Science.gov

Sample records for genetically homogeneous population

  1. Low genetic diversity and strong but shallow population differentiation suggests genetic homogenization by metapopulation dynamics in a social spider.

    PubMed

    Settepani, V; Bechsgaard, J; Bilde, T

    2014-12-01

    Mating systems and population dynamics influence genetic diversity and structure. Species that experience inbreeding and limited gene flow are expected to evolve isolated, divergent genetic lineages. Metapopulation dynamics with frequent extinctions and colonizations may, on the other hand, deplete and homogenize genetic variation, if extinction rate is sufficiently high compared to the effect of drift in local demes. We investigated these theoretical predictions empirically in social spiders that are highly inbred. Social spiders show intranest mating, female-biased sex ratio, and frequent extinction and colonization events, factors that deplete genetic diversity within nests and populations and limit gene flow. We characterized population genetic structure in Stegodyphus sarasinorum, a social spider distributed across the Indian subcontinent. Species-wide genetic diversity was estimated over approximately 2800 km from Sri Lanka to Himalayas, by sequencing 16 protein-coding nuclear loci. We found 13 SNPs in 6592 bp (π = 0.00045) indicating low species-wide nucleotide diversity. Three genetic lineages were strongly differentiated; however, only one fixed difference among them suggests recent divergence. This is consistent with a scenario of metapopulation dynamics that homogenizes genetic diversity across the species' range. Ultimately, low standing genetic variation may hamper a species' ability to track environmental change and render social inbreeding spiders 'evolutionary dead-ends'. PMID:25348843

  2. Anthropogenics: human influence on global and genetic homogenization of parasite populations.

    PubMed

    Zarlenga, Dante S; Hoberg, Eric; Rosenthal, Benjamin; Mattiucci, Simonetta; Nascetti, Giuseppe

    2014-12-01

    environmental change now plays a primary role in defining where hosts, parasites, and other pathogens occur. This review examines how anthropogenic factors serve as drivers of globalization and genetic homogenization of parasite populations and demonstrates the impact that human intervention has had on the global dissemination of parasites and the accompanying diseases. PMID:25198251

  3. FADS genetic variants and ω-6 polyunsaturated fatty acid metabolism in a homogeneous island population[S

    PubMed Central

    Mathias, Rasika A.; Vergara, Candelaria; Gao, Li; Rafaels, Nicholas; Hand, Tracey; Campbell, Monica; Bickel, Carol; Ivester, Priscilla; Sergeant, Susan; Barnes, Kathleen C.; Chilton, Floyd H.

    2010-01-01

    Long-chain polyunsaturated fatty acids (PUFA) orchestrate immunity and inflammation through their capacity to be converted to potent inflammatory mediators. We assessed associations of FADS gene cluster polymorphisms and fasting serum PUFA concentrations in a fully ascertained, geographically isolated founder population of European descent. Concentrations of 22 PUFAs were determined by gas chromatography, of which ten fatty acids and five ratios defining FADS1 and FADS2 activity were tested for genetic association against 16 single nucleotide polymorphisms (SNP) in 224 individuals. A cluster of SNPs in tight linkage disequilibrium in the FADS1 gene (rs174537, rs174545, rs174546, rs174553, rs174556, rs174561, rs174568, and rs99780) were strongly associated with arachidonic acid (AA) (P = 5.8 × 10−7 – 1.7 × 10−8) among other PUFAs, but the strongest associations were with the ratio measuring FADS1 activity in the ω-6 series (P = 2.11 × 10−13 – 1.8 × 10−20). The minor allele across all SNPs was consistently associated with decreased ω-6 PUFAs, with the exception of dihomo-γ-linoleic acid (DHGLA), where the minor allele was consistently associated with increased levels. Our findings in a geographically isolated population with a homogenous dietary environment suggest that variants in the Δ-5 desaturase enzymatic step likely regulate the efficiency of conversion of medium-chain PUFAs to potentially inflammatory PUFAs, such as AA. PMID:20562440

  4. Genetic Structure and Demographic History Should Inform Conservation: Chinese Cobras Currently Treated as Homogenous Show Population Divergence

    PubMed Central

    Lin, Long-Hui; Qu, Yan-Fu; Li, Hong; Zhou, Kai-Ya; Ji, Xiang

    2012-01-01

    An understanding of population structure and genetic diversity is crucial for wildlife conservation and for determining the integrity of wildlife populations. The vulnerable Chinese cobra (Naja atra) has a distribution from the mouth of the Yangtze River down to northern Vietnam and Laos, within which several large mountain ranges and water bodies may influence population structure. We combined 12 microsatellite loci and 1117 bp of the mitochondrial cytochrome b gene to explore genetic structure and demographic history in this species, using 269 individuals from various localities in Mainland China and Vietnam. High levels of genetic variation were identified for both mtDNA and microsatellites. mtDNA data revealed two main (Vietnam + southern China + southwestern China; eastern + southeastern China) and one minor (comprising only two individuals from the westernmost site) clades. Microsatellite data divided the eastern + southeastern China clade further into two genetic clusters, which include individuals from the eastern and southeastern regions, respectively. The Luoxiao and Nanling Mountains may be important barriers affecting the diversification of lineages. In the haplotype network of cytchrome b, many haplotypes were represented within a “star” cluster and this and other tests suggest recent expansion. However, microsatellite analyses did not yield strong evidence for a recent bottleneck for any population or genetic cluster. The three main clusters identified here should be considered as independent management units for conservation purposes. The release of Chinese cobras into the wild should cease unless their origin can be determined, and this will avoid problems arising from unnatural homogenization. PMID:22558439

  5. Detecting immigrants in a highly genetically homogeneous spiny lobster population (Palinurus elephas) in the northwest Mediterranean Sea.

    PubMed

    Elphie, Hamdi; Raquel, Goñi; David, Dìaz; Serge, Planes

    2012-10-01

    We investigated the genetic structure of early benthic juveniles of the spiny lobster Palinurus elephas in the northwest Mediterranean Sea by means of ten polymorphic microsatellite markers. Non-metric Multidimensional Scaling coupled with assignment tests were used as a new approach to further delimit a reference population inside a genetically homogeneous pool of individuals and test for the presence of long distance immigrants. From this approach, we found that most early benthic juveniles collected while settling in the northwest Mediterranean Sea originated from a common larval pool. However, 4.2% of the individuals were classified as immigrants from other genetically differentiated populations, with more immigrants in the south than in the north of the sampled basin. Given currents in the northwest Mediterranean Sea and the long pelagic larval phase of P. elephas that lasts several months, this result suggest a restricted homogenized zone in the studied basin with some individuals probably coming from more differentiated populations through the Almeria-Oran Front or the Strait of Sicily. PMID:23145326

  6. Homogenous Population Genetic Structure of the Non-Native Raccoon Dog (Nyctereutes procyonoides) in Europe as a Result of Rapid Population Expansion

    PubMed Central

    Drygala, Frank; Korablev, Nikolay; Ansorge, Hermann; Fickel, Joerns; Isomursu, Marja; Elmeros, Morten; Kowalczyk, Rafał; Baltrunaite, Laima; Balciauskas, Linas; Saarma, Urmas; Schulze, Christoph; Borkenhagen, Peter; Frantz, Alain C.

    2016-01-01

    The extent of gene flow during the range expansion of non-native species influences the amount of genetic diversity retained in expanding populations. Here, we analyse the population genetic structure of the raccoon dog (Nyctereutes procyonoides) in north-eastern and central Europe. This invasive species is of management concern because it is highly susceptible to fox rabies and an important secondary host of the virus. We hypothesized that the large number of introduced animals and the species’ dispersal capabilities led to high population connectivity and maintenance of genetic diversity throughout the invaded range. We genotyped 332 tissue samples from seven European countries using 16 microsatellite loci. Different algorithms identified three genetic clusters corresponding to Finland, Denmark and a large ‘central’ population that reached from introduction areas in western Russia to northern Germany. Cluster assignments provided evidence of long-distance dispersal. The results of an Approximate Bayesian Computation analysis supported a scenario of equal effective population sizes among different pre-defined populations in the large central cluster. Our results are in line with strong gene flow and secondary admixture between neighbouring demes leading to reduced genetic structuring, probably a result of its fairly rapid population expansion after introduction. The results presented here are remarkable in the sense that we identified a homogenous genetic cluster inhabiting an area stretching over more than 1500km. They are also relevant for disease management, as in the event of a significant rabies outbreak, there is a great risk of a rapid virus spread among raccoon dog populations. PMID:27064784

  7. Homogenous Population Genetic Structure of the Non-Native Raccoon Dog (Nyctereutes procyonoides) in Europe as a Result of Rapid Population Expansion.

