among Indians could potentially influence the design of case-control studies for autoimmune disorders in the south Indian population. A total of 12 single nucleotide variations (SNVs) related to genes associated with autoimmune disorders were genotyped in 370 healthy individuals belonging to six different caste groups in southern India. Allele frequencies were estimated; genetic divergence and phylogenetic relationship within the various caste groups and other HapMap populations were ascertained. Allele frequencies for all genotyped SNVs did not vary significantly among the different groups studied. Wright's FSTwas 0.001 per cent among study population and 0.38 per cent when compared with Gujarati in Houston (GIH) population on HapMap data. The analysis of molecular variance results showed a 97 per cent variation attributable to differences within the study population and <1 per cent variation due to differences between castes. Phylogenetic analysis showed a separation of Dravidian population from other HapMap populations and particularly from GIH population. Despite the complex genetic origins of the Indian population, our study indicated a low level of genetic differentiation among Dravidian language-speaking people of south India. Case-control studies of association among Dravidians of south India may not require stratification based on language and caste.

Evaluation of genetic diversity of Panicum turgidum Forssk from Saudi Arabia.

PubMed

Assaeed, Abdulaziz M; Al-Faifi, Sulieman A; Migdadi, Hussein M; El-Bana, Magdy I; Al Qarawi, Abdulaziz A; Khan, Mohammad Altaf

2018-01-01

The genetic diversity of 177 accessions of Panicum turgidum Forssk, representing ten populations collected from four geographical regions in Saudi Arabia, was analyzed using amplified fragment length polymorphism (AFLP) markers. A set of four primer-pairs with two/three selective nucleotides scored 836 AFLP amplified fragments (putative loci/genome landmarks), all of which were polymorphic. Populations collected from the southern region of the country showed the highest genetic diversity parameters, whereas those collected from the central regions showed the lowest values. Analysis of molecular variance (AMOVA) revealed that 78% of the genetic variability was attributable to differences within populations. Pairwise values for population differentiation and genetic structure were statistically significant for all variances. The UPGMA dendrogram, validated by principal coordinate analysis-grouped accessions, corresponded to the geographical origin of the accessions. Mantel's test showed that there was a significant correlation between the genetic and geographical distances ( r  = 0.35, P  < 0.04). In summary, the AFLP assay demonstrated the existence of substantial genetic variation in P. turgidum . The relationship between the genetic diversity and geographical source of P. turgidum populations of Saudi Arabia, as revealed through this comprehensive study, will enable effective resource management and restoration of new areas without compromising adaptation and genetic diversity.

Assessment of Population Exposure to Coarse and Fine Particulate Matter in the Urban Areas of Chennai, India.

PubMed

Prasannavenkatesh, Ramachandran; Andimuthu, Ramachandran; Kandasamy, Palanivelu; Rajadurai, Geetha; Kumar, Divya Subash; Radhapriya, Parthasarathy; Ponnusamy, Malini

2015-01-01

Research outcomes from the epidemiological studies have found that the course (PM10) and the fine particulate matter (PM2.5) are mainly responsible for various respiratory health effects for humans. The population-weighted exposure assessment is used as a vital decision-making tool to analyze the vulnerable areas where the population is exposed to critical concentrations of pollutants. Systemic sampling was carried out at strategic locations of Chennai to estimate the various concentration levels of particulate pollution during November 2013-January 2014. The concentration of the pollutants was classified based on the World Health Organization interim target (IT) guidelines. Using geospatial information systems the pollution and the high-resolution population data were interpolated to study the extent of the pollutants at the urban scale. The results show that approximately 28% of the population resides in vulnerable locations where the coarse particulate matter exceeds the prescribed standards. Alarmingly, the results of the analysis of fine particulates show that about 94% of the inhabitants live in critical areas where the concentration of the fine particulates exceeds the IT guidelines. Results based on human exposure analysis show the vulnerability is more towards the zones which are surrounded by prominent sources of pollution.

Assessment of Population Exposure to Coarse and Fine Particulate Matter in the Urban Areas of Chennai, India

PubMed Central

Prasannavenkatesh, Ramachandran; Andimuthu, Ramachandran; Kandasamy, Palanivelu; Rajadurai, Geetha; Subash Kumar, Divya; Radhapriya, Parthasarathy; Ponnusamy, Malini

2015-01-01

Research outcomes from the epidemiological studies have found that the course (PM10) and the fine particulate matter (PM2.5) are mainly responsible for various respiratory health effects for humans. The population-weighted exposure assessment is used as a vital decision-making tool to analyze the vulnerable areas where the population is exposed to critical concentrations of pollutants. Systemic sampling was carried out at strategic locations of Chennai to estimate the various concentration levels of particulate pollution during November 2013–January 2014. The concentration of the pollutants was classified based on the World Health Organization interim target (IT) guidelines. Using geospatial information systems the pollution and the high-resolution population data were interpolated to study the extent of the pollutants at the urban scale. The results show that approximately 28% of the population resides in vulnerable locations where the coarse particulate matter exceeds the prescribed standards. Alarmingly, the results of the analysis of fine particulates show that about 94% of the inhabitants live in critical areas where the concentration of the fine particulates exceeds the IT guidelines. Results based on human exposure analysis show the vulnerability is more towards the zones which are surrounded by prominent sources of pollution. PMID:26258167

Population Change and Farm Dependence: Temporal and Spatial Variation in the U.S. Great Plains, 1900–2000

PubMed Central

CURTIS WHITE, KATHERINE J.

2008-01-01

I investigate the relationship between county population change and farm dependence in the Great Plains region during the twentieth century, using spatial data analysis techniques. This research is rooted in a long-standing sociological and demographic interest in population responses to economic transitions and informs the theoretical understanding of urbanization processes. Using census and environmental data, the analysis challenges earlier assertions of a simple transition in the relationship between farm dependence and population change that accompanied modern technological advancements, namely tractors (the mechanization thesis). Rather than observing the proposed positive-to-negative shift, study results show a negative association throughout the pre- and post-mechanization periods. Partial support is found if the thesis is revised to consider the relationship between population change and the change in farm dependence rather than the level of farm dependence. Findings show mixed support for an alternative argument that nonfarm industries moderate the influence of farm dependence (the industry complex thesis). In contrast to earlier applications of the thesis, industrial relations in the Great Plains context are characterized by specialization rather than cooperation. PMID:18613486

Human mtDNA hypervariable regions, HVR I and II, hint at deep common maternal founder and subsequent maternal gene flow in Indian population groups.

PubMed

Sharma, Swarkar; Saha, Anjana; Rai, Ekta; Bhat, Audesh; Bamezai, Ramesh

2005-01-01

We have analysed the hypervariable regions (HVR I and II) of human mitochondrial DNA (mtDNA) in individuals from Uttar Pradesh (UP), Bihar (BI) and Punjab (PUNJ), belonging to the Indo-European linguistic group, and from South India (SI), that have their linguistic roots in Dravidian language. Our analysis revealed the presence of known and novel mutations in both hypervariable regions in the studied population groups. Median joining network analyses based on mtDNA showed extensive overlap in mtDNA lineages despite the extensive cultural and linguistic diversity. MDS plot analysis based on Fst distances suggested increased maternal genetic proximity for the studied population groups compared with other world populations. Mismatch distribution curves, respective neighbour joining trees and other statistical analyses showed that there were significant expansions. The study revealed an ancient common ancestry for the studied population groups, most probably through common founder female lineage(s), and also indicated that human migrations occurred (maybe across and within the Indian subcontinent) even after the initial phase of female migration to India.

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.

DNA Barcoding of the Mexican Sedative and Anxiolytic Plant Galphimia glauca

PubMed Central

Sharma, Ashutosh; Folch, Jorge Luis; Cardoso-Taketa, Alexandre; Lorence, Argelia; Villarreal, María Luisa

2015-01-01

Ethnopharmacology relevance Galphimiaglauca (Malpighiaceae) is a Mexican plant popularly used as a tranquilizer in the treatment of nervous system disorders, although it is also used to treat other common illnesses. Aim of the study The aim of this investigation is to find out if populations of Galphimiaglauca collected in different regions and ecosystems in Mexico actually belong to the same species by using the contemporary technique of DNA barcodes. Our previous metabolic profiling study demonstrates that different collections of this plant obtained from various geographical areas exhibited diverse chemical profiles in terms of the active compounds named Galphimines. We expected the DNA barcodes apart from indicating the different species of Galphimia would indicate the active populations. Materials and methods We employed matK, rpoC1 and rbcL DNA barcodes to indicate the different species. Furthermore to investigate the possible impact of the several different ecosystems where the seven populations were collected, thin layer chromatography was employed to create a partial chemical profile, which was then compared with the metabolic profiles obtained by 1H-NMR and multivariate data analysis. Results and conclusions This study showed that the seven populations here analyzed contain at least three different species of the genus Galphimia, although each individual population is homogeneous. Interestingly our TLC analysis clearly showed that the active populations displayed a distinctively unique chemical profile. This work also showed that the use of DNA barcodes combined with chemical profile analysis is an excellent approach to solve the problems of quality control in the development of Galphimia-based medicines, as well as for any breeding programs for this species. PMID:23010364

Statistical properties of the radiation belt seed population

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

Boyd, A. J.; Spence, H. E.; Huang, C. -L.

Here, we present a statistical analysis of phase space density data from the first 26 months of the Van Allen Probes mission. In particular, we investigate the relationship between the tens and hundreds of keV seed electrons and >1 MeV core radiation belt electron population. Using a cross-correlation analysis, we find that the seed and core populations are well correlated with a coefficient of ≈0.73 with a time lag of 10–15 h. We present evidence of a seed population threshold that is necessary for subsequent acceleration. The depth of penetration of the seed population determines the inner boundary of themore » acceleration process. However, we show that an enhanced seed population alone is not enough to produce acceleration in the higher energies, implying that the seed population of hundreds of keV electrons is only one of several conditions required for MeV electron radiation belt acceleration.« less

Genetic variation in Indian populations of Scirpophaga incertulas as revealed by RAPD-PCR analysis.

PubMed

Kumar, L S; Sawant, A S; Gupta, V S; Ranjekar, P K

2001-02-01

Scirpophaga incertulas, commonly referred to as yellow stem borer, is a predominant pest of rice causing serious losses in its yield. Genetic variation among populations of Scirpophaga incertulas collected from 28 hotspot locations in India was examined using the randomly amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR). In all, 32 primers were used and 354 amplification products were observed. No RAPD-PCR bands diagnostic to the pest population from any specific region were identified. Cluster analysis using UPGMA showed that, with the exception of the pest population from Pattambi, all the populations cluster as one group with GD values in the range of 6-22%, suggesting that gene flow between populations is independent of geographic distance and appears to be unrestricted. The relatively high GD value of 48% exhibited by the pest population from Pattambi was the only exception.

Statistical properties of the radiation belt seed population

DOE PAGES

Boyd, A. J.; Spence, H. E.; Huang, C. -L.; ...

2016-07-25

Here, we present a statistical analysis of phase space density data from the first 26 months of the Van Allen Probes mission. In particular, we investigate the relationship between the tens and hundreds of keV seed electrons and >1 MeV core radiation belt electron population. Using a cross-correlation analysis, we find that the seed and core populations are well correlated with a coefficient of ≈0.73 with a time lag of 10–15 h. We present evidence of a seed population threshold that is necessary for subsequent acceleration. The depth of penetration of the seed population determines the inner boundary of themore » acceleration process. However, we show that an enhanced seed population alone is not enough to produce acceleration in the higher energies, implying that the seed population of hundreds of keV electrons is only one of several conditions required for MeV electron radiation belt acceleration.« less

Fasting insulin, insulin resistance and risk of hypertension in the general population: A meta-analysis.

PubMed

Wang, Feng; Han, Lili; Hu, Dayi

2017-01-01

Studies on the association of fasting insulin concentrations or insulin resistance with subsequent risk of hypertension have yielded conflicting results. To quantitatively assess the association of fasting insulin concentrations or homeostasis model assessment insulin resistance (HOMA-IR) with incident hypertension in a general population by performing a meta-analysis. We searched the PubMed and Embase databases until August 31, 2016 for prospective observational studies investigating the elevated fasting insulin concentrations or HOMA-IR with subsequent risk of hypertension in the general population. Pooled risk ratio (RR) and 95% confidence interval (CI) of hypertension was calculated for the highest versus the lowest category of fasting insulin or HOMA-IR. Eleven studies involving 10,230 hypertension cases were identified from 55,059 participants. Meta-analysis showed that the pooled adjusted RR of hypertension was 1.54 (95% CI 1.34-1.76) for fasting insulin concentrations and 1.43 (95% CI 1.27-1.62) for HOMA-IR comparing the highest to the lowest category. Subgroup analysis results showed that the association of fasting insulin concentrations with subsequent risk of hypertension seemed more pronounced in women (RR 2.07; 95% CI 1.19-3.60) than in men (RR 1.48; 95% CI 1.17-1.88). This meta-analysis suggests that elevated fasting insulin concentrations or insulin resistance as estimated by homeostasis model assessment is independently associated with an exacerbated risk of hypertension in the general population. Early intervention of hyperinsulinemia or insulin resistance may help clinicians to identify the high risk of hypertensive population. Copyright © 2016 Elsevier B.V. All rights reserved.

Comparative karyotypic analysis in the Alstroemeria hookeri Lodd. (Alstroemeriaceae) complex sensu Bayer (1987)

PubMed Central

2010-01-01

Alstroemeria L. (Alstroemeriaceae) is an American genus of monocots with two principal distribution centers in Chile and Brazil. In Chile, it is represented by about 32 species, most of them in central Chile, an area known for its high level of endemism. The “complex” Alstroemeriahookeri is endemic to Chile, where it is distributed from the Coquimbo to the Bío-Bío Region. We analyzed the karyotypes of 36 populations of this complex along its natural distribution. Ten metaphases per population were used for chromosome measurements. All analyzed subspecies presented a well defined asymmetric karyotype. The populations of A. hookeri subsp. hookeri collected in the coastal range of the Bío-Bío Region and the populations from the Central Valley of this Region (Pangal del Laja) presented striking morphological differences in the karyotype, mainly on chromosome 3. The population of A. hookeri subsp. recumbens from Pichicuy showed a polymorphism on chromosome 7, which differed from the other analyzed populations of this subspecies. Phenetic analysis suggested that A. hookeri subsp. cummingiana, which showed a more symmetrical karyotype and did not grow in sandy soil, should be alocated to A. cummingiana rather than considered as part of the hookeri complex. PMID:21637614

Model of Numerical Spatial Classification for Sustainable Agriculture in Badung Regency and Denpasar City, Indonesia

NASA Astrophysics Data System (ADS)

Trigunasih, N. M.; Lanya, I.; Subadiyasa, N. N.; Hutauruk, J.

2018-02-01

Increasing number and activity of the population to meet the needs of their lives greatly affect the utilization of land resources. Land needs for activities of the population continue to grow, while the availability of land is limited. Therefore, there will be changes in land use. As a result, the problems faced by land degradation and conversion of agricultural land become non-agricultural. The objectives of this research are: (1) to determine parameter of spatial numerical classification of sustainable food agriculture in Badung Regency and Denpasar City (2) to know the projection of food balance in Badung Regency and Denpasar City in 2020, 2030, 2040, and 2050 (3) to specify of function of spatial numerical classification in the making of zonation model of sustainable agricultural land area in Badung regency and Denpasar city (4) to determine the appropriate model of the area to protect sustainable agricultural land in spatial and time scale in Badung and Denpasar regencies. The method used in this research was quantitative method include: survey, soil analysis, spatial data development, geoprocessing analysis (spatial analysis of overlay and proximity analysis), interpolation of raster digital elevation model data, and visualization (cartography). Qualitative methods consisted of literature studies, and interviews. The parameters observed for a total of 11 parameters Badung regency and Denpasar as much as 9 parameters. Numerical classification parameter analysis results used the standard deviation and the mean of the population data and projections relationship rice field in the food balance sheet by modelling. The result of the research showed that, the number of different numerical classification parameters in rural areas (Badung) and urban areas (Denpasar), in urban areas the number of parameters is less than the rural areas. The based on numerical classification weighting and scores generate population distribution parameter analysis results of a standard deviation and average value. Numerical classification produced 5 models, which was divided into three zones are sustainable neighbourhood, buffer and converted in Denpasar and Badung. The results of Population curve parameter analysis in Denpasar showed normal curve, in contrast to the Badung regency showed abnormal curve, therefore Denpasar modeling carried out throughout the region, while in the Badung regency modeling done in each district. Relationship modelling and projections lands role in food balance in Badung views of sustainable land area whereas in Denpasar seen from any connection to the green open spaces in the spatial plan Denpasar 2011-2031. Modelling in Badung (rural) is different in Denpasar (urban), as well as population curve parameter analysis results in Badung showed abnormal curve while in Denpasar showed normal curve. Relationship modelling and projections lands role in food balance in the Badung regency sustainable in terms of land area, while in Denpasar in terms of linkages with urban green space in Denpasar City’s regional landuse plan of 2011-2031.

Money Income and Poverty Status of Families and Persons in the United States: 1985. (Advance Data from the March 1986 Current Population Survey).

ERIC Educational Resources Information Center

Current Population Reports, 1986

1986-01-01

Analysis of information gained from the March 1986 Current Population Survey (CPS) conducted by the Bureau of the Census shows the following results for the year 1985: (1) median family money income continued to move ahead of inflation; (2) the median earnings of men showed no statistically significant change from 1984, but the earnings of women…

[Analysis of Camellia rosthorniana populations fecundity].

PubMed

Cao, Guoxing; Zhong, Zhangcheng; Xie, Deti; Liu, Yun

2004-03-01

With the method of space substituting time, the structure of Camellia rosthorniana populations in three forest communities, i.e., Jiant bamboo forest, coniferous and broad-leaved mixed forest, and evergreen broad-leaved forest in Mt. Jinyun was investigated, and based on static life-tables, the fecundity tables and reproductive value tables of C. rosthorniana populations were constructed. Each reproductive parameter and its relation to bionomic strategies of C. rosthorniana populations were also analyzed. The results indicated that in evergreen broad-leaved forest, C. rosthorniana population had the longest life span and the greatest fitness. The stage of maximum reproductive value increased with increasing stability of the community. The sum of each population's reproductive value, residual reproductive value and total reproductive value for the whole life-history of C. rosthorniana also increased with increasing maturity of the community, showing their inherent relationships with reproductive fitness. As regards to bionomic strategy, C. rosthorniana showed mainly the characteristics of a k-strategies, but in less stable community, the reproductive parameters were greatly changed, showing some characteristics of a r-strategies.

Genetic Diversity and Population Structure of Saccharomyces cerevisiae Strains Isolated from Different Grape Varieties and Winemaking Regions

PubMed Central

Schuller, Dorit; Cardoso, Filipa; Sousa, Susana; Gomes, Paula; Gomes, Ana C.; Santos, Manuel A. S.; Casal, Margarida

2012-01-01

We herein evaluate intraspecific genetic diversity of fermentative vineyard-associated S. cerevisiae strains and evaluate relationships between grape varieties and geographical location on populational structures. From the musts obtained from 288 grape samples, collected from two wine regions (16 vineyards, nine grape varieties), 94 spontaneous fermentations were concluded and 2820 yeast isolates were obtained that belonged mainly (92%) to the species S. cerevisiae. Isolates were classified in 321 strains by the use of ten microsatellite markers. A high strain diversity (8–43 strains per fermentation) was associated with high percentage (60–100%) of fermenting samples per vineyard, whereas a lower percentage of spontaneous fermentations (0–40%) corresponded to a rather low strain diversity (1–10 strains per fermentation). For the majority of the populations, observed heterozygosity (Ho) was about two to five times lower than the expected heterozygosity (He). The inferred ancestry showed a very high degree of admixture and divergence was observed between both grape variety and geographical region. Analysis of molecular variance showed that 81–93% of the total genetic variation existed within populations, while significant differentiation within the groups could be detected. Results from AMOVA analysis and clustering of allelic frequencies agree in the distinction of genetically more dispersed populations from the larger wine region compared to the less extended region. Our data show that grape variety is a driver of populational structures, because vineyards with distinct varieties harbor genetically more differentiated S. cerevisiae populations. Conversely, S. cerevisiae strains from vineyards in close proximity (5–10 km) that contain the same grape variety tend to be less divergent. Populational similarities did not correlate with the distance between vineyards of the two wine regions. Globally, our results show that populations of S. cerevisiae in vineyards may occur locally due to multi-factorial influences, one of them being the grape variety. PMID:22393409

Morphology and genetics of Anadenanthera colubrina var. cebil (Fabaceae) tree from salta (Northwestern Argentina).

PubMed

de Viana, Marta L; Giamminola, Eugenia; Russo, Roberta; Ciaccio, Mirella

2014-06-01

Anadenanthera colubrina var. cebil is an important tree species for its cultural, economic, and medicinal uses in South America. In order to characterize A. colubrina populations, we collected fruits from four different sites (San Bernardo, El Cebilar, Metán and El Gallinato) within the species distribution area in Salta Province, Northwestern Argentina. For this, a total of 75 fruits and seeds per site were collected and described using morphological (fruits size and weight; seed weight and number per fruit) and genetic descriptors (ribosomic DNA extraction and PCR; nucleotide alignment and phylogenetic analysis) with standard protocols. Our results showed that the San Bernardo population had the heaviest fruits and seeds (7.89 +/- 0.2g and 0.19 +/- 0.002, respectively), and the Cebilar population the lightest (6.25 +/- 0.18g and 0.15 +/- 0.002g, respectively). Fruits and seeds from Metán and El Gallinato showed similar and intermediate values. The proportion viable (39 to 55%) and aborted (43 to 57%) seeds was different, while the proportion of predated (1.7 to 4.2%) seeds was similar among populations. The genetic analysis showed variability of ITS sequences within the especies, and also when compared with the same Brazilian species. Both, morphologic and genetic descriptors showed a high level of similarity between San Bernardo and Metán, and between El Cebilar and El Gallinato populations. Further studies are needed to assess levels of phenotypic and genetic variability within and between populations of different plant species, since this information is crucial for biodiversity and germplasm long-term conservation.

The Age Specific Incidence Anomaly Suggests that Cancers Originate During Development

NASA Astrophysics Data System (ADS)

Brody, James P.

The accumulation of genetic alterations causes cancers. Since this accumulation takes time, the incidence of most cancers is thought to increase exponentially with age. However, careful measurements of the age-specific incidence show that the specific incidence for many forms of cancer rises with age to a maximum, and then decreases. This decrease in the age-specific incidence with age is an anomaly. Understanding this anomaly should lead to a better understanding of how tumors develop and grow. Here we derive the shape of the age-specific incidence, showing that it should follow the shape of a Weibull distribution. Measurements indicate that the age-specific incidence for colon cancer does indeed follow a Weibull distribution. This analysis leads to the interpretation that for colon cancer two subpopulations exist in the general population: a susceptible population and an immune population. Colon tumors will only occur in the susceptible population. This analysis is consistent with the developmental origins of disease hypothesis and generalizable to many other common forms of cancer.

Control for Population Structure and Relatedness for Binary Traits in Genetic Association Studies via Logistic Mixed Models

PubMed Central

Chen, Han; Wang, Chaolong; Conomos, Matthew P.; Stilp, Adrienne M.; Li, Zilin; Sofer, Tamar; Szpiro, Adam A.; Chen, Wei; Brehm, John M.; Celedón, Juan C.; Redline, Susan; Papanicolaou, George J.; Thornton, Timothy A.; Laurie, Cathy C.; Rice, Kenneth; Lin, Xihong

2016-01-01

Linear mixed models (LMMs) are widely used in genome-wide association studies (GWASs) to account for population structure and relatedness, for both continuous and binary traits. Motivated by the failure of LMMs to control type I errors in a GWAS of asthma, a binary trait, we show that LMMs are generally inappropriate for analyzing binary traits when population stratification leads to violation of the LMM’s constant-residual variance assumption. To overcome this problem, we develop a computationally efficient logistic mixed model approach for genome-wide analysis of binary traits, the generalized linear mixed model association test (GMMAT). This approach fits a logistic mixed model once per GWAS and performs score tests under the null hypothesis of no association between a binary trait and individual genetic variants. We show in simulation studies and real data analysis that GMMAT effectively controls for population structure and relatedness when analyzing binary traits in a wide variety of study designs. PMID:27018471

The hOGG1 Ser326Cys Gene Polymorphism and Breast Cancer Risk in Saudi Population.

PubMed

Alanazi, Mohammed; Pathan, Akbar Ali Khan; Shaik, Jilani P; Alhadheq, Abdullah; Khan, Zahid; Khan, Wajahatullah; Al Naeem, Abdulrahman; Parine, Narasimha Reddy

2017-07-01

The purpose of this study was to test the association between human 8-oxoguanine glycosylase 1 (hOGG1) gene polymorphisms and susceptibility to breast cancer in Saudi population. We have also aimed to screen the hOGG1 Ser326Cys polymorphism effect on structural and functional properties of the hOGG1 protein using in silico tools. We have analyzed four SNPs of hOGG1 gene among Saudi breast cancer patients along with healthy controls. Genotypes were screened using TaqMan SNP genotype analysis method. Experimental data was analyzed using Chi-square, t test and logistic regression analysis using SPSS software (v.16). In silco analysis was conducted using discovery studio and HOPE program. Genotypic analysis showed that hOGG1 rs1052133 (Ser326Cys) is significantly associated with breast cancer samples in Saudi population, however rs293795 (T >C), rs2072668 (C>G) and rs2075747 (G >A) did not show any association with breast cancer. The hOGG1 SNP rs1052133 (Ser326Cys) minor allele T showed a significant association with breast cancer samples (OR = 1.78, χ2 = 7.86, p = 0.02024). In silico structural analysis was carried out to compare the wild type (Ser326) and mutant (Cys326) protein structures. The structural prediction studies revealed that Ser326Cys variant may destabilize the protein structure and it may disturb the hOGG1 function. Taken together this is the first In silico study report to confirm Ser326Cys variant effect on structural and functional properties of hOGG1 gene and Ser326Cys role in breast cancer susceptibility in Saudi population.

Genetic variation among wild lake trout populations: the 'wanted' and the 'unwanted'

USGS Publications Warehouse

Burnham-Curtis, Mary K.; Kallemeyn, Larry W.; Bronte, Charles R.; Greswell, Robert E.; Dwyer, Pat; Hamre, R.H.

1997-01-01

In this study we examine genetic variation within and among self-sustaining lake trout populations from the Great Lakes basin, the Rainy Lake basin, and Yellowstone Lake. We used RFLP analysis and direct sequencing to examine DNA sequence variation among several mitochondrial and nuclear genes, including highly conserved loci (e.g. cytochrome b, nuclear exon regions) and highly variable loci (e.g. mitochondrial d-loop and nuclear intron regions). Native Lake Superior lake trout populations show high levels of genetic diversity, while populations from the Rainy Lake basin show little or none. The lake trout population sampled from Yellowstone Lake shows moderate genetic diversity, possibly representative of a relatively large source population closely related to lake trout from Lewis Lake, Wyoming. There has been significant social and management controversy involving these lake trout populations, particularly those that are located in National Parks. In the Great Lakes and Rainy Lake basins, the controversy involves the degree to which hatchery supplementation can contribute to or negatively impact self-sustaining populations which are highly desired by recreational and commercial fisheries. In Yellowstone Lake, the lake trout are viewed as an undesirable intruder that may interfere with resident populations of highly prized native cutthroat trout.

CLU rs2279590 polymorphism contributes to Alzheimer's disease susceptibility in Caucasian and Asian populations.

PubMed

Zhang, Shuyan; Zhang, Donghui; Jiang, Yongshuai; Wu, Lina; Shang, Hong; Liu, Jiafeng; Feng, Rennan; Liao, Mingzhi; Zhang, Liangcai; Liu, Yong; Liu, Guiyou; Li, Keshen

2015-03-01

It is reported that CLU rs2279590 polymorphism is significantly associated with Alzheimer's disease (AD) in European ancestry. Recent studies investigated rs2279590 polymorphism in Asian population (Chinese, Japanese and Korean). Four studies showed negative association and two studies showed weak association between rs2279590 and AD. We believe that the weak association or no association may be caused by the relatively small sample size in Asian population. Here, we reinvestigated the association in Asian population. Meanwhile, to investigate the genetic heterogeneity of the rs2279590 polymorphism in Asian and Caucasian populations, we searched the PubMed and AlzGene databases and selected 11 independent studies (6 studies in Asian population and 5 studies in Caucasian population) including 20,655 individuals (8,605 cases and 12,050 controls) for meta-analysis. Our results showed significant association between rs2279590 polymorphism and AD in Asian population with P = 2.00E-04 and P = 2.00E-04 using additive and recessive models, respectively. We observed no significant heterogeneity between Asian and Caucasian populations. We believe that our results may be helpful to understand the mechanisms of CLU in AD pathogenesis and will be useful for future genetic studies in AD.

Effective Population Size, Genetic Variation, and Their Relevance for Conservation: The Bighorn Sheep in Tiburon Island and Comparisons with Managed Artiodactyls

PubMed Central

Gasca-Pineda, Jaime; Cassaigne, Ivonne; Alonso, Rogelio A.; Eguiarte, Luis E.

2013-01-01

The amount of genetic diversity in a finite biological population mostly depends on the interactions among evolutionary forces and the effective population size (N e) as well as the time since population establishment. Because the N e estimation helps to explore population demographic history, and allows one to predict the behavior of genetic diversity through time, N e is a key parameter for the genetic management of small and isolated populations. Here, we explored an N e-based approach using a bighorn sheep population on Tiburon Island, Mexico (TI) as a model. We estimated the current (N crnt) and ancestral stable (N stbl) inbreeding effective population sizes as well as summary statistics to assess genetic diversity and the demographic scenarios that could explain such diversity. Then, we evaluated the feasibility of using TI as a source population for reintroduction programs. We also included data from other bighorn sheep and artiodactyl populations in the analysis to compare their inbreeding effective size estimates. The TI population showed high levels of genetic diversity with respect to other managed populations. However, our analysis suggested that TI has been under a genetic bottleneck, indicating that using individuals from this population as the only source for reintroduction could lead to a severe genetic diversity reduction. Analyses of the published data did not show a strict correlation between H E and N crnt estimates. Moreover, we detected that ancient anthropogenic and climatic pressures affected all studied populations. We conclude that the estimation of N crnt and N stbl are informative genetic diversity estimators and should be used in addition to summary statistics for conservation and population management planning. PMID:24147115

Testing for Non-Random Mating: Evidence for Ancestry-Related Assortative Mating in the Framingham Heart Study

PubMed Central

Sebro, Ronnie; Hoffman, Thomas J.; Lange, Christoph; Rogus, John J.; Risch, Neil J.

2013-01-01

Population stratification leads to a predictable phenomenon—a reduction in the number of heterozygotes compared to that calculated assuming Hardy-Weinberg Equilibrium (HWE). We show that population stratification results in another phenomenon—an excess in the proportion of spouse-pairs with the same genotypes at all ancestrally informative markers, resulting in ancestrally related positive assortative mating. We use principal components analysis to show that there is evidence of population stratification within the Framingham Heart Study, and show that the first principal component correlates with a North-South European cline. We then show that the first principal component is highly correlated between spouses (r=0.58, p=0.0013), demonstrating that there is ancestrally related positive assortative mating among the Framingham Caucasian population. We also show that the single nucleotide polymorphisms loading most heavily on the first principal component show an excess of homozygotes within the spouses, consistent with similar ancestry-related assortative mating in the previous generation. This nonrandom mating likely affects genetic structure seen more generally in the North American population of European descent today, and decreases the rate of decay of linkage disequilibrium for ancestrally informative markers. PMID:20842694

Different level of population differentiation among human genes.

PubMed

Wu, Dong-Dong; Zhang, Ya-Ping

2011-01-14

During the colonization of the world, after dispersal out of African, modern humans encountered changeable environments and substantial phenotypic variations that involve diverse behaviors, lifestyles and cultures, were generated among the different modern human populations. Here, we study the level of population differentiation among different populations of human genes. Intriguingly, genes involved in osteoblast development were identified as being enriched with higher FST SNPs, a result consistent with the proposed role of the skeletal system in accounting for variation among human populations. Genes involved in the development of hair follicles, where hair is produced, were also found to have higher levels of population differentiation, consistent with hair morphology being a distinctive trait among human populations. Other genes that showed higher levels of population differentiation include those involved in pigmentation, spermatid, nervous system and organ development, and some metabolic pathways, but few involved with the immune system. Disease-related genes demonstrate excessive SNPs with lower levels of population differentiation, probably due to purifying selection. Surprisingly, we find that Mendelian-disease genes appear to have a significant excessive of SNPs with high levels of population differentiation, possibly because the incidence and susceptibility of these diseases show differences among populations. As expected, microRNA regulated genes show lower levels of population differentiation due to purifying selection. Our analysis demonstrates different level of population differentiation among human populations for different gene groups.

Cost effectiveness of population based BRCA1 founder mutation testing in Sephardi Jewish women.

PubMed

Patel, Shreeya; Legood, Rosa; Evans, D Gareth; Turnbull, Clare; Antoniou, Antonis C; Menon, Usha; Jacobs, Ian; Manchanda, Ranjit

2018-04-01

Population-based BRCA1/BRCA2 founder-mutation testing has been demonstrated as cost effective compared with family history based testing in Ashkenazi Jewish women. However, only 1 of the 3 Ashkenazi Jewish BRCA1/BRCA2 founder mutations (185delAG[c.68_69delAG]), 5382insC[c.5266dupC]), and 6174delT[c.5946delT]) is found in the Sephardi Jewish population (185delAG[c.68_69delAG]), and the overall prevalence of BRCA mutations in the Sephardi Jewish population is accordingly lower (0.7% compared with 2.5% in the Ashkenazi Jewish population). Cost-effectiveness analyses of BRCA testing have not previously been performed at these lower BRCA prevalence levels seen in the Sephardi Jewish population. Here we present a cost-effectiveness analysis for UK and US populations comparing population testing with clinical criteria/family history-based testing in Sephardi Jewish women. A Markov model was built comparing the lifetime costs and effects of population-based BRCA1 testing, with testing using family history-based clinical criteria in Sephardi Jewish women aged ≥30 years. BRCA1 carriers identified were offered magnetic resonance imaging/mammograms and risk-reducing surgery. Costs are reported at 2015 prices. Outcomes include breast cancer, ovarian cancer, and excess deaths from heart disease. All costs and outcomes are discounted at 3.5%. The time horizon is lifetime, and perspective is payer. The incremental cost-effectiveness ratio per quality-adjusted life-year was calculated. Parameter uncertainty was evaluated through 1-way and probabilistic sensitivity analysis. Population testing resulted in gain in life expectancy of 12 months (quality-adjusted life-year = 1.00). The baseline discounted incremental cost-effectiveness ratio for UK population-based testing was £67.04/quality-adjusted life-year and for US population was $308.42/quality-adjusted life-year. Results were robust in the 1-way sensitivity analysis. The probabilistic sensitivity analysis showed 100% of simulations were cost effective at £20,000/quality-adjusted life-year UK and the $100,000/quality-adjusted life-year US willingness-to-pay thresholds. Scenario analysis showed that population testing remains cost effective in UK and US populations, even if premenopausal oophorectomy does not reduce breast cancer risk or if hormone replacement therapy compliance is nil. Population-based BRCA1 testing is highly cost effective compared with clinical criteria-driven approach in Sephardi Jewish women. This supports changing the paradigm to population-based BRCA testing in the Jewish population, regardless of Ashkenazi/Sephardi ancestry. Copyright © 2017 Elsevier Inc. All rights reserved.

Individualized head-related transfer functions based on population grouping.

PubMed

Xu, Song; Li, Zhizhong; Salvendy, Gavriel

2008-11-01

A method is proposed to divide a population into different groups for partial individualization of head-related transfer functions (HRTFs). Borrowing the basic idea in sizing system design, factor analysis is used to identify the most representative measurements which are then in a case study used to group the population. The comparison between the group mean HRTFs and the population mean HRTFs shows that the group mean HRTFs could greatly reduce spectral distortion at most sampled positions.

CR1 rs3818361 Polymorphism Contributes to Alzheimer's Disease Susceptibility in Chinese Population.

PubMed

Li, Yongning; Song, Dongjing; Jiang, Yongshuai; Wang, Jingwei; Feng, Rennan; Zhang, Liangcai; Wang, Guangyu; Chen, Zugen; Wang, Renzhi; Jiang, Qinghua; Liu, Guiyou

2016-08-01

Recent genome-wide association studies (GWAS) reported CR1 rs3818361 polymorphism to be an Alzheimer's disease (AD) susceptibility variant in European ancestry. Three independent studies investigated this association in Chinese population. However, these studies reported weak or no significant association. Here, we reinvestigated the association using all the samples from three independent studies in Chinese population (N = 4047, 1244 AD cases and 2803 controls). We also selected three independent studies in European ancestry population (N = 11787, 3939 AD cases and 7848 controls) to evaluate the effect of rs3818361 polymorphism on AD risk in different ethnic backgrounds. In Chinese population, we did not identified significant heterogeneity using additive, recessive, and dominant genetic models. Meta-analysis showed significant association between rs3818361 and AD with P = 6.00E-03 and P = 5.00E-03. We further identified no heterogeneity of rs3818361 polymorphism between Chinese and European populations. We found that rs3818361 polymorphism contributed to AD with similar genetic risk in Chinese and European populations. In summary, this is the first study to show significant association between rs3818361 polymorphism and AD in Chinese population by a meta-analysis method. Our findings indicate that the effect of CR1 rs3818361 polymorphism on AD risk in Chinese cohorts is consistent with the increased risk observed in European AD cohorts.

Long-term on-farm participatory maize breeding by stratified mass selection retains molecular diversity while improving agronomic performance.

PubMed

Alves, Mara Lisa; Belo, Maria; Carbas, Bruna; Brites, Cláudia; Paulo, Manuel; Mendes-Moreira, Pedro; Brites, Carla; Bronze, Maria do Rosário; Šatović, Zlatko; Vaz Patto, Maria Carlota

2018-02-01

Modern maize breeding programs gave rise to genetically uniform varieties that can affect maize's capacity to cope with increasing climate unpredictability. Maize populations, genetically more heterogeneous, can evolve and better adapt to a broader range of edaphic-climatic conditions. These populations usually suffer from low yields; it is therefore desirable to improve their agronomic performance while maintaining their valuable diversity levels. With this objective, a long-term participatory breeding/on-farm conservation program was established in Portugal. In this program, maize populations were subject to stratified mass selection. This work aimed to estimate the effect of on-farm stratified mass selection on the agronomic performance, quality, and molecular diversity of two historical maize populations. Multilocation field trials, comparing the initial populations with the derived selection cycles, showed that this selection methodology led to agronomic improvement for one of the populations. The molecular diversity analysis, using microsatellites, revealed that overall genetic diversity in both populations was maintained throughout selection. The comparison of quality parameters between the initial populations and the derived selection cycles was made using kernel from a common-garden experiment. This analysis showed that the majority of the quality traits evaluated progressed erratically over time. In conclusion, this breeding approach, through simple and low-cost methodologies, proved to be an alternative strategy for genetic resources' on-farm conservation.

Classification accuracy on the family planning participation status using kernel discriminant analysis

NASA Astrophysics Data System (ADS)

Kurniawan, Dian; Suparti; Sugito

2018-05-01

Population growth in Indonesia has increased every year. According to the population census conducted by the Central Bureau of Statistics (BPS) in 2010, the population of Indonesia has reached 237.6 million people. Therefore, to control the population growth rate, the government hold Family Planning or Keluarga Berencana (KB) program for couples of childbearing age. The purpose of this program is to improve the health of mothers and children in order to manifest prosperous society by controlling births while ensuring control of population growth. The data used in this study is the updated family data of Semarang city in 2016 that conducted by National Family Planning Coordinating Board (BKKBN). From these data, classifiers with kernel discriminant analysis will be obtained, and also classification accuracy will be obtained from that method. The result of the analysis showed that normal kernel discriminant analysis gives 71.05 % classification accuracy with 28.95 % classification error. Whereas triweight kernel discriminant analysis gives 73.68 % classification accuracy with 26.32 % classification error. Using triweight kernel discriminant for data preprocessing of family planning participation of childbearing age couples in Semarang City of 2016 can be stated better than with normal kernel discriminant.

Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle

PubMed Central

Upadhyay, M R; Chen, W; Lenstra, J A; Goderie, C R J; MacHugh, D E; Park, S D E; Magee, D A; Matassino, D; Ciani, F; Megens, H-J; van Arendonk, J A M; Groenen, M A M; Marsan, P A; Balteanu, V; Dunner, S; Garcia, J F; Ginja, C; Kantanen, J

2017-01-01

The domestication of taurine cattle initiated ~10 000 years ago in the Near East from a wild aurochs (Bos primigenius) population followed by their dispersal through migration of agriculturalists to Europe. Although gene flow from wild aurochs still present at the time of this early dispersion is still debated, some of the extant primitive cattle populations are believed to possess the aurochs-like primitive features. In this study, we use genome-wide single nucleotide polymorphisms to assess relationship, admixture patterns and demographic history of an ancient aurochs sample and European cattle populations, several of which have primitive features and are suitable for extensive management. The principal component analysis, the model-based clustering and a distance-based network analysis support previous works suggesting different histories for north-western and southern European cattle. Population admixture analysis indicates a zebu gene flow in the Balkan and Italian Podolic cattle populations. Our analysis supports the previous report of gene flow between British and Irish primitive cattle populations and local aurochs. In addition, we show evidence of aurochs gene flow in the Iberian cattle populations indicating wide geographical distribution of the aurochs. Runs of homozygosity (ROH) reveal that demographic processes like genetic isolation and breed formation have contributed to genomic variations of European cattle populations. The ROH also indicate recent inbreeding in southern European cattle populations. We conclude that in addition to factors such as ancient human migrations, isolation by distance and cross-breeding, gene flow between domestic and wild-cattle populations also has shaped genomic composition of European cattle populations. PMID:27677498

Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle.

PubMed

Upadhyay, M R; Chen, W; Lenstra, J A; Goderie, C R J; MacHugh, D E; Park, S D E; Magee, D A; Matassino, D; Ciani, F; Megens, H-J; van Arendonk, J A M; Groenen, M A M

2017-02-01

The domestication of taurine cattle initiated ~10 000 years ago in the Near East from a wild aurochs (Bos primigenius) population followed by their dispersal through migration of agriculturalists to Europe. Although gene flow from wild aurochs still present at the time of this early dispersion is still debated, some of the extant primitive cattle populations are believed to possess the aurochs-like primitive features. In this study, we use genome-wide single nucleotide polymorphisms to assess relationship, admixture patterns and demographic history of an ancient aurochs sample and European cattle populations, several of which have primitive features and are suitable for extensive management. The principal component analysis, the model-based clustering and a distance-based network analysis support previous works suggesting different histories for north-western and southern European cattle. Population admixture analysis indicates a zebu gene flow in the Balkan and Italian Podolic cattle populations. Our analysis supports the previous report of gene flow between British and Irish primitive cattle populations and local aurochs. In addition, we show evidence of aurochs gene flow in the Iberian cattle populations indicating wide geographical distribution of the aurochs. Runs of homozygosity (ROH) reveal that demographic processes like genetic isolation and breed formation have contributed to genomic variations of European cattle populations. The ROH also indicate recent inbreeding in southern European cattle populations. We conclude that in addition to factors such as ancient human migrations, isolation by distance and cross-breeding, gene flow between domestic and wild-cattle populations also has shaped genomic composition of European cattle populations.

Population studies of Glossina pallidipes in Ethiopia: emphasis on cuticular hydrocarbons and wing morphometric analysis.

PubMed

Getahun, M N; Cecchi, G; Seyoum, E

2014-10-01

Tsetse flies, like many insects, use pheromones for inter- and intra-specific communication. Several of their pheromones are cuticular hydrocarbons (CHCs) that are perceived by contact at close range. We hypothesized that for a successful implementation of the Sterile Insect Technique (SIT), along with proper identification of target area and target species, the target tsetse populations and the sterile flies must chemically communicate with each other. To study the population structuring of Glossina pallidipes in Ethiopia, CHCs were extracted and analyzed from three tsetse belts. As a comparative approach, wing morphometric analysis was performed. The analysis of the relative abundance of CHCs revealed that populations of G. pallidipes from the Rift Valley tsetse belt showed a distinct clustering compared to populations from the other two belts. The spatial pattern of CHC differences was complemented by the wing morphometric analysis. Our data suggest that CHCs of known biological and ecological role, when combined with wing morphometric data, will provide an alternative means for the study of population structuring of Glossina populations. This could aid the planning of area wide control strategies using SIT, which is dependent on sexual competence. Copyright © 2014 International Atomic Energy Agency 2014. Published by Elsevier B.V. All rights reserved.

Phylogeography, intraspecific structure and sex-biased dispersal of Dall's porpoise, Phocoenoides dalli, revealed by mitochondrial and microsatellite DNA analyses.

PubMed

Escorza-Treviño, S; Dizon, A E

2000-08-01

Mitochondrial DNA (mtDNA) control-region sequences and microsatellite loci length polymorphisms were used to estimate phylogeographical patterns (historical patterns underlying contemporary distribution), intraspecific population structure and gender-biased dispersal of Phocoenoides dalli dalli across its entire range. One-hundred and thirteen animals from several geographical strata were sequenced over 379 bp of mtDNA, resulting in 58 mtDNA haplotypes. Analysis using F(ST) values (based on haplotype frequencies) and phi(ST) values (based on frequencies and genetic distances between haplotypes) yielded statistically significant separation (bootstrap values P < 0.05) among most of the stocks currently used for management purposes. A minimum spanning network of haplotypes showed two very distinctive clusters, differentially occupied by western and eastern populations, with some common widespread haplotypes. This suggests some degree of phyletic radiation from west to east, superimposed on gene flow. Highly male-biased migration was detected for several population comparisons. Nuclear microsatellite DNA markers (119 individuals and six loci) provided additional support for population subdivision and gender-biased dispersal detected in the mtDNA sequences. Analysis using F(ST) values (based on allelic frequencies) yielded statistically significant separation between some, but not all, populations distinguished by mtDNA analysis. R(ST) values (based on frequencies of and genetic distance between alleles) showed no statistically significant subdivision. Again, highly male-biased dispersal was detected for all population comparisons, suggesting, together with morphological and reproductive data, the existence of sexual selection. Our molecular results argue for nine distinct dalli-type populations that should be treated as separate units for management purposes.

Interethnic genetic differentiation: HLA class I antigens in the population of Mongolia.

PubMed

Chimge, Nyam-Osorin; Batsuuri, Jamiyangiin

1999-09-01

A total of 1668 individuals representing 10 major Mongolian ethnic groups were serologically typed for HLA-A, -B, and -C antigens. Antigens A2, A24, B61, B51, B58, Cw3, Cw7, and Cw6 were the most frequent specificities in Mongolians and no case of B42 was noted in all ethnic groups. The cluster analysis of Principal Components I and II shows that Mongolian speaking groups form one cluster vs Turkic-speaking Kazakhs. The analysis reveals a low, but significant differentiation of Mongolian ethnic groups as measured by F(ST) = 0.0100 (P < 0.001). Gene diversity analysis shows that the genetic diversity of the Mongolian population can be attributed largely to its ethnic component, which makes up 64% of total genetic variation. The low degree of interpopulation variation and high level of intrapopulation diversity can be explained by the nomadic way of life of this indigenous population. Three-locus haplotypes A24-B61-Cw3, A33-B58-Cw3 are the most common haplotypic associations in Mongolians. The presence of antigens characteristic of Mongoloid, Caucasoid, and Negroid populations in Mongolians suggests a unique genetic background of this indigenous population. The three-locus haplotype distribution among Mongolians relative to other world populations supports the migration of ancient people from Central Asia to the New World, Korean Peninsula, and Southeast Asia. Am. J. Hum. Biol. 11:603-618, 1999. Copyright 1999 Wiley-Liss, Inc.

GIS-based poverty and population distribution analysis in China

NASA Astrophysics Data System (ADS)

Cui, Jing; Wang, Yingjie; Yan, Hong

2009-07-01

Geographically, poverty status is not only related with social-economic factors but also strongly affected by geographical environment. In the paper, GIS-based poverty and population distribution analysis method is introduced for revealing their regional differences. More than 100000 poor villages and 592 national key poor counties are chosen for the analysis. The results show that poverty distribution tends to concentrate in most of west China and mountainous rural areas of mid China. Furthermore, the fifth census data are overlaid to those poor areas in order to gain its internal diversity of social-economic characteristics. By overlaying poverty related social-economic parameters, such as sex ratio, illiteracy, education level, percentage of ethnic minorities, family composition, finding shows that poverty distribution is strongly correlated with high illiteracy rate, high percentage minorities, and larger family member.

Global analysis of genetic variation in human arsenic (+ 3 oxidation state) methyltransferase (AS3MT)

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

Fujihara, Junko; Soejima, Mikiko; Yasuda, Toshihiro

2010-03-15

Human arsenic (+ 3 oxidation state) methyltransferase (AS3MT) is known to catalyze the methylation of arsenite. The objective of this study was to investigate the diversity of the AS3MT gene at the global level. The distribution of 18 single nucleotide polymorphisms (SNPs) in AS3MT was performed in 827 individuals from 10 populations (Japanese, Korean, Chinese, Mongolian, Tibetans, Sri Lankan Tamils, Sri Lankan Sinhalese, Nepal Tamangs, Ovambo, and Ghanaian). In the African populations, the A allele in A6144T was not observed; the allele frequencies of C35587 were much lower than those in other populations; the allele frequencies of A37616 and C37950more » were relatively higher than those in other populations. Among Asian populations, Mongolians showed a different genotype distribution pattern. A lower C3963 and T6144 frequencies were observed, and, in the C37616A and T37950C polymorphism, the Mongolian population showed higher A37616 and C37950 allele frequencies than other Asian populations, similarly to the African populations. A total of 66 haplotypes were observed in the Ovambo, 48, in the Ghanaian, 99, in the Japanese, 103, in the Korean, 103, in the South Chinese, 20, in the Sri Lankan Tamil, 12, in the Sri Lankan Sinhalese, 21, in the Nepal Tamang, 50, in the Tibetan, and 45, in the Mongolian populations. The D' values between the SNP pairs were extremely high in the Sri Lankan Sinhalese population. Relatively higher D' values were observed in Mongolian and Sri Lankan Tamil populations. Network analysis showed two clusters that may have different origins, African and Asians (Chinese and/or Japanese). The present study is the first to demonstrate the existence of genetic heterogeneity in a world wide distribution of 18 SNPs in AS3MT.« less

Assessment of Azorean ancestry by Alu insertion polymorphisms.

PubMed

Branco, Claudia C; Palla, Raquel; Lino, Sílvia; Pacheco, Paula R; Cabral, Rita; De Fez, Laura; Peixoto, Bernardo R; Mota-Vieira, Luisa

2006-01-01

Knowledge of population ancestry from genetic markers is essential, for example, to understand the history of human migration and to carry out admixture and association studies. Here we assess the genome ancestry of the Azorean population through analysis of six Alu polymorphic sites (TPA-25, ACE, APO, B65, PV92, and D1) in 65 Azoreans and 30 Portuguese unrelated blood donors and compare data for the Y-chromosome and mtDNA. Allele frequencies were calculated by direct counting. Statistical analysis was performed using Arlequin 2.0. Nei's genetic distance was calculated with DISPAN software, and trees were constructed by neighbor joining (NJ) using PHYLIP 3.63. The results show that all Alu insertions were polymorphic. APO is the closest to fixation. The less frequent insertions are PV92 and D1 in the Azores and Portugal, respectively. ACE and TPA-25 show the highest values of heterozygosity in both populations. Allele frequencies are very similar to those obtained in European populations. These results are validated by the Y-chromosome and mtDNA data, where the majority of the maternal and paternal lineages are European. Overall, these data are reflected in the phylogenetic tree, in which the Azoreans and the Portuguese branch with Catalans, Andalusians, Moroccans, and Algerians. We conclude that the population of the Azores shows no significant genetic differences from that of mainland Portugal and that it is an outbred population. Moreover, the data validate the use of Alu insertion polymorphisms to assess the origin and history of human populations. Am. J. Hum. Biol. 18:223-226, 2006. (c) 2006 Wiley-Liss, Inc.

Economic level and human longevity: Spatial and temporal variations and correlation analysis of per capita GDP and longevity indicators in China.

PubMed

Wang, Shaobin; Luo, Kunli; Liu, Yonglin; Zhang, Shixi; Lin, Xiaoxu; Ni, Runxiang; Tian, Xinglei; Gao, Xing

2015-01-01

We show the variation of longevity indicators in China during the past 60 years and its correlation patterns with per capita GDP (GDPpc) both at provincial and inner-provincial level. Population data from six national population censuses in China (1953-2010) at provincial level and in several typical provinces in 2010 at county-level were selected. Four main longevity indicators were calculated. Pearson's r and distributed lags time series analysis between longevity indicators and GDPpc were conducted. The results show that Guangxi and Hainan Provinces maintain relatively high long-lived population (population over the age of 90) across various population censuses. The distributions of the population over the age of 80 and life expectancy are significantly affected by both contemporaneous and historical GDPpc at provincial level. However, areas of high long-lived population (over the age of 90) exhibit continuously stable features that lack any significant correlation with GDPpc both at provincial and inner-provincial level. Our results indicate a mixed distribution pattern of several longevity indexes and different relation to GDPpc. It shows consistent trend with Preston curve, that is, economic conditions may have limited influence on human longevity, especially for those who live longer than 90 years old. This study suggests that the economic development may favor the local residents to have access to live as old as 80 years old, but it is still difficult for most residents to reach the level of centenarians. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Deficits in facial affect recognition among antisocial populations: a meta-analysis.

PubMed

Marsh, Abigail A; Blair, R J R

2008-01-01

Individuals with disorders marked by antisocial behavior frequently show deficits in recognizing displays of facial affect. Antisociality may be associated with specific deficits in identifying fearful expressions, which would implicate dysfunction in neural structures that subserve fearful expression processing. A meta-analysis of 20 studies was conducted to assess: (a) if antisocial populations show any consistent deficits in recognizing six emotional expressions; (b) beyond any generalized impairment, whether specific fear recognition deficits are apparent; and (c) if deficits in fear recognition are a function of task difficulty. Results show a robust link between antisocial behavior and specific deficits in recognizing fearful expressions. This impairment cannot be attributed solely to task difficulty. These results suggest dysfunction among antisocial individuals in specified neural substrates, namely the amygdala, involved in processing fearful facial affect.

A hierarchical model for regional analysis of population change using Christmas Bird Count data, with application to the American Black Duck

USGS Publications Warehouse

Link, W.A.; Sauer, J.R.; Niven, D.K.

2006-01-01

Analysis of Christmas Bird Count (CBC) data is complicated by the need to account for variation in effort on counts and to provide summaries over large geographic regions. We describe a hierarchical model for analysis of population change using CBC data that addresses these needs. The effect of effort is modeled parametrically, with parameter values varying among strata as identically distributed random effects. Year and site effects are modeled hierarchically, accommodating large regional variation in number of samples and precision of estimates. The resulting model is complex, but a Bayesian analysis can be conducted using Markov chain Monte Carlo techniques. We analyze CBC data for American Black Ducks (Anas rubripes), a species of considerable management interest that has historically been monitored using winter surveys. Over the interval 1966-2003, Black Duck populations showed distinct regional patterns of population change. The patterns shown by CBC data are similar to those shown by the Midwinter Waterfowl Inventory for the United States.

Molecular analysis and genetic diversity of Aedes albopictus (Diptera, Culicidae) from China.

PubMed

Ruiling, Zhang; Peien, Leng; Xuejun, Wang; Zhong, Zhang

2018-05-01

Aedes albopictus is one of the most invasive species, which can carry Dengue virus, Yellow fever virus and more than twenty arboviruses. Based on mitochondrial gene cytochrome c oxidase I (COI) and samples collected from 17 populations, we investigated the molecular character and genetic diversity of Ae. albopictus from China. Altogether, 25 haplotypes were detected, including 10 shared haplotypes and 15 private haplotypes. H1 was the dominant haplotype, which is widely distributed in 13 populations. Tajima'D value of most populations was significantly negative, demonstrating that populations experienced rapid range expansion recently. Most haplotypes clustered together both in phylogenetic and median-joining network analysis without clear phylogeographic patterns. However, neutrality tests revealed shallow divergences among Hainan and Guangxi with other populations (0.15599 ≤ F ST ≤ 0.75858), which probably due to interrupted gene flow, caused by geographical isolations. In conclusion, Ae. albopictus populations showed low genetic diversity in China.

Life-history, substrate choice and Cytochrome Oxidase I variations in sandy beach peracaridans along the Rio de la Plata estuary

NASA Astrophysics Data System (ADS)

Fanini, L.; Zampicinini, G.; Tsigenopoulos, C. S.; Barboza, F. R.; Lozoya, J. P.; Gómez, J.; Celentano, E.; Lercari, D.; Marchetti, G. M.; Defeo, O.

2017-03-01

Life-history, substrate choice and Cytochrome Oxidase I (COI) sequences were analysed in populations of two peracaridans, the supralittoral talitrid Atlantorchestoidea brasiliensis and the intertidal cirolanid Excirolana armata. Three populations of each species, from beaches with similar grain size and located at different points along the natural gradient generated by the Rio de la Plata estuary were analysed. Abundance of E. armata increased with distance from the estuary, while the opposite trend was observed for A. brasiliensis. The proportion of females decreased towards high salinities for both species, significantly for E. armata. A test on substrate salinity preference revealed the absence of patterns due to active choice in E. armata. By contrast, A. brasiliensis showed no preference for the population closer to the estuary, while individuals from the other two sites significantly preferred high salinity substrates. Mitochondrial COI sequences were obtained from A. brasiliensis specimens tested for behaviour. Sequence analysis showed the population from the intermediate site to differ significantly from the other two. No significant genetic differentiation was instead found between populations from the two most distant sites, nor between individuals that expressed different salinity preference. Results showed that diverse sets of traits at the population level enable sandy beach species to cope with local environmental changes: life-history and behavioural traits appear to change in response to different ecological conditions, and, in the case of A brasiliensis, independently of the population structure inferred from COI sequence variation. Information from multiple traits allowed detection of population profiles, highlighting the relevance of multidisciplinary information and the concurrent analysis of field data and laboratory experiments, to detect responses of resident biota to environmental changes.

Evolution of Fitness in Experimental Populations of Vesicular Stomatitis Virus

PubMed Central

Elena, S. F.; Gonzalez-Candelas, F.; Novella, I. S.; Duarte, E. A.; Clarke, D. K.; Domingo, E.; Holland, J. J.; Moya, A.

1996-01-01

The evolution of fitness in experimental clonal populations of vesicular stomatitis virus (VSV) has been compared under different genetic (fitness of initial clone) and demographic (population dynamics) regimes. In spite of the high genetic heterogeneity among replicates within experiments, there is a clear effect of population dynamics on the evolution of fitness. Those populations that went through strong periodic bottlenecks showed a decreased fitness in competition experiments with wild type. Conversely, mutant populations that were transferred under the dynamics of continuous population expansions increased their fitness when compared with the same wild type. The magnitude of the observed effect depended on the fitness of the original viral clone. Thus, high fitness clones showed a larger reduction in fitness than low fitness clones under dynamics with included periodic bottleneck. In contrast, the gain in fitness was larger the lower the initial fitness of the viral clone. The quantitative genetic analysis of the trait ``fitness'' in the resulting populations shows that genetic variation for the trait is positively correlated with the magnitude of the change in the same trait. The results are interpreted in terms of the operation of MULLER's ratchet and genetic drift as opposed to the appearance of beneficial mutations. PMID:8849878

Reappraisal of fetal abdominal circumference in an Asian population: analysis of 50,131 records.

PubMed

Lu, Szu-Ching; Chang, Chiung-Hsin; Yu, Chen-Hsiang; Kang, Lin; Tsai, Pei-Ying; Chang, Fong-Ming

2008-03-01

Fetuses from different populations may show different growth patterns. In obstetrics, fetal abdominal circumference (AC) is a very useful index for assessing fetal growth. In this study, we attempted to establish the normal fetal growth curves of AC in an Asian population in South Taiwan. We reviewed our computer ultrasound database of fetal AC records from January 1991 to December 2006. During the study period of 16 years, only the fetuses examined by ultrasonography with gestational age between 14 and 41 weeks were included. We excluded extreme bilateral records after initial analysis. Eventually, 50,131 records of AC were included for final analysis. The observed gestation-specific AC values and the predicted AC values were calculated. The best-fit regression equation of AC versus gestational age is a second-order polynomial equation. In general, fetal AC values in our population showed similar patterns to those in Western populations. Besides, we established a table of the predicted AC values based on specific gestational age, including the 5 th , 10 th , 50 th , 90 th and 95 th centiles, for clinical reference. To the best of our knowledge, our series is the largest sample of AC reported in the medical literature. We believe that the gestational age-specific nomogram of fetal AC is important for further clinical assessment of fetal growth.

No longer a deadly encounter?

PubMed

Ferreira, Marcelo U; Castro, Marcia C

2015-01-01

A careful analysis shows that the mortality rates associated with epidemics following the contact between Amazonian indigenous communities and the external word have decreased in recent years. However, whether isolated indigenous populations can be contacted safely is still open to debate; many will argue that these populations should remain uncontacted in order to survive.

Isolation of mouse pancreatic alpha, beta, duct and acinar populations with cell surface markers.

PubMed

Dorrell, Craig; Grompe, Maria T; Pan, Fong Cheng; Zhong, Yongping; Canaday, Pamela S; Shultz, Leonard D; Greiner, Dale L; Wright, Chris V; Streeter, Philip R; Grompe, Markus

2011-06-06

Tools permitting the isolation of live pancreatic cell subsets for culture and/or molecular analysis are limited. To address this, we developed a collection of monoclonal antibodies with selective surface labeling of endocrine and exocrine pancreatic cell types. Cell type labeling specificity and cell surface reactivity were validated on mouse pancreatic sections and by gene expression analysis of cells isolated using FACS. Five antibodies which marked populations of particular interest were used to isolate and study viable populations of purified pancreatic ducts, acinar cells, and subsets of acinar cells from whole pancreatic tissue or of alpha or beta cells from isolated mouse islets. Gene expression analysis showed the presence of known endocrine markers in alpha and beta cell populations and revealed that TTR and DPPIV are primarily expressed in alpha cells whereas DGKB and GPM6A have a beta cell specific expression profile. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Genetic diversity and population structure analysis between Indian red jungle fowl and domestic chicken using microsatellite markers.

PubMed

Kumar, Vinay; Shukla, Sanjeev K; Mathew, Jose; Sharma, Deepak

2015-01-01

The present study was conducted to assess the genetic diversity, population structure, and relatedness in Indian red jungle fowl (RJF, Gallus gallus murgi) from northern India and three domestic chicken populations (gallus gallus domesticus), maintained at the institute farms, namely White Leghorn (WL), Aseel (AS) and Red Cornish (RC) using 25 microsatellite markers. All the markers were polymorphic, the number of alleles at each locus ranged from five (MCW0111) to forty-three (LEI0212) with an average number of 19 alleles per locus. Across all loci, the mean expected heterozygosity and polymorphic information content were 0.883 and 0.872, respectively. Population-specific alleles were found in each population. A UPGMA dendrogram based on shared allele distances clearly revealed two major clusters among the four populations; cluster I had genotypes from RJF and WL whereas cluster II had AS and RC genotypes. Furthermore, the estimation of population structure was performed to understand how genetic variation is partitioned within and among populations. The maximum ▵K value was observed for K = 4 with four identified clusters. Furthermore, factorial analysis clearly showed four clustering; each cluster represented the four types of population used in the study. These results clearly, demonstrate the potential of microsatellite markers in elucidating the genetic diversity, relationships, and population structure analysis in RJF and domestic chicken populations.

Community characteristics that attract physicians in Japan: a cross-sectional analysis of community demographic and economic factors.

PubMed

Matsumoto, Masatoshi; Inoue, Kazuo; Noguchi, Satomi; Toyokawa, Satoshi; Kajii, Eiji

2009-02-18

In many countries, there is a surplus of physicians in some communities and a shortage in others. Population size is known to be correlated with the number of physicians in a community, and is conventionally considered to represent the power of communities to attract physicians. However, associations between other demographic/economic variables and the number of physicians in a community have not been fully evaluated. This study seeks other parameters that correlate with the physician population and show which characteristics of a community determine its "attractiveness" to physicians. Associations between the number of physicians and selected demographic/economic/life-related variables of all of Japan's 3132 municipalities were examined. In order to exclude the confounding effect of community size, correlations between the physician-to-population ratio and other variable-to-population ratios or variable-to-area ratios were evaluated with simple correlation and multiple regression analyses. The equity of physician distribution against each variable was evaluated by the orenz curve and Gini index. Among the 21 variables selected, the service industry workers-to-population ratio (0.543), commercial land price (0.527), sales of goods per person (0.472), and daytime population density (0.451) were better correlated with the physician-to-population ratio than was population density (0.409). Multiple regression analysis showed that the service industry worker-to-population ratio, the daytime population density, and the elderly rate were each independently correlated with the physician-to-population ratio (standardized regression coefficient 0.393, 0.355, 0.089 respectively; each p<0.001). Equity of physician distribution was higher against service industry population (Gini index=0.26) and daytime population (0.28) than against population (0.33). Daytime population and service industry population in a municipality are better parameters of community attractiveness to physicians than population. Because attractiveness is supposed to consist of medical demand and the amenities of urban life, the two parameters may represent the amount of medical demand and/or the extent of urban amenities of the community more precisely than population does. The conventional demand-supply analysis based solely on population as the demand parameter may overestimate the inequity of the physician distribution among communities.

The effects of Medieval dams on genetic divergence and demographic history in brown trout populations

PubMed Central

2014-01-01

Background Habitat fragmentation has accelerated within the last century, but may have been ongoing over longer time scales. We analyzed the timing and genetic consequences of fragmentation in two isolated lake-dwelling brown trout populations. They are from the same river system (the Gudenå River, Denmark) and have been isolated from downstream anadromous trout by dams established ca. 600–800 years ago. For reference, we included ten other anadromous populations and two hatchery strains. Based on analysis of 44 microsatellite loci we investigated if the lake populations have been naturally genetically differentiated from anadromous trout for thousands of years, or have diverged recently due to the establishment of dams. Results Divergence time estimates were based on 1) Approximate Bayesian Computation and 2) a coalescent-based isolation-with-gene-flow model. Both methods suggested divergence times ca. 600–800 years bp, providing strong evidence for establishment of dams in the Medieval as the factor causing divergence. Bayesian cluster analysis showed influence of stocked trout in several reference populations, but not in the focal lake and anadromous populations. Estimates of effective population size using a linkage disequilibrium method ranged from 244 to > 1,000 in all but one anadromous population, but were lower (153 and 252) in the lake populations. Conclusions We show that genetic divergence of lake-dwelling trout in two Danish lakes reflects establishment of water mills and impassable dams ca. 600–800 years ago rather than a natural genetic population structure. Although effective population sizes of the two lake populations are not critically low they may ultimately limit response to selection and thereby future adaptation. Our results demonstrate that populations may have been affected by anthropogenic disturbance over longer time scales than normally assumed. PMID:24903056

The effects of Medieval dams on genetic divergence and demographic history in brown trout populations.

PubMed

Hansen, Michael M; Limborg, Morten T; Ferchaud, Anne-Laure; Pujolar, José-Martin

2014-06-05

Habitat fragmentation has accelerated within the last century, but may have been ongoing over longer time scales. We analyzed the timing and genetic consequences of fragmentation in two isolated lake-dwelling brown trout populations. They are from the same river system (the Gudenå River, Denmark) and have been isolated from downstream anadromous trout by dams established ca. 600-800 years ago. For reference, we included ten other anadromous populations and two hatchery strains. Based on analysis of 44 microsatellite loci we investigated if the lake populations have been naturally genetically differentiated from anadromous trout for thousands of years, or have diverged recently due to the establishment of dams. Divergence time estimates were based on 1) Approximate Bayesian Computation and 2) a coalescent-based isolation-with-gene-flow model. Both methods suggested divergence times ca. 600-800 years bp, providing strong evidence for establishment of dams in the Medieval as the factor causing divergence. Bayesian cluster analysis showed influence of stocked trout in several reference populations, but not in the focal lake and anadromous populations. Estimates of effective population size using a linkage disequilibrium method ranged from 244 to > 1,000 in all but one anadromous population, but were lower (153 and 252) in the lake populations. We show that genetic divergence of lake-dwelling trout in two Danish lakes reflects establishment of water mills and impassable dams ca. 600-800 years ago rather than a natural genetic population structure. Although effective population sizes of the two lake populations are not critically low they may ultimately limit response to selection and thereby future adaptation. Our results demonstrate that populations may have been affected by anthropogenic disturbance over longer time scales than normally assumed.

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.

Neutral polymorphisms in putative housekeeping genes and tandem repeats unravels the population genetics and evolutionary history of Plasmodium vivax in India.

PubMed

Prajapati, Surendra K; Joshi, Hema; Carlton, Jane M; Rizvi, M Alam

2013-01-01

The evolutionary history and age of Plasmodium vivax has been inferred as both recent and ancient by several studies, mainly using mitochondrial genome diversity. Here we address the age of P. vivax on the Indian subcontinent using selectively neutral housekeeping genes and tandem repeat loci. Analysis of ten housekeeping genes revealed a substantial number of SNPs (n = 75) from 100 P. vivax isolates collected from five geographical regions of India. Neutrality tests showed a majority of the housekeeping genes were selectively neutral, confirming the suitability of housekeeping genes for inferring the evolutionary history of P. vivax. In addition, a genetic differentiation test using housekeeping gene polymorphism data showed a lack of geographical structuring between the five regions of India. The coalescence analysis of the time to the most recent common ancestor estimate yielded an ancient TMRCA (232,228 to 303,030 years) and long-term population history (79,235 to 104,008) of extant P. vivax on the Indian subcontinent. Analysis of 18 tandem repeat loci polymorphisms showed substantial allelic diversity and heterozygosity per locus, and analysis of potential bottlenecks revealed the signature of a stable P. vivax population, further corroborating our ancient age estimates. For the first time we report a comparable evolutionary history of P. vivax inferred by nuclear genetic markers (putative housekeeping genes) to that inferred from mitochondrial genome diversity.