    PubMed

    Drygala, Frank; Korablev, Nikolay; Ansorge, Hermann; Fickel, Joerns; Isomursu, Marja; Elmeros, Morten; Kowalczyk, Rafał; Baltrunaite, Laima; Balciauskas, Linas; Saarma, Urmas; Schulze, Christoph; Borkenhagen, Peter; Frantz, Alain C

    2016-01-01

    The extent of gene flow during the range expansion of non-native species influences the amount of genetic diversity retained in expanding populations. Here, we analyse the population genetic structure of the raccoon dog (Nyctereutes procyonoides) in north-eastern and central Europe. This invasive species is of management concern because it is highly susceptible to fox rabies and an important secondary host of the virus. We hypothesized that the large number of introduced animals and the species' dispersal capabilities led to high population connectivity and maintenance of genetic diversity throughout the invaded range. We genotyped 332 tissue samples from seven European countries using 16 microsatellite loci. Different algorithms identified three genetic clusters corresponding to Finland, Denmark and a large 'central' population that reached from introduction areas in western Russia to northern Germany. Cluster assignments provided evidence of long-distance dispersal. The results of an Approximate Bayesian Computation analysis supported a scenario of equal effective population sizes among different pre-defined populations in the large central cluster. Our results are in line with strong gene flow and secondary admixture between neighbouring demes leading to reduced genetic structuring, probably a result of its fairly rapid population expansion after introduction. The results presented here are remarkable in the sense that we identified a homogenous genetic cluster inhabiting an area stretching over more than 1500km. They are also relevant for disease management, as in the event of a significant rabies outbreak, there is a great risk of a rapid virus spread among raccoon dog populations. PMID:27064784

  8. Anthropogenics: Human influence on global and genetic homogenization of parasite populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The distribution, abundance, and diversity of life on Earth have been greatly shaped by human activities. This is no truer than in the geographic expansion of parasites; however, measuring the extent to which humans have influenced the dissemination and population structure of parasites has been cha...

  9. Y-chromosome based evidence for pre-neolithic origin of the genetically homogeneous but diverse Sardinian population: inference for association scans.

    PubMed

    Contu, Daniela; Morelli, Laura; Santoni, Federico; Foster, Jamie W; Francalacci, Paolo; Cucca, Francesco

    2008-01-01

    The island of Sardinia shows a unique high incidence of several autoimmune diseases with multifactorial inheritance, particularly type 1 diabetes and multiple sclerosis. The prior knowledge of the genetic structure of this population is fundamental to establish the optimal design for association studies in these diseases. Previous work suggested that the Sardinians are a relatively homogenous population, but some reports were contradictory and data were largely based on variants subject to selection. For an unbiased assessment of genetic structure, we studied a combination of neutral Y-chromosome variants, 21 biallelic and 8 short tandem repeats (STRs) in 930 Sardinian males. We found a high degree of interindividual variation but a homogenous distribution of the detected variability in samples from three separate regions of the island. One haplogroup, I-M26, is rare or absent outside Sardinia and is very common (0.37 frequency) throughout the island, consistent with a founder effect. A Bayesian full likelihood analysis (BATWING) indicated that the time from the most recent common ancestor (TMRCA) of I-M26, was 21.0 (16.0-25.5) thousand years ago (KYA) and that the population began to expand 14.0 (7.8-22.0) KYA. These results suggest a largely pre-Neolithic settlement of the island with little subsequent gene flow from outside populations. Consequently, Sardinia is an especially attractive venue for case-control genome wide association scans in common multifactorial diseases. Concomitantly, the high degree of interindividual variation in the current population facilitates fine mapping efforts to pinpoint the aetiologic polymorphisms. PMID:18183308

  10. Genetics of population isolates.

    PubMed

    Arcos-Burgos, M; Muenke, M

    2002-04-01

    Genetic isolates, as shown empirically by the Finnish, Old Order Amish, Hutterites, Sardinian and Jewish communities among others, represent a most important and powerful tool in genetically mapping inherited disorders. The main features associated with that genetic power are the existence of multigenerational pedigrees which are mostly descended from a small number of founders a short number of generations ago, environmental and phenotypic homogeneity, restricted geographical distribution, the presence of exhaustive and detailed records correlating individuals in very well ascertained pedigrees, and inbreeding as a norm. On the other hand, the presence of a multifounder effect or admixture among divergent populations in the founder time (e.g. the Finnish and the Paisa community from Colombia) will theoretically result in increased linkage disequilibrium among adjacent loci. The present review evaluates the historical context and features of some genetic isolates with emphasis on the basic population genetic concepts of inbreeding and genetic drift, and also the state-of-the-art in mapping traits, both Mendelian and complex, on genetic isolates. PMID:12030885

  11. Degeneracy allows for both apparent homogeneity and diversification in populations

    PubMed Central

    Whitacre, James M.; Atamas, Sergei P.

    2013-01-01

    Trait diversity – the substrate for natural selection – is necessary for adaptation through selection, particularly in populations faced with environmental changes that diminish population fitness. In habitats that remain unchanged for many generations, stabilizing selection maximizes exploitation of resources by reducing trait diversity to a narrow optimal range. One might expect that such ostensibly homogeneous populations would have a reduced potential for heritable adaptive responses when faced with fitness-reducing environmental changes. However, field studies have documented populations that, even after long periods of evolutionary stasis, can still rapidly evolve in response to changed environmental conditions. We argue that degeneracy, the ability of diverse population elements to function similarly, can satisfy both the current need to maximize fitness and the future need for diversity. Degenerate ensembles appear functionally redundant in certain environmental contexts and functionally diverse in others. We propose that genetic variation not contributing to the observed range of phenotypes in a current population, also known as cryptic genetic variation (CGV), is a specific case of degeneracy. We argue that CGV, which gradually accumulates in static populations in stable environments, reveals hidden trait differences when environments change. By allowing CGV accumulation, static populations prepare themselves for future rapid adaptations to environmental novelty. A greater appreciation of degeneracy’s role in resolving the inherent tension between current stabilizing selection and future directional selection has implications in conservation biology and may be applied in social and technological systems to maximize current performance while strengthening the potential for future changes. PMID:22910487

  12. Population genetics of Lithuanians.

    PubMed

    Ku inskas, V

    2001-01-01

    The primary objective of this article was to overview the present-day knowledge on genetic features of the Lithuanian population. Genetic differentiation within the Lithuanian population and the relationship between Lithuanians and other European populations was analysed by means of blood groups, serum protein polymorphisms and DNA markers including mtDNA. The results of the research have shown small differences between present-day Lithuanian ethnolinguistic groups, which probably go back to the prehistoric Baltic tribal structure. The Baltic peoples show a mixture of eastern and western genetic traits, e.g. a high frequency of the blood group B combined with a very high frequency of the Rh-negative blood group. Studies of the Baltic 'tribal gene' LWb indicate the presence of a considerable Baltic admixture in the neighbouring Finno-Ugric and Slavic populations. PMID:11201326

  13. Population Dynamics of Genetic Regulatory Networks

    NASA Astrophysics Data System (ADS)

    Braun, Erez

    2005-03-01

    Unlike common objects in physics, a biological cell processes information. The cell interprets its genome and transforms the genomic information content, through the action of genetic regulatory networks, into proteins which in turn dictate its metabolism, functionality and morphology. Understanding the dynamics of a population of biological cells presents a unique challenge. It requires to link the intracellular dynamics of gene regulation, through the mechanism of cell division, to the level of the population. We present experiments studying adaptive dynamics of populations of genetically homogeneous microorganisms (yeast), grown for long durations under steady conditions. We focus on population dynamics that do not involve random genetic mutations. Our experiments follow the long-term dynamics of the population distributions and allow to quantify the correlations among generations. We focus on three interconnected issues: adaptation of genetically homogeneous populations following environmental changes, selection processes on the population and population variability and expression distributions. We show that while the population exhibits specific short-term responses to environmental inputs, it eventually adapts to a robust steady-state, largely independent of external conditions. Cycles of medium-switch show that the adapted state is imprinted in the population and that this memory is maintained for many generations. To further study population adaptation, we utilize the process of gene recruitment whereby a gene naturally regulated by a specific promoter is placed under a different regulatory system. This naturally occurring process has been recognized as a major driving force in evolution. We have recruited an essential gene to a foreign regulatory network and followed the population long-term dynamics. Rewiring of the regulatory network allows us to expose their complex dynamics and phase space structure.