Assessing population exposure for landslide risk analysis using dasymetric cartography

NASA Astrophysics Data System (ADS)

Garcia, Ricardo A. C.; Oliveira, Sergio C.; Zezere, Jose L.

2015-04-01

Exposed Population is a major topic that needs to be taken into account in a full landslide risk analysis. Usually, risk analysis is based on an accounting of inhabitants number or inhabitants density, applied over statistical or administrative terrain units, such as NUTS or parishes. However, this kind of approach may skew the obtained results underestimating the importance of population, mainly in territorial units with predominance of rural occupation. Furthermore, the landslide susceptibility scores calculated for each terrain unit are frequently more detailed and accurate than the location of the exposed population inside each territorial unit based on Census data. These drawbacks are not the ideal setting when landslide risk analysis is performed for urban management and emergency planning. Dasymetric cartography, which uses a parameter or set of parameters to restrict the spatial distribution of a particular phenomenon, is a methodology that may help to enhance the resolution of Census data and therefore to give a more realistic representation of the population distribution. Therefore, this work aims to map and to compare the population distribution based on a traditional approach (population per administrative terrain units) and based on dasymetric cartography (population by building). The study is developed in the Region North of Lisbon using 2011 population data and following three main steps: i) the landslide susceptibility assessment based on statistical models independently validated; ii) the evaluation of population distribution (absolute and density) for different administrative territorial units (Parishes and BGRI - the basic statistical unit in the Portuguese Census); and iii) the dasymetric population's cartography based on building areal weighting. Preliminary results show that in sparsely populated administrative units, population density differs more than two times depending on the application of the traditional approach or the dasymetric cartography. This work was supported by the FCT - Portuguese Foundation for Science and Technology.

Genetic diversity in populations of Isatis glauca Aucher ex Boiss. ssp. from Central Anatolia in Turkey, as revealed by AFLP analysis.

PubMed

Özbek, Özlem; Görgülü, Elçin; Yıldırımlı, Şinasi

2013-12-01

Isatidae L. is a complex and systematically difficult genus in Brassicaceae. The genus displays great morphological polymorphism, which makes the classification of species and subspecies difficult as it is observed in Isatis glauca Aucher ex Boiss. The aim of this study is characterization of the genetic diversity in subspecies of Isatis glauca Aucher ex Boiss. distributed widely in Central Anatolia, in Turkey by using Amplified Fragment Length Polymorphism (AFLP) technique. Eight different Eco RI-Mse I primer combinations produced 805 AFLP loci, 793 (98.5%) of which were polymorphic in 67 accessions representing nine different populations. The data obtained by AFLP was computed with using GDA (Genetic Data Analysis) and STRUCTURE (version 2.3.3) software programs for population genetics. The mean proportion of the polymorphic locus (P), the mean number of alleles (A), the number of unique alleles (U) and the mean value of gene diversity (He) were 0.59, 1.59, 20, and 0.23 respectively. The coancestry coefficient (ϴ) was 0.24. The optimal number of K was identified as seven. The principal component analysis (PCA) explained 85.61% of the total genetic variation. Isatis glauca ssp. populations showed a high level of genetic diversity, and the AFLP analysis revealed that high polymorphism and differentiated subspecies could be used conveniently for population genetic studies. The principal coordinate analysis (PCoA) based on the dissimilarity matrix, the dendrogram drawn with UPGMA method and STRUCTURE cluster analysis distinguished the accessions successfully. The accessions formed distinctive population structures for populations AA, AB, E, K, and S. Populations AG1 and AG2 seemed to have similar genetic content, in addition, in both populations several hybrid individuals were observed. The accessions did not formed distinctive population structures for both populations AI and ANP. Consequently, Ankara province might be the area, where species Isatis glauca Aucher ex Boiss. originated.

Analysis of Pvama1 genes from China-Myanmar border reveals little regional genetic differentiation of Plasmodium vivax populations.

PubMed

Zhu, Xiaotong; Zhao, Pan; Wang, Si; Liu, Fei; Liu, Jun; Wang, Jian; Yang, Zhaoqing; Yan, Guiyun; Fan, Qi; Cao, Yaming; Cui, Liwang

2016-11-29

With the premise of diminishing parasite genetic diversity following the reduction of malaria incidence, the analysis of polymorphic antigenic markers may provide important information about the impact of malaria control on local parasite populations. Here we evaluated the genetic diversity of Plasmodium vivax apical membrane antigen 1 (Pvama1) gene in a parasite population from the China-Myanmar border and compared it with global P. vivax populations. We performed evolutionary analysis to examine the genetic diversity, natural selection, and population differentiation of 73 Pvama1 sequences acquired from the China-Myanmar border as well as 615 publically available Pvama1 sequences from seven global P. vivax populations. A total of 308 Pvama1 haplotypes were identified among the global P. vivax isolates. The overall nucleotide diversity of Pvama1 gene among the 73 China-Myanmar border parasite isolates was 0.008 with 41 haplotypes being identified (Hd = 0.958). Domain I (DI) harbored the majority (26/33) of the polymorphic sites. The McDonald Kreitman test showed a significant positive selection across the ectodomain and the DI of Pvama1. The fixation index (F ST ) estimation between the China-Myanmar border, Thailand (0.01) and Myanmar (0.10) showed only slight geographical genetic differentiation. Notably, the Sal-I haplotype was not detected in any of the analyzed global isolates, whereas the Belem strain was restricted to the Thai population. The detected mutations are mapped outside the overlapped region of the predicted B-cell epitopes and intrinsically unstructured/disordered regions. This study revealed high levels of genetic diversity of Pvama1 in the P. vivax parasite population from the China-Myanmar border with DI displaying stronger diversifying selection than other domains. There were low levels of population subdivision among parasite populations from the Greater Mekong Subregion.

Genetic and phenotypic variability of iris color in Buenos Aires population

PubMed Central

Hohl, Diana María; Bezus, Brenda; Ratowiecki, Julia; Catanesi, Cecilia Inés

2018-01-01

Abstract The aim of this work was to describe the phenotypic and genotypic variability related to iris color for the population of Buenos Aires province (Argentina), and to assess the usefulness of current methods of analysis for this country. We studied five Single Nucleotide Polymorphisms (SNPs) included in the IrisPlex kit, in 118 individuals, and we quantified eye color with Digital Iris Analysis Tool. The markers fit Hardy-Weinberg equilibrium for the whole sample, but not for rs12913832 within the group of brown eyes (LR=8.429; p=0.004). We found a remarkable association of HERC2 rs12913832 GG with blue color (p < 0.01) but the other markers did not show any association with iris color. The results for the Buenos Aires population differ from those of other populations of the world for these polymorphisms (p < 0,01). The differences we found might respond to the admixed ethnic composition of Argentina; therefore, methods of analysis used in European populations should be carefully applied when studying the population of Argentina. These findings reaffirm the importance of this investigation in the Argentinian population for people identification based on iris color. PMID:29658972

An anthropometric data bank for the Iranian working population with ethnic diversity.

PubMed

Sadeghi, Fatemeh; Mazloumi, Adel; Kazemi, Zeinab

2015-05-01

This study constructed an anthropometric data bank for the Iranian working population. In total, thirty-seven body dimensions were measured among 3720 Iranian workers with different ethnicities (3000 male and 720 female; aged 20-60 years). Statistical analysis revealed significant differences for most of body dimensions among the ethnical groups. Moreover, the authors compared Iranian anthropometric characteristics with those of four Asian populations: Taiwanese, Chinese, Japanese, and Korean. Overall, 16 body dimensions for the five Asian populations were selected and compared. Accordingly, different morphological characteristics of these five populations were observed. The Iranian population showed wide shoulders and hips and long legs; the Chinese population showed narrow hips and shoulders and a short height relative to the other populations. The Korean sample recorded moderate body size comparing the other populations. The Taiwanese had large hands, relatively wide shoulders and short upper limbs. These differences in population dimensions should be taken into consideration for product and process design when expanding regional markets. Copyright © 2014 Elsevier Ltd and The Ergonomics Society. All rights reserved.

Relationship between regional population and healthcare delivery in Japan.

PubMed

Niga, Takeo; Mori, Maiko; Kawahara, Kazuo

2016-01-01

In order to address regional inequality in healthcare delivery in Japan, healthcare districts were established in 1985. However, regional healthcare delivery has now become a national issue because of population migration and the aging population. In this study, the state of healthcare delivery at the district level is examined by analyzing population, the number of physicians, and the number of hospital beds. The results indicate a continuing disparity in healthcare delivery among districts. We find that the rate of change in population has a strong positive correlation with that in the number of physicians and a weak positive correlation with that in the number of hospital beds. In addition, principal component analysis is performed on three variables: the rate of change in population, the number of physicians per capita, and the number of hospital beds per capita. This analysis suggests that the two principal components contribute 90.1% of the information. The first principal component is thought to show the effect of the regulations on hospital beds. The second principal component is thought to show the capacity to recruit physicians. This study indicates that an adjustment to the regulations on hospital beds as well as physician allocation by public funds may be key to resolving the impending issue of regionally disproportionate healthcare delivery.

Chromosomal Mapping of Repetitive DNA Sequences in the Genus Bryconamericus (Characidae) and DNA Barcoding to Differentiate Populations.

PubMed

Santos, Angélica Rossotti Dos; Usso, Mariana Campaner; Gouveia, Juceli Gonzalez; Araya-Jaime, Cristian; Frantine-Silva, Wilson; Giuliano-Caetano, Lucia; Foresti, Fausto; Dias, Ana Lúcia

2017-06-01

The mapping of repetitive DNA sites by fluorescence in situ hybridization has been widely used for karyotype studies in different species of fish, especially when dealing with related species or even genera presenting high chromosome variability. This study analyzed three populations of Bryconamericus, with diploid number preserved, but with different karyotype formulae. Bryconamericus ecai, from the Forquetinha river/RS, presented three new cytotypes, increasing the number of karyotype forms to seven in this population. Other two populations of Bryconamericus sp. from the Vermelho stream/PR and Cambuta river/PR exhibited interpopulation variation. The chromosome mapping of rDNA sites revealed unique markings among the three populations, showing inter- and intrapopulation variability located in the terminal region. The molecular analysis using DNA barcoding complementing the cytogenetic analysis also showed differentiation among the three populations. The U2 small nuclear DNA repetitive sequence exhibited conserved features, being located in the interstitial region of a single chromosome pair. This is the first report on its occurrence in the genus Bryconamericus. Data obtained revealed a karyotype variability already assigned to the genus, along with polymorphism of ribosomal sites, demonstrating that this group of fish can be undergoing a divergent evolutionary process, constituting a substantive model for studies of chromosomal evolution.

Impact of constitutional copy number variants on biological pathway evolution.

PubMed

Poptsova, Maria; Banerjee, Samprit; Gokcumen, Omer; Rubin, Mark A; Demichelis, Francesca

2013-01-23

Inherited Copy Number Variants (CNVs) can modulate the expression levels of individual genes. However, little is known about how CNVs alter biological pathways and how this varies across different populations. To trace potential evolutionary changes of well-described biological pathways, we jointly queried the genomes and the transcriptomes of a collection of individuals with Caucasian, Asian or Yoruban descent combining high-resolution array and sequencing data. We implemented an enrichment analysis of pathways accounting for CNVs and genes sizes and detected significant enrichment not only in signal transduction and extracellular biological processes, but also in metabolism pathways. Upon the estimation of CNV population differentiation (CNVs with different polymorphism frequencies across populations), we evaluated that 22% of the pathways contain at least one gene that is proximal to a CNV (CNV-gene pair) that shows significant population differentiation. The majority of these CNV-gene pairs belong to signal transduction pathways and 6% of the CNV-gene pairs show statistical association between the copy number states and the transcript levels. The analysis suggested possible examples of positive selection within individual populations including NF-kB, MAPK signaling pathways, and Alu/L1 retrotransposition factors. Altogether, our results suggest that constitutional CNVs may modulate subtle pathway changes through specific pathway enzymes, which may become fixed in some populations.

Impact of constitutional copy number variants on biological pathway evolution

PubMed Central

2013-01-01

Background Inherited Copy Number Variants (CNVs) can modulate the expression levels of individual genes. However, little is known about how CNVs alter biological pathways and how this varies across different populations. To trace potential evolutionary changes of well-described biological pathways, we jointly queried the genomes and the transcriptomes of a collection of individuals with Caucasian, Asian or Yoruban descent combining high-resolution array and sequencing data. Results We implemented an enrichment analysis of pathways accounting for CNVs and genes sizes and detected significant enrichment not only in signal transduction and extracellular biological processes, but also in metabolism pathways. Upon the estimation of CNV population differentiation (CNVs with different polymorphism frequencies across populations), we evaluated that 22% of the pathways contain at least one gene that is proximal to a CNV (CNV-gene pair) that shows significant population differentiation. The majority of these CNV-gene pairs belong to signal transduction pathways and 6% of the CNV-gene pairs show statistical association between the copy number states and the transcript levels. Conclusions The analysis suggested possible examples of positive selection within individual populations including NF-kB, MAPK signaling pathways, and Alu/L1 retrotransposition factors. Altogether, our results suggest that constitutional CNVs may modulate subtle pathway changes through specific pathway enzymes, which may become fixed in some populations. PMID:23342974

Cost-effectiveness analysis of HPV vaccination: comparing the general population with socially vulnerable individuals.

PubMed

Han, Kyu-Tae; Kim, Sun Jung; Lee, Seo Yoon; Park, Eun-Cheol

2014-01-01

After the WHO recommended HPV vaccination of the general population in 2009, government support of HPV vaccination programs was increased in many countries. However, this policy was not implemented in Korea due to perceived low cost-effectiveness. Thus, the aim of this study was to analyze the cost-utility of HPV vaccination programs targeted to high risk populations as compared to vaccination programs for the general population. Each study population was set to 100,000 people in a simulation study to determine the incremental cost-utility ratio (ICUR), then standard prevalence rates, cost, vaccination rates, vaccine efficacy, and the Quality-Adjusted Life-Years (QALYs) were applied to the analysis. In addition, sensitivity analysis was performed by assuming discounted vaccination cost. In the socially vulnerable population, QALYs gained through HPV vaccination were higher than that of the general population (General population: 1,019, Socially vulnerable population: 5,582). The results of ICUR showed that the cost of HPV vaccination was higher for the general population than the socially vulnerable population. (General population: 52,279,255 KRW, Socially vulnerable population: 9,547,347 KRW). Compared with 24 million KRW/QALYs as the social threshold, vaccination of the general population was not cost-effective. In contrast, vaccination of the socially vulnerable population was strongly cost-effective. The results suggest the importance and necessity of government support of HPV vaccination programs targeted to socially vulnerable populations because a targeted approach is much more cost-effective. The implementation of government support for such vaccination programs is a critical strategy for decreasing the burden of HPV infection in Korea.

Bovine GDF10 gene polymorphism analysis and its association with body measurement traits in Chinese indigenous cattle.

PubMed

Adoligbe, C; Zan, Linsen; Farougou, S; Wang, Hongbao; Ujjan, J A

2012-04-01

The objective of this research was to detect bovine GDF10 gene polymorphism and analyze its association with body measurement traits (BMT) of animals sampled from 6 different Chinese indigenous cattle populations. The populations included Xuelong (Xl), Luxi (Lx), Qinchuan (Qc), Jiaxian red (Jx), Xianang (Xn) and Nanyang (Ny). Blood samples were taken from a total of 417 female animals stratified into age categories of 12-36 months. Polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) was employed to find out GDF10 single polymorphism nucleotide (SNPs) and explore their possible association with BMT. Sequence analysis of GDF10 gene revealed 3 SNPs in total: 1 in exon1 (G142A) and 2 in exon3 (A11471G, and T12495C). G142A and T12495C SNPs are both synonymous mutation. They showed 2 genotypes namely respectively (GG, GA) and (PP and PB). A11471G SNP is a missense mutation leading to the change of Alanine to Threonine amino acid. It showed three genotypes namely AA, BB and AB. Analysis of association of polymorphism with body measurement traits at the three locus showed that there were significant effects on BMT in Qc, Jx and Ny cattle population. These results suggest that the GDF10 gene might have potential effects on body measurement traits in the above mentioned cattle populations and could be used for marker-assisted selection.

Identification of TNIP1 Polymorphisms by High Resolution Melting Analysis with Unlabelled Probe: Association with Systemic Lupus Erythematosus

PubMed Central

Zhang, Jie; Chen, Yuewen; Shao, Yong; Wu, Qi; Guan, Ming; Zhang, Wei; Wan, Jun; Yu, Bo

2012-01-01

Background. TNFα-induced protein 3 (TNFAIP3) interacting with protein 1 (TNIP1) acts as a negative regulator of NF-κB and plays an important role in maintaining the homeostasis of immune system. A recent genome-wide association study (GWAS) showed that the polymorphism of TNIP1 was associated with the disease risk of SLE in Caucasian. In this study, we investigated whether the association of TNIP1 with SLE was replicated in Chinese population. Methods. The association of TNIP1 SNP rs7708392 (G/C) was determined by high resolution melting (HRM) analysis with unlabeled probe in 285 SLE patients and 336 healthy controls. Results. A new SNP rs79937737 located on 5 bp upstream of rs7708392 was discovered during the HRM analysis. No association of rs7708392 or rs79937737 with the disease risk of SLE was found. Furthermore, rs7708392 and rs79937737 were in weak linkage disequilibrium (LD). Hypotypes analysis of the two SNPs also showed no association with SLE in Chinese population. Conclusions. High resolution melting analysis with unlabeled probes proves to be a powerful and efficient genotyping method for identifying and screening SNPs. No association of rs7708392 or rs79937737 with the disease risk of SLE was observed in Chinese population. PMID:22852072

Changes in exposure to ‘life stressors’ in the Aboriginal and Torres Strait Islander population, 2002 to 2008

PubMed Central

2014-01-01

Background The Negative Life Events Scale (NLES) has been included in nationally representative surveys of the Indigenous and Australian population since 2002 as a measure of exposure to a range of ‘life stressors’. There has been limited reporting or analysis of estimates of the NLES from these surveys. This paper reports changes in exposure to stressors from 2002 to 2008 for the Indigenous population, and examines inter-relationships between eleven NLES items. Data for the 2006 Australian population is also included for comparative purposes. Methods Data from the 2002 and 2008 National Aboriginal and Torres Strait Islander Social Surveys (NATSISS) and the 2006 General Social Survey (GSS) were accessed from the Australia Bureau of Statistics in order to determine significant changes in exposure to stressors for the 2002 and 2008 Indigenous population by remoteness and to compare this with the 2006 Australian population. Factor analysis was used to assess the inter-relationships between stressors for the Indigenous and Australian population by remoteness. Results In remote locations, between 2002 and 2008, exposure to life stressors decreased significantly for the Indigenous population across seven of the eleven stressors. In non-remote locations, exposure to four of the stressors increased significantly. Exposure to stressors in the 2002 and 2008 non-remote Indigenous population were significantly higher than those for the 2006 Australian population for all items, except ‘alcohol and/or drug problems’ and ‘trouble with the police’, which showed no evidence of a difference. The factor analysis of the NLES for the 2002 and 2008 remote and non-remote Indigenous populations and the 2006 Australian population showed a consistent clustering of items into three groups: social transgressions; grief and trauma; and labour market stressors. Conclusions The reduction in exposure to life stressors for the remote Indigenous population may be related to policy and practice changes (e.g. more police, income quarantining, housing construction). The differential change in exposure to life stressors between remote and non-remote locations highlights the importance of presenting data for these geographic locations separately. PMID:24512200

How Close Do We Live to Water? A Global Analysis of Population Distance to Freshwater Bodies

PubMed Central

Kummu, Matti; de Moel, Hans; Ward, Philip J.; Varis, Olli

2011-01-01

Traditionally, people have inhabited places with ready access to fresh water. Today, over 50% of the global population lives in urban areas, and water can be directed via tens of kilometres of pipelines. Still, however, a large part of the world's population is directly dependent on access to natural freshwater sources. So how are inhabited places related to the location of freshwater bodies today? We present a high-resolution global analysis of how close present-day populations live to surface freshwater. We aim to increase the understanding of the relationship between inhabited places, distance to surface freshwater bodies, and climatic characteristics in different climate zones and administrative regions. Our results show that over 50% of the world's population lives closer than 3 km to a surface freshwater body, and only 10% of the population lives further than 10 km away. There are, however, remarkable differences between administrative regions and climatic zones. Populations in Australia, Asia, and Europe live closest to water. Although populations in arid zones live furthest away from freshwater bodies in absolute terms, relatively speaking they live closest to water considering the limited number of freshwater bodies in those areas. Population distributions in arid zones show statistically significant relationships with a combination of climatic factors and distance to water, whilst in other zones there is no statistically significant relationship with distance to water. Global studies on development and climate adaptation can benefit from an improved understanding of these relationships between human populations and the distance to fresh water. PMID:21687675

Morphological versus molecular markers to describe variability in Juniperus excelsa subsp. excelsa (Cupressaceae).

PubMed

Douaihy, Bouchra; Sobierajska, Karolina; Jasińska, Anna Katarzyna; Boratyńska, Krystyna; Ok, Tolga; Romo, Angel; Machon, Nathalie; Didukh, Yakiv; Bou Dagher-Kharrat, Magda; Boratyński, Adam

2012-01-01

Juniperus excelsa M.-Bieb. is a major forest element in the mountains of the eastern part of Mediterranean and sub-Mediterranean regions. This study comprises the first morphological investigation covering a large part of the geographical range of J. excelsa and aims to verify the congruency between the morphological results and molecular results of a previous study. We studied 14 populations sampled from Greece, Cyprus, Ukraine, Turkey and Lebanon, 11 of which have previously been investigated using molecular markers. Three hundred and ninety-four individuals of J. excelsa were examined using nine biometric features characterizing cones, seeds and shoots, and eight derived ratios. Statistical analyses were conducted in order to evaluate the intra- and inter-population morphological variability. The level of intra-population variability observed did not show any geographical trends. The total variation mostly depended on the ratios of cone diameter/seed width and seed width/seed length. The discrimination analysis, the Ward agglomeration method and barrier analysis results showed a separation of the sampled populations into three main clusters. These results confirmed, in part, the geographical differentiation revealed by molecular markers with a lower level of differentiation and a less clear geographical pattern. The most differentiated populations using both markers corresponded to old, isolated populations in the high altitudes of Lebanon (>2000 m). Moreover, a separation of the northern Turkish population from the southern Turkish populations was observed using both markers. Morphological variation together with genetic and biogeographic studies make an effective tool for detecting relict plant populations and also populations subjected to more intensive selection.

Phylogeography of Trichuris populations isolated from different Cricetidae rodents.

PubMed

Callejón, Rocío; De Rojas, Manuel; Feliú, Carlos; Balao, Francisco; Marrugal, Angela; Henttonen, Heikki; Guevara, Diego; Cutillas, Cristina

2012-11-01

The phylogeography of Trichuris populations (Nematoda) collected from Cricetidae rodents (Muroidea) from different geographical regions was studied. Ribosomal DNA (Internal Transcribed Spacers 1 and 2, and mitochondrial DNA (cytochrome c- oxidase subunit 1 partial gene) have been used as molecular markers. The nuclear internal transcribed spacers (ITSs) 1 and 2 showed 2 clear-cut geographical and genetic lineages: one of the Nearctic region (Oregon), although the second was widespread throughout the Palaearctic region and appeared as a star-like structure in the minimum spanning network. The mitochondrial results revealed that T. arvicolae populations from the Palaearctic region were separated into 3 clear-cut geographical and genetic lineages: populations from Northern Europe, populations from Southern (Spain) and Eastern Europe (Croatia, Belarus, Kazahstan), and populations from Italy and France (Eastern Pyrénean Mountains). Phylogenetic analysis obtained on the basis of ITS1-5·8S-ITS2 rDNA sequences did not show a differential geographical structure; however, these markers suggest a new Trichuris species parasitizing Chionomys roberti and Cricetulus barabensis. The mitochondrial results revealed that Trichuris populations from arvicolinae rodents show signals of a post-glacial northward population expansion starting from the Pyrenees and Italy. Apparently, the Pyrenees and the Alps were not barriers to the dispersal of Trichuris populations.

Assessment of diversity among populations of Rauvolfia serpentina Benth. Ex. Kurtz. from Southern Western Ghats of India, based on chemical profiling, horticultural traits and RAPD analysis.

PubMed

Nair, Vadakkemuriyil Divya; Raj, Rajan Pillai Dinesh; Panneerselvam, Rajaram; Gopi, Ragupathi

2014-01-01

Genetic, morphological and chemical variations of ten natural populations of Rauvolfia serpentina Benth. Ex. Kurtz. from Southern Western Ghats of India were assessed using RAPD markers reserpine content and morphological traits. An estimate of genetic diversity and differentiation between genotypes of breeding germplasm is of key importance for its improvement. Populations were collected from different geographical regions. Data obtained through three different methods were compared and the correlation among them was estimated. Statistical analysis showed significant differences for all horticultural characteristics among the accessions suggesting that selection for relevant characteristics could be possible. Variation in the content of Reserpine ranges from 0.192 g/100 g (population from Tusharagiri) to 1.312 g/100 g (population from Aryankavu). A high diversity within population and high genetic differentiation among them based on RAPDs were revealed caused both by habitat fragmentation of the low size of most populations and the low level of gene flow among them. The UPGMA dendrogram and PCA analysis based on reserpine content yielded higher separation among populations indicated specific adaptation of populations into clusters each of them including populations closed to their geographical origin. Genetic, chemical and morphological data were correlated based on Mantel test. Given the high differentiation among populations conservation strategies should take into account genetic diversity and chemical variation levels in relation to bioclimatic and geographic location of populations. Our results also indicate that RAPD approach along with horticultural analysis seemed to be best suited for assessing with high accuracy the genetic relationships among distinct R. serpentina accessions. © 2013.

Selective sweeps in the homoploid hybrid species Helianthus deserticola: evolution in concert across populations and across origins

PubMed Central

GROSS, BRIANA L.; TURNER, KATHRYN G.; RIESEBERG, LOREN H.

2008-01-01

The evolution of different populations within a species in response to selective pressures can potentially happen in three different ways. It can occur in parallel, where similar changes occur independently in each population in response to selection; in concert, where the spread of an adaptive mutation across a species’ range results in a single allele fixing in each population; or populations can diverge in response to local selective pressures. We explored these possibilities in populations of the homoploid hybrid species Helianthus deserticola relative to its parental species Helianthus annuus and Helianthus petiolaris using an analysis of variation in 96 expressed sequence tag-based microsatellites. A total of nine loci showed evidence consistent with recent selection at either the species or population level, although two of these genes were discarded because the apparent sweep did not occur relative to the parent from which the locus was derived. Between one and five loci showed a putative sweep across the entire species range with the same microsatellite allele fixed in each population. This pattern is consistent with evolution in concert despite geographical isolation and potential independent origins of the populations. Only one population of H. deserticola showed candidate sweeps that were unique compared to the rest of the species, and this population has also potentially experienced recent admixture with the parental species. PMID:18092993

Unraveling the efficiency of RAPD and SSR markers in diversity analysis and population structure estimation in common bean.

PubMed

Zargar, Sajad Majeed; Farhat, Sufia; Mahajan, Reetika; Bhakhri, Ayushi; Sharma, Arjun

2016-01-01

Increase in food production viz-a-viz quality of food is important to feed the growing human population to attain food as well as nutritional security. The availability of diverse germplasm of any crop is an important genetic resource to mine the genes that may assist in attaining food as well as nutritional security. Here we used 15 RAPD and 23 SSR markers to elucidate diversity among 51 common bean genotypes mostly landraces collected from the Himalayan region of Jammu and Kashmir, India. We observed that both the markers are highly polymorphic. The discriminatory power of these markers was determined using various parameters like; percent polymorphism, PIC, resolving power and marker index. 15 RAPDs produced 171 polymorphic bands, while 23 SSRs produced 268 polymorphic bands. SSRs showed a higher PIC value (0.300) compared to RAPDs (0.243). Further the resolving power of SSRs was 5.241 compared to 3.86 for RAPDs. However, RAPDs showed a higher marker index (2.69) compared to SSRs (1.279) that may be attributed to their higher multiplex ratio. The dendrograms generated with hierarchical UPGMA cluster analysis grouped genotypes into two main clusters with various degrees of sub clustering within the cluster. Here we observed that both the marker systems showed comparable accuracy in grouping genotypes of common bean according to their area of cultivation. The model based STRUCTURE analysis using 15 RAPD and 23 SSR markers identified a population with 3 sub-populations which corresponds to distance based groupings. High level of genetic diversity was observed within the population. These findings have further implications in common bean breeding as well as conservation programs.

Waterfalls drive parallel evolution in a freshwater goby

PubMed Central

Kano, Yuichi; Nishida, Shin; Nakajima, Jun

2012-01-01

Waterfalls may affect fish distribution and genetic structure within drainage networks even to the extent of leading evolutionary events. Here, parallel evolution was studied by focusing on waterfall and the landlocked freshwater goby Rhinogobius sp. YB (YB), which evolved from amphidromous R. brunneus (BR). The fish fauna was surveyed at 30 sites in 11 rivers on Iriomote Island, Japan, the geography of which was characterized by terraces/tablelands with many waterfalls. We found that all YB individuals were distributed only above waterfalls (height 6.8–58.7 m), whereas BR, and other fishes, were mostly distributed below waterfalls. Mitochondrial DNA analysis showed that every YB local population above the waterfall was independently evolved from BR. In contrast, cluster analysis of nine morphological characters, such as fin color and body pattern, showed that the morphology of YB individuals held a similarity beyond the genetic divergence, suggesting parallel evolution has occurred relating to their morphology. Genetic distance between each YB local population and BR was significantly correlated with waterfall height (r2 = 0.94), suggesting that the waterfalls have been heightened due to the constant geological erosion and that their height represents the isolation period of YB local populations from BR (ca. 11,000–88,000 years). Each local population of BR was once landlocked in upstream by waterfall formation, consequently evolving to YB in each site. Although the morphology of YB had a high degree of similarity among local populations, finer scale analysis showed that the morphology of YB was significantly correlated with the genetic distance from BR. Consequently, there could be simultaneous multiple phases of allopatric/parallel evolution of the goby due to variations in waterfall height on this small island. PMID:22957183

Effects of English admixture and geographic distance on anthropometric variation and genetic structure in 19th-century Ireland.

PubMed

Relethford, J H

1988-05-01

The analysis of anthropometric data often allows investigation of patterns of genetic structure in historical populations. This paper focuses on interpopulational anthropometric variation in seven populations in Ireland using data collected in the 1890s. The seven populations were located within a 120-km range along the west coast of Ireland and include islands and mainland isolates. Two of the populations (the Aran Islands and Inishbofin) have a known history of English admixture in earlier centuries. Ten anthropometric measures (head length, breadth, and height; nose length and breadth; bizygomatic and bigonial breadth; stature; hand length; and forearm length) on 259 adult Irish males were analyzed following age adjustment. Discriminant and canonical variates analysis were used to determine the degree and pattern of among-group variation. Mahalanobis' distance measure, D2, was computed between each pair of populations and compared to distance measures based on geographic distance and English admixture (a binary measure indicating whether either of a pair of populations had historical indications of admixture). In addition, surname frequencies were used to construct distance measures based on random isonymy. Correlations were computed between distance measures, and their probabilities were derived using the Mantel matrix permutation method. English admixture has the greatest effect on anthropometric variation among these populations, followed by geographic distance. The correlation between anthropometric distance and geographic distance is not significant (r = -0.081, P = .590), but the correlation of admixture and anthropometric distance is significant (r = 0.829, P = .047). When the two admixed populations are removed from the analysis the correlation between geographic and anthropometric distance becomes significant (r = 0.718, P = .025). Isonymy distance shows a significant correlation with geographic distance (r = 0.425, P = .046) but not with admixture distance (r = -0.052, P = .524). The fact that anthropometrics show past patterns of gene flow and surnames do not reflects the greater impact of stochastic processes on surnames, along with the continued extinction of surnames. This study shows that 1) anthropometrics can be extremely useful in assessing population structure and history, 2) differential gene flow into populations can have a major impact on local genetic structure, and 3) microevolutionary processes can have different effects on biological characters and surnames.

Characterization of the genetic diversity and population structure for the yellow cattle in Taiwan based on microsatellite markers.

PubMed

Tu, Po-An; Lin, Der-Yuh; Li, Guang-Fu; Huang, Jan-Chi; Wang, De-Chi; Wang, Pei-Hwa

2014-01-01

In recent years, the population size of Taiwan yellow cattle has drastically declined, even become endangered. A preservation project, Taiwan Yellow Cattle Genetic Preservation Project (TYCGPP), was carried out at the Livestock Research Institute (LRI) Hengchun branch (1988-present). An analysis of intra- and inter- population variability was performed to be the first step to preserve this precious genetic resource. In this work, a total number of 140 individuals selected from the five Taiwan yellow cattle populations were analyzed using 12 microsatellite markers (loci). These markers determined the level of genetic variation within and among populations as well as the phylogenetic structure. The total number of alleles detected (122, 10.28 per locus) and the expected heterozygosity (0.712) indicated that these five populations had a high level of genetic variability. Bayesian cluster analysis showed that the most likely number of groups was 2 (K = 2). Genetic differentiation among clusters was moderate (F ST = 0.095). The result of AMOVA showed that yellow cattle in Taiwan had maintained a high level of within-population genetic differentiation (91%), the remainder being accounted for by differentiation among subpopulations (4%), and by differentiation among regions (5%). The results of STRUCTURE and principal component analysis (PCA) revealed two divergent clusters. The individual unrooted phylogenetic tree showed that some Kinmen yellow cattle in the Hengchun facility (KMHC individuals) were overlapped with Taiwan yellow cattle (TW) and Taiwan yellow cattle Hengchun (HC) populations. Also, they were overlapped with Kinmen × Taiwan (KT) and Kinmen yellow cattle (KM) populations. It is possible that KMHC kept similar phenotypic characteristics and analogous genotypes between TW and KM. A significant inbreeding coefficient (F IS = 0.185; P < 0.01) was detected, suggesting a medium level of inbreeding for yellow cattle in Taiwan. The hypothesis that yellow cattle in Taiwan were derived from two different clusters was also supported by the phylogenetic tree constructed by the UPGMA, indicating that the yellow cattle in Taiwan and in Kinmen should be treated as two different management units. This result will be applied to maintain a good level of genetic variability and rusticity (stress-resistance) and to avoid further inbreeding for yellow cattle population in Taiwan.

Prevalence, distribution and intraspecific variation of Heterodera schachtii populations from semiarid environment

PubMed Central

Haidar, Asma M.; Al-Assas, Khaled M.; Dawabah, Ahmed A.M.

2015-01-01

A two-year survey study was carried-out to identify and determine the distribution, community characteristics and intraspecific variation of the sugar beet cyst nematode, Heterodera schachtii populations collected from the six major sugar beet-producing governorates in Syria, west Asia. A total of 178 composite rhizosphere soil samples were collected from the six governorates during 2009 and 2010 growing seasons as follows: Aleppo (26), Ar Raqqah (17), Dayr az Zawr (33), Idlib (34), Hamah (41) and Homs (27 samples). The nematode was originally identified on the basis of morphometrics and morphological features of the cyst vulvar cones and second-stage juveniles (J2). The communities of H. schachtii were then analyzed using the criteria of frequency of occurrence (FO%), mean population density (PD) and prominence value (PV). Results showed that H. schachtii was the most frequent and prominent in Homs (FO% = 70.37% and PV = 23472.37) and the least frequent and prominent in Ar Raqqah (FO% = 5.88% and PV = 28.86). The highest nematode population density was also recorded in Homs in 2009 (50,545 J2 + eggs/100 g soil) while the least was recorded in Ar Raqqah in 2010 (119 J2 + eggs/100 g soil). The morphometric data of cyst vulvar cone, second-stage juveniles (J2) and eggs were also subjected to a multivariate principal component analysis to analyze the relationships between the studied populations, and to identify the variables that show the highest multiple correlations with these populations. Results showed that at the high order of hierarchical cluster analysis, four populations (Idlib, Hamah, Homs and Aleppo) formed one main cluster, while Dair az Zawr and Ar Raqqah failed to form clusters and separated individually. However, at low distance value, the main cluster further subdivided to separate the Aleppo population from Idlib, Hamah and Homs populations. The morphometric distance values ranged from 0.07 to 0.61. Hamah and Homs were the closest populations while Dair az Zawr showed the most diverse population. This study also revealed the value of J2 body length, egg length and width, fenestral length and width and the number of bullae inside the cyst vulvar cone in determining the intraspecific variations among the Syrian populations of H. schachtii. PMID:26981013

[Genetic polymorphism of Tulipa gesneriana L. evaluated on the basis of the ISSR marking data].

PubMed

Kashin, A S; Kritskaya, T A; Schanzer, I A

2016-10-01

Using the method of ISSR analysis, the genetic diversity of 18 natural populations of Tulipa gesneriana L. from the north of the Lower Volga region was examined. The ten ISSR primers used in the study provided identification of 102 PCR fragments, of which 50 were polymorphic (49.0%). According to the proportion of polymorphic markers, two population groups were distinguished: (1) the populations in which the proportion of polymorphic markers ranged from 0.35 to 0.41; (2) the populations in which the proportion of polymorphic markers ranged from 0.64 to 0.85. UPGMA clustering analysis provided subdivision of the sample into two large clusters. The unrooted tree constructed using the Neighbor Joining algorithm had similar topology. The first cluster included slightly variable populations and the second cluster included highly variable populations. The AMOVA analysis showed statistically significant differences (F CT = 0.430; p = 0.000) between the two groups. Local populations are considerably genetically differentiated from each other (F ST = 0.632) and have almost no links via modern gene flow, as evidenced by the results of the Mantel test (r =–0.118; p = 0.819). It is suggested that the degree of genetic similarities and differences between the populations depends on the time and the species dispersal patterns on these territories.

Comparative analyses of genetic/epigenetic diversities and structures in a wild barley species (Hordeum brevisubulatum) using MSAP, SSAP and AFLP.

PubMed

Shan, X H; Li, Y D; Liu, X M; Wu, Y; Zhang, M Z; Guo, W L; Liu, B; Yuan, Y P

2012-08-17

We analyzed genetic diversity and population genetic structure of four artificial populations of wild barley (Hordeum brevisubulatum); 96 plants collected from the Songnen Prairie in northeastern China were analyzed using amplified fragment length polymorphism (AFLP), specific-sequence amplified polymorphism (SSAP) and methylation-sensitive amplified polymorphism (MSAP) markers. Indices of (epi-)genetic diversity, (epi-)genetic distance, gene flow, genotype frequency, cluster analysis, PCA analysis and AMOVA analysis generated from MSAP, AFLP and SSAP markers had the same trend. We found a high level of correlation in the artificial populations between MSAP, SSAP and AFLP markers by the Mantel test (r > 0.8). This is incongruent with previous findings showing that there is virtually no correlation between DNA methylation polymorphism and classical genetic variation; the high level of genetic polymorphism could be a result of epigenetic regulation. We compared our results with data from natural populations. The population diversity of the artificial populations was lower. However, different from what was found using AFLP and SSAP, based on MSAP results the methylation polymorphism of the artificial populations was not significantly reduced. This leads us to suggest that the DNA methylation pattern change in H. brevisubulatum populations is not only related to DNA sequence variation, but is also regulated by other controlling systems.

Phylogeographic patterns of Lygus pratensis (Hemiptera: Miridae): Evidence for weak genetic structure and recent expansion in northwest China.

PubMed

Zhang, Li-Juan; Cai, Wan-Zhi; Luo, Jun-Yu; Zhang, Shuai; Wang, Chun-Yi; Lv, Li-Min; Zhu, Xiang-Zhen; Wang, Li; Cui, Jin-Jie

2017-01-01

Lygus pratensis (L.) is an important cotton pest in China, especially in the northwest region. Nymphs and adults cause serious quality and yield losses. However, the genetic structure and geographic distribution of L. pratensis is not well known. We analyzed genetic diversity, geographical structure, gene flow, and population dynamics of L. pratensis in northwest China using mitochondrial and nuclear sequence datasets to study phylogeographical patterns and demographic history. L. pratensis (n = 286) were collected at sites across an area spanning 2,180,000 km2, including the Xinjiang and Gansu-Ningxia regions. Populations in the two regions could be distinguished based on mitochondrial criteria but the overall genetic structure was weak. The nuclear dataset revealed a lack of diagnostic genetic structure across sample areas. Phylogenetic analysis indicated a lack of population level monophyly that may have been caused by incomplete lineage sorting. The Mantel test showed a significant correlation between genetic and geographic distances among the populations based on the mtDNA data. However the nuclear dataset did not show significant correlation. A high level of gene flow among populations was indicated by migration analysis; human activities may have also facilitated insect movement. The availability of irrigation water and ample cotton hosts makes the Xinjiang region well suited for L. pratensis reproduction. Bayesian skyline plot analysis, star-shaped network, and neutrality tests all indicated that L. pratensis has experienced recent population expansion. Climatic changes and extensive areas occupied by host plants have led to population expansion of L. pratensis. In conclusion, the present distribution and phylogeographic pattern of L. pratensis was influenced by climate, human activities, and availability of plant hosts.

High prices for rare species can drive large populations extinct: the anthropogenic Allee effect revisited.

PubMed

Holden, Matthew H; McDonald-Madden, Eve

2017-09-21

Consumer demand for plant and animal products threatens many populations with extinction. The anthropogenic Allee effect (AAE) proposes that such extinctions can be caused by prices for wildlife products increasing with species rarity. This price-rarity relationship creates financial incentives to extract the last remaining individuals of a population, despite higher search and harvest costs. The AAE has become a standard approach for conceptualizing the threat of economic markets on endangered species. Despite its potential importance for conservation, AAE theory is based on a simple graphical model with limited analysis of possible population trajectories. By specifying a general class of functions for price-rarity relationships, we show that the classic theory can understate the risk of species extinction. AAE theory proposes that only populations below a critical Allee threshold will go extinct due to increasing price-rarity relationships. Our analysis shows that this threshold can be much higher than the original theory suggests, depending on initial harvest effort. More alarmingly, even species with population sizes above this Allee threshold, for which AAE predicts persistence, can be destined to extinction. Introducing even a minimum price for harvested individuals, close to zero, can cause large populations to cross the classic anthropogenic Allee threshold on a trajectory towards extinction. These results suggest that traditional AAE theory may give a false sense of security when managing large harvested populations. Copyright © 2017 Elsevier Ltd. All rights reserved.

Demography of black-tailed prairie dog populations reoccupying sites treated with rodenticide

Treesearch

R. P. Cincotta; Daniel W. Uresk; R. M. Hansen

1987-01-01

A rodenticide, zinc phosphide, was applied to remove black-tailed prairie dogs (Cynomys ludovicianus) from 6 haofa prairie dog colony in southwestern South Dakota. Another adjacent 6 ha was left untreated. The removal experiment was repeated two consecutive years. Contingency table analysis showed that the resultant population was not homogeneous;...

Spectral Study of Measles Epidemics: The Dependence of Spectral Gradient on the Population Size of the Community

NASA Astrophysics Data System (ADS)

Sumi, Ayako; Olsen, Lars Folke; Ohtomo, Norio; Tanaka, Yukio; Sawamura, Sadashi

2003-02-01

We have carried out spectral analysis of measles notifications in several communities in Denmark, UK and USA. The results confirm that each power spectral density (PSD) shows exponential characteristics, which are universally observed in the PSD for time series generated from nonlinear dynamical system. The exponential gradient increases with the population size. For almost all communities, many spectral lines observed in each PSD can be fully assigned to linear combinations of several fundamental periods, suggesting that the measles data are substantially noise-free. The optimum least squares fitting curve calculated using these fundamental periods essentially reproduces an underlying variation of the measles data, and an extension of the curve can be used to predict measles epidemics. For the communities with large population sizes, some PSD patterns obtained from segment time series analysis show a close resemblance to the PSD patterns at the initial stages of a period-doubling bifurcation process for the so-called susceptible/exposed/infectious/recovered (SEIR) model with seasonal forcing. The meaning of the relationship between the exponential gradient and the population size is discussed.

Control for Population Structure and Relatedness for Binary Traits in Genetic Association Studies via Logistic Mixed Models.

PubMed

Chen, Han; Wang, Chaolong; Conomos, Matthew P; Stilp, Adrienne M; Li, Zilin; Sofer, Tamar; Szpiro, Adam A; Chen, Wei; Brehm, John M; Celedón, Juan C; Redline, Susan; Papanicolaou, George J; Thornton, Timothy A; Laurie, Cathy C; Rice, Kenneth; Lin, Xihong

2016-04-07

Linear mixed models (LMMs) are widely used in genome-wide association studies (GWASs) to account for population structure and relatedness, for both continuous and binary traits. Motivated by the failure of LMMs to control type I errors in a GWAS of asthma, a binary trait, we show that LMMs are generally inappropriate for analyzing binary traits when population stratification leads to violation of the LMM's constant-residual variance assumption. To overcome this problem, we develop a computationally efficient logistic mixed model approach for genome-wide analysis of binary traits, the generalized linear mixed model association test (GMMAT). This approach fits a logistic mixed model once per GWAS and performs score tests under the null hypothesis of no association between a binary trait and individual genetic variants. We show in simulation studies and real data analysis that GMMAT effectively controls for population structure and relatedness when analyzing binary traits in a wide variety of study designs. Copyright © 2016 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

No population genetic structure in a widespread aquatic songbird from the Neotropics

USGS Publications Warehouse

Cadena, Carlos Daniel; Gutierrez-Pinto, Natalia; Davila, Nicolas; Chesser, R. Terry

2011-01-01

Neotropical lowland organisms often show marked population genetic structure, suggesting restricted migration among populations. However, most phylogeographic studies have focused on species inhabiting humid forest interior. Little attention has been devoted to the study of species with ecologies conducive to dispersal, such as those of more open and variable environments associated with watercourses. Using mtDNA sequences, we examined patterns of genetic variation in a widely distributed Neotropical songbird of aquatic environments, the Yellow-hooded Blackbird (Icteridae, Chrysomus icterocephalus). In contrast to many forest species, Yellow-hooded Blackbirds showed no detectable genetic structure across their range, which includes lowland populations on both sides of the Andes, much of northeastern South America, Amazonia, as well as a phenotypically distinct highland population in Colombia. A coalescent-based analysis of the species indicated that its effective population size has increased considerably, suggesting a range expansion. Our results support the hypothesis that species occurring in open habitats and tracking temporally dynamic environments should show increased dispersal propensities (hence gene flow) relative to species from closed and more stable environments. The phenotypic and behavioral variation among populations of our study species appears to have arisen recently and perhaps in the face of gene flow.

Molecular genetic and morphological analyses of the African wild dog (Lycaon pictus).

PubMed

Girman, D J; Kat, P W; Mills, M G; Ginsberg, J R; Borner, M; Wilson, V; Fanshawe, J H; Fitzgibbon, C; Lau, L M; Wayne, R K

1993-01-01

African wild dog populations have declined precipitously during the last 100 years in eastern Africa. The possible causes of this decline include a reduction in prey abundance and habitat; disease; and loss of genetic variability accompanied by inbreeding depression. We examined the levels of genetic variability and distinctiveness among populations of African wild dogs using mitochondrial DNA (mtDNA) restriction site and sequence analyses and multivariate analysis of cranial and dental measurements. Our results indicate that the genetic variability of eastern African wild dog populations is comparable to that of southern Africa and similar to levels of variability found in other large canids. Southern and eastern populations of wild dogs show about 1% divergence in mtDNA sequence and form two monophyletic assemblages containing three mtDNA genotypes each. No genotypes are shared between the two regions. With one exception, all wild dogs examined from zoos had southern African genotypes. Morphological analysis supports the distinction of eastern and southern African wild dog populations, and we suggest they should be considered separate subspecies. An eastern African wild dog breeding program should be initiated to ensure preservation of the eastern African form and to slow the loss of genetic variability that, while not yet apparent, will inevitably occur if wild populations continue to decline. Finally, we examined the phylogenetic relationships of wild dogs to other wolf-like canids through analysis of 736 base pairs (bp) of cytochrome b sequence and showed wild dogs to belong to a phylogenetically distinct lineage of the wolf-like canids.

Thin-plate spline analysis of the cranial base in African, Asian and European populations and its relationship with different malocclusions.

PubMed

Rosas, Antonio; Bastir, Markus; Alarcón, Jose Antonio; Kuroe, Kazuto

2008-09-01

To test the hypothesis that midline basicranial orientation and posterior cranial base length are discriminating factors between adults of different populations and its potential maxillo/mandibular disharmonies. Twenty-nine 2D landmarks of the midline cranial base, the face and the mandible of dry skull X-rays from three major populations (45 Asians, 34 Africans, 64 Europeans) were digitized and analysed by geometric morphometrics. We used, first, MANOVA to test for mean shape differences between populations; then, principal components analysis (PCA) to assess the overall variation in the sample and finally, canonical variate analysis (CVA) with jack-knife validations (N=1000) to analyse the anatomical features that best distinguished among populations. Significant mean shapes differences were shown between populations (P<0.001). CVA revealed two significant axes of discrimination (P<0.001). Jack-knife validation correctly identified 92% of 15,000 unknowns. In Africans the whole cranial base is rotated into a forward-downward position, while in Asians it is rotated in the opposite way. The Europeans occupied an intermediate position. African and Asian samples showed a maxillo/mandibular prognathism. African prognathism was produced by an anterior positioned maxilla, Asian prognathism by retruded anterior cranial base and increase of the posterior cranial base length. Europeans showed a trend towards retracted mandibles with relatively shorter posterior cranial bases. The results supported the hypothesis that basicranial orientation and posterior cranial base length are valid factors to distinguish between geographic groups. The whole craniofacial configuration underlying a particular maxillo-facial disharmony must be considered in diagnosis, growth predictions and resulting treatment planning.

Origin and expansion of the Yunnan Shoot Borer, Tomicus yunnanensis (coleoptera: scolytinae): a mixture of historical natural expansion and contemporary human-mediated relocation.

PubMed

Lü, Jun; Hu, Shao-ji; Ma, Xue-yu; Chen, Jin-min; Li, Qing-qing; Ye, Hui

2014-01-01

The Yunnan shoot borer, Tomicus yunnanensis, is a recently-discovered, aggressive pest of the Yunnan pine stands in southwestern China. Despite many bionomics studies and massive controlling efforts, research on its population genetics is extremely limited. The present study, aimed at investigating the origin and dispersal of this important forestry pest, analyzed the population genetic structure and demographic history using a mitochondrial cox1 gene fragment. Our results showed that T. yunnanensis most likely originated from the Central-Yunnan Altiplano, and the divergence time analysis placed the origin approximately 0.72 million-years ago. Host separation and specialization might have caused the speciation of T. yunnanensis. Genetic structure analyses identified two population groups, with six populations near the origin area forming one group and the remaining six populations from western and eastern Yunnan and southwestern Sichuan comprising the other. Divergence time analysis placed the split of the two groups at approximately 0.60 million-years ago, and haplotype phylogenetic tree, network, as well as migration rate suggested that populations of the latter group were established via a small number of individuals from the former one. Migration analysis also showed a certain degree of recent expansion from southwestern Sichuan to eastern Yunnan. Our findings implied that T. yunnanensis underwent both historical expansion and recent dispersal. The historical expansion may relate to the oscillation of regional climate due to glacial and interglacial periods in the Pleistocene, while human-mediated transportation of pine-wood material might have assisted the relocation and establishment of this pest in novel habitats.

A Genome-wide Analysis of Admixture in Uyghurs and a High-Density Admixture Map for Disease-Gene Discovery

PubMed Central

Xu, Shuhua; Jin, Li

2008-01-01

Following up on our previous study, we conducted a genome-wide analysis of admixture for two Uyghur population samples (HGDP-UG and PanAsia-UG), collected from the northern and southern regions of Xinjiang in China, respectively. Both HGDP-UG and PanAsia-UG showed a substantial admixture of East-Asian (EAS) and European (EUR) ancestries, with an empirical estimation of ancestry contribution of 53:47 (EAS:EUR) and 48:52 for HGDP-UG and PanAsia-UG, respectively. The effective admixture time under a model with a single pulse of admixture was estimated as 110 generations and 129 generations, or admixture events occurred about 2200 and 2580 years ago for HGDP-UG and PanAsia-UG, respectively, assuming an average of 20 yr per generation. Despite Uyghurs' earlier history compared to other admixture populations, admixture mapping, holds promise for this population, because of its large size and its mixture of ancestry from different continents. We screened multiple databases and identified a genome-wide single-nucleotide polymorphism panel that can distinguish EAS and EUR ancestry of chromosomal segments in Uyghurs. The panel contains 8150 ancestry-informative markers (AIMs) showing large frequency differences between EAS and EUR populations (FST > 0.25, mean FST = 0.43) but small frequency differences (7999 AIMs validated) within both populations (FST < 0.05, mean FST < 0.01). We evaluated the effectiveness of this admixture map for localizing disease genes in two Uyghur populations. To our knowledge, our map constitutes the first practical resource for admixture mapping in Uyghurs, and it will enable studies of diseases showing differences in genetic risk between EUR and EAS populations. PMID:18760393

Natural selection among Kinnaura of the Himalayan highland: A comparative analysis with other Indian and Himalayan populations

PubMed Central

Gautam, Rajesh K.; Kapoor, Anup K.; Kshatriya, G. K.

2009-01-01

The present investigation on fertility and mortality differential among Kinnaura of the Himalayan highland is based on data collected from 160 post-menopausal women belonging to the middle and high altitude region of Kinnaur district of Himachal Pradesh (Indian Himalayas). Selection potential based on differential fertility and mortality was computed for middle-and high-altitude women. Irrespective of the methodology, the total index of selection was found to be highest among middle-altitude women (0.386) as compared with high-altitude (0.370) women, whereas for the total population it is estimated to be 0.384. It was found that the Kinnaura of the Himalayan highland showing moderate index of total selection and relative contribution of the mortality component (Im) to the index of total selection is higher than the corresponding fertility component (If). The analysis of embryonic and post-natal mortality components shows that the post-natal mortality components are higher in comparison with the embryonic mortality components among highlanders and needs special intervention and health care. The present findings are compared with other Indian tribes as well as non-tribes of the Himalayan region and other parts of the country. It reveals that this index among Kinnaura is moderate than the other population groups; among the Himalayan population, the highest was reported for Galong (It = 1.07) of Arunachal, whereas the lowest was reported from Ahom (It = 0.218) of Manipur. The correlation and regression analysis between total index of selection (It) and fertility (If) and mortality (Im) components for pooled data of populations of the Indian Himalayan states show that If and Im account for 21.6 and 29.1% variability, respectively. In Crow's total index of selection (It) along with strong association, which is significant at the 1% level, this indicates that mortality plays a greater role in natural selection in comparison with fertility among populations of the Indian Himalayas. PMID:21088718

Isolation by distance and vicariance drive genetic structure of a coral reef fish in the Pacific Ocean.

PubMed

Planes, S; Fauvelot, C

2002-02-01

We studied the genetic diversity of a coral reef fish species to investigate the origin of the differentiation. A total of 727 Acanthurus triostegus collected from 15 locations throughout the Pacific were analyzed for 20 polymorphic loci. The genetic structure showed limited internal disequilibrium within each population; 3.7% of the loci showed significant Hardy-Weinberg disequilibrium, mostly associated with Adh*, and we subsequently removed this locus from further analysis of geographic pattern. The genetic structure of A. triostegus throughout the tropical Pacific Ocean revealed a strong geographic pattern. Overall, there was significant population differentiation (multilocus F(ST) = 0.199), which was geographically structured according to bootstraps of neighbor-joining analysis on Nei's unbiased genetic distances and AMOVA analysis. The genetic structure revealed five geographic groups in the Pacific Ocean: western Pacific (Guam, Philippines, Palau, and Great Barrier Reef); central Pacific (Solomons, New Caledonia, and Fiji); and three groups made up of the eastern populations, namely Hawaiian Archipelago (north), Marquesas (equatorial), and southern French Polynesia (south) that incorporates Clipperton Island located in the northeastern Pacific. In addition, heterozygosity values were found to be geographically structured with higher values grouped within Polynesian and Clipperton populations, which exhibited lower population size. Finally, the genetic differentiation (F(ST)) was significantly correlated with geographic distance when populations from the Hawaiian and Marquesas archipelagos were separated from all the other locations. These results show that patterns of differentiation vary within the same species according to the spatial scale, with one group probably issued from vicariance, whereas the other followed a pattern of isolation by distance. The geographic pattern for A. triostegus emphasizes the diversity of the evolutionary processes that lead to the present genetic structure with some being more influential in certain areas or according to a particular spatial scale.

Dietary reconstruction from trace element analysis and dental microwear in an Early Medieval population from Gán (Galanta district, Slovakia).

PubMed

Bodoriková, Silvia; Tibenská, Kristína Domonkosová; Katina, Stanislav; Uhrová, Petra; Dörnhöferová, Michaela; Takács, Michal; Urminský, Jozef

2013-01-01

The aim of the study was to determine the diet of an historical human population using the trace elements in dental tissues and dental buccal microwear. Although 38 individuals had been buried in the cemetery, preservation of the remains did not allow analysis of all of them. A total of 13 individuals were analysed, of which the samples for trace-element analysis consisted of 12 permanent premolars from 12 individuals. Buccal microwear was studied in a sample of nine teeth from nine individuals. Both trace-element and microwear analyses were performed on eight individuals. All analyzed teeth were intact, with fully developed roots, without dental calculus and macro-abrasion. Concentrations of Sr, Zn, and Ca, and their ratios, were used to determine the relative proportions of plant and animal protein in the diet. Samples were analyzed using optical emission spectrometry with inductively coupled plasma. The values of the Sr and Zn concentrations indicate that a diet of the investigated population was of a mixed character with approximately the same proportion of plants and meat in their food. Buccal microwear was studied in molds ofbuccal surfaces and observed at 100x magnification with a scanning electron microscope (SEM). Length and orientation of striations were determined with the SigmaScan Pro 5.0 image analysis program. The results obtained from microwear analysis correspond with those from trace-element analysis and showed that the population consumed a mixed diet. The density of the scratches indicates that the diet contained a considerable vegetable component. The high number of vertical scratches and their high average length suggest that individuals also consumed a large portion of meat. The results of both analyses showed that there were also individuals whose diet had probably been poor, i.e. richer in animal protein, which probably could be related to their health or social status in the population.

Genetic structure in four West African population groups

PubMed Central

Adeyemo, Adebowale A; Chen, Guanjie; Chen, Yuanxiu; Rotimi, Charles

2005-01-01

Background Africa contains the most genetically divergent group of continental populations and several studies have reported that African populations show a high degree of population stratification. In this regard, it is important to investigate the potential for population genetic structure or stratification in genetic epidemiology studies involving multiple African populations. The presences of genetic sub-structure, if not properly accounted for, have been reported to lead to spurious association between a putative risk allele and a disease. Within the context of the Africa America Diabetes Mellitus (AADM) Study (a genetic epidemiologic study of type 2 diabetes mellitus in West Africa), we have investigated population structure or stratification in four ethnic groups in two countries (Akan and Gaa-Adangbe from Ghana, Yoruba and Igbo from Nigeria) using data from 372 autosomal microsatellite loci typed in 493 unrelated persons (986 chromosomes). Results There was no significant population genetic structure in the overall sample. The smallest probability is associated with an inferred cluster of 1 and little of the posterior probability is associated with a higher number of inferred clusters. The distribution of members of the sample to inferred clusters is consistent with this finding; roughly the same proportion of individuals from each group is assigned to each cluster with little variation between the ethnic groups. Analysis of molecular variance (AMOVA) showed that the between-population component of genetic variance is less than 0.1% in contrast to 99.91% for the within population component. Pair-wise genetic distances between the four ethnic groups were also very similar. Nonetheless, the small between-population genetic variance was sufficient to distinguish the two Ghanaian groups from the two Nigerian groups. Conclusion There was little evidence for significant population substructure in the four major West African ethnic groups represented in the AADM study sample. Ethnicity apparently did not introduce differential allele frequencies that may affect analysis and interpretation of linkage and association studies. These findings, although not entirely surprising given the geographical proximity of these groups, provide important insights into the genetic relationships between the ethnic groups studied and confirm previous results that showed close genetic relationship between most studied West African groups. PMID:15978124

Genetic admixture and lineage separation in a southern Andean plant

PubMed Central

Morello, Santiago; Sede, Silvana M.

2016-01-01

Mountain uplifts have generated new ecologic opportunities for plants, and triggered evolutionary processes, favouring an increase on the speciation rate in all continents. Moreover, mountain ranges may act as corridors or barriers for plant lineages and populations. In South America a high rate of diversification has been linked to Andean orogeny during Pliocene/Miocene. More recently, Pleistocene glacial cycles have also shaped species distribution and demography. The endemic genus Escallonia is known to have diversified in the Andes. Species with similar morphology obscure species delimitation and plants with intermediate characters occur naturally. The aim of this study is to characterize genetic variation and structure of two widespread species of Escallonia: E. alpina and E. rubra. We analyzed the genetic variation of populations of the entire distribution range of the species and we also included those with intermediate morphological characters; a total of 94 accessions from 14 populations were used for the Amplified Fragment Length Polymorphism (AFLP) analysis. Plastid DNA sequences (trnS-trnG, 3′trnV-ndhC intergenic spacers and the ndhF gene) from sixteen accessions of Escallonia species were used to construct a Statistical Parsimony network. Additionally, we performed a geometric morphometrics analysis on 88 leaves from 35 individuals of the two E. alpina varieties to further study their differences. Wright’s Fst and analysis of molecular variance tests performed on AFLP data showed a significant level of genetic structure at the species and population levels. Intermediate morphology populations showed a mixed genetic contribution from E. alpina var. alpina and E. rubra both in the Principal Coordinates Analysis (PCoA) and STRUCTURE. On the other hand, E. rubra and the two varieties of E. alpina are well differentiated and assigned to different genetic clusters. Moreover, the Statistical Parsimony network showed a high degree of divergence between the varieties of E. alpina: var. alpina is more closely related to E. rubra and other species than to its own counterpart E. alpina var. carmelitana. Geometric morphometrics analysis (Elliptic Fourier descriptors) revealed significant differences in leaf shape between varieties. We found that diversity in Escallonia species analyzed here is geographically structured and deep divergence between varieties of E. alpina could be associated to ancient evolutionary events like orogeny. Admixture in southern populations could be the result of hybridization at the margins of the parental species’ distribution range. PMID:27179539

Comparative analysis of qualitative dermatoglyphic traits of Albanian and Turkish populations living in the area of Dukagjin Valley in Kosovo.

PubMed

Temaj, Gazmend; Krajacić, Petra; Milicić, Jasna; Jurić, Tatjana Skarić; Behluli, Ibrahim; Narancić, Nina Smolej; Hadziselimović, Rifat; Nefić, Hilda; Sopi, Ramadan; Belegu, Mazllan; Jakupi, Muharrem; Rudan, Pavao

2011-09-01

Dermatoglyphic prints were collected from 800 inhabitants of Dukagjin valley in Kosovo. The sample consisted of two ethnically different sub-populations who refer themselves as Albanians (N = 400) and Turks (N = 400). Qualitative analysis of prints concerned the frequency of the patterns on fingers (arch, ulnar and radial loop, whorl, accidental whorl) and on palms (Thenar and I, II, III, and IV interdigital area and the hypothenar, main line index, and the axial "t" triradius position). As was expected due to previous study of quantitative dermatoglyphic traits, in the same population the Alba-nians and Turks showed to be significantly different in most explored qualitative dermatoglyphic variables. Found differences indicated that the reproductive isolation between the Albanian and Turkish population in Kosovo is substantial, despite the fact that those two ethnic sub-populations live in the close vicinity through several centuries.

Population-genetics approach to the genetics of human behaviour.

PubMed

Bulaeva, K B; Isaichev, S A; Pavlova, T A

1990-04-01

Invariant values of inheritance factors within and between different populations can show the existence of and measure the degree of genetic determination of behavioural characters. The absence of inbred depression of quantitative behavioural characters in isolated populations of highland inhabitants of Daghestan is demonstrated by means of comparative analysis of the mean population values of psychophysiological characters in outbred, moderately isolated, and extremely isolated (and inbred) populations. The absence of pronounced adverse effects of inbred marriages, known as the 'Daghestan phenomenon', is explained by the antiquity of the native populations and the severe ecological conditions under which these populations live which have led to elimination of carriers of hereditary diseases and other detrimental phenotypes.

Validation of Warwick-Edinburgh Mental Well-being Scale (WEMWBS) in a population of people using Secondary Care Mental Health Services.

PubMed

Bass, Malcolm; Dawkin, Mathew; Muncer, Steven; Vigurs, Scott; Bostock, Janet

2016-08-01

The Warwick-Edinburgh Mental Well-being Scale (WEMWBS) is a relatively new measure and to date has been validated in a number of populations, including student, general and adolescent samples across the UK. There is increasing interest in measuring the mental well-being of users of secondary care mental health services and therefore it is apt to validate WEMWBS for this population. To investigate the validity of WEMWBS in a secondary care mental health service user population. Data was collected from two NHS Trusts and one charity. Analyses are based on 1180 completed WEMWBS. WEMWBS scores for this population are significantly lower than those in a general population (Mean 34.9, SD 13.8). Overall the data analyses supported the use of WEMWBS in this population sample. The Rasch analysis found that the majority of the items can be seen as measuring one dimension. The confirmatory factor analysis supports a one factor solution and thus, measures a single underlying concept. The findings from this study show WEMWBS to be a valid and reliable measure for this population sample.

Stability and bifurcation analysis of three-species predator-prey model with non-monotonic delayed predator response

NASA Astrophysics Data System (ADS)

Balilo, Aldrin T.; Collera, Juancho A.

2018-03-01

In this paper, we consider delayed three-species predator-prey model with non-monotonic functional response where two predator populations feed on a single prey population. Response function in both predator populations includes a time delay which represents the gestation period of the predator populations. We call a positive equlibrium solution of the form E*S=(x*,y*,y*) as a symmetric equilibrium. The goal of this paper is to determine the effect of the difference in gestation periods of predator populations to the local dynamics of symmetric equilibria. Our results include conditions on the existence of equilibrium solutions, and stability and bifurcations of symmetric equilibria as the gestation periods of predator populations are varied. A numerical bifurcation analysis tool is also used to illustrate our results. Stability switch occurs at a Hopf bifurcation. Moreover, a branch of stable periodic solutions, obtained using numerical continuation, emerges from the Hopf bifurcation. This shows that the predator population with longer gestation period oscillates higher than the predator population with shorter gestation period.

A Comparative Analysis of Genetic Ancestry and Admixture in the Colombian Populations of Chocó and Medellín

PubMed Central

Conley, Andrew B.; Rishishwar, Lavanya; Norris, Emily T.; Valderrama-Aguirre, Augusto; Mariño-Ramírez, Leonardo; Medina-Rivas, Miguel A.; Jordan, I. King

2017-01-01

At least 20% of Colombians identify as having African ancestry, yielding the second largest population of Afro-descendants in Latin America. To date, there have been relatively few studies focused on the genetic ancestry of Afro-Latino populations. We report a comparative analysis of the genetic ancestry of Chocó, a state located on Colombia’s Pacific coast with a population that is >80% Afro-Colombian. We compared genome-wide patterns of genetic ancestry and admixture for Chocó to six other admixed American populations, with an emphasis on a Mestizo population from the nearby Colombian city of Medellín. One hundred sample donors from Chocó were genotyped across 610,545 genomic sites and compared with 94 publicly available whole genome sequences from Medellín. At the continental level, Chocó shows mostly African genetic ancestry (76%) with a nearly even split between European (13%) and Native American (11%) fractions, whereas Medellín has primarily European ancestry (75%), followed by Native American (18%) and African (7%). Sample donors from Chocó self-identify as having more African ancestry, and conversely less European and Native American ancestry, than can be genetically inferred, as opposed to what we previously found for Medellín, where individuals tend to overestimate levels of European ancestry. We developed a novel approach for subcontinental ancestry assignment, which allowed us to characterize subcontinental source populations for each of the three distinct continental ancestry fractions separately. Despite the clear differences between Chocó and Medellín at the level of continental ancestry, the two populations show overall patterns of subcontinental ancestry that are highly similar. Their African subcontinental ancestries are only slightly different, with Chocó showing more exclusive shared ancestry with the modern Yoruba (Nigerian) population, and Medellín having relatively more shared ancestry with West African populations in Sierra Leone and Gambia. Both populations show very similar Spanish ancestry within Europe and virtually identical patterns of Native American ancestry, with main contributions from the Embera and Waunana tribes. When the three subcontinental ancestry components are considered jointly, the populations of Chocó and Medellín are shown to be most closely related, to the exclusion of the other admixed American populations that we analyzed. We consider the implications of the existence of shared subcontinental ancestries for Colombian populations that appear, at first glance, to be clearly distinct with respect to competing notions of national identity that emphasize ethnic mixing (mestizaje) vs. group-specific identities (multiculturalism). PMID:28855283

Conservation biology of the Cross River gorilla (Gorilla gorilla diehli)

NASA Astrophysics Data System (ADS)

Bergl, Richard Alexander

The Cross River gorilla (Gorilla gorilla diehli), a recently revived fourth subspecies of gorilla, is the most endangered and poorly studied ape taxon. Only about 300 Cross River gorillas remain and these gorillas occur in at least eleven different localities. This dissertation presents a population-wide assessment of threats to this population based on molecular genetic data, satellite imagery and demographic modeling. I used DNA extracted from non-invasively collected fecal samples to amplify eleven microsatellite loci for population genetic analysis. Microsatellite data suggested that a complex population structure is present in the Cross River gorilla, with three genetically identifiable subpopulations present. Though levels of gene flow between certain subpopulations were low, there is evidence that reproductive contact persists between many of the subpopulations. The genetic data also demonstrate that levels of diversity in the Cross River population are not evenly distributed across subpopulations, and that one subpopulation has higher levels of variability than the others. In a genus-wide comparison, levels of genetic diversity in the Cross River gorilla were comparable to those of the similarly small populations of the mountain gorilla ( Gorilla beringei beringei) in Bwindi and the Virunga volcanoes, but showed lower levels of diversity than a sample from a large, continuous population of Gorilla gorilla gorilla at Mondika, Central African Republic. Genetic data also showed strong evidence of a population bottleneck in the Cross River gorilla, but not in the other three gorilla populations examined. I used analysis of remotely-sensed data from the Landsat satellite to assess the extent and pattern of land cover distribution across the Cross River gorilla's range. Considerable potential gorilla habitat remains within the range of the Cross River gorilla and each gorilla locality is at least tenuously connected by forest. Finally, I developed a model-based population viability analysis for the Cross River gorilla. Demographic modeling suggested that both population structure and variables associated with female reproductive output most influence population growth in the Cross River gorilla. Taken together, the results of my study are encouraging for the conservation of the Cross River gorilla population, and highlight the resilience of these animals in the face of human activities. Conservation efforts should promote connectivity between gorilla localities and foster the growth of their population. The methods I applied could provide useful insights into patterns of population structure and migration for a wide range of animal taxa.

Detecting population–environmental interactions with mismatched time series data

PubMed Central

Ferguson, Jake M.; Reichert, Brian E.; Fletcher, Robert J.; Jager, Henriëtte I.

2017-01-01

Time series analysis is an essential method for decomposing the influences of density and exogenous factors such as weather and climate on population regulation. However, there has been little work focused on understanding how well commonly collected data can reconstruct the effects of environmental factors on population dynamics. We show that, analogous to similar scale issues in spatial data analysis, coarsely sampled temporal data can fail to detect covariate effects when interactions occur on timescales that are fast relative to the survey period. We propose a method for modeling mismatched time series data that couples high-resolution environmental data to low-resolution abundance data. We illustrate our approach with simulations and by applying it to Florida’s southern Snail kite population. Our simulation results show that our method can reliably detect linear environmental effects and that detecting nonlinear effects requires high-resolution covariate data even when the population turnover rate is slow. In the Snail kite analysis, our approach performed among the best in a suite of previously used environmental covariates explaining Snail kite dynamics and was able to detect a potential phenological shift in the environmental dependence of Snail kites. Our work provides a statistical framework for reliably detecting population–environment interactions from coarsely surveyed time series. An important implication of this work is that the low predictability of animal population growth by weather variables found in previous studies may be due, in part, to how these data are utilized as covariates. PMID:28759123

Genetic diversity of the Tibetan antelope (Pantholops hodgsonii) population of Ladakh, India, its relationship with other populations and conservation implications.

PubMed

Ahmad, Khursheed; Kumar, Ved P; Joshi, Bheem Dutt; Raza, Mohamed; Nigam, Parag; Khan, Anzara Anjum; Goyal, Surendra P

2016-10-21

The Tibetan antelope (Pantholops hodgsonii), or chiru, is an endangered antelope, distributed in China [Xinjiang, Xizang, Qinghai, Zhuolaihu Lake (Breeding habitat)], and India (Aksai Chin and Ladakh). There is a global demand for the species prized wool, which is used in weaving shahtoosh shawls. Over the years, the population of the Tibetan antelope has drastically declined from more than a million to a few thousand individuals, mainly due to poaching. Field studies undertaken in Ladakh, India also indicated winter migration of the population to Tibet. Migration between winter and calving habitats is well established to be female-biased across the Qinghai Tibetan Plateau (QTP). For effective conservation planning, genetic characterization is considered the best way to understand the likely impact of threats for ensuring the long-term viability of the population. In this regard, genetic characteristics of all Chinese populations are well-studied using mitochondrial and microsatellite markers, but information is lacking for the Indian population. Therefore, using the control region marker, we document for the first time the genetic variation of the Indian population of the Tibetan antelope, the extent of migration and its relationships with other populations of China. The partial fragment of control region (259 bp) marker was successfully amplified in 30 Tibetan antelope samples that were collected from the Chang Chenmo Valley in eastern Ladakh, India. We also retrieved control region sequences (n = 88) available in the public domain from GenBank of different Chinese populations. Low levels of nucleotide (π; 0.004) and haplotype (hd; 0.543) diversity were observed in the Indian population when compared to Chinese populations (π = 0.01357-0.02048 and hd = 0.889-0.986). Commonly used indices (Tajima's D and Fu's Fs) were analyzed for inferring the demographic history of the Indian populations, and all values were negative indicating population expansion or demographic equilibrium, though nonsignificant. We observed five haplotypes in the Indian population, and these were not reported in previously studied populations of QTP. Bayesian-based phylogenetic analysis indicates the presence of four clades, however, the posterior probability support for three of these clades is weak (<0.5). Of these, the Indian population formed a distinct clade, whereas the Chinese populations exhibited shared haplotypes, and no geographic structure was observed. Median-joining network analysis was conducted for 46 haplotypes in the overall population, except the samples from India which showed a star-like topology. The Indian population is separated by one median vector from the Chinese population. The present study revealed the presence of different sub-clades in the Bayesian phylogenetic tree and five new haplotypes only in the Indian population or sampling location. Furthermore, in the phylogenetic tree, Indian haplotypes of Tibetan antelopes were clustered with the haplotype reported in the Chinese population of the Xinjiang region. Median-joining network analysis showed shared haplotypes pattern in all populations of QTP except the samples from India which showed new haplotypes. Given the presence of low nucleotide and haplotype diversity in eastern Ladakh populations and limited information available for populations of the western side in its range, we suggest to include genetic studies of Tibetan antelope populations around Aksai Chin (Fig. 1) under the proposed transboundary agenda between India and China and assess relationships with other populations. Such understanding would enable the planning of conservation strategies for ensuring long-term survival of westernmost populations in its range, and if required, it would establish connectivity with the other populations.

Population stratification effect on cancer susceptibility in an admixed population from Brazilian Amazon.

PubMed

Vieira, Priscilla Cristina Moura; Burbano, Rommel Mario Rodríguez; Fernandes, Débora Christina Ricardo Oliveira; Montenegro, Raquel Carvalho; Dos Santos, Sidney Emanuel Batista; Sortica, Vinicius Albuquerque; Assumpção, Paulo Pimentel; Ribeiro-Dos-Santos, Ândrea Kely Campos; Carvalho, Antônio Alberto; Dos Santos, Ney Pereira Carneiro

2015-04-01

Many efforts have been made to identify candidate genes involved in cancer susceptibility. The present study aimed to investigate the association between Arg194Trp (XRCC1), Ala222Val (MTHFR) and Arg521Lys (EGFR) polymorphisms (SNPs) and their susceptibility to gastric and breast carcinoma cancer in patients from Brazilian Amazon, controlling population structure interference. The SNPs were genotyped by TaqMan® SNP Genotyping Assays. Ancestry was estimated by analysis of a panel with 48 ancestry informative markers. Logistic regression analysis showed an inverse association with a 10% increase in African and European ancestry and cancer risk (odds ratio (OR)=1.919 and 0.676, respectively). In a preliminary Chi-square analysis a positive association between Arg521Lys (EGFR) polymorphism and carcinoma susceptibility was found (p=0.037); however, when two different methodologies to control population structure bias were utilized, this association was lost (p=0.064 and p=0.256). Genetic ancestry influence gastric and breast cancer risk and highlight the importance of population structure inference in association studies in highly admixed populations, such as those from Brazilian Amazon. Copyright© 2015 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

Association between Vitamin D level and/or deficiency, and systemic lupus erythematosus: a meta-analysis.

PubMed

Bae, Sang-Cheol; Lee, Young Ho

2018-01-31

This study aimed to evaluate the relationship between the level of 25-hydroxyvitamin D [25(OH)D] and systemic lupus erythematosus (SLE). We searched the PUBMED, EMBASE, and Cochrane databases and performed a meta-analysis examining the vitamin D level and/or deficiency in patients with SLE, compared with that in healthy controls. In total, 18 studies consisting of 1,083 patients with SLE and 1,273 controls were included. Vitamin D level was significantly lower in the SLE group than in the control group (standardized mean difference [SMD] = -0.938, 95% CI = -1.352 to -0.524, p = 9.0 × 10-6). Stratification by ethnicity showed a significantly decreased vitamin D level in the SLE group in the European and Arab populations (SMD = -1.485, 95% CI = -2.427 to -0.543, p = 0.002; SMD = -1.067, 95% CI = -1.251 to -0.883, p < 1.0 × 10-8), and an association tendency between decreased vitamin D level and SLE in the Asian population (SMD = -0.874, 95% CI = -2.073 to -0.324, p = 0.153). Subgroup analysis by sample size showed a significantly lower vitamin D level in the SLE group in small- (n ≤ 100) and large-sample (n > 100) populations (SMD = -1.008, 95% CI = -1.672 to -0.344, p = 0.003; SMD = -0.863, 95% CI = -1.444 to -0.293, p = 0.003). Meta-analysis revealed a significant association between SLE and vitamin D deficiency (RR = 2.321, 95% CI = 1.361-3.960, p = 0.002). Stratification by ethnicity showed a significant association between SLE and vitamin D deficiency in European and Arab populations (RR = 2.182, 95% CI = 1.024-4.648, p = 0.043; RR = 4.550, 95% CI = 3.471-5.965, p < 1.0 × 10-8). Our meta-analysis demonstrates that compared with controls, patients with SLE show significantly low serum levels of vitamin D, and that a deficiency of vitamin D is associated with SLE.

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

PubMed

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

2008-08-01

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

Using parentage analysis to examine gene flow and spatial genetic structure.

PubMed

Kane, Nolan C; King, Matthew G

2009-04-01

Numerous approaches have been developed to examine recent and historical gene flow between populations, but few studies have used empirical data sets to compare different approaches. Some methods are expected to perform better under particular scenarios, such as high or low gene flow, but this, too, has rarely been tested. In this issue of Molecular Ecology, Saenz-Agudelo et al. (2009) apply assignment tests and parentage analysis to microsatellite data from five geographically proximal (2-6 km) and one much more distant (1500 km) panda clownfish populations, showing that parentage analysis performed better in situations of high gene flow, while their assignment tests did better with low gene flow. This unusually complete data set is comprised of multiple exhaustively sampled populations, including nearly all adults and large numbers of juveniles, enabling the authors to ask questions that in many systems would be impossible to answer. Their results emphasize the importance of selecting the right analysis to use, based on the underlying model and how well its assumptions are met by the populations to be analysed.

Low Divergence of Clonorchis sinensis in China Based on Multilocus Analysis

PubMed Central

Sun, Jiufeng; Huang, Yan; Huang, Huaiqiu; Liang, Pei; Wang, Xiaoyun; Mao, Qiang; Men, Jingtao; Chen, Wenjun; Deng, Chuanhuan; Zhou, Chenhui; Lv, Xiaoli; Zhou, Juanjuan; Zhang, Fan; Li, Ran; Tian, Yanli; Lei, Huali; Liang, Chi; Hu, Xuchu; Xu, Jin; Li, Xuerong; XinbingYu

2013-01-01

Clonorchis sinensis, an ancient parasite that infects a number of piscivorous mammals, attracts significant public health interest due to zoonotic exposure risks in Asia. The available studies are insufficient to reflect the prevalence, geographic distribution, and intraspecific genetic diversity of C. sinensis in endemic areas. Here, a multilocus analysis based on eight genes (ITS1, act, tub, ef-1a, cox1, cox3, nad4 and nad5 [4.986 kb]) was employed to explore the intra-species genetic construction of C. sinensis in China. Two hundred and fifty-six C. sinensis isolates were obtained from environmental reservoirs from 17 provinces of China. A total of 254 recognized Multilocus Types (MSTs) showed high diversity among these isolates using multilocus analysis. The comparison analysis of nuclear and mitochondrial phylogeny supports separate clusters in a nuclear dendrogram. Genetic differentiation analysis of three clusters (A, B, and C) showed low divergence within populations. Most isolates from clusters B and C are geographically limited to central China, while cluster A is extraordinarily genetically diverse. Further genetic analyses between different geographic distributions, water bodies and hosts support the low population divergence. The latter haplotype analyses were consistent with the phylogenetic and genetic differentiation results. A recombination network based on concatenated sequences showed a concentrated linkage recombination population in cox1, cox3, nad4 and nad5, with spatial structuring in ITS1. Coupled with the history record and archaeological evidence of C. sinensis infection in mummified desiccated feces, these data point to an ancient origin of C. sinensis in China. In conclusion, we present a likely phylogenetic structure of the C. sinensis population in mainland China, highlighting its possible tendency for biogeographic expansion. Meanwhile, ITS1 was found to be an effective marker for tracking C. sinensis infection worldwide. Thus, the present study improves our understanding of the global epidemiology and evolution of C. sinensis. PMID:23825605

Bacterial community structure analysis of sediment in the Sagami River, Japan using a rapid approach based on two-dimensional DNA gel electrophoresis mapping with selective primer pairs.

PubMed

Liu, Guo-hua; Rajendran, Narasimmalu; Amemiya, Takashi; Itoh, Kiminori

2011-11-01

A rapid approach based on two-dimensional DNA gel electrophroesis (2-DGE) mapping with selective primer pairs was employed to analyze bacterial community structure in sediments from upstream, midstream and downstream of Sagami River in Japan. The 2-DGE maps indicated that Alpha- and Delta-proteobacteria were major bacterial populations in the upstream and midstream sediments. Further bacterial community structure analysis showed that richness proportion of Alpha- and Delta-proteobacterial groups reflected a trend toward decreasing from the upstream to downstream sediments. The biomass proportion of bacterial populations in the midstream sediment showed a significantly difference from that in the other sediments, suggesting that there may be an environmental pressure on the midstream bacterial community. Lorenz curves, together with Gini coefficients were successfully applied to the 2-DGE mapping data for resolving evenness of bacterial populations, and showed that the plotted curve from high-resolution 2-DGE mapping became less linear and more an exponential function than that of the 1-DGE methods such as chain length analysis and denaturing gradient gel electrophoresis, suggesting that the 2-DGE mapping may achieve a more detailed evaluation of bacterial community. In conclusion, the 2-DGE mapping combined with the selective primer pairs enables bacterial community structure analysis in river sediment and thus it can also monitor sediment pollution based on the change of bacterial community structure.

Comparisons of Lasker's coefficient of relationship in a Venezuelan town in two different periods.

PubMed

Pinto-Cisternas, J; Zimmer, E; Barrai, I

1990-01-01

A formula for the standard error of Lasker's coefficient of relationship Ri derived from isonymy is proposed, and used to test for differences in relationship in two groups of pairs of spouses from the town of Quibor in Venezuela sampled one century apart. From analysis of the relationship, it was possible to attribute population growth also to immigration. Further, the study of the values of Ri showed that the surnames belonging to the male line are more frequent and stable in this population, which is characterized by a predominantly agricultural activity. From the analysis of the coefficients of relationship, the population of Quibor is also classified as patrilocal.

Morphological versus molecular markers to describe variability in Juniperus excelsa subsp. excelsa (Cupressaceae)

PubMed Central

Douaihy, Bouchra; Sobierajska, Karolina; Jasińska, Anna Katarzyna; Boratyńska, Krystyna; Ok, Tolga; Romo, Angel; Machon, Nathalie; Didukh, Yakiv; Bou Dagher-Kharrat, Magda; Boratyński, Adam

2012-01-01

Background and aims Juniperus excelsa M.-Bieb. is a major forest element in the mountains of the eastern part of Mediterranean and sub-Mediterranean regions. This study comprises the first morphological investigation covering a large part of the geographical range of J. excelsa and aims to verify the congruency between the morphological results and molecular results of a previous study. Methodology We studied 14 populations sampled from Greece, Cyprus, Ukraine, Turkey and Lebanon, 11 of which have previously been investigated using molecular markers. Three hundred and ninety-four individuals of J. excelsa were examined using nine biometric features characterizing cones, seeds and shoots, and eight derived ratios. Statistical analyses were conducted in order to evaluate the intra- and inter-population morphological variability. Principal results The level of intra-population variability observed did not show any geographical trends. The total variation mostly depended on the ratios of cone diameter/seed width and seed width/seed length. The discrimination analysis, the Ward agglomeration method and barrier analysis results showed a separation of the sampled populations into three main clusters. These results confirmed, in part, the geographical differentiation revealed by molecular markers with a lower level of differentiation and a less clear geographical pattern. The most differentiated populations using both markers corresponded to old, isolated populations in the high altitudes of Lebanon (>2000 m). Moreover, a separation of the northern Turkish population from the southern Turkish populations was observed using both markers. Conclusions Morphological variation together with genetic and biogeographic studies make an effective tool for detecting relict plant populations and also populations subjected to more intensive selection. PMID:22822421

[Inverse probability weighting (IPW) for evaluating and "correcting" selection bias].

PubMed

Narduzzi, Silvia; Golini, Martina Nicole; Porta, Daniela; Stafoggia, Massimo; Forastiere, Francesco

2014-01-01

the Inverse probability weighting (IPW) is a methodology developed to account for missingness and selection bias caused by non-randomselection of observations, or non-random lack of some information in a subgroup of the population. to provide an overview of IPW methodology and an application in a cohort study of the association between exposure to traffic air pollution (nitrogen dioxide, NO₂) and 7-year children IQ. this methodology allows to correct the analysis by weighting the observations with the probability of being selected. The IPW is based on the assumption that individual information that can predict the probability of inclusion (non-missingness) are available for the entire study population, so that, after taking account of them, we can make inferences about the entire target population starting from the nonmissing observations alone.The procedure for the calculation is the following: firstly, we consider the entire population at study and calculate the probability of non-missing information using a logistic regression model, where the response is the nonmissingness and the covariates are its possible predictors.The weight of each subject is given by the inverse of the predicted probability. Then the analysis is performed only on the non-missing observations using a weighted model. IPW is a technique that allows to embed the selection process in the analysis of the estimates, but its effectiveness in "correcting" the selection bias depends on the availability of enough information, for the entire population, to predict the non-missingness probability. In the example proposed, the IPW application showed that the effect of exposure to NO2 on the area of verbal intelligence quotient of children is stronger than the effect showed from the analysis performed without regard to the selection processes.

Management of Uncomplicated Acute Appendicitis as Day Case Surgery: Feasibility and a Critical Analysis of Exclusion Criteria and Treatment Failure.

PubMed

Grelpois, Gérard; Sabbagh, Charles; Cosse, Cyril; Robert, Brice; Chapuis-Roux, Emilie; Ntouba, Alexandre; Lion, Thierry; Regimbeau, Jean-Marc

2016-11-01

Day case surgery (DCS) for uncomplicated acute appendicitis (NCAA) is evaluated. The objective of this prospective, single-center, descriptive, nonrandomized, intention-to-treat cohort study was to assess the feasibility of DCS for NCAA with a critical analysis of the reasons for exclusion and treatment failures and a focus on patients discharged to home and admitted for DCS on the following day. From April 2013 to December 2015, NCAA patients meeting the inclusion criteria were included in the study. The primary end point was the success rate for DCS (length of stay less than 12 hours) in the intention-to-treat population (all NCAA) and in the per-protocol population (no pre- or perioperative exclusion criteria). The secondary end points were morbidity, DCS quality criteria, predictive factors for successful DCS, patient satisfaction, quality of life, and reasons for pre- or perioperative exclusion. A subgroup of patients discharged to home the day before operation was also analyzed. A total of 240 patients were included. The success rate of DCS was 31.5% in the intention-to-treat population and 91.5% in the per-protocol population. The rates of unplanned consultations, hospitalization, and reoperation were 13%, 4%, and 1%, respectively. An analysis of the reasons for DCS exclusion showed that 73% could have been modified. For the 68 patients discharged to home on the day before operation, the DCS success rate was 91%. Day case surgery is feasible in NCAA. A critical analysis of the reasons for exclusion from DCS showed that it should be possible to dramatically increase the eligible population. Copyright © 2016 American College of Surgeons. Published by Elsevier Inc. All rights reserved.

Which System Variables Carry Robust Early Signs of Upcoming Phase Transition? An Ecological Example.

PubMed

Negahbani, Ehsan; Steyn-Ross, D Alistair; Steyn-Ross, Moira L; Aguirre, Luis A

2016-01-01

Growth of critical fluctuations prior to catastrophic state transition is generally regarded as a universal phenomenon, providing a valuable early warning signal in dynamical systems. Using an ecological fisheries model of three populations (juvenile prey J, adult prey A and predator P), a recent study has reported silent early warning signals obtained from P and A populations prior to saddle-node (SN) bifurcation, and thus concluded that early warning signals are not universal. By performing a full eigenvalue analysis of the same system we demonstrate that while J and P populations undergo SN bifurcation, A does not jump to a new state, so it is not expected to carry early warning signs. In contrast with the previous study, we capture a significant increase in the noise-induced fluctuations in the P population, but only on close approach to the bifurcation point; it is not clear why the P variance initially shows a decaying trend. Here we resolve this puzzle using observability measures from control theory. By computing the observability coefficient for the system from the recordings of each population considered one at a time, we are able to quantify their ability to describe changing internal dynamics. We demonstrate that precursor fluctuations are best observed using only the J variable, and also P variable if close to transition. Using observability analysis we are able to describe why a poorly observable variable (P) has poor forecasting capabilities although a full eigenvalue analysis shows that this variable undergoes a bifurcation. We conclude that observability analysis provides complementary information to identify the variables carrying early-warning signs about impending state transition.

Identification of a unique hepatocellular carcinoma line, Li-7, with CD13(+) cancer stem cells hierarchy and population change upon its differentiation during culture and effects of sorafenib.

PubMed

Yamada, Takeshi; Abei, Masato; Danjoh, Inaho; Shirota, Ryoko; Yamashita, Taro; Hyodo, Ichinosuke; Nakamura, Yukio

2015-04-11

Cancer stem cell (CSC) research has highlighted the necessity of developing drugs targeting CSCs. We investigated a hepatocellular carcinoma (HCC) cell line that not only has CSC hierarchy but also shows phenotypic changes (population changes) upon differentiation of CSC during culture and can be used for screening drugs targeting CSC. Based on a hypothesis that the CSC proportion should decrease upon its differentiation into progenitors (population change), we tested HCC cell lines (HuH-7, Li-7, PLC/PRF/5, HLF, HLE) before and after 2 months culture for several markers (CD13, EpCAM, CD133, CD44, CD90, CD24, CD166). Tumorigenicity was tested using nude mice. To evaluate the CSC hierarchy, we investigated reconstructivity, proliferation, ALDH activity, spheroid formation, chemosensitivity and microarray analysis of the cell populations sorted by FACS. Only Li-7 cells showed a population change during culture: the proportion of CD13 positive cells decreased, while that of CD166 positive cells increased. The high tumorigenicity of the Li-7 was lost after the population change. CD13(+)/CD166(-) cells showed slow growth and reconstructed the bulk Li-7 populations composed of CD13(+)/CD166(-), CD13(-)/CD166(-) and CD13(-)/CD166(+) fractions, whereas CD13(-)/CD166(+) cells showed rapid growth but could not reproduce any other population. CD13(+)/CD166(-) cells showed high ALDH activity, spheroid forming ability and resistance to 5-fluorouracil. Microarray analysis demonstrated higher expression of stemness-related genes in CD166(-) than CD166(+) fraction. These results indicated a hierarchy in Li-7 cells, in which CD13(+)/CD166(-) and CD13(-)/CD166(+) cells serve as slow growing CSCs and rapid growing progenitors, respectively. Sorafenib selectively targeted the CD166(-) fraction, including CD13(+) CSCs, which exhibited higher mRNA expression for FGF3 and FGF4, candidate biomarkers for sorafenib. 5-fluorouracil followed by sorafenib inhibited the growth of bulk Li-7 cells more effectively than the reverse sequence or either alone. We identified a unique HCC line, Li-7, which not only shows heterogeneity for a CD13(+) CSC hierarchy, but also undergoes a "population change" upon CSC differentiation. Sorafenib targeted the CSC in vitro, supporting the use of this model for screening drugs targeting the CSC. This type of "heterogeneous, unstable" cell line may prove more useful in the CSC era than conventional "homogeneous, stable" cell lines.

Fleeing to Fault Zones: Incorporating Syrian Refugees into Earthquake Risk Analysis along the East Anatolian and Dead Sea Rift Fault Zones

NASA Astrophysics Data System (ADS)

Wilson, B.; Paradise, T. R.

2016-12-01

The influx of millions of Syrian refugees into Turkey has rapidly changed the population distribution along the Dead Sea Rift and East Anatolian Fault zones. In contrast to other countries in the Middle East where refugees are accommodated in camp environments, the majority of displaced individuals in Turkey are integrated into cities, towns, and villages—placing stress on urban settings and increasing potential exposure to strong shaking. Yet, displaced populations are not traditionally captured in data sources used in earthquake risk analysis or loss estimations. Accordingly, we present a district-level analysis assessing the spatial overlap of earthquake hazards and refugee locations in southeastern Turkey to determine how migration patterns are altering seismic risk in the region. Using migration estimates from the U.S. Humanitarian Information Unit, we create three district-level population scenarios that combine official population statistics, refugee camp populations, and low, median, and high bounds for integrated refugee populations. We perform probabilistic seismic hazard analysis alongside these population scenarios to map spatial variations in seismic risk between 2011 and late 2015. Our results show a significant relative southward increase of seismic risk for this period due to refugee migration. Additionally, we calculate earthquake fatalities for simulated earthquakes using a semi-empirical loss estimation technique to determine degree of under-estimation resulting from forgoing migration data in loss modeling. We find that including refugee populations increased casualties by 11-12% using median population estimates, and upwards of 20% using high population estimates. These results communicate the ongoing importance of placing environmental hazards in their appropriate regional and temporal context which unites physical, political, cultural, and socio-economic landscapes. Keywords: Earthquakes, Hazards, Loss-Estimation, Syrian Crisis, Migration, Refugees

Diversity and population structure of a dominant deciduous tree based on morphological and genetic data

PubMed Central

Zhang, Qin-di; Jia, Rui-Zhi; Meng, Chao; Ti, Chao-Wen; Wang, Yi-Ling

2015-01-01

Knowledge of the genetic diversity and structure of tree species across their geographic ranges is essential for sustainable use and management of forest ecosystems. Acer grosseri Pax., an economically and ecologically important maple species, is mainly distributed in North China. In this study, the genetic diversity and population differentiation of 24 natural populations of this species were evaluated using sequence-related amplified polymorphism markers and morphological characters. The results show that highly significant differences occurred in 32 morphological traits. The coefficient of variation of 34 characters was 18.19 %. Principal component analysis indicated that 18 of 34 traits explained 60.20 % of the total variance. The phenotypic differentiation coefficient (VST) was 36.06 % for all morphological traits. The Shannon–Wiener index of 34 morphological characters was 6.09, while at the population level, it was 1.77. The percentage of polymorphic bands of all studied A. grosseri populations was 82.14 %. Nei's gene diversity (He) and Shannon's information index (I) were 0.35 and 0.50, respectively. Less genetic differentiation was detected among the natural populations (GST = 0.20, ΦST = 0.10). Twenty-four populations of A. grosseri formed two main clusters, which is consistent with morphological cluster analysis. Principal coordinates analysis and STRUCTURE analysis supported the UPGMA-cluster dendrogram. There was no significant correlation between genetic and geographical distances among populations. Both molecular and morphological data suggested that A. grosseri is rich in genetic diversity. The high level of genetic variation within populations could be affected by the biological characters, mating system and lifespan of A. grosseri, whereas the lower genetic diversity among populations could be caused by effective gene exchange, selective pressure from environmental heterogeneity and the species' geographical range. PMID:26311734

Contrasting results from molecular and pedigree-based population diversity measures in captive zebra highlight challenges facing genetic management of zoo populations.

PubMed

Ito, Hideyuki; Ogden, Rob; Langenhorst, Tanya; Inoue-Murayama, Miho

2017-01-01

Zoo conservation breeding programs manage the retention of population genetic diversity through analysis of pedigree records. The range of demographic and genetic indices determined through pedigree analysis programs allows the conservation of diversity to be monitored relative to the particular founder population for a species. Such approaches are based on a number of well-documented founder assumptions, however without knowledge of actual molecular genetic diversity there is a risk that pedigree-based measures will be misinterpreted and population genetic diversity misunderstood. We examined the genetic diversity of the captive populations of Grevy's zebra, Hartmann's mountain zebra and plains zebra in Japan and the United Kingdom through analysis of mitochondrial DNA sequences. Very low nucleotide variability was observed in Grevy's zebra. The results were evaluated with respect to current and historic diversity in the wild, and indicate that low genetic diversity in the captive population is likely a result of low founder diversity, which in turn suggests relatively low wild genetic diversity prior to recent population declines. Comparison of molecular genetic diversity measures with analogous diversity indices generated from the studbook data for Grevy's zebra and Hartmann's mountain zebra show contrasting patterns, with Grevy's zebra displaying markedly less molecular diversity than mountain zebra, despite studbook analysis indicating that the Grevy's zebra population has substantially more founders, greater effective population size, lower mean kinship, and has suffered less loss of gene diversity. These findings emphasize the need to validate theoretical estimates of genetic diversity in captive breeding programs with empirical molecular genetic data. Zoo Biol. 36:87-94, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Evaluation of the genetic structure of sika deer (Cervus nippon) in Japan's Kanto and Tanzawa mountain areas, based on microsatellite markers.

PubMed

Konishi, Sayaka; Hata, Shoko; Matsuda, Sayumi; Arai, Kazushi; Mizoguchi, Yasushi

2017-11-01

The browsing habits of sika deer (Cervus nippon) in Japan have caused serious ecological problems. Appropriate management of sika deer populations requires understanding the different genetic structures of local populations. In the present study, we used 10 microsatellite polymorphisms to explore the genetic structures of sika deer populations (162 individuals) living in the Kanto region. The expected heterozygosity of the Tanzawa mountain range population (Group I) was lower than that of the populations in the Kanto mountain areas (Group II). Our results suggest that moderate gene flow has occurred between the sika deer populations in the Kanto mountain areas (Group II), but not to or from the Tanzawa mountain range population (Group I). Also, genetic structure analysis showed that the Tanzawa population was separated from the other populations. This is probably attributable to a genetic bottleneck that developed in the Tanzawa sika deer population in the 1950s. However, we found that the Tanzawa population has since recovered from the bottleneck situation and now exhibits good genetic diversity. Our results show that it is essential to periodically evaluate the genetic structures of deer populations to develop conservation strategies appropriate to the specific structures of individual populations at any given time. © 2017 Japanese Society of Animal Science.

Genetic diversity analysis of cultivated Korarima [Aframomum corrorima (Braun) P.C.M. Jansen] populations from southwestern Ethiopia using inter simple sequence repeats (ISSR) marker.

PubMed

Chombe, Dagmawit; Bekele, Endashaw

2018-12-01

Korarima ( Aframomum corrorima ) is a perennial and aromatic herb native and widely distributed in southwestern Ethiopia. It is known for its fine flavor as a spice in various Ethiopian traditional dishes. Few molecular studies have been performed on this species so far. In the present paper, the ISSR technique was employed to study the genetic diversity in populations of cultivated A. corrorima . Seven ISSR primers produced a total of 86 clearly scorable DNA bands. High levels of genetic diversity were detected in cultivated A. corrorima (percentage of polymorphic bands = 97.67%, gene diversity = 0.35, Shannon's information index = 0.52). Analysis of molecular variance (AMOVA) showed that 27.47% of the variation is attributed to the variation among populations and 72.53% to the variation within populations. The F st (0.28) value showed a significant ( p  < 0.0001) genetic differentiation among populations. This was supported by the high coefficient of gene differentiation (G st  = 0.32) and low estimated gene flow (Nm = 1.08). A neighbor-joining dendrogram showed that the thirteen cultivated populations were separated into three clusters, which was in good accordance with the results provided by the two dimensional and three dimensional coordinate analyses. However, the clusters did not reveal clear pattern of populations clustering according to their geographic origin. This could be due to human mediated transfer of genetic material among different localities. The genetic diversity in populations of A. corrorima from the southwestern part of Ethiopia was relatively high. This finding should be taken into account when conservation actions, management policies for the species and site identification for in situ and ex situ conservation strategies are developed. Mizan Teferi II population displayed the highest genetic diversity; this population should be considered as the key site in designing conservation strategies for this crop. In addition, Jimma I and Jimma II populations with lowest genetic diversity, should also be considered due to the putative risk of extinction that they face because of the low genetic diversity.

High genetic diversity in the offshore island populations of the tephritid fruit fly Bactrocera dorsalis.

PubMed

Yi, Chunyan; Zheng, Chunyan; Zeng, Ling; Xu, Yijuan

2016-10-13

Geographic isolation is an important factor that limit species dispersal and thereby affects genetic diversity. Because islands are often small and surrounded by a natural water barrier to dispersal, they generally form discrete isolated habitats. Therefore, islands may play a key role in the distribution of the genetic diversity of insects, including flies. To characterize the genetic structure of island populations of Bactrocera dorsalis, we analyzed a dataset containing both microsatellite and mtDNA loci of B. dorsalis samples collected from six offshore islands in Southern China. The microsatellite data revealed a high level of genetic diversity among these six island populations based on observed heterozygosity (Ho), expected heterozygosity (H E ), Nei's standard genetic distance (D), genetic identity (I) and the percentage of polymorphic loci (PIC). These island populations had low F ST values (F ST  = 0.04161), and only 4.16 % of the total genetic variation in the species was found on these islands, as determined by an analysis of molecular variance. Based on the mtDNA COI data, high nucleotide diversity (0.9655) and haplotype diversity (0.00680) were observed in all six island populations. F-statistics showed that the six island populations exhibited low or medium levels of genetic differentiation among some island populations. To investigate the population differentiation between the sampled locations, a factorial correspondence analysis and both the unweighted pair-group method with arithmetic mean and Bayesian clustering methods were used to analyze the microsatellite data. The results showed that Hebao Island, Weizhou Island and Dong'ao Island were grouped together in one clade. Another clade consisted of Shangchuan Island and Naozhou Island, and a final, separate clade contained only the Wailingding Island population. Phylogenetic analysis of the mtDNA COI sequences revealed that the populations on each of these six islands were closely related to different populations on mainland China. Our study suggests that these island populations have high genetic diversity, experience frequent gene flow and exhibit low or medium levels of genetic differentiation among some island populations. Therefore, the geographic isolation of the six islands does not appear to be a major dispersal barrier to B. dorsalis. Such knowledge is helpful for a better understanding of evolutionary processes of the species of island populations.

Carbon dioxide emissions, GDP, energy use, and population growth: a multivariate and causality analysis for Ghana, 1971-2013.

PubMed

Asumadu-Sarkodie, Samuel; Owusu, Phebe Asantewaa

2016-07-01

In this study, the relationship between carbon dioxide emissions, GDP, energy use, and population growth in Ghana was investigated from 1971 to 2013 by comparing the vector error correction model (VECM) and the autoregressive distributed lag (ARDL). Prior to testing for Granger causality based on VECM, the study tested for unit roots, Johansen's multivariate co-integration and performed a variance decomposition analysis using Cholesky's technique. Evidence from the variance decomposition shows that 21 % of future shocks in carbon dioxide emissions are due to fluctuations in energy use, 8 % of future shocks are due to fluctuations in GDP, and 6 % of future shocks are due to fluctuations in population. There was evidence of bidirectional causality running from energy use to GDP and a unidirectional causality running from carbon dioxide emissions to energy use, carbon dioxide emissions to GDP, carbon dioxide emissions to population, and population to energy use. Evidence from the long-run elasticities shows that a 1 % increase in population in Ghana will increase carbon dioxide emissions by 1.72 %. There was evidence of short-run equilibrium relationship running from energy use to carbon dioxide emissions and GDP to carbon dioxide emissions. As a policy implication, the addition of renewable energy and clean energy technologies into Ghana's energy mix can help mitigate climate change and its impact in the future.

Genetic variation in scaly hair-fin anchovy Setipinna tenuifilis (Engraulididae) based on the mitochondrial DNA control region.

PubMed

Xu, Shengyong; Song, Na; Lu, Zhichuang; Wang, Jun; Cai, Shanshan; Gao, Tianxiang

2014-06-01

Scaly hair-fin anchovy (Setipinna tenuifilis) is a small, pelagic and economical species and widely distributed in Chinese coastal water. However, resources of S. tenuifilis have been reduced due to overfishing. For better fishery management, it is necessary to understand the pattern of S. tenuifilis's biogeography. Genetic analyses were taken place to detect their population genetic variation. A total of 153 individuals from 7 locations (Dongying, Yantai, Qingdao, Nantong, Wenzhou, Xiamen and Beibu Bay) were sequenced at the 5' end of mtDNA control region. A 39-bp tandem repeated sequence was found at the 5' end of the segment and a polymorphism of tandem repeated sequence was detected among 7 populations. Both mismatch distribution analysis and neutrality tests showed S. tenuifilis had experienced a recent population expansion. The topology of neighbor-joining tree and Bayesian evolutionary tree showed no significant genealogical branches or clusters of samples corresponding to sampling locality. Hierarchical analysis of molecular variance and conventional pairwise population Fst value at group hierarchical level implied that there might have genetic divergence between southern group (population WZ, XM and BB) and northern group (population DY, YT, QD and NT). We concluded that there might have three different fishery management groups of S. tenuifilis and the late Pleistocene glacial event might have a crucial effect on present-day demography of S. tenuifilis in this region.

Genetic analysis of floating Enteromorpha prolifera in the Yellow Sea with AFLP marker

NASA Astrophysics Data System (ADS)

Liu, Cui; Zhang, Jing; Sun, Xiaoyu; Li, Jian; Zhang, Xi; Liu, Tao

2011-09-01

Extremely large accumulation of green algae Enteromorpha prolifera floated along China' coastal region of the Yellow Sea ever since the summer of 2008. Amplified Fragment Length Polymorphism (AFLP) analysis was applied to assess the genetic diversity and relationships among E. prolifera samples collected from 9 affected areas of the Yellow Sea. Two hundred reproducible fragments were generated with 8 AFLP primer combinations, of which 194 (97%) were polymorphic. The average Nei's genetic diversity, the coefficiency of genetic differentiation (Gst), and the average gene flow estimated from Gst in the 9 populations were 0.4018, 0.6404 and 0.2807 respectively. Cluster analysis based on the unweighed pair group method with arithmetic averages (UPGMA) showed that the genetic relationships within one population or among different populations were all related to their collecting locations and sampling time. Large genetic differentiation was detected among the populations. The E. prolifera originated from different areas and were undergoing a course of mixing.

Genetic Diversity and Differentiation of Colletotrichum spp. Isolates Associated with Leguminosae Using Multigene Loci, RAPD and ISSR

PubMed Central

Mahmodi, Farshid; Kadir, J. B.; Puteh, A.; Pourdad, S. S.; Nasehi, A.; Soleimani, N.

2014-01-01

Genetic diversity and differentiation of 50 Colletotrichum spp. isolates from legume crops studied through multigene loci, RAPD and ISSR analysis. DNA sequence comparisons by six genes (ITS, ACT, Tub2, CHS-1, GAPDH, and HIS3) verified species identity of C. truncatum, C. dematium and C. gloeosporiodes and identity C. capsici as a synonym of C. truncatum. Based on the matrix distance analysis of multigene sequences, the Colletotrichum species showed diverse degrees of intera and interspecific divergence (0.0 to 1.4%) and (15.5–19.9), respectively. A multilocus molecular phylogenetic analysis clustered Colletotrichum spp. isolates into 3 well-defined clades, representing three distinct species; C. truncatum, C. dematium and C. gloeosporioides. The ISSR and RAPD and cluster analysis exhibited a high degree of variability among different isolates and permitted the grouping of isolates of Colletotrichum spp. into three distinct clusters. Distinct populations of Colletotrichum spp. isolates were genetically in accordance with host specificity and inconsistent with geographical origins. The large population of C. truncatum showed greater amounts of genetic diversity than smaller populations of C. dematium and C. gloeosporioides species. Results of ISSR and RAPD markers were congruent, but the effective maker ratio and the number of private alleles were greater in ISSR markers. PMID:25288981

Genetic characterization and phylogenetic analysis of porcine circovirus type 2 (PCV2) in Serbia.

PubMed

Savic, Bozidar; Milicevic, Vesna; Jakic-Dimic, Dobrila; Bojkovski, Jovan; Prodanovic, Radisa; Kureljusic, Branislav; Potkonjak, Aleksandar; Savic, Borivoje

2012-01-01

Porcine circovirus type 2 (PCV2) is the main causative agent of postweaning multisystemic wasting syndrome (PMWS). To characterize and determine the genetic diversity of PCV2 in the porcine population of Serbia, nucleotide and deduced amino acid sequences of the open reading frame 2 (ORF2) of PCV2 collected from the tissues of pigs that either had died as a result of PMWS or did not exhibit disease symptoms were analyzed. Sequencing and phylogenetic analysis showed considerable diversity among PCV2 ORF2 sequences and the existence of two main PCV2 genotypes, PCV2b and PCV2a, with at least three clusters, 1A/B, 1C and 2D. In order to provide further proof that the 1C strain is circulating in the porcine population, the whole viral genome of one PCV2 isolate was sequenced. Genotyping and phylogenetic analysis using the entire viral genome sequences confirmed that there was a PMWS-associated 1C strain emerging in Serbia. Our analysis also showed that PCV2b is dominant in the porcine population, and that it is exclusively associated with PMWS occurrences in the country. These data constitute a useful basis for further epidemiological studies regarding the heterogeneity of PCV2 strains on the European continent.

Genetic analysis identifies the region of origin of smuggled peach palm seeds.

PubMed

Cristo-Araújo, Michelly; Molles, David Bronze; Rodrigues, Doriane Picanço; Clement, Charles R

2017-04-01

Seeds of a plant, supposedly a palm tree known popularly as peach palm (Bactris gasipaes), were seized by the Federal Police in the state of Pará, Brazil, without documentation of legal origin to authorize transportation and marketing in Brazil. They were alleged to be from the western part of Amazonas, Brazil, near the frontier with Peru and Colombia, justifying the lack of documentation. The species was confirmed to be peach palm. To determine the likely place of origin, a genetic analysis was performed to determine the relationship between the seized seeds and representative populations of peach palm from all of Amazonia, maintained in the Peach palm Core Collection, at the National Research Institute for Amazonia, using nine microsatellite loci. Reynolds' coancestry analysis showed a strong relationship between the seeds and the Pampa Hermosa landrace, around Yurimaguas, Peru. The Structure program, used to infer the probability of an individual belonging to a given population, showed that most seeds grouped with populations close to Yurimaguas, Peru, corroborating the coancestry analysis. The Pampa Hermosa landrace is the main source of spineless peach palm seeds used in the Brazilian heart-of-palm agribusiness, which motivated the smugglers to attempt this biopiracy. Copyright © 2017 Elsevier B.V. All rights reserved.

Global Prevalence of Elder Abuse: A Meta-analysis and Meta-regression.

PubMed

Ho, C Sh; Wong, S Y; Chiu, M M; Ho, R Cm

2017-06-01

Elder abuse is increasingly recognised as a global public health and social problem. There has been limited inter-study comparison of the prevalence and risk factors for elder abuse. This study aimed to estimate the pooled and subtype prevalence of elder abuse worldwide and identify significant associated risk factors. We conducted a meta-analysis and meta-regression of 34 population-based and 17 non-population-based studies. The pooled prevalences of elder abuse were 10.0% (95% confidence interval, 5.2%-18.6%) and 34.3% (95% confidence interval, 22.9%-47.8%) in population-based studies and third party- or caregiver-reported studies, respectively. Being in a marital relationship was found to be a significant moderator using random-effects model. This meta-analysis revealed that third parties or caregivers were more likely to report abuse than older abused adults. Subgroup analyses showed that females and those resident in non-western countries were more likely to be abused. Emotional abuse was the most prevalent elder abuse subtype and financial abuse was less commonly reported by third parties or caregivers. Heterogeneity in the prevalence was due to the high proportion of married older adults in the sample. Subgroup analysis showed that cultural factors, subtypes of abuse, and gender also contributed to heterogeneity in the pooled prevalence of elder abuse.

Advance notification letters increase adherence in colorectal cancer screening: a population-based randomized trial.

PubMed

van Roon, A H C; Hol, L; Wilschut, J A; Reijerink, J C I Y; van Vuuren, A J; van Ballegooijen, M; Habbema, J D F; van Leerdam, M E; Kuipers, Ernst J

2011-06-01

The population benefit of screening depends not only on the effectiveness of the test, but also on adherence, which, for colorectal cancer (CRC) screening remains low. An advance notification letter may increase adherence, however, no population-based randomized trials have been conducted to provide evidence of this. In 2008, a representative sample of the Dutch population (aged 50-74 years) was randomized. All 2493 invitees in group A were sent an advance notification letter, followed two weeks later by a standard invitation. The 2507 invitees in group B only received the standard invitation. Non-respondents in both groups were sent a reminder 6 weeks after the invitation. The advance notification letters resulted in a significantly higher adherence (64.4% versus 61.1%, p-value 0.019). Multivariate logistic regression analysis showed no significant interactions between group and age, sex, or socio-economic status. Cost analysis showed that the incremental cost per additional detected advanced neoplasia due to sending an advance notification letter was € 957. This population-based randomized trial demonstrates that sending an advance notification letter significantly increases adherence by 3.3%. The incremental cost per additional detected advanced neoplasia is acceptable. We therefore recommend that such letters are incorporated within the standard CRC-screening invitation process. Copyright © 2011 Elsevier Inc. All rights reserved.

Essential Oil Composition of Pinus peuce Griseb. Needles and Twigs from Two National Parks of Kosovo.

PubMed

Hajdari, Avni; Mustafa, Behxhet; Nebija, Dashnor; Selimi, Hyrmete; Veselaj, Zeqir; Breznica, Pranvera; Quave, Cassandra Leah; Novak, Johannes

The principal aim of this study was to analyze the chemical composition and qualitative and quantitative variability of essential oils obtained from seven naturally grown populations of the Pinus peuce Grisebach, Pinaceae in Kosovo. Plant materials were collected from three populations in the Sharri National Park and from four other populations in the Bjeshkët e Nemuna National Park, in Kosovo. Essential oils were obtained by steam distillation and analyzed by GC-FID (Gas Chromatography-Flame Ionization Detection) and GC-MS (Gas Chromatography-Mass Spectrometry). The results showed that the yield of essential oils (v/w dry weight) varied depending on the origin of population and the plant organs and ranged from 0.7 to 3.3%. In total, 51 compounds were identified. The main compounds were α-pinene (needles: 21.6-34.9%; twigs: 11.0-24%), β-phellandrene (needles: 4.1-27.7; twigs: 29.0-49.8%), and β-pinene (needles: 10.0-16.1; twigs: 6.9-20.7%). HCA (Hierarchical Cluster Analysis) and PCA (Principal Component Analyses) were used to assess geographical variations in essential oil composition. Statistical analysis showed that the analyzed populations are grouped in three main clusters which seem to reflect microclimatic conditions on the chemical composition of the essential oils.

East Greenland and Barents Sea polar bears (Ursus maritimus): adaptive variation between two populations using skull morphometrics as an indicator of environmental and genetic differences.

PubMed

Pertoldi, Cino; Sonne, Christian; Wiig, Øystein; Baagøe, Hans J; Loeschcke, Volker; Bechshøft, Thea Østergaard

2012-06-01

A morphometric study was conducted on four skull traits of 37 male and 18 female adult East Greenland polar bears (Ursus maritimus) collected 1892-1968, and on 54 male and 44 female adult Barents Sea polar bears collected 1950-1969. The aim was to compare differences in size and shape of the bear skulls using a multivariate approach, characterizing the variation between the two populations using morphometric traits as an indicator of environmental and genetic differences. Mixture analysis testing for geographic differentiation within each population revealed three clusters for Barents Sea males and three clusters for Barents Sea females. East Greenland consisted of one female and one male cluster. A principal component analysis (PCA) conducted on the clusters defined by the mixture analysis, showed that East Greenland and Barents Sea polar bear populations overlapped to a large degree, especially with regards to females. Multivariate analyses of variance (MANOVA) showed no significant differences in morphometric means between the two populations, but differences were detected between clusters from each respective geographic locality. To estimate the importance of genetics and environment in the morphometric differences between the bears, a PCA was performed on the covariance matrix derived from the skull measurements. Skull trait size (PC1) explained approx. 80% of the morphometric variation, whereas shape (PC2) defined approx. 15%, indicating some genetic differentiation. Hence, both environmental and genetic factors seem to have contributed to the observed skull differences between the two populations. Overall, results indicate that many Barents Sea polar bears are morphometrically similar to the East Greenland ones, suggesting an exchange of individuals between the two populations. Furthermore, a subpopulation structure in the Barents Sea population was also indicated from the present analyses, which should be considered with regards to future management decisions. © 2012 The Authors.

Spinocerebellar ataxia 7 (SCA7) in Indian population: predilection of ATXN7-CAG expansion mutation in an ethnic population

PubMed Central

Faruq, Mohammed; Srivastava, Achal Kumar; Singh, Suman; Gupta, Rohit; Dada, Tanuj; Garg, Ajay; Behari, Madhuri; Mukerji, Mitali

2015-01-01

Background & objectives: Spinocerebellar ataxia 7 (SCA7) is a rare form of neurodegenerative disorder with the clinical manifestation of cerebellar ataxia and retinal degeneration. In this study we describe the clinico-genetic characteristics of nine SCA7 families of Indian origin and cross compare these with other available worldwide studies. Methods: Thirty five individuals from nine SCA7 families were clinico-genetically characterized and CAG repeat distribution analysis was carried out in 382 control DNA samples from healthy controls (derived from 21 diverse Indian populations based on ethnic and linguistic and geographical location). Results: Of the nine families studied, 22 affected individuals and one asymptomatic carrier were identified. The average age at disease onset was 23.4±12.6 yr. The length of expanded CAG ranged from 40-94 with mean value of 53.2±13.9. The main clinical findings in affecteds individuals included cerebellar ataxia, and retinal degeneration along with hyper-reflexia (95%), slow saccades (85%) and spasticity (45%). Analysis of the association of number of CAG repeats with disease onset revealed that<49 repeats were associated with earlier age at onset in South East Asians compared to European populations. Further analysis of CAG repeats from 21 diverse Indian populations showed pre-mutable repeats (28-34) alleles in the IE-N-LP2 population. Six of the nine families identified in this study belonged to the same ethnic population. Interpretations & conclusion: Our results show that presenece of SCA7 is relatively rare and confined to one ethnic group from Haryana region of India. We observed a homogeneous phenotypic expression of SCA7 mutation as described earlier and an earlier age of onset in our patients with CAG <49. The identification of pre-mutable allele in IE-N-LP2 suggests this population to be at the risk of SCA7. PMID:25900954

AFLP-Based Analysis of Genetic Diversity, Population Structure, and Relationships with Agronomic Traits in Rice Germplasm from North Region of Iran and World Core Germplasm Set.

PubMed

Sorkheh, Karim; Masaeli, Mohammad; Chaleshtori, Maryam Hosseini; Adugna, Asfaw; Ercisli, Sezai

2016-04-01

Analysis of the genetic diversity and population structure of crops is very important for use in breeding programs and for genetic resources conservation. We analyzed the genetic diversity and population structure of 47 rice genotypes from diverse origins using amplified fragment length polymorphism (AFLP) markers and morphological characters. The 47 genotypes, which were composed of four populations: Iranian native varieties, Iranian improved varieties, International Rice Research Institute (IRRI) rice varieties, and world rice collections, were analyzed using ten primer combinations. A total of 221 scorable bands were produced with an average of 22.1 alleles per pair of primers, of which 120 (54.30%) were polymorphic. The polymorphism information content (PIC) values varied from 0.32 to 0.41 with an average of 0.35. The high percentage of polymorphic bands (%PB) was found to be 64.71 and the resolving power (R p) collections were 63.36. UPGMA clustering based on numerical data from AFLP patterns clustered all 47 genotypes into three large groups. The genetic similarity between individuals ranged from 0.54 to 0.94 with an average of 0.74. Population genetic tree showed that Iranian native cultivars formed far distant cluster from the other populations, which may indicate that these varieties had minimal genetic change over time. Analysis of molecular variance (AMOVA) revealed that the largest proportion of the variation (84%) to be within populations showing the inbreeding nature of rice. Therefore, Iranian native varieties (landraces) may have unique genes, which can be used for future breeding programs and there is a need to conserve this unique diversity. Furthermore, crossing of Iranian genotypes with the genetically distant genotypes in the other three populations may result in useful combinations, which can be used as varieties and/or lines for future rice breeding programs.

Genetic structure of Mount Huang honey bee (Apis cerana) populations: evidence from microsatellite polymorphism.

PubMed

Liu, Fang; Shi, Tengfei; Huang, Sisi; Yu, Linsheng; Bi, Shoudong

2016-01-01

The Mount Huang eastern honey bees ( Apis cerana ) are an endemic population, which is well adapted to the local agricultural and ecological environment. In this study, the genetic structure of seven eastern honey bees ( A. cerana ) populations from Mount Huang in China were analyzed by SSR (simple sequence repeat) markers. The results revealed that 16 pairs of primers used amplified a total of 143 alleles. The number of alleles per locus ranged from 6 to 13, with a mean value of 8.94 alleles per locus. Observed and expected heterozygosities showed mean values of 0.446 and 0.831 respectively. UPGMA cluster analysis grouped seven eastern honey bees in three groups. The results obtained show a high genetic diversity in the honey bee populations studied in Mount Huang, and high differentiation among all the populations, suggesting that scarce exchange of honey bee species happened in Mount Huang. Our study demonstrated that the Mount Huang honey bee populations still have a natural genome worth being protected for conservation.

[Intercensal reconstruction of population and descriptive epidemiological measures in Italy: what is the impact on the cancer incidence rates?].

PubMed

Rashid, Ivan; Giacomin, Adriano; Michiara, Maria; Minerba, Sante; Sgargi, Paolo; Mincuzzi, Antonia; Silvestrini, Angela

2016-01-01

to test the effect on cancer incidence rates when using precensal computation (computed population) or intercensal reconstruction of population (reconstructed population). comparison between computed and reconstructed population by area and period in 2002-2011; evaluation of the effect on cancer rates using Italian cancer registries data. Setting e participants: population data from the Italian National Institute for Statistics, cancer data from Italian cancer registries; specific analysis involves data from Parma (Emilia-Romagna Region, Northern Italy) and Taranto (Apulia Region, Southern Italy) cancer registries. ratio between computed and reconstructed population by area, gender, age, and period; ratio between corresponding age-standardized incidence rates. Italian population estimates by precensal computation for years 2002-2011 was generally higher than that obtained by intercensal reconstruction especially in 2011, when this has been found in more than 86% of Italian Municipalities. In the same year a smaller proportion of Municipalities (11%) showed an inverse population ratio. Among the most populated Municipalities, the City of Milan showed the higher precensal to intercensal population ratio (1.076), while the City of Taranto showed the lower precensal to intercensal population ratio (0.956). The ratios between age standardized rates obtained with precensal population to those obtained with intercensal population show similar differences; in particular, for all cancer in males and females they were, respectively, 0.985 and 0.982 in the Province of Parma, 0.974 and 0.968 in the City of Parma, 1.023 and 1.013 in the Province of Taranto, and 1.08 and 1.051 in the City of Taranto. using precensal population as denominator for the year 2002- 2011 produces a remarkable distortion of both temporal trend and geographical comparisons. It is, therefore, necessary that researchers take into account this possible distortion when reporting descriptive measures in the years between the last two censuses in Italy.

[Optimum population analysis of Jilin Province, China based on comprehensive carrying capacity.

PubMed

Li, Xiu Xia; Meng, Mei

2017-10-01

The regional moderate population model was constructed using state-space method, and the weights of relevant factors were obtained using principal component analysis. The optimum population of Jilin Province during 2005-2014 was calculated and the causes for its formation were discussed. The results showed that the optimum population of Jilin Province was in deficit from 2005-2014, and the imbalance existed between the population, resources and environment. The resources carrying population was significantly higher than the economic carrying and the ecological carrying population, indicating that the economic development of Jilin Province was established at the expense of destroying the environment. Moreover, the land resources carrying population was substantially higher than the water and energy carrying population, which was at a deficit, indicating that the economic development of Jilin Province was based on the depletion of energy and water resources. In the future, water resources carrying capacity should be improved according to the local conditions, the energy efficiency should be enhanced via the development of new energy sources, the extensive and consumption-based resource utilization should be transformed to the intensive and low-carbon type, and the production mode and consumption patterns should be changed to protect the ecological environment.

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

NASA Astrophysics Data System (ADS)

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

2006-09-01

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

Using population viability analysis, genomics, and habitat suitability to forecast future population patterns of Little Owl Athene noctua across Europe.

PubMed

Andersen, Line Holm; Sunde, Peter; Pellegrino, Irene; Loeschcke, Volker; Pertoldi, Cino

2017-12-01

The agricultural scene has changed over the past decades, resulting in a declining population trend in many species. It is therefore important to determine the factors that the individual species depend on in order to understand their decline. The landscape changes have also resulted in habitat fragmentation, turning once continuous populations into metapopulations. It is thus increasingly important to estimate both the number of individuals it takes to create a genetically viable population and the population trend. Here, population viability analysis and habitat suitability modeling were used to estimate population viability and future prospects across Europe of the Little Owl Athene noctua , a widespread species associated with agricultural landscapes. The results show a high risk of population declines over the coming 100 years, especially toward the north of Europe, whereas populations toward the southeastern part of Europe have a greater probability of persistence. In order to be considered genetically viable, individual populations must count 1,000-30,000 individuals. As Little Owl populations of several countries count <30,000, and many isolated populations in northern Europe count <1,000 individuals, management actions resulting in exchange of individuals between populations or even countries are probably necessary to prevent losing <1% genetic diversity over a 100-year period. At a continental scale, a habitat suitability analysis suggested Little Owl to be affected positively by increasing temperatures and urban areas, whereas an increased tree cover, an increasing annual rainfall, grassland, and sparsely vegetated areas affect the presence of the owl negatively. However, the low predictive power of the habitat suitability model suggests that habitat suitability might be better explained at a smaller scale.

Population genetic variation in the tree fern Alsophila spinulosa (Cyatheaceae): effects of reproductive strategy.

PubMed

Wang, Ting; Su, Yingjuan; Li, Yuan

2012-01-01

Essentially all ferns can perform both sexual and asexual reproduction. Their populations represent suitable study objects to test the population genetic effects of different reproductive systems. Using the diploid homosporous fern Alsophila spinulosa as an example species, the main purpose of this study was to assess the relative impact of sexual and asexual reproduction on the level and structure of population genetic variation. Inter-simple sequence repeats analysis was conducted on 140 individuals collected from seven populations (HSG, LCH, BPC, MPG, GX, LD, and ZHG) in China. Seventy-four polymorphic bands discriminated a total of 127 multilocus genotypes. Character compatibility analysis revealed that 50.0 to 70.0% of the genotypes had to be deleted in order to obtain a tree-like structure in the data set from populations HSG, LCH, MPG, BPC, GX, and LD; and there was a gradual decrease of conflict in the data set when genotypes with the highest incompatibility counts were successively deleted. In contrast, in population ZHG, only 33.3% of genotypes had to be removed to achieve complete compatibility in the data set, which showed a sharp decline in incompatibility upon the deletion of those genotypes. All populations examined possessed similar levels of genetic variation. Population ZHG was not found to be more differentiated than the other populations. Sexual recombination is the predominant source of genetic variation in most of the examined populations of A. spinulosa. However, somatic mutation contributes most to the genetic variation in population ZHG. This change of the primary mode of reproduction does not cause a significant difference in the population genetic composition. Character compatibility analysis represents an effective approach to separate the role of sexual and asexual components in shaping the genetic pattern of fern populations.

Early detection of nonnative alleles in fish populations: When sample size actually matters

USGS Publications Warehouse

Croce, Patrick Della; Poole, Geoffrey C.; Payne, Robert A.; Gresswell, Bob

2017-01-01

Reliable detection of nonnative alleles is crucial for the conservation of sensitive native fish populations at risk of introgression. Typically, nonnative alleles in a population are detected through the analysis of genetic markers in a sample of individuals. Here we show that common assumptions associated with such analyses yield substantial overestimates of the likelihood of detecting nonnative alleles. We present a revised equation to estimate the likelihood of detecting nonnative alleles in a population with a given level of admixture. The new equation incorporates the effects of the genotypic structure of the sampled population and shows that conventional methods overestimate the likelihood of detection, especially when nonnative or F-1 hybrid individuals are present. Under such circumstances—which are typical of early stages of introgression and therefore most important for conservation efforts—our results show that improved detection of nonnative alleles arises primarily from increasing the number of individuals sampled rather than increasing the number of genetic markers analyzed. Using the revised equation, we describe a new approach to determining the number of individuals to sample and the number of diagnostic markers to analyze when attempting to monitor the arrival of nonnative alleles in native populations.

Complete mitochondrial genome of Concholepas concholepas inferred by 454 pyrosequencing and mtDNA expression in two mollusc populations.

PubMed

Núñez-Acuña, Gustavo; Aguilar-Espinoza, Andrea; Gallardo-Escárate, Cristian

2013-03-01

Despite the great relevance of mitochondrial genome analysis in evolutionary studies, there is scarce information on how the transcripts associated with the mitogenome are expressed and their role in the genetic structuring of populations. This work reports the complete mitochondrial genome of the marine gastropod Concholepas concholepas, obtained by 454 pryosequencing, and an analysis of mitochondrial transcripts of two populations 1000 km apart along the Chilean coast. The mitochondrion of C. concholepas is 15,495 base pairs (bp) in size and contains the 37 subunits characteristic of metazoans, as well as a non-coding region of 330 bp. In silico analysis of mitochondrial gene variability showed significant differences among populations. In terms of levels of relative abundance of transcripts associated with mitochondrion in the two populations (assessed by qPCR), the genes associated with complexes III and IV of the mitochondrial genome had the highest levels of expression in the northern population while transcripts associated with the ATP synthase complex had the highest levels of expression in the southern population. Moreover, fifteen polymorphic SNPs were identified in silico between the mitogenomes of the two populations. Four of these markers implied different amino acid substitutions (non-synonymous SNPs). This work contributes novel information regarding the mitochondrial genome structure and mRNA expression levels of C. concholepas. Copyright © 2012 Elsevier Inc. All rights reserved.

Ecomorphology of the external flight apparatus of blackcaps (Sylvia atricapilla) with different migration behavior.

PubMed

Fiedler, Wolfgang

2005-06-01

An analysis of the external flight apparatus of 700 blackcaps from eight different populations (sedentary to long-distance migrators) is presented. With increasing migration distances of populations, (1) wing length, aspect ratio, and wing pointedness increase; (2) wing load decreases; (3) slots on the wing tips become relatively shorter; (4) the alula tends to be shorter in relation to wing length; and (5) the tail is shorter in relation to wing length. Although body mass increases from southern to northern populations, changes in wing length and wing area are two to three times larger than expected for simple isometric relationships. Regarding the aerodynamic background of these changes, it can be stated that traits for energy-effective flight are more strongly developed and traits for maneuverability are less developed in birds traveling longer distances, presumably as a consequence of trade-offs. Nonmigratory blackcaps from Madeira and the Cape Verde islands do not always show the traits we would expect in view of their sedentary behavior. This can be seen as a result of recent colonization of these islands by migrants or of selection by factors other than migration behavior. In migratory populations, changes between the first and the second set of primaries during first complete molt show almost the same pattern as the changes from nonmigratory to migratory populations. During molt of the primaries, blackcaps of nonmigratory populations do not show these changes. Hybrids between migrating and nonmigrating blackcap populations (Moscow and Madeira) showed intermediate values between parent populations in wing length, wing shape, and wing area; in the other variables they resembled either parent population.

Genetic analysis of Trichuris suis and Trichuris trichiura recovered from humans and pigs in a sympatric setting in Uganda.

PubMed

Nissen, Sofie; Al-Jubury, Azmi; Hansen, Tina V A; Olsen, Annette; Christensen, Henrik; Thamsborg, Stig M; Nejsum, Peter

2012-08-13

The whipworms Trichuris trichiura and Trichuris suis in humans and pigs, respectively, are believed to be two different species yet closely related. Morphologically, adult worms, eggs and larvae of the two species are indistinguishable. The aim of this study was to examine the genetic variation of Trichuris sp. mainly recovered from natural infected pigs and humans. Worm material isolated from humans and pigs living in the same geographical region in Uganda were analyzed by PCR, cloning and sequencing. Measurements of morphometric characters were also performed. The analysis of the ITS-2 (internal transcribed spacer) region showed a high genetic variation in the human-derived worms with two sequence types, designated type 1 and type 2, differing with up to 45%, the type 2 being identical to the sequence found in pig-derived worms. A single human-derived worm showed exclusively the type 2-genotype (T. suis-type) and three cases of 'heterozygote' worms in humans were identified. However, the analysis showed that sympatric Trichuris primarily assorted with host origin. Sequence analysis of a part of the genetically conserved β-tubulin gene confirmed two separate populations/species but also showed that the 'heterozygote' worms had a T. suis-like β-tubulin gene. A PCR-RFLP on the ITS-2 region was developed, that could distinguish between worms of the pig, human and 'heterozygote' type. The data suggest that Trichuris in pigs and humans belong to two different populations (i.e. are two different species). However, the data presented also suggest that cross-infections of humans with T. suis takes place. Further studies on sympatric Trichuris populations are highly warranted in order to explore transmission dynamics and unravel the zoonotic potential of T. suis. Copyright © 2012 Elsevier B.V. All rights reserved.

Copy Number Variation across European Populations

PubMed Central

Chen, Wanting; Hayward, Caroline; Wright, Alan F.; Hicks, Andrew A.; Vitart, Veronique; Knott, Sara; Wild, Sarah H.; Pramstaller, Peter P.; Wilson, James F.; Rudan, Igor; Porteous, David J.

2011-01-01

Genome analysis provides a powerful approach to test for evidence of genetic variation within and between geographical regions and local populations. Copy number variants which comprise insertions, deletions and duplications of genomic sequence provide one such convenient and informative source. Here, we investigate copy number variants from genome wide scans of single nucleotide polymorphisms in three European population isolates, the island of Vis in Croatia, the islands of Orkney in Scotland and the South Tyrol in Italy. We show that whereas the overall copy number variant frequencies are similar between populations, their distribution is highly specific to the population of origin, a finding which is supported by evidence for increased kinship correlation for specific copy number variants within populations. PMID:21829696

Nonlinear Analysis of Time Series in Genome-Wide Linkage Disequilibrium Data

NASA Astrophysics Data System (ADS)

Hernández-Lemus, Enrique; Estrada-Gil, Jesús K.; Silva-Zolezzi, Irma; Fernández-López, J. Carlos; Hidalgo-Miranda, Alfredo; Jiménez-Sánchez, Gerardo

2008-02-01

The statistical study of large scale genomic data has turned out to be a very important tool in population genetics. Quantitative methods are essential to understand and implement association studies in the biomedical and health sciences. Nevertheless, the characterization of recently admixed populations has been an elusive problem due to the presence of a number of complex phenomena. For example, linkage disequilibrium structures are thought to be more complex than their non-recently admixed population counterparts, presenting the so-called ancestry blocks, admixed regions that are not yet smoothed by the effect of genetic recombination. In order to distinguish characteristic features for various populations we have implemented several methods, some of them borrowed or adapted from the analysis of nonlinear time series in statistical physics and quantitative physiology. We calculate the main fractal dimensions (Kolmogorov's capacity, information dimension and correlation dimension, usually named, D0, D1 and D2). We also have made detrended fluctuation analysis and information based similarity index calculations for the probability distribution of correlations of linkage disequilibrium coefficient of six recently admixed (mestizo) populations within the Mexican Genome Diversity Project [1] and for the non-recently admixed populations in the International HapMap Project [2]. Nonlinear correlations showed up as a consequence of internal structure within the haplotype distributions. The analysis of these correlations as well as the scope and limitations of these procedures within the biomedical sciences are discussed.

Genetic studies among seven endogamous populations of the Koshi Zone, Bihar (India).

PubMed

Pandey, B N; Das, P K; Husain, S; Anwer, Md Rauf; Jha, A K

2003-09-01

The distribution of AB0 and Rhesus blood groups, PTC taste sensitivity and colour blindness was studied among seven endogamous populations (Tharu, Mushar, Santal, Dhobi, Julaha, Kulhaiya and Karan Kayastha) in the Koshi Zone of Bihar (India). The phenotype and allele frequencies of the four gene loci (AB0, RH, PTC and colour blindness) show considerable differences between these populations. The measurement of genetic distances revealed, that the lowest genetic distance is seen between Dhobi and Julaha, the highest between Mushar and Tharu. From the genetic distance analysis there is some evidence for a close genetic relationship among the population groups belonging to the same region, irrespective of their caste, religion, linguistic or any other affinities. It may be concluded that all these populations have arisen through a common ancestor and changed gene frequencies among them is due to evolutionary forces like mutation, selection, migration, temporal variation and genetic drift. However, these populations retain their separate entities by practising endogamy. Gene diversity analysis reveals that these populations are at an early stage of genetic differentiation.

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 connectivity of the moth pollinated tree Glionnetia sericea in a highly fragmented habitat.