  14. Genetics and population history of Caucasus populations.

    PubMed

    Bulayeva, Kazima; Jorde, Lynn B; Ostler, Christopher; Watkins, Scott; Bulayev, Oleg; Harpending, Henry

    2003-12-01

    We describe aspects of genetic diversity in several ethnic populations of the Caucasus Mountains of Daghestan using mitochondrial DNA sequences and a sample of 100 polymorphic Alu insertion loci. The mitochondrial DNA (mtDNA) sequences are like those of Europe. Principal coordinates and nearest neighbor statistics show that there is little detectable structure in the distances among populations computed from mtDNA. The Alu frequencies of the Caucasus populations suggest that they have undergone more genetic drift than most other groups since the dispersal of modern humans. Genetic differences among these populations are not large; instead, they are of the same order as distances among populations of Europe. We compare two methods of inference about the demography of ancient colonizing populations from Africa, one based on conventional FST statistics and one based on mean Alu insertion frequencies. The two approaches agree reasonably well if we assume that there was demographic growth in Africa before the diaspora of ancestors of contemporary regional human groups outside Africa. PMID:15018034

  15. Genetic differentiation of Jewish populations.

    PubMed

    Klitz, W; Gragert, L; Maiers, M; Fernandez-Viña, M; Ben-Naeh, Y; Benedek, G; Brautbar, C; Israel, S

    2010-12-01

    The Jewish diaspora can be viewed as a natural process in population dispersion and differentiation. We extend genetic studies on the Jewish diaspora to an analysis of human leukocyte antigen (HLA) haplotype distributions in the Jewish peoples, and show the value of this information for the design of Jewish marrow donor registries. HLA data from the Hadassah Bone Marrow Registry having parental country-of-origin information comprise samples of geographically discrete regions. We analyzed the HLA allele and haplotype frequencies for each national sample using population genetic and clustering methods. Population differentiation among diaspora populations was shown on the basis of HLA haplotype frequencies, including differences within the more recently diverged European groups. A method of haplotype and population clustering showed patterns of unique haplotype affinities associated with specific Jewish populations. The evidence showed that diaspora Jewish populations can be sorted into distinct clades of which the Ashkenazi are but one. Relationships among Jewish populations are interpretable in light of the historical record. We suggest that a major contributing factor to the genetic divergence between Jewish groups may have been admixture with local host populations, while, at the same time, threads of Eastern Mediterranean ancestry remain evident. PMID:20860586

  16. Genetic homogeneity in the commercial pink shrimp Farfantepenaeus paulensis revealed by COI barcoding gene

    NASA Astrophysics Data System (ADS)

    Teodoro, S. S. A.; Terossi, M.; Costa, R. C.; Mantelatto, F. L.

    2015-12-01

    The pink shrimp Farfantepenaeus paulensis is one of the most commercially exploited species in Brazil's South and Southeastern regions. Specific information about the status of its genetic variation is necessary to promote more effective management procedures. The genetic variation of the population of F. paulensis was investigated in five localities along southern and southeastern coast of Brazil. Sampling was performed with a commercial fishing boat. Total genomic DNA was extracted from abdominal muscle tissues and was used to DNA amplification by PCR. The COI gene was used as a DNA barcoding marker. The 570 bp COI gene sequences were obtained from all 45 individuals. The haplotype network showed no genetic variability among the population stocks, which was confirmed by Molecular Variance Analysis. The final alignment showed that inside species there is haplotype sharing among the sampled localities, since one haplotype is shared by 38 individuals belonging to all the five sampled regions, with no biogeographic pattern. This result is reasonable since there are no geographical barriers or habitat disjunction that might serve as a barrier to gene flow among the sampled localities. Possible reasons and consequences of the genetic homogeneity found are discussed. The results complement ecological studies concerning the offseason: since it is a single stock, the same protection strategy can be applied. However, the genetic homogeneity found in this study combined with the intensive fishery effort and the species biology can result in severe consequences for the F. paulensis.

  17. [Population genetics of plant pathogens].

    PubMed

    Zhu, Wen; Zhan, Jia-Sui

    2012-02-01

    Comparing to natural ecosystems, the evolution of plant pathogens in agricultural ecosystems is generally faster due to high-density monocultures, large-scale application of agrochemicals, and international trade in agricultural products. Knowledge of the population genetics and evolutionary biology of plant pathogens is necessary to understand disease epidemiology, effectively breed and use resistant cultivars, and control plant diseases. In this article, we outlined the aims of population genetic studies in plant pathogens, discuss contributions of five evolutionary forces (i.e., mutation, gene flow, recombination, random genetic drift, and natural selection) to origin, maintenance, and distribution of genetic variation in time and space, and gave an overview of current research status in this field. PMID:22382057

  18. Mantel test in population genetics

    PubMed Central

    Diniz-Filho, José Alexandre F.; Soares, Thannya N.; Lima, Jacqueline S.; Dobrovolski, Ricardo; Landeiro, Victor Lemes; de Campos Telles, Mariana Pires; Rangel, Thiago F.; Bini, Luis Mauricio

    2013-01-01

    The comparison of genetic divergence or genetic distances, estimated by pairwise FST and related statistics, with geographical distances by Mantel test is one of the most popular approaches to evaluate spatial processes driving population structure. There have been, however, recent criticisms and discussions on the statistical performance of the Mantel test. Simultaneously, alternative frameworks for data analyses are being proposed. Here, we review the Mantel test and its variations, including Mantel correlograms and partial correlations and regressions. For illustrative purposes, we studied spatial genetic divergence among 25 populations of Dipteryx alata (“Baru”), a tree species endemic to the Cerrado, the Brazilian savannas, based on 8 microsatellite loci. We also applied alternative methods to analyze spatial patterns in this dataset, especially a multivariate generalization of Spatial Eigenfunction Analysis based on redundancy analysis. The different approaches resulted in similar estimates of the magnitude of spatial structure in the genetic data. Furthermore, the results were expected based on previous knowledge of the ecological and evolutionary processes underlying genetic variation in this species. Our review shows that a careful application and interpretation of Mantel tests, especially Mantel correlograms, can overcome some potential statistical problems and provide a simple and useful tool for multivariate analysis of spatial patterns of genetic divergence. PMID:24385847

  19. Apparent genetic homogeneity of spawning striped bass in the upper Chesapeak Bay

    SciTech Connect

    Sidell, B.D.; Otto, R.G.; Powers, D.A. Karweit, M.; Smith, J.

    1980-01-01

    The possible existence of genetically distinct populations of spawning striped bass (Morone saxatilis) in the river systems of the upper Chesapeake Bay was investigated by a biochemical genetic approach. Samples of blood and liver from adult fish were obtained during the 1976 spawning runs from the Rappanhannock (Virginia), Potomac, Choptank, Sassafras, Bohemia, and Elk rivers (Maryland), and Maryland waters of the Chesapeake and Delaware Canal. Samples were analyzed for frequency of occurrence of a polymorphic liver enzyme, glycerol-3-phosphate dehydrogenase, and variable serum proteins which were not correlated with age or sex. Multivariate and Bayesian analyses of these data indicate apparent genetic homogeneity of spawning bass within the upper Chesapeake Bay. If natal stream homing occurs, a sufficient number of wanderers may provide significant gene flow among river systems. The results suggest that long-term management of the fishery need not be totally on the basis of separate river units.

  20. Homogeneity of Powassan virus populations in naturally infected Ixodes scapularis

    SciTech Connect

    Brackney, Doug E.; Brown, Ivy K.; Nofchissey, Robert A.; Fitzpatrick, Kelly A.; Ebel, Gregory D.

    2010-07-05

    Powassan virus (POWV, Flaviviridae: Flavivirus) is the sole North American member of the tick-borne encephalitis complex and consists of two distinct lineages that are maintained in ecologically discrete enzootic transmission cycles. The underlying genetic mechanisms that lead to niche partitioning in arboviruses are poorly understood. Therefore, intra- and interhost genetic diversity was analyzed to determine if POWV exists as a quasispecies in nature and quantify selective pressures within and between hosts. In contrast to previous reports for West Nile virus (WNV), significant intrahost genetic diversity was not observed. However, pN (0.238) and d{sub N}/d{sub S} ratios (0.092) for interhost diversity were similar to those of WNV. Combined, these data suggest that purifying selection and/or population bottlenecks constrain quasispecies diversity within ticks. These same selective and stochastic mechanisms appear to drive minor sequence changes between ticks. Moreover, Powassan virus populations seem not to be structured as quasispecies in naturally infected adult deer ticks.

  1. Does genetic diversity limit disease spread in natural host populations?

    PubMed Central

    King, K C; Lively, C M

    2012-01-01

    It is a commonly held view that genetically homogenous host populations are more vulnerable to infection than genetically diverse populations. The underlying idea, known as the ‘monoculture effect,' is well documented in agricultural studies. Low genetic diversity in the wild can result from bottlenecks (that is, founder effects), biparental inbreeding or self-fertilization, any of which might increase the risk of epidemics. Host genetic diversity could buffer populations against epidemics in nature, but it is not clear how much diversity is required to prevent disease spread. Recent theoretical and empirical studies, particularly in Daphnia populations, have helped to establish that genetic diversity can reduce parasite transmission. Here, we review the present theoretical work and empirical evidence, and we suggest a new focus on finding ‘diversity thresholds.' PMID:22713998

  2. Natural selection of altruism in inelastic viscous homogeneous populations.

    PubMed

    Grafen, Alan; Archetti, Marco

    2008-06-21

    Biological explanations are given of three main uninterpreted theoretical results on the selection of altruism in inelastic viscous homogeneous populations, namely that non-overlapping generations hinder the evolution of altruism, fecundity effects are more conducive to altruism than survival effects, and one demographic regime (so-called death-birth) permits altruism whereas another (so-called birth-death) does not. The central idea is 'circles of compensation', which measure how far the effects of density dependence extend from a focal individual. Relatednesses can then be calculated that compensate for density dependence. There is very generally a 'balancing circle of compensation', at which the viscosity of the population slows up selection of altruism, but does not affect its direction, and this holds for altruism towards any individual, not just immediate neighbours. These explanations are possible because of recent advances in the theory of inclusive fitness on graphs. The assumption of node bitransitivity in that recent theory is relaxed to node transitivity and symmetry of the dispersal matrix, and new formulae show how to calculate relatedness from dispersal and vice versa. PMID:18371985

  3. (Genetic structure of natural populations)

    SciTech Connect

    Not Available

    1988-01-01

    Our efforts in the first eight months were concentrated in obtaining a genomic clone of the copper-zinc superoxide dismutase (SOD) in Drosophila melanogaster and other Drosophila species. This we have now successfully accomplished. We seek to understand the role of SOD in radioresistance; how genetic variation in this enzyme is maintained in populations; and relevant aspects of its evolution that may contribute to these goals as well as to an understanding of molecular evolution in general. To accomplish these goals we are undertaking the following experiments: cloning and sequencing of (at least) one F allele, one S allele, and the null allele for SOD; cloning and sequencing SOD from species related to D. melanogaster; and cloning and sequencing the SOD gene from several independently sampled S and F alleles in D. melanogaster. We are also preparing to test the radioprotective effects of SOD. 67 refs.