PubMed

Finger, Aline; Kaiser-Bunbury, Christopher N; Kettle, Chris J; Valentin, Terence; Ghazoul, Jaboury

2014-01-01

Long-distance gene flow is thought to be one prerequisite for the persistence of plant species in fragmented environments. Human influences have led to severe fragmentation of native habitats in the Seychelles islands, with many species surviving only in small and isolated populations. The endangered Seychelles endemic tree Glionnetia sericea is restricted to altitudes between 450 m and 900 m where the native forest vegetation has been largely lost and replaced with exotic invasives over the last 200 years. This study explores the genetic and ecological consequences of population fragmentation in this species by analysing patterns of genetic diversity in a sample of adults, juveniles and seeds, and by using controlled pollination experiments. Our results show no decrease in genetic diversity and no increase in genetic structuring from adult to juvenile cohorts. Despite significant inbreeding in some populations, there is no evidence of higher inbreeding in juvenile cohorts relative to adults. A Bayesian structure analysis and a tentative paternity analysis indicate extensive historical and contemporary gene flow among remnant populations. Pollination experiments and a paternity analysis show that Glionnetia sericea is self-compatible. Nevertheless, outcrossing is present with 7% of mating events resulting from pollen transfer between populations. Artificial pollination provided no evidence for pollen limitation in isolated populations. The highly mobile and specialized hawkmoth pollinators (Agrius convolvuli and Cenophodes tamsi; Sphingidae) appear to promote extensive gene flow, thus mitigating the potential negative ecological and genetic effects of habitat fragmentation in this species. We conclude that contemporary gene flow is sufficient to maintain genetic connectivity in this rare and restricted Seychelles endemic, in contrast to other island endemic tree species with limited contemporary gene flow.

Genetic Connectivity of the Moth Pollinated Tree Glionnetia sericea in a Highly Fragmented Habitat

PubMed Central

Finger, Aline; Valentin, Terence; Ghazoul, Jaboury

2014-01-01

Long-distance gene flow is thought to be one prerequisite for the persistence of plant species in fragmented environments. Human influences have led to severe fragmentation of native habitats in the Seychelles islands, with many species surviving only in small and isolated populations. The endangered Seychelles endemic tree Glionnetia sericea is restricted to altitudes between 450 m and 900 m where the native forest vegetation has been largely lost and replaced with exotic invasives over the last 200 years. This study explores the genetic and ecological consequences of population fragmentation in this species by analysing patterns of genetic diversity in a sample of adults, juveniles and seeds, and by using controlled pollination experiments. Our results show no decrease in genetic diversity and no increase in genetic structuring from adult to juvenile cohorts. Despite significant inbreeding in some populations, there is no evidence of higher inbreeding in juvenile cohorts relative to adults. A Bayesian structure analysis and a tentative paternity analysis indicate extensive historical and contemporary gene flow among remnant populations. Pollination experiments and a paternity analysis show that Glionnetia sericea is self-compatible. Nevertheless, outcrossing is present with 7% of mating events resulting from pollen transfer between populations. Artificial pollination provided no evidence for pollen limitation in isolated populations. The highly mobile and specialized hawkmoth pollinators (Agrius convolvuli and Cenophodes tamsi; Sphingidae) appear to promote extensive gene flow, thus mitigating the potential negative ecological and genetic effects of habitat fragmentation in this species. We conclude that contemporary gene flow is sufficient to maintain genetic connectivity in this rare and restricted Seychelles endemic, in contrast to other island endemic tree species with limited contemporary gene flow. PMID:25347541

Investigation of extended Y chromosome STR haplotypes in Sardinia.

PubMed

Lacerenza, D; Aneli, S; Di Gaetano, C; Critelli, R; Piazza, A; Matullo, G; Culigioni, C; Robledo, R; Robino, C; Calò, C

2017-03-01

Y-chromosomal variation of selected single nucleotide polymorphisms (SNPs) and 32 short tandem repeat (STR) loci was evaluated in Sardinia in three open population groups (Northern Sardinia, n=40; Central Sardinia, n=56; Southern Sardinia, n=91) and three isolates (Desulo, n=34; Benetutti, n=45, Carloforte, n=42). The tested Y-STRs consisted of Yfiler ® Plus markers and the seven rapidly mutating (RM) loci not included in the YFiler ® Plus kit (DYF399S1, DYF403S1ab, DYF404S1, DYS526ab, DYS547, DYS612, and DYS626). As expected, inclusion of additional Y-STR loci increased haplotype diversity (h), though complete differentiation of male lineages was impossible even by means of RM Y-STRs (h=0.99997). Analysis of molecular variance indicated that the three open populations were fairly homogeneous, whereas signs of genetic heterogeneity could be detected when the three isolates were also included in the analysis. Multidimensional scaling analysis showed that, even for extended haplotypes including RM Y-STR markers, Sardinians were clearly differentiated from populations of the Italian peninsula and Sicily. The only exception was represented by the Carloforte sample that, in accordance with its peculiar population history, clustered with Northern/Central Italian populations. The introduction of extended forensic Y-STR panels, including highly variable RM Y-STR markers, is expected to reduce the impact of population structure on haplotype frequency estimations. However, our results show that the availability of geographically detailed reference databases is still important for the assessment of the evidential value of a Y-haplotype match. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

The Contribution of Genetic Diversity to Subdivide Populations Living in the Silk Road of China

PubMed Central

Gui, Hongsheng; Yuan, Zuyi; Li, Shengbin

2014-01-01

There are several indigenous ethnic populations along the silk road in the Northwest of China that display clear differences in culture and social customs, perhaps as a result of geographic isolation and different linguistic traditions. However, extensive trade and other interactions probably facilitated the admixture of different gene pools between these populations over the last two millennia. To further explore the evolutionary relationships of the 13 ethnic populations residing in Northwest China and to reveal the features of population admixture, the 9 most-commonly employed CODIS loci (D3S1358, TH01, D5S818, D13S317, D7S820, CSF1PO, vWA, TPOX, FGA) were selected for genotyping and further analysis. Phylogenetic tree and principal component analysis revealed clear pattern of population differentiation between 4 populations living in Sinkiang Uighur Autonomous Region and other 9 populations dwelled in the upper regions of Silk Road. R matrix regression showed high-level gene flow and population admixture dose exist among these ethic populations in the Northwest region of China. Furthermore, the Mantel test suggests that larger percent of genetic variance (21.58% versus 2.3%) can be explained by geographic isolation than linguistic barriers, which matched with the contribution of geographic factors to other world populations. PMID:24828511

Border Disease Virus: An Exceptional Driver of Chamois Populations Among Other Threats.

PubMed

Serrano, Emmanuel; Colom-Cadena, Andreu; Gilot-Fromont, Emmanuelle; Garel, Mathieu; Cabezón, Oscar; Velarde, Roser; Fernández-Sirera, Laura; Fernández-Aguilar, Xavier; Rosell, Rosa; Lavín, Santiago; Marco, Ignasi

2015-01-01

Though it is accepted that emerging infectious diseases are a threat to planet biodiversity, little information exists about their role as drivers of species extinction. Populations are also affected by natural catastrophes and other pathogens, making it difficult to estimate the particular impact of emerging infectious diseases. Border disease virus genogroup 4 (BDV-4) caused a previously unreported decrease in populations of Pyrenean chamois (Rupicapra pyrenaica pyrenaica) in Spain. Using a population viability analysis, we compared probabilities of extinction of a virtual chamois population affected by winter conditions, density dependence, keratoconjunctivitis, sarcoptic mange, and BD outbreaks. BD-affected populations showed double risk of becoming extinct in 50 years, confirming the exceptional ability of this virus to drive chamois populations.

Recurrent jellyfish blooms are a consequence of global oscillations.

PubMed

Condon, Robert H; Duarte, Carlos M; Pitt, Kylie A; Robinson, Kelly L; Lucas, Cathy H; Sutherland, Kelly R; Mianzan, Hermes W; Bogeberg, Molly; Purcell, Jennifer E; Decker, Mary Beth; Uye, Shin-ichi; Madin, Laurence P; Brodeur, Richard D; Haddock, Steven H D; Malej, Alenka; Parry, Gregory D; Eriksen, Elena; Quiñones, Javier; Acha, Marcelo; Harvey, Michel; Arthur, James M; Graham, William M

2013-01-15

A perceived recent increase in global jellyfish abundance has been portrayed as a symptom of degraded oceans. This perception is based primarily on a few case studies and anecdotal evidence, but a formal analysis of global temporal trends in jellyfish populations has been missing. Here, we analyze all available long-term datasets on changes in jellyfish abundance across multiple coastal stations, using linear and logistic mixed models and effect-size analysis to show that there is no robust evidence for a global increase in jellyfish. Although there has been a small linear increase in jellyfish since the 1970s, this trend was unsubstantiated by effect-size analysis that showed no difference in the proportion of increasing vs. decreasing jellyfish populations over all time periods examined. Rather, the strongest nonrandom trend indicated jellyfish populations undergo larger, worldwide oscillations with an approximate 20-y periodicity, including a rising phase during the 1990s that contributed to the perception of a global increase in jellyfish abundance. Sustained monitoring is required over the next decade to elucidate with statistical confidence whether the weak increasing linear trend in jellyfish after 1970 is an actual shift in the baseline or part of an oscillation. Irrespective of the nature of increase, given the potential damage posed by jellyfish blooms to fisheries, tourism, and other human industries, our findings foretell recurrent phases of rise and fall in jellyfish populations that society should be prepared to face.

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

Evaluation of forensic and anthropological potential of D9S1120 in Mestizos and Amerindian populations from Mexico

PubMed Central

Rangel-Villalobos, Héctor; Sánchez-Gutiérrez, Viviana M; Botello-Ruiz, Miriam; Salazar-Flores, Joel; Martínez-Cortés, Gabriela; Muñoz-Valle, José F; Phillips, Christopher

2012-01-01

Aim To carry out a deeper forensic and anthropological evaluation of the short tandem repeat (STR) D9S1120 in five Mestizo populations and eight Amerindian groups from Mexico. Methods We amplified the STR D9S1120 based on primers and conditions described by Phillips et al, followed by capillary electrophoresis in the genetic analyzer ABI Prism 310. Genotypes were analyzed with the GeneMapper ID software. In each population we estimated statistical parameters of forensic importance and Hardy-Weinberg equilibrium. Heterozygosity and FST-values were compared with those previously obtained with nine STRs of the Combined DNA Index System (CODIS-STRs). Results Amerindian and Mestizo populations showed high frequencies of the allele 9 and 16, respectively. Population structure analysis (AMOVA) showed a significant differentiation between Amerindian groups (FST = 2.81%; P < 0.0001), larger than between Mestizos (FST = 0.44%; P = 0.187). D9S1120 showed less genetic diversity but better population differentiation estimates than CODIS-STRs between Amerindian groups and between Amerindians and Mestizos, but not between Mestizo groups. Conclusion This study evaluated the ability of D9S1120 to be used for human identification purposes and demonstrated its anthropological potential to differentiate Mestizos and Amerindian populations. PMID:23100204

Geochemical characteristics of Heavy metals of river sediment from the main rivers at Texas, USA.

NASA Astrophysics Data System (ADS)

Matsumoto, I.; Hoffman, D.; MacAlister, J.; Ishiga, H.

2008-12-01

Trinity River is one of the biggest rivers which flows through Dallas and Fort Worth two big cities of USA and are highly populated. Trinity river drains into the Gulf of Mexico. Sediment samples collected from various points along the upper and lower streams were subjected to content analysis and elution analysis (using liquate (flow) out test) on the heavy metals like Cd, CN, Pb, Cr, As, Hg, Ni, Zn and Cu from the river sediment for the purpose of environment assessment. A total of 22 sample points were identified from upper stream to lower stream and samples were collected such that almost the whole stream length of Trinity River is covered. Results show that heavy metal content through out the river stream is below the recommended limits posing no immediate environmental threat. However, the experimental results show clear impact of human population in bigger cities on heavy metal concentrations in the river sediments as compared to smaller cities with low human population. It could be seen from the analysis that all the heavy metals show relatively high content and high elution value in Dallas and Fort Worth. As we move away from the big cities, the value of content and elution of sediment decreased by natural dilution effect by the river. And we also present the data of the Colorado and San Antonio rivers.

Analysis of genetic diversity and population structure of oil palm (Elaeis guineensis) from China and Malaysia based on species-specific simple sequence repeat markers.

PubMed

Zhou, L X; Xiao, Y; Xia, W; Yang, Y D

2015-12-08

Genetic diversity and patterns of population structure of the 94 oil palm lines were investigated using species-specific simple sequence repeat (SSR) markers. We designed primers for 63 SSR loci based on their flanking sequences and conducted amplification in 94 oil palm DNA samples. The amplification result showed that a relatively high level of genetic diversity was observed between oil palm individuals according a set of 21 polymorphic microsatellite loci. The observed heterozygosity (Ho) was 0.3683 and 0.4035, with an average of 0.3859. The Ho value was a reliable determinant of the discriminatory power of the SSR primer combinations. The principal component analysis and unweighted pair-group method with arithmetic averaging cluster analysis showed the 94 oil palm lines were grouped into one cluster. These results demonstrated that the oil palm in Hainan Province of China and the germplasm introduced from Malaysia may be from the same source. The SSR protocol was effective and reliable for assessing the genetic diversity of oil palm. Knowledge of the genetic diversity and population structure will be crucial for establishing appropriate management stocks for this species.

Pattern of morphological variation and diversity of Cocos nucifera (Arecaceae) in Mexico.

PubMed

Zizumbo-Villarreal, D; Piñero, D

1998-06-01

The pattern of morphological variation of Cocos nucifera in Mexico was statistically and numerically evaluated. Forty-one populations were analyzed, using 17 morphological fruit characters. Principal components and cluster analyses indicated four main groups of coconut populations that showed high similarity with four different genotypes recently imported into Mexico from areas that could be the origin of Mexican coconut populations. These four genotypes were evaluated with regard to the lethal yellowing disease in Jamaica and showed a differential susceptibility. Therefore it is possible to speculate upon a difference in susceptibility of the Mexican genotypes. The analysis of correlation between morphological and geographical distances showed a high positive correlation that supports: (1) historical evidence that indicates early introductions of coconut from different regions of the world, (2) that on both coasts of Mexico two different patterns of dispersal were involved: continuous and in jumps. Collectively these results suggest that the impact of the lethal yellowing disease on coconut populations will vary depending on the specific area and the origin of its coconuts.

Genetic polymorphisms of nine X-STR loci in four population groups from Inner Mongolia, China.

PubMed

Hou, Qiao-Fang; Yu, Bin; Li, Sheng-Bin

2007-02-01

Nine short tandem repeat (STR) markers on the X chromosome (DXS101, DXS6789, DXS6799, DXS6804, DXS7132, DXS7133, DXS7423, DXS8378, and HPRTB) were analyzed in four population groups (Mongol, Ewenki, Oroqen, and Daur) from Inner Mongolia, China, in order to learn about the genetic diversity, forensic suitability, and possible genetic affinities of the populations. Frequency estimates, Hardy-Weinberg equilibrium, and other parameters of forensic interest were computed. The results revealed that the nine markers have a moderate degree of variability in the population groups. Most heterozygosity values for the nine loci range from 0.480 to 0.891, and there are evident differences of genetic variability among the populations. A UPGMA tree constructed on the basis of the generated data shows very low genetic distance between Mongol and Han (Xi'an) populations. Our results based on genetic distance analysis are consistent with the results of earlier studies based on linguistics and the immigration history and origin of these populations. The minisatellite loci on the X chromosome studied here are not only useful in showing significant genetic variation between the populations, but also are suitable for human identity testing among Inner Mongolian populations.

The B chromosome polymorphism of the grasshopper Eyprepocnemis plorans in North Africa. IV. Transmission of rare B chromosome variants.

PubMed

Bakkali, M; Camacho, J P M

2004-01-01

In addition to the principal B chromosome (B(1)) in Moroccan populations of the grasshopper Eyprepocnemis plorans, nine B chromosome variants appeared at low frequency. The transmission of five of these rare B chromosome variants through females was analysed in three natural populations. Sixteen controlled crosses provided useful information on the transmission of B(M2), B(M6) and B(M7) in Smir, B(M3) and B(M6) in SO.DE.A. (Société de Développement Agricole lands near Ksar-el-Kebir city), and B(M2) and B(M10) in Mechra, all located in Morocco. Since six female parents carried two different B variants, a total of 22 progeny analyses could be studied. Intraindividual variation in B transmission rate (k(B)) was observed among the successive egg pods in 26.7 % of the females, but this variation did not show a consistent temporal pattern. Only the B(M2) and B(M6) variants in Smir showed net drive, although variation was high among crosses, especially for B(M2). These two variants are thus good candidates for future regenerations (the replacement of a neutralized B, B(1) in this case, by a new driving variant, B(M2) or B(M6)) in Smir, the northern population where the B polymorphism is presumably older. The analysis of all crosses performed in the three populations, including those reported previously for the analysis of B(1) transmission, showed that the largest variance in k(B) among crosses stands at the individual level, and not at population or type of B levels. The implications of these findings for the occurrence of possible regeneration processes in Moroccan populations are discussed. Copyright 2004 S. Karger AG, Basel

Sympatric speciation revealed by genome-wide divergence in the blind mole rat Spalax.

PubMed

Li, Kexin; Hong, Wei; Jiao, Hengwu; Wang, Guo-Dong; Rodriguez, Karl A; Buffenstein, Rochelle; Zhao, Yang; Nevo, Eviatar; Zhao, Huabin

2015-09-22

Sympatric speciation (SS), i.e., speciation within a freely breeding population or in contiguous populations, was first proposed by Darwin [Darwin C (1859) On the Origins of Species by Means of Natural Selection] and is still controversial despite theoretical support [Gavrilets S (2004) Fitness Landscapes and the Origin of Species (MPB-41)] and mounting empirical evidence. Speciation of subterranean mammals generally, including the genus Spalax, was considered hitherto allopatric, whereby new species arise primarily through geographic isolation. Here we show in Spalax a case of genome-wide divergence analysis in mammals, demonstrating that SS in continuous populations, with gene flow, encompasses multiple widespread genomic adaptive complexes, associated with the sharply divergent ecologies. The two abutting soil populations of S. galili in northern Israel habituate the ancestral Senonian chalk population and abutting derivative Plio-Pleistocene basalt population. Population divergence originated ∼0.2-0.4 Mya based on both nuclear and mitochondrial genome analyses. Population structure analysis displayed two distinctly divergent clusters of chalk and basalt populations. Natural selection has acted on 300+ genes across the genome, diverging Spalax chalk and basalt soil populations. Gene ontology enrichment analysis highlights strong but differential soil population adaptive complexes: in basalt, sensory perception, musculature, metabolism, and energetics, and in chalk, nutrition and neurogenetics are outstanding. Population differentiation of chemoreceptor genes suggests intersoil population's mate and habitat choice substantiating SS. Importantly, distinctions in protein degradation may also contribute to SS. Natural selection and natural genetic engineering [Shapiro JA (2011) Evolution: A View From the 21st Century] overrule gene flow, evolving divergent ecological adaptive complexes. Sharp ecological divergences abound in nature; therefore, SS appears to be an important mode of speciation as first envisaged by Darwin [Darwin C (1859) On the Origins of Species by Means of Natural Selection].

Genetic diversity of 38 insertion-deletion polymorphisms in Jewish populations.

PubMed

Ferragut, J F; Pereira, R; Castro, J A; Ramon, C; Nogueiro, I; Amorim, A; Picornell, A

2016-03-01

Population genetic data of 38 non-coding biallelic autosomal indels are reported for 466 individuals, representing six populations with Jewish ancestry (Ashkenazim, Mizrahim, Sephardim, North African, Chuetas and Bragança crypto-Jews). Intra-population diversity and forensic parameters values showed that this set of indels was highly informative for forensic applications in the Jewish populations studied. Genetic distance analysis demonstrated that this set of markers efficiently separates populations from different continents, but does not seem effective for molecular anthropology studies in Mediterranean region. Finally, it is important to highlight that although the genetic distances between Jewish populations were small, significant differences were observed for Chuetas and Bragança Jews, and therefore, specific databases must be used for these populations. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Population Pharmacokinetics and Therapeutic Efficacy of Febuxostat in Patients with Severe Renal Impairment.

PubMed

Hira, Daiki; Chisaki, Yugo; Noda, Satoshi; Araki, Hisazumi; Uzu, Takashi; Maegawa, Hiroshi; Yano, Yoshitaka; Morita, Shin-Ya; Terada, Tomohiro

2015-01-01

The aim of the present study was to determine the influence of severe renal dysfunction (estimated glomerular filtration rate <30 ml/min/1.73 m(2), including hemodialysis) on the pharmacokinetics and therapeutic effects of febuxostat using a population pharmacokinetic analysis. This study recruited patients with hyperuricemia who were initially treated with allopurinol, but were switched to febuxostat, and it consists of 2 sub-studies: a pharmacokinetic study (26 patients) and retrospective efficacy evaluation study (51 patients). The demographic and clinical data of patients were collected from electronic medical records. Plasma febuxostat concentrations were obtained at each hospital visit. Population pharmacokinetic modeling was performed with NONMEM version 7.2. A total of 128 plasma febuxostat concentrations from 26 patients were used in the population pharmacokinetic analysis. The data were best described by a 1-compartment model with first order absorption. Covariate analysis revealed that renal function did not influence the pharmacokinetics of febuxostat, whereas actual body weight significantly influenced apparent clearance and apparent volume of distribution. The retrospective efficacy analysis showed the favorable therapeutic response of febuxostat switched from allopurinol in patients with moderate to severe renal impairment. No serious adverse event associated with febuxostat was observed irrespective of renal function. The population pharmacokinetic analysis and therapeutic analysis of febuxostat revealed that severe renal dysfunction had no influence on the pharmacokinetic parameters of febuxostat. These results suggest that febuxostat is tolerated well by patients with severe renal impairment. © 2015 S. Karger AG, Basel.

Chromosome 9p21 In Ischemic Stroke: Population Structure and Meta-Analysis

PubMed Central

Anderson, CD; Biffi, A; Rost, NS; Cortellini, L; Furie, KL; Rosand, J

2011-01-01

Background and Purpose Sequence variants on chromosome 9p21.3 are implicated in coronary artery disease (CAD) and myocardial infarction (MI), but studies in ischemic stroke have produced inconsistent results. We investigated whether these conflicting findings were due to false positive studies confounded by population stratification, or false negative studies that failed to account for effects specific to certain stroke subtypes. Methods After assessing for population stratification at 9p21.3 using genome-wide data, we meta-analyzed 8 ischemic stroke studies. This analysis focused on two single nucleotide polymorphisms (SNPs), rs1537378 and rs10757278, as these variants are in strong linkage disequilibrium with most SNPs analyzed in prior studies of the region. Results Principal component analysis of the genome-wide data showed no evidence of population stratification at that locus. Meta-analysis confirmed that both rs1537378 and rs10757278 are risk factors for ischemic stroke (odds ratios 1.09, [p = 0.0014], and 1.11, [p = 0.001] respectively). Subtype analysis revealed a substantial increase in the effect of each SNP for risk of large artery (LA) stroke, achieving an effect size similar to that seen in CAD/MI. Conclusions Variants on 9p21.3 are associated with ischemic stroke, and restriction of analysis to LA stroke increases effect size towards that observed in prior association studies of CAD/MI. Previous inconsistent findings are best explained by this subtype-specificity rather than any unmeasured confounding by population stratification. PMID:20395606

Effect of interleukin-6 polymorphism on risk of preterm birth within population strata: a meta-analysis.

PubMed

Wu, Wilfred; Clark, Erin A S; Stoddard, Gregory J; Watkins, W Scott; Esplin, M Sean; Manuck, Tracy A; Xing, Jinchuan; Varner, Michael W; Jorde, Lynn B

2013-04-25

Because of the role of inflammation in preterm birth (PTB), polymorphisms in and near the interleukin-6 gene (IL6) have been association study targets. Several previous studies have assessed the association between PTB and a single nucleotide polymorphism (SNP), rs1800795, located in the IL6 gene promoter region. Their results have been inconsistent and SNP frequencies have varied strikingly among different populations. We therefore conducted a meta-analysis with subgroup analysis by population strata to: (1) reduce the confounding effect of population structure, (2) increase sample size and statistical power, and (3) elucidate the association between rs1800975 and PTB. We reviewed all published papers for PTB phenotype and SNP rs1800795 genotype. Maternal genotype and fetal genotype were analyzed separately and the analyses were stratified by population. The PTB phenotype was defined as gestational age (GA) < 37 weeks, but results from earlier GA were selected when available. All studies were compared by genotype (CC versus CG+GG), based on functional studies.For the maternal genotype analysis, 1,165 PTBs and 3,830 term controls were evaluated. Populations were stratified into women of European descent (for whom the most data were available) and women of heterogeneous origin or admixed populations. All ancestry was self-reported. Women of European descent had a summary odds ratio (OR) of 0.68, (95% confidence interval (CI) 0.51 - 0.91), indicating that the CC genotype is protective against PTB. The result for non-European women was not statistically significant (OR 1.01, 95% CI 0.59 - 1.75). For the fetal genotype analysis, four studies were included; there was no significant association with PTB (OR 0.98, 95% CI 0.72 - 1.33). Sensitivity analysis showed that preterm premature rupture of membrane (PPROM) may be a confounding factor contributing to phenotype heterogeneity. IL6 SNP rs1800795 genotype CC is protective against PTB in women of European descent. It is not significant in other heterogeneous or admixed populations, or in fetal genotype analysis.Population structure is an important confounding factor that should be controlled for in studies of PTB.

Optimization and Management of Naval Hospital Bremerton’s Military-Medicare Population by Market Analysis of the Naval Hospital Bremerton Empanelled Population

DTIC Science & Technology

2001-04-30

coworkers, published in this issues, showed that shorter office visits were associated with more inappropriate prescribing of non - steroidal anti ... inflammatory drugs ( NSAIDs )” (Davidoff, 1997, p. 483). The article found that shorter visits lead to provider failure to obtain history that would have been...Population Information It is generally noted that the elderly have more contacts with medical providers than do the non - elderly . According to the

A cautionary note on Bayesian estimation of population size by removal sampling with diffuse priors.

PubMed

Bord, Séverine; Bioche, Christèle; Druilhet, Pierre

2018-05-01

We consider the problem of estimating a population size by removal sampling when the sampling rate is unknown. Bayesian methods are now widespread and allow to include prior knowledge in the analysis. However, we show that Bayes estimates based on default improper priors lead to improper posteriors or infinite estimates. Similarly, weakly informative priors give unstable estimators that are sensitive to the choice of hyperparameters. By examining the likelihood, we show that population size estimates can be stabilized by penalizing small values of the sampling rate or large value of the population size. Based on theoretical results and simulation studies, we propose some recommendations on the choice of the prior. Then, we applied our results to real datasets. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A MAYAN FOUNDER MUTATION IS A COMMON CAUSE OF DEAFNESS IN GUATEMALA

PubMed Central

Carranza, Claudia; Menendez, Ibis; Herrera, Mariana; Castellanos, Patricia; Amado, Carlos; Maldonado, Fabiola; Rosales, Luisa; Escobar, Nancy; Guerra, Mariela; Alvarez, Darwin; Foster, Joseph; Guo, Shengru; Blanton, Susan H.; Bademci, Guney; Tekin, Mustafa

2017-01-01

SUMMARY Over 5% of the world population have varying degrees of hearing loss. Mutations in GJB2 are the most common cause of autosomal recessive non-syndromic hearing loss (NSHL) in many populations. The frequency and type of mutations are influenced by ethnicity. Guatemala is a multi-ethnic country with four major populations: Maya, Ladino, Xinca, and Garifuna. To determine the mutation profile of GJB2 in a NSHL population from Guatemala, we sequenced both exons of GJB2 in 133 unrelated families. A total of six pathogenic variants were detected. The most frequent pathogenic variant is c.131G>A (p.Trp44*) detected in 21 of 266 alleles. We show that c.131G>A is associated with a conserved haplotype in Guatemala suggesting a single founder. The majority of Mayan population lives in the west region of the country from where all c.131G>A carriers originated. Further analysis of genome-wide variation of individuals carrying the c.131G>A mutation compared to those of Native American, European, and African populations shows a close match with the Mayan population. PMID:26346709

Population Pharmacokinetics and Exposure Response Assessment of CC-292, a Potent BTK Inhibitor, in Patients With Chronic Lymphocytic Leukemia.

PubMed

Li, Yan; Ramírez-Valle, Francisco; Xue, Yongjun; Ventura, Judith I; Gouedard, Olivier; Mei, Jay; Takeshita, Kenichi; Palmisano, Maria; Zhou, Simon

2017-10-01

CC-292, a potent Bruton tyrosine kinase inhibitor, is under development for the treatment of B-cell malignancies. An analysis was performed to develop a population pharmacokinetic model of CC-292 and assess the influence of demographics and disease-related covariates on CC-292 exposure and to assess the exposure-response (overall response rate) relationship in patients with chronic lymphocytic leukemia. Population pharmacokinetic analysis was based on a 2-compartment base model conducted in NONMEM. Categorical exposure-response analysis was performed using logistic regression in SAS. The population pharmacokinetic analysis results indicated that CC-292 pharmacokinetic disposition is similar between healthy subjects and patients. CC-292 showed a larger central compartment volume of distribution than the peripheral compartment volume of distribution (158 L and 72 L, respectively) and a faster clearance than intercompartmental clearance (134 L/h and 18.7 L/h, respectively), indicating that for CC-292, clearance from blood occurs faster than distribution into deep tissues and organs. CC-292 clearance is not affected by demographics or baseline clinical lab factors, except for sex. Although sex significantly reduced variation of apparent clearance, the sex effect on apparent clearance is unlikely to be clinically relevant. The exposure-response analysis suggested that higher drug exposure is linearly correlated with higher overall response rate. A twice-daily dose regimen showed higher overall response rate as compared to once-daily dosing, consistent with a threshold concentration of approximately 300 ng/mL, above which the probability of overall response rate significantly increases. © 2017, The Authors. The Journal of Clinical Pharmacology Published by Wiley Periodicals, Inc. on behalf of American College of Clinical Pharmacology.

Puerto Ricans in the United States: A Changing Reality.

ERIC Educational Resources Information Center

Rivera-Batiz, Francisco L.; Santiago, Carlos

This report shows that the face of the Puerto Rican population in the United States has changed dramatically in recent years. The analysis is based largely on data from the 1980 and 1990 Censuses of Population, but it is supplemented by other sources. The number of Puerto Ricans in the United States has increased from close to 2 million in 1980 to…

Population growth, economic security, and cultural change in wilderness counties

Treesearch

Paul A. Lorah

2000-01-01

A familiar version of the “jobs versus the environment” argument asserts that wilderness areas limit economic growth by locking up potentially productive natural resources. Analysis of the development paths of rural Western counties shows that this is unlikely: the presence of Wilderness is correlated with income, employment and population growth. Similarly, Wilderness...

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.

Association between KCNJ11 gene polymorphisms and risk of type 2 diabetes mellitus in East Asian populations: a meta-analysis in 42,573 individuals.

PubMed

Yang, Lijuan; Zhou, Xianghai; Luo, Yingying; Sun, Xiuqin; Tang, Yong; Guo, Wulan; Han, Xueyao; Ji, Linong

2012-01-01

A number of studies have been performed to identify the association between potassium inwardly-rectifying channel, subfamily J, member 11 (KCNJ11) gene and type 2 diabetes mellitus (T2DM) in East Asian populations, with inconsistent results. The main aim of this work was to evaluate more precisely the genetic influence of KCNJ11 on T2DM in East Asian populations by means of a meta-analysis. We identified 20 articles for qualitative analysis and 16 were eligible for quantitative analysis (meta-analysis) by database searching up to May 2010. The association was assessed under different genetic models, and the pooled odds ratios (ORs) with 95% confidence intervals (95% CIs) were calculated. The allelic and genotypic contrast demonstrated that the association between KCNJ11 and T2DM was significant for rs5210. However, not all results for rs5215 and rs5218 showed significant associations. For rs5219, the combined ORs (95% CIs) for allelic contrast, dominant and recessive models contrast (with allelic frequency and genotypic distribution data) were 1.139 (1.093-1.188), 1.177 (1.099-1.259) and 1.207 (1.094-1.332), respectively (random effect model). The analysis on the most completely adjusted ORs (95% CIs) by the covariates of rs5219 all presented significant associations under different genetic models. Population-stratified analysis (Korean, Japanese and Chinese) and sensitivity analysis verified the significant results. Cumulative meta-analysis including publication time and sample size illustrated the exaggerated genetic effect in the earliest studies. Heterogeneity and publication bias were assessed. Our study verified that single nucleotide polymorphisms (SNPs) of KCNJ11 gene were significantly associated with the risk of T2DM in East Asian populations.

Molecular phylogeny, population genetics, and evolution of heterocystous cyanobacteria using nifH gene sequences.

PubMed

Singh, Prashant; Singh, Satya Shila; Elster, Josef; Mishra, Arun Kumar

2013-06-01

In order to assess phylogeny, population genetics, and approximation of future course of cyanobacterial evolution based on nifH gene sequences, 41 heterocystous cyanobacterial strains collected from all over India have been used in the present study. NifH gene sequence analysis data confirm that the heterocystous cyanobacteria are monophyletic while the stigonematales show polyphyletic origin with grave intermixing. Further, analysis of nifH gene sequence data using intricate mathematical extrapolations revealed that the nucleotide diversity and recombination frequency is much greater in Nostocales than the Stigonematales. Similarly, DNA divergence studies showed significant values of divergence with greater gene conversion tracts in the unbranched (Nostocales) than the branched (Stigonematales) strains. Our data strongly support the origin of true branching cyanobacterial strains from the unbranched strains.

[Karyological studies of two populations of Juniperus communis L. in west Siberia].

PubMed

Mikheeva, N A; Muratova, E N

2005-01-01

Results of a karyological study of Juniperus communis L. populations under swamp and dry conditions are presented. The chromosome number of J. communis are 2n = 22. Analysis of morphological chromosome parameters showed a similarity between karyotypes of both populations. It is possible to identify one pair of asymmetric chromosomes (VIII pair); this chromosome pair is close to submetacentric type. Three pairs of chromosomes (I, VII, VIII) have secondary constrictions. Other metacentric chromosomes form groups of five long (II--VI) and three short (IX-XI) pairs. Differences between two populations in absolute chromosomal length are observed.

Detecting hybridization between Iranian wild wolf (Canis lupus pallipes) and free-ranging domestic dog (Canis familiaris) by analysis of microsatellite markers.

PubMed

Khosravi, Rasoul; Rezaei, Hamid Reza; Kaboli, Mohammad

2013-01-01

The genetic threat due to hybridization with free-ranging dogs is one major concern in wolf conservation. The identification of hybrids and extent of hybridization is important in the conservation and management of wolf populations. Genetic variation was analyzed at 15 unlinked loci in 28 dogs, 28 wolves, four known hybrids, two black wolves, and one dog with abnormal traits in Iran. Pritchard's model, multivariate ordination by principal component analysis and neighbor joining clustering were used for population clustering and individual assignment. Analysis of genetic variation showed that genetic variability is high in both wolf and dog populations in Iran. Values of H(E) in dog and wolf samples ranged from 0.75-0.92 and 0.77-0.92, respectively. The results of AMOVA showed that the two groups of dog and wolf were significantly different (F(ST) = 0.05 and R(ST) = 0.36; P < 0.001). In each of the three methods, wolf and dog samples were separated into two distinct clusters. Two dark wolves were assigned to the wolf cluster. Also these models detected D32 (dog with abnormal traits) and some other samples, which were assigned to more than one cluster and could be a hybrid. This study is the beginning of a genetic study in wolf populations in Iran, and our results reveal that as in other countries, hybridization between wolves and dogs is sporadic in Iran and can be a threat to wolf populations if human perturbations increase.

Population Structure of Hispanics in the United States: The Multi-Ethnic Study of Atherosclerosis

PubMed Central

Manichaikul, Ani; Palmas, Walter; Rodriguez, Carlos J.; Peralta, Carmen A.; Divers, Jasmin; Guo, Xiuqing; Chen, Wei-Min; Wong, Quenna; Williams, Kayleen; Kerr, Kathleen F.; Taylor, Kent D.; Tsai, Michael Y.; Goodarzi, Mark O.; Sale, Michèle M.; Diez-Roux, Ana V.; Rich, Stephen S.; Rotter, Jerome I.; Mychaleckyj, Josyf C.

2012-01-01

Using ∼60,000 SNPs selected for minimal linkage disequilibrium, we perform population structure analysis of 1,374 unrelated Hispanic individuals from the Multi-Ethnic Study of Atherosclerosis (MESA), with self-identification corresponding to Central America (n = 93), Cuba (n = 50), the Dominican Republic (n = 203), Mexico (n = 708), Puerto Rico (n = 192), and South America (n = 111). By projection of principal components (PCs) of ancestry to samples from the HapMap phase III and the Human Genome Diversity Panel (HGDP), we show the first two PCs quantify the Caucasian, African, and Native American origins, while the third and fourth PCs bring out an axis that aligns with known South-to-North geographic location of HGDP Native American samples and further separates MESA Mexican versus Central/South American samples along the same axis. Using k-means clustering computed from the first four PCs, we define four subgroups of the MESA Hispanic cohort that show close agreement with self-identification, labeling the clusters as primarily Dominican/Cuban, Mexican, Central/South American, and Puerto Rican. To demonstrate our recommendations for genetic analysis in the MESA Hispanic cohort, we present pooled and stratified association analysis of triglycerides for selected SNPs in the LPL and TRIB1 gene regions, previously reported in GWAS of triglycerides in Caucasians but as yet unconfirmed in Hispanic populations. We report statistically significant evidence for genetic association in both genes, and we further demonstrate the importance of considering population substructure and genetic heterogeneity in genetic association studies performed in the United States Hispanic population. PMID:22511882

Population clustering based on copy number variations detected from next generation sequencing data.

PubMed

Duan, Junbo; Zhang, Ji-Gang; Wan, Mingxi; Deng, Hong-Wen; Wang, Yu-Ping

2014-08-01

Copy number variations (CNVs) can be used as significant bio-markers and next generation sequencing (NGS) provides a high resolution detection of these CNVs. But how to extract features from CNVs and further apply them to genomic studies such as population clustering have become a big challenge. In this paper, we propose a novel method for population clustering based on CNVs from NGS. First, CNVs are extracted from each sample to form a feature matrix. Then, this feature matrix is decomposed into the source matrix and weight matrix with non-negative matrix factorization (NMF). The source matrix consists of common CNVs that are shared by all the samples from the same group, and the weight matrix indicates the corresponding level of CNVs from each sample. Therefore, using NMF of CNVs one can differentiate samples from different ethnic groups, i.e. population clustering. To validate the approach, we applied it to the analysis of both simulation data and two real data set from the 1000 Genomes Project. The results on simulation data demonstrate that the proposed method can recover the true common CNVs with high quality. The results on the first real data analysis show that the proposed method can cluster two family trio with different ancestries into two ethnic groups and the results on the second real data analysis show that the proposed method can be applied to the whole-genome with large sample size consisting of multiple groups. Both results demonstrate the potential of the proposed method for population clustering.

Siberian population of the New Stone Age: mtDNA haplotype diversity in the ancient population from the Ust'-Ida I burial ground, dated 4020-3210 BC by 14C.

PubMed

Naumova O, Y u; Rychkov S, Y u

1998-03-01

On the basis of analysis of mtDNA from skeletal remains, dated by 14C 4020-3210 BC, from the Ust'-Ida I Neolithic burial ground in Cis-Baikal area of Siberia, we obtained genetic characteristics of the ancient Mongoloid population. Using the 7 restriction enzymes for the analysis of site's polymorphism in 16,106-16,545 region of mtDNA, we studied the structure of the most frequent DNA haplotypes, and estimated the intrapopulational nucleotide diversity of the Neolithic population. Comparison of the Neolithic and modern indigeneous populations from Siberia, Mongolia and Ural showed, that the ancient Siberian population is one of the ancestors of the modern population of Siberia. From genetic distance, in the assumption of constant nucleotide substitution rate, we estimated the divergence time between the Neolithic and the modern Siberian population. This divergence time (5572 years ago) is conformed to the age of skeletal remains (5542-5652 years). With use of the 14C dates of the skeletal remains, nucleotide substitution rate in mtDNA was estimated as 1% sequence divergence for 8938-9115 years.

The genetics of East African populations: a Nilo-Saharan component in the African genetic landscape

PubMed Central

Dobon, Begoña; Hassan, Hisham Y.; Laayouni, Hafid; Luisi, Pierre; Ricaño-Ponce, Isis; Zhernakova, Alexandra; Wijmenga, Cisca; Tahir, Hanan; Comas, David; Netea, Mihai G.; Bertranpetit, Jaume

2015-01-01

East Africa is a strategic region to study human genetic diversity due to the presence of ethnically, linguistically, and geographically diverse populations. Here, we provide new insight into the genetic history of populations living in the Sudanese region of East Africa by analysing nine ethnic groups belonging to three African linguistic families: Niger-Kordofanian, Nilo-Saharan and Afro-Asiatic. A total of 500 individuals were genotyped for 200,000 single-nucleotide polymorphisms. Principal component analysis, clustering analysis using ADMIXTURE, FST statistics, and the three-population test were used to investigate the underlying genetic structure and ancestry of the different ethno-linguistic groups. Our analyses revealed a genetic component for Sudanese Nilo-Saharan speaking groups (Darfurians and part of Nuba populations) related to Nilotes of South Sudan, but not to other Sudanese populations or other sub-Saharan populations. Populations inhabiting the North of the region showed close genetic affinities with North Africa, with a component that could be remnant of North Africans before the migrations of Arabs from Arabia. In addition, we found very low genetic distances between populations in genes important for anti-malarial and anti-bacterial host defence, suggesting similar selective pressures on these genes and stressing the importance of considering functional pathways to understand the evolutionary history of populations. PMID:26017457

Large genetic differentiation and low variation in vector competence for dengue and yellow fever viruses of Aedes albopictus from Brazil, the United States, and the Cayman Islands.

PubMed

Lourenço de Oliveira, Ricardo; Vazeille, Marie; de Filippis, Ana Maria Bispo; Failloux, Anna-Bella

2003-07-01

We conducted a population genetic analysis of Aedes albopictus collected from 20 sites in Brazil, the United States (Florida, Georgia, and Illinois), and the Cayman Islands. Using isoenzyme analysis, we examined genetic diversity and patterns of gene flow. High genetic differentiation was found among Brazilian samples, and between them and North American samples. Regression analysis of genetic differentiation according to geographic distances indicated that Ae. albopictus samples from Florida were genetically isolated by distance. Infection rates with dengue and yellow fever viruses showed greater differences between two Brazilian samples than between the two North American samples or between a Brazilian sample and a North American sample. Introductions and establishments of new Ae. albopictus populations in the Americas are still in progress, shaping population genetic composition and potentially modifying both dengue and yellow fever transmission patterns.

A Bibliometric Analysis on Cancer Population Science with Topic Modeling.

PubMed

Li, Ding-Cheng; Rastegar-Mojarad, Majid; Okamoto, Janet; Liu, Hongfang; Leichow, Scott

2015-01-01

Bibliometric analysis is a research method used in library and information science to evaluate research performance. It applies quantitative and statistical analyses to describe patterns observed in a set of publications and can help identify previous, current, and future research trends or focus. To better guide our institutional strategic plan in cancer population science, we conducted bibliometric analysis on publications of investigators currently funded by either Division of Cancer Preventions (DCP) or Division of Cancer Control and Population Science (DCCPS) at National Cancer Institute. We applied two topic modeling techniques: author topic modeling (AT) and dynamic topic modeling (DTM). Our initial results show that AT can address reasonably the issues related to investigators' research interests, research topic distributions and popularities. In compensation, DTM can address the evolving trend of each topic by displaying the proportion changes of key words, which is consistent with the changes of MeSH headings.

Exploration of Urban Spatial Planning Evaluation Based on Humanland Harmony

NASA Astrophysics Data System (ADS)

Hu, X. S.; Ma, Q. R.; Liang, W. Q.; Wang, C. X.; Xiong, X. Q.; Han, X. H.

2017-09-01

This study puts forward a new concept, "population urbanization level forecast - driving factor analysis - urban spatial planning analysis" for achieving efficient and intensive development of urbanization considering human-land harmony. We analyzed big data for national economic and social development, studied the development trends of population urbanization and its influencing factors using the grey system model in Chengmai county of Hainan province, China. In turn, we calculated the population of Chengmai coming years based on the forecasting urbanization rate and the corresponding amount of urban construction land, and evaluated the urban spatial planning with GIS spatial analysis method in the study area. The result shows that the proposed concept is feasible for evaluation of urban spatial planning, and is meaningful for guiding the rational distribution of urban space, controlling the scale of development, improving the quality of urbanization and thus promoting highly-efficient and intensive use of limited land resource.

Analysis of Genetic Diversity and Population Structure of Rice Germplasm from North-Eastern Region of India and Development of a Core Germplasm Set

PubMed Central

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

2014-01-01

The North-Eastern region (NER) of India, comprising of Arunachal Pradesh, Assam, Manipur, Meghalaya, Mizoram, Nagaland and Tripura, is a hot spot for genetic diversity and the most probable origin of rice. North-east rice collections are known to possess various agronomically important traits like biotic and abiotic stress tolerance, unique grain and cooking quality. The genetic diversity and associated population structure of 6,984 rice accessions, originating from NER, were assessed using 36 genome wide unlinked single nucleotide polymorphism (SNP) markers distributed across the 12 rice chromosomes. All of the 36 SNP loci were polymorphic and bi-allelic, contained five types of base substitutions and together produced nine types of alleles. The polymorphic information content (PIC) ranged from 0.004 for Tripura to 0.375 for Manipur and major allele frequency ranged from 0.50 for Assam to 0.99 for Tripura. Heterozygosity ranged from 0.002 in Nagaland to 0.42 in Mizoram and gene diversity ranged from 0.006 in Arunachal Pradesh to 0.50 in Manipur. The genetic relatedness among the rice accessions was evaluated using an unrooted phylogenetic tree analysis, which grouped all accessions into three major clusters. For determining population structure, populations K = 1 to K = 20 were tested and population K = 3 was present in all the states, with the exception of Meghalaya and Manipur where, K = 5 and K = 4 populations were present, respectively. Principal Coordinate Analysis (PCoA) showed that accessions were distributed according to their population structure. AMOVA analysis showed that, maximum diversity was partitioned at the individual accession level (73% for Nagaland, 58% for Arunachal Pradesh and 57% for Tripura). Using POWERCORE software, a core set of 701 accessions was obtained, which accounted for approximately 10% of the total NE India collections, representing 99.9% of the allelic diversity. The rice core set developed will be a valuable resource for future genomic studies and crop improvement strategies. PMID:25412256

A Comparative Analysis of Genetic Ancestry and Admixture in the Colombian Populations of Chocó and Medellín.

PubMed

Conley, Andrew B; Rishishwar, Lavanya; Norris, Emily T; Valderrama-Aguirre, Augusto; Mariño-Ramírez, Leonardo; Medina-Rivas, Miguel A; Jordan, I King

2017-10-05

At least 20% of Colombians identify as having African ancestry, yielding the second largest population of Afro-descendants in Latin America. To date, there have been relatively few studies focused on the genetic ancestry of Afro-Latino populations. We report a comparative analysis of the genetic ancestry of Chocó, a state located on Colombia's Pacific coast with a population that is >80% Afro-Colombian. We compared genome-wide patterns of genetic ancestry and admixture for Chocó to six other admixed American populations, with an emphasis on a Mestizo population from the nearby Colombian city of Medellín. One hundred sample donors from Chocó were genotyped across 610,545 genomic sites and compared with 94 publicly available whole genome sequences from Medellín. At the continental level, Chocó shows mostly African genetic ancestry (76%) with a nearly even split between European (13%) and Native American (11%) fractions, whereas Medellín has primarily European ancestry (75%), followed by Native American (18%) and African (7%). Sample donors from Chocó self-identify as having more African ancestry, and conversely less European and Native American ancestry, than can be genetically inferred, as opposed to what we previously found for Medellín, where individuals tend to overestimate levels of European ancestry. We developed a novel approach for subcontinental ancestry assignment, which allowed us to characterize subcontinental source populations for each of the three distinct continental ancestry fractions separately. Despite the clear differences between Chocó and Medellín at the level of continental ancestry, the two populations show overall patterns of subcontinental ancestry that are highly similar. Their African subcontinental ancestries are only slightly different, with Chocó showing more exclusive shared ancestry with the modern Yoruba (Nigerian) population, and Medellín having relatively more shared ancestry with West African populations in Sierra Leone and Gambia. Both populations show very similar Spanish ancestry within Europe and virtually identical patterns of Native American ancestry, with main contributions from the Embera and Waunana tribes. When the three subcontinental ancestry components are considered jointly, the populations of Chocó and Medellín are shown to be most closely related, to the exclusion of the other admixed American populations that we analyzed. We consider the implications of the existence of shared subcontinental ancestries for Colombian populations that appear, at first glance, to be clearly distinct with respect to competing notions of national identity that emphasize ethnic mixing ( mestizaje ) vs. group-specific identities (multiculturalism). Copyright © 2017 Conley et al.

Population Trend and Elasticities of Vital Rates for Steller Sea Lions (Eumetopias jubatus) in the Eastern Gulf of Alaska: A New Life-History Table Analysis

PubMed Central

Maniscalco, John M.; Springer, Alan M.; Adkison, Milo D.; Parker, Pamela

2015-01-01

Steller sea lion (Eumetopias jubatus) numbers are beginning to recover across most of the western distinct population segment following catastrophic declines that began in the 1970s and ended around the turn of the century. This study makes use of contemporary vital rate estimates from a trend-site rookery in the eastern Gulf of Alaska (a sub-region of the western population) in a matrix population model to estimate the trend and strength of the recovery across this region between 2003 and 2013. The modeled population trend was projected into the future based on observed variation in vital rates and a prospective elasticity analysis was conducted to determine future trends and which vital rates pose the greatest threats to recovery. The modeled population grew at a mean rate of 3.5% per yr between 2003 and 2013 and was correlated with census count data from the local rookery and throughout the eastern Gulf of Alaska. If recent vital rate estimates continue with little change, the eastern Gulf of Alaska population could be fully recovered to pre-decline levels within 23 years. With density dependent growth, the population would need another 45 years to fully recover. Elasticity analysis showed that, as expected, population growth rate (λ) was most sensitive to changes in adult survival, less sensitive to changes in juvenile survival, and least sensitive to changes in fecundity. A population decline could be expected with only a 6% decrease in adult survival, whereas a 32% decrease in fecundity would be necessary to bring about a population decline. These results have important implications for population management and suggest current research priorities should be shifted to a greater emphasis on survival rates and causes of mortality. PMID:26488901

Sex expression and floral diversity in Jatropha curcas: a population study in its center of origin

PubMed Central

Adriano-Anaya, María de Lourdes; Pérez-Castillo, Edilma; Salvador-Figueroa, Miguel; Ruiz-González, Sonia; Vázquez-Ovando, Alfredo; Grajales-Conesa, Julieta

2016-01-01

Sex expression and floral morphology studies are central to understand breeding behavior and to define the productive potential of plant genotypes. In particular, the new bioenergy crop Jatropha curcas L. has been classified as a monoecious species. Nonetheless, there is no information about its reproductive diversity in the Mesoamerican region, which is considered its center of origin and diversification. Thus, we determined sex expression and floral morphology in J. curcas populations from southern Mexico and Guatemala. Our results showed that most of J. curcas specimens had typical inflorescences with separate sexes (monoecious); meanwhile, the rest were atypical (gynoecious, androecious, andromonoecious, androgynomonoecious). The most important variables to group these populations, based on a discriminant analysis, were: male flower diameter, female petal length and male nectary length. From southern Mexico “Guerrero” was the most diverse population, and “Centro” had the highest variability among the populations from Chiapas. A cluster analysis showed that the accessions from southern Mexico were grouped without showing any correlation with the geographical origin, while those accessions with atypical sexuality were grouped together. To answer the question of how informative are floral morphological traits compared to molecular markers, we perform a Mantel correlation test between the distance matrix generated in this study and the genetic distance matrix (AFLP) previously reported for the same accessions. We found significant correlation between data at the level of accessions. Our results contribute to design genetic improvement programs by using sexually and morphologically contrasting plants from the center of origin. PMID:27257548

Disease invasion risk in a growing population.

PubMed

Yuan, Sanling; van den Driessche, P; Willeboordse, Frederick H; Shuai, Zhisheng; Ma, Junling

2016-09-01

The spread of an infectious disease may depend on the population size. For simplicity, classic epidemic models assume homogeneous mixing, usually standard incidence or mass action. For standard incidence, the contact rate between any pair of individuals is inversely proportional to the population size, and so the basic reproduction number (and thus the initial exponential growth rate of the disease) is independent of the population size. For mass action, this contact rate remains constant, predicting that the basic reproduction number increases linearly with the population size, meaning that disease invasion is easiest when the population is largest. In this paper, we show that neither of these may be true on a slowly evolving contact network: the basic reproduction number of a short epidemic can reach its maximum while the population is still growing. The basic reproduction number is proportional to the spectral radius of a contact matrix, which is shown numerically to be well approximated by the average excess degree of the contact network. We base our analysis on modeling the dynamics of the average excess degree of a random contact network with constant population input, proportional deaths, and preferential attachment for contacts brought in by incoming individuals (i.e., individuals with more contacts attract more incoming contacts). In addition, we show that our result also holds for uniform attachment of incoming contacts (i.e., every individual has the same chance of attracting incoming contacts), and much more general population dynamics. Our results show that a disease spreading in a growing population may evade control if disease control planning is based on the basic reproduction number at maximum population size.

Multi-InDel Analysis for Ancestry Inference of Sub-Populations in China

PubMed Central

Sun, Kuan; Ye, Yi; Luo, Tao; Hou, Yiping

2016-01-01

Ancestry inference is of great interest in diverse areas of scientific researches, including the forensic biology, medical genetics and anthropology. Various methods have been published for distinguishing populations. However, few reports refer to sub-populations (like ethnic groups) within Asian populations for the limitation of markers. Several InDel loci located very tightly in physical positions were treated as one marker by us, which is multi-InDel. The multi-InDel shows potential as Ancestry Inference Marker (AIM). In this study, we performed a genome-wide scan for multi-InDels as AIM. After examining the FST distributions in the 1000 Genomes Database, 12 candidates were selected and validated for eastern Asian populations. A multiplexed assay was developed as a panel to genotype 12 multi-InDel markers simultaneously. Ancestry component analysis with STRUCTURE and principal component analysis (PCA) were employed to estimate its capability for ancestry inference. Furthermore, ancestry assignments of trial individuals were conducted. It proved to be very effective when 210 samples from Han and Tibetan individuals in China were tested. The panel consisting of multi-InDel markers exhibited considerable potency in ancestry inference, and was suggested to be applied in forensic practices and genetic population studies. PMID:28004788

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.

Trends in incidence of lung cancer in Croatia from 2001 to 2013: gender and regional differences

PubMed Central

Siroglavić, Katarina-Josipa; Polić Vižintin, Marina; Tripković, Ingrid; Šekerija, Mario; Kukulj, Suzana

2017-01-01

Aim To provide an overview of the lung cancer incidence trends in the City of Zagreb (Zagreb), Split-Dalmatia County (SDC), and Croatia in the period from 2001 to 2013. Method Incidence data were obtained from the Croatian National Cancer Registry. For calculating incidence rates per 100 000 population, we used population estimates for the period 2001-2013 from the Croatian Bureau of Statistics. Age-standardized rates of lung cancer incidence were calculated by the direct standardization method using the European Standard Population. To describe incidence trends, we used joinpoint regression analysis. Results Joinpoint analysis showed a statistically significant decrease in lung cancer incidence in men in all regions, with an annual percentage change (APC) of -2.2% for Croatia, 1.9% for Zagreb, and -2.0% for SDC. In women, joinpoint analysis showed a statistically significant increase in the incidence for Croatia, with APC of 1.4%, a statistically significant increase of 1.0% for Zagreb, and no significant change in trend for SDC. In both genders, joinpoint analysis showed a significant decrease in age-standardized incidence rates of lung cancer, with APC of -1.3% for Croatia, -1.1% for Zagreb, and -1.6% for SDC. Conclusion There was an increase in female lung cancer incidence rate and a decrease in male lung cancer incidence rate in Croatia in 2001-20013 period, with similar patterns observed in all the investigated regions. These results highlight the importance of smoking prevention and cessation policies, especially among women and young people. PMID:29094814

Association between glutathione S-transferase P1 Ile (105) Val gene polymorphism and chronic obstructive pulmonary disease: A meta-analysis based on seventeen case-control studies.

PubMed

Yang, Lingjing; Li, Xixia; Tong, Xiang; Fan, Hong

2015-12-01

Previous studies have shown that glutathione S-transferase P1 (GSTP1) was associated with chronic obstructive pulmonary disease (COPD). However, the association between GSTP1 Ile (105) Val gene polymorphism and COPD remains controversial. To drive a more precise estimation, we performed a meta-analysis based on published case-control studies. An electronic search of PubMed, EMBASE, Cochrane library, Web of Science and China Knowledge Resource Integrated (CNKI) Database for papers on GSTP1 Ile (105) Val gene polymorphism and COPD risk was performed. The pooled odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the strength of association in the homozygote model, heterozygote model, dominant model, recessive model and an additive mode. Statistical heterogeneity, test of publication bias and sensitivity analysis was performed. The software STATA (Version 13.0) was used data analysis. Overall, seventeen studies with 1892 cases and 2012 controls were included in this meta-analysis. The GSTP1 Ile (105) Val polymorphism showed pooled odds ratios for the homozygote comparison (OR = 1.501, 95%CI [0.862, 2.614]), heterozygote comparison (OR = 0.924, 95%CI [0.733, 1.165]), dominant model (OR = 1.003, 95%CI [0.756, 1.331]), recessive model (OR = 1.510, 95%CI [0.934, 2.439]), and an additive model (OR = 1.072, 95%CI [0.822, 1.398]). In conclusion, the current meta-analysis, based on the most updated information, showed no significant association between GSTP1 Ile (105) Val gene polymorphism and COPD risk in any genetic models. The results of subgroup analysis also showed no significant association between GSTP1 Ile (105) Val gene polymorphism and COPD risk in Asian population and Caucasian population. Further studies involving large populations and careful control with age, sex, ethnicity, and cigarette smoking are greatly needed.

Association between glutathione S-transferase P1 Ile (105) Val gene polymorphism and chronic obstructive pulmonary disease: A meta-analysis based on seventeen case–control studies

PubMed Central

Yang, Lingjing; Li, Xixia; Tong, Xiang; Fan, Hong

2015-01-01

Introduction Previous studies have shown that glutathione S-transferase P1 (GSTP1) was associated with chronic obstructive pulmonary disease (COPD). However, the association between GSTP1 Ile (105) Val gene polymorphism and COPD remains controversial. To drive a more precise estimation, we performed a meta-analysis based on published case–control studies. Methods An electronic search of PubMed, EMBASE, Cochrane library, Web of Science and China Knowledge Resource Integrated (CNKI) Database for papers on GSTP1 Ile (105) Val gene polymorphism and COPD risk was performed. The pooled odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the strength of association in the homozygote model, heterozygote model, dominant model, recessive model and an additive mode. Statistical heterogeneity, test of publication bias and sensitivity analysis was performed. The software STATA (Version 13.0) was used data analysis. Results Overall, seventeen studies with 1892 cases and 2012 controls were included in this meta-analysis. The GSTP1 Ile (105) Val polymorphism showed pooled odds ratios for the homozygote comparison (OR = 1.501, 95%CI [0.862, 2.614]), heterozygote comparison (OR = 0.924, 95%CI [0.733, 1.165]), dominant model (OR = 1.003, 95%CI [0.756, 1.331]), recessive model (OR = 1.510, 95%CI [0.934, 2.439]), and an additive model (OR = 1.072, 95%CI [0.822, 1.398]). Conclusions In conclusion, the current meta-analysis, based on the most updated information, showed no significant association between GSTP1 Ile (105) Val gene polymorphism and COPD risk in any genetic models. The results of subgroup analysis also showed no significant association between GSTP1 Ile (105) Val gene polymorphism and COPD risk in Asian population and Caucasian population. Further studies involving large populations and careful control with age, sex, ethnicity, and cigarette smoking are greatly needed. PMID:26504746

Genetic diversity and relatedness within and between species of the genus Oligoryzomys (Rodentia; Sigmodontinae).

PubMed

Trott, A; Callegari-Jacques, S M; Oliveira, L F B; Langguth, A; Mattevi, M S

2007-02-01

A RAPD analysis on six species of the rodent genus Oligoryzomys trapped in a wide area (ranging from 01 degrees N to 32 degrees S) of Brazilian territory was performed in order to determine the levels of genetic variability within and between its populations and species. One-hundred and ninety-three animals were collected in 13 different sites (corresponding to 17 samples) located at Pampas, Atlantic Rain Forest, Cerrado, and Amazon domains. Oligoryzomys sp., O. nigripes (8 populations), O. flavescens (4 populations), O. moojeni, O. stramineus, and O. fornesi were the taxa analyzed. Of the 20 primers tested, 4 generated a total of 75 polymorphic products simultaneously amplified in 151 specimens. Various diversity estimators analyzed showed considerable differences between species and populations, indicating a great genetic variation occurring in the Oligoryzomys taxa investigated. A cluster analysis was made using Nei's standard genetic distances, however, it did not correlate the genetic heterogeneity of the species and populations with the geographical areas.

Development of an unbiased, semi-automated approach for classifying plasma cell immunophenotype following multicolor flow cytometry of bone marrow aspirates.

PubMed

Post, Steven R; Post, Ginell R; Nikolic, Dejan; Owens, Rebecca; Insuasti-Beltran, Giovanni

2018-03-24

Despite increased usage of multiparameter flow cytometry (MFC) to assess diagnosis, prognosis, and therapeutic efficacy (minimal residual disease, MRD) in plasma cell neoplasms (PCNs), standardization of methodology and data analysis is suboptimal. We investigated the utility of using the mean and median fluorescence intensities (FI) obtained from MFC to objectively describe parameters that distinguish plasma cell (PC) phenotypes. In this retrospective study, flow cytometry results from bone marrow aspirate specimens from 570 patients referred to the Myeloma Institute at UAMS were evaluated. Mean and median FI data were obtained from 8-color MFC of non-neoplastic, malignant, and mixed PC populations using antibodies to CD38, CD138, CD19, CD20, CD27, CD45, CD56, and CD81. Of 570 cases, 252 cases showed only non-neoplastic PCs, 168 showed only malignant PCs, and 150 showed mixed PC populations. Statistical analysis of median FI data for each CD marker showed no difference in expression intensity on non-neoplastic and malignant PCs, between pure and mixed PC populations. ROC analysis of the median FI of CD expression in non-neoplastic and malignant PCs was used to develop an algorithm to convert quantitative FI values to qualitative assessments including "negative," "positive," "dim," and "heterogeneous" expression. FI data derived from 8-color MFC can be used to define marker expression on PCs. Translation of FI data from Infinicyt software to an Excel worksheet streamlines workflow and eliminates transcriptional errors when generating flow reports. © 2018 International Clinical Cytometry Society. © 2018 International Clinical Cytometry Society.

Partial AZFc duplications not deletions are associated with male infertility in the Yi population of Yunnan Province, China.

PubMed

Ye, Jun-jie; Ma, Li; Yang, Li-juan; Wang, Jin-huan; Wang, Yue-li; Guo, Hai; Gong, Ning; Nie, Wen-hui; Zhao, Shu-hua

2013-09-01

There are many reports on associations between spermatogenesis and partial azoospermia factor c (AZFc) deletions as well as duplications; however, results are conflicting, possibly due to differences in methodology and ethnic background. The purpose of this study is to investigate the association of AZFc polymorphisms and male infertility in the Yi ethnic population, residents within Yunnan Province, China. A total of 224 infertile patients and 153 fertile subjects were selected in the Yi ethnic population. The study was performed by sequence-tagged site plus/minus (STS+/-) analysis followed by gene dosage and gene copy definition analysis. Y haplotypes of 215 cases and 115 controls were defined by 12 binary markers using single nucleotide polymorphism on Y chromosome (Y-SNP) multiplex assays based on single base primer extension technology. The distribution of Y haplotypes was not significantly different between the case and control groups. The frequencies of both gr/gr (7.6% vs. 8.5%) and b2/b3 (6.3% vs. 8.5%) deletions do not show significant differences. Similarly, single nucleotide variant (SNV) analysis shows no significant difference of gene copy definition between the cases and controls. However, the frequency of partial duplications in the infertile group (4.0%) is significantly higher than that in the control group (0.7%). Further, we found a case with sY1206 deletion which had two CDY1 copies but removed half of DAZ genes. Our results show that male infertility is associated with partial AZFc duplications, but neither gr/gr nor b2/b3 deletions, suggesting that partial AZFc duplications rather than deletions are risk factors for male infertility in Chinese-Yi population.

Social deprivation and population density are not associated with small area risk of amyotrophic lateral sclerosis.

PubMed

Rooney, James P K; Tobin, Katy; Crampsie, Arlene; Vajda, Alice; Heverin, Mark; McLaughlin, Russell; Staines, Anthony; Hardiman, Orla

2015-10-01

Evidence of an association between areal ALS risk and population density has been previously reported. We aim to examine ALS spatial incidence in Ireland using small areas, to compare this analysis with our previous analysis of larger areas and to examine the associations between population density, social deprivation and ALS incidence. Residential area social deprivation has not been previously investigated as a risk factor for ALS. Using the Irish ALS register, we included all cases of ALS diagnosed in Ireland from 1995-2013. 2006 census data was used to calculate age and sex standardised expected cases per small area. Social deprivation was assessed using the pobalHP deprivation index. Bayesian smoothing was used to calculate small area relative risk for ALS, whilst cluster analysis was performed using SaTScan. The effects of population density and social deprivation were tested in two ways: (1) as covariates in the Bayesian spatial model; (2) via post-Bayesian regression. 1701 cases were included. Bayesian smoothed maps of relative risk at small area resolution matched closely to our previous analysis at a larger area resolution. Cluster analysis identified two areas of significant low risk. These areas did not correlate with population density or social deprivation indices. Two areas showing low frequency of ALS have been identified in the Republic of Ireland. These areas do not correlate with population density or residential area social deprivation, indicating that other reasons, such as genetic admixture may account for the observed findings. Copyright © 2015 Elsevier Inc. All rights reserved.

A molecular analysis of the patterns of genetic diversity in local chickens from western Algeria in comparison with commercial lines and wild jungle fowls.

PubMed

Mahammi, F Z; Gaouar, S B S; Laloë, D; Faugeras, R; Tabet-Aoul, N; Rognon, X; Tixier-Boichard, M; Saidi-Mehtar, N

2016-02-01

The objectives of this study were to characterize the genetic variability of village chickens from three agro-ecological regions of western Algeria: coastal (CT), inland plains (IP) and highlands (HL), to reveal any underlying population structure, and to evaluate potential genetic introgression from commercial lines into local populations. A set of 233 chickens was genotyped with a panel of 23 microsatellite markers. Geographical coordinates were individually recorded. Eight reference populations were included in the study to investigate potential gene flow: four highly selected commercial pure lines and four lines of French slow-growing chickens. Two populations of wild red jungle fowls were also genotyped to compare the range of diversity between domestic and wild fowls. A genetic diversity analysis was conducted both within and between populations. Multivariate redundancy analyses were performed to assess the relative influence of geographical location among Algerian ecotypes. The results showed a high genetic variability within the Algerian population, with 184 alleles and a mean number of 8.09 alleles per locus. The values of heterozygosity (He and Ho) ranged from 0.55 to 0.62 in Algerian ecotypes and were smaller than values found in Jungle fowl populations and higher than values found in commercial populations. Although the structuring analysis of genotypes did not reveal clear subpopulations within Algerian ecotypes, the supervised approach using geographical data showed a significant (p < 0.01) differentiation between the three ecotypes which was mainly due to altitude. Thus, the genetic diversity of Algerian ecotypes may be under the influence of two factors with contradictory effects: the geographical location and climatic conditions may induce some differentiation, whereas the high level of exchanges and gene flow may suppress it. Evidence of gene flow between commercial and Algerian local populations was observed, which may be due to unrecorded crossing with commercial chickens. Chicken ecotypes from western Algeria are characterized by a high genetic diversity and must be safeguarded as an important reservoir of genetic diversity. © 2015 Blackwell Verlag GmbH.

Anatomy and genetic diversity of two populations of Schinus terebinthifolius (Anacardiaceae) from the Tibagi River basin in Paraná, Brazil.

PubMed

Ruas, E A; Ruas, C F; Medri, P S; Medri, C; Medri, M E; Bianchini, E; Pimenta, J A; Rodrigues, L A; Ruas, P M

2011-03-29

Knowledge of the effects of flooding on plant survival is relevant for the efficiency of management and conservation programs. Schinus terebinthifolius is a tree of economic and ecological importance that is common in northeast Brazil. Flooding tolerance and genetic variation were investigated in two riparian populations of S. terebinthifolius distributed along two different ecological regions of the Tibagi River basin. Flooding tolerance was evaluated through the investigation of young plants, submitted to different flooding intensities to examine the morphological and anatomical responses to this stress. The growth rate of S. terebinthifolius was not affected by flooding, but total submersion proved to be lethal for 100% of the plants. Morphological alterations such as hypertrophied lenticels were observed in both populations and lenticel openings were significantly higher in plants from one population. Genetic analysis using DNA samples obtained from both populations showed a moderate degree of genetic variation between populations (13.7%); most of the variation was found within populations (86.3%). These results show that for conservation purposes and management of degraded areas, both populations should be preserved and could be used in programs that intend to recompose riparian forests.

Admixture into and within sub-Saharan Africa.

PubMed

Busby, George Bj; Band, Gavin; Si Le, Quang; Jallow, Muminatou; Bougama, Edith; Mangano, Valentina D; Amenga-Etego, Lucas N; Enimil, Anthony; Apinjoh, Tobias; Ndila, Carolyne M; Manjurano, Alphaxard; Nyirongo, Vysaul; Doumba, Ogobara; Rockett, Kirk A; Kwiatkowski, Dominic P; Spencer, Chris Ca

2016-06-21

Similarity between two individuals in the combination of genetic markers along their chromosomes indicates shared ancestry and can be used to identify historical connections between different population groups due to admixture. We use a genome-wide, haplotype-based, analysis to characterise the structure of genetic diversity and gene-flow in a collection of 48 sub-Saharan African groups. We show that coastal populations experienced an influx of Eurasian haplotypes over the last 7000 years, and that Eastern and Southern Niger-Congo speaking groups share ancestry with Central West Africans as a result of recent population expansions. In fact, most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of gene-flow within the last 4000 years. Our in-depth analysis provides insight into haplotype sharing across different ethno-linguistic groups and the recent movement of alleles into new environments, both of which are relevant to studies of genetic epidemiology.

Analysing the natural population growth of a large marine mammal after a depletive harvest.

PubMed

Romero, M A; Grandi, M F; Koen-Alonso, M; Svendsen, G; Ocampo Reinaldo, M; García, N A; Dans, S L; González, R; Crespo, E A

2017-07-13

An understanding of the underlying processes and comprehensive history of population growth after a harvest-driven depletion is necessary when assessing the long-term effectiveness of management and conservation strategies. The South American sea lion (SASL), Otaria flavescens, is the most conspicuous marine mammal along the South American coasts, where it has been heavily exploited. As a consequence of this exploitation, many of its populations were decimated during the early 20th century but currently show a clear recovery. The aim of this study was to assess SASL population recovery by applying a Bayesian state-space modelling framework. We were particularly interested in understanding how the population responds at low densities, how human-induced mortality interplays with natural mechanisms, and how density-dependence may regulate population growth. The observed population trajectory of SASL shows a non-linear relationship with density, recovering with a maximum increase rate of 0.055. However, 50 years after hunting cessation, the population still represents only 40% of its pre-exploitation abundance. Considering that the SASL population in this region represents approximately 72% of the species abundance within the Atlantic Ocean, the present analysis provides insights into the potential mechanisms regulating the dynamics of SASL populations across the global distributional range of the species.

Digitoxin medication and cancer; case control and internal dose-response studies

PubMed Central

Haux, Johan; Klepp, Olbjørn; Spigset, Olav; Tretli, Steinar

2001-01-01

Background Digitoxin induces apoptosis in different human malignant cell lines in vitro. In this paper we investigated if patients taking digitoxin for cardiac disease have a different cancer incidence compared to the general population. Methods Computer stored data on digitoxin concentrations in plasma from 9271 patients with cardiac disease were used to define a user population. Age and sex matched controls from the Norwegian Cancer Registry were used to calculate the number of expected cancer cases. Results The population on digitoxin showed a higher incidence of cancer compared to the control population. However, an additional analysis showed that the population on digitoxin had a general increased risk of cancer already, before the start on digitoxin. Leukemia/lymphoma were the cancer types which stood out with the highest risk in the digitoxin population before starting on digitoxin. This indicates that yet unknown risk factors exist for cardiovascular disease and lymphoproliferative cancer. An internal dose-response analysis revealed a relationship between high plasma concentration of digitoxin and a lower risk for leukemia/lymphoma and for cancer of the kidney/urinary tract. Conclusion Morbidity and mortality are high in the population on digitoxin, due to high age and cardiac disease.These factors disturb efforts to isolate an eventual anticancer effect of digitoxin in this setting. Still, the results may indicate an anticancer effect of digitoxin for leukemia/lymphoma and kidney/urinary tract cancers. Prospective clinical cancer trials have to be done to find out if digitoxin and other cardiac glycosides are useful as anticancer agents. PMID:11532201

Forensic parameters and admixture in Mestizos from five geographic regions of Mexico based on 20 autosomal STRs (Powerplex 21 system).

PubMed

Aguilar-Velázquez, J A; Martínez-Cortés, G; Inclán-Sánchez, A; Favela-Mendoza, A F; Velarde-Félix, J S; Rangel-Villalobos, H

2018-03-01

We analyzed Mestizo (admixed) population samples from different geographic regions of Mexico (n = 1283) with 20 autosomal STRs (PowerPlex® 21, Promega Corp.). Allele frequencies and forensic parameters from the Northwest, Northeast, West, Center, and Southeast regions are reported, as well as from the pooled Mexican population sample. The combined PD and PE for this 20 STR system were > 0.9999999999 and > 0.99999996593% in all five population samples, respectively. Analysis of molecular variance (AMOVA) of these Mexican population samples, plus Monterrey (Northeast) and Mexico (Center) Cities, showed low but significant differences among Mexican-Mestizos from the seven populations (Fst = 0.20%; p = 0.0000). Structure analysis showed the highest proportion of Native American ancestry in Mexico City, Center, and Southeast regions, respectively, which was in agreement with the estimated genetic distances represented in a MDS plot and a NJ tree. The best fit of population clusters (K = 4) obtained with the Structure software indicates that Mexican-Mestizos are mainly composed by European, African, and two Native American ancestries. The European and Native American ancestries displayed a contrary gradient, increasing toward the North-West and South-Southeast, respectively. These 20 autosomal STR loci improved the admixture estimation regarding previous studies with the 13 CODIS-STRs, as supported by the higher similarity with previous estimates based on genome-wide SNP. In brief, this study validates the confident use of the PowerPlex® 21 system for human identification purposes in Mestizo populations throughout the Mexican territory.

Maximization of Markers Linked in Coupling for Tetraploid Potatoes via Monoparental Haploids

PubMed Central

Bartkiewicz, Annette M.; Chilla, Friederike; Terefe-Ayana, Diro; Lübeck, Jens; Strahwald, Josef; Tacke, Eckhard; Hofferbert, Hans-Reinhard; Linde, Marcus; Debener, Thomas

2018-01-01

Haploid potato populations derived from a single tetraploid donor constitute an efficient strategy to analyze markers segregating from a single donor genotype. Analysis of marker segregation in populations derived from crosses between polysomic tetraploids is complicated by a maximum of eight segregating alleles, multiple dosages of the markers and problems related to linkage analysis of marker segregation in repulsion. Here, we present data on two monoparental haploid populations generated by prickle pollination of two tetraploid cultivars with Solanum phureja and genotyped with the 12.8 k SolCAP single nucleotide polymorphism (SNP) array. We show that in a population of monoparental haploids, the number of biallelic SNP markers segregating in linkage to loci from the tetraploid donor genotype is much larger than in putative crosses of this genotype to a diverse selection of 125 tetraploid cultivars. Although this strategy is more laborious than conventional breeding, the generation of haploid progeny for efficient marker analysis is straightforward if morphological markers and flow cytometry are utilized to select true haploid progeny. The level of introgressed fragments from S. phureja, the haploid inducer, is very low, supporting its suitability for genetic analysis. Mapping with single-dose markers allowed the analysis of quantitative trait loci (QTL) for four phenotypic traits. PMID:29868076

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.

Genetic diversity in a Poincianella pyramidalis (Tul.) L.P. Queiroz population assessed by RAPD molecular markers.

PubMed

Belarmino, K S; Rêgo, M M; Bruno, R L A; Medeiros, G D A; Andrade, A P; Rêgo, E R

2017-08-31

Poincianella pyramidalis (Tul.) L.P. Queiroz is an endemic Caatinga (Brazilian savannah biome) species that has been exploited for different purposes, although information is necessary about still existing natural populations. The objective of this study was to evaluate the genetic diversity among 20 P. pyramidalis individuals occurring in a population localized in the Caatinga biome of Paraíba State, aiming at seed collection, using RAPD markers. For the DNA extraction, young shoots of the individuals were used, and amplification was carried out using 20 primers. The obtained markers were converted to a binary matrix, from which a genetic dissimilarity matrix was built using the arithmetic complement of Jaccard's coefficient, and the dendrogram was built by the UPGMA analysis. No amplified fragment was monomorphic, resulting in 100% polymorphism of the analyzed population. The mean genetic diversity among the matrices was 63.28%, ranging from 30.9 to 97.7%. Individuals 09 and 17 showed relevant genetic proximity, and thus planting their seedlings at close sites would not be indicated. The population evaluated in this study showed high genetic diversity, originating twelve groups from the UPGMA hierarchical cluster analysis. Based on the results, individuals 09 and 17 can provide plant material for the evaluation of the physiological performance of P. pyramidalis seeds, and the set of individuals of this population has a high genetic diversity that characterizes them as adequate matrices for projects of restoration and conservation of the seed species.

Genome-Wide Landscapes of Human Local Adaptation in Asia

PubMed Central

Lu, Dongsheng; Xu, Shuhua

2013-01-01

Genetic studies of human local adaptation have been facilitated greatly by recent advances in high-throughput genotyping and sequencing technologies. However, few studies have investigated local adaptation in Asian populations on a genome-wide scale and with a high geographic resolution. In this study, taking advantage of the dense population coverage in Southeast Asia, which is the part of the world least studied in term of natural selection, we depicted genome-wide landscapes of local adaptations in 63 Asian populations representing the majority of linguistic and ethnic groups in Asia. Using genome-wide data analysis, we discovered many genes showing signs of local adaptation or natural selection. Notable examples, such as FOXQ1, MAST2, and CDH4, were found to play a role in hair follicle development and human cancer, signal transduction, and tumor repression, respectively. These showed strong indications of natural selection in Philippine Negritos, a group of aboriginal hunter-gatherers living in the Philippines. MTTP, which has associations with metabolic syndrome, body mass index, and insulin regulation, showed a strong signature of selection in Southeast Asians, including Indonesians. Functional annotation analysis revealed that genes and genetic variants underlying natural selections were generally enriched in the functional category of alternative splicing. Specifically, many genes showing significant difference with respect to allele frequency between northern and southern Asian populations were found to be associated with human height and growth and various immune pathways. In summary, this study contributes to the overall understanding of human local adaptation in Asia and has identified both known and novel signatures of natural selection in the human genome. PMID:23349834

Evaluation of Association of ADRA2A rs553668 and ACE I/D Gene Polymorphisms with Obesity Traits in the Setapak Population, Malaysia.

PubMed

Shunmugam, Vicneswari; Say, Yee-How

2016-02-01

α-adrenergic receptor 2A (ADRA2A) and angiotensin-converting enzyme (ACE) genes have been variably associated with obesity and its related phenotypes in different populations worldwide. This cross-sectional study aims to investigate the association of adrenergic receptor α2A (ADRA2A) rs553668 and angiotensin-converting enzyme (ACE) I/D single nucleotide polymorphisms (SNPs) with obesity traits (body mass index-BMI; waist-hip ratio-WHR; total body fat percentage - TBF) in a Malaysian population. Demographic and clinical variables were initially collected from 230 subjects via convenience sampling among residents and workers in Setapak, Malaysia, but in the end only 214 multi-ethnic Malaysians (99 males; 45 Malays, 116 ethnic Chinese, and 53 ethnic Indians) were available for statistical analysis. Genotyping was performed by polymerase chain reaction using DNA extracted from mouthwash samples. The overall minor allele frequencies (MAFs) for ADRA2A rs553668 and ACE I/D were 0.55 and 0.56, respectively. Allele distribution of ACE I/D was significantly associated with ethnicity and WHR class. Logistic regression analysis showed that subjects with the ACE II genotype and I allele were, respectively, 2.15 and 1.55 times more likely to be centrally obese, but when adjusted for age and ethnicity, this association was abolished. Covariate analysis controlling for age, gender, and ethnicity also showed similar results, where subjects carrying the II genotype or I allele did not have significantly higher WHR. Combinatory genotype and allele analysis for ADRA2A rs553668 and ACE I/D showed that subjects with both ADRA2A rs553668 GG and ACE I/D II genotypes had significant lowest WHR compared to other genotype combinations. The ACE II genotype might be a protective factor against central adiposity risk among the Malaysian population when in combination with the ADRA2A rs553668 GG genotype.

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

PubMed Central

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

2017-01-01

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

[Evaluation of Molecular Genetic Diversity of Wild Apple Malus sieversii Populations from Zailiysky Alatau by Microsatellite Markers].

PubMed

Omasheva, M E; Chekalin, S V; Galiakparov, N N

2015-07-01

The territory of Kazakhstan is part of the distribution range of Malus sieversii, which is one of the ancestors of cultivated apple tree varieties. The collected samples of Sievers apple leaves from five populations growing in the Zailiysky Alatau region served as a source not only for the creation of a bank of genomic DNA but also for determination ofthe wild apple genetic polymorphism. The seven microsatellite markers used in this study revealed 86 alleles with different frequencies, as well as the characteristic pools of rare alleles for each of the populations. Molecular genetic analysis showed a high level of genetic diversity (H(o) = 0.704; PIC = 0.752; I = 1.617). Moreover, interpopulation variability accounted only for 7.5% of total variability, confirming the genetic closeness of the populations examined. Based on phylogenetic analysis, it was demonstrated that the Bel'bulak and Almaty Reserve populations were closest to each other, while the most distant were the Ketmen and Great Almaty gorge populations, which suggests the dependence of genetic distance on the geographical.

Latitudinal Gradient in Otolith Shape among Local Populations of Atlantic Herring (Clupea harengus L.) in Norway

PubMed Central

Libungan, Lísa Anne; Slotte, Aril; Husebø, Åse; Godiksen, Jane A.; Pálsson, Snæbjörn

2015-01-01

Otolith shape analysis of Atlantic herring (Clupea harengus) in Norwegian waters shows significant differentiation among fjords and a latitudinal gradient along the coast where neighbouring populations are more similar to each other than to those sampled at larger distances. The otolith shape was obtained using quantitative shape analysis, the outlines were transformed with Wavelet and analysed with multivariate methods. The observed morphological differences are likely to reflect environmental differences but indicate low dispersal among the local herring populations. Otolith shape variation suggests also limited exchange between the local populations and their oceanic counterparts, which could be due to differences in spawning behaviour. Herring from the most northerly location (69°N) in Balsfjord, which is genetically more similar to Pacific herring (Clupea pallasii), differed in otolith shape from all the other populations. Our results suggest that the semi-enclosed systems, where the local populations live and breed, are efficient barriers for dispersal. Otolith shape can thus serve as a marker to identify the origin of herring along the coast of Norway. PMID:26101885

Influence of harvesting pressure on demographic tactics: Implications for wildlife management

USGS Publications Warehouse

Servanty, S.; Gaillard, J.-M.; Ronchi, F.; Focardi, S.; Baubet, E.; Gimenez, O.

2011-01-01

Demographic tactics within animal populations are shaped by selective pressures. Exploitation exerts additional pressures so that differing demographic tactics might be expected among populations with differences in levels of exploitation. Yet little has been done so far to assess the possible consequences of exploitation on the demographic tactics of mammals, even though such information could influence the choice of effective management strategies. Compared with similar-sized ungulate species, wild boar Sus scrofa has high reproductive capabilities, which complicates population management. Using a perturbation analysis, we investigated how population growth rates (??) and critical life-history stages differed between two wild boar populations monitored for several years, one of which was heavily harvested and the other lightly harvested. Asymptotic ?? was 1??242 in the lightly hunted population and 1??115 in the heavily hunted population, while the ratio between the elasticity of adult survival and juvenile survival was 2??63 and 1??27, respectively. A comparative analysis including 21 other ungulate species showed that the elasticity ratio in the heavily hunted population was the lowest ever observed. Compared with expected generation times of similar-sized ungulates (more than 6years), wild boar has a fast life-history speed, especially when facing high hunting pressure. This is well illustrated by our results, where generation times were 3??6years in the lightly hunted population and only 2??3years in the heavily hunted population. High human-induced mortality combined with non-limiting food resources accounted for the accelerated life history of the hunted population because of earlier reproduction. Synthesis and applications. For wild boar, we show that when a population is facing a high hunting pressure, increasing the mortality in only one age-class (e.g. adults or juveniles) may not allow managers to limit population growth. We suggest that simulations of management strategies based on context-specific demographic models are useful for selecting interventions for population control. This type of approach allows the assessment of population response to exploitation by considering a range of plausible scenarios, improving the chance of selecting appropriate management actions. ?? 2011 The Authors. Journal of Applied Ecology ?? 2011 British Ecological Society.

Interplay of secondary structures and side-chain contacts in the denatured state of BBA1

NASA Astrophysics Data System (ADS)

Wen, Edward Z.; Luo, Ray

2004-08-01

The denatured state of a miniprotein BBA1 is studied under the native condition with the AMBER/Poisson-Boltzmann energy model and with the self-guided enhanced sampling technique. Forty independent trajectories are collected to sample the highly diversified denatured structures. Our simulation data show that the denatured BBA1 contains high percentage of native helix and native turn, but low percentage of native hairpin. Conditional population analysis indicates that the native helix formation and the native hairpin formation are not cooperative in the denatured state. Side-chain analysis shows that the native hydrophobic contacts are more preferred than the non-native hydrophobic contacts in the denatured BBA1. In contrast, the salt-bridge contacts are more or less nonspecific even if their populations are higher than those of hydrophobic contacts. Analysis of the trajectories shows that the native helix mostly initiates near the N terminus and propagates to the C terminus, and mostly forms from 310-helix/turn to α helix. The same analysis shows that the native turn is important but not necessary in its formation in the denatured BBA1. In addition, the formations of the two strands in the native hairpin are rather asymmetric, demonstrating the likely influence of the protein environment. Energetic analysis shows that the native helix formation is largely driven by electrostatic interactions in denatured BBA1. Further, the native helix formation is associated with the breakup of non-native salt-bridge contacts and the accumulation of native salt-bridge contacts. However, the native hydrophobic contacts only show a small increase upon the native helix formation while the non-native hydrophobic contacts stay essentially the same, different from the evolution of hydrophobic contacts observed in an isolated helix folding.

Molecular reclassification of Crohn's disease: a cautionary note on population stratification.

PubMed

Maus, Bärbel; Jung, Camille; Mahachie John, Jestinah M; Hugot, Jean-Pierre; Génin, Emmanuelle; Van Steen, Kristel

2013-01-01

Complex human diseases commonly differ in their phenotypic characteristics, e.g., Crohn's disease (CD) patients are heterogeneous with regard to disease location and disease extent. The genetic susceptibility to Crohn's disease is widely acknowledged and has been demonstrated by identification of over 100 CD associated genetic loci. However, relating CD subphenotypes to disease susceptible loci has proven to be a difficult task. In this paper we discuss the use of cluster analysis on genetic markers to identify genetic-based subgroups while taking into account possible confounding by population stratification. We show that it is highly relevant to consider the confounding nature of population stratification in order to avoid that detected clusters are strongly related to population groups instead of disease-specific groups. Therefore, we explain the use of principal components to correct for population stratification while clustering affected individuals into genetic-based subgroups. The principal components are obtained using 30 ancestry informative markers (AIM), and the first two PCs are determined to discriminate between continental origins of the affected individuals. Genotypes on 51 CD associated single nucleotide polymorphisms (SNPs) are used to perform latent class analysis, hierarchical and Partitioning Around Medoids (PAM) cluster analysis within a sample of affected individuals with and without the use of principal components to adjust for population stratification. It is seen that without correction for population stratification clusters seem to be influenced by population stratification while with correction clusters are unrelated to continental origin of individuals.

Molecular Reclassification of Crohn’s Disease: A Cautionary Note on Population Stratification

PubMed Central

Maus, Bärbel; Jung, Camille; Mahachie John, Jestinah M.; Hugot, Jean-Pierre; Génin, Emmanuelle; Van Steen, Kristel

2013-01-01

Complex human diseases commonly differ in their phenotypic characteristics, e.g., Crohn’s disease (CD) patients are heterogeneous with regard to disease location and disease extent. The genetic susceptibility to Crohn’s disease is widely acknowledged and has been demonstrated by identification of over 100 CD associated genetic loci. However, relating CD subphenotypes to disease susceptible loci has proven to be a difficult task. In this paper we discuss the use of cluster analysis on genetic markers to identify genetic-based subgroups while taking into account possible confounding by population stratification. We show that it is highly relevant to consider the confounding nature of population stratification in order to avoid that detected clusters are strongly related to population groups instead of disease-specific groups. Therefore, we explain the use of principal components to correct for population stratification while clustering affected individuals into genetic-based subgroups. The principal components are obtained using 30 ancestry informative markers (AIM), and the first two PCs are determined to discriminate between continental origins of the affected individuals. Genotypes on 51 CD associated single nucleotide polymorphisms (SNPs) are used to perform latent class analysis, hierarchical and Partitioning Around Medoids (PAM) cluster analysis within a sample of affected individuals with and without the use of principal components to adjust for population stratification. It is seen that without correction for population stratification clusters seem to be influenced by population stratification while with correction clusters are unrelated to continental origin of individuals. PMID:24147066

Measurement of the distribution of non-structural carbohydrate composition in onion populations by a high-throughput microplate enzymatic assay.

PubMed

Revanna, Roopashree; Turnbull, Matthew H; Shaw, Martin L; Wright, Kathryn M; Butler, Ruth C; Jameson, Paula E; McCallum, John A

2013-08-15

Non-structural carbohydrate (NSC; glucose, fructose, sucrose and fructan) composition of onions (Allium cepa L.) varies widely and is a key determinant of market usage. To analyse the physiology and genetics of onion carbohydrate metabolism and to enable selective breeding, an inexpensive, reliable and practicable sugar assay is required to phenotype large numbers of samples. A rapid, reliable and cost-effective microplate-based assay was developed for NSC analysis in onions and used to characterise variation in tissue hexose, sucrose and fructan content in open-pollinated breeding populations and in mapping populations developed from a wide onion cross. Sucrose measured in microplates employing maltase as a hydrolytic enzyme was in agreement with HPLC-PAD results. The method revealed significant variation in bulb fructan content within open-pollinated 'Pukekohe Longkeeper' breeding populations over a threefold range. Very wide segregation from 80 to 600 g kg(-1) in fructan content was observed in bulbs of F2 genetic mapping populations from the wide onion cross 'Nasik Red × CUDH2150'. The microplate enzymatic assay is a reliable and practicable method for onion sugar analysis for genetics, breeding and food technology. Open-pollinated onion populations may harbour extensive within-population variability in carbohydrate content, which may be quantified and exploited using this method. The phenotypic data obtained from genetic mapping populations show that the method is well suited to detailed genetic and physiological analysis. © 2013 Society of Chemical Industry.

Construction of population-specific Indian MRI brain template: Morphometric comparison with Chinese and Caucasian templates.

PubMed

Bhalerao, Gaurav Vivek; Parlikar, Rujuta; Agrawal, Rimjhim; Shivakumar, Venkataram; Kalmady, Sunil V; Rao, Naren P; Agarwal, Sri Mahavir; Narayanaswamy, Janardhanan C; Reddy, Y C Janardhan; Venkatasubramanian, Ganesan

2018-06-01

Spatial normalization of brain MR images is highly dependent on the choice of target brain template. Morphological differences caused by factors like genetic and environmental exposures, generates a necessity to construct population specific brain templates. Brain image analysis performed using brain templates from Caucasian population may not be appropriate for non-Caucasian population. In this study, our objective was to construct an Indian brain template from a large population (N = 157 subjects) and compare the morphometric parameters of this template with that of Chinese-56 and MNI-152 templates. In addition, using an independent MRI data of 15 Indian subjects, we also evaluated the potential registration accuracy differences using these three templates. Indian brain template was constructed using iterative routines as per established procedures. We compared our Indian template with standard MNI-152 template and Chinese template by measuring global brain features. We also examined accuracy of registration by aligning 15 new Indian brains to Indian, Chinese and MNI templates. Furthermore, we supported our measurement protocol with inter-rater and intra-rater reliability analysis. Our results showed that there were significant differences in global brain features of Indian template in comparison with Chinese and MNI brain templates. The results of registration accuracy analysis revealed that fewer deformations are required when Indian brains are registered to Indian template as compared to Chinese and MNI templates. This study concludes that population specific Indian template is likely to be more appropriate for structural and functional image analysis of Indian population. Copyright © 2018 Elsevier B.V. All rights reserved.

Age-Sex Structure of the Population and Demographic Processes in Environmentally Challenged Mining Region (on the example of Kemerovo region)

NASA Astrophysics Data System (ADS)

Leshukov, Timofey; Brel, Olga; Zaytseva, Anna; Kaizer, Philipp; Makarov, Kirill

2017-11-01

The main goal of the article is to show the influence of the age-sex structure of the population on the basic demographic processes in the Kemerovo region. During research the authors have established correlation links between the sex-age structure of the population and the main demographic indicators (birth and mortality rate, morbidity rate, migration and others) based on the analysis of official statistical data. The direct influence of internal and external factors on the age-sex structure of the population is revealed. Conclusions about the impact of demographic processes on the sex-age structure of the population of the Kemerovo region are drawn.

Population structure in the Island of Ugljan--demographic processes and marital migration.

PubMed

Malnar, Ana

2008-12-01

This research on the basic demographic processes and marital migrations of the population on Ugljan Island in the period from 1857 to 2001 was conducted within the context of the long-term anthropological research of the population structure of Croatia's islands. The analysis was based on the study of the origin of 5 244 married couples from Preko, Kali, Kukljica, Lukoran and Ugljan and carried out using data preserved in the old Registers of Marriages. The results show a high level of endogamy and reproductive isolation of the population in all the villages and they also confirm the importance of using historical and demographic sources for researching the shaping of population structures.

Application of Semiparametric Spline Regression Model in Analyzing Factors that In uence Population Density in Central Java

NASA Astrophysics Data System (ADS)

Sumantari, Y. D.; Slamet, I.; Sugiyanto

2017-06-01

Semiparametric regression is a statistical analysis method that consists of parametric and nonparametric regression. There are various approach techniques in nonparametric regression. One of the approach techniques is spline. Central Java is one of the most densely populated province in Indonesia. Population density in this province can be modeled by semiparametric regression because it consists of parametric and nonparametric component. Therefore, the purpose of this paper is to determine the factors that in uence population density in Central Java using the semiparametric spline regression model. The result shows that the factors which in uence population density in Central Java is Family Planning (FP) active participants and district minimum wage.

Genetic diversity of Leishmania tropica strains isolated from clinical forms of cutaneous leishmaniasis in rural districts of Herat province, Western Afghanistan, based on ITS1-rDNA.

PubMed

Fakhar, Mahdi; Pazoki Ghohe, Hossein; Rasooli, Sayed Abobakar; Karamian, Mehdi; Mohib, Abdul Satar; Ziaei Hezarjaribi, Hajar; Pagheh, Abdol Sattar; Ghatee, Mohammad Amin

2016-07-01

Despite the high incidence of cutaneous leishmaniasis (CL) in Afghanistan, there is a little information concerning epidemiological status of the disease and phylogenetic relationship and population structure of causative agents. This study was conducted to determine the prevalence and distribution of CL cases and investigate the Leishmania tropica population structure in rural districts of Heart province in the West of Afghanistan in comparison to neighboring foci. Overall, 4189 clinically suspected CL cases from 177 villages (including 12 districts) in Herat province were enrolled in the referral laboratory of WHO sub-office in Herat city from January 2012 to December 2013. 3861 cases were confirmed as CL by microscopic examination of Giemsa-stained slides. ITS1 PCR-RFLP analysis showed dominance of L. tropica (more than 98%) among 127 randomly chosen samples. Analysis of the ITS1 sequences revealed 4 sequence types among the 21 L. tropica isolates. Comparison of sequence types from Herat rural districts with the representatives of L. tropica from Iran, India, and Herat city showed two main population groups (cluster A and B). All isolates from Herat province, India and Southeast, East, and Central Iran were found exclusively in cluster A. The close proximity of West Afghanistan focus and Birjand county as the capital of Southern Khorasan province in East Iran can explain relatively equal to the genetic composition of L. tropica in these two neighboring regions. In addition, two populations were found among L. tropica isolates from Herat rural districts. Main population showed more similarity to some isolates from Birjand county in East Iran while minor population probably originated from the Southeast and East Iranian L. tropica. Recent study provided valuable information concerning the population structure of L. tropica and epidemiology of ACL in the West of Afghanistan, which could be the basis for molecular epidemiology studies in other regions of Afghanistan. Copyright © 2016 Elsevier B.V. All rights reserved.

Comparison of Y-STR polymorphisms in three different Slovak population groups.

PubMed

Petrejcíková, Eva; Siváková, Daniela; Soták, Miroslav; Bernasovská, Jarmila; Bernasovský, Ivan; Rebała, Krzysztof; Boronová, Iveta; Bôziková, Alexandra; Sovicová, Adriana; Gabriková, Dana; Maceková, Sona; Svícková, Petra; Carnogurská, Jana

2010-01-01

Eleven Y-chromosomal microsatellite loci included in the Powerplex Y multiplex kit were analyzed in different Slovak population samples: Habans (n = 39), Romanies (n = 100) and Slovak Caucasian (n = 148) individuals, respectively, from different regions of Slovakia. The analysis of molecular variance between populations indicated that 89.27% of the haplotypic variations were found within populations and only 10.72% between populations (Fst = 0.1027; p = 0.0000). The haplotype diversities were ranging from 0.9258 to 0.9978, and indicated a high potential for differentiating between male individuals. The study reports differences in allele frequencies between the Romanies, Habans and Slovak Caucasian men. Selected loci showed that both the Romany and Haban population belonged to endogamous and relatively small founder population groups, which developed in relatively reproductive isolated groups surrounded by the Slovak Caucasian population.

Long-term dynamics of natural populations of Schistosoma mansoni among Rattus rattus in patchy environment.

PubMed

Théron, A; Pointier, J P; Morand, S; Imbert-Establet, D; Borel, G

1992-04-01

Dynamics of natural populations of Schistosoma mansoni were studied during 8 consecutive years among Rattus rattus populations from 8 transmission sites of the marshy forest focus of Guadeloupe (French West Indies). The schistosome population is over-dispersed (k = 0.119) within the murine hosts and ecological factors linked to the patchy environment may be responsible for such aggregated distribution. Analysis of the spatio-temporal variations in prevalences, intensities and abundances showed limited variations of the infection during the 8 years at the level of the whole parasite population but great spatial heterogeneity at the level of local schistosome populations. Inter-populational genetic variability linked to the degree of adaptation of this human parasite to the murine host may explain differences in transmission dynamics between the local populations of S. mansoni.

[Spatial structure analysis and distribution simulation of Therioaphis trifolii population based on geostatistics and GIS].

PubMed

Zhang, Rong; Leng, Yun-fa; Zhu, Meng-meng; Wang, Fang

2007-11-01

Based on geographic information system and geostatistics, the spatial structure of Therioaphis trifolii population of different periods in Yuanzhou district of Guyuan City, the southern Ningxia Province, was analyzed. The spatial distribution of Therioaphis trifolii population was also simulated by ordinary Kriging interpretation. The results showed that Therioaphis trifolii population of different periods was correlated spatially in the study area. The semivariograms of Therioaphis trifolii could be described by exponential model, indicating an aggregated spatial arrangement. The spatial variance varied from 34.13%-48.77%, and the range varied from 8.751-12.049 km. The degree and direction of aggregation showed that the trend was increased gradually from southwest to northeast. The dynamic change of Therioaphis trifolii population in different periods could be analyzed intuitively on the simulated maps of the spatial distribution from the two aspects of time and space, The occurrence position and degree of Therioaphis trifolii to a state of certain time could be determined easily.

Changes in muscle fiber conduction velocity indicate recruitment of distinct motor unit populations.

PubMed

Houtman, C J; Stegeman, D F; Van Dijk, J P; Zwarts, M J

2003-09-01

To obtain more insight into the changes in mean muscle fiber conduction velocity (MFCV) during sustained isometric exercise at relatively low contraction levels, we performed an in-depth study of the human tibialis anterior muscle by using multichannel surface electromyogram. The results show an increase in MFCV after an initial decrease of MFCV at 30 or 40% maximum voluntary contraction in all of the five subjects studied. With a peak velocity analysis, we calculated the distribution of conduction velocities of action potentials in the bipolar electromyogram signal. It shows two populations of peak velocities occurring simultaneously halfway through the exercise. The MFCV pattern implies the recruitment of two different populations of motor units. Because of the lowering of MFCV of the first activated population of motor units, the newly recruited second population of motor units becomes visible. It is most likely that the MFCV pattern can be ascribed to the fatiguing of already recruited predominantly type I motor units, followed by the recruitment of fresh, predominantly type II, motor units.

Temporal Genetic Dynamics of an Invasive Species, Frankliniella occidentalis (Pergande), in an Early Phase of Establishment.

PubMed

Yang, Xian-Ming; Lou, Heng; Sun, Jing-Tao; Zhu, Yi-Ming; Xue, Xiao-Feng; Hong, Xiao-Yue

2015-07-03

Many species can successfully colonize new areas despite their propagules having low genetic variation. We assessed whether the decreased genetic diversity could result in temporal fluctuations of genetic parameters of the new populations of an invasive species, western flower thrips, Frankliniella occidentalis, using mitochondrial and microsatellite markers. This study was conducted in eight localities from four climate regions in China, where F. occidentalis was introduced in the year 2000 and had lower genetic diversity than its native populations. We also tested the level of genetic differentiation in these introduced populations. The genetic diversity of the samples at different years in the same locality was not significantly different from each other in most localities. FST and STRUCTURE analysis also showed that most temporal population comparisons from the same sites were not significantly differentiated. Our results showed that the invasive populations of F. occidentalis in China can maintain temporal stability in genetic composition at an early phase of establishment despite having lower genetic diversity than in their native range.

Microgeographic Genetic Variation of the Malaria Vector Anopheles darlingi Root (Diptera: Culicidae) from Córdoba and Antioquia, Colombia

PubMed Central

Gutiérrez, Lina A.; Gómez, Giovan F.; González, John J.; Castro, Martha I.; Luckhart, Shirley; Conn, Jan E.; Correa, Margarita M.

2010-01-01

Anopheles darlingi is an important vector of Plasmodium spp. in several malaria-endemic regions of Colombia. This study was conducted to test genetic variation of An. darlingi at a microgeographic scale (approximately 100 km) from localities in Córdoba and Antioquia states, in western Colombia, to better understand the potential contribution of population genetics to local malaria control programs. Microsatellite loci: nuclear white and cytochrome oxidase subunit I (COI) gene sequences were analyzed. The northern white gene lineage was exclusively distributed in Córdoba and Antioquia and shared COI haplotypes were highly represented in mosquitoes from both states. COI analyses showed these An. darlingi are genetically closer to Central American populations than southern South American populations. Overall microsatellites and COI analysis showed low to moderate genetic differentiation among populations in northwestern Colombia. Given the existence of high gene flow between An. darlingi populations of Córdoba and Antioquia, integrated vector control strategies could be developed in this region of Colombia. PMID:20595475

Molecular characterization of Belgian pseudorabies virus isolates from domestic swine and wild boar.

PubMed

Verpoest, Sara; Cay, Ann Brigitte; De Regge, Nick

2014-08-06

Aujeszky's disease is an economically important disease in domestic swine caused by suid herpesvirus 1, also called pseudorabies virus (PRV). In several European countries, including Belgium, the virus has successfully been eradicated from the domestic swine population. The presence of PRV in the wild boar population however poses a risk for possible reintroduction of the virus into the domestic pig population. It is therefore important to assess the genetic relatedness between circulating strains and possible epidemiological links. In this study, nine historical Belgian domestic swine isolates that circulated before 1990 and five recent wild boar isolates obtained since 2006 from Belgium and the Grand Duchy of Luxembourg were genetically characterized by restriction fragment length polymorphism (RFLP) analysis and phylogenetic analysis. While all wild boar isolates were characterized as type I RFLP genotypes, the RFLP patterns of the domestic swine isolates suggest that a shift from genotype I to genotype II might have occurred in the 1980s in the domestic population. By phylogenetic analysis, Belgian wild boar isolates belonging to both clade A and B were observed, while all domestic swine isolates clustered within clade A. The joint phylogenetic analysis of both wild boar and domestic swine strains showed that some isolates with identical sequences were present within both populations, raising the question whether these strains represent an increased risk for reintroduction of the virus into the domestic population. Copyright © 2014 Elsevier B.V. All rights reserved.

Development of a scale to assess cancer stigma in the non-patient population.

PubMed

Marlow, Laura A V; Wardle, Jane

2014-04-23

Illness-related stigma has attracted considerable research interest, but few studies have specifically examined stigmatisation of cancer in the non-patient population. The present study developed and validated a Cancer Stigma Scale (CASS) for use in the general population. An item pool was developed on the basis of previous research into illness-related stigma in the general population and patients with cancer. Two studies were carried out. The first study used Exploratory factor analysis to explore the structure of items in a sample of 462 postgraduate students recruited through a London university. The second study used Confirmatory factor analysis to confirm the structure among 238 adults recruited through an online market research panel. Internal reliability, test-retest reliability and construct validity were also assessed. Exploratory factor analysis suggested six subscales, representing: Awkwardness, Severity, Avoidance, Policy Opposition, Personal Responsibility and Financial Discrimination. Confirmatory factor analysis confirmed this structure with a 25-item scale. All subscales showed adequate to good internal and test-retest reliability in both samples. Construct validity was also good, with mean scores for each subscale varying in the expected directions by age, gender, experience of cancer, awareness of lifestyle risk factors for cancer, and social desirability. Means for the subscales were consistent across the two samples. These findings highlight the complexity of cancer stigma and provide the Cancer Stigma Scale (CASS) which can be used to compare populations, types of cancer and evaluate the effects of interventions designed to reduce cancer stigma in non-patient populations.

Microsatellite DNA Analysis Revealed a Drastic Genetic Change of Plasmodium vivax Population in the Republic of Korea During 2002 and 2003

PubMed Central

Iwagami, Moritoshi; Hwang, Seung-Young; Kim, So-Hee; Park, So-Jung; Lee, Ga-Young; Matsumoto-Takahashi, Emilie Louise Akiko; Kho, Weon-Gyu; Kano, Shigeyuki

2013-01-01

Background Vivax malaria was successfully eliminated in the Republic of Korea (South Korea) in the late 1970s, but it was found to have re-emerged from 1993. In order to control malaria and evaluate the effectiveness of malaria controls, it is important to develop a spatiotemporal understanding of the genetic structure of the parasite population. Here, we estimated the population structure and temporal dynamics of the transmission of Plasmodium vivax in South Korea by analyzing microsatellite DNA markers of the parasite. Methodology/Principal Findings We analyzed 14 microsatellite DNA loci of the P. vivax genome from 163 South Korean isolates collected from 1994 to 2008. Allelic data were used to analyze linkage disequilibrium (LD), genetic differentiation and population structure, in order to make a detailed estimate of temporal change in the parasite population. The LD analysis showed a gradual decrease in LD levels, while the levels of genetic differentiation between successive years and analysis of the population structure based on the Bayesian approach suggested that a drastic genetic change occurred in the South Korean population during 2002 and 2003. Conclusions/Significance Although relapse and asymptomatic parasite carriage might influence the population structure to some extent, our results suggested the continual introduction of P. vivax into South Korea through other parasite population sources. One possible source, particularly during 2002 and 2003, is North Korea. Molecular epidemiology using microsatellite DNA of the P. vivax population is effective for assessing the population structure and temporal dynamics of parasite transmission; information that can assist in the elimination of vivax malaria in endemic areas. PMID:24205429

Stochastic population dynamics of a montane ground-dwelling squirrel.

PubMed

Hostetler, Jeffrey A; Kneip, Eva; Van Vuren, Dirk H; Oli, Madan K

2012-01-01

Understanding the causes and consequences of population fluctuations is a central goal of ecology. We used demographic data from a long-term (1990-2008) study and matrix population models to investigate factors and processes influencing the dynamics and persistence of a golden-mantled ground squirrel (Callospermophilus lateralis) population, inhabiting a dynamic subalpine habitat in Colorado, USA. The overall deterministic population growth rate λ was 0.94±SE 0.05 but it varied widely over time, ranging from 0.45±0.09 in 2006 to 1.50±0.12 in 2003, and was below replacement (λ<1) for 9 out of 18 years. The stochastic population growth rate λ(s) was 0.92, suggesting a declining population; however, the 95% CI on λ(s) included 1.0 (0.52-1.60). Stochastic elasticity analysis showed that survival of adult females, followed by survival of juvenile females and litter size, were potentially the most influential vital rates; analysis of life table response experiments revealed that the same three life history variables made the largest contributions to year-to year changes in λ. Population viability analysis revealed that, when the influences of density dependence and immigration were not considered, the population had a high (close to 1.0 in 50 years) probability of extinction. However, probability of extinction declined to as low as zero when density dependence and immigration were considered. Destabilizing effects of stochastic forces were counteracted by regulating effects of density dependence and rescue effects of immigration, which allowed our study population to bounce back from low densities and prevented extinction. These results suggest that dynamics and persistence of our study population are determined synergistically by density-dependence, stochastic forces, and immigration.

Stochastic Population Dynamics of a Montane Ground-Dwelling Squirrel

PubMed Central

Hostetler, Jeffrey A.; Kneip, Eva; Van Vuren, Dirk H.; Oli, Madan K.

2012-01-01

Understanding the causes and consequences of population fluctuations is a central goal of ecology. We used demographic data from a long-term (1990–2008) study and matrix population models to investigate factors and processes influencing the dynamics and persistence of a golden-mantled ground squirrel (Callospermophilus lateralis) population, inhabiting a dynamic subalpine habitat in Colorado, USA. The overall deterministic population growth rate λ was 0.94±SE 0.05 but it varied widely over time, ranging from 0.45±0.09 in 2006 to 1.50±0.12 in 2003, and was below replacement (λ<1) for 9 out of 18 years. The stochastic population growth rate λs was 0.92, suggesting a declining population; however, the 95% CI on λs included 1.0 (0.52–1.60). Stochastic elasticity analysis showed that survival of adult females, followed by survival of juvenile females and litter size, were potentially the most influential vital rates; analysis of life table response experiments revealed that the same three life history variables made the largest contributions to year-to year changes in λ. Population viability analysis revealed that, when the influences of density dependence and immigration were not considered, the population had a high (close to 1.0 in 50 years) probability of extinction. However, probability of extinction declined to as low as zero when density dependence and immigration were considered. Destabilizing effects of stochastic forces were counteracted by regulating effects of density dependence and rescue effects of immigration, which allowed our study population to bounce back from low densities and prevented extinction. These results suggest that dynamics and persistence of our study population are determined synergistically by density-dependence, stochastic forces, and immigration. PMID:22479616

Cost-effectiveness of population based BRCA testing with varying Ashkenazi Jewish ancestry.

PubMed

Manchanda, Ranjit; Patel, Shreeya; Antoniou, Antonis C; Levy-Lahad, Ephrat; Turnbull, Clare; Evans, D Gareth; Hopper, John L; Macinnis, Robert J; Menon, Usha; Jacobs, Ian; Legood, Rosa

2017-11-01

Population-based BRCA1/BRCA2 testing has been found to be cost-effective compared with family history-based testing in Ashkenazi-Jewish women were >30 years old with 4 Ashkenazi-Jewish grandparents. However, individuals may have 1, 2, or 3 Ashkenazi-Jewish grandparents, and cost-effectiveness data are lacking at these lower BRCA prevalence estimates. We present an updated cost-effectiveness analysis of population BRCA1/BRCA2 testing for women with 1, 2, and 3 Ashkenazi-Jewish grandparents. Decision analysis model. Lifetime costs and effects of population and family history-based testing were compared with the use of a decision analysis model. 56% BRCA carriers are missed by family history criteria alone. Analyses were conducted for United Kingdom and United States populations. Model parameters were obtained from the Genetic Cancer Prediction through Population Screening trial and published literature. Model parameters and BRCA population prevalence for individuals with 3, 2, or 1 Ashkenazi-Jewish grandparent were adjusted for the relative frequency of BRCA mutations in the Ashkenazi-Jewish and general populations. Incremental cost-effectiveness ratios were calculated for all Ashkenazi-Jewish grandparent scenarios. Costs, along with outcomes, were discounted at 3.5%. The time horizon of the analysis is "life-time," and perspective is "payer." Probabilistic sensitivity analysis evaluated model uncertainty. Population testing for BRCA mutations is cost-saving in Ashkenazi-Jewish women with 2, 3, or 4 grandparents (22-33 days life-gained) in the United Kingdom and 1, 2, 3, or 4 grandparents (12-26 days life-gained) in the United States populations, respectively. It is also extremely cost-effective in women in the United Kingdom with just 1 Ashkenazi-Jewish grandparent with an incremental cost-effectiveness ratio of £863 per quality-adjusted life-years and 15 days life gained. Results show that population-testing remains cost-effective at the £20,000-30000 per quality-adjusted life-years and $100,000 per quality-adjusted life-years willingness-to-pay thresholds for all 4 Ashkenazi-Jewish grandparent scenarios, with ≥95% simulations found to be cost-effective on probabilistic sensitivity analysis. Population-testing remains cost-effective in the absence of reduction in breast cancer risk from oophorectomy and at lower risk-reducing mastectomy (13%) or risk-reducing salpingo-oophorectomy (20%) rates. Population testing for BRCA mutations with varying levels of Ashkenazi-Jewish ancestry is cost-effective in the United Kingdom and the United States. These results support population testing in Ashkenazi-Jewish women with 1-4 Ashkenazi-Jewish grandparent ancestry. Copyright © 2017 Elsevier Inc. All rights reserved.

Detection of damage on single- or double-stranded DNA in a population exposed to arsenic in drinking water.

PubMed

Jiménez-Villarreal, J; Rivas-Armendariz, D I; Pineda-Belmontes, C P; Betancourt-Martínez, N D; Macías-Corral, M A; Guerra-Alanis, A J; Niño-Castañeda, M S; Morán-Martínez, J

2017-05-18

Different studies have suggested an association between arsenic (As) exposure and damage to single-stranded DNA by reactive oxygen species derived from the biotransformation of arsenic. The single strand damages are converted to double strand damage upon interaction with ultraviolet radiation. Analysis of genomic integrity is important for assessing the genotoxicity caused by environmental pollutants. In this study, we compared the concentration of As in drinking water, nutritional status, lifestyle variables, and the level of genotoxicity in an exposed population and a control group. Arsenic content of water was determined using a portable Arsenator ® kit. DNA fragmentation was determined using the two-tailed comet assay. Our results show that the exposed population had low nutritional consumption compared to the control group (P < 0.05). Furthermore, the water consumed by the exposed group had As concentration of 14.3 ± 8.4 mg/L, whereas the As level in the water consumed by the control group was 7.7 ± 3.5 mg/L. Analysis shows that the frequency of double strand break (DSB) fragmentation was higher in the population exposed to higher levels of As compared to that of the control group. These results suggest a possible association between the concentration of As in drinking water and lifestyle variables, with increasing fragmentation of DSBs in the exposed population.

Essential Oil Composition of Pinus peuce Griseb. Needles and Twigs from Two National Parks of Kosovo

PubMed Central

Hajdari, Avni; Mustafa, Behxhet; Selimi, Hyrmete; Veselaj, Zeqir; Breznica, Pranvera; Novak, Johannes

2016-01-01

The principal aim of this study was to analyze the chemical composition and qualitative and quantitative variability of essential oils obtained from seven naturally grown populations of the Pinus peuce Grisebach, Pinaceae in Kosovo. Plant materials were collected from three populations in the Sharri National Park and from four other populations in the Bjeshkët e Nemuna National Park, in Kosovo. Essential oils were obtained by steam distillation and analyzed by GC-FID (Gas Chromatography-Flame Ionization Detection) and GC-MS (Gas Chromatography-Mass Spectrometry). The results showed that the yield of essential oils (v/w dry weight) varied depending on the origin of population and the plant organs and ranged from 0.7 to 3.3%. In total, 51 compounds were identified. The main compounds were α-pinene (needles: 21.6–34.9%; twigs: 11.0–24%), β-phellandrene (needles: 4.1–27.7; twigs: 29.0–49.8%), and β-pinene (needles: 10.0–16.1; twigs: 6.9–20.7%). HCA (Hierarchical Cluster Analysis) and PCA (Principal Component Analyses) were used to assess geographical variations in essential oil composition. Statistical analysis showed that the analyzed populations are grouped in three main clusters which seem to reflect microclimatic conditions on the chemical composition of the essential oils. PMID:27579344

Correlation of human papilloma virus with oral squamous cell carcinoma in Chinese population.

PubMed

Zhou, Jingping; Tao, Detao; Tang, Daofang; Gao, Zhenlin

2015-01-01

Previous studies indicated that oral squamous cell carcinomas (OSCC) might be related to human papilloma virus (HPV) infection. However, the relationship between OSCC in a Chinese population and oral HPV infection is still unclear. In this study, we evaluate the relationship of OSCC with HPV infection in a Chinese population via a meta-analysis. The reports on HPV and OSCC in a Chinese population published between January, 1994, and October, 2015 were retrieved via CNKI/WANFANG/pubmed databases. According to the inclusion criteria, we selected 26 eligible case-control studies. After testing the heterogeneity of the studies by the Cochran Q test, the meta-analyses for HPV and HPV16 were performed using the random effects model. Quantitative meta-analyses showed that, compared with normal oral mucosa the combined odds ratio of OSCC with HPV infection were 1.98 (95% CI: 1.34-2.92). The test for overall effect showed that the P value was less than 0.05 (Z = 3.46). Forest plot analyses were seen in Figures 2 and 3. Publication bias and bias risk analysis using RevMan 5.3 software were measured indicators of the graphics of the basic symmetry. High incidences of HPV infection were found in the samples of Chinese OSCC. For the Chinese population, HPV infection elevates the risk of OSCC tumorigenesis.

Development and Characterization of 18 Novel EST-SSRs from the Western Flower Thrips, Frankliniella occidentalis (Pergande)

PubMed Central

Yang, Xian-Ming; Sun, Jing-Tao; Xue, Xiao-Feng; Zhu, Wen-Chao; Hong, Xiao-Yue

2012-01-01

The western flower thrips, Frankliniella occidentalis (Pergande), is an invasive species and the most economically important pest within the insect order Thysanoptera. For a better understanding of the genetic makeup and migration patterns of F. occidentalis throughout the world, we characterized 18 novel polymorphic EST-derived microsatellites. The mutational mechanism of these EST-SSRs was also investigated to facilitate the selection of appropriate combinations of markers for population genetic studies. Genetic diversity of these novel markers was assessed in 96 individuals from three populations in China (Harbin, Dali, and Guiyang). The results showed that all these 18 loci were highly polymorphic; the number of alleles ranged from 2 to 15, with an average of 5.50 alleles per locus. The observed (HO) and expected (HE) heterozygosities ranged from 0.072 to 0.707 and 0.089 to 0.851, respectively. Furthermore, only two locus/population combinations (WFT144 in Dali and WFT50 in Guiyang) significantly deviated from Hardy–Weinberg equilibrium (HWE). Pairwise FST analysis showed a low but significant differentiation (0.026 < FST < 0.032) among all three pairwise population comparisons. Sequence analysis of alleles per locus revealed a complex mutational pattern of these EST-SSRs. Thus, these EST-SSRs are useful markers but greater attention should be paid to the mutational characteristics of these microsatellites when they are used in population genetic studies. PMID:22489130

Development and characterization of 18 novel EST-SSRs from the western flower Thrips, Frankliniella occidentalis (Pergande).

PubMed

Yang, Xian-Ming; Sun, Jing-Tao; Xue, Xiao-Feng; Zhu, Wen-Chao; Hong, Xiao-Yue

2012-01-01

The western flower thrips, Frankliniella occidentalis (Pergande), is an invasive species and the most economically important pest within the insect order Thysanoptera. For a better understanding of the genetic makeup and migration patterns of F. occidentalis throughout the world, we characterized 18 novel polymorphic EST-derived microsatellites. The mutational mechanism of these EST-SSRs was also investigated to facilitate the selection of appropriate combinations of markers for population genetic studies. Genetic diversity of these novel markers was assessed in 96 individuals from three populations in China (Harbin, Dali, and Guiyang). The results showed that all these 18 loci were highly polymorphic; the number of alleles ranged from 2 to 15, with an average of 5.50 alleles per locus. The observed (H(O)) and expected (H(E)) heterozygosities ranged from 0.072 to 0.707 and 0.089 to 0.851, respectively. Furthermore, only two locus/population combinations (WFT144 in Dali and WFT50 in Guiyang) significantly deviated from Hardy-Weinberg equilibrium (HWE). Pairwise F(ST) analysis showed a low but significant differentiation (0.026 < F(ST) < 0.032) among all three pairwise population comparisons. Sequence analysis of alleles per locus revealed a complex mutational pattern of these EST-SSRs. Thus, these EST-SSRs are useful markers but greater attention should be paid to the mutational characteristics of these microsatellites when they are used in population genetic studies.

Effect of interacting second- and third-order stimulus-dependent correlations on population-coding asymmetries.

PubMed

Montangie, Lisandro; Montani, Fernando

2016-10-01

Spike correlations among neurons are widely encountered in the brain. Although models accounting for pairwise interactions have proved able to capture some of the most important features of population activity at the level of the retina, the evidence shows that pairwise neuronal correlation analysis does not resolve cooperative population dynamics by itself. By means of a series expansion for short time scales of the mutual information conveyed by a population of neurons, the information transmission can be broken down into firing rate and correlational components. In a proposed extension of this framework, we investigate the information components considering both second- and higher-order correlations. We show that the existence of a mixed stimulus-dependent correlation term defines a new scenario for the interplay between pairwise and higher-than-pairwise interactions in noise and signal correlations that would lead either to redundancy or synergy in the information-theoretic sense.

Composition and Variability of the Essential Oil of the Flowers of Lavandula stoechas from Various Geographical Sources.

PubMed

La Bella, Salvatore; Tuttolomondo, Teresa; Dugo, Giacomo; Ruberto, Giuseppe; Leto, Claudio; Napoli, Edoardo M; Potorti, Angela Giorgia; Fede, Maria Rita; Virga, Giuseppe; Leone, Raffaele; D'Anna, Eleonora; Licata, Mario

2015-11-01

Samples of flowers of wild Lavandula stoechas L. spp. stoechas populations were collected in three areas of Sicily (Italy) and were characterized in agronomic and chemical terms. Essential oil (EO) was extracted by hydrodistillation and analyzed by GC-FID and GC-MS. GC-FID and GC-MS analyses permitted identification of 89 compounds from the EO. The samples were separated into 3 groups using PCA (Principal Component Analysis) statistical method, with reference to the chemical composition of the EO. All three Sicilian populations of lavender were identified as the fenchone chemotype with percentage content ranged between 52.8-71.1%. The population of Partinico showed the highest dry weight of flowers per plant (221.3 g), but the lowest EO yield (0.37%). The essential oils of the three wild Sicilian populations of L. stoechas L. spp. stoechas showed a greater chemical differentiation than those obtained from other Mediterranean areas.

Logistic analysis of shovel and Carabelli's tooth traits in a Caucasoid population.

PubMed

Hsu, J W; Tsai, P; Liu, K; Ferguson, D

1997-09-19

Caucasoid populations differ from Mongoloids by having a high prevalence of Carabelli's trait and a low prevalence of shovel trait. This study was conducted to investigate the association between the shovel and the Carabelli's traits in a Caucasoid population. The research design sought a Caucasoid population at Milwaukee of Wisconsin in United States. The Caucasoid group selected for study was the European descendant. The effects of sex and age on Carabelli's trait were controlled in this investigation, as was the association between tooth size and Carabelli's trait. Results show that males were more likely to have Carabelli's trait expressed on teeth than females. The buccolingual diameter of Carabelli's trait teeth was larger than that of teeth without the trait. After adjusting for sex, age, and tooth size, the existence of the shovel trait decreased the likelihood of having Carabelli's trait which shows an significant effect.

Genetic analysis of haplotype data for 23 Y-chromosome short tandem repeat loci in the Turkish population recently settled in Sarajevo, Bosnia and Herzegovina.

PubMed

Dogan, Serkan; Primorac, Dragan; Marjanović, Damir

2014-10-01

To explore the distribution and polymorphisms of 23 short tandem repeat (STR) loci on the Y chromosome in the Turkish population recently settled in Sarajevo, Bosnia and Herzegovina and to investigate its genetic relationships with the homeland Turkish population and neighboring populations. This study included 100 healthy unrelated male individuals from the Turkish population living in Sarajevo. Buccal swab samples were collected as a DNA source. Genomic DNA was extracted using the salting out method and amplification was performed using PowerPlex Y 23 amplification kit. The studied population was compared to other populations using pairwise genetic distances, which were represented with a multi-dimensional scaling plot. Haplotype and allele frequencies of the sample population were calculated and the results showed that all 100 samples had unique haplotypes. The most polymorphic locus was DYS458, and the least polymorphic DYS391. The observed haplotype diversity was 1.0000 ± 0.0014, with a discrimination capacity of 1.00 and the match probability of 0.01. Rst values showed that our sample population was closely related in both dimensions to the Lebanese and Iraqi populations, while it was more distant from Bosnian, Croatian, and Macedonian populations. Turkish population residing in Sarajevo could be observed as a representative Turkish population, since our results were consistent with those previously published for the homeland Turkish population. Also, this study once again proved that geographically close populations were genetically more related to each other.

Pheromonally mediated sexual isolation among denning populations of red-sided garter snakes, Thamnophis sirtalis parietalis.

PubMed

Lemaster, Michael P; Mason, Robert T

2003-04-01

Utilizing behavioral experiments and chemical analyses, we examined whether pheromonally mediated sexual isolation exists between denning populations of red-sided garter snakes (Thamtnophis sirtalis parietalis) in Manitoba, Canada. Simultaneous choice tests conducted during the breeding season revealed that adult males from a hibernaculum in central Manitoba displayed a strong courtship preference for females from their own population over females from a hibernaculum in western Manitoba, whereas males from the western Manitoba hibernaculum showed no such preference. In addition. trailing experiments testing the response of males from the two hibernacula to familiar and unfamiliar female trails showed similar results, demonstrating that the observed male preference is mediated through chemical cues. Subsequent chemical analysis of the female sexual attractiveness pheromone. a homologous series of long-chain saturated and (omega-9 cis-unsaturated methyl ketones responsible for eliciting male courtship behavior and trailing behavior in garter snakes, showed significant variation in the composition of the pheromone between the two populations. Specifically, the two populations varied in the relative concentrations of individual unsaturated methyl ketones expressed by females. These results suggest that sexual isolation exists to a degree among denning populations of red-sided garter snakes due to variation in the expression of the female sexual attractiveness pheromone.

Effects of Sample Selection Bias on the Accuracy of Population Structure and Ancestry Inference

PubMed Central

Shringarpure, Suyash; Xing, Eric P.

2014-01-01

Population stratification is an important task in genetic analyses. It provides information about the ancestry of individuals and can be an important confounder in genome-wide association studies. Public genotyping projects have made a large number of datasets available for study. However, practical constraints dictate that of a geographical/ethnic population, only a small number of individuals are genotyped. The resulting data are a sample from the entire population. If the distribution of sample sizes is not representative of the populations being sampled, the accuracy of population stratification analyses of the data could be affected. We attempt to understand the effect of biased sampling on the accuracy of population structure analysis and individual ancestry recovery. We examined two commonly used methods for analyses of such datasets, ADMIXTURE and EIGENSOFT, and found that the accuracy of recovery of population structure is affected to a large extent by the sample used for analysis and how representative it is of the underlying populations. Using simulated data and real genotype data from cattle, we show that sample selection bias can affect the results of population structure analyses. We develop a mathematical framework for sample selection bias in models for population structure and also proposed a correction for sample selection bias using auxiliary information about the sample. We demonstrate that such a correction is effective in practice using simulated and real data. PMID:24637351

Population bottlenecks, genetic diversity and breeding ability of the three-spined stickleback (Gasterosteus aculeatus) from three polluted English Rivers.

PubMed

Santos, Eduarda M; Hamilton, Patrick B; Coe, Tobias S; Ball, Jonathan S; Cook, Alastair C; Katsiadaki, Ioanna; Tyler, Charles R

2013-10-15

Pollution is a significant environmental pressure on fish populations in both freshwater and marine environments. Populations subjected to chronic exposure to pollutants can experience impacts ranging from altered reproductive capacity to changes in population genetic structure. Few studies, however, have examined the reproductive vigor of individuals within populations inhabiting environments characterized by chronic pollution. In this study we undertook an analysis of populations of three-spined sticklebacks (Gasterosteus aculeatus) from polluted sites, to determine levels of genetic diversity, assess for evidence of historic population genetic bottlenecks and determine the reproductive competitiveness of males from these locations. The sites chosen included locations in the River Aire, the River Tees and the River Birket, English rivers that have been impacted by pollution from industrial and/or domestic effluents for over 100 years. Male reproductive competitiveness was determined via competitive breeding experiments with males and females derived from a clean water site, employing DNA microsatellites to determine parentage outcome. Populations of stickleback collected from the three historically polluted sites showed evidence of recent population bottlenecks, although only the River Aire population showed low genetic diversity. In contrast, fish collected from two relatively unpolluted sites within the River Gowy and Houghton Springs showed weak, or no evidence of such bottlenecks. Nevertheless, males derived from polluted sites were able to reproduce successfully in competition with males derived from clean water exposures, indicating that these bottlenecks have not resulted in any substantial loss of reproductive fitness in males. Copyright © 2013 Elsevier B.V. All rights reserved.

Artificial neural network models for prediction of cardiovascular autonomic dysfunction in general Chinese population

PubMed Central

2013-01-01

Background The present study aimed to develop an artificial neural network (ANN) based prediction model for cardiovascular autonomic (CA) dysfunction in the general population. Methods We analyzed a previous dataset based on a population sample consisted of 2,092 individuals aged 30–80 years. The prediction models were derived from an exploratory set using ANN analysis. Performances of these prediction models were evaluated in the validation set. Results Univariate analysis indicated that 14 risk factors showed statistically significant association with CA dysfunction (P < 0.05). The mean area under the receiver-operating curve was 0.762 (95% CI 0.732–0.793) for prediction model developed using ANN analysis. The mean sensitivity, specificity, positive and negative predictive values were similar in the prediction models was 0.751, 0.665, 0.330 and 0.924, respectively. All HL statistics were less than 15.0. Conclusion ANN is an effective tool for developing prediction models with high value for predicting CA dysfunction among the general population. PMID:23902963

Assessment of Facial Golden Proportions among North Maharashtri-an Population

PubMed Central

Sunilkumar, L N; Jadhav, Kalpana S; Nazirkar, Girish; Singh, Shailendra; Nagmode, Pradnya S; Ali, Fareedi Mukram

2013-01-01

Background: Divine Proportion in Orthodontics and Prosthodontics has always been intriguing. This was applied to the North Maharashtrian population to evaluate the relationship between facial esthetics and the golden proportions. Materials & Methods: Facial proportions were assessed by examining photographs of sum total of 300 subjects of North Maharashtrian population. Young adults with a skeletal and dental Class 1 occlusion, competent lips, and balanced facial proportion were selected. Photographic prints were taken and manually parameters were plotted and analysis was done. Results: The measurements of anterior facial height showed proportionality with the total facial height. The values showed shorter lower anterior facial height and deviation of facial width parameters from the divine proportion indicating small mouth, nose, and narrow-set eyes with respect to the inter-temporal width. Conclusion: There is soft-tissue facial balance of North Maharashtrian population in comparison with the golden proportion. However, certain parameters show some deviation from the divine proportion.. How to cite this article: Sunilkumar L N, Jadhav K S, Nazirkar G, Singh S, Nagmode P S, Ali F M. Assessment of Facial Golden Proportions among North Maharashtrian Population. J Int Oral Health 2013; 5(3):48-54. PMID:24155602

Morphological and Molecular Data Reveal Three Distinct Populations of Indian Wild Rice Oryza rufipogon Griff. Species Complex.

PubMed

Singh, Balwant; Singh, Nisha; Mishra, Shefali; Tripathi, Kabita; Singh, Bikram P; Rai, Vandna; Singh, Ashok K; Singh, Nagendra K

2018-01-01

Wild relatives of crops possess adaptive mutations for agronomically important traits, which could play significant role in crop improvement for sustainable agriculture. However, global climate change and human activities pose serious threats to the natural habitats leading to erosion of genetic diversity of wild rice populations. The purpose of this study was to explore and characterize India's huge untapped wild rice diversity in Oryza rufipogon Griff. species complex from a wide range of ecological niches. We made strategic expeditions around diversity hot spots in 64 districts of nine different agro-climatic zones of the country and collected 418 wild rice accessions. Significant variation was observed among the accessions for 46 morphological descriptors, allowing classification into O. nivara, O. rufipogon , and O. sativa f. spontanea morpho-taxonomic groups. Genome-specific pSINE1 markers confirmed all the accessions having AA genome, which were further classified using ecotype-specific pSINE1 markers into annual, perennial, intermediate, and an unknown type. Principal component analysis revealed continuous variation for the morphological traits in each ecotype group. Genetic diversity analysis based on multi-allelic SSR markers clustered these accessions into three major groups and analysis of molecular variance for nine agro-climatic zones showed that 68% of the genetic variation was inherent amongst individuals while only 11% of the variation separated the zones, though there was significant correlation between genetic and spatial distances of the accessions. Model based population structure analysis using genome wide bi-allelic SNP markers revealed three sub-populations designated 'Pro-Indica,' 'Pro-Aus,' and 'Mid-Gangetic,' which showed poor correspondence with the morpho - taxonomic classification or pSINE1 ecotypes. There was Pan-India distribution of the 'Pro-Indica' and 'Pro-Aus' sub-populations across agro-climatic zones, indicating a more fundamental grouping based on the ancestry closely related to 'Indica' and 'Aus' groups of rice cultivars. The Pro-Indica population has substantial presence in the Eastern Himalayan Region and Lower Gangetic Plains, whereas 'Pro-Aus' sub-population was predominant in the Upper Gangetic Plains, Western Himalayan Region, Gujarat Plains and Hills, and Western Coastal Plains. In contrast 'Mid-Gangetic' population was largely concentrated in the Mid Gangetic Plains. The information presented here will be useful in the utilization of wild rice resources for varietal improvement.

Behavioural adaptations in talitrids from two Atlantic beaches

NASA Astrophysics Data System (ADS)

Rossano, Claudia; Gambineri, Simone; Fanini, Lucia; Durier, Virginie; Rivault, Colette; Scapini, Felicita

2009-12-01

The aim of the present study was to test sun orientation and rhythmic activity of two sandhopper populations from two Atlantic macro-tidal beaches. A population from Le Verger beach (orientated to 346°, Ille et Vilaine, Brittany, France) and a population from Damgan (orientated to 195°, Morbihan, Brittany, France), were tested on the beach under clear sky discriminating for landscape vision. For both populations locomotor activity rhythm was recorded in the laboratory. The two beaches differed for climatic features, tidal range and for human use. Both talitrid populations resulted very well orientated toward the shoreline, and both used solar position and landscape vision to orient. However the multiple regression analysis of orientation with climatic features showed a different use of local cues by the two populations and a slight influence of tidal regime (ebbing and rising tide), in spite of the supralittoral zonation of sandhoppers. In the laboratory they showed a well defined rhythmic behaviour as well as a bimodal rhythmicity, explained as a tidal one. These results are a new brick in the complex picture of orientation and rhythm studies on sandy beach invertebrates.

Crash and rebound of indigenous populations in lowland South America

NASA Astrophysics Data System (ADS)

Hamilton, Marcus J.; Walker, Robert S.; Kesler, Dylan C.

2014-04-01

Lowland South America has long been a battle-ground between European colonization and indigenous survival. Initial waves of European colonization brought disease epidemics, slavery, and violence that had catastrophic impacts on indigenous cultures. In this paper we focus on the demography of 238 surviving populations in Brazil. We use longitudinal censuses from all known indigenous Brazilian societies to quantify three demographic metrics: 1) effects of European contact on indigenous populations; 2) empirical estimates of minimum viable population sizes; and 3) estimates of post-contact population growth rates. We use this information to conduct population viability analysis (PVA). Our results show that all surviving populations suffered extensive mortality during, and shortly after, contact. However, most surviving populations exhibit positive growth rates within the first decade post-contact. Our findings paint a positive demographic outlook for these indigenous populations, though long-term survival remains subject to powerful externalities, including politics, economics, and the pervasive illegal exploitation of indigenous lands.

Genetic differentiation and origin of the Jordanian population: an analysis of Alu insertion polymorphisms.

PubMed

Bahri, Raoudha; El Moncer, Wifak; Al-Batayneh, Khalid; Sadiq, May; Esteban, Esther; Moral, Pedro; Chaabani, Hassen

2012-05-01

Although much of Jordan is covered by desert, its north-western region forms part of the Fertile Crescent region that had given a rich past to Jordanians. This past, scarcely described by historians, is not yet clarified by sufficient genetic data. Thus in this paper we aim to determine the genetic differentiation of the Jordanian population and to discuss its origin. A total of 150 unrelated healthy Jordanians were investigated for ten Alu insertion polymorphisms. Genetic relationships among populations were estimated by a principal component (PC) plot based on the analyses of the R-matrix software. Statistical analysis showed that the Jordanian population is not significantly different from the United Arab Emirates population or the North Africans. This observation, well represented in PC plot, suggests a common origin of these populations belonging respectively to ancient Mesopotamia, Arabia, and North Africa. Our results are compatible with ancient peoples' movements from Arabia to ancient Mesopotamia and North Africa as proposed by historians and supported by previous genetic results. The original genetic profile of the Jordanian population, very likely Arabian Semitic, has not been subject to significant change despite the succession of several civilizations.

The Flavin-Containing Monooxygenase 3 Gene and Essential Hypertension: The Joint Effect of Polymorphism E158K and Cigarette Smoking on Disease Susceptibility

PubMed Central

Bushueva, Olga; Solodilova, Maria; Churnosov, Mikhail; Ivanov, Vladimir; Polonikov, Alexey

2014-01-01

Gene encoding flavin-containing monooxygenase 3 (FMO3), a microsomal antioxidant defense enzyme, has been suggested to contribute to essential hypertension (EH). The present study was designed to investigate whether common functional polymorphism E158K (rs2266782) of the FMO3 gene is associated with EH susceptibility in a Russian population. A total of 2 995 unrelated subjects from Kursk (1 362 EH patients and 843 healthy controls) and Belgorod (357 EH patients and 422 population controls) regions of Central Russia were recruited for this study. DNA samples from all study participants were genotyped for the FMO3 gene polymorphism through PCR followed by RFLP analysis. We found that the polymorphism E158K is associated with increased risk of essential hypertension in both discovery population from Kursk region (OR 1.36 95% CI 1.09–1.69, P = 0.01) and replication population from Belgorod region (OR 1.54 95% CI 1.07–1.89, P = 0.02) after adjustment for gender and age using logistic regression analysis. Further analysis showed that the increased hypertension risk in carriers of genotype 158KK gene occurred in cigarette smokers, whereas nonsmoker carriers of this genotype did not show the disease risk. This is the first study reporting the association of the FMO3 gene polymorphism and the risk of essential hypertension. PMID:25243081

Associations between suicidal behavior and childhood abuse and neglect: A meta-analysis.