  4. Genetics of growth in piglets and the association with homogeneity of body weight within litters.

    PubMed

    Canario, L; Lundgren, H; Haandlykken, M; Rydhmer, L

    2010-04-01

    The objective of this study was to examine the genetic basis of homogeneity in piglets and the genetic correlations with litter size and growth during lactation. Genetic parameters for variation in piglet BW within litters at birth and at 3 wk of age, and in the BW of individual piglets at 3 wk (BW3) were estimated from the Norwegian Landrace nucleus population. Data on BW3 were collected from 146,572 piglets from 14,045 litters in 58 herds. Body weight at birth and at 3 wk of age was recorded for 13,318 piglets from 5 nucleus herds. Litter data were evaluated using multivariate trait models. The heritability estimates for the SD of BW at birth and at 3 wk (SDBW3) were in agreement with the literature (0.10 and 0.08, respectively). The genetic correlation for the number of piglets born alive and the mean BW at 3 wk was negative (-0.40 +/- 0.07), and the correlation of number of piglets born alive with SDBW3 was close to zero (-0.03 +/- 0.11). The genetic correlation between the SD of BW at birth and SDBW3 was moderate (0.51 +/- 0.31). The mean BW at birth was genetically correlated with mean BW at 3 wk (0.59 +/- 0.16) but was independent of SDBW3 (0.08 +/- 0.27). The estimates of direct and maternal heritability for BW3 were 0.03 and 0.07, respectively, and the genetic correlation between the 2 components was negative (-0.43 +/- 0.10). The genetic correlation of SDBW3 with the maternal effect on BW3 was positive and strong (0.66 +/- 0.08), whereas a negative correlation was found with the direct effect on BW3 (-0.18 +/- 0.14). These results suggest that it is possible to select for mean BW at birth without an increase in within-litter heterogeneity at 3 wk of age. A more efficient strategy would be to consider both the direct and the maternal effects on BW3 in the genetic evaluation, together with SDBW3. Thus, it is possible to avoid the increase in within-litter heterogeneity that would occur as a result of selection performed at 3 wk on a litter trait such as

  5. Genetic background of clinical homogeneity of phenylketonuria in Poland.

    PubMed Central

    Jaruzelska, J; Matuszak, R; Lyonnet, S; Rey, F; Rey, J; Filipowicz, J; Borski, K; Munnich, A

    1993-01-01

    In order to elucidate the clinical homogeneity and severity of the hyperphenylalaninaemias in Poland, a total of 71 children with typical phenylketonuria (PKU) originating from western and northern Poland were screened for 13 mutations in the phenylalanine hydroxylase (PAH) gene. Eighty percent of all PKU alleles tested were found to carry an identified mutation. One mutation, namely the R408W mutation, accounted for more than 63% of mutant PAH alleles in Poland, the other 27% being accounted for by six mutations: IVS12nt1 (5%), IVSnt546 (5%), Y414C (4%), R252W (1.5%), R261Q (< 1%), and G272ter (< 1%). The predominance of the R408W mutation resulted in a high rate of homozygotes (35.2%) and compound heterozygotes for this mutation in children from western and northern Poland. The frequency and deleterious nature of this mutation probably accounts for the clinical homogeneity and severity of the hyperphenylalaninaemias in Poland. In addition, the high rate of the R408W mutation and its association with mutant haplotype 2 at the PAH locus in Poland give additional support to the Balto-Slavic origin of this mutant gene. PMID:8097262

  6. Genetic analysis of 12 unrelated CADASIL families: Demonstration of genetic homogeneity: Physical mapping of the gene

    SciTech Connect

    Tournier-Lasserve, E.; Nibbio, A.; Vahedi, K.

    1994-09-01

    CADASIL is the acronym (Cerebral Autosomal Dominant Arteriopathy with Subcortical Ischemic Strokes and Leukoencephalopathy) designating a recently identified mendelian cerebral arteriopathy characterized by the recurrence of ischemic sensory and motor deficits leading to a progressive subcortical dementia. Magnetic resonance imaging of the brain shows extensive areas of increased signal in the hemispheric white matter. We recently mapped the CADASIL locus in 2 large families on chromosome 19 in a 14 cM interval bracketed by D19S221 and D19S215{sup *}. Forty additional families have been collected. Twelve of them including more than 200 members have already been genotyped with a set of 10 highly polymorphic markers located between D19S221 and D19S215. All families are significantly linked to chromosome 19 demonstrating genetic homogeneity. Combined lod scores for several of these markers are above 30. The size of the mapping interval has been reduced to 2 cM. Genetic testing for presymptomatic individuals is now possible with respect to all ethical rules in this severe condition. Lastly, physical mapping of the affected gene has been started and data will be presented at the meeting.

  7. Dynamic regimes of local homogeneous population model with time lag

    NASA Astrophysics Data System (ADS)

    Neverova, Galina; Frisman, Efim

    2016-06-01

    We investigated Moran - Ricker model with time lag 1. It is made analytical and numerical study of the model. It is shown there is co-existence of various dynamic regimes under the same values of parameters. The model simultaneously possesses several different limit regimes: stable state, periodic fluctuations, and chaotic attractor. The research results show if present population size substantially depends on population number of previous year then it is observed quasi-periodic oscillations. Fluctuations with period 2 occur when the growth of population size is regulated by density dependence in the current year.

  8. Investigating Population History Using Temporal Genetic Differentiation

    PubMed Central

    Skoglund, Pontus; Sjödin, Per; Skoglund, Tobias; Lascoux, Martin; Jakobsson, Mattias

    2014-01-01

    The rapid advance of sequencing technology, coupled with improvements in molecular methods for obtaining genetic data from ancient sources, holds the promise of producing a wealth of genomic data from time-separated individuals. However, the population-genetic properties of time-structured samples have not been extensively explored. Here, we consider the implications of temporal sampling for analyses of genetic differentiation and use a temporal coalescent framework to show that complex historical events such as size reductions, population replacements, and transient genetic barriers between populations leave a footprint of genetic differentiation that can be traced through history using temporal samples. Our results emphasize explicit consideration of the temporal structure when making inferences and indicate that genomic data from ancient individuals will greatly increase our ability to reconstruct population history. PMID:24939468

  9. Can Population Genetics Adapt to Rapid Evolution?

    PubMed

    Messer, Philipp W; Ellner, Stephen P; Hairston, Nelson G

    2016-07-01

    Population genetics largely rests on a 'standard model' in which random genetic drift is the dominant force, selective sweeps occur infrequently, and deleterious mutations are purged from the population by purifying selection. Studies of phenotypic evolution in nature reveal a very different picture, with strong selection and rapid heritable trait changes being common. The time-rate scaling of phenotypic evolution suggests that selection on phenotypes is often fluctuating in direction, allowing phenotypes to respond rapidly to environmental fluctuations while remaining within relatively constant bounds over longer periods. Whether such rapid phenotypic evolution undermines the standard model will depend on how many genomic loci typically contribute to strongly selected traits and how phenotypic evolution impacts the dynamics of genetic variation in a population. Population-level sequencing will allow us to dissect the genetic basis of phenotypic evolution and study the evolutionary dynamics of genetic variation through direct measurement of polymorphism trajectories over time. PMID:27185237

  10. What Use Is Population Genetics?

    PubMed

    Charlesworth, Brian

    2015-07-01

    The Genetic Society of America's Thomas Hunt Morgan Medal is awarded to an individual GSA member for lifetime achievement in the field of genetics. For over 40 years, 2015 recipient Brian Charlesworth has been a leader in both theoretical and empirical evolutionary genetics, making substantial contributions to our understanding of how evolution acts on genetic variation. Some of the areas in which Charlesworth's research has been most influential are the evolution of sex chromosomes, transposable elements, deleterious mutations, sexual reproduction, and life history. He also developed the influential theory of background selection, whereby the recurrent elimination of deleterious mutations reduces variation at linked sites, providing a general explanation for the correlation between recombination rate and genetic variation. PMID:26170438

  11. What Use Is Population Genetics?

    PubMed Central

    Charlesworth, Brian

    2015-01-01

    The Genetic Society of America’s Thomas Hunt Morgan Medal is awarded to an individual GSA member for lifetime achievement in the field of genetics. For over 40 years, 2015 recipient Brian Charlesworth has been a leader in both theoretical and empirical evolutionary genetics, making substantial contributions to our understanding of how evolution acts on genetic variation. Some of the areas in which Charlesworth’s research has been most influential are the evolution of sex chromosomes, transposable elements, deleterious mutations, sexual reproduction, and life history. He also developed the influential theory of background selection, whereby the recurrent elimination of deleterious mutations reduces variation at linked sites, providing a general explanation for the correlation between recombination rate and genetic variation. PMID:26170438

  12. Genetic homogeneity of autoimmune polyglandular disease type I

    SciTech Connect

    Bjoerses, P.; Aaltonen, J.; Vikman, A.