PubMed

Liu, Jianbo; Fang, Yumin; Gong, Jingbo; Cui, Xilong; Meng, Tiantian; Xiao, Bo; He, Yuqiong; Shen, Yanmei; Luo, Xuerong

2017-10-01

Relationships of some types of childhood maltreatment and suicidal behavior remain controversial and inconclusive. Medline, Embase, PsycINFO and Cochrane library were searched for eligible studies, and the results were synthesized in meta-analyses. childhood maltreatment was associated positively with suicidal behavior in the total population and maltreatment subgroups. Emotional abuse had the strongest effect (OR =2.33, SMD =0.660, P<0.001). Subgroup analyses showed that the effects of childhood abuse (OR =1.55, SMD =0.523) and neglect (OR =1.25, SMD =0.31) were significant. According to the analysis of dichotomous outcomes, childhood maltreatment was associated positively with suicidal behavior in men and women (women: OR =4.84, P<0.001; men: OR =1.03, P<0.001). Among populations, childhood maltreatment had the strongest effect on suicidal behavior in the general population (OR =3.78, P<0.001). However, the analysis of continuous outcomes showed that the effect was strongest in patients with chronic schizophrenia (SMD =0.89, P<0.001). In addition, childhood maltreatment was associated positively with suicide attempt (OR =1.11, SMD =0.48, P<0.001), but not with suicidal ideation. Some subgroup samples were not sufficiently large. Childhood maltreatment increases the risk of suicidal behavior. Emotional abuse had the strongest effect among the five types of maltreatment. The risk of suicidal behavior is higher in the general population, women, and individuals with chronic schizophrenia who have histories of childhood maltreatment. Copyright © 2017. Published by Elsevier B.V.

Recurrent jellyfish blooms are a consequence of global oscillations

PubMed Central

Condon, Robert H.; Duarte, Carlos M.; Pitt, Kylie A.; Robinson, Kelly L.; Lucas, Cathy H.; Sutherland, Kelly R.; Mianzan, Hermes W.; Bogeberg, Molly; Purcell, Jennifer E.; Decker, Mary Beth; Uye, Shin-ichi; Madin, Laurence P.; Brodeur, Richard D.; Haddock, Steven H. D.; Malej, Alenka; Parry, Gregory D.; Eriksen, Elena; Quiñones, Javier; Acha, Marcelo; Harvey, Michel; Arthur, James M.; Graham, William M.

2013-01-01

A perceived recent increase in global jellyfish abundance has been portrayed as a symptom of degraded oceans. This perception is based primarily on a few case studies and anecdotal evidence, but a formal analysis of global temporal trends in jellyfish populations has been missing. Here, we analyze all available long-term datasets on changes in jellyfish abundance across multiple coastal stations, using linear and logistic mixed models and effect-size analysis to show that there is no robust evidence for a global increase in jellyfish. Although there has been a small linear increase in jellyfish since the 1970s, this trend was unsubstantiated by effect-size analysis that showed no difference in the proportion of increasing vs. decreasing jellyfish populations over all time periods examined. Rather, the strongest nonrandom trend indicated jellyfish populations undergo larger, worldwide oscillations with an approximate 20-y periodicity, including a rising phase during the 1990s that contributed to the perception of a global increase in jellyfish abundance. Sustained monitoring is required over the next decade to elucidate with statistical confidence whether the weak increasing linear trend in jellyfish after 1970 is an actual shift in the baseline or part of an oscillation. Irrespective of the nature of increase, given the potential damage posed by jellyfish blooms to fisheries, tourism, and other human industries, our findings foretell recurrent phases of rise and fall in jellyfish populations that society should be prepared to face. PMID:23277544

A Cross‐Study Analysis Evaluating the Effects of Food on the Pharmacokinetics of Rivaroxaban in Clinical Studies

PubMed Central

Peters, Gary; Haskell, Lloyd; Patel, Purve; Nandy, Partha; Moore, Kenneth Todd

2017-01-01

Abstract US prescribing guidelines recommend that 15‐ and 20‐mg doses of rivaroxaban be administered with food for the treatment of deep vein thrombosis (DVT) and pulmonary embolism (PE) and for reduction in the risk of recurrence of DVT and PE. In addition, the US prescribing guidelines recommend these doses be administered with an evening meal to reduce the risk of stroke and systemic embolism in patients with nonvalvular atrial fibrillation (AF). The purpose of this model‐based cross‐study comparison was to examine the impact of food, with regard to both meal timing and content, on the pharmacokinetics (PK) of rivaroxaban, using data collected during its clinical development. Results of this analysis showed that a PK model built from pooled data in the AF population (for whom rivaroxaban was administered with an evening meal) and in the DVT population (for whom rivaroxaban was administered with a morning meal) can describe both data sets well. Furthermore, the PK model built from data in the AF population alone can adequately predict the PK profile of the DVT population and vice versa. This cross‐study analysis also confirmed the findings from previous clinical pharmacology studies, which showed that meal content does not have a clinically relevant impact on the PK of rivaroxaban at 20 mg. Therefore, although the administration of rivaroxaban with food is necessary for maintaining high bioavailability, neither meal timing nor meal content appears to affect the PK of rivaroxaban. PMID:28679020

Analysis of Neural Stem Cells from Human Cortical Brain Structures In Vitro.

PubMed

Aleksandrova, M A; Poltavtseva, R A; Marei, M V; Sukhikh, G T

2016-05-01

Comparative immunohistochemical analysis of the neocortex from human fetuses showed that neural stem and progenitor cells are present in the brain throughout the gestation period, at least from week 8 through 26. At the same time, neural stem cells from the first and second trimester fetuses differed by the distribution, morphology, growth, and quantity. Immunocytochemical analysis of neural stem cells derived from fetuses at different gestation terms and cultured under different conditions showed their differentiation capacity. Detailed analysis of neural stem cell populations derived from fetuses on gestation weeks 8-9, 18-20, and 26 expressing Lex/SSEA1 was performed.

Phylodynamic and Phylogeographic Patterns of the HIV Type 1 Subtype F1 Parenteral Epidemic in Romania

PubMed Central

Hué, Stéphane; Buckton, Andrew J.; Myers, Richard E.; Duiculescu, Dan; Ene, Luminita; Oprea, Cristiana; Tardei, Gratiela; Rugina, Sorin; Mardarescu, Mariana; Floch, Corinne; Notheis, Gundula; Zöhrer, Bettina; Cane, Patricia A.; Pillay, Deenan

2012-01-01

Abstract In the late 1980s an HIV-1 epidemic emerged in Romania that was dominated by subtype F1. The main route of infection is believed to be parenteral transmission in children. We sequenced partial pol coding regions of 70 subtype F1 samples from children and adolescents from the PENTA-EPPICC network of which 67 were from Romania. Phylogenetic reconstruction using the sequences and other publically available global subtype F sequences showed that 79% of Romanian F1 sequences formed a statistically robust monophyletic cluster. The monophyletic cluster was epidemiologically linked to parenteral transmission in children. Coalescent-based analysis dated the origins of the parenteral epidemic to 1983 [1981–1987; 95% HPD]. The analysis also shows that the epidemic's effective population size has remained fairly constant since the early 1990s suggesting limited onward spread of the virus within the population. Furthermore, phylogeographic analysis suggests that the root location of the parenteral epidemic was Bucharest. PMID:22251065

Groupwise shape analysis of the hippocampus using spectral matching

NASA Astrophysics Data System (ADS)

Shakeri, Mahsa; Lombaert, Hervé; Lippé, Sarah; Kadoury, Samuel

2014-03-01

The hippocampus is a prominent subcortical feature of interest in many neuroscience studies. Its subtle morphological changes often predicate illnesses, including Alzheimer's, schizophrenia or epilepsy. The precise location of structural differences requires a reliable correspondence between shapes across a population. In this paper, we propose an automated method for groupwise hippocampal shape analysis based on a spectral decomposition of a group of shapes to solve the correspondence problem between sets of meshes. The framework generates diffeomorphic correspondence maps across a population, which enables us to create a mean shape. Morphological changes are then located between two groups of subjects. The performance of the proposed method was evaluated on a dataset of 42 hippocampus shapes and compared with a state-of-the-art structural shape analysis approach, using spherical harmonics. Difference maps between mean shapes of two test groups demonstrates that the two approaches showed results with insignificant differences, while Gaussian curvature measures calculated between matched vertices showed a better fit and reduced variability with spectral matching.

Analysis of genetic population structure in Acacia caven (Leguminosae, Mimosoideae), comparing one exploratory and two Bayesian-model-based methods.

PubMed

Pometti, Carolina L; Bessega, Cecilia F; Saidman, Beatriz O; Vilardi, Juan C

2014-03-01

Bayesian clustering as implemented in STRUCTURE or GENELAND software is widely used to form genetic groups of populations or individuals. On the other hand, in order to satisfy the need for less computer-intensive approaches, multivariate analyses are specifically devoted to extracting information from large datasets. In this paper, we report the use of a dataset of AFLP markers belonging to 15 sampling sites of Acacia caven for studying the genetic structure and comparing the consistency of three methods: STRUCTURE, GENELAND and DAPC. Of these methods, DAPC was the fastest one and showed accuracy in inferring the K number of populations (K = 12 using the find.clusters option and K = 15 with a priori information of populations). GENELAND in turn, provides information on the area of membership probabilities for individuals or populations in the space, when coordinates are specified (K = 12). STRUCTURE also inferred the number of K populations and the membership probabilities of individuals based on ancestry, presenting the result K = 11 without prior information of populations and K = 15 using the LOCPRIOR option. Finally, in this work all three methods showed high consistency in estimating the population structure, inferring similar numbers of populations and the membership probabilities of individuals to each group, with a high correlation between each other.

Applications of chemiluminescence to bacterial analysis

NASA Technical Reports Server (NTRS)

Searle, N. D.

1975-01-01

Luminol chemiluminescence method for detecting bacteria was based on microbial activation of the oxidation of the luminol monoanion by hydrogen peroxide. Elimination of the prior lysing step, previously used in the chemiluminescence technique, was shown to improve considerably the reproducibility and accuracy of the method in addition to simplifying it. An inexpensive, portable photomultiplier detector was used to measure the maximum light intensity produced when the sample is added to the reagent. Studies of cooling tower water show that the luminol chemiluminescence technique can be used to monitor changes in viable cell population both under normal conditions and during chlorine treatment. Good correlation between chemiluminescence and plate counts was also obtained in the analysis of process water used in paper mills. This method showed good potential for monitoring the viable bacteria populations in activated sludge used in waste treatment plants to digest organic matter.

Genetic variation and population structure in Jamunapari goats using microsatellites, mitochondrial DNA, and milk protein genes.

PubMed

Rout, P K; Thangraj, K; Mandal, A; Roy, R

2012-01-01

Jamunapari, a dairy goat breed of India, has been gradually declining in numbers in its home tract over the years. We have analysed genetic variation and population history in Jamunapari goats based on 17 microsatellite loci, 2 milk protein loci, mitochondrial hypervariable region I (HVRI) sequencing, and three Y-chromosomal gene sequencing. We used the mitochondrial DNA (mtDNA) mismatch distribution, microsatellite data, and bottleneck tests to infer the population history and demography. The mean number of alleles per locus was 9.0 indicating that the allelic variation was high in all the loci and the mean heterozygosity was 0.769 at nuclear loci. Although the population size is smaller than 8,000 individuals, the amount of variability both in terms of allelic richness and gene diversity was high in all the microsatellite loci except ILST 005. The gene diversity and effective number of alleles at milk protein loci were higher than the 10 other Indian goat breeds that they were compared to. Mismatch analysis was carried out and the analysis revealed that the population curve was unimodal indicating the expansion of population. The genetic diversity of Y-chromosome genes was low in the present study. The observed mean M ratio in the population was above the critical significance value (Mc) and close to one indicating that it has maintained a slowly changing population size. The mode-shift test did not detect any distortion of allele frequency and the heterozygosity excess method showed that there was no significant departure from mutation-drift equilibrium detected in the population. However, the effects of genetic bottlenecks were observed in some loci due to decreased heterozygosity and lower level of M ratio. There were two observed genetic subdivisions in the population supporting the observations of farmers in different areas. This base line information on genetic diversity, bottleneck analysis, and mismatch analysis was obtained to assist the conservation decision and management of the breed.

Genetic Variation and Population Structure in Jamunapari Goats Using Microsatellites, Mitochondrial DNA, and Milk Protein Genes

PubMed Central

Rout, P. K.; Thangraj, K.; Mandal, A.; Roy, R.

2012-01-01

Jamunapari, a dairy goat breed of India, has been gradually declining in numbers in its home tract over the years. We have analysed genetic variation and population history in Jamunapari goats based on 17 microsatellite loci, 2 milk protein loci, mitochondrial hypervariable region I (HVRI) sequencing, and three Y-chromosomal gene sequencing. We used the mitochondrial DNA (mtDNA) mismatch distribution, microsatellite data, and bottleneck tests to infer the population history and demography. The mean number of alleles per locus was 9.0 indicating that the allelic variation was high in all the loci and the mean heterozygosity was 0.769 at nuclear loci. Although the population size is smaller than 8,000 individuals, the amount of variability both in terms of allelic richness and gene diversity was high in all the microsatellite loci except ILST 005. The gene diversity and effective number of alleles at milk protein loci were higher than the 10 other Indian goat breeds that they were compared to. Mismatch analysis was carried out and the analysis revealed that the population curve was unimodal indicating the expansion of population. The genetic diversity of Y-chromosome genes was low in the present study. The observed mean M ratio in the population was above the critical significance value (Mc) and close to one indicating that it has maintained a slowly changing population size. The mode-shift test did not detect any distortion of allele frequency and the heterozygosity excess method showed that there was no significant departure from mutation-drift equilibrium detected in the population. However, the effects of genetic bottlenecks were observed in some loci due to decreased heterozygosity and lower level of M ratio. There were two observed genetic subdivisions in the population supporting the observations of farmers in different areas. This base line information on genetic diversity, bottleneck analysis, and mismatch analysis was obtained to assist the conservation decision and management of the breed. PMID:22606053

Allee effects and the spatial dynamics of a locally endangered butterfly, the high brown fritillary (Argynnis adippe).

PubMed

Bonsall, Michael B; Dooley, Claire A; Kasparson, Anna; Brereton, Tom; Roy, David B; Thomas, Jeremy A

2014-01-01

Conservation of endangered species necessitates a full appreciation of the ecological processes affecting the regulation, limitation, and persistence of populations. These processes are influenced by birth, death, and dispersal events, and characterizing them requires careful accounting of both the deterministic and stochastic processes operating at both local and regional population levels. We combined ecological theory and observations on Allee effects by linking mathematical analysis and the spatial and temporal population dynamics patterns of a highly endangered butterfly, the high brown fritillary, Argynnis adippe. Our theoretical analysis showed that the role of density-dependent feedbacks in the presence of local immigration can influence the strength of Allee effects. Linking this theory to the analysis of the population data revealed strong evidence for both negative density dependence and Allee effects at the landscape or regional scale. These regional dynamics are predicted to be highly influenced by immigration. Using a Bayesian state-space approach, we characterized the local-scale births, deaths, and dispersal effects together with measurement and process uncertainty in the metapopulation. Some form of an Allee effect influenced almost three-quarters of these local populations. Our joint analysis of the deterministic and stochastic dynamics suggests that a conservation priority for this species would be to increase resource availability in currently occupied and, more importantly, in unoccupied sites.

Population pharmacokinetic (PK) analysis of laromustine, an emerging alkylating agent, in cancer patients.

PubMed

Nassar, Ala F; Wisnewski, Adam V; King, Ivan

2017-05-01

1. Alkylating agents are capable of introducing an alkyl group into nucleophilic sites on DNA or RNA through covalent bond. Laromustine is an active member of a relatively new class of sulfonylhydrazine prodrugs under development as antineoplastic alkylating agents, and displays significant single-agent activity. 2. This is the first report of the population pharmacokinetic analysis of laromustine, 106 patients, 66 with hematologic malignancies and 40 with solid tumors, participated in five clinical trials worldwide. Of these, 104 patients were included in the final NONMEM analysis. 3. The population estimates for total clearance (CL) and volume of distribution of the central compartment (V 1 ) were 96.3 L/h and 45.9 L, associated with high inter-patient variability of 52.9% and 79.8% and inter-occasion variability of 26.7% and 49.3%, respectively. The population estimates for Q and V 2 were 73.2 L/h and 29.9 L, and inter-patient variability in V 2 was 63.1%, respectively. 4. The estimate of V ss (75.8 L) exceeds total body water, indicating that laromustine is distributed to tissues. The half-life is short, less than 1 h, reflecting rapid clearance. Population PK analysis showed laromustine pharmacokinetics to be independent of dose and organ function with no effect on subsequent dosing cycles.

Genetic population structure of the lionfish Pterois miles (Scorpaenidae, Pteroinae) in the Gulf of Aqaba and northern Red Sea.

PubMed

Kochzius, Marc; Blohm, Dietmar

2005-03-14

The aim of this study is to reveal gene flow between populations of the coral reef dwelling lionfish Pterois miles in the Gulf of Aqaba and northern Red Sea. Due to the fjord-like hydrography and topology of the Gulf of Aqaba, isolation of populations might be possible. Analysis of 5' mitochondrial control region sequences from 94 P. miles specimens detected 32 polymorphic sites, yielding 38 haplotypes. Sequence divergence among different haplotypes ranged from 0.6% to 9.9% and genetic diversity was high (h=0.85, pi=1.9%). AMOVA indicates panmixia between the Gulf of Aqaba and northern Red Sea, but analysis of migration pattern shows an almost unidirectional migration originating from the Red Sea.

A population-based case-control teratologic study of furazidine, a nitrofuran-derivative treatment during pregnancy.

PubMed

Czeizel, A E; Rockenbauer, M; Sørensen, H T; Olsen, J

2000-04-01

To study human teratogenic potential of furazidine treatment during pregnancy. Pair analysis of cases with congenital abnormalities and matched population controls. The Hungarian Case-Control Surveillance of Congenital Abnormalities. 38,151 pregnant women who had newborn infants without any defects (population control group) and 22,865 pregnant women who had newborns or fetuses with congenital abnormalities between 1980 and 1996. In the case group, 157 (0.7%) and in the control group, 254 (0.7%) pregnant women were treated with furazidine. The case-control pair analysis did not indicate a teratogenic potential of furazidine use during the second to third months of gestation, i.e. in the critical period for major congenital abnormalities. Treatment with furazidine during pregnancy did not show teratogenic risk to the fetus.

Analysis on the Climate Change Characteristics of Dianchi Lake Basin under the Background of Global Warming

NASA Astrophysics Data System (ADS)

Zhenyu, Yu; Luo, Yi; Yang, Kun; Qiongfei, Deng

2017-05-01

Based on the data published by the State Statistical Bureau and the weather station data, the annual mean temperature, wind speed, humidity, light duration and precipitation of Dianchi Lake in 1990 ~ 2014 were analysed. Combined with the population The results show that the climatic changes in Dianchi Lake basin are related to the climatic change in the past 25 years, and the correlation between these factors and the main climatic factors are analysed by linear regression, Mann-Kendall test, cumulative anomaly, R/S and Morlet wavelet analysis. Population, housing construction area growth and other aspects of the correlation trends and changes in the process, revealing the population expansion and housing construction area growth on the climate of the main factors of the cycle tendency of significant impact.

Identification of different nutritional status groups in institutionalized elderly people by cluster analysis.

PubMed

López-Contreras, María José; López, Maria Ángeles; Canteras, Manuel; Candela, María Emilia; Zamora, Salvador; Pérez-Llamas, Francisca

2014-03-01

To apply a cluster analysis to groups of individuals of similar characteristics in an attempt to identify undernutrition or the risk of undernutrition in this population. A cross-sectional study. Seven public nursing homes in the province of Murcia, on the Mediterranean coast of Spain. 205 subjects aged 65 and older (131 women and 74 men). Dietary intake (energy and nutrients), anthropometric (body mass index, skinfold thickness, mid-arm muscle circumference, mid-arm muscle area, corrected arm muscle area, waist to hip ratio) and biochemical and haematological (serum albumin, transferrin, total cholesterol, total lymphocyte count). Variables were analyzed by cluster analysis. The results of the cluster analysis, including intake, anthropometric and analytical data showed that, of the 205 elderly subjects, 66 (32.2%) were over - weight/obese, 72 (35.1%) had an adequate nutritional status and 67 (32.7%) were undernourished or at risk of undernutrition. The undernourished or at risk of undernutrition group showed the lowest values for dietary intake and the anthropometric and analytical parameters measured. Our study shows that cluster analysis is a useful statistical method for assessing the nutritional status of institutionalized elderly populations. In contrast, use of the specific reference values frequently described in the literature might fail to detect real cases of undernourishment or those at risk of undernutrition. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

Genetic comparisons between seed bank and Stipa krylovii plant populations.

PubMed

Han, B; Zhao, M

2011-09-01

The soil seed bank represents the potential plant population since it is the source for population replacement. The genetic structure of a Stipa krylovii (Roshev.) plant population and its soil seed bank was investigated in the Xilinguole Steppe of Inner Mongolia using random amplified polymorphic DNA (RAPD) analyses. The population was sampled at two sites that were in close proximity to each other (0.5 km apart). Thirty plants and 18 seed bank samples were taken from each site to determine the genetic diversity between sites and between sources (plant or seed). The material was analyzed using 13 primers to produce 92 loci. Eighty-six were multi-loci, of which 23 loci (26.74%) of allele frequencies showed significant differences (P < or = 0.05). The genetic similarity between two seed bank sites was 0.9843 while the genetic similarity between two plant sites was 0.9619. Their similarities were all greater than that between the seed bank and plant populations. An analysis of their genetic structure showed that 87.86% of total variation was derived by two-loci. Genetic structures between plant and soil seed bank populations in S. krylovii were different due to the variance of mean gametic disequilibria and mean gene diversity. AMOVA results showed that the majority of variance (88.62%) occurred within sites, 12.75% was from between-groups. Further research is needed to investigate the selective function in maintaining the genetic diversity of Stipa krylovii plant populations.

Aboriginal population prospects.

PubMed

Gray, A; Tesfaghiorghis, H

1993-11-01

The authors examine data from the 1986 and 1991 Australian censuses to assess discrepancies between the census data and past projections of the size and structure of the Aboriginal population. They also "comment on ways in which determinants of Aboriginal population change are diverging from the parameters used for previous projections. We pay particular attention to mortality prospects.... We note the evidence for under-enumeration of the Aboriginal population in particular age groups in the 1991 Census as in previous censuses, and estimate the size of adjustments necessary to correct for some, but not all, of these deficiencies. The analysis shows that Aboriginal fertility increased in the second half of the 1980s." excerpt

Genomic microsatellites identify shared Jewish ancestry intermediate between Middle Eastern and European populations.

PubMed

Kopelman, Naama M; Stone, Lewi; Wang, Chaolong; Gefel, Dov; Feldman, Marcus W; Hillel, Jossi; Rosenberg, Noah A

2009-12-08

Genetic studies have often produced conflicting results on the question of whether distant Jewish populations in different geographic locations share greater genetic similarity to each other or instead, to nearby non-Jewish populations. We perform a genome-wide population-genetic study of Jewish populations, analyzing 678 autosomal microsatellite loci in 78 individuals from four Jewish groups together with similar data on 321 individuals from 12 non-Jewish Middle Eastern and European populations. We find that the Jewish populations show a high level of genetic similarity to each other, clustering together in several types of analysis of population structure. Further, Bayesian clustering, neighbor-joining trees, and multidimensional scaling place the Jewish populations as intermediate between the non-Jewish Middle Eastern and European populations. These results support the view that the Jewish populations largely share a common Middle Eastern ancestry and that over their history they have undergone varying degrees of admixture with non-Jewish populations of European descent.

Genomic microsatellites identify shared Jewish ancestry intermediate between Middle Eastern and European populations

PubMed Central

2009-01-01

Background Genetic studies have often produced conflicting results on the question of whether distant Jewish populations in different geographic locations share greater genetic similarity to each other or instead, to nearby non-Jewish populations. We perform a genome-wide population-genetic study of Jewish populations, analyzing 678 autosomal microsatellite loci in 78 individuals from four Jewish groups together with similar data on 321 individuals from 12 non-Jewish Middle Eastern and European populations. Results We find that the Jewish populations show a high level of genetic similarity to each other, clustering together in several types of analysis of population structure. Further, Bayesian clustering, neighbor-joining trees, and multidimensional scaling place the Jewish populations as intermediate between the non-Jewish Middle Eastern and European populations. Conclusion These results support the view that the Jewish populations largely share a common Middle Eastern ancestry and that over their history they have undergone varying degrees of admixture with non-Jewish populations of European descent. PMID:19995433

Molecular evidence for a single taxon, Anopheles nuneztovari s. l., from two endemic malaria regions in Colombia

PubMed Central

Jaramillo, Luz Marina; Gutiérrez, Lina A; Luckhart, Shirley; Conn, Jan E; Correa, Margarita M

2012-01-01

To elucidate the Anopheles nuneztovari s.l. taxonomic status at a microgeographic level in four malaria endemic localities from Antioquia and Córdoba, Colombia, fragments of the Cytochrome oxidase subunit I (COI) and the white gene were used. The COI analysis showed low genetic differentiation with FST levels between −0.02 and 0.137 and Nm values between 3 and infinity, indicating the presence of high gene flow among An. nuneztovari s.l. populations from the four localities. The COI network showed a single most common haplotype, 1 (n=55), present in all localities, as the likely ancestral haplotype. Analysis of the white gene showed that An. nuneztovari s.l. populations from both departments grouped with haplotypes 19 and 20, which are part of lineage 3 previously reported. The results of the present study suggest that An. nuneztovari s.l. is a single taxon in the area of the present study. PMID:22241127

A geometric morphometric analysis of hominin upper second and third molars, with particular emphasis on European Pleistocene populations.

PubMed

Gómez-Robles, Aida; Bermúdez de Castro, José María; Martinón-Torres, María; Prado-Simón, Leyre; Arsuaga, Juan Luis

2012-09-01

The study of dental morphology by means of geometric morphometric methods allows for a detailed and quantitative comparison of hominin species that is useful for taxonomic assignment and phylogenetic reconstruction. Upper second and third molars have been studied in a comprehensive sample of Plio- and Pleistocene hominins from African, Asian and European sites in order to complete our analysis of the upper postcanine dentition. Intraspecific variation in these two molars is high, but some interspecific trends can be identified. Both molars exhibit a strong reduction of the distal cusps in recent hominin species, namely European Homo heidelbergensis, Homo neanderthalensis and Homo sapiens, but this reduction shows specific patterns and proportions in the three groups. Second molars tend to show four well developed cusps in earlier hominin species and their morphology is only marginally affected by allometric effects. Third molars can be incipiently reduced in earlier species and they evince a significant allometric component, identified both inter- and intraspecifically. European Middle Pleistocene fossils from Sima de los Huesos (SH) show a very strong reduction of these two molars, even more marked than the reduction observed in Neanderthals and in modern human populations. The highly derived shape of SH molars points to an early acquisition of typical Neanderthal dental traits by pre-Neanderthal populations and to a deviation of this population from mean morphologies of other European Middle Pleistocene groups. Copyright © 2012 Elsevier Ltd. All rights reserved.

Gastroesophageal reflux disease symptoms and dietary behaviors are significant correlates of short sleep duration in the general population: the Nagahama Study.

PubMed

Murase, Kimihiko; Tabara, Yasuharu; Takahashi, Yoshimitsu; Muro, Shigeo; Yamada, Ryo; Setoh, Kazuya; Kawaguchi, Takahisa; Kadotani, Hiroshi; Kosugi, Shinji; Sekine, Akihiro; Nakayama, Takeo; Mishima, Michiaki; Chiba, Tsutomu; Chin, Kazuo; Matsuda, Fumihiko

2014-11-01

To examine relationships among gastroesophageal reflux disease (GERD) symptoms, dietary behaviors, and sleep duration in the general population. Cross-sectional. Community-based. There were 9,643 participants selected from the general population (54 ± 13 y). None. Sleep duration, sleep habits, and unfavorable dietary behaviors of each participant were assessed with a structured questionnaire. Participants were categorized into five groups according to their sleep duration: less than 5 h, 5 to less than 6 h, 6 to less than 7 h, 7 to less than 8 h, and 8 or more h per day. GERD was evaluated using the Frequency Scale for the Symptoms of GERD (FSSG) and participants having an FSSG score of 8 or more or those under treatment of GERD were defined as having GERD. Trend analysis showed that both the FSSG score and the number of unfavorable dietary habits increased with decreasing sleep duration. Further, multiple logistic regression analysis showed that both the presence of GERD (odds ratio = 1.19, 95% confidence interval (CI) = 1.07-1.32) and the number of unfavorable dietary behaviors (odds ratio = 1.19, 95% CI = 1.13-1.26) were independent and potent factors to identify participants with short sleep duration even after controlling for other confounding factors. The current study showed that both GERD symptoms and unfavorable dietary behaviors were significant correlates of short sleep duration independently of each other in a large sample from the general population.

Sensitivity of chloride efflux vs. transepithelial measurements in mixed CF and normal airway epithelial cell populations.

PubMed

Illek, Beate; Lei, Dachuan; Fischer, Horst; Gruenert, Dieter C

2010-01-01

While the Cl(-) efflux assays are relatively straightforward, their ability to assess the efficacy of phenotypic correction in cystic fibrosis (CF) tissue or cells may be limited. Accurate assessment of therapeutic efficacy, i.e., correlating wild type CF transmembrane conductance regulator (CFTR) levels with phenotypic correction in tissue or individual cells, requires a sensitive assay. Radioactive chloride ((36)Cl) efflux was compared to Ussing chamber analysis for measuring cAMP-dependent Cl(-) transport in mixtures of human normal (16HBE14o-) and cystic fibrosis (CF) (CFTE29o- or CFBE41o-, respectively) airway epithelial cells. Cell mixtures with decreasing amounts of 16HBE14o- cells were evaluated. Efflux and Ussing chamber studies on mixed populations of normal and CF airway epithelial cells showed that, as the number of CF cells within the population was progressively increased, the cAMP-dependent Cl(-) decreased. The (36)Cl efflux assay was effective for measuring Cl(-) transport when ≥ 25% of the cells were normal. If < 25% of the cells were phenotypically wild-type (wt), the (36)Cl efflux assay was no longer reliable. Polarized CFBE41o- cells, also homozygous for the ΔF508 mutation, were used in the Ussing chamber studies. Ussing analysis detected cAMP-dependent Cl(-) currents in mixtures with ≥1% wild-type cells indicating that Ussing analysis is more sensitive than (36)Cl efflux analysis for detection of functional CFTR. Assessment of CFTR function by Ussing analysis is more sensitive than (36)Cl efflux analysis. Ussing analysis indicates that cell mixtures containing 10% 16HBE14o- cells showed 40-50% of normal cAMP-dependent Cl(-) transport that drops off exponentially between 10-1% wild-type cells. Copyright © 2010 S. Karger AG, Basel.

Indicators of AEI applied to the Delaware Estuary.

PubMed

Barnthouse, Lawrence W; Heimbuch, Douglas G; Anthony, Vaughn C; Hilborn, Ray W; Myers, Ransom A

2002-05-18

We evaluated the impacts of entrainment and impingement at the Salem Generating Station on fish populations and communities in the Delaware Estuary. In the absence of an agreed-upon regulatory definition of "adverse environmental impact" (AEI), we developed three independent benchmarks of AEI based on observed or predicted changes that could threaten the sustainability of a population or the integrity of a community. Our benchmarks of AEI included: (1) disruption of the balanced indigenous community of fish in the vicinity of Salem (the "BIC" analysis); (2) a continued downward trend in the abundance of one or more susceptible fish species (the "Trends" analysis); and (3) occurrence of entrainment/impingement mortality sufficient, in combination with fishing mortality, to jeopardize the future sustainability of one or more populations (the "Stock Jeopardy" analysis). The BIC analysis utilized nearly 30 years of species presence/absence data collected in the immediate vicinity of Salem. The Trends analysis examined three independent data sets that document trends in the abundance of juvenile fish throughout the estuary over the past 20 years. The Stock Jeopardy analysis used two different assessment models to quantify potential long-term impacts of entrainment and impingement on susceptible fish populations. For one of these models, the compensatory capacities of the modeled species were quantified through meta-analysis of spawner-recruit data available for several hundred fish stocks. All three analyses indicated that the fish populations and communities of the Delaware Estuary are healthy and show no evidence of an adverse impact due to Salem. Although the specific models and analyses used at Salem are not applicable to every facility, we believe that a weight of evidence approach that evaluates multiple benchmarks of AEI using both retrospective and predictive methods is the best approach for assessing entrainment and impingement impacts at existing facilities.

Analysis of intraspecific seed diversity in Astragalus aquilanus (Fabaceae), an endemic species of Central Apennine.

PubMed

Di Cecco, V; Di Musciano, M; D'Archivio, A A; Frattaroli, A R; Di Martino, L

2018-05-20

This work aims to study seeds of the endemic species Astragalus aquilanus from four different populations of central Italy. We investigated seed morpho-colorimetric features (shape and size) and chemical differences (through infrared spectroscopy) among populations and between dark and light seeds. Seed morpho-colorimetric quantitative variables, describing shape, size and colour traits, were measured using image analysis techniques. Fourier transform infrared (FT-IR) spectroscopy was used to attempt seed chemical characterisation. The measured data were analysed by step-wise linear discriminant analysis (LDA). Moreover, we analysed the correlation between the four most important traits and six climatic variables extracted from WorldClim 2.0. The LDA on seeds traits shows clear differentiation of the four populations, which can be attributed to different chemical composition, as confirmed by Wilk's lambda test (P < 0.001). A strong correlation between morphometric traits and temperature (annual mean temperature, mean temperature of the warmest and coolest quarter), colorimetric traits and precipitation (annual precipitation, precipitation of wettest and driest quarter) was observed. The characterisation of A. aquilanus seeds shows large intraspecific plasticity both in morpho-colorimetric and chemical composition. These results confirm the strong relationship between the type of seed produced and the climatic variables. © 2018 German Society for Plant Sciences and The Royal Botanical Society of the Netherlands.

Deeper Insights into the Circumgalactic Medium using Multivariate Analysis Methods

NASA Astrophysics Data System (ADS)

Lewis, James; Churchill, Christopher W.; Nielsen, Nikole M.; Kacprzak, Glenn

2017-01-01

Drawing from a database of galaxies whose surrounding gas has absorption from MgII, called the MgII-Absorbing Galaxy Catalog (MAGIICAT, Neilsen et al 2013), we studied the circumgalactic medium (CGM) for a sample of 47 galaxies. Using multivariate analysis, in particular the k-means clustering algorithm, we determined that simultaneously examining column density (N), rest-frame B-K color, virial mass, and azimuthal angle (the projected angle between the galaxy major axis and the quasar line of sight) yields two distinct populations: (1) bluer, lower mass galaxies with higher column density along the minor axis, and (2) redder, higher mass galaxies with lower column density along the major axis. We support this grouping by running (i) two-sample, two-dimensional Kolmogorov-Smirnov (KS) tests on each of the six bivariate planes and (ii) two-sample KS tests on each of the four variables to show that the galaxies significantly cluster into two independent populations. To account for the fact that 16 of our 47 galaxies have upper limits on N, we performed Monte-Carlo tests whereby we replaced upper limits with random deviates drawn from a Schechter distribution fit, f(N). These tests strengthen the results of the KS tests. We examined the behavior of the MgII λ2796 absorption line equivalent width and velocity width for each galaxy population. We find that equivalent width and velocity width do not show similar characteristic distinctions between the two galaxy populations. We discuss the k-means clustering algorithm for optimizing the analysis of populations within datasets as opposed to using arbitrary bivariate subsample cuts. We also discuss the power of the k-means clustering algorithm in extracting deeper physical insight into the CGM in relationship to host galaxies.

Protective Factors in the Inuit Population of Nunavut: A Comparative Study of People Who Died by Suicide, People Who Attempted Suicide, and People Who Never Attempted Suicide

PubMed Central

Beaudoin, Véronique; Séguin, Monique; Chawky, Nadia; Affleck, William; Chachamovich, Eduardo; Turecki, Gustavo

2018-01-01

Epidemiological data shows an alarming prevalence of suicide in Aboriginal populations around the world. In Canada, the highest rates are found in Inuit communities. In this article, we present the findings of a secondary analysis conducted with data previously collected as part of a larger study of psychological autopsies conducted in Nunavut, Canada. The objective of this secondary analysis was to identify protective factors in the Inuit population of Nunavut by comparing people who died by suicide, people from the general population who attempted suicide, and people from the general population who never attempted suicide. This case-control study included 90 participants, with 30 participants in each group who were paired by birth date, sex, and community. Content analysis was first conducted on the clinical vignettes from the initial study in order to codify the presence of protective variables. Then, inferential analyses were conducted to highlight differences between each group in regards to protection. Findings demonstrated that (a) people with no suicide attempt have more protective variables throughout their lifespan than people who died by suicide and those with suicide attempts within the environmental, social, and individual dimensions; (b) people with suicide attempts significantly differ from the two other groups in regards to the use of services; and (c) protective factors that stem from the environmental dimension show the greatest difference between the three groups, being significantly more present in the group with no suicide attempt. Considering these findings, interventions could focus on enhancing environmental stability in Inuit communities as a suicide prevention strategy. PMID:29337928

Effect of sociocultural cleavage on genetic differentiation: a study from North India.

PubMed

Khan, Faisal; Pandey, Atul Kumar; Borkar, Meenal; Tripathi, Manorma; Talwar, Sudha; Bisen, P S; Agrawal, Suraksha

2008-06-01

Indian populations possess an exclusive genetic profile primarily due to the many migratory events, which caused an extensive range of genetic diversity, and also due to stringent and austere sociocultural barriers that structure these populations into different endogamous groups. In the present study we attempt to explore the genetic relationships between various endogamous North Indian populations and to determine the effect of stringent social regulations on their gene pool. Twenty STR markers were genotyped in 1,800 random North Indians from 9 endogamous populations belonging to upper-caste and middle-caste Hindus and Muslims. All nine populations had high allelic diversity (176 alleles) and average observed heterozygosity (0.742 +/- 0.06), suggesting strong intrapopulation diversity. The average F(ST) value over all loci was as low as 0.0084. However, within-group F(ST) and genetic distance analysis showed that populations of the same group were genetically closer to each other. The genetic distance of Muslims from middle castes (F(ST) = 0.0090; DA = 0.0266) was significantly higher than that of Muslims from upper castes (F(ST) = 0.0050; DA = 0.0148). Phylogenetic trees (neighbor-joining and maximum-likelihood) show the basal cluster pattern of three clusters corresponding to Muslims, upper-caste, and middle-caste populations, with Muslims clustered with upper-caste populations. Based on the results, we conclude that the extensive gene flow through a series of migrations and invasions has created an enormous amount of genetic diversity. The interpopulation differences are minimal but have a definite pattern, in which populations of different socioreligious groups have more genetic similarity within the same group and are genetically more distant from populations of other groups. Finally, North Indian Muslims show a differential genetic relationship with upper- and middle-caste populations.

Population genetic analysis among five Indian population groups using six microsatellite markers.

PubMed

Ghosh, Anu; Das, Birajalaxmi; Seshadri, M

2003-04-01

Genetic variation at six tetranucleotide microsatellites (HUMTHO1, HUMVWA, F13A01, D3S1359, D12S66, and D12S67) has heen determined in five endogamous ethnic population groups of India belonging to two major linguistic families. The populations analyzed were Konkanastha Brahmins and Marathas (Maharashtra state) from the Indo-Aryan linguistic family and Nairs, Ezhavas, and Muslims (Kerala state) from the Dravidian family. All six loci show high gene diversity, ranging from 0.63 +/- 0.04 to 0.84 +/- 0.02. The average GST value observed was 1.7%, indicating that the differences between the populations account for less than 2% of the diversity, while the genetic variation is high within the five population groups studied (>98%). The phylogenetic tree fails to show any clear cluster. The absence of any cluster along with low average GST is suggestive of substantial genetic similarity among the studied populations, in spite of clear geographical, linguistic, and cultural barriers. This similarity indicates either a greater gene flow between these groups or, alternatively, may reflect a recent evolution for them, considering that the Indian caste system evolved only about 3000 years ago.

A Mayan founder mutation is a common cause of deafness in Guatemala.

PubMed

Carranza, C; Menendez, I; Herrera, M; Castellanos, P; Amado, C; Maldonado, F; Rosales, L; Escobar, N; Guerra, M; Alvarez, D; Foster, J; Guo, S; Blanton, S H; Bademci, G; Tekin, M

2015-09-08

Over 5% of the world's population has varying degrees of hearing loss. Mutations in GJB2 are the most common cause of autosomal recessive non-syndromic hearing loss (ARNHL) in many populations. The frequency and type of mutations are influenced by ethnicity. Guatemala is a multi-ethnic country with four major populations: Maya, Ladino, Xinca, and Garifuna. To determine the mutation profile of GJB2 in a ARNHL population from Guatemala, we sequenced both exons of GJB2 in 133 unrelated families. A total of six pathogenic variants were detected. The most frequent pathogenic variant is c.131G>A (p.Trp44*) detected in 21 of 266 alleles. We show that c.131G>A is associated with a conserved haplotype in Guatemala suggesting a single founder. The majority of Mayan population lives in the west region of the country from where all c.131G>A carriers originated. Further analysis of genome-wide variation of individuals carrying the c.131G>A mutation compared with those of Native American, European, and African populations shows a close match with the Mayan population. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

[Respondent-Driven Sampling: a new sampling method to study visible and hidden populations].

PubMed

Mantecón, Alejandro; Juan, Montse; Calafat, Amador; Becoña, Elisardo; Román, Encarna

2008-01-01

The paper introduces a variant of chain-referral sampling: respondent-driven sampling (RDS). This sampling method shows that methods based on network analysis can be combined with the statistical validity of standard probability sampling methods. In this sense, RDS appears to be a mathematical improvement of snowball sampling oriented to the study of hidden populations. However, we try to prove its validity with populations that are not within a sampling frame but can nonetheless be contacted without difficulty. The basics of RDS are explained through our research on young people (aged 14 to 25) who go clubbing, consume alcohol and other drugs, and have sex. Fieldwork was carried out between May and July 2007 in three Spanish regions: Baleares, Galicia and Comunidad Valenciana. The presentation of the study shows the utility of this type of sampling when the population is accessible but there is a difficulty deriving from the lack of a sampling frame. However, the sample obtained is not a random representative one in statistical terms of the target population. It must be acknowledged that the final sample is representative of a 'pseudo-population' that approximates to the target population but is not identical to it.

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

PubMed

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

2014-01-01

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

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

PubMed Central

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

2014-01-01

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

Sex difference in blood pressure among South Asian diaspora in Europe and North America and the role of BMI: a meta-analysis.

PubMed

de Munter, J S L; Agyemang, C; van Valkengoed, I G; Bhopal, R; Stronks, K

2011-07-01

It is unclear whether the sex difference that is known to occur in blood pressure (BP) is similar in some South Asian populations. This study presents a meta-analysis of the sex difference in BP, hypertension and the role of body mass index (BMI) in South Asian diaspora compared with populations of European descent. We systematically searched for studies that reported BP and hypertension among South Asian descent populations living in Europe and North America. Weighted mean differences in BP and risk ratios (RR) for hypertension were calculated for men and women. We included 11 studies in this meta-analysis. In general, men had a higher BP and prevalence of hypertension than women, for example, systolic BP was higher in men than in women among the Indian (7.21 mm Hg, 95% confidence interval (CI): 4.46-9.95) and European populations (6.12 mm Hg, 95% CI: 4.45-7.80). The difference was less in the Pakistani population (4.00 mm Hg, 95% CI: 2.65-5.36). The Bangladeshi population showed a comparatively small sex difference in systolic (2.93 mm Hg, 95% CI: 1.20-4.66) and diastolic BP (0.68 mm Hg, 95% CI: -1.76 to 3.12) and prevalence of hypertension (RR 1.28, 95% CI: 0.66-2.46). Sex differences in BMI for the South Asian populations were greater than those in Europeans. The Indian population had similar sex differences in BP and hypertension compared with Europeans, but Pakistani and Bangladeshi had smaller sex differences. Sex differences in BMI might relate to the blunted sex differences in BP in Pakistani and Bangladeshi populations. Further research should focus on factors that underlie this intriguing sex difference among South Asian populations.

Smoking and Genetic Risk Variation across Populations of European, Asian, and African-American Ancestry - A Meta-analysis of Chromosome 15q25

PubMed Central

Chen, Li-Shiun; Saccone, Nancy L.; Culverhouse, Robert C.; Bracci, Paige M.; Chen, Chien-Hsiun; Dueker, Nicole; Han, Younghun; Huang, Hongyan; Jin, Guangfu; Kohno, Takashi; Ma, Jennie Z.; Przybeck, Thomas R.; Sanders, Alan R.; Smith, Jennifer A.; Sung, Yun Ju; Wenzlaff, Angie S.; Wu, Chen; Yoon, Dankyu; Chen, Ying-Ting; Cheng, Yu-Ching; Cho, Yoon Shin; David, Sean P.; Duan, Jubao; Eaton, Charles B.; Furberg, Helena; Goate, Alison M.; Gu, Dongfeng; Hansen, Helen M.; Hartz, Sarah; Hu, Zhibin; Kim, Young Jin; Kittner, Steven J.; Levinson, Douglas F.; Mosley, Thomas H.; Payne, Thomas J.; Rao, DC; Rice, John P.; Rice, Treva K.; Schwantes-An, Tae-Hwi; Shete, Sanjay S.; Shi, Jianxin; Spitz, Margaret R.; Sun, Yan V.; Tsai, Fuu-Jen; Wang, Jen C.; Wrensch, Margaret R.; Xian, Hong; Gejman, Pablo V.; He, Jiang; Hunt, Steven C.; Kardia, Sharon L.; Li, Ming D.; Lin, Dongxin; Mitchell, Braxton D.; Park, Taesung; Schwartz, Ann G.; Shen, Hongbing; Wiencke, John K.; Wu, Jer-Yuarn; Yokota, Jun; Amos, Christopher I.; Bierut, Laura J.

2012-01-01

Recent meta-analyses of European ancestry subjects show strong evidence for association between smoking quantity and multiple genetic variants on chromosome 15q25. This meta-analysis extends the examination of association between distinct genes in the CHRNA5-CHRNA3-CHRNB4 region and smoking quantity to Asian and African American populations to confirm and refine specific reported associations. Association results for a dichotomized cigarettes smoked per day (CPD) phenotype in 27 datasets (European ancestry (N=14,786), Asian (N=6,889), and African American (N=10,912) for a total of 32,587 smokers) were meta-analyzed by population and results were compared across all three populations. We demonstrate association between smoking quantity and markers in the chromosome 15q25 region across all three populations, and narrow the region of association. Of the variants tested, only rs16969968 is associated with smoking (p < 0.01) in each of these three populations (OR=1.33, 95%C.I.=1.25–1.42, p=1.1×10−17 in meta-analysis across all population samples). Additional variants displayed a consistent signal in both European ancestry and Asian datasets, but not in African Americans. The observed consistent association of rs16969968 with heavy smoking across multiple populations, combined with its known biological significance, suggests rs16969968 is most likely a functional variant that alters risk for heavy smoking. We interpret additional association results that differ across populations as providing evidence for additional functional variants, but we are unable to further localize the source of this association. Using the cross-population study paradigm provides valuable insights to narrow regions of interest and inform future biological experiments. PMID:22539395

Smoking and genetic risk variation across populations of European, Asian, and African American ancestry--a meta-analysis of chromosome 15q25.

PubMed

Chen, Li-Shiun; Saccone, Nancy L; Culverhouse, Robert C; Bracci, Paige M; Chen, Chien-Hsiun; Dueker, Nicole; Han, Younghun; Huang, Hongyan; Jin, Guangfu; Kohno, Takashi; Ma, Jennie Z; Przybeck, Thomas R; Sanders, Alan R; Smith, Jennifer A; Sung, Yun Ju; Wenzlaff, Angie S; Wu, Chen; Yoon, Dankyu; Chen, Ying-Ting; Cheng, Yu-Ching; Cho, Yoon Shin; David, Sean P; Duan, Jubao; Eaton, Charles B; Furberg, Helena; Goate, Alison M; Gu, Dongfeng; Hansen, Helen M; Hartz, Sarah; Hu, Zhibin; Kim, Young Jin; Kittner, Steven J; Levinson, Douglas F; Mosley, Thomas H; Payne, Thomas J; Rao, D C; Rice, John P; Rice, Treva K; Schwantes-An, Tae-Hwi; Shete, Sanjay S; Shi, Jianxin; Spitz, Margaret R; Sun, Yan V; Tsai, Fuu-Jen; Wang, Jen C; Wrensch, Margaret R; Xian, Hong; Gejman, Pablo V; He, Jiang; Hunt, Steven C; Kardia, Sharon L; Li, Ming D; Lin, Dongxin; Mitchell, Braxton D; Park, Taesung; Schwartz, Ann G; Shen, Hongbing; Wiencke, John K; Wu, Jer-Yuarn; Yokota, Jun; Amos, Christopher I; Bierut, Laura J

2012-05-01

Recent meta-analyses of European ancestry subjects show strong evidence for association between smoking quantity and multiple genetic variants on chromosome 15q25. This meta-analysis extends the examination of association between distinct genes in the CHRNA5-CHRNA3-CHRNB4 region and smoking quantity to Asian and African American populations to confirm and refine specific reported associations. Association results for a dichotomized cigarettes smoked per day phenotype in 27 datasets (European ancestry (N = 14,786), Asian (N = 6,889), and African American (N = 10,912) for a total of 32,587 smokers) were meta-analyzed by population and results were compared across all three populations. We demonstrate association between smoking quantity and markers in the chromosome 15q25 region across all three populations, and narrow the region of association. Of the variants tested, only rs16969968 is associated with smoking (P < 0.01) in each of these three populations (odds ratio [OR] = 1.33, 95% CI = 1.25-1.42, P = 1.1 × 10(-17) in meta-analysis across all population samples). Additional variants displayed a consistent signal in both European ancestry and Asian datasets, but not in African Americans. The observed consistent association of rs16969968 with heavy smoking across multiple populations, combined with its known biological significance, suggests rs16969968 is most likely a functional variant that alters risk for heavy smoking. We interpret additional association results that differ across populations as providing evidence for additional functional variants, but we are unable to further localize the source of this association. Using the cross-population study paradigm provides valuable insights to narrow regions of interest and inform future biological experiments. © 2012 Wiley Periodicals, Inc.

The projection of a test genome onto a reference population and applications to humans and archaic hominins.

PubMed

Yang, Melinda A; Harris, Kelley; Slatkin, Montgomery

2014-12-01

We introduce a method for comparing a test genome with numerous genomes from a reference population. Sites in the test genome are given a weight, w, that depends on the allele frequency, x, in the reference population. The projection of the test genome onto the reference population is the average weight for each x, [Formula: see text]. The weight is assigned in such a way that, if the test genome is a random sample from the reference population, then [Formula: see text]. Using analytic theory, numerical analysis, and simulations, we show how the projection depends on the time of population splitting, the history of admixture, and changes in past population size. The projection is sensitive to small amounts of past admixture, the direction of admixture, and admixture from a population not sampled (a ghost population). We compute the projections of several human and two archaic genomes onto three reference populations from the 1000 Genomes project-Europeans, Han Chinese, and Yoruba-and discuss the consistency of our analysis with previously published results for European and Yoruba demographic history. Including higher amounts of admixture between Europeans and Yoruba soon after their separation and low amounts of admixture more recently can resolve discrepancies between the projections and demographic inferences from some previous studies. Copyright © 2014 by the Genetics Society of America.

Genetic structure of the threatened Hopea chinensis in the Quang Ninh Province, Vietnam.

PubMed

Trang, N T P; Triest, L

2016-04-29

Hopea chinensis Hand-Mazz (synonym H. hongayensis Tardieu), is a wind and insect pollinated species. It is a threatened species known only from two locations: Quang Ninh (Vietnam) and Guangxi (China). As an endemic species, it is worth preserving both for dipterocarp biodiversity, as well as for its medicinal use and economic importance as a fine wood. The genetic diversity and population genetic structure of H. chinensis was investigated, using natural populations distributed throughout the Ba Mun and Cai Lim islands, Quang Ninh Province, Vietnam. A total of 65 alleles were detected. The adult allelic richness was higher than that found in juveniles and seedlings in both populations. Inbreeding was found to be significant in Ba Mun adults (F(ST) = 0.139), as well as in Cai Lim juveniles and seedlings (F(ST) = 0.283 and 0.345, respectively). Evidence of a bottleneck could be detected in the juveniles and seedlings of the Cai Lim population. A Bayesian analysis and F(ST) values suggested high genetic differentiation among the age classes of the Ba Mun and Cai Lim populations. Whereas the adults of the Ba Mun population showed evidence of inbreeding, the next generations showed more potential heterozygotes. In contrast, the adults in the Cai Lim population showed no significant inbreeding, but the observed heterozygosity in the next generation was lower than expected, suggesting significant inbreeding. The H. chinensis populations on islands are developed well and showed re-generation under good condition. Thus, the forestry protector should conserve and protect the natural spatial structure of H. chinensis on each island as their natural habitats and keep them through natural regeneration.

Philopatry drives genetic differentiation in an island archipelago: comparative population genetics of Galapagos Nazca boobies (Sula granti) and great frigatebirds (Fregata minor)

PubMed Central

Levin, Iris I; Parker, Patricia G

2012-01-01

Seabirds are considered highly mobile, able to fly great distances with few apparent barriers to dispersal. However, it is often the case that seabird populations exhibit strong population genetic structure despite their potential vagility. Here we show that Galapagos Nazca booby (Sula granti) populations are substantially differentiated, even within the small geographic scale of this archipelago. On the other hand, Galapagos great frigatebird (Fregata minor) populations do not show any genetic structure. We characterized the genetic differentiation by sampling five colonies of both species in the Galapagos archipelago and analyzing eight microsatellite loci and three mitochondrial genes. Using an F-statistic approach on the multilocus data, we found significant differentiation between nearly all island pairs of Nazca booby populations and a Bayesian clustering analysis provided support for three distinct genetic clusters. Mitochondrial DNA showed less differentiation of Nazca booby colonies; only Nazca boobies from the island of Darwin were significantly differentiated from individuals throughout the rest of the archipelago. Great frigatebird populations showed little to no evidence for genetic differentiation at the same scale. Only two island pairs (Darwin – Wolf, N. Seymour – Wolf) were significantly differentiated using the multilocus data, and only two island pairs had statistically significant φST values (N. Seymour – Darwin, N. Seymour – Wolf) according to the mitochondrial data. There was no significant pattern of isolation by distance for either species calculated using both markers. Seven of the ten Nazca booby migration rates calculated between island pairs were in the south or southeast to north or northwest direction. The population differentiation found among Galapagos Nazca booby colonies, but not great frigatebird colonies, is most likely due to differences in natal and breeding philopatry. PMID:23170212

Allometric shape change and heterochrony in the freeliving coral Trachyphyllia bilobata (Duncan)

NASA Astrophysics Data System (ADS)

Foster, Ann Budd; Johnson, Kenneth G.; Schultz, Lori L.

1988-05-01

Regression analysis has been used to study the relationship between age, size, shape, and surface area in two ancestral-descendant populations of the Neogene Caribbean coral Trachyphyllia bilobata. Analyses of the relationship between size and age show that the relationship is isometric and that little difference occurs between populations in mean corallite length or height and in their rates of growth. Onset of columella growth is significantly earlier, however, in the descendant population. Studies of the relationship between size and shape show that growth is allometric, with shape change occurring in both corallum elongation and pinching of the corallite wall during ontogeny. In the descendant population, pinching and elongation initiate earlier in the ontogeny of the coral. These results suggest that the evolutionary development of the meandroid form in freeliving corals has been accomplished by heterochrony, involving a complex set of disassociated peramorphic changes in ontogeny accompanied by paedomorphic changes in astogeny. Further analyses show that the observed heterochronic changes serve to decrease corallum surface area which may in turn enhance sediment removal and nutrition in unstable habitats.

Climate change threatens polar bear populations: a stochastic demographic analysis.

PubMed

Hunter, Christine M; Caswell, Hal; Runge, Michael C; Regehr, Eric V; Amstrup, Steve C; Stirling, Ian

2010-10-01

The polar bear (Ursus maritimus) depends on sea ice for feeding, breeding, and movement. Significant reductions in Arctic sea ice are forecast to continue because of climate warming. We evaluated the impacts of climate change on polar bears in the southern Beaufort Sea by means of a demographic analysis, combining deterministic, stochastic, environment-dependent matrix population models with forecasts of future sea ice conditions from IPCC general circulation models (GCMs). The matrix population models classified individuals by age and breeding status; mothers and dependent cubs were treated as units. Parameter estimates were obtained from a capture-recapture study conducted from 2001 to 2006. Candidate statistical models allowed vital rates to vary with time and as functions of a sea ice covariate. Model averaging was used to produce the vital rate estimates, and a parametric bootstrap procedure was used to quantify model selection and parameter estimation uncertainty. Deterministic models projected population growth in years with more extensive ice coverage (2001-2003) and population decline in years with less ice coverage (2004-2005). LTRE (life table response experiment) analysis showed that the reduction in lambda in years with low sea ice was due primarily to reduced adult female survival, and secondarily to reduced breeding. A stochastic model with two environmental states, good and poor sea ice conditions, projected a declining stochastic growth rate, log lambdas, as the frequency of poor ice years increased. The observed frequency of poor ice years since 1979 would imply log lambdas approximately - 0.01, which agrees with available (albeit crude) observations of population size. The stochastic model was linked to a set of 10 GCMs compiled by the IPCC; the models were chosen for their ability to reproduce historical observations of sea ice and were forced with "business as usual" (A1B) greenhouse gas emissions. The resulting stochastic population projections showed drastic declines in the polar bear population by the end of the 21st century. These projections were instrumental in the decision to list the polar bear as a threatened species under the U.S. Endangered Species Act.

Climate change threatens polar bear populations: A stochastic demographic analysis

USGS Publications Warehouse

Hunter, C.M.; Caswell, H.; Runge, M.C.; Regehr, E.V.; Amstrup, Steven C.; Stirling, I.

2010-01-01

The polar bear (Ursus maritimus) depends on sea ice for feeding, breeding, and movement. Significant reductions in Arctic sea ice are forecast to continue because of climate warming. We evaluated the impacts of climate change on polar bears in the southern Beaufort Sea by means of a demographic analysis, combining deterministic, stochastic, environment-dependent matrix population models with forecasts of future sea ice conditions from IPCC general circulation models (GCMs). The matrix population models classified individuals by age and breeding status; mothers and dependent cubs were treated as units. Parameter estimates were obtained from a capture-recapture study conducted from 2001 to 2006. Candidate statistical models allowed vital rates to vary with time and as functions of a sea ice covariate. Model averaging was used to produce the vital rate estimates, and a parametric bootstrap procedure was used to quantify model selection and parameter estimation uncertainty. Deterministic models projected population growth in years with more extensive ice coverage (2001-2003) and population decline in years with less ice coverage (2004-2005). LTRE (life table response experiment) analysis showed that the reduction in ?? in years with low sea ice was due primarily to reduced adult female survival, and secondarily to reduced breeding. A stochastic model with two environmental states, good and poor sea ice conditions, projected a declining stochastic growth rate, log ??s, as the frequency of poor ice years increased. The observed frequency of poor ice years since 1979 would imply log ??s ' - 0.01, which agrees with available (albeit crude) observations of population size. The stochastic model was linked to a set of 10 GCMs compiled by the IPCC; the models were chosen for their ability to reproduce historical observations of sea ice and were forced with "business as usual" (A1B) greenhouse gas emissions. The resulting stochastic population projections showed drastic declines in the polar bear population by the end of the 21st century. These projections were instrumental in the decision to list the polar bear as a threatened species under the U.S. Endangered Species Act. ?? 2010 by the Ecological Society of America.

Distribution and Differentiation of Wild, Feral, and Cultivated Populations of Perennial Upland Cotton (Gossypium hirsutum L.) in Mesoamerica and the Caribbean

PubMed Central

Coppens d'Eeckenbrugge, Geo; Lacape, Jean-Marc

2014-01-01

Perennial forms of Gossypium hirsutum are classified under seven races. Five Mesoamerican races would have been derived from the wild race ‘yucatanense’ from northern Yucatán. ‘Marie-Galante’, the main race in the Caribbean, would have developed from introgression with G. barbadense. The racial status of coastal populations from the Caribbean has not been clearly defined. We combined Ecological Niche Modeling with an analysis of SSR marker diversity, to elucidate the relationships among cultivated, feral and wild populations of perennial cottons. Out of 954 records of occurrence in Mesoamerica and the Caribbean, 630 were classified into four categories cultivated, feral (disturbed and secondary habitats), wild/feral (protected habitats), and truly wild cotton (TWC) populations. The widely distributed three first categories cannot be differentiated on ecological grounds, indicating they mostly belong to the domesticated pool. In contrast, TWC are restricted to the driest and hottest littoral habitats, in northern Yucatán and in the Caribbean (from Venezuela to Florida), as confirmed by their climatic envelope in the factorial analysis. Extrapolating this TWC climatic model to South America and the Pacific Ocean points towards places where other wild representatives of tetraploid Gossypium species have been encountered. The genetic analysis sample comprised 42 TWC accessions from 12 sites and 68 feral accessions from 18 sites; at nine sites, wild and feral accessions were collected in close vicinity. Principal coordinate analysis, neighbor joining, and STRUCTURE consistently showed a primary divergence between TWC and feral cottons, and a secondary divergence separating ‘Marie-Galante’ from all other feral accessions. This strong genetic structure contrasts strikingly with the absence of geographic differentiation. Our results show that TWC populations of Mesoamerica and the Caribbean constitute a homogenous gene pool. Furthermore, the relatively low genetic divergence between the Mesoamerican and Caribbean domesticated pools supports the hypothesis of domestication of G. hirsutum in northern Yucatán. PMID:25198534

[Fenetic analysis of aboriginal and introduced sable (Martes zibellina) populations in Russia].

PubMed

Monakhov, V G

2001-09-01

Using standard and mulivariate statistic methods, an epigenetic character--foramina in fossa condyloidei inferior, FFCI--was studied in sable populations. This character was shown to be most frequent in southeastern populations of the species (Primorye and the Baikal region) while its distribution in the remaining part of the range was polyclinal. The expression of FFCI was directly associated with coat color and longitude, and inversely associated with skull size. This trend was broken by some western populations formed in the 1950s by introduction, which exhibited stable morphological differences with adjacent aboriginal sable populations. Most populations of the species exhibit differences in the manifestation of the character. Frequency of the FFCI manifestation can be used as an additional population characteristic, an associative diagnostic character that shows high discriminating capability in detecting phenogenetic relationships of intraspecific groups.

Rasch validation of the PHQ-9 in people with visual impairment in South India.

PubMed

Gothwal, Vijaya K; Bagga, Deepak K; Sumalini, Rebecca

2014-01-01

The Patient-Health Questionnaire (PHQ-9) is a widely used screening instrument for depression. Recently, its properties as a measure were investigated using Rasch analysis in an Australian population with visual impairment (VI) and it was demonstrated to possess excellent measurement properties, but the response scale required shortening (modified PHQ-9). However, further validation was recommended to substantiate its use with the growing population of VI. Therefore, we aimed to use Rasch analysis to evaluate the measurement properties of the modified PHQ-9 in an Indian population with VI. 303 patients with VI (mean age 40.2 years; 71% male) referred to Vision Rehabilitation Centres were administered the PHQ-9 by trained interviewer. Rasch analysis was used to investigate the psychometric properties of the modified PHQ-9. Rasch analysis showed good fit to the model, no misfitting items and an acceptable person separation reliability (0.82). Dimensionality testing supported combining 9 items to create a total score. Targeting was sub-optimal (-1.30 logits); more difficult items are needed. One item ('trouble falling asleep') showed notable differential item functioning, DIF (1.18 logits) by duration of VI. The generalisability of these results might be restricted to patients with VI presenting to a tertiary eye care centre. Except for DIF, the performance of the modified PHQ-9 is consistent with that of the original, albeit in a different cultural context (Indian population with VI). Clinicians/researchers can readily use the modified PHQ-9 without formal training in Rasch procedures given the provision of ready-to-use spreadsheets that convert raw to Rasch-scaled scores. However the conversions will apply only if the sample being tested is similar to that of the present study. Copyright © 2014 Elsevier B.V. All rights reserved.

The functional spectrum of low-frequency coding variation.

PubMed

Marth, Gabor T; Yu, Fuli; Indap, Amit R; Garimella, Kiran; Gravel, Simon; Leong, Wen Fung; Tyler-Smith, Chris; Bainbridge, Matthew; Blackwell, Tom; Zheng-Bradley, Xiangqun; Chen, Yuan; Challis, Danny; Clarke, Laura; Ball, Edward V; Cibulskis, Kristian; Cooper, David N; Fulton, Bob; Hartl, Chris; Koboldt, Dan; Muzny, Donna; Smith, Richard; Sougnez, Carrie; Stewart, Chip; Ward, Alistair; Yu, Jin; Xue, Yali; Altshuler, David; Bustamante, Carlos D; Clark, Andrew G; Daly, Mark; DePristo, Mark; Flicek, Paul; Gabriel, Stacey; Mardis, Elaine; Palotie, Aarno; Gibbs, Richard

2011-09-14

Rare coding variants constitute an important class of human genetic variation, but are underrepresented in current databases that are based on small population samples. Recent studies show that variants altering amino acid sequence and protein function are enriched at low variant allele frequency, 2 to 5%, but because of insufficient sample size it is not clear if the same trend holds for rare variants below 1% allele frequency. The 1000 Genomes Exon Pilot Project has collected deep-coverage exon-capture data in roughly 1,000 human genes, for nearly 700 samples. Although medical whole-exome projects are currently afoot, this is still the deepest reported sampling of a large number of human genes with next-generation technologies. According to the goals of the 1000 Genomes Project, we created effective informatics pipelines to process and analyze the data, and discovered 12,758 exonic SNPs, 70% of them novel, and 74% below 1% allele frequency in the seven population samples we examined. Our analysis confirms that coding variants below 1% allele frequency show increased population-specificity and are enriched for functional variants. This study represents a large step toward detecting and interpreting low frequency coding variation, clearly lays out technical steps for effective analysis of DNA capture data, and articulates functional and population properties of this important class of genetic variation.

The history of introduction of the African baobab (Adansonia digitata, Malvaceae: Bombacoideae) in the Indian subcontinent

PubMed Central

Bell, Karen L.; Rangan, Haripriya; Kull, Christian A.; Murphy, Daniel J.

2015-01-01

To investigate the pathways of introduction of the African baobab, Adansonia digitata, to the Indian subcontinent, we examined 10 microsatellite loci in individuals from Africa, India, the Mascarenes and Malaysia, and matched this with historical evidence of human interactions between source and destination regions. Genetic analysis showed broad congruence of African clusters with biogeographic regions except along the Zambezi (Mozambique) and Kilwa (Tanzania), where populations included a mixture of individuals assigned to at least two different clusters. Individuals from West Africa, the Mascarenes, southeast India and Malaysia shared a cluster. Baobabs from western and central India clustered separately from Africa. Genetic diversity was lower in populations from the Indian subcontinent than in African populations, but the former contained private alleles. Phylogenetic analysis showed Indian populations were closest to those from the Mombasa-Dar es Salaam coast. The genetic results provide evidence of multiple introductions of African baobabs to the Indian subcontinent over a longer time period than previously assumed. Individuals belonging to different genetic clusters in Zambezi and Kilwa may reflect the history of trafficking captives from inland areas to supply the slave trade between the fifteenth and nineteenth centuries. Baobabs in the Mascarenes, southeast India and Malaysia indicate introduction from West Africa through eighteenth and nineteenth century European colonial networks. PMID:26473060

The history of introduction of the African baobab (Adansonia digitata, Malvaceae: Bombacoideae) in the Indian subcontinent.

PubMed

Bell, Karen L; Rangan, Haripriya; Kull, Christian A; Murphy, Daniel J

2015-09-01

To investigate the pathways of introduction of the African baobab, Adansonia digitata, to the Indian subcontinent, we examined 10 microsatellite loci in individuals from Africa, India, the Mascarenes and Malaysia, and matched this with historical evidence of human interactions between source and destination regions. Genetic analysis showed broad congruence of African clusters with biogeographic regions except along the Zambezi (Mozambique) and Kilwa (Tanzania), where populations included a mixture of individuals assigned to at least two different clusters. Individuals from West Africa, the Mascarenes, southeast India and Malaysia shared a cluster. Baobabs from western and central India clustered separately from Africa. Genetic diversity was lower in populations from the Indian subcontinent than in African populations, but the former contained private alleles. Phylogenetic analysis showed Indian populations were closest to those from the Mombasa-Dar es Salaam coast. The genetic results provide evidence of multiple introductions of African baobabs to the Indian subcontinent over a longer time period than previously assumed. Individuals belonging to different genetic clusters in Zambezi and Kilwa may reflect the history of trafficking captives from inland areas to supply the slave trade between the fifteenth and nineteenth centuries. Baobabs in the Mascarenes, southeast India and Malaysia indicate introduction from West Africa through eighteenth and nineteenth century European colonial networks.

The variability of lower third molar development in Northeast Malaysian population with application to age estimation.

PubMed

Johan, N A; Khamis, M F; Abdul Jamal, N Sk; Ahmad, B; Mahanani, E S

2012-07-01

This study aimed to assess the variability of the lower third molar (tooth 38 and 48) development in Northeast Malaysian population with respect to the side of dentition, to generate age prediction models and to compare the outcome with other studies. A total of 1080 orthopantomograms of Northeast Malaysian population aged between 14 and 25 years (540 males and 540 females) from the Hospital Universiti Sains Malaysia's archive which met the inclusion and exclusion criteria were selected and the maturity stages of tooth 38 and 48 were scored using Demirjian's stages (A-H). The findings showed a wide variation of the development of lower third molars in the Northeast Malaysian population. The roots developed earlier in males than in females. The development of the dentition on opposite sides of the mandible was synchronously in females and males. A multiple regression analysis shows that 71.1% of variance in age was explained by sex and developmental stage of tooth 48. An age prediction model was generated from the regression analysis: [Age = 7.117 + 1.907*(stage of tooth 48) - 0.432*(sex)] with mean prediction errors between -0.17 to 3.14 years. The obtained data in the current study are useful for references and determining age of unidentified human remains for identification investigation.

[New risks of addiction for new populations: the example of hackers].

PubMed

Tisserand, I N

2000-10-01

Our purpose was to examine recent social and technical habits related to high-tech environments. Our goal was to show that the prevention of risk behaviors due to training in data processing, requires an interdisciplinary approach where medical anthropology could benefit from and exchange of complementary information sources (particularly from psychiatrics and psychoanalysis). We used this approach to search for solutions regarding new kinds of addiction. When identifying pathological conditions and proposing appropriate care, these solutions must take into consideration the progressive loss of human nature in data processing environments and the very important and highly sophisticated relationship established between the human being and the computer. We looked at the hacker population as a modern tribe and marginal group. Our analysis led to a better understanding of this kind of artificial culture, sometimes called a "high-tech" or "cyber" culture. The hacker population is integrating new rituals, languages and special rhythms which induce addictions. We show how high-tech environments operating in e-time and e-life induce addictions. This work illustrates a classical anthropological approach to the question (ethnological fields, interviews, literature analysis). The major challenge is to explain how high-tech environments present high risks for dependency in the hacker population and other, unwarned, computer (ab)users.

Does marital status predict the odds of suicidal death in taiwan? A seven-year population-based study.

PubMed

Yeh, Jui-Yuan; Xirasagar, Sudha; Liu, Tsai-Ching; Li, Chong-Yi; Lin, Herng-Ching

2008-06-01

Using nationwide, 7-year population-based data for 1997-2003, we examined marital status to see if it predicted suicide among the ethnic Chinese population of Taiwan. Using cause of death data, with a case-control design, two groups-total adult suicide deaths, n = 17,850, the study group, and adult deaths other than suicide, n = 71,400 (randomly selected from age, sex, and geographic region matched controls, four per suicide)-were studied. Using multiple logistic regression analysis including age-marital status interaction, adjusted estimates show divorced status to be the most detrimental for suicide propensity, with males showing stronger effect size. Females never married, aged below 35 and 65-plus, and widowed 65-plus had lower suicide odds.

Effects of urbanization on benthic macroinvertebrate communities in streams, Anchorage, Alaska

USGS Publications Warehouse

Ourso, Robert T.

2001-01-01

The effect of urbanization on stream macroinvertebrate communities was examined by using data gathered during a 1999 reconnaissance of 14 sites in the Municipality of Anchorage, Alaska. Data collected included macroinvertebrate abundance, water chemistry, and trace elements in bed sediments. Macroinvertebrate relative-abundance data were edited and used in metric and index calculations. Population density was used as a surrogate for urbanization. Cluster analysis (unweighted-paired-grouping method) using arithmetic means of macroinvertebrate presence-absence data showed a well-defined separation between urbanized and nonurbanized sites as well as extracted sites that did not cleanly fall into either category. Water quality in Anchorage generally declined with increasing urbanization (population density). Of 59 variables examined, 31 correlated with urbanization. Local regression analysis extracted 11 variables that showed a significant impairment threshold response and 6 that showed a significant linear response. Significant biological variables for determining the impairment threshold in this study were the Margalef diversity index, Ephemeroptera-Plecoptera-Trichoptera taxa richness, and total taxa richness. Significant thresholds were observed in the water-chemistry variables conductivity, dissolved organic carbon, potassium, and total dissolved solids. Significant thresholds in trace elements in bed sediments included arsenic, iron, manganese, and lead. Results suggest that sites in Anchorage that have ratios of population density to road density greater than 70, storm-drain densities greater than 0.45 miles per square mile, road densities greater than 4 miles per square mile, or population densities greater than 125-150 persons per square mile may require further monitoring to determine if the stream has become impaired. This population density is far less than the 1,000 persons per square mile used by the U.S. Census Bureau to define an urban area.

Relationship between blood manganese and blood pressure in the Korean general population according to KNHANES 2008

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

Lee, Byung-Kook; Kim, Yangho, E-mail: yanghokm@nuri.net

Introduction: We present data on the association of manganese (Mn) level with hypertension in a representative sample of the adult Korean population who participated in the Korean National Health and Nutrition Examination Survey (KNHANES) 2008. Methods: This study was based on the data obtained by KNHANES 2008, which was conducted for three years (2007-2009) using a rolling sampling design involving a complex, stratified, multistage, probability-cluster survey of a representative sample of the noninstitutionalized civilian population of South Korea. Results: Multiple regression analysis after controlling for covariates, including gender, age, regional area, education level, smoking, drinking status, hemoglobin, and serum creatinine,more » showed that the beta coefficients of log blood Mn were 3.514, 1.878, and 2.517 for diastolic blood pressure, and 3.593, 2.449, and 2.440 for systolic blood pressure in female, male, and all participants, respectively. Multiple regression analysis including three other blood metals, lead, mercury, and cadmium, revealed no significant effects of the three metals on blood pressure and showed no effect on the association between blood Mn and blood pressure. In addition, doubling the blood Mn increased the risk of hypertension 1.828, 1.573, and 1.567 fold in women, men, and all participants, respectively, after adjustment for covariates. The addition of blood lead, mercury, and cadmium as covariates did not affect the association between blood Mn and the prevalence of hypertension. Conclusion: Blood Mn level was associated with an increased risk of hypertension in a representative sample of the Korean adult population. - Highlights: {yields} We showed the association of manganese with hypertension in Korean population. {yields} This study was based on the data obtained by KNHANES 2008. {yields} Blood manganese level was associated with an increased risk of hypertension.« less

Population genetics of the westernmost distribution of the glaciations-surviving black truffle Tuber melanosporum.

PubMed

García-Cunchillos, Iván; Sánchez, Sergio; Barriuso, Juan José; Pérez-Collazos, Ernesto

2014-04-01

The black truffle (Tuber melanosporum Vittad.) is an important natural resource due to its relevance as a delicacy in gastronomy. Different aspects of this hypogeous fungus species have been studied, including population genetics of French and Italian distribution ranges. Although those studies include some Spanish populations, this is the first time that the genetic diversity and genetic structure of the wide geographical range of the natural Spanish populations have been analysed. To achieve this goal, 23 natural populations were sampled across the Spanish geographical distribution. ISSR technique demonstrated its reliability and capability to detect high levels of polymorphism in the species. Studied populations showed high levels of genetic diversity (h N  = 0.393, h S  = 0.678, Hs = 0.418), indicating a non threatened genetic conservation status. These high levels may be a consequence of the wide distribution range of the species, of its spore dispersion by animals, and by its evolutionary history. AMOVA analysis showed a high degree of genetic structure among populations (47.89%) and other partitions as geographical ranges. Bayesian genetic structure analyses differentiated two main Spanish groups separated by the Iberian Mountain System, and showed the genetic uniqueness of some populations. Our results suggest the survival of some of these populations during the last glaciation, the Spanish southern distribution range perhaps surviving as had occurred in France and Italy, but it is also likely that specific northern areas may have acted as a refugia for the later dispersion to other calcareous areas in the Iberian Peninsula and probably France.

Landscape genomics and pathway analysis to understand genetic adaptation of South African indigenous goat populations.

PubMed

Mdladla, K; Dzomba, E F; Muchadeyi, F C

2018-04-01

In Africa, extensively raised livestock populations in most smallholder farming communities are exposed to harsh and heterogeneous climatic conditions and disease pathogens that they adapt to in order to survive. Majority of these livestock species, including goats, are of non-descript and uncharacterized breeds and their response to natural selection presented by heterogeneous environments is still unresolved. This study investigated genetic diversity and its association with environmental and geographic conditions in 194 South African indigenous goats from different geographic locations genotyped on the Illumina goat SNP50K panel. Population structure analysis revealed a homogeneous genetic cluster of the Tankwa goats, restricted to the Northern Cape province. Overall, the Boer, Kalahari Red, and Savanna showed a wide geographic spread of shared genetic components, whereas the village ecotypes revealed a longitudinal distribution. The relative importance of environmental factors on genetic variation of goat populations was assessed using redundancy analysis (RDA). Climatic and geographic variables explained 22% of the total variation while climatic variables alone accounted for 17% of the diversity. Geographic variables solitarily explained 1% of the total variation. The first axis (Model I) of the RDA analysis revealed 329 outlier SNPs. Landscape genomic approaches of spatial analysis method (SAM) identified a total of 843 (1.75%) SNPs, while latent factor mixed models (LFMM) identified 714 (1.48%) SNPs significantly associated with environmental variables. Significant markers were within genes involved in biological functions potentially important for environmental adaptation. Overall, the study suggested environmental factors to have some effect in shaping the genetic variation of South African indigenous goat populations. Loci observed to be significant and under selection may be responsible for the adaption of the goat populations to local production systems.

Correspondence regarding Zhong et al., BMC Bioinformatics 2013 Mar 7;14:89.

PubMed

Kuhn, Alexandre

2014-11-28

Computational expression deconvolution aims to estimate the contribution of individual cell populations to expression profiles measured in samples of heterogeneous composition. Zhong et al. recently proposed Digital Sorting Algorithm (BMC Bioinformatics 2013 Mar 7;14:89) and showed that they could accurately estimate population-specific expression levels and expression differences between two populations. They compared DSA with Population-Specific Expression Analysis (PSEA), a previous deconvolution method that we developed to detect expression changes occurring within the same population between two conditions (e.g. disease versus non-disease). However, Zhong et al. compared PSEA-derived specific expression levels across different cell populations. Specific expression levels obtained with PSEA cannot be directly compared across different populations as they are on a relative scale. They are accurate as we demonstrate by deconvolving the same dataset used by Zhong et al. and, importantly, allow for comparison of population-specific expression across conditions.

Heterogeneous Suppression of Sequential Effects in Random Sequence Generation, but Not in Operant Learning.

PubMed

Shteingart, Hanan; Loewenstein, Yonatan

2016-01-01

There is a long history of experiments in which participants are instructed to generate a long sequence of binary random numbers. The scope of this line of research has shifted over the years from identifying the basic psychological principles and/or the heuristics that lead to deviations from randomness, to one of predicting future choices. In this paper, we used generalized linear regression and the framework of Reinforcement Learning in order to address both points. In particular, we used logistic regression analysis in order to characterize the temporal sequence of participants' choices. Surprisingly, a population analysis indicated that the contribution of the most recent trial has only a weak effect on behavior, compared to more preceding trials, a result that seems irreconcilable with standard sequential effects that decay monotonously with the delay. However, when considering each participant separately, we found that the magnitudes of the sequential effect are a monotonous decreasing function of the delay, yet these individual sequential effects are largely averaged out in a population analysis because of heterogeneity. The substantial behavioral heterogeneity in this task is further demonstrated quantitatively by considering the predictive power of the model. We show that a heterogeneous model of sequential dependencies captures the structure available in random sequence generation. Finally, we show that the results of the logistic regression analysis can be interpreted in the framework of reinforcement learning, allowing us to compare the sequential effects in the random sequence generation task to those in an operant learning task. We show that in contrast to the random sequence generation task, sequential effects in operant learning are far more homogenous across the population. These results suggest that in the random sequence generation task, different participants adopt different cognitive strategies to suppress sequential dependencies when generating the "random" sequences.

Y-chromosomal analysis of Greek Cypriots reveals a primarily common pre-Ottoman paternal ancestry with Turkish Cypriots

PubMed Central

Fernández-Domínguez, Eva; Bertoncini, Stefania; Chimonas, Marios; Christofi, Vasilis; King, Jonathan; Budowle, Bruce; Manoli, Panayiotis

2017-01-01

Genetics can provide invaluable information on the ancestry of the current inhabitants of Cyprus. A Y-chromosome analysis was performed to (i) determine paternal ancestry among the Greek Cypriot (GCy) community in the context of the Central and Eastern Mediterranean and the Near East; and (ii) identify genetic similarities and differences between Greek Cypriots (GCy) and Turkish Cypriots (TCy). Our haplotype-based analysis has revealed that GCy and TCy patrilineages derive primarily from a single gene pool and show very close genetic affinity (low genetic differentiation) to Calabrian Italian and Lebanese patrilineages. In terms of more recent (past millennium) ancestry, as indicated by Y-haplotype sharing, GCy and TCy share much more haplotypes between them than with any surrounding population (7–8% of total haplotypes shared), while TCy also share around 3% of haplotypes with mainland Turks, and to a lesser extent with North Africans. In terms of Y-haplogroup frequencies, again GCy and TCy show very similar distributions, with the predominant haplogroups in both being J2a-M410, E-M78, and G2-P287. Overall, GCy also have a similar Y-haplogroup distribution to non-Turkic Anatolian and Southwest Caucasian populations, as well as Cretan Greeks. TCy show a slight shift towards Turkish populations, due to the presence of Eastern Eurasian (some of which of possible Ottoman origin) Y-haplogroups. Overall, the Y-chromosome analysis performed, using both Y-STR haplotype and binary Y-haplogroup data puts Cypriot in the middle of a genetic continuum stretching from the Levant to Southeast Europe and reveals that despite some differences in haplotype sharing and haplogroup structure, Greek Cypriots and Turkish Cypriots share primarily a common pre-Ottoman paternal ancestry. PMID:28622394

Y-chromosomal analysis of Greek Cypriots reveals a primarily common pre-Ottoman paternal ancestry with Turkish Cypriots.

PubMed

Heraclides, Alexandros; Bashiardes, Evy; Fernández-Domínguez, Eva; Bertoncini, Stefania; Chimonas, Marios; Christofi, Vasilis; King, Jonathan; Budowle, Bruce; Manoli, Panayiotis; Cariolou, Marios A

2017-01-01

Genetics can provide invaluable information on the ancestry of the current inhabitants of Cyprus. A Y-chromosome analysis was performed to (i) determine paternal ancestry among the Greek Cypriot (GCy) community in the context of the Central and Eastern Mediterranean and the Near East; and (ii) identify genetic similarities and differences between Greek Cypriots (GCy) and Turkish Cypriots (TCy). Our haplotype-based analysis has revealed that GCy and TCy patrilineages derive primarily from a single gene pool and show very close genetic affinity (low genetic differentiation) to Calabrian Italian and Lebanese patrilineages. In terms of more recent (past millennium) ancestry, as indicated by Y-haplotype sharing, GCy and TCy share much more haplotypes between them than with any surrounding population (7-8% of total haplotypes shared), while TCy also share around 3% of haplotypes with mainland Turks, and to a lesser extent with North Africans. In terms of Y-haplogroup frequencies, again GCy and TCy show very similar distributions, with the predominant haplogroups in both being J2a-M410, E-M78, and G2-P287. Overall, GCy also have a similar Y-haplogroup distribution to non-Turkic Anatolian and Southwest Caucasian populations, as well as Cretan Greeks. TCy show a slight shift towards Turkish populations, due to the presence of Eastern Eurasian (some of which of possible Ottoman origin) Y-haplogroups. Overall, the Y-chromosome analysis performed, using both Y-STR haplotype and binary Y-haplogroup data puts Cypriot in the middle of a genetic continuum stretching from the Levant to Southeast Europe and reveals that despite some differences in haplotype sharing and haplogroup structure, Greek Cypriots and Turkish Cypriots share primarily a common pre-Ottoman paternal ancestry.

Expression of depressive symptoms in a nonclinical Brazilian adolescent sample.

PubMed

Gorenstein, Clarice; Andrade, Laura; Zanolo, Elaine; Artes, Rinaldo

2005-03-01

This study aimed to detect the prevalence of depressive symptomatology and its expression in a nonclinical Brazilian adolescent student sample. A sample of students from private and public schools (n = 1555, aged 13 to 17 years) answered the Beck Depression Inventory (BDI). We performed factor analysis of the BDI as an indicator of the expression of depressive symptomatology. The following cut-off scores defined nonclinical subgroups: "nondepressed," BDI < 15; "dysphoria," BDI 16 to 20; and "depressed," BDI > 20. We used discriminant analysis to test whether these subgroups could be separated by the depression-specific and nonspecific items. The point prevalence of depression was 7.6%, according to the BDI cut-off of 20. Girls had higher scores than boys in several items. Scores increased with age. Students from public schools had higher scores than did private school students. Factor analysis showed 2 common factors for the total sample and for each sex: the cognitive affective dimension and the somatic nonspecific dimension. In the adolescents showing clinical depression, items related to self-depreciation, sense of failure, guilty feelings, self-dislike, suicidal wishes, and distortion of body image were common components of BDI factors. Discriminant analysis showed that the BDI highly discriminates depressive symptomatology in adolescent students and also measures specific aspects of depression. The BDI is useful as a measure of specific aspects of depression in nonclinical adolescent samples; it was able to detect depression in approximately 7% of the surveyed population. The expression of depressive symptoms in a Brazilian adolescent population is compatible with international studies in this age group. Detecting depressive symptoms in a school population is a critical preventive strategy; to avoid damage to the learning process, it should be followed with further referral to treatment when needed.

Two decades of demography reveals that seed and seedling transitions limit population persistence in a translocated shrub

PubMed Central

Gross, C. L.; Mackay, D.

2014-01-01

Background and Aims Olearia flocktoniae is an endangered shrub that was passively translocated from its natural ecosystem, where it has since gone extinct. This study aimed to determine sensitivities vital to populations persisting in human-created areas. Methods Population colonization, longevity and extinction were investigated over 20 years using 133 populations. Seed-bank longevity was determined from germination trials of seeds exhumed from extinct and extant sites via a 10-year glasshouse trial and by in situ sowing experiments. From 27 populations, 98 cohorts were followed and matrix models of transitions from seeds to adults were used to evaluate the intrinsic rate of population growth against disturbance histories. Ten populations (38 cohorts) with different disturbance histories were used to evaluate sensitivities in vital rates. Key Results Most populations had few individuals (∼30) and were transient (<5 years above ground). The intrinsic population growth rate was rarely >1 and all but two populations were extinct at year 20. Seeds were short-lived in situ. Although >1000 seeds per plant were produced annually in most populations, sensitivity analysis showed that the transition to the seed bank and the transition from the seed bank to seedlings are key vulnerabilities in the life-cycle. Conclusions Seedling establishment is promoted by recent disturbance. Increasing the number of disturbance events in populations, even severe disturbances that almost extirpate populations, significantly increases longer-term population persistence. Only populations that were disturbed annually survived the full 20 years of the study. The results show that translocated populations of O. flocktoniae will fail to persist without active management. PMID:24844983

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

Equilibrium analysis of a yellow Fever dynamical model with vaccination.

PubMed

Martorano Raimundo, Silvia; Amaku, Marcos; Massad, Eduardo

2015-01-01

We propose an equilibrium analysis of a dynamical model of yellow fever transmission in the presence of a vaccine. The model considers both human and vector populations. We found thresholds parameters that affect the development of the disease and the infectious status of the human population in the presence of a vaccine whose protection may wane over time. In particular, we derived a threshold vaccination rate, above which the disease would be eradicated from the human population. We show that if the mortality rate of the mosquitoes is greater than a given threshold, then the disease is naturally (without intervention) eradicated from the population. In contrast, if the mortality rate of the mosquitoes is less than that threshold, then the disease is eradicated from the populations only when the growing rate of humans is less than another threshold; otherwise, the disease is eradicated only if the reproduction number of the infection after vaccination is less than 1. When this reproduction number is greater than 1, the disease will be eradicated from the human population if the vaccination rate is greater than a given threshold; otherwise, the disease will establish itself among humans, reaching a stable endemic equilibrium. The analysis presented in this paper can be useful, both to the better understanding of the disease dynamics and also for the planning of vaccination strategies.

Population genetic analysis of Mountain Plover using mitochondrial DNA sequence data

USGS Publications Warehouse

Oyler-McCance, S.J.; St. John, J.; Knopf, F.L.; Quinn, T.W.

2005-01-01

Mountain Plover (Charadrius montanus) distribution and abundance have been reduced drastically in the past 30 years and the conversion of shortgrass prairie to agriculture has caused breeding populations to become geographically isolated. This, coupled with the fact that Mountain Plovers are thought to show fidelity to breeding grounds, leads to the prediction that the isolated breeding populations would be genetically distinct. This pattern, if observed, would have important management implications for a species at risk of extinction. Our study examined genetic variation at two mitochondrial regions for 20–30 individuals from each of four breeding sites. We found no evidence of significant population differentiation in the data from the control region or the ATPase 6/8 region. Nested-clade analysis revealed no relationship between haplotype phylogeny, and geography among the 47 control region haplotypes. In the ATPase 6/8 region, however, one of the two clades provided information suggesting that, historically, there has been continuous range expansion. Analysis of mismatch distributions and Tajima's D suggest that the Mountain Plover underwent a population expansion, following the Pleistocene glacial period. To explain the lack of detectable genetic differentiation among populations, despite their geographic isolation and fidelity to breeding locations, we speculate that there is sufficient female-mediated gene flow to homogenize gene pools among populations. Such gene flow might ensue if pair bonds are formed in mixed flocks on wintering grounds rather than on the summer breeding grounds.

Polymorphisms of HLA-DRB1, -DQA1 and -DQB1 in inhabitants of Astana, the capital city of Kazakhstan.

PubMed

Kuranov, Alexandr B; Vavilov, Mikhail N; Abildinova, Gulshara Zh; Akilzhanova, Ainur R; Iskakova, Aisha N; Zholdybayeva, Elena V; Boldyreva, Margarita N; Müller, Claudia A; Momynaliev, Kuvat T

2014-01-01

Kazakhstan has been inhabited by different populations, such as the Kazakh, Kyrgyz, Uzbek and others. Here we investigate allelic and haplotypic polymorphisms of human leukocyte antigen (HLA) genes at DRB1, DQA1 and DQB1 loci in the Kazakh ethnic group, and their genetic relationship between world populations. A total of 157 unrelated Kazakh ethnic individuals from Astana were genotyped using sequence based typing (SBT-Method) for HLA-DRB1, -DQA1 and -DQB1 loci. Allele frequencies, neighbor-joining method, and multidimensional scaling analysis have been obtained for comparison with other world populations. Statistical analyses were performed using Arlequin v3.11. Applying the software PAST v. 2.17 the resulting genetic distance matrix was used for a multidimensional scaling analysis (MDS). Respectively 37, 17 and 19 alleles were observed at HLA-DRB1, -DQA1 and -DQB1 loci. The most frequent alleles were HLA-DRB1*07:01 (13.1%), HLA-DQA1*03:01 (13.1%) and HLA-DQB1*03:01 (17.6%). In the observed group of Kazakhs DRB1*07:01-DQA1*02:01-DQB1*02:01 (8.0%) was the most common three loci haplotype. DRB1*10:01-DQB1*05:01 showed the strongest linkage disequilibrium. The Kazakh population shows genetic kinship with the Kazakhs from China, Uyghurs, Mongolians, Todzhinians, Tuvinians and as well as with other Siberians and Asians. The HLA-DRB1, -DQA1 and -DQB1 loci are highly polymorphic in the Kazakh population, and this population has the closest relationship with other Asian and Siberian populations.

Population Fisher information matrix and optimal design of discrete data responses in population pharmacodynamic experiments.

PubMed

Ogungbenro, Kayode; Aarons, Leon

2011-08-01

In the recent years, interest in the application of experimental design theory to population pharmacokinetic (PK) and pharmacodynamic (PD) experiments has increased. The aim is to improve the efficiency and the precision with which parameters are estimated during data analysis and sometimes to increase the power and reduce the sample size required for hypothesis testing. The population Fisher information matrix (PFIM) has been described for uniresponse and multiresponse population PK experiments for design evaluation and optimisation. Despite these developments and availability of tools for optimal design of population PK and PD experiments much of the effort has been focused on repeated continuous variable measurements with less work being done on repeated discrete type measurements. Discrete data arise mainly in PDs e.g. ordinal, nominal, dichotomous or count measurements. This paper implements expressions for the PFIM for repeated ordinal, dichotomous and count measurements based on analysis by a mixed-effects modelling technique. Three simulation studies were used to investigate the performance of the expressions. Example 1 is based on repeated dichotomous measurements, Example 2 is based on repeated count measurements and Example 3 is based on repeated ordinal measurements. Data simulated in MATLAB were analysed using NONMEM (Laplace method) and the glmmML package in R (Laplace and adaptive Gauss-Hermite quadrature methods). The results obtained for Examples 1 and 2 showed good agreement between the relative standard errors obtained using the PFIM and simulations. The results obtained for Example 3 showed the importance of sampling at the most informative time points. Implementation of these expressions will provide the opportunity for efficient design of population PD experiments that involve discrete type data through design evaluation and optimisation.

A population of wheat multiple synthetic derivatives: an effective platform to explore, harness and utilize genetic diversity of Aegilops tauschii for wheat improvement.

PubMed

Gorafi, Yasir Serag Alnor; Kim, June-Sik; Elbashir, Awad Ahmed Elawad; Tsujimoto, Hisashi

2018-04-28

The multiple synthetic derivatives platform described in this study will provide an opportunity for effective utilization of Aegilops tauschii traits and genes for wheat breeding. Introducing genes from wild relatives is the best option to increase genetic diversity and discover new alleles necessary for wheat improvement. A population harboring genomic fragments from the diploid wheat progenitor Aegilops tauschii Coss. in the background of bread wheat (Triticum aestivum L.) was developed by crossing and backcrossing 43 synthetic wheat lines with the common wheat cultivar Norin 61. We named this population multiple synthetic derivatives (MSD). To validate the suitability of this population for wheat breeding and genetic studies, we randomly selected 400 MSD lines and genotyped them by using Diversity Array Technology sequencing markers. We scored black glume as a qualitative trait and heading time in two environments in Sudan as a quantitative trait. Our results showed high genetic diversity and less recombination which is expected from the nature of the population. Genome-wide association (GWA) analysis showed one QTL at the short arm of chromosome 1D different from those alleles reported previously indicating that black glume in the MSD population is controlled by new allele at the same locus. For heading time, from the two environments, GWA analysis revealed three QTLs on the short arms of chromosomes 2A, 2B and 2D and two on the long arms of chromosomes 5A and 5D. Using the MSD population, which represents the diversity of 43 Ae. tauschii accessions representing most of its natural habitat, QTLs or genes and desired phenotypes (such as drought, heat and salinity tolerance) could be identified and selected for utilization in wheat breeding.

The reliability and validity of the SF-8 with a conflict-affected population in northern Uganda.

PubMed

Roberts, Bayard; Browne, John; Ocaka, Kaducu Felix; Oyok, Thomas; Sondorp, Egbert

2008-12-02

The SF-8 is a health-related quality of life instrument that could provide a useful means of assessing general physical and mental health amongst populations affected by conflict. The purpose of this study was to test the validity and reliability of the SF-8 with a conflict-affected population in northern Uganda. A cross-sectional multi-staged, random cluster survey was conducted with 1206 adults in camps for internally displaced persons in Gulu and Amuru districts of northern Uganda. Data quality was assessed by analysing the number of incomplete responses to SF-8 items. Response distribution was analysed using aggregate endorsement frequency. Test-retest reliability was assessed in a separate smaller survey using the intraclass correlation test. Construct validity was measured using principal component analysis, and the Pearson Correlation test for item-summary score correlation and inter-instrument correlations. Known groups validity was assessed using a two sample t-test to evaluates the ability of the SF-8 to discriminate between groups known to have, and not have, physical and mental health problems. The SF-8 showed excellent data quality. It showed acceptable item response distribution based upon analysis of aggregate endorsement frequencies. Test-retest showed a good intraclass correlation of 0.61 for PCS and 0.68 for MCS. The principal component analysis indicated strong construct validity and concurred with the results of the validity tests by the SF-8 developers. The SF-8 also showed strong construct validity between the 8 items and PCS and MCS summary score, moderate inter-instrument validity, and strong known groups validity. This study provides evidence on the reliability and validity of the SF-8 amongst IDPs in northern Uganda.

The reliability and validity of the SF-8 with a conflict-affected population in northern Uganda

PubMed Central

Roberts, Bayard; Browne, John; Ocaka, Kaducu Felix; Oyok, Thomas; Sondorp, Egbert

2008-01-01

Background The SF-8 is a health-related quality of life instrument that could provide a useful means of assessing general physical and mental health amongst populations affected by conflict. The purpose of this study was to test the validity and reliability of the SF-8 with a conflict-affected population in northern Uganda. Methods A cross-sectional multi-staged, random cluster survey was conducted with 1206 adults in camps for internally displaced persons in Gulu and Amuru districts of northern Uganda. Data quality was assessed by analysing the number of incomplete responses to SF-8 items. Response distribution was analysed using aggregate endorsement frequency. Test-retest reliability was assessed in a separate smaller survey using the intraclass correlation test. Construct validity was measured using principal component analysis, and the Pearson Correlation test for item-summary score correlation and inter-instrument correlations. Known groups validity was assessed using a two sample t-test to evaluates the ability of the SF-8 to discriminate between groups known to have, and not have, physical and mental health problems. Results The SF-8 showed excellent data quality. It showed acceptable item response distribution based upon analysis of aggregate endorsement frequencies. Test-retest showed a good intraclass correlation of 0.61 for PCS and 0.68 for MCS. The principal component analysis indicated strong construct validity and concurred with the results of the validity tests by the SF-8 developers. The SF-8 also showed strong construct validity between the 8 items and PCS and MCS summary score, moderate inter-instrument validity, and strong known groups validity. Conclusion This study provides evidence on the reliability and validity of the SF-8 amongst IDPs in northern Uganda. PMID:19055716

Analysis of genetic diversity of Chinese dairy goats via microsatellite markers.

PubMed

Wang, G Z; Chen, S S; Chao, T L; Ji, Z B; Hou, L; Qin, Z J; Wang, J M

2017-05-01

In this study, 15 polymorphic microsatellite markers were used to analyze the genetic structure and phylogenetic relationships of 6 dairy goat breeds in China, including 4 native developed breeds and 2 introduced breeds. The results showed that a total of 172 alleles were detected in 347 samples of the dairy goat breeds included in this study. The mean number of effective alleles per locus was 4.92. Except for BMS0812, all of the remaining microsatellite loci were highly polymorphic (polymorphism information content [PIC] > 0.5). The analysis of genetic diversity parameters, including the number of effective alleles, PIC, and heterozygosity, revealed that the native developed dairy goat breeds in China harbored a rich genetic diversity. However, these breeds showed a low breeding degree and a high population intermix degree, with a certain degree of inbreeding and within-subpopulation inbreeding coefficient ( > 0). The analysis of population genetic differentiation and phylogenetic tree topologies showed a moderate state of genetic differentiation among subpopulations of native developed breed dairy goats in China (0.05 < gene fixation coefficient [] < 0.15). The native developed breeds shared a common ancestor, namely, the Saanen dairy goat, originating from Europe. The results showed that there was a close genetic relationship between Wendeng and Laoshan dairy goats while the Guanzhong dairy goat and the Xinong Saanen dairy goat were also found to have a close genetic relationship, which were both in agreement with the formation history and geographical distribution of the breeds. This study revealed that adopting genetic management strategies, such as expanding pedigree source and strengthening multi-trait selection, is useful in maintaining the genetic diversity of native developed breeds and improving the population uniformity of dairy goats.

First report of Perkinsus beihaiensis in Crassostrea madrasensis from the Indian subcontinent.

PubMed

Sanil, N K; Suja, G; Lijo, J; Vijayan, K K

2012-04-26

Protozoan parasites of the genus Perkinsus are considered important pathogens responsible for mass mortalities in many wild and farmed bivalve populations. The present study was initiated to screen populations of the Indian edible oyster Crassostrea madrasensis, a promising candidate for aquaculture along the Indian coasts, for the presence of Perkinsus spp. The study reports the presence of P. beihaiensis for the first time in C. madrasensis populations from the Indian subcontinent and south Asia. Samples collected from the east and west coasts of India were subjected to Ray's fluid thioglycollate medium (RFTM) culture and histology which indicated the presence of Perkinsus spp. PCR screening of the tissues using specific primers amplified the product specific to the genus Perkinsus. The taxonomic affinities of the parasites were determined by sequencing both internal transcribed spacer (ITS) and actin genes followed by basic local alignment search tool (BLAST) analysis. Analysis based on the ITS sequences showed 98 to 100% identity to Perkinsus spp. (P. beihaiensis and Brazilian Perkinsus sp.). The pairwise genetic distance values and phylogenetic analysis confirmed that 2 of the present samples belonged to the P. beihaiensis clade while the other 4 showed close affinities with the Brazilian Perkinsus sp. clade. The genetic divergence data, close affinity with the Brazilian Perkinsus sp., and co-existence with P. beihaiensis in the same host species in the same habitat show that the remaining 4 samples exhibit some degree of variation from P. beihaiensis. As expected, the sequencing of actin genes did not show any divergence among the samples studied. They probably could be intraspecific variants of P. beihaiensis having a separate lineage in the process of evolution.

Development of EMS-induced mutation population for amylose and resistant starch variation in bread wheat (Triticum aestivum) and identification of candidate genes responsible for amylose variation.

PubMed

Mishra, Ankita; Singh, Anuradha; Sharma, Monica; Kumar, Pankaj; Roy, Joy

2016-10-06

Starch is a major part of cereal grain. It comprises two glucose polymer fractions, amylose (AM) and amylopectin (AP), that make up about 25 and 75 % of total starch, respectively. The ratio of the two affects processing quality and digestibility of starch-based food products. Digestibility determines nutritional quality, as high amylose starch is considered a resistant or healthy starch (RS type 2) and is highly preferred for preventive measures against obesity and related health conditions. The topic of nutrition security is currently receiving much attention and consumer demand for food products with improved nutritional qualities has increased. In bread wheat (Triticum aestivum L.), variation in amylose content is narrow, hence its limited improvement. Therefore, it is necessary to produce wheat lines or populations showing wide variation in amylose/resistant starch content. In this study, a set of EMS-induced M4 mutant lines showing dynamic variation in amylose/resistant starch content were produced. Furthermore, two diverse mutant lines for amylose content were used to study quantitative expression patterns of 20 starch metabolic pathway genes and to identify candidate genes for amylose biosynthesis. A population comprising 101 EMS-induced mutation lines (M4 generation) was produced in a bread wheat (Triticum aestivum) variety. Two methods of amylose measurement in grain starch showed variation in amylose content ranging from ~3 to 76 % in the population. The method of in vitro digestion showed variation in resistant starch content from 1 to 41 %. One-way ANOVA analysis showed significant variation (p < 0.05) in amylose and resistant starch content within the population. A multiple comparison test (Dunnett's test) showed that significant variation in amylose and resistant starch content, with respect to the parent, was observed in about 89 and 38 % of the mutant lines, respectively. Expression pattern analysis of 20 starch metabolic pathway genes in two diverse mutant lines (low and high amylose mutants) showed higher expression of key genes of amylose biosynthesis (GBSSI and their isoforms) in the high amylose mutant line, in comparison to the parent. Higher expression of amylopectin biosynthesis (SBE) was observed in the low amylose mutant lines. An additional six candidate genes showed over-expression (BMY, SPA) and reduced-expression (SSIII, SBEI, SBEIII, ISA3) in the high amylose mutant line, indicating that other starch metabolic genes may also contribute to amylose biosynthesis. In this study a set of 101 EMS-induced mutant lines (M4 generation) showing variation in amylose and resistant starch content in seed were produced. This population serves as useful germplasm or pre-breeding material for genome-wide study and improvement of starch-based processing and nutrition quality in wheat. It is also useful for the study of the genetic and molecular basis of amylose/resistant starch variation in wheat. Furthermore, gene expression analysis of 20 starch metabolic genes in the two diverse mutant lines (low and high amylose mutants) indicates that in addition to key genes, several other genes (such as phosphorylases, isoamylases, and pullulanases) may also be involved in contributing to amylose/amylopectin biosynthesis.

Mobilizing support for the extreme right: a discursive analysis of minority leadership.

PubMed

Rooyackers, Ilse N; Verkuyten, Maykel

2012-03-01

This study uses a tripolar model of minority influence to investigate social category constructions of extreme right politicians. The analysis focuses on Geert Wilders, leader of the extreme right Party For Freedom (PVV) in the Netherlands. It is examined how this popular politician construes the interdependent relations between himself, the population, and mainstream politicians, and discursively manages his controversial standpoints and proposals. Four parliamentary debates are analysed. The analysis shows that by defining national identity, Wilders invokes a self-image as a prototypical member of the population. Furthermore, and in contrast to other politicians, Wilders works up a self-image of a responsible and realistic politician who is group oriented. In addition, the analysis suggests that being a minority can be of strategic political value and therefore a position to foster. The relevance of the analysis for social psychological approaches to leadership and political minorities is discussed. © 2011 The British Psychological Society.

An evaluation of treatment strategies for head and neck cancer in an African American population.

PubMed

Ignacio, D N; Griffin, J J; Daniel, M G; Serlemitsos-Day, M T; Lombardo, F A; Alleyne, T A

2013-07-01

This study evaluated treatment strategies for head and neck cancers in a predominantly African American population. Data were collected utilizing medical records and the tumour registry at the Howard University Hospital. Kaplan-Meier method was used for survival analysis and Cox proportional hazards regression analysis predicted the hazard of death. Analysis revealed that the main treatment strategy was radiation combined with platinum for all stages except stage I. Cetuximab was employed in only 1% of cases. Kaplan-Meier analysis revealed stage II patients had poorer outcome than stage IV while Cox proportional hazard regression analysis (p = 0.4662) showed that stage I had a significantly lower hazard of death than stage IV (HR = 0.314; p = 0.0272). Contributory factors included tobacco and alcohol but body mass index (BMI) was inversely related to hazard of death. There was no difference in survival using any treatment modality for African Americans.

Temporal genetic analysis of the endangered tidewater goby: extinction-colonization dynamics or drift in isolation?

PubMed

Kinziger, Andrew P; Hellmair, Michael; McCraney, W Tyler; Jacobs, David K; Goldsmith, Greg

2015-11-01

Extinction and colonization dynamics are critical to understanding the evolution and conservation of metapopulations. However, traditional field studies of extinction-colonization are potentially fraught with detection bias and have rarely been validated. Here, we provide a comparison of molecular and field-based approaches for assessment of the extinction-colonization dynamics of tidewater goby (Eucyclogobius newberryi) in northern California. Our analysis of temporal genetic variation across 14 northern California tidewater goby populations failed to recover genetic change expected with extinction-colonization cycles. Similarly, analysis of site occupancy data from field studies (94 sites) indicated that extinction and colonization are very infrequent for our study populations. Comparison of the approaches indicated field data were subject to imperfect detection, and falsely implied extinction-colonization cycles in several instances. For northern California populations of tidewater goby, we interpret the strong genetic differentiation between populations and high degree of within-site temporal stability as consistent with a model of drift in the absence of migration, at least over the past 20-30 years. Our findings show that tidewater goby exhibit different population structures across their geographic range (extinction-colonization dynamics in the south vs. drift in isolation in the north). For northern populations, natural dispersal is too infrequent to be considered a viable approach for recolonizing extirpated populations, suggesting that species recovery will likely depend on artificial translocation in this region. More broadly, this work illustrates that temporal genetic analysis can be used in combination with field data to strengthen inference of extinction-colonization dynamics or as a stand-alone tool when field data are lacking. © 2015 John Wiley & Sons Ltd.

Predicting Performance on State Achievement Tests Using Curriculum-Based Measurement in Reading: A Multilevel Meta-Analysis

ERIC Educational Resources Information Center

Yeo, Seungsoo

2010-01-01

The purpose of this synthesis was to examine the relationship between Curriculum-Based Measurement (CBM) and statewide achievement tests in reading. A multilevel meta-analysis was used to calculate the correlation coefficient of the population for 27 studies that met the inclusion criteria. Results showed an overall large correlation coefficient…

Uniparental Markers of Contemporary Italian Population Reveals Details on Its Pre-Roman Heritage

PubMed Central

Álvarez-Iglesias, Vanesa; Fondevila, Manuel; Blanco-Verea, Alejandro; Carracedo, Ángel; Pascali, Vincenzo L.; Capelli, Cristian

2012-01-01

Background According to archaeological records and historical documentation, Italy has been a melting point for populations of different geographical and ethnic matrices. Although Italy has been a favorite subject for numerous population genetic studies, genetic patterns have never been analyzed comprehensively, including uniparental and autosomal markers throughout the country. Methods/Principal Findings A total of 583 individuals were sampled from across the Italian Peninsula, from ten distant (if homogeneous by language) ethnic communities — and from two linguistic isolates (Ladins, Grecani Salentini). All samples were first typed for the mitochondrial DNA (mtDNA) control region and selected coding region SNPs (mtSNPs). This data was pooled for analysis with 3,778 mtDNA control-region profiles collected from the literature. Secondly, a set of Y-chromosome SNPs and STRs were also analyzed in 479 individuals together with a panel of autosomal ancestry informative markers (AIMs) from 441 samples. The resulting genetic record reveals clines of genetic frequencies laid according to the latitude slant along continental Italy – probably generated by demographical events dating back to the Neolithic. The Ladins showed distinctive, if more recent structure. The Neolithic contribution was estimated for the Y-chromosome as 14.5% and for mtDNA as 10.5%. Y-chromosome data showed larger differentiation between North, Center and South than mtDNA. AIMs detected a minor sub-Saharan component; this is however higher than for other European non-Mediterranean populations. The same signal of sub-Saharan heritage was also evident in uniparental markers. Conclusions/Significance Italy shows patterns of molecular variation mirroring other European countries, although some heterogeneity exists based on different analysis and molecular markers. From North to South, Italy shows clinal patterns that were most likely modulated during Neolithic times. PMID:23251386

Uniparental markers of contemporary Italian population reveals details on its pre-Roman heritage.

PubMed

Brisighelli, Francesca; Álvarez-Iglesias, Vanesa; Fondevila, Manuel; Blanco-Verea, Alejandro; Carracedo, Angel; Pascali, Vincenzo L; Capelli, Cristian; Salas, Antonio

2012-01-01

According to archaeological records and historical documentation, Italy has been a melting point for populations of different geographical and ethnic matrices. Although Italy has been a favorite subject for numerous population genetic studies, genetic patterns have never been analyzed comprehensively, including uniparental and autosomal markers throughout the country. A total of 583 individuals were sampled from across the Italian Peninsula, from ten distant (if homogeneous by language) ethnic communities--and from two linguistic isolates (Ladins, Grecani Salentini). All samples were first typed for the mitochondrial DNA (mtDNA) control region and selected coding region SNPs (mtSNPs). This data was pooled for analysis with 3,778 mtDNA control-region profiles collected from the literature. Secondly, a set of Y-chromosome SNPs and STRs were also analyzed in 479 individuals together with a panel of autosomal ancestry informative markers (AIMs) from 441 samples. The resulting genetic record reveals clines of genetic frequencies laid according to the latitude slant along continental Italy--probably generated by demographical events dating back to the Neolithic. The Ladins showed distinctive, if more recent structure. The Neolithic contribution was estimated for the Y-chromosome as 14.5% and for mtDNA as 10.5%. Y-chromosome data showed larger differentiation between North, Center and South than mtDNA. AIMs detected a minor sub-Saharan component; this is however higher than for other European non-Mediterranean populations. The same signal of sub-Saharan heritage was also evident in uniparental markers. Italy shows patterns of molecular variation mirroring other European countries, although some heterogeneity exists based on different analysis and molecular markers. From North to South, Italy shows clinal patterns that were most likely modulated during Neolithic times.

Illicit drug consumption in school populations measured by wastewater analysis.

PubMed

Zuccato, Ettore; Gracia-Lor, Emma; Rousis, Nikolaos I; Parabiaghi, Alberto; Senta, Ivan; Riva, Francesco; Castiglioni, Sara

2017-09-01

Analysis of student consumption of illicit drugs (ID) by school population surveys (SPS) provides information useful for prevention, but the results may be influenced by subjective factors. We explored wastewater (WW) analysis to improve the information. We used WW analysis to measure ID consumption in eight secondary schools in Italy in 2010-13 (students aged 15-19). Samples were collected from the sewage pipes of the schools during lessons for one week each year. Samples were analysed by mass spectrometry to measure ID and consumption by students was compared to that of the general population. We found THCCOOH (human metabolite of THC) concentrations in 2010 indicating significant consumption of cannabis in all the schools and benzoylecgonine (human metabolite of cocaine) suggesting a limited consumption of cocaine in all but one school. Morphine was only found in traces, and amphetamine, methamphetamine, ecstasy, ketamine and mephedrone were not detectable. Repeated analysis showed cannabis stable until 2012 with increases in 2013, low cocaine and morphine levels, and none of the other ID. WW analysis suggested that students used amounts of cannabis comparable to the general population, with low, sporadic use of cocaine and opioids, but excluded the use of significant amounts of amphetamine, methamphetamine, ecstasy, ketamine and mephedrone. WW analysis was useful to confirm SPS figures and provides complementary findings for effective prevention strategies. This is the first time WW analysis has been used to investigate consumption of a large number of ID and new psychoactive substances (NPS) in schools. Copyright © 2017 Elsevier B.V. All rights reserved.

Comparing Sociodemographic Factors Associated with Disability between Immigrants and the Chilean-Born: Are There Different Stories to Tell?

PubMed Central

Cabieses, Baltica; Pickett, Kate E.; Tunstall, Helena

2012-01-01

This study explored a range of sociodemographic factors associated with disability among international immigrants in Chile, and compared them to the Chilean-born. Secondary data analysis of the Chilean population-based survey CASEN-2006 was conducted (268,873 participants). Main health outcomes: any disability and six different types of disability: visual, hearing, learning, physical, psychiatric and speaking (binary outcomes). Sociodemographic variables: Demographic factors (age, sex, marital status, urban/rural, ethnicity), socioeconomic status (SES: income, education, employment status, and an integrated indicator combining the SES measures through cluster analysis for the immigrant population), material factors (overcrowding, sanitation, housing quality) and migration related (country of origin and length of stay). Immigrants reported a significantly lower prevalence of any disability (3.55%), visual (1.00%) and physical disability (0.38%). Factors associated with any disability among immigrants were age, low SES or over 20 years duration of residence in Chile; while a range of sociodemographic factors were associated with disability in the Chilean-born. Conditional regression models by age group varied between populations, but SES remained significantly associated with disability across immigrants and the Chilean-born. However, there are no similar patterns of factors associated to different types of disability between the populations under study. Factors associated with disability varied between populations under study, but SES showed a consistent association with any disability in immigrants and the Chilean-born. Types of disability showed different patterns of factors associated to them between populations, which suggest the great complexity of underlying mechanisms related to disability in Chile. PMID:23211607

Comparing sociodemographic factors associated with disability between immigrants and the Chilean-born: are there different stories to tell?

PubMed

Cabieses, Baltica; Pickett, Kate E; Tunstall, Helena

2012-12-04

This study explored a range of sociodemographic factors associated with disability among international immigrants in Chile, and compared them to the Chilean-born. Secondary data analysis of the Chilean population-based survey CASEN-2006 was conducted (268,873 participants). Main health outcomes: any disability and six different types of disability: visual, hearing, learning, physical, psychiatric and speaking (binary outcomes). Sociodemographic variables: Demographic factors (age, sex, marital status, urban/rural, ethnicity), socioeconomic status (SES: income, education, employment status, and an integrated indicator combining the SES measures through cluster analysis for the immigrant population), material factors (overcrowding, sanitation, housing quality) and migration related (country of origin and length of stay). Immigrants reported a significantly lower prevalence of any disability (3.55%), visual (1.00%) and physical disability (0.38%). Factors associated with any disability among immigrants were age, low SES or over 20 years duration of residence in Chile; while a range of sociodemographic factors were associated with disability in the Chilean-born. Conditional regression models by age group varied between populations, but SES remained significantly associated with disability across immigrants and the Chilean-born. However, there are no similar patterns of factors associated to different types of disability between the populations under study. Factors associated with disability varied between populations under study, but SES showed a consistent association with any disability in immigrants and the Chilean-born. Types of disability showed different patterns of factors associated to them between populations, which suggest the great complexity of underlying mechanisms related to disability in Chile.

Identification of dietary patterns in urban population of Argentina: study on diet-obesity relation in population-based prevalence study.

PubMed

Pou, Sonia Alejandra; Del Pilar Díaz, María; De La Quintana, Ana Gabriela; Forte, Carla Antonella; Aballay, Laura Rosana

2016-12-01

In Argentina, obesity prevalence rose from 14.6% in 2005 to 20.8% in 2013. Although the number of studies on noncommunicable diseases and dietary patterns as a unique dietary exposure measure has increased, information on this topic remains scarce in developing countries. This is the first population-based study investigating the association between diet and obesity using a dietary pattern approach in Argentina. We aimed (a) to identify current dietary patterns of the population of Córdoba city, (b) to investigate its association with obesity prevalence, and (c) to identify and describe dietary patterns from the subgroup of people with obesity. The Córdoba Obesity and Diet Study (CODIES) was conducted in Córdoba city by using a random sample of n = 4,327 subjects between 2005 and 2012. Empirically derived dietary patterns were identified through principal component factor analysis. A multiple logistic regression analysis was used to investigate the association of dietary patterns with obesity. Four dietary patterns were identified, called " Starchy-Sugar ", " Prudent ", " Western ", and " Sugary drinks ". High scores for the " Western " pattern (with strongest factor loading on meats/eggs, processed meats, and alcohol) showed a positive association with obesity (OR: 1.33, 95% CI: 1.06-1.67, for third versus first tertile of factor score). " Meats/Cheeses " and " Snacks/Alcohol " patterns emerged in people with obesity. The findings suggest that high adherence to the " Western " pattern promoted obesity in this urban population. In addition, people with obesity showed characteristic dietary patterns that differ from those identified in the overall population.

Genome-wide detection and characterization of positive selection in human populations.

PubMed

Sabeti, Pardis C; Varilly, Patrick; Fry, Ben; Lohmueller, Jason; Hostetter, Elizabeth; Cotsapas, Chris; Xie, Xiaohui; Byrne, Elizabeth H; McCarroll, Steven A; Gaudet, Rachelle; Schaffner, Stephen F; Lander, Eric S; Frazer, Kelly A; Ballinger, Dennis G; Cox, David R; Hinds, David A; Stuve, Laura L; Gibbs, Richard A; Belmont, John W; Boudreau, Andrew; Hardenbol, Paul; Leal, Suzanne M; Pasternak, Shiran; Wheeler, David A; Willis, Thomas D; Yu, Fuli; Yang, Huanming; Zeng, Changqing; Gao, Yang; Hu, Haoran; Hu, Weitao; Li, Chaohua; Lin, Wei; Liu, Siqi; Pan, Hao; Tang, Xiaoli; Wang, Jian; Wang, Wei; Yu, Jun; Zhang, Bo; Zhang, Qingrun; Zhao, Hongbin; Zhao, Hui; Zhou, Jun; Gabriel, Stacey B; Barry, Rachel; Blumenstiel, Brendan; Camargo, Amy; Defelice, Matthew; Faggart, Maura; Goyette, Mary; Gupta, Supriya; Moore, Jamie; Nguyen, Huy; Onofrio, Robert C; Parkin, Melissa; Roy, Jessica; Stahl, Erich; Winchester, Ellen; Ziaugra, Liuda; Altshuler, David; Shen, Yan; Yao, Zhijian; Huang, Wei; Chu, Xun; He, Yungang; Jin, Li; Liu, Yangfan; Shen, Yayun; Sun, Weiwei; Wang, Haifeng; Wang, Yi; Wang, Ying; Xiong, Xiaoyan; Xu, Liang; Waye, Mary M Y; Tsui, Stephen K W; Xue, Hong; Wong, J Tze-Fei; Galver, Luana M; Fan, Jian-Bing; Gunderson, Kevin; Murray, Sarah S; Oliphant, Arnold R; Chee, Mark S; Montpetit, Alexandre; Chagnon, Fanny; Ferretti, Vincent; Leboeuf, Martin; Olivier, Jean-François; Phillips, Michael S; Roumy, Stéphanie; Sallée, Clémentine; Verner, Andrei; Hudson, Thomas J; Kwok, Pui-Yan; Cai, Dongmei; Koboldt, Daniel C; Miller, Raymond D; Pawlikowska, Ludmila; Taillon-Miller, Patricia; Xiao, Ming; Tsui, Lap-Chee; Mak, William; Song, You Qiang; Tam, Paul K H; Nakamura, Yusuke; Kawaguchi, Takahisa; Kitamoto, Takuya; Morizono, Takashi; Nagashima, Atsushi; Ohnishi, Yozo; Sekine, Akihiro; Tanaka, Toshihiro; Tsunoda, Tatsuhiko; Deloukas, Panos; Bird, Christine P; Delgado, Marcos; Dermitzakis, Emmanouil T; Gwilliam, Rhian; Hunt, Sarah; Morrison, Jonathan; Powell, Don; Stranger, Barbara E; Whittaker, Pamela; Bentley, David R; Daly, Mark J; de Bakker, Paul I W; Barrett, Jeff; Chretien, Yves R; Maller, Julian; McCarroll, Steve; Patterson, Nick; Pe'er, Itsik; Price, Alkes; Purcell, Shaun; Richter, Daniel J; Sabeti, Pardis; Saxena, Richa; Schaffner, Stephen F; Sham, Pak C; Varilly, Patrick; Altshuler, David; Stein, Lincoln D; Krishnan, Lalitha; Smith, Albert Vernon; Tello-Ruiz, Marcela K; Thorisson, Gudmundur A; Chakravarti, Aravinda; Chen, Peter E; Cutler, David J; Kashuk, Carl S; Lin, Shin; Abecasis, Gonçalo R; Guan, Weihua; Li, Yun; Munro, Heather M; Qin, Zhaohui Steve; Thomas, Daryl J; McVean, Gilean; Auton, Adam; Bottolo, Leonardo; Cardin, Niall; Eyheramendy, Susana; Freeman, Colin; Marchini, Jonathan; Myers, Simon; Spencer, Chris; Stephens, Matthew; Donnelly, Peter; Cardon, Lon R; Clarke, Geraldine; Evans, David M; Morris, Andrew P; Weir, Bruce S; Tsunoda, Tatsuhiko; Johnson, Todd A; Mullikin, James C; Sherry, Stephen T; Feolo, Michael; Skol, Andrew; Zhang, Houcan; Zeng, Changqing; Zhao, Hui; Matsuda, Ichiro; Fukushima, Yoshimitsu; Macer, Darryl R; Suda, Eiko; Rotimi, Charles N; Adebamowo, Clement A; Ajayi, Ike; Aniagwu, Toyin; Marshall, Patricia A; Nkwodimmah, Chibuzor; Royal, Charmaine D M; Leppert, Mark F; Dixon, Missy; Peiffer, Andy; Qiu, Renzong; Kent, Alastair; Kato, Kazuto; Niikawa, Norio; Adewole, Isaac F; Knoppers, Bartha M; Foster, Morris W; Clayton, Ellen Wright; Watkin, Jessica; Gibbs, Richard A; Belmont, John W; Muzny, Donna; Nazareth, Lynne; Sodergren, Erica; Weinstock, George M; Wheeler, David A; Yakub, Imtaz; Gabriel, Stacey B; Onofrio, Robert C; Richter, Daniel J; Ziaugra, Liuda; Birren, Bruce W; Daly, Mark J; Altshuler, David; Wilson, Richard K; Fulton, Lucinda L; Rogers, Jane; Burton, John; Carter, Nigel P; Clee, Christopher M; Griffiths, Mark; Jones, Matthew C; McLay, Kirsten; Plumb, Robert W; Ross, Mark T; Sims, Sarah K; Willey, David L; Chen, Zhu; Han, Hua; Kang, Le; Godbout, Martin; Wallenburg, John C; L'Archevêque, Paul; Bellemare, Guy; Saeki, Koji; Wang, Hongguang; An, Daochang; Fu, Hongbo; Li, Qing; Wang, Zhen; Wang, Renwu; Holden, Arthur L; Brooks, Lisa D; McEwen, Jean E; Guyer, Mark S; Wang, Vivian Ota; Peterson, Jane L; Shi, Michael; Spiegel, Jack; Sung, Lawrence M; Zacharia, Lynn F; Collins, Francis S; Kennedy, Karen; Jamieson, Ruth; Stewart, John

2007-10-18

With the advent of dense maps of human genetic variation, it is now possible to detect positive natural selection across the human genome. Here we report an analysis of over 3 million polymorphisms from the International HapMap Project Phase 2 (HapMap2). We used 'long-range haplotype' methods, which were developed to identify alleles segregating in a population that have undergone recent selection, and we also developed new methods that are based on cross-population comparisons to discover alleles that have swept to near-fixation within a population. The analysis reveals more than 300 strong candidate regions. Focusing on the strongest 22 regions, we develop a heuristic for scrutinizing these regions to identify candidate targets of selection. In a complementary analysis, we identify 26 non-synonymous, coding, single nucleotide polymorphisms showing regional evidence of positive selection. Examination of these candidates highlights three cases in which two genes in a common biological process have apparently undergone positive selection in the same population:LARGE and DMD, both related to infection by the Lassa virus, in West Africa;SLC24A5 and SLC45A2, both involved in skin pigmentation, in Europe; and EDAR and EDA2R, both involved in development of hair follicles, in Asia.

Meta-analysis confirms the LCE3C_LCE3B deletion as a risk factor for psoriasis in several ethnic groups and finds interaction with HLA-Cw6

PubMed Central

Riveira-Munoz, Eva; He, Su-Min; Escaramís, Georgia; Stuart, Philip E; Hüffmeier, Ulrike; Lee, Catherine; Kirby, Brian; Oka, Akira; Giardina, Emiliano; Liao, Wilson; Bergboer, Judith; Kainu, Kati; de Cid, Rafael; Munkhbat, Batmunkh; Zeeuwen, Patrick L J M; Armour, John A L; Poon, Annie; Mabuchi, Tomotaka; Ozawa, Akira; Zawirska, Agnieszka; Burden, David A; Barker, Jonathan N; Capon, Francesca; Traupe, Heiko; Sun, Liang-Dan; Cui, Yong; Yin, Xian-Yong; Chen, Gang; Lim, Henry; Nair, Rajan; Voorhess, John; Tejasvi, Trilokraj; Pujol, Ramón; Munkhtuvshin, Namid; Fischer, Judith; Kere, Juha; Schalkwijk, Joost; Bowcock, Anne; Kwok, Pui-Yan; Novelli, Giuseppe; Inoko, Hidetoshi; Ryan, Anthony W; Trembath, Richard C; Reis, André; Zhang, Xue-Jun; Elder, James T; Estivill, Xavier

2012-01-01

A multicenter meta-analysis including data from 9389 psoriasis patients and 9477 control subjects was performed to investigate the contribution of the deletion of genes LCE3C and LCE3B, involved in skin barrier defense, to psoriasis susceptibility in different populations. The study confirms that the deletion of LCE3C and LCE3B is a common genetic factor for susceptibility to psoriasis in European populations [OROverall = 1.21 (1.15–1.27)], and for the first time directly demonstrated the deletion's association with psoriasis in [Chinese OR = 1.27 (1.16–1.34); Mongolian OR = 2.08 (1.44–2.99)] populations. The analysis of the HLA-Cw6 locus showed significant differences in the epistatic interaction with the LCE3C and LCE3B deletion in at least some European populations, indicating epistatic effects between these two major genetic contributors to psoriasis. The study highlights the value of examining genetic risk factors in multiple populations to identify genetic interactions, and indicates the need of further studies to understand the interaction of the skin barrier and the immune system in susceptibility to psoriasis. PMID:21107349

Variation in mitochondrial DNA and allozymes discriminates early and late forms of Chinook salmon Oncorhynchus tshawytscha in the Kenai and Kasilof Rivers, AK

USGS Publications Warehouse

Adams, Noah S.; Spearman, William J.; Burger, Carl V.; Currens, Kenneth P.; Schreck, Carl B.; Li, Hiram W.

1994-01-01

Genetic differences between early and late forms of Alaskan chinook salmon (Oncorhynchus tshawytscha) were identified using two genetic approaches: mitochondrial DNA (mtDNA) analysis, and protein electrophoresis. Study populations consisted of early and late runs in each of the Kenai and Kasilof rivers in Alaska, and a population from the Minam River, Oregon. Two segments of mtDNA were amplified using the polymerase chain reaction (PCR) and digested with 14–16 restriction enzymes. Results showed that early runs were genetically similar to each other but different from the late runs. The late runs were different from each other based on the frequency of the common haplotypes. Frequency differences in shared haplotypes together with the presence of a unique haplotype separated the Minam River stock from those in Alaska. In the protein analysis, each population was examined at 30 allozyme loci. Based on 14 polymorphic loci, Minam River salmon were genetically distinct from the Alaskan populations. Within the Alaskan populations, early runs were most similar to each other but different from the late runs; the late runs were also genetically most similar to each other. Both mtDNA and allozyme analysis suggest that chinook salmon may segregate into genetically different early and late forms within a drainage.

The influence of hydrology and waterway distance on population structure of Chinook salmon Oncorhynchus tshawytscha in a large river.

PubMed

Olsen, J B; Beacham, T D; Wetklo, M; Seeb, L W; Smith, C T; Flannery, B G; Wenburg, J K

2010-04-01

Adult Chinook salmon Oncorhynchus tshawytscha navigate in river systems using olfactory cues that may be influenced by hydrologic factors such as flow and the number, size and spatial distribution of tributaries. Thus, river hydrology may influence both homing success and the level of straying (gene flow), which in turn influences population structure. In this study, two methods of multivariate analysis were used to examine the extent to which four indicators of hydrology and waterway distance explained population structure of O. tshawytscha in the Yukon River. A partial Mantel test showed that the indicators of hydrology were positively associated with broad-scale (Yukon basin) population structure, when controlling for the influence of waterway distance. Multivariate multiple regression showed that waterway distance, supplemented with the number and flow of major drainage basins, explained more variation in broad-scale population structure than any single indicator. At an intermediate spatial scale, indicators of hydrology did not appear to influence population structure after accounting for waterway distance. These results suggest that habitat changes in the Yukon River, which alter hydrology, may influence the basin-wide pattern of population structure in O. tshawytscha. Further research is warranted on the role of hydrology in concert with waterway distance in influencing population structure in Pacific salmon.

Methodological assessment of 2b-RAD genotyping technique for population structure inferences in yellowfin tuna (Thunnus albacares).

PubMed

Pecoraro, Carlo; Babbucci, Massimiliano; Villamor, Adriana; Franch, Rafaella; Papetti, Chiara; Leroy, Bruno; Ortega-Garcia, Sofia; Muir, Jeff; Rooker, Jay; Arocha, Freddy; Murua, Hilario; Zudaire, Iker; Chassot, Emmanuel; Bodin, Nathalie; Tinti, Fausto; Bargelloni, Luca; Cariani, Alessia

2016-02-01

Global population genetic structure of yellowfin tuna (Thunnus albacares) is still poorly understood despite its relevance for the tuna fishery industry. Low levels of genetic differentiation among oceans speak in favour of the existence of a single panmictic population worldwide of this highly migratory fish. However, recent studies indicated genetic structuring at a much smaller geographic scales than previously considered, pointing out that YFT population genetic structure has not been properly assessed so far. In this study, we demonstrated for the first time, the utility of 2b-RAD genotyping technique for investigating population genetic diversity and differentiation in high gene-flow species. Running de novo pipeline in Stacks, a total of 6772 high-quality genome-wide SNPs were identified across Atlantic, Indian and Pacific population samples representing all major distribution areas. Preliminary analyses showed shallow but significant population structure among oceans (FST=0.0273; P-value<0.01). Discriminant Analysis of Principal Components endorsed the presence of genetically discrete yellowfin tuna populations among three oceanic pools. Although such evidence needs to be corroborated by increasing sample size, these results showed the efficiency of this genotyping technique in assessing genetic divergence in a marine fish with high dispersal potential. Copyright © 2015 Elsevier B.V. All rights reserved.

Mathematical Modeling of Extinction of Inhomogeneous Populations

PubMed Central

Karev, G.P.; Kareva, I.

2016-01-01

Mathematical models of population extinction have a variety of applications in such areas as ecology, paleontology and conservation biology. Here we propose and investigate two types of sub-exponential models of population extinction. Unlike the more traditional exponential models, the life duration of sub-exponential models is finite. In the first model, the population is assumed to be composed clones that are independent from each other. In the second model, we assume that the size of the population as a whole decreases according to the sub-exponential equation. We then investigate the “unobserved heterogeneity”, i.e. the underlying inhomogeneous population model, and calculate the distribution of frequencies of clones for both models. We show that the dynamics of frequencies in the first model is governed by the principle of minimum of Tsallis information loss. In the second model, the notion of “internal population time” is proposed; with respect to the internal time, the dynamics of frequencies is governed by the principle of minimum of Shannon information loss. The results of this analysis show that the principle of minimum of information loss is the underlying law for the evolution of a broad class of models of population extinction. Finally, we propose a possible application of this modeling framework to mechanisms underlying time perception. PMID:27090117

Study of Streptococcus thermophilus population on a world-wide and historical collection by a new MLST scheme.

PubMed

Delorme, Christine; Legravet, Nicolas; Jamet, Emmanuel; Hoarau, Caroline; Alexandre, Bolotin; El-Sharoud, Walid M; Darwish, Mohamed S; Renault, Pierre

2017-02-02

We analyzed 178 Streptococcus thermophilus strains isolated from diverse products, from around the world, over a 60-year period with a new multilocus sequence typing (MLST) scheme. This collection included isolates from two traditional cheese-making sites with different starter-use practices, in sampling campaigns carried out over a three years period. The nucleotide diversity of the S. thermophilus population was limited, but 116 sequence types (ST) were identified. Phylogenetic analysis of the concatenated sequences of the six housekeeping genes revealed the existence of groups confirmed by eBURST analysis. Deeper analyses performed on 25 strains by CRISPR and whole-genome analysis showed that phylogenies obtained by MLST and whole-genome analysis were in agreement but differed from that inferred by CRISPR analysis. Strains isolated from traditional products could cluster in specific groups indicating their origin, but also be mixed in groups containing industrial starter strains. In the traditional cheese-making sites, we found that S. thermophilus persisted on dairy equipment, but that occasionally added starter strains may become dominant. It underlined the impact of starter use that may reshape S. thermophilus populations including in traditional products. This new MLST scheme thus provides a framework for analyses of S. thermophilus populations and the management of its biodiversity. Copyright © 2016 Elsevier B.V. All rights reserved.

Analysis of serotonin receptor 2A gene (HTR2A): association study with autism spectrum disorder in the Indian population and investigation of the gene expression in peripheral blood leukocytes.

PubMed

Guhathakurta, Subhrangshu; Singh, Asem Surindro; Sinha, Swagata; Chatterjee, Anindita; Ahmed, Shabina; Ghosh, Saurabh; Usha, Rajamma

2009-12-01

Several studies suggest involvement of serotoninergic system in the pathophysiology of Autism Spectrum Disorder (ASD). The 5-HT receptor binding studies using (3)H-lysergic acid diethylamide ((3)H-LSD) and linkage analysis provided evidences to consider HTR2A as a potential candidate gene for ASD. The three SNPs, -1438A/G (rs6311), 102T/C (rs6313) and 1354C/T (rs6314) of HTR2A have been well studied in the etiology of various neuropsychiatric disorders. But studies on association of this gene with ASD are limited to two reports from American and Korean populations. Additionally there are reports, which demonstrated paternal imprinting of HTR2A with expression from only one allele. So far no reports are available on HTR2A and its association with any neuropsychiatric disorders from Indian population. Therefore, the present study investigates association of the above mentioned three markers of HTR2A with ASD in Indian population using population and family-based approaches. The study also deals with allelic expression pattern of HTR2A in Peripheral Blood Leukocytes (PBLs) to understand the parental imprinting status. The genotyping analyses were carried out for probands, parents and controls. The subsequent association analyses did not show association of these markers with ASD. So, HTR2A is unlikely to be a genetic marker for ASD in Indian population. The expression analyses showed absence of monoallelic expression, suggesting lack of parental imprinting of HTR2A gene. However, we noticed methylation of the CpG sites at -1438A/G and 102T/C loci of HTR2A gene. Further bioinformatics analysis revealed absence of CpG islands in the promoter of the gene supporting biallelic expression pattern of HTR2A in PBLs.

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

NASA Astrophysics Data System (ADS)

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

2016-11-01

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

Genetic analysis of haplotype data for 23 Y-chromosome short tandem repeat loci in the Turkish population recently settled in Sarajevo, Bosnia and Herzegovina

PubMed Central

Dogan, Serkan; Primorac, Dragan; Marjanović, Damir

2014-01-01

Aim To explore the distribution and polymorphisms of 23 short tandem repeat (STR) loci on the Y chromosome in the Turkish population recently settled in Sarajevo, Bosnia and Herzegovina and to investigate its genetic relationships with the homeland Turkish population and neighboring populations. Methods This study included 100 healthy unrelated male individuals from the Turkish population living in Sarajevo. Buccal swab samples were collected as a DNA source. Genomic DNA was extracted using the salting out method and amplification was performed using PowerPlex Y 23 amplification kit. The studied population was compared to other populations using pairwise genetic distances, which were represented with a multi-dimensional scaling plot. Results Haplotype and allele frequencies of the sample population were calculated and the results showed that all 100 samples had unique haplotypes. The most polymorphic locus was DYS458, and the least polymorphic DYS391. The observed haplotype diversity was 1.0000 ± 0.0014, with a discrimination capacity of 1.00 and the match probability of 0.01. Rst values showed that our sample population was closely related in both dimensions to the Lebanese and Iraqi populations, while it was more distant from Bosnian, Croatian, and Macedonian populations. Conclusion Turkish population residing in Sarajevo could be observed as a representative Turkish population, since our results were consistent with those previously published for the homeland Turkish population. Also, this study once again proved that geographically close populations were genetically more related to each other. PMID:25358886

Spatiotemporal analysis and mapping of oral cancer risk in changhua county (taiwan): an application of generalized bayesian maximum entropy method.