    1996-10-01

    Autoimmune polyglandular disease type I (APECED) is an autosomal recessive autoimmune disease (MIM 240300) characterized by hypoparathyroidism, primary adrenocortical failure, and chronic mucocutaneous candidiasis. The disease is highly prevalent in two isolated populations, the Finnish population and the Iranian Jewish one. Sporadic cases have been identified in many other countries, including almost all European countries. The APECED locus has previously been assigned to chromosome 21q22.3 by linkage analyses in 14 Finnish families. Locus heterogeneity is a highly relevant question in this disease affecting multiple tissues and with great phenotypic diversity. To solve this matter, we performed linkage and haplotype analyses on APECED families rising from different populations. Six microsatellite markers on the critical chromosomal region of 2.6 cM on 21q22.3 were analyzed. Pair-wise linkage analyses revealed significant LOD scores for all these markers, maximum LOD score being 10.23. The obtained haplotype data and the geographic distribution of the great-grandparents of the Finnish APECED patients suggest the presence of one major, relatively old mutation responsible for {approximately}90% of the Finnish cases. Similar evidence for one founder mutation was also found in analyses of Iranian Jewish APECED haplotypes. These haplotypes, however, differed totally from the Finnish ones. The linkage analyses in 21 non-Finnish APECED families originating from several European countries provided independent evidence for linkage to the same chromosomal region on 21q22.3 and revealed no evidence for locus heterogeneity. The haplotype analyses of APECED chromosomes suggest that in different populations APECED is due to a spectrum of mutations in a still unknown gene on chromosome 21. 21 refs., 3 figs., 3 tabs.

  13. The genetic structure of the Kuwaiti population: mtDNA Inter- and intra-population variation.

    PubMed

    Theyab, Jasem B; Al-Bustan, Suzanne; Crawford, Michael H

    2012-08-01

    This study investigated: (1) the mitochondrial DNA (mtDNA) genetic variation in 116 unrelated individuals who originated from the Arabian Peninsula, Iran, or were of Bedouin ethnicity and (2) the genetic structure of Kuwaiti populations and compared it to their neighboring populations. These subpopulations were tested for genetic homogeneity and shown to be heterogeneous. Restriction fragment length polymorphism (RFLP) and mtDNA sequencing analyses of HVRI were used to reconstruct the genetic structure of Kuwait. The results indicated that the combined Kuwaiti population has a high frequency of haplogroup R0 (17%), J (12%), and U (12%) similar to other Arabian populations. In addition, contemporary African gene flow was detected through the presence of sub-haplogroup L (L1 and L2) (2%) and the absence of L3 which is reflective of an earlier migration. Furthermore, the multidimensional scaling (MDS) plot showed that the Kuwaiti population clusters with neighboring populations, including Iran and Saudi Arabia indicating gene flow into Kuwait. According to this study, the Kuwaiti population may be undergoing an expansion in a relatively short period of time, and the maternal genetic structure of Kuwait resembles both Saudi Arabia and Iran. PMID:23249314

  14. Genetics of autoimmune diseases: insights from population genetics

    PubMed Central

    Ramos, Paula S; Shedlock, Andrew M; Langefeld, Carl D

    2015-01-01

    Human genetic diversity is the result of population genetic forces. This genetic variation influences disease risk and contributes to health disparities. Autoimmune diseases (ADs) are a family of complex heterogeneous disorders with similar underlying mechanisms characterized by immune responses against self. Collectively, ADs are common, exhibit gender and ethnic disparities, and increasing incidence. As natural selection is an important influence on human genetic variation, and immune function genes are enriched for signals of positive selection, it is thought that the prevalence of AD risk alleles seen in different population is partially the result of differing selective pressures (for example, due to pathogens). With the advent of high-throughput technologies, new analytical methodologies and large-scale projects, evidence for the role of natural selection in contributing to the heritable component of ADs keeps growing. This review summarizes the genetic regions associated with susceptibility to different ADs and concomitant evidence for selection, including known agents of selection exerting selective pressure in these regions. Examples of specific adaptive variants with phenotypic effects are included as an evidence of natural selection increasing AD susceptibility. Many of the complexities of gene effects in different ADs can be explained by population genetics phenomena. Integrating AD susceptibility studies with population genetics to investigate how natural selection has contributed to genetic variation that influences disease risk will help to identify functional variants and elucidate biological mechanisms. As such, the study of population genetics in human population holds untapped potential for elucidating the genetic causes of human disease and more rapidly focusing to personalized medicine. PMID:26223182

  15. Ocean currents help explain population genetic structure

    PubMed Central

    White, Crow; Selkoe, Kimberly A.; Watson, James; Siegel, David A.; Zacherl, Danielle C.; Toonen, Robert J.

    2010-01-01

    Management and conservation can be greatly informed by considering explicitly how environmental factors influence population genetic structure. Using simulated larval dispersal estimates based on ocean current observations, we demonstrate how explicit consideration of frequency of exchange of larvae among sites via ocean advection can fundamentally change the interpretation of empirical population genetic structuring as compared with conventional spatial genetic analyses. Both frequency of larval exchange and empirical genetic difference were uncorrelated with Euclidean distance between sites. When transformed into relative oceanographic distances and integrated into a genetic isolation-by-distance framework, however, the frequency of larval exchange explained nearly 50 per cent of the variance in empirical genetic differences among sites over scales of tens of kilometres. Explanatory power was strongest when we considered effects of multiple generations of larval dispersal via intermediary locations on the long-term probability of exchange between sites. Our results uncover meaningful spatial patterning to population genetic structuring that corresponds with ocean circulation. This study advances our ability to interpret population structure from complex genetic data characteristic of high gene flow species, validates recent advances in oceanographic approaches for assessing larval dispersal and represents a novel approach to characterize population connectivity at small spatial scales germane to conservation and fisheries management. PMID:20133354

  16. Using noise to control heterogeneity of isogenic populations in homogenous environments

    NASA Astrophysics Data System (ADS)

    Szymańska, Paulina; Gritti, Nicola; Keegstra, Johannes M.; Soltani, Mohammad; Munsky, Brian

    2015-07-01

    We explore the extent to which the phenotypes of individual, genetically identical cells can be controlled independently from each other using only a single homogeneous environmental input. We show that such control is theoretically impossible if restricted to a deterministic setting, but it can be achieved readily if one exploits heterogeneities introduced at the single-cell level due to stochastic fluctuations in gene regulation. Using stochastic analyses of a bistable genetic toggle switch, we develop a control strategy that maximizes the chances that a chosen cell will express one phenotype, while the rest express another. The control mechanism uses UV radiation to enhance identically protein degradation in all cells. Control of individual cells is made possible only by monitoring stochastic protein fluctuations and applying UV control at favorable times and levels. For two identical cells, our stochastic control law can drive protein expression of a chosen cell above its neighbor with a better than 99% success rate. In a population of 30 identical cells, we can drive a given cell to remain consistently within the top 20%. Although cellular noise typically impairs predictability for biological responses, our results show that it can also simultaneously improve controllability for those same responses.

  17. Relevant genetic differentiation among Brazilian populations of Anastrepha fraterculus (Diptera, Tephritidae).

    PubMed

    Manni, Mosè; Lima, Kátia Manuela; Guglielmino, Carmela Rosalba; Lanzavecchia, Silvia Beatriz; Juri, Marianela; Vera, Teresa; Cladera, Jorge; Scolari, Francesca; Gomulski, Ludvik; Bonizzoni, Mariangela; Gasperi, Giuliano; Silva, Janisete Gomes; Malacrida, Anna Rodolfa

    2015-01-01

    We used a population genetic approach to detect the presence of genetic diversity among six populations of Anastrepha fraterculus across Brazil. To this aim, we used Simple Sequence Repeat (SSR) markers, which may capture the presence of differentiative processes across the genome in distinct populations. Spatial analyses of molecular variance were used to identify groups of populations that are both genetically and geographically homogeneous while also being maximally differentiated from each other. The spatial analysis of genetic diversity indicates that the levels of diversity among the six populations vary significantly on an eco-geographical basis. Particularly, altitude seems to represent a differentiating adaptation, as the main genetic differentiation is detected between the two populations present at higher altitudes and the other four populations at sea level. The data, together with the outcomes from different cluster analyses, identify a genetic diversity pattern that overlaps with the distribution of the known morphotypes in the Brazilian area. PMID:26798258

  18. Relevant genetic differentiation among Brazilian populations of Anastrepha fraterculus (Diptera, Tephritidae)

    PubMed Central

    Manni, Mosè; Lima, Kátia Manuela; Guglielmino, Carmela Rosalba; Lanzavecchia, Silvia Beatriz; Juri, Marianela; Vera, Teresa; Cladera, Jorge; Scolari, Francesca; Gomulski, Ludvik; Bonizzoni, Mariangela; Gasperi, Giuliano; Silva, Janisete Gomes; Malacrida, Anna Rodolfa

    2015-01-01

    Abstract We used a population genetic approach to detect the presence of genetic diversity among six populations of Anastrepha fraterculus across Brazil. To this aim, we used Simple Sequence Repeat (SSR) markers, which may capture the presence of differentiative processes across the genome in distinct populations. Spatial analyses of molecular variance were used to identify groups of populations that are both genetically and geographically homogeneous while also being maximally differentiated from each other. The spatial analysis of genetic diversity indicates that the levels of diversity among the six populations vary significantly on an eco-geographical basis. Particularly, altitude seems to represent a differentiating adaptation, as the main genetic differentiation is detected between the two populations present at higher altitudes and the other four populations at sea level. The data, together with the outcomes from different cluster analyses, identify a genetic diversity pattern that overlaps with the distribution of the known morphotypes in the Brazilian area. PMID:26798258

  19. Making a Game of Population Genetics

    ERIC Educational Resources Information Center

    Thornton, Kent W.; Ashley, David C.

    1977-01-01

    Describes a game that illustrates the principles of population genetics and helps explain the occurrence of evolution through changes in gene frequencies. Demonstrates the importance of genetic variability in evolution: winning is achieved by a player's species becoming "completely heterozygous" for six characteristics. Players move directed by…

  20. A genomewide association study of autism using the Simons Simplex Collection: Does reducing phenotypic heterogeneity in autism increase genetic homogeneity?

    PubMed Central

    Chaste, Pauline; Klei, Lambertus; Sanders, Stephan J.; Hus, Vanessa; Murtha, Michael T.; Lowe, Jennifer K.; Willsey, A. Jeremy; Moreno-De-Luca, Daniel; Yu, Timothy W.; Fombonne, Eric; Geschwind, Daniel; Grice, Dorothy E.; Ledbetter, David H.; Mane, Shrikant M.; Martin, Donna M.; Morrow, Eric M.; Walsh, Christopher A.; Sutcliffe, James S.; Martin, Christa Lese; Beaudet, Arthur L.; Lord, Catherine; State, Matthew W.; Cook, Edwin H.; Devlin, Bernie

    2014-01-01

    Background Phenotypic heterogeneity in autism has long been conjectured to be a major hindrance to the discovery of genetic risk factors, leading to numerous attempts to stratify children based on phenotype to increase power of discovery studies. This approach, however, is based on the hypothesis that phenotypic heterogeneity closely maps to genetic variation, which has not been tested. Our study examines the impact of sub-phenotyping of a well-characterized ASD sample on genetic homogeneity and the ability to discover common genetic variants conferring liability to ASD. Methods Genome-wide genotypic data of 2576 families from the Simons Simplex Collection (SSC) were analyzed in the overall sample and phenotypic subgroups defined on the basis of diagnosis, IQ, and symptom profiles. We conducted a family-based association study as well as estimating heritability and evaluating allele scores for each phenotypic subgroup. Results Association analyses revealed no genome-wide significant association signal. Sub-phenotyping did not increase power substantially. Moreover, allele scores built from the most associated SNPs, based on the odds ratio in the full sample, predicted case status in subsets of the sample equally well and heritability estimates were very similar for all subgroups. Conclusions In genome-wide association analysis of the SSC sample, reducing phenotypic heterogeneity had at most a modest impact on genetic homogeneity. Our results are based on a relatively small sample, one with greater homogeneity than the entire population; if they apply more broadly, they imply that analysis of sub-phenotypes is not a productive path forward for discovering genetic risk variants in ASD. PMID:25534755

  1. Genetic and Metabolite Diversity of Sardinian Populations of Helichrysum italicum

    PubMed Central

    Melito, Sara; Sias, Angela; Petretto, Giacomo L.; Chessa, Mario; Pintore, Giorgio; Porceddu, Andrea

    2013-01-01

    Background Helichrysum italicum (Asteraceae) is a small shrub endemic to the Mediterranean Basin, growing in fragmented and diverse habitats. The species has attracted attention due to its secondary metabolite content, but little effort has as yet been dedicated to assessing the genetic and metabolite diversity present in these populations. Here, we describe the diversity of 50 H. italicum populations collected from a range of habitats in Sardinia. Methods H. italicum plants were AFLP fingerprinted and the composition of their leaf essential oil characterized by GC-MS. The relationships between the genetic structure of the populations, soil, habitat and climatic variables and the essential oil chemotypes present were evaluated using Bayesian clustering, contingency analyses and AMOVA. Key results The Sardinian germplasm could be partitioned into two AFLP-based clades. Populations collected from the southwestern region constituted a homogeneous group which remained virtually intact even at high levels of K. The second, much larger clade was more diverse. A positive correlation between genetic diversity and elevation suggested the action of natural purifying selection. Four main classes of compounds were identified among the essential oils, namely monoterpenes, oxygenated monoterpenes, sesquiterpenes and oxygenated sesquiterpenes. Oxygenated monoterpene levels were significantly correlated with the AFLP-based clade structure, suggesting a correspondence between gene pool and chemical diversity. Conclusions The results suggest an association between chemotype, genetic diversity and collection location which is relevant for the planning of future collections aimed at identifying valuable sources of essential oil. PMID:24260149

  2. Genetic structure of forensic populations.

    PubMed Central

    Morton, N E

    1992-01-01

    DNA-based identification depends on the probability that two different individuals have the same phenotype, which is given by kinship theory. Together with the large and consistent body of evidence on human population structure, kinship theory provides a sound basis for forensic use of DNA markers. PMID:1557360

  3. Population genetics of ice age brown bears.

    PubMed

    Leonard, J A; Wayne, R K; Cooper, A

    2000-02-15

    The Pleistocene was a dynamic period for Holarctic mammal species, complicated by episodes of glaciation, local extinctions, and intercontinental migration. The genetic consequences of these events are difficult to resolve from the study of present-day populations. To provide a direct view of population genetics in the late Pleistocene, we measured mitochondrial DNA sequence variation in seven permafrost-preserved brown bear (Ursus arctos) specimens, dated from 14,000 to 42,000 years ago. Approximately 36,000 years ago, the Beringian brown bear population had a higher genetic diversity than any extant North American population, but by 15,000 years ago genetic diversity appears similar to the modern day. The older, genetically diverse, Beringian population contained sequences from three clades now restricted to local regions within North America, indicating that current phylogeographic patterns may provide misleading data for evolutionary studies and conservation management. The late Pleistocene phylogeographic data also indicate possible colonization routes to areas south of the Cordilleran ice sheet. PMID:10677513

  4. An elaboration of theory about preventing outbreaks in homogeneous populations to include heterogeneity or preferential mixing.

    PubMed

    Feng, Zhilan; Hill, Andrew N; Smith, Philip J; Glasser, John W

    2015-12-01

    The goal of many vaccination programs is to attain the population immunity above which pathogens introduced by infectious people (e.g., travelers from endemic areas) will not cause outbreaks. Using a simple meta-population model, we demonstrate that, if sub-populations either differ in characteristics affecting their basic reproduction numbers or if their members mix preferentially, weighted average sub-population immunities cannot be compared with the proportionally-mixing homogeneous population-immunity threshold, as public health practitioners are wont to do. Then we review the effect of heterogeneity in average per capita contact rates on the basic meta-population reproduction number. To the extent that population density affects contacts, for example, rates might differ in urban and rural sub-populations. Other differences among sub-populations in characteristics affecting their basic reproduction numbers would contribute similarly. In agreement with more recent results, we show that heterogeneous preferential mixing among sub-populations increases the basic meta-population reproduction number more than homogeneous preferential mixing does. Next we refine earlier results on the effects of heterogeneity in sub-population immunities and preferential mixing on the effective meta-population reproduction number. Finally, we propose the vector of partial derivatives of this reproduction number with respect to the sub-population immunities as a fundamentally new tool for targeting vaccination efforts. PMID:26375548

  5. Philosophy of race meets population genetics.

    PubMed

    Spencer, Quayshawn

    2015-08-01

    In this paper, I respond to four common semantic and metaphysical objections that philosophers of race have launched at scholars who interpret recent human genetic clustering results in population genetics as evidence for biological racial realism. I call these objections 'the discreteness objection', 'the visibility objection', 'the very important objection', and 'the objectively real objection.' After motivating each objection, I show that each one stems from implausible philosophical assumptions about the relevant meaning of 'race' or the nature of biological racial realism. In order to be constructive, I end by offering some advice for how we can productively critique attempts to defend biological racial realism based on recent human genetic clustering results. I also offer a clarification of the relevant human-population genetic research. PMID:25963045