PubMed

Yu, Hwa-Lung; Chiang, Chi-Ting; Lin, Shu-De; Chang, Tsun-Kuo

2010-02-01

Incidence rate of oral cancer in Changhua County is the highest among the 23 counties of Taiwan during 2001. However, in health data analysis, crude or adjusted incidence rates of a rare event (e.g., cancer) for small populations often exhibit high variances and are, thus, less reliable. We proposed a generalized Bayesian Maximum Entropy (GBME) analysis of spatiotemporal disease mapping under conditions of considerable data uncertainty. GBME was used to study the oral cancer population incidence in Changhua County (Taiwan). Methodologically, GBME is based on an epistematics principles framework and generates spatiotemporal estimates of oral cancer incidence rates. In a way, it accounts for the multi-sourced uncertainty of rates, including small population effects, and the composite space-time dependence of rare events in terms of an extended Poisson-based semivariogram. The results showed that GBME analysis alleviates the noises of oral cancer data from population size effect. Comparing to the raw incidence data, the maps of GBME-estimated results can identify high risk oral cancer regions in Changhua County, where the prevalence of betel quid chewing and cigarette smoking is relatively higher than the rest of the areas. GBME method is a valuable tool for spatiotemporal disease mapping under conditions of uncertainty. 2010 Elsevier Inc. All rights reserved.

Development of a scale to assess cancer stigma in the non-patient population

PubMed Central

2014-01-01

Background Illness-related stigma has attracted considerable research interest, but few studies have specifically examined stigmatisation of cancer in the non-patient population. The present study developed and validated a Cancer Stigma Scale (CASS) for use in the general population. Methods An item pool was developed on the basis of previous research into illness-related stigma in the general population and patients with cancer. Two studies were carried out. The first study used Exploratory factor analysis to explore the structure of items in a sample of 462 postgraduate students recruited through a London university. The second study used Confirmatory factor analysis to confirm the structure among 238 adults recruited through an online market research panel. Internal reliability, test-retest reliability and construct validity were also assessed. Results Exploratory factor analysis suggested six subscales, representing: Awkwardness, Severity, Avoidance, Policy Opposition, Personal Responsibility and Financial Discrimination. Confirmatory factor analysis confirmed this structure with a 25-item scale. All subscales showed adequate to good internal and test-retest reliability in both samples. Construct validity was also good, with mean scores for each subscale varying in the expected directions by age, gender, experience of cancer, awareness of lifestyle risk factors for cancer, and social desirability. Means for the subscales were consistent across the two samples. Conclusions These findings highlight the complexity of cancer stigma and provide the Cancer Stigma Scale (CASS) which can be used to compare populations, types of cancer and evaluate the effects of interventions designed to reduce cancer stigma in non-patient populations. PMID:24758482

Signatures of criticality arise from random subsampling in simple population models.

PubMed

Nonnenmacher, Marcel; Behrens, Christian; Berens, Philipp; Bethge, Matthias; Macke, Jakob H

2017-10-01

The rise of large-scale recordings of neuronal activity has fueled the hope to gain new insights into the collective activity of neural ensembles. How can one link the statistics of neural population activity to underlying principles and theories? One attempt to interpret such data builds upon analogies to the behaviour of collective systems in statistical physics. Divergence of the specific heat-a measure of population statistics derived from thermodynamics-has been used to suggest that neural populations are optimized to operate at a "critical point". However, these findings have been challenged by theoretical studies which have shown that common inputs can lead to diverging specific heat. Here, we connect "signatures of criticality", and in particular the divergence of specific heat, back to statistics of neural population activity commonly studied in neural coding: firing rates and pairwise correlations. We show that the specific heat diverges whenever the average correlation strength does not depend on population size. This is necessarily true when data with correlations is randomly subsampled during the analysis process, irrespective of the detailed structure or origin of correlations. We also show how the characteristic shape of specific heat capacity curves depends on firing rates and correlations, using both analytically tractable models and numerical simulations of a canonical feed-forward population model. To analyze these simulations, we develop efficient methods for characterizing large-scale neural population activity with maximum entropy models. We find that, consistent with experimental findings, increases in firing rates and correlation directly lead to more pronounced signatures. Thus, previous reports of thermodynamical criticality in neural populations based on the analysis of specific heat can be explained by average firing rates and correlations, and are not indicative of an optimized coding strategy. We conclude that a reliable interpretation of statistical tests for theories of neural coding is possible only in reference to relevant ground-truth models.

Laser fluorescence fluctuation excesses in molecular immunology experiments

NASA Astrophysics Data System (ADS)

Galich, N. E.; Filatov, M. V.

2007-04-01

A novel approach to statistical analysis of flow cytometry fluorescence data have been developed and applied for population analysis of blood neutrophils stained with hydroethidine during respiratory burst reaction. The staining based on intracellular oxidation hydroethidine to ethidium bromide, which intercalate into cell DNA. Fluorescence of the resultant product serves as a measure of the neutrophil ability to generate superoxide radicals after induction respiratory burst reaction by phorbol myristate acetate (PMA). It was demonstrated that polymorphonuclear leukocytes of persons with inflammatory diseases showed a considerably changed response. Cytofluorometric histograms obtained have unique information about condition of neutrophil population what might to allow a determination of the pathology processes type connecting with such inflammation. A novel approach to histogram analysis is based on analysis of high-momentum dynamic of distribution. The features of fluctuation excesses of distribution have unique information about disease under consideration.

Genome-Wide Analysis in Brazilian Xavante Indians Reveals Low Degree of Admixture

PubMed Central

Kuhn, Patricia C.; Horimoto, Andréa R. V. Russo.; Sanches, José Maurício; Vieira Filho, João Paulo B.; Franco, Luciana; Fabbro, Amaury Dal; Franco, Laercio Joel; Pereira, Alexandre C.; Moises, Regina S

2012-01-01

Characterization of population genetic variation and structure can be used as tools for research in human genetics and population isolates are of great interest. The aim of the present study was to characterize the genetic structure of Xavante Indians and compare it with other populations. The Xavante, an indigenous population living in Brazilian Central Plateau, is one of the largest native groups in Brazil. A subset of 53 unrelated subjects was selected from the initial sample of 300 Xavante Indians. Using 86,197 markers, Xavante were compared with all populations of HapMap Phase III and HGDP-CEPH projects and with a Southeast Brazilian population sample to establish its population structure. Principal Components Analysis showed that the Xavante Indians are concentrated in the Amerindian axis near other populations of known Amerindian ancestry such as Karitiana, Pima, Surui and Maya and a low degree of genetic admixture was observed. This is consistent with the historical records of bottlenecks experience and cultural isolation. By calculating pair-wise Fst statistics we characterized the genetic differentiation between Xavante Indians and representative populations of the HapMap and from HGDP-CEPH project. We found that the genetic differentiation between Xavante Indians and populations of Ameridian, Asian, European, and African ancestry increased progressively. Our results indicate that the Xavante is a population that remained genetically isolated over the past decades and can offer advantages for genome-wide mapping studies of inherited disorders. PMID:22900041

Genome-wide analysis in Brazilian Xavante Indians reveals low degree of admixture.

PubMed

Kuhn, Patricia C; Horimoto, Andréa R V Russo; Sanches, José Maurício; Vieira Filho, João Paulo B; Franco, Luciana; Fabbro, Amaury Dal; Franco, Laercio Joel; Pereira, Alexandre C; Moises, Regina S

2012-01-01

Characterization of population genetic variation and structure can be used as tools for research in human genetics and population isolates are of great interest. The aim of the present study was to characterize the genetic structure of Xavante Indians and compare it with other populations. The Xavante, an indigenous population living in Brazilian Central Plateau, is one of the largest native groups in Brazil. A subset of 53 unrelated subjects was selected from the initial sample of 300 Xavante Indians. Using 86,197 markers, Xavante were compared with all populations of HapMap Phase III and HGDP-CEPH projects and with a Southeast Brazilian population sample to establish its population structure. Principal Components Analysis showed that the Xavante Indians are concentrated in the Amerindian axis near other populations of known Amerindian ancestry such as Karitiana, Pima, Surui and Maya and a low degree of genetic admixture was observed. This is consistent with the historical records of bottlenecks experience and cultural isolation. By calculating pair-wise F(st) statistics we characterized the genetic differentiation between Xavante Indians and representative populations of the HapMap and from HGDP-CEPH project. We found that the genetic differentiation between Xavante Indians and populations of Ameridian, Asian, European, and African ancestry increased progressively. Our results indicate that the Xavante is a population that remained genetically isolated over the past decades and can offer advantages for genome-wide mapping studies of inherited disorders.

Stochastic seasonality and nonlinear density-dependent factors regulate population size in an African rodent

USGS Publications Warehouse

Leirs, H.; Stenseth, N.C.; Nichols, J.D.; Hines, J.E.; Verhagen, R.; Verheyen, W.

1997-01-01

Ecology has long been troubled by the controversy over how populations are regulated. Some ecologists focus on the role of environmental effects, whereas others argue that density-dependent feedback mechanisms are central. The relative importance of both processes is still hotly debated, but clear examples of both processes acting in the same population are rare. Keyfactor analysis (regression of population changes on possible causal factors) and time-series analysis are often used to investigate the presence of density dependence, but such approaches may be biased and provide no information on actual demographic rates. Here we report on both density-dependent and density-independent effects in a murid rodent pest species, the multimammate rat Mastomys natalensis (Smith, 1834), using statistical capture-recapture models. Both effects occur simultaneously, but we also demonstrate that they do not affect all demographic rates in the same way. We have incorporated the obtained estimates of demographic rates in a population dynamics model and show that the observed dynamics are affected by stabilizing nonlinear density-dependent components coupled with strong deterministic and stochastic seasonal components.

Seasonal and Cyclical Changes in Genetic Composition of the Marine Intertidal Rock Pool Copepod Tigriopus brevicornis.

PubMed

Van Wormhoudt, Alain

2015-06-01

Tigriopus brevicornis is a marine rock pool copepod widely distributed along Atlantic coasts. Due to the absence of a known dispersal mechanism by free swimming stages, exchanges between populations over long distances are questionable. In order to analyse the evolution of an isolated supralittoral rock pool population, sampling of the copepod was performed monthly during 1 year and compared to samplings over 5 years in the same rock pool, as well as from other rock pools. Using ITS1 analysis, cyclical changes in genetic composition were detected. Our results give clear indications concerning the segregation of the rock pool population and a lack of gene flow among outside populations. A network analysis shows the presence of several shared dominant haplotypes and also singletons differing by one mutation point. F(st) analyses indicate that the main changes occur in autumn and winter. The few analogies of ITS1 sequences with nearby populations may indicate that new migrants must re-colonise the pools from surrounding rock crevices in the intertidal habitat where they may have found a refuge after bad weather conditions.

Population limitation in a non-cyclic arctic fox population in a changing climate.

PubMed

Pálsson, Snæbjörn; Hersteinsson, Páll; Unnsteinsdóttir, Ester R; Nielsen, Ólafur K

2016-04-01

Arctic foxes Vulpes lagopus (L.) display a sharp 3- to 5-year fluctuation in population size where lemmings are their main prey. In areas devoid of lemmings, such as Iceland, they do not experience short-term fluctuations. This study focusses on the population dynamics of the arctic fox in Iceland and how it is shaped by its main prey populations. Hunting statistics from 1958-2003 show that the population size of the arctic fox was at a maximum in the 1950s, declined to a minimum in the 1970s, and increased steadily until 2003. Analysis of the arctic fox population size and their prey populations suggests that fox numbers were limited by rock ptarmigan numbers during the decline period. The recovery of the arctic fox population was traced mostly to an increase in goose populations, and favourable climatic conditions as reflected by the Subpolar Gyre. These results underscore the flexibility of a generalist predator and its responses to shifting food resources and climate changes.

Genetic portrait of Jewish populations based on three sets of X-chromosome markers: Indels, Alu insertions and STRs.

PubMed

Ferragut, J F; Bentayebi, K; Pereira, R; Castro, J A; Amorim, A; Ramon, C; Picornell, A

2017-11-01

Population genetic data for 53 X-chromosome markers (32 X-indels, 9 X-Alu insertions and 12 X-STRs) are reported for five populations with Jewish ancestry (Sephardim, North African Jews, Middle Eastern Jews, Ashkenazim, and Chuetas) and Majorca, as the host population of Chuetas. Genetic distances between these populations demonstrated significant differences, except between Sephardic and North African Jews, with the Chuetas as the most differentiated group, in accordance with the particular demographic history of this population. X-chromosome analysis and a comparison with autosomal data suggest a generally sex-biased demographic history in Jewish populations. Asymmetry was found between female and male effective population sizes both in the admixture processes between Jewish communities, and between them and their respective non-Jewish host populations. Results further show that these X-linked markers are highly informative for forensic purposes, and highlight the need for specific databases for differentiated Jewish populations. Copyright © 2017 Elsevier B.V. All rights reserved.

Prenatal diagnosis in a cystic fibrosis family: a combined molecular strategy for a precise diagnosis.

PubMed

Chávez-Saldaña, Margarita; García-Cavazos, Ricardo; Vigueras, Rosa María; Orozco, Lorena

2011-01-01

The high genetic heterogeneity in populations with a wide spectrum of mutations in the CF transmembrane conductance regulator gene (CFTR), makes the detection of mutations a very hard and difficult task, thereby limiting the accurate diagnosis of the disease, mainly in patients with uncharacterized mutations. Molecular strategies, like targeted identification of the most frequent CFTR mutations in Mexican population combined with linkage analysis using markers, is very useful for carrier detection and for prenatal diagnosis in affected families with CF. In this paper we show that the combination of methodologies was a crucial alternative to reach a precise prenatal CF diagnosis. We documented CF diagnosis in a 14th-week fetus combining the screening of the most common mutations in Mexican population with linkage analysis of two extragenic polymorphisms (XV2C/TaqI and KM19/PstI). We determined that the fetus inherited the PG542X mutation from its mother and an unknown mutation from its father through the chromosomal phases analysis.

Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise

PubMed Central

Lah, Ljerka; Trense, Daronja; Benke, Harald; Berggren, Per; Gunnlaugsson, Þorvaldur; Lockyer, Christina; Öztürk, Ayaka; Öztürk, Bayram; Pawliczka, Iwona; Roos, Anna; Siebert, Ursula; Víkingsson, Gísli; Tiedemann, Ralph

2016-01-01

The population structure of the highly mobile marine mammal, the harbor porpoise (Phocoena phocoena), in the Atlantic shelf waters follows a pattern of significant isolation-by-distance. The population structure of harbor porpoises from the Baltic Sea, which is connected with the North Sea through a series of basins separated by shallow underwater ridges, however, is more complex. Here, we investigated the population differentiation of harbor porpoises in European Seas with a special focus on the Baltic Sea and adjacent waters, using a population genomics approach. We used 2872 single nucleotide polymorphisms (SNPs), derived from double digest restriction-site associated DNA sequencing (ddRAD-seq), as well as 13 microsatellite loci and mitochondrial haplotypes for the same set of individuals. Spatial principal components analysis (sPCA), and Bayesian clustering on a subset of SNPs suggest three main groupings at the level of all studied regions: the Black Sea, the North Atlantic, and the Baltic Sea. Furthermore, we observed a distinct separation of the North Sea harbor porpoises from the Baltic Sea populations, and identified splits between porpoise populations within the Baltic Sea. We observed a notable distinction between the Belt Sea and the Inner Baltic Sea sub-regions. Improved delineation of harbor porpoise population assignments for the Baltic based on genomic evidence is important for conservation management of this endangered cetacean in threatened habitats, particularly in the Baltic Sea proper. In addition, we show that SNPs outperform microsatellite markers and demonstrate the utility of RAD-tags from a relatively small, opportunistically sampled cetacean sample set for population diversity and divergence analysis. PMID:27783621

Population structure in Japanese rice population

PubMed Central

Yamasaki, Masanori; Ideta, Osamu

2013-01-01

It is essential to elucidate genetic diversity and relationships among even related individuals and populations for plant breeding and genetic analysis. Since Japanese rice breeding has improved agronomic traits such as yield and eating quality, modern Japanese rice cultivars originated from narrow genetic resource and closely related. To resolve the population structure and genetic diversity in Japanese rice population, we used a total of 706 alleles detected by 134 simple sequence repeat markers in a total of 114 cultivars composed of 94 improved varieties and 20 landraces, which are representative and important for Japanese rice breeding. The landraces exhibit greater gene diversity than improved lines, suggesting that landraces can provide additional genetic diversity for future breeding. Model-based Bayesian clustering analysis revealed six subgroups and admixture situation in the cultivars, showing good agreement with pedigree information. This method could be superior to phylogenetic method in classifying a related population. The leading Japanese rice cultivar, Koshihikari is unique due to the specific genome constitution. We defined Japanese rice diverse sets that capture the maximum number of alleles for given sample sizes. These sets are useful for a variety of genetic application in Japanese rice cultivars. PMID:23641181

The Alburnus benthopelagic fish species of the Western Balkan Peninsula: An assessment of their sustainable use.

PubMed

Simić, Vladica; Simić, Snežana; Paunović, Momir; Radojković, Nataša; Petrović, Ana; Talevski, Trajče; Milošević, Djuradj

2016-01-01

In this study, we aimed to assess the population status of bleak (Alburnus spp.) over the Western Balkan Peninsula in terms of its sustainable use. A second objective was to determine key factors important for fishery management planning. Two different basins, continental (the Danube Basin and the Sava River sub-basin) and marine (the Adriatic and the Aegean Sea Basins) were examined. A sustainability assessment and factor analysis were conducted using the adjusted ESHIPPOfishing model, extended with additional socio-economic sub-elements, and the categorical principal components analysis (CATPCA), respectively. The results of the assessment revealed the bleak populations in the Danube Basin and the Sava River sub-basin to be highly sustainable. The population characteristics with abiotic and biotic factors were responsible for this status, while the influence of socio-economic factors was insignificant. The sustainability status of the bleak populations of the Mediterranean basin varied, with the populations from Ohrid and Skadar Lakes showing a high and those from Prespa and Dojran Lakes a medium status. Socio-economic factors with traditional fishing were the most important for the Mediterranean bleak populations. Copyright © 2015 Elsevier B.V. All rights reserved.

Apolipoprotein C3 Gene Polymorphisms Are Not a Risk Factor for Developing Non-Alcoholic Fatty Liver Disease: A Meta-Analysis

PubMed Central

Zhang, Haiying; Chen, Lizhen; Xin, Yongning; Lou, Yuangui; Liu, Yang; Xuan, Shiying

2014-01-01

Context: Our objective was to evaluate the effect of gene polymorphisms of apolipoprotein C3 (APOC3) on the development of non-alcoholic fatty liver disease (NAFLD) in different populations. Evidence Acquisition: We performed a meta-analysis of all relevant studies published in the literature. A total of 115 clinical trials or reports were identified, but only seven trials met our inclusion criteria. A meta-analysis was performed according to the Cochrane Reviewers’ Handbook recommendations. Results: Five hospital-based and two population-based case-control studies were included in the final analysis. The overall frequency of APOC3 gene polymorphisms was 67.5% (1177/1745) in NAFLD and 68.8% (988/1437) in controls. The summary odds ratio for the association of gene polymorphisms of APOC3 and the risk of NAFLD was 1.03 (95% CI: 0.89-1.22),which was not statistically significant (P > 0.05). Conclusions: Our meta-analysis, while not ruling out possible publication bias, showed no association between gene polymorphisms of APOC3 and the risk of NAFLD development in different populations in the world. PMID:25477977

Genetic Diversity and Structure of the Apiosporina morbosa Populations on Prunus spp.

PubMed

Zhang, Jinxiu; Fernando, W G Dilantha; Remphrey, William R

2005-08-01

ABSTRACT Populations of Apiosporina morbosa collected from 15 geographic locations in Canada and the United States and three host species, Prunus virginiana, P. pensylvanica, and P. padus, were evaluated using the sequence-related amplified polymorphism (SRAP) technique to determine their genetic diversity and population differentiation. Extensive diversity was detected in the A. morbosa populations, including 134 isolates from Canada and the United States, regardless of the origin of the population. The number of polymorphic loci varied from 6.9 to 82.8% in the geographic populations, and from 41.4 to 79.3% in the populations from four host genotypes based on 58 polymorphic fragments. In all, 44 to 100% of isolates in the geographic populations and 43.6 to 76.2% in populations from four host genotypes represented unique genotypes. Values of heterozygosity (H) varied from 2.8 to 28.3% in the geographic populations and 10.2 to 26.1% in the populations from four host genotypes. In general, the A. morbosa populations sampled from wild chokecherry showed a higher genetic diversity than those populations collected from other host species, whereas the populations isolated from cultivated chokecherry, P. virginiana 'Shubert Select', showed a reduction of genetic diversity compared with populations from wild P. virginiana. Significant population differentiation was found among both the geographic populations (P < 0.05) and populations from different host genotypes (P < 0.02). In the geographic populations, most of populations from cultivated and wild P. virginiana were closely clustered, and no population differentiation was detected except for the populations from Morris, Morden, and Winnipeg, Manitoba, Canada. Furthermore, the populations from P. virginiana in the same geographic locations had higher genetic identity and closer genetic distance to each other compared with those from different locations. Four populations from P. virginiana, P. pensylvanica, and P. padus, were significantly differentiated from each other (P < 0.02), except there was no differentiation between the Shubert Select and wild chokecherry populations (>P> = 0.334). Indirect estimation of gene flow showed that significant restricted gene flow existed between populations from different regions and host species. Gene flow rates (Nm) varied from <1 to 12.5, with higher gene flow rates among population pairs from the same host species (P = 1.000). The analysis of molecular variance revealed that a major genetic variance source came from the genetic variation among isolates within populations regardless of the origin and host genotype of the population. Although some locations had a limited number of isolates, the results of this study clearly showed that the genetic diversity and population differentiation of A. morbosa were closely associated with host genotypes and geographic locations, but mostly with the former.

Analyzing ion distributions around DNA: sequence-dependence of potassium ion distributions from microsecond molecular dynamics

PubMed Central

Pasi, Marco; Maddocks, John H.; Lavery, Richard

2015-01-01

Microsecond molecular dynamics simulations of B-DNA oligomers carried out in an aqueous environment with a physiological salt concentration enable us to perform a detailed analysis of how potassium ions interact with the double helix. The oligomers studied contain all 136 distinct tetranucleotides and we are thus able to make a comprehensive analysis of base sequence effects. Using a recently developed curvilinear helicoidal coordinate method we are able to analyze the details of ion populations and densities within the major and minor grooves and in the space surrounding DNA. The results show higher ion populations than have typically been observed in earlier studies and sequence effects that go beyond the nature of individual base pairs or base pair steps. We also show that, in some special cases, ion distributions converge very slowly and, on a microsecond timescale, do not reflect the symmetry of the corresponding base sequence. PMID:25662221

Power laws governing epidemics in isolated populations

NASA Astrophysics Data System (ADS)

Rhodes, C. J.; Anderson, R. M.

1996-06-01

TEMPORAL changes in the incidence of measles virus infection within large urban communities in the developed world have been the focus of much discussion in the context of the identification and analysis of nonlinear and chaotic patterns in biological time series1-11. In contrast, the measles records for small isolated island populations are highly irregular, because of frequent fade-outs of infection12-14, and traditional analysis15 does not yield useful insight. Here we use measurements of the distribution of epidemic sizes and duration to show that regularities in the dynamics of such systems do become apparent. Specifically, these biological systems are characterized by well-defined power laws in a manner reminiscent of other nonlinear, spatially extended dynamical systems in the physical sciences16-19. We further show that the observed power-law exponents are well described by a simple lattice-based model which reflects the social interaction between individual hosts.

Methylenetetrahydrofolate reductase gene polymorphism and risk of chronic myelogenous leukemia: a meta-analysis.

PubMed

Li, Chen; Yichao, Jin; Jiaxin, Lin; Yueting, Zhang; Qin, Lu; Tonghua, Yang

2015-01-01

Reported evidence supports a role for methylenetetrahydrofolate reductase (MTHFR) in the risk of chronic myelogenous leykemia (CML). However, these reports arrived at non-conclusive and even conflicting results regarding the association between two common MTHFR polymorphisms (C677T and A1298C) and CML risk. Thus, a meta-analysis was carried out to clarify a more precise association between these two polymorphisms and the CML risk by updating the available publications. Pooled odds ratios (OR) with corresponding 95% confidence interval (95% CI) and stratification analysis were performed to estimate the relationship between MTHFR polymorphisms and the risk of CML under different genetic comparison models. Data from the meta-analysis showed no significant association between MTHFR C677T polymorphism and CML risk. However, significant associations were found between MTHFR A1298C variants and CML risk under homozygous comparison model (CC vs AA, OR=1.62, 95% CI=1.11-2.36, p=0.01) and dominant comparison model (CC+AC vs AA, OR=1.68, 95% CI=1.17-2.43, p=0.005) in overall population; especially more obvious impacts were noticed for Asian populations in subgroup analysis for homozygous model (CC vs AA, OR=2.00, 95% CI=1.25-3.21, p=0.004) and dominant model (CC+AC vs AA, OR=2.49, 95% CI=1.42-4.36, p=0.001), but this did not apply in Caucasian populations. The results of this meta-analysis suggested no significant association between MTHFR C677T polymorphism and CML risk, while an increased CML risk was noticed for 1298C variant carriers, especially in Asian populations but not in Caucasian populations, which suggested ethnicity differences between MTHFR A1298C polymorphisms and risk of CML.

Construction of a High-Density Genetic Map from RNA-Seq Data for an Arabidopsis Bay-0 × Shahdara RIL Population

PubMed Central

Serin, Elise A. R.; Snoek, L. B.; Nijveen, Harm; Willems, Leo A. J.; Jiménez-Gómez, Jose M.; Hilhorst, Henk W. M.; Ligterink, Wilco

2017-01-01

High-density genetic maps are essential for high resolution mapping of quantitative traits. Here, we present a new genetic map for an Arabidopsis Bayreuth × Shahdara recombinant inbred line (RIL) population, built on RNA-seq data. RNA-seq analysis on 160 RILs of this population identified 30,049 single-nucleotide polymorphisms (SNPs) covering the whole genome. Based on a 100-kbp window SNP binning method, 1059 bin-markers were identified, physically anchored on the genome. The total length of the RNA-seq genetic map spans 471.70 centimorgans (cM) with an average marker distance of 0.45 cM and a maximum marker distance of 4.81 cM. This high resolution genotyping revealed new recombination breakpoints in the population. To highlight the advantages of such high-density map, we compared it to two publicly available genetic maps for the same population, comprising 69 PCR-based markers and 497 gene expression markers derived from microarray data, respectively. In this study, we show that SNP markers can effectively be derived from RNA-seq data. The new RNA-seq map closes many existing gaps in marker coverage, saturating the previously available genetic maps. Quantitative trait locus (QTL) analysis for published phenotypes using the available genetic maps showed increased QTL mapping resolution and reduced QTL confidence interval using the RNA-seq map. The new high-density map is a valuable resource that facilitates the identification of candidate genes and map-based cloning approaches. PMID:29259624

QTL mapping for downy mildew resistance in cucumber via bulked segregant analysis using next-generation sequencing and conventional methods.

PubMed

Win, Khin Thanda; Vegas, Juan; Zhang, Chunying; Song, Kihwan; Lee, Sanghyeob

2017-01-01

QTL mapping using NGS-assisted BSA was successfully applied to an F 2 population for downy mildew resistance in cucumber. QTLs detected by NGS-assisted BSA were confirmed by conventional QTL analysis. Downy mildew (DM), caused by Pseudoperonospora cubensis, is one of the most destructive foliar diseases in cucumber. QTL mapping is a fundamental approach for understanding the genetic inheritance of DM resistance in cucumber. Recently, many studies have reported that a combination of bulked segregant analysis (BSA) and next-generation sequencing (NGS) can be a rapid and cost-effective way of mapping QTLs. In this study, we applied NGS-assisted BSA to QTL mapping of DM resistance in cucumber and confirmed the results by conventional QTL analysis. By sequencing two DNA pools each consisting of ten individuals showing high resistance and susceptibility to DM from a F 2 population, we identified single nucleotide polymorphisms (SNPs) between the two pools. We employed a statistical method for QTL mapping based on these SNPs. Five QTLs, dm2.2, dm4.1, dm5.1, dm5.2, and dm6.1, were detected and dm2.2 showed the largest effect on DM resistance. Conventional QTL analysis using the F 2 confirmed dm2.2 (R 2  = 10.8-24 %) and dm5.2 (R 2  = 14-27.2 %) as major QTLs and dm4.1 (R 2  = 8 %) as two minor QTLs, but could not detect dm5.1 and dm6.1. A new QTL on chromosome 2, dm2.1 (R 2  = 28.2 %) was detected by the conventional QTL method using an F 3 population. This study demonstrated the effectiveness of NGS-assisted BSA for mapping QTLs conferring DM resistance in cucumber and revealed the unique genetic inheritance of DM resistance in this population through two distinct major QTLs on chromosome 2 that mainly harbor DM resistance.

Sea ice occurrence predicts genetic isolation in the Arctic fox.

PubMed

Geffen, Eli; Waidyaratne, Sitara; Dalén, Love; Angerbjörn, Anders; Vila, Carles; Hersteinsson, Pall; Fuglei, Eva; White, Paula A; Goltsman, Michael; Kapel, Christian M O; Wayne, Robert K

2007-10-01

Unlike Oceanic islands, the islands of the Arctic Sea are not completely isolated from migration by terrestrial vertebrates. The pack ice connects many Arctic Sea islands to the mainland during winter months. The Arctic fox (Alopex lagopus), which has a circumpolar distribution, populates numerous islands in the Arctic Sea. In this study, we used genetic data from 20 different populations, spanning the entire distribution of the Arctic fox, to identify barriers to dispersal. Specifically, we considered geographical distance, occurrence of sea ice, winter temperature, ecotype, and the presence of red fox and polar bear as nonexclusive factors that influence the dispersal behaviour of individuals. Using distance-based redundancy analysis and the BIOENV procedure, we showed that occurrence of sea ice is the key predictor and explained 40-60% of the genetic distance among populations. In addition, our analysis identified the Commander and Pribilof Islands Arctic populations as genetically unique suggesting they deserve special attention from a conservation perspective.

Genetic diversity of Trichomonas vaginalis clinical isolates from Henan province in central China.

PubMed

Mao, Meng; Liu, Hui Li

2015-07-01

Trichomonas vaginalis is a flagellated protozoan parasite that infects the human urogenital tract, causing the most common non-viral, sexually transmitted disease worldwide. In this study, genetic variants of T. vaginalis were identified in Henan Province, China. Fragments of the small subunit of nuclear ribosomal RNA (18S rRNA) were amplified from 32 T. vaginalis isolates obtained from seven regions of Henan Province. Overall, 18 haplotypes were determined from the 18S rRNA sequences. Each sampled population and the total population displayed high haplotype diversity (Hd), accompanied by very low nucleotide diversity (Pi). In these molecular genetic variants, 91.58% genetic variation was derived from intra-regions. Phylogenetic analysis revealed no correlation between phylogeny and geographic distribution. Demographic analysis supported population expansion of T. vaginalis isolates from central China. Our findings showing moderate-to-high genetic variations in the 32 isolates of T. vaginalis provide useful knowledge for monitoring changes in parasite populations for the development of future control strategies.

Admixture into and within sub-Saharan Africa

PubMed Central

Busby, George BJ; Band, Gavin; Si Le, Quang; Jallow, Muminatou; Bougama, Edith; Mangano, Valentina D; Amenga-Etego, Lucas N; Enimil, Anthony; Apinjoh, Tobias; Ndila, Carolyne M; Manjurano, Alphaxard; Nyirongo, Vysaul; Doumba, Ogobara; Rockett, Kirk A; Kwiatkowski, Dominic P; Spencer, Chris CA

2016-01-01

Similarity between two individuals in the combination of genetic markers along their chromosomes indicates shared ancestry and can be used to identify historical connections between different population groups due to admixture. We use a genome-wide, haplotype-based, analysis to characterise the structure of genetic diversity and gene-flow in a collection of 48 sub-Saharan African groups. We show that coastal populations experienced an influx of Eurasian haplotypes over the last 7000 years, and that Eastern and Southern Niger-Congo speaking groups share ancestry with Central West Africans as a result of recent population expansions. In fact, most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of gene-flow within the last 4000 years. Our in-depth analysis provides insight into haplotype sharing across different ethno-linguistic groups and the recent movement of alleles into new environments, both of which are relevant to studies of genetic epidemiology. DOI: http://dx.doi.org/10.7554/eLife.15266.001 PMID:27324836

Adaptation and major chromosomal changes in populations of Saccharomyces cerevisiae.

PubMed

Adams, J; Puskas-Rozsa, S; Simlar, J; Wilke, C M

1992-07-01

Thirteen independent populations of Saccharomyces cerevisiae (nine haploid and four diploid) were maintained in continuous culture for up to approximately 1000 generations, with growth limited by the concentration of organic phosphates in medium buffered at pH 6. Analysis of clones isolated from these populations showed that a number (17) of large-scale chromosomal-length variants and rearrangements were present in the populations at their termination. Nine of the 16 yeast chromosomes were involved in such changes. Few of the changes could be explained by copy-number increases in the structural loci for acid phosphatase. Several considerations concerning the nature and frequency of the chromosome-length variants observed lead us to conclude that they are selectively advantageous.

On the effects of nonlinear boundary conditions in diffusive logistic equations on bounded domains

NASA Astrophysics Data System (ADS)

Cantrell, Robert Stephen; Cosner, Chris

We study a diffusive logistic equation with nonlinear boundary conditions. The equation arises as a model for a population that grows logistically inside a patch and crosses the patch boundary at a rate that depends on the population density. Specifically, the rate at which the population crosses the boundary is assumed to decrease as the density of the population increases. The model is motivated by empirical work on the Glanville fritillary butterfly. We derive local and global bifurcation results which show that the model can have multiple equilibria and in some parameter ranges can support Allee effects. The analysis leads to eigenvalue problems with nonstandard boundary conditions.

Expression of interest: transcriptomics and the designation of conservation units.

PubMed

Hansen, Michael M

2010-05-01

An important task within conservation genetics consists in defining intraspecific conservation units. Most conceptual frameworks involve two steps: (i) identifying demographically independent units, and (ii) evaluating their degree of adaptive divergence. Whereas a plethora of methods are available for delineating genetic population structure, assessment of functional genetic divergence remains a challenge. In this issue, Tymchuk et al. (2010) study Atlantic salmon (Salmo salar) populations using both microsatellite markers and analysis of global gene expression. They show that important gene expression differences exist that can be interpreted in the context of different ecological conditions experienced by the populations, along with the populations' histories. This demonstrates an important potential role of transcriptomics for designating conservation units.

Genetic diversity of Brazilian natural populations of Anthonomus grandis Boheman (Coleoptera: Curculionidae), the major cotton pest in the New World.

PubMed

Martins, W F S; Ayres, C F J; Lucena, W A

2007-01-27

Twenty-five RAPD loci and 6 isozyme loci were studied to characterize the genetic variability of natural populations of Anthonomus grandis from two agroecosystems of Brazil. The random-amplified polymorphic DNA data disclosed a polymorphism that varied from 52 to 84% and a heterozygosity of 0.189 to 0.347. The index of genetic differentiation (GST) among the six populations was 0.258. The analysis of isozymes showed a polymorphism and a heterozygosity ranging from 25 to 100% and 0.174 to 0.277, respectively. The genetic differentiation (FST) among the populations obtained by isozyme data was 0.544. It was possible to observe rare alleles in the populations from the Northeast region. The markers examined allowed us to distinguish populations from large-scale, intensive farming region (cotton belts) versus populations from areas of small-scale farming

RAPID-COMMUNICATION Genetic diversity and differentiation in natural populations of Arapaima gigas from lower Amazon revealed by microsatellites.

PubMed

Fazzi-Gomes, P F; Melo, N; Palheta, G; Guerreiro, S; Amador, M; Ribeiro-Dos-Santos, A K; Santos, S; Hamoy, I

2017-02-08

Genetic variability is one of the important criteria for species conservation decisions. This study aimed to analyze the genetic diversity and the population differentiation of two natural populations of Arapaima gigas, a species with a long history of being commercially exploited. We collected 87 samples of A. gigas from Grande Curuai Lake and Paru Lake, located in the Lower Amazon region of Amazônia, Brazil, and genotyped these samples using a multiplex panel of microsatellite markers. Our results showed that the populations of A. gigas analyzed had high levels of genetic variability, which were similar to those described in previous studies. These two populations had a significant population differentiation supported by the estimates of F ST and R ST (0.06), by Bayesian analysis (K = 2), and by population assignment tests, which revealed a moderate genetic distance.

Analysis of genetic population structure in Acacia caven (Leguminosae, Mimosoideae), comparing one exploratory and two Bayesian-model-based methods

PubMed Central

Pometti, Carolina L.; Bessega, Cecilia F.; Saidman, Beatriz O.; Vilardi, Juan C.

2014-01-01

Bayesian clustering as implemented in STRUCTURE or GENELAND software is widely used to form genetic groups of populations or individuals. On the other hand, in order to satisfy the need for less computer-intensive approaches, multivariate analyses are specifically devoted to extracting information from large datasets. In this paper, we report the use of a dataset of AFLP markers belonging to 15 sampling sites of Acacia caven for studying the genetic structure and comparing the consistency of three methods: STRUCTURE, GENELAND and DAPC. Of these methods, DAPC was the fastest one and showed accuracy in inferring the K number of populations (K = 12 using the find.clusters option and K = 15 with a priori information of populations). GENELAND in turn, provides information on the area of membership probabilities for individuals or populations in the space, when coordinates are specified (K = 12). STRUCTURE also inferred the number of K populations and the membership probabilities of individuals based on ancestry, presenting the result K = 11 without prior information of populations and K = 15 using the LOCPRIOR option. Finally, in this work all three methods showed high consistency in estimating the population structure, inferring similar numbers of populations and the membership probabilities of individuals to each group, with a high correlation between each other. PMID:24688293

Differential dynamics of spatial attention, position, and color coding within the parietofrontal network.

PubMed

Astrand, Elaine; Ibos, Guilhem; Duhamel, Jean-René; Ben Hamed, Suliann

2015-02-18

Despite an ever growing knowledge on how parietal and prefrontal neurons encode low-level spatial and color information or higher-level information, such as spatial attention, an understanding of how these cortical regions process neuronal information at the population level is still missing. A simple assumption would be that the function and temporal response profiles of these neuronal populations match that of its constituting individual cells. However, several recent studies suggest that this is not necessarily the case and that the single-cell approach overlooks dynamic changes in how information is distributed over the neuronal population. Here, we use a time-resolved population pattern analysis to explore how spatial position, spatial attention and color information are differentially encoded and maintained in the macaque monkey prefrontal (frontal eye fields) and parietal cortex (lateral intraparietal area). Overall, our work brings about three novel observations. First, we show that parietal and prefrontal populations operate in two distinct population regimens for the encoding of sensory and cognitive information: a stationary mode and a dynamic mode. Second, we show that the temporal dynamics of a heterogeneous neuronal population brings about complementary information to that of its functional subpopulations. Thus, both need to be investigated in parallel. Last, we show that identifying the neuronal configuration in which a neuronal population encodes given information can serve to reveal this same information in a different context. All together, this work challenges common views on neural coding in the parietofrontal network. Copyright © 2015 the authors 0270-6474/15/353174-16$15.00/0.

A rapid screening of ancestry for genetic association studies in an admixed population from Pernambuco, Brazil.

PubMed

Coelho, A V C; Moura, R R; Cavalcanti, C A J; Guimarães, R L; Sandrin-Garcia, P; Crovella, S; Brandão, L A C

2015-03-31

Genetic association studies determine how genes influence traits. However, non-detected population substructure may bias the analysis, resulting in spurious results. One method to detect substructure is to genotype ancestry informative markers (AIMs) besides the candidate variants, quantifying how much ancestral populations contribute to the samples' genetic background. The present study aimed to use a minimum quantity of markers, while retaining full potential to estimate ancestries. We tested the feasibility of a subset of the 12 most informative markers from a previously established study to estimate influence from three ancestral populations: European, African and Amerindian. The results showed that in a sample with a diverse ethnicity (N = 822) derived from 1000 Genomes database, the 12 AIMs had the same capacity to estimate ancestries when compared to the original set of 128 AIMs, since estimates from the two panels were closely correlated. Thus, these 12 SNPs were used to estimate ancestry in a new sample (N = 192) from an admixed population in Recife, Northeast Brazil. The ancestry estimates from Recife subjects were in accordance with previous studies, showing that Northeastern Brazilian populations show great influence from European ancestry (59.7%), followed by African (23.0%) and Amerindian (17.3%) ancestries. Ethnicity self-classification according to skin-color was confirmed to be a poor indicator of population substructure in Brazilians, since ancestry estimates overlapped between classifications. Thus, our streamlined panel of 12 markers may substitute panels with more markers, while retaining the capacity to control for population substructure and admixture, thereby reducing sample processing time.

Identification and expression profiles of fifteen delta-class glutathione S-transferase genes from a stored-product pest, Liposcelis entomophila (Enderlein) (Psocoptera: Liposcelididae).

PubMed

Jing, Tian-Xing; Wu, Yu-Xian; Li, Ting; Wei, Dan-Dan; Smagghe, Guy; Wang, Jin-Jun

2017-04-01

Glutathione S-transferases (GSTs) comprise a diverse family of enzymes found ubiquitously in aerobic organisms and they play important roles in insecticide resistance. In this study, we tested the sensitivities of Liposcelis entomophila, collected from four different field populations, to three insecticides. The results showed that the insects from Tongliang population had a relatively higher tolerance to malathion and propuxor than insects from other field populations. The insecticide sensitivities of different populations detected in psocids may be due to the different control practices. Through sequence mining and phylogenetic analyses, we identified 15 delta class GST genes that contained the conserved motifs of the GSTs. Quantitative real-time PCR (Q-PCR) analysis indicated that the 15 GST genes were expressed at all tested developmental stages, and 12 GST genes had significantly higher expression levels in adulthood than in egg stage. The expression levels of 15 GST genes in different field populations showed that 9 GST genes were significantly higher in Tongliang population compared to other populations. Furthermore, Q-PCR confirmed that the expression of several delta class GSTs was upregulated at different times after malathion, propuxor and deltamethrine exposure with the LC 50 concentration of insecticide. Taken together, these findings showed that delta class GST genes have various expression levels in different developmental stages and different field populations, and they were up-regulated in response to insecticide exposure, which suggested that these GSTs may be associated with insecticide metabolism in psocids. Copyright © 2017 Elsevier Inc. All rights reserved.

Dentine morphology of Atapuerca-Sima de los Huesos lower molars: Evolutionary implications through three-dimensional geometric morphometric analysis.

PubMed

Hanegraef, Hester; Martinón-Torres, María; Martínez de Pinillos, Marina; Martín-Francés, Laura; Vialet, Amélie; Arsuaga, Juan Luis; Bermúdez de Castro, José María

2018-06-01

This study aims to explore the affinities of the Sima de los Huesos (SH) population in relation to Homo neanderthalensis, Arago, and early and contemporary Homo sapiens. By characterizing SH intra-population variation, we test current models to explain the Neanderthal origins. Three-dimensional reconstructions of dentine surfaces of lower first and second molars were produced by micro-computed tomography. Landmarks and sliding semilandmarks were subjected to generalized Procrustes analysis and principal components analysis. SH is often similar in shape to Neanderthals, and both groups are generally discernible from Homo sapiens. For example, the crown height of SH and Neanderthals is lower than for modern humans. Differences in the presence of a mid-trigonid crest are also observed, with contemporary Homo sapiens usually lacking this feature. Although SH and Neanderthals show strong affinities, they can be discriminated based on certain traits. SH individuals are characterized by a lower intra-population variability, and show a derived dental reduction in lower second molars compared to Neanderthals. SH also differs in morphological features from specimens that are often classified as Homo heidelbergensis, such as a lower crown height and less pronounced mid-trigonid crest in the Arago fossils. Our results are compatible with the idea that multiple evolutionary lineages or populations coexisted in Europe during the Middle Pleistocene, with the SH paradigm phylogenetically closer to Homo neanderthalensis. Further research could support the possibility of SH as a separate taxon. Alternatively, SH could be a subspecies of Neanderthals, with the variability of this clade being remarkably higher than previously thought. © 2018 Wiley Periodicals, Inc.

Origin and dynamics of admixture in Brazilians and its effect on the pattern of deleterious mutations.

PubMed

Kehdy, Fernanda S G; Gouveia, Mateus H; Machado, Moara; Magalhães, Wagner C S; Horimoto, Andrea R; Horta, Bernardo L; Moreira, Rennan G; Leal, Thiago P; Scliar, Marilia O; Soares-Souza, Giordano B; Rodrigues-Soares, Fernanda; Araújo, Gilderlanio S; Zamudio, Roxana; Sant Anna, Hanaisa P; Santos, Hadassa C; Duarte, Nubia E; Fiaccone, Rosemeire L; Figueiredo, Camila A; Silva, Thiago M; Costa, Gustavo N O; Beleza, Sandra; Berg, Douglas E; Cabrera, Lilia; Debortoli, Guilherme; Duarte, Denise; Ghirotto, Silvia; Gilman, Robert H; Gonçalves, Vanessa F; Marrero, Andrea R; Muniz, Yara C; Weissensteiner, Hansi; Yeager, Meredith; Rodrigues, Laura C; Barreto, Mauricio L; Lima-Costa, M Fernanda; Pereira, Alexandre C; Rodrigues, Maíra R; Tarazona-Santos, Eduardo

2015-07-14

While South Americans are underrepresented in human genomic diversity studies, Brazil has been a classical model for population genetics studies on admixture. We present the results of the EPIGEN Brazil Initiative, the most comprehensive up-to-date genomic analysis of any Latin-American population. A population-based genome-wide analysis of 6,487 individuals was performed in the context of worldwide genomic diversity to elucidate how ancestry, kinship, and inbreeding interact in three populations with different histories from the Northeast (African ancestry: 50%), Southeast, and South (both with European ancestry >70%) of Brazil. We showed that ancestry-positive assortative mating permeated Brazilian history. We traced European ancestry in the Southeast/South to a wider European/Middle Eastern region with respect to the Northeast, where ancestry seems restricted to Iberia. By developing an approximate Bayesian computation framework, we infer more recent European immigration to the Southeast/South than to the Northeast. Also, the observed low Native-American ancestry (6-8%) was mostly introduced in different regions of Brazil soon after the European Conquest. We broadened our understanding of the African diaspora, the major destination of which was Brazil, by revealing that Brazilians display two within-Africa ancestry components: one associated with non-Bantu/western Africans (more evident in the Northeast and African Americans) and one associated with Bantu/eastern Africans (more present in the Southeast/South). Furthermore, the whole-genome analysis of 30 individuals (42-fold deep coverage) shows that continental admixture rather than local post-Columbian history is the main and complex determinant of the individual amount of deleterious genotypes.

Origin and dynamics of admixture in Brazilians and its effect on the pattern of deleterious mutations

PubMed Central

Kehdy, Fernanda S. G.; Gouveia, Mateus H.; Machado, Moara; Magalhães, Wagner C. S.; Horimoto, Andrea R.; Horta, Bernardo L.; Moreira, Rennan G.; Leal, Thiago P.; Scliar, Marilia O.; Soares-Souza, Giordano B.; Rodrigues-Soares, Fernanda; Araújo, Gilderlanio S.; Zamudio, Roxana; Sant Anna, Hanaisa P.; Santos, Hadassa C.; Duarte, Nubia E.; Fiaccone, Rosemeire L.; Figueiredo, Camila A.; Silva, Thiago M.; Costa, Gustavo N. O.; Beleza, Sandra; Berg, Douglas E.; Cabrera, Lilia; Debortoli, Guilherme; Duarte, Denise; Ghirotto, Silvia; Gilman, Robert H.; Gonçalves, Vanessa F.; Marrero, Andrea R.; Muniz, Yara C.; Weissensteiner, Hansi; Yeager, Meredith; Rodrigues, Laura C.; Barreto, Mauricio L.; Lima-Costa, M. Fernanda; Pereira, Alexandre C.; Rodrigues, Maíra R.; Tarazona-Santos, Eduardo

2015-01-01

While South Americans are underrepresented in human genomic diversity studies, Brazil has been a classical model for population genetics studies on admixture. We present the results of the EPIGEN Brazil Initiative, the most comprehensive up-to-date genomic analysis of any Latin-American population. A population-based genome-wide analysis of 6,487 individuals was performed in the context of worldwide genomic diversity to elucidate how ancestry, kinship, and inbreeding interact in three populations with different histories from the Northeast (African ancestry: 50%), Southeast, and South (both with European ancestry >70%) of Brazil. We showed that ancestry-positive assortative mating permeated Brazilian history. We traced European ancestry in the Southeast/South to a wider European/Middle Eastern region with respect to the Northeast, where ancestry seems restricted to Iberia. By developing an approximate Bayesian computation framework, we infer more recent European immigration to the Southeast/South than to the Northeast. Also, the observed low Native-American ancestry (6–8%) was mostly introduced in different regions of Brazil soon after the European Conquest. We broadened our understanding of the African diaspora, the major destination of which was Brazil, by revealing that Brazilians display two within-Africa ancestry components: one associated with non-Bantu/western Africans (more evident in the Northeast and African Americans) and one associated with Bantu/eastern Africans (more present in the Southeast/South). Furthermore, the whole-genome analysis of 30 individuals (42-fold deep coverage) shows that continental admixture rather than local post-Columbian history is the main and complex determinant of the individual amount of deleterious genotypes. PMID:26124090

Genetic distance of Malaysian mousedeer based on mitochondrial DNA cytochrome oxidase I (COI) and D-loop region sequences

NASA Astrophysics Data System (ADS)

Bakar, Mohamad-Azam Akmal Abu; Rovie-Ryan, Jeffrine Japning; Ampeng, Ahmad; Yaakop, Salmah; Nor, Shukor Md; Md-Zain, Badrul Munir

2018-04-01

Mousedeer is one of the primitive mammals that can be found mainly in Southeast-Asia region. There are two species of mousedeer in Malaysia which are Tragulus kanchil and Tragulus napu. Both species can be distinguish by size, coat coloration, and throat pattern but clear diagnosis still cannot be found. The objective of the study is to show the genetic distance relationship between T. kanchil and T. napu and their population based on mitochondrial DNA (mtDNA) cytochrome oxidase I (COI) and D-loop region. There are 42 sample of mousedeer were used in this study collected by PERHILITAN from different locality. Another 29 D-loop sequence were retrieved from Genbank for comparative analysis. All sample were amplified using universal primer and species-specific primer for COI and D-loop genes via PCR process. The amplified sequences were analyzed to determine genetic distance of T. kanchil and T. napu. From the analysis, the average genetic distance between T. kanchil and T. napu based on locus COI and D-loop were 0.145 and 0.128 respectively. The genetic distance between populations of T. kanchil based on locus COI was between 0.003-0.013. For locus D-loop, genetic distance analysis showed distance in relationship between west-coast populations to east-coast population of T. kanchil. COI and D-loop mtDNA region provided a clear picture on the relationship within the mousedeer species. Last but not least, conservation effort toward protecting this species can be done by study the molecular genetics and prevent the extinction of this species.

Genetic diversity and genetic structure of consecutive breeding generations of golden mandarin fish (Siniperca scherzeri Steindachner) using microsatellite markers.

PubMed

Luo, X N; Yang, M; Liang, X F; Jin, K; Lv, L Y; Tian, C X; Yuan, Y C; Sun, J

2015-09-25

In this study, 12 polymorphic microsatellites were inves-tigated to determine the genetic diversity and structure of 5 consecu-tive selected populations of golden mandarin fish (Siniperca scherzeri Steindachner). The total numbers of alleles, average heterozyosity, and average polymorphism information content showed that the genetic diversity of these breeding populations was decreasing. Additionally, pairwise fixation index FST values among populations and Da values in-creased from F1 generation to subsequent generations (FST values from 0.0221-0.1408; Da values from 0.0608-0.1951). Analysis of molecular variance indicated that most genetic variations arise from individuals within populations (about 92.05%), while variation among populations accounted for only 7.95%. The allele frequency of the loci SC75-220 and SC101-222 bp changed regularly in the 5 breeding generations. Their frequencies were gradually increased and showed an enrichment trend, indicating that there may be genetic correlations between these 2 loci and breeding traits. Our study indicated that microsatellite markers are effective for assessing the genetic variability in the golden mandarin fish breeding program.

Heterogeneous Structure of Stem Cells Dynamics: Statistical Models and Quantitative Predictions

PubMed Central

Bogdan, Paul; Deasy, Bridget M.; Gharaibeh, Burhan; Roehrs, Timo; Marculescu, Radu

2014-01-01

Understanding stem cell (SC) population dynamics is essential for developing models that can be used in basic science and medicine, to aid in predicting cells fate. These models can be used as tools e.g. in studying patho-physiological events at the cellular and tissue level, predicting (mal)functions along the developmental course, and personalized regenerative medicine. Using time-lapsed imaging and statistical tools, we show that the dynamics of SC populations involve a heterogeneous structure consisting of multiple sub-population behaviors. Using non-Gaussian statistical approaches, we identify the co-existence of fast and slow dividing subpopulations, and quiescent cells, in stem cells from three species. The mathematical analysis also shows that, instead of developing independently, SCs exhibit a time-dependent fractal behavior as they interact with each other through molecular and tactile signals. These findings suggest that more sophisticated models of SC dynamics should view SC populations as a collective and avoid the simplifying homogeneity assumption by accounting for the presence of more than one dividing sub-population, and their multi-fractal characteristics. PMID:24769917

Temporal Genetic Dynamics of an Invasive Species, Frankliniella occidentalis (Pergande), in an Early Phase of Establishment

PubMed Central

Yang, Xian-Ming; Lou, Heng; Sun, Jing-Tao; Zhu, Yi-Ming; Xue, Xiao-Feng; Hong, Xiao-Yue

2015-01-01

Many species can successfully colonize new areas despite their propagules having low genetic variation. We assessed whether the decreased genetic diversity could result in temporal fluctuations of genetic parameters of the new populations of an invasive species, western flower thrips, Frankliniella occidentalis, using mitochondrial and microsatellite markers. This study was conducted in eight localities from four climate regions in China, where F. occidentalis was introduced in the year 2000 and had lower genetic diversity than its native populations. We also tested the level of genetic differentiation in these introduced populations. The genetic diversity of the samples at different years in the same locality was not significantly different from each other in most localities. FST and STRUCTURE analysis also showed that most temporal population comparisons from the same sites were not significantly differentiated. Our results showed that the invasive populations of F. occidentalis in China can maintain temporal stability in genetic composition at an early phase of establishment despite having lower genetic diversity than in their native range. PMID:26138760

Genetic variability in captive populations of the stingless bee Tetragonisca angustula.

PubMed

Santiago, Leandro R; Francisco, Flávio O; Jaffé, Rodolfo; Arias, Maria C

2016-08-01

Low genetic variability has normally been considered a consequence of animal husbandry and a major contributing factor to declining bee populations. Here, we performed a molecular analysis of captive and wild populations of the stingless bee Tetragonisca angustula, one of the most commonly kept species across South America. Microsatellite analyses showed similar genetic variability between wild and captive populations However, captive populations showed lower mitochondrial genetic variability. Male-mediated gene flow, transport and division of nests are suggested as the most probable explanations for the observed patterns of genetic structure. We conclude that increasing the number of colonies kept through nest divisions does not negatively affect nuclear genetic variability, which seems to be maintained by small-scale male dispersal and human-mediated nest transport. However, the transport of nests from distant localities should be practiced with caution given the high genetic differentiation observed between samples from western and eastern areas. The high genetic structure verified is the result of a long-term evolutionary process, and bees from distant localities may represent unique evolutionary lineages.

A fully-stochasticized, age-structured population model for population viability analysis of fish: Lower Missouri River endangered pallid sturgeon example

USGS Publications Warehouse

Wildhaber, Mark L.; Albers, Janice; Green, Nicholas; Moran, Edward H.

2017-01-01

We develop a fully-stochasticized, age-structured population model suitable for population viability analysis (PVA) of fish and demonstrate its use with the endangered pallid sturgeon (Scaphirhynchus albus) of the Lower Missouri River as an example. The model incorporates three levels of variance: parameter variance (uncertainty about the value of a parameter itself) applied at the iteration level, temporal variance (uncertainty caused by random environmental fluctuations over time) applied at the time-step level, and implicit individual variance (uncertainty caused by differences between individuals) applied within the time-step level. We found that population dynamics were most sensitive to survival rates, particularly age-2+ survival, and to fecundity-at-length. The inclusion of variance (unpartitioned or partitioned), stocking, or both generally decreased the influence of individual parameters on population growth rate. The partitioning of variance into parameter and temporal components had a strong influence on the importance of individual parameters, uncertainty of model predictions, and quasiextinction risk (i.e., pallid sturgeon population size falling below 50 age-1+ individuals). Our findings show that appropriately applying variance in PVA is important when evaluating the relative importance of parameters, and reinforce the need for better and more precise estimates of crucial life-history parameters for pallid sturgeon.

Genetic Diversity of Ascaris in China Assessed Using Simple Sequence Repeat Markers.

PubMed

Zhou, Chunhua; Jian, Shaoqing; Peng, Weidong; Li, Min

2018-04-01

The giant roundworm Ascaris infects pigs and people worldwide and causes serious diseases. The taxonomic relationship between Ascaris suum and Ascaris lumbricoides is still unclear. The purpose of the present study was to investigate the genetic diversity and population genetic structure of 258 Ascaris specimens from humans and pigs from 6 sympatric regions in Ascaris -endemic regions of China using existing simple sequence repeat data. The microsatellite markers showed a high level of allelic richness and genetic diversity in the samples. Each of the populations demonstrated excess homozygosity (Ho0). According to a genetic differentiation index (Fst=0.0593), there was a high-level of gene flow in the Ascaris populations. A hierarchical analysis on molecular variance revealed remarkably high levels of variation within the populations. Moreover, a population structure analysis indicated that Ascaris populations fell into 3 main genetic clusters, interpreted as A. suum , A. lumbricoides , and a hybrid of the species. We speculated that humans can be infected with A. lumbricoides , A. suum , and the hybrid, but pigs were mainly infected with A. suum . This study provided new information on the genetic diversity and population structure of Ascaris from human and pigs in China, which can be used for designing Ascaris control strategies. It can also be beneficial to understand the introgression of host affiliation.

Ancient DNA evidence supports the contribution of Di-Qiang people to the han Chinese gene pool.

PubMed

Zhao, Yong-Bin; Li, Hong-Jie; Li, Sheng-Nan; Yu, Chang-Chun; Gao, Shi-Zhu; Xu, Zhi; Jin, Li; Zhu, Hong; Zhou, Hui

2011-02-01

Han Chinese is the largest ethnic group in the world. During its development, it gradually integrated with many neighboring populations. To uncover the origin of the Han Chinese, ancient DNA analysis was performed on the remains of 46 humans (1700 to 1900 years ago) excavated from the Taojiazhai site in Qinghai province, northwest of China, where the Di-Qiang populations had previously lived. In this study, eight mtDNA haplogroups (A, B, D, F, M*, M10, N9a, and Z) and one Y-chromosome haplogroup (O3) were identified. All analyses show that the Taojiazhai population presents close genetic affinity to Tibeto-Burman populations (descendants of Di-Qiang populations) and Han Chinese, suggesting that the Di-Qiang populations may have contributed to the Han Chinese genetic pool. 2010 Wiley-Liss, Inc.

Genetic analysis and ethnic affinities from two Scytho-Siberian skeletons.

PubMed

Ricaut, François-Xavier; Keyser-Tracqui, Christine; Cammaert, Laurence; Crubézy, Eric; Ludes, Bertrand

2004-04-01

We extracted DNA from two skeletons belonging to the Sytho-Siberian population, which were excavated from the Sebÿstei site (dating back 2,500 years) in the Altai Republic (Central Asia). Ancient DNA was analyzed by autosomal short tandem repeats (STRs) and by the sequencing of the hypervariable region 1 (HV1) of the mitochondrial DNA (mtDNA) control region. The results showed that these two skeletons were not close relatives. Moreover, their haplogroups were characteristic of Asian populations. Comparison with the haplogroup of 3,523 Asian and American individuals linked one skeleton with a putative ancestral paleo-Asiatic population and the other with Chinese populations. It appears that the genetic study of ancient populations of Central Asia brings important elements to the understanding of human population movements in Asia. Copyright 2003 Wiley-Liss, Inc.

Genetic evidence for an East Asian origin of Chinese Muslim populations Dongxiang and Hui

PubMed Central

Yao, Hong-Bing; Wang, Chuan-Chao; Tao, Xiaolan; Shang, Lei; Wen, Shao-Qing; Zhu, Bofeng; Kang, Longli; Jin, Li; Li, Hui

2016-01-01

There is a long-going debate on the genetic origin of Chinese Muslim populations, such as Uygur, Dongxiang, and Hui. However, genetic information for those Muslim populations except Uygur is extremely limited. In this study, we investigated the genetic structure and ancestry of Chinese Muslims by analyzing 15 autosomal short tandem repeats in 652 individuals from Dongxiang, Hui, and Han Chinese populations in Gansu province. Both genetic distance and Bayesian-clustering methods showed significant genetic homogeneity between the two Muslim populations and East Asian populations, suggesting a common genetic ancestry. Our analysis found no evidence of substantial gene flow from Middle East or Europe into Dongxiang and Hui people during their Islamization. The dataset generated in present study are also valuable for forensic identification and paternity tests in China. PMID:27924949

Genetic analysis of the Venezuelan Criollo horse.

PubMed

Cothran, E G; Canelon, J L; Luis, C; Conant, E; Juras, R

2011-10-07

Various horse populations in the Americas have an origin in Spain; they are remnants of the first livestock introduced to the continent early in the colonial period (16th and 17th centuries). We evaluated genetic variability within the Venezuelan Criollo horse and its relationship with other horse breeds. We observed high levels of genetic diversity within the Criollo breed. Significant population differentiation was observed between all South American breeds. The Venezuelan Criollo horse showed high levels of genetic diversity, and from a conservation standpoint, there is no immediate danger of losing variation unless there is a large drop in population size.

Data Mining Applied to Analysis of Contraceptive Methods Among College Students.

PubMed

Simões, Priscyla Waleska; Cesconetto, Samuel; Dalló, Eduardo Daminelli; de Souza Pires, Maria Marlene; Comunello, Eros; Borges Tomaz, Felipe; Xavier, Eduardo Pícolo; da Rosa Brunel Alves, Pedro Antonio; Ceretta, Luciane Bisognin; Manenti, Sandra Aparecida

2017-01-01

The aim of this study was to use the Data Mining to analyze the profile of the use of contraceptive methods in a university population. We used a database about sexuality performed on a university population in southern Brazil. The results obtained by the generated rules are largely in line with the literature and epidemiology worldwide, showing significant points of vulnerability in the university population. Validation measures of the study, as such, accuracy, sensitivity, specificity, and area under the ROC curve were higher or at least similar as compared to recent studies using the same methodology.

Worldwide analysis of multiple microsatellites: language diversity has a detectable influence on DNA diversity.

PubMed

Belle, Elise M S; Barbujani, Guido

2007-08-01

Previous studies of the correlations between the languages spoken by human populations and the genes carried by the members of those populations have been limited by the small amount of genetic markers available and by approximations in the treatment of linguistic data. In this study we analyzed a large collection of polymorphic microsatellite loci (377), distributed on all autosomes, and used Ruhlen's linguistic classification, to investigate the relative roles of geography and language in shaping the distribution of human DNA diversity at a worldwide scale. For this purpose, we performed three different kinds of analysis: (i) we partitioned genetic variances at three hierarchical levels of population subdivision according to language group by means of a molecular analysis of variance (AMOVA); (ii) we quantified by a series of Mantel's tests the correlation between measures of genetic and linguistic differentiation; and (iii) we tested whether linguistic differences are increased across known zones of increased genetic change between populations. Genetic differences appear to more closely reflect geographic than linguistic differentiation. However, our analyses show that language differences also have a detectable effect on DNA diversity at the genomic level, above and beyond the effects of geographic distance. (c) 2007 Wiley-Liss, Inc.

Analysis of current assessments and perspectives of ESR tooth dosimetry for radiation dose reconstruction of the population residing near the Semipalatinsk nuclear test site.

PubMed

Romanyukha, Alex; Schauer, David A; Malikov, Yurii K

2006-02-01

Between 1949 and 1989 the Semipalatinsk nuclear test site (SNTS), an area of 19,000 square km in northeastern Kazakhstan, was the location of over 400 nuclear test explosions with a total explosive energy of 6.6 Mt TNT (trinitrotoluene or trotyl) equivalent. It is estimated that the bulk of the radiation exposure to the population resulted from three tests, conducted in 1949, 1951, and 1953 although estimations of radiation doses received by the local population have varied significantly. Analysis of the published ESR dose reconstruction results for residents of the villages near the SNTS show that they do not correlate well with other methods of dose assessment (e.g. model dose calculation and thermo luminescence dosimetry (TLD) in bricks). The most significant difference in dose estimations was found for the population of Dolon, which was exposed as result of the first Soviet nuclear test in 1949. Published results of ESR measurements in tooth enamel are considerably lower than other dose estimations. Detailed analysis of these results is provided and a possible explanation for this discrepancy and ways to eliminate it are suggested.

Analysis of promoter polymorphism in monoamine oxidase A (MAOA) gene in completed suicide on Slovenian population.

PubMed

Uršič, Katarina; Zupanc, Tomaž; Paska, Alja Videtič

2018-04-23

Suicide is a well-defined public health problem and is a complex phenomenon influenced by a number of different risk factors, including genetic ones. Numerous studies have examined serotonin system genes. Monoamine oxidase A (MAO-A) is an outer mitochondrial membrane enzyme which is involved in the metabolic pathway of serotonin degradation. Upstream variable number of tandem repeats (uVNTR) in the promoter region of MAOA gene affects the activity of transcription. In the present study we genotyped MAOA-uVNTR polymorphism in 266 suicide victims and 191 control subjects of Slovenian population, which ranks among the European and world populations with the highest suicide rate. Genotyping was performed with polymerase chain reaction and agarose gel electrophoresis. Using a separate statistical analysis for female and male subjects we determined the differences in genotype distributions of MAOA-uVNTR polymorphism between the studied groups. Statistical analysis showed a trend towards 3R allele and suicide, and associated 3R allele with non-violent suicide method on stratified data (20 suicide victims). This is the first study associating highly suicidal Slovenian population with MAOA-uVNTR polymorphism. Copyright © 2018 Elsevier B.V. All rights reserved.

Rapid genome-wide evolution in Brassica rapa populations following drought revealed by sequencing of ancestral and descendant gene pools.

PubMed

Franks, Steven J; Kane, Nolan C; O'Hara, Niamh B; Tittes, Silas; Rest, Joshua S

2016-08-01

There is increasing evidence that evolution can occur rapidly in response to selection. Recent advances in sequencing suggest the possibility of documenting genetic changes as they occur in populations, thus uncovering the genetic basis of evolution, particularly if samples are available from both before and after selection. Here, we had a unique opportunity to directly assess genetic changes in natural populations following an evolutionary response to a fluctuation in climate. We analysed genome-wide differences between ancestors and descendants of natural populations of Brassica rapa plants from two locations that rapidly evolved changes in multiple phenotypic traits, including flowering time, following a multiyear late-season drought in California. These ancestor-descendant comparisons revealed evolutionary shifts in allele frequencies in many genes. Some genes showing evolutionary shifts have functions related to drought stress and flowering time, consistent with an adaptive response to selection. Loci differentiated between ancestors and descendants (FST outliers) were generally different from those showing signatures of selection based on site frequency spectrum analysis (Tajima's D), indicating that the loci that evolved in response to the recent drought and those under historical selection were generally distinct. Very few genes showed similar evolutionary responses between two geographically distinct populations, suggesting independent genetic trajectories of evolution yielding parallel phenotypic changes. The results show that selection can result in rapid genome-wide evolutionary shifts in allele frequencies in natural populations, and highlight the usefulness of combining resurrection experiments in natural populations with genomics for studying the genetic basis of adaptive evolution. © 2016 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Genetic Analysis of Aedes aegypti Using Random Amplified Polymorphic DNA (RAPD) Markers from Dengue Outbreaks in Pakistan.

PubMed

Ashraf, Hafiz Muhammad; Zahoor, Muhammad Kashif; Nasir, Shabab; Majeed, Humara Naz; Zahoor, Sarwat

2016-12-01

Keeping in view the havoc situation of dengue fever in Pakistan, the current study was designed to demonstrate the genetic variations, gene flow and rate of migration from Lahore and Faisalabad. The larvae were collected from both natural and artificial breeding places from each collection site. The adult mosquitoes were collected by means of sweep net and battery-operated aspirator. DNA extraction was performed using TNE buffer method. Ten GeneLink-A series RAPD primers were used for PCR amplification and the data was analyzed through POPGENE. The number of amplification products produced per primer varied from 8-12, ranging from 200 to 2000 bp with an average of 10.0 bands per primer. The percentage of polymorphic loci amplified by each primer varied from 22.5 to 51%. The UPGMA dendrogram demonstrates two distinct groups from Faisalabad and Lahore populations. The genetic diversity ranged from 0.260 in Faisalabad to 0.294 in Lahore with a total heterozygosity of 0.379. The G ST value for nine populations within Lahore was 0.131 (Nm= 3.317), whereas for nine populations in Faisalabad G ST value was 0.117 (Nm= 3.773). The overall genetic variation among eighteen populations showed G ST = 0.341 and Nm= 1.966. The genetic relatedness and Nm value show that Ae . aegypti populations exhibit intra-population gene flow both in Faisalabad and Lahore. Although, both cities show a distinct pattern of genetic structure; however, few areas from both the cities show genetic similarity. The gene flow and the genetic relatedness in few populations of Lahore and Faisalabad cities need further investigation.