  6. A Population Genetic Signal of Polygenic Adaptation

    PubMed Central

    Berg, Jeremy J.; Coop, Graham

    2014-01-01

    Adaptation in response to selection on polygenic phenotypes may occur via subtle allele frequencies shifts at many loci. Current population genomic techniques are not well posed to identify such signals. In the past decade, detailed knowledge about the specific loci underlying polygenic traits has begun to emerge from genome-wide association studies (GWAS). Here we combine this knowledge from GWAS with robust population genetic modeling to identify traits that may have been influenced by local adaptation. We exploit the fact that GWAS provide an estimate of the additive effect size of many loci to estimate the mean additive genetic value for a given phenotype across many populations as simple weighted sums of allele frequencies. We use a general model of neutral genetic value drift for an arbitrary number of populations with an arbitrary relatedness structure. Based on this model, we develop methods for detecting unusually strong correlations between genetic values and specific environmental variables, as well as a generalization of comparisons to test for over-dispersion of genetic values among populations. Finally we lay out a framework to identify the individual populations or groups of populations that contribute to the signal of overdispersion. These tests have considerably greater power than their single locus equivalents due to the fact that they look for positive covariance between like effect alleles, and also significantly outperform methods that do not account for population structure. We apply our tests to the Human Genome Diversity Panel (HGDP) dataset using GWAS data for height, skin pigmentation, type 2 diabetes, body mass index, and two inflammatory bowel disease datasets. This analysis uncovers a number of putative signals of local adaptation, and we discuss the biological interpretation and caveats of these results. PMID:25102153

  7. Genetic improvement of wild fish populations.

    PubMed

    Moav, R; Brody, T; Hulata, G

    1978-09-22

    A plan for the genetic improvement of commercially exploited wild animals is presented. It consists of crossing wild with domesticated breeds to produce heterotic hybrids and to upgrade the wild stocks. Empirical evidence is presented from experiments with the carp. Procedures for monitoring the manipulated populations are outlined. The suggested plan is ecologically reasonable and would counteract the negative genetic changes caused by excessive commercial exploitation of many species. PMID:17830305

  8. Genetic sources of population epigenomic variation.

    PubMed

    Taudt, Aaron; Colomé-Tatché, Maria; Johannes, Frank

    2016-06-01

    The field of epigenomics has rapidly progressed from the study of individual reference epigenomes to surveying epigenomic variation in populations. Recent studies in a number of species, from yeast to humans, have begun to dissect the cis- and trans-regulatory genetic mechanisms that shape patterns of population epigenomic variation at the level of single epigenetic marks, as well as at the level of integrated chromatin state maps. We show that this information is paving the way towards a more complete understanding of the heritable basis underlying population epigenomic variation. We also highlight important conceptual challenges when interpreting results from these genetic studies, particularly in plants, in which epigenomic variation can be determined both by genetic and epigenetic inheritance. PMID:27156976

  9. Population extinction and the genetics of adaptation.

    PubMed

    Orr, H Allen; Unckless, Robert L

    2008-08-01

    Theories of adaptation typically ignore the effect of environmental change on population size. But some environmental challenges--challenges to which populations must adapt--may depress absolute fitness below 1, causing populations to decline. Under this scenario, adaptation is a race; beneficial alleles that adapt a population to the new environment must sweep to high frequency before the population becomes extinct. We derive simple, though approximate, solutions to the probability of successful adaptation (population survival) when adaptation involves new mutations, the standing genetic variation, or a mixture of the two. Our results show that adaptation to such environmental challenges can be difficult when relying on new mutations at one or a few loci, and populations will often decline to extinction. PMID:18662122

  10. Bacterial Population Genetics in a Forensic Context

    SciTech Connect

    Velsko, S P

    2009-11-02

    This report addresses the recent Department of Homeland Security (DHS) call for a Phase I study to (1) assess gaps in the forensically relevant knowledge about the population genetics of eight bacterial agents of concern, (2) formulate a technical roadmap to address those gaps, and (3) identify new bioinformatics tools that would be necessary to analyze and interpret population genetic data in a forensic context. The eight organisms that were studied are B. anthracis, Y. pestis, F. tularensis, Brucella spp., E. coli O157/H7, Burkholderia mallei, Burkholderia pseudomallei, and C. botulinum. Our study focused on the use of bacterial population genetics by forensic investigators to test hypotheses about the possible provenance of an agent that was used in a crime or act of terrorism. Just as human population genetics underpins the calculations of match probabilities for human DNA evidence, bacterial population genetics determines the level of support that microbial DNA evidence provides for or against certain well-defined hypotheses about the origins of an infecting strain. Our key findings are: (1) Bacterial population genetics is critical for answering certain types of questions in a probabilistic manner, akin (but not identical) to 'match probabilities' in DNA forensics. (2) A basic theoretical framework for calculating likelihood ratios or posterior probabilities for forensic hypotheses based on microbial genetic comparisons has been formulated. This 'inference-on-networks' framework has deep but simple connections to the population genetics of mtDNA and Y-STRs in human DNA forensics. (3) The 'phylogeographic' approach to identifying microbial sources is not an adequate basis for understanding bacterial population genetics in a forensic context, and has limited utility, even for generating 'leads' with respect to strain origin. (4) A collection of genotyped isolates obtained opportunistically from international locations augmented by phylogenetic representations

  11. Genetic Heterogeneity in Algerian Human Populations

    PubMed Central

    Deba, Tahria; Calafell, Francesc; Benhamamouch, Soraya; Comas, David

    2015-01-01

    The demographic history of human populations in North Africa has been characterized by complex processes of admixture and isolation that have modeled its current gene pool. Diverse genetic ancestral components with different origins (autochthonous, European, Middle Eastern, and sub-Saharan) and genetic heterogeneity in the region have been described. In this complex genetic landscape, Algeria, the largest country in Africa, has been poorly covered, with most of the studies using a single Algerian sample. In order to evaluate the genetic heterogeneity of Algeria, Y-chromosome, mtDNA and autosomal genome-wide makers have been analyzed in several Berber- and Arab-speaking groups. Our results show that the genetic heterogeneity found in Algeria is not correlated with geography or linguistics, challenging the idea of Berber groups being genetically isolated and Arab groups open to gene flow. In addition, we have found that external sources of gene flow into North Africa have been carried more often by females than males, while the North African autochthonous component is more frequent in paternally transmitted genome regions. Our results highlight the different demographic history revealed by different markers and urge to be cautious when deriving general conclusions from partial genomic information or from single samples as representatives of the total population of a region. PMID:26402429

  12. The population genetics of the Jewish people.

    PubMed

    Ostrer, Harry; Skorecki, Karl

    2013-02-01

    Adherents to the Jewish faith have resided in numerous geographic locations over the course of three millennia. Progressively more detailed population genetic analysis carried out independently by multiple research groups over the past two decades has revealed a pattern for the population genetic architecture of contemporary Jews descendant from globally dispersed Diaspora communities. This pattern is consistent with a major, but variable component of shared Near East ancestry, together with variable degrees of admixture and introgression from the corresponding host Diaspora populations. By combining analysis of monoallelic markers with recent genome-wide variation analysis of simple tandem repeats, copy number variations, and single-nucleotide polymorphisms at high density, it has been possible to determine the relative contribution of sex-specific migration and introgression to map founder events and to suggest demographic histories corresponding to western and eastern Diaspora migrations, as well as subsequent microevolutionary events. These patterns have been congruous with the inferences of many, but not of all historians using more traditional tools such as archeology, archival records, linguistics, comparative analysis of religious narrative, liturgy and practices. Importantly, the population genetic architecture of Jews helps to explain the observed patterns of health and disease-relevant mutations and phenotypes which continue to be carefully studied and catalogued, and represent an important resource for human medical genetics research. The current review attempts to provide a succinct update of the more recent developments in a historical and human health context. PMID:23052947

  13. Population Genetics in ex situ Conservation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The role of population genetics in assessing the quality and maintenance of ex situ variation is a critical component of genebanking operations worldwide. New analytical approaches developed for whole genome characterization of model organisms can be effectively used to gain insight into the ex sit...

  14. Population genetics of malaria resistance in humans.

    PubMed

    Hedrick, P W

    2011-10-01

    The high mortality and widespread impact of malaria have resulted in this disease being the strongest evolutionary selective force in recent human history, and genes that confer resistance to malaria provide some of the best-known case studies of strong positive selection in modern humans. I begin by reviewing JBS Haldane's initial contribution to the potential of malaria genetic resistance in humans. Further, I discuss the population genetics aspects of many of the variants, including globin, G6PD deficiency, Duffy, ovalocytosis, ABO and human leukocyte antigen variants. Many of the variants conferring resistance to malaria are 'loss-of-function' mutants and appear to be recent polymorphisms from the last 5000-10 000 years or less. I discuss estimation of selection coefficients from case-control data and make predictions about the change for S, C and G6PD-deficiency variants. In addition, I consider the predicted joint changes when the two β-globin alleles S and C are both variable in the same population and when there is a variation for α-thalassemia and S, two unlinked, but epistatic variants. As more becomes known about genes conferring genetic resistance to malaria in humans, population genetics approaches can contribute both to investigating past selection and predicting the consequences in future generations for these variants. PMID:21427751

  15. Population genetics of malaria resistance in humans

    PubMed Central

    Hedrick, P W

    2011-01-01

    The high mortality and widespread impact of malaria have resulted in this disease being the strongest evolutionary selective force in recent human history, and genes that confer resistance to malaria provide some of the best-known case studies of strong positive selection in modern humans. I begin by reviewing JBS Haldane's initial contribution to the potential of malaria genetic resistance in humans. Further, I discuss the population genetics aspects of many of the variants, including globin, G6PD deficiency, Duffy, ovalocytosis, ABO and human leukocyte antigen variants. Many of the variants conferring resistance to malaria are ‘loss-of-function' mutants and appear to be recent polymorphisms from the last 5000–10 000 years or less. I discuss estimation of selection coefficients from case–control data and make predictions about the change for S, C and G6PD-deficiency variants. In addition, I consider the predicted joint changes when the two β-globin alleles S and C are both variable in the same population and when there is a variation for α-thalassemia and S, two unlinked, but epistatic variants. As more becomes known about genes conferring genetic resistance to malaria in humans, population genetics approaches can contribute both to investigating past selection and predicting the consequences in future generations for these variants. PMID:21427751

  16. Spatial genetic structure patterns of phenotype-limited and boundary-limited expanding populations: a simulation study.

    PubMed

    Dai, Qiang; Zhan, Xiangjiang; Lu, Bin; Fu, Jinzhong; Wang, Qian; Qi, Dunwu

    2014-01-01

    Range expansions may create a unique spatial genetic pattern characterized by alternate genetically homogeneous domains and allele frequency clines. Previous attempts to model range expansions have mainly focused on the loss of genetic diversity during expansions. Using individual-based models, we examined spatial genetic patterns under two expansion scenarios, boundary-limited range expansions (BLRE) and phenotype-limited range expansions (PhLRE). Our simulation revealed that the genetic diversity within populations lost quickly during the range expansion, while the genetic difference accumulated between populations. Consequently, accompanying the expansions, the overall diversity featured a slow decrease. Specifically, during BLREs, high speed of boundary motion facilitated the maintenance of total genetic diversity and sharpened genetic clines. Very slight constraints on boundary motion of BLREs drastically narrowed the homogeneous domains and increased the allele frequency fluctuations from those levels exhibited by PhLREs. Even stronger constraints, however, surprisingly brought the width of homogeneous domains and the allele frequency fluctuations back to the normal levels of PhLREs. Furthermore, high migration rates maintained a higher total genetic diversity than low ones did during PhLREs. Whereas, the total genetic diversities during BLREs showed a contrary pattern: higher when migration was low than those when migration was high. Besides, the increase of migration rates helped maintain a greater number of homogeneous domains during PhLREs, but their effects on the number of homogeneous domains during BLREs were not monotonous. Previous studies have showed that the homogenous domains can merge to form a few broad domains as the expansion went on, leading to fewer homogeneous domains. Our simulations, meanwhile, revealed that the range expansions could also rebuild homogeneous domains from the clines during the range expansion. It is possible that that the

  17. Deep Learning for Population Genetic Inference

    PubMed Central

    Sheehan, Sara; Song, Yun S.

    2016-01-01

    Given genomic variation data from multiple individuals, computing the likelihood of complex population genetic models is often infeasible. To circumvent this problem, we introduce a novel likelihood-free inference framework by applying deep learning, a powerful modern technique in machine learning. Deep learning makes use of multilayer neural networks to learn a feature-based function from the input (e.g., hundreds of correlated summary statistics of data) to the output (e.g., population genetic parameters of interest). We demonstrate that deep learning can be effectively employed for population genetic inference and learning informative features of data. As a concrete application, we focus on the challenging problem of jointly inferring natural selection and demography (in the form of a population size change history). Our method is able to separate the global nature of demography from the local nature of selection, without sequential steps for these two factors. Studying demography and selection jointly is motivated by Drosophila, where pervasive selection confounds demographic analysis. We apply our method to 197 African Drosophila melanogaster genomes from Zambia to infer both their overall demography, and regions of their genome under selection. We find many regions of the genome that have experienced hard sweeps, and fewer under selection on standing variation (soft sweep) or balancing selection. Interestingly, we find that soft sweeps and balancing selection occur more frequently closer to the centromere of each chromosome. In addition, our demographic inference suggests that previously estimated bottlenecks for African Drosophila melanogaster are too extreme. PMID:27018908

  18. Deep Learning for Population Genetic Inference.

    PubMed

    Sheehan, Sara; Song, Yun S

    2016-03-01

    Given genomic variation data from multiple individuals, computing the likelihood of complex population genetic models is often infeasible. To circumvent this problem, we introduce a novel likelihood-free inference framework by applying deep learning, a powerful modern technique in machine learning. Deep learning makes use of multilayer neural networks to learn a feature-based function from the input (e.g., hundreds of correlated summary statistics of data) to the output (e.g., population genetic parameters of interest). We demonstrate that deep learning can be effectively employed for population genetic inference and learning informative features of data. As a concrete application, we focus on the challenging problem of jointly inferring natural selection and demography (in the form of a population size change history). Our method is able to separate the global nature of demography from the local nature of selection, without sequential steps for these two factors. Studying demography and selection jointly is motivated by Drosophila, where pervasive selection confounds demographic analysis. We apply our method to 197 African Drosophila melanogaster genomes from Zambia to infer both their overall demography, and regions of their genome under selection. We find many regions of the genome that have experienced hard sweeps, and fewer under selection on standing variation (soft sweep) or balancing selection. Interestingly, we find that soft sweeps and balancing selection occur more frequently closer to the centromere of each chromosome. In addition, our demographic inference suggests that previously estimated bottlenecks for African Drosophila melanogaster are too extreme. PMID:27018908

  19. Turkish Population Structure and Genetic Ancestry Reveal Relatedness among Eurasian Populations

    PubMed Central

    Hodoğlugil, Uğur; Mahley, Robert W.

    2013-01-01

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

  20. Population differentiation in Pacific salmon: local adaptation, genetic drift, or the environment?

    USGS Publications Warehouse

    Adkison, M.D.

    1995-01-01

    Morphological, behavioral, and life-history differences between Pacific salmon (Oncorhynchus spp.) populations are commonly thought to reflect local adaptation, and it is likewise common to assume that salmon populations separated by small distances are locally adapted. Two alternatives to local adaptation exist: random genetic differentiation owing to genetic drift and founder events, and genetic homogeneity among populations, in which differences reflect differential trait expression in differing environments. Population genetics theory and simulations suggest that both alternatives are possible. With selectively neutral alleles, genetic drift can result in random differentiation despite many strays per generation. Even weak selection can prevent genetic drift in stable populations; however, founder effects can result in random differentiation despite selective pressures. Overlapping generations reduce the potential for random differentiation. Genetic homogeneity can occur despite differences in selective regimes when straying rates are high. In sum, localized differences in selection should not always result in local adaptation. Local adaptation is favored when population sizes are large and stable, selection is consistent over large areas, selective diffeentials are large, and straying rates are neither too high nor too low. Consideration of alternatives to local adaptation would improve both biological research and salmon conservation efforts.

  1. Population Genetics of Three Dimensional Range Expansions

    NASA Astrophysics Data System (ADS)

    Lavrentovich, Maxim; Nelson, David

    2014-03-01

    We develop a simple model of genetic diversity in growing spherical cell clusters, where the growth is confined to the cluster surface. This kind of growth occurs in cells growing in soft agar, and can also serve as a simple model of avascular tumors. Mutation-selection balance in these radial expansions is strongly influenced by scaling near a neutral, voter model critical point and by the inflating frontier. We develop a scaling theory to describe how the dynamics of mutation-selection balance is cut off by inflation. Genetic drift, i.e., local fluctuations in the genetic diversity, also plays an important role, and can lead to the extinction even of selectively advantageous strains. We calculate this extinction probability, taking into account the effect of rough population frontiers.

  2. Genetic structure of populations of Legionella pneumophila.

    PubMed Central

    Selander, R K; McKinney, R M; Whittam, T S; Bibb, W F; Brenner, D J; Nolte, F S; Pattison, P E

    1985-01-01

    The genetic structure of populations of Legionella pneumophila was defined by an analysis of electrophoretically demonstrable allelic variation at structural genes encoding 22 enzymes in 292 isolates from clinical and environmental sources. Nineteen of the loci were polymorphic, and 62 distinctive electrophoretic types (ETs), representing multilocus genotypes, were identified. Principal coordinates and clustering analyses demonstrated that isolates received as L. pneumophila were a heterogeneous array of genotypes that included two previously undescribed species. For 50 ETs of L. pneumophila (strict sense), mean genetic diversity per locus was 0.312, and diversity was equivalent in ETs represented by isolates recovered from clinical sources and those collected from environmental sources. Cluster analysis revealed four major groups or lineages of ETs in L. pneumophila. Genetic diversity among ETs of the same serotype was, on average, 93% of that in the total sample of ETs. Isolates marked by particular patterns of reactivity to a panel of nine monoclonal antibodies were also genetically heterogeneous, mean diversity within patterns being about 75% of the total. Both Pontiac fever and the pneumonic form of legionellosis may be caused by isolates of the same ET. The genetic structure of L. pneumophila is clonal, and many clones apparently are worldwide in distribution. The fact that L. pneumophila is only 60% as variable as Escherichia coli raises the possibility that isolates recovered from clinical cases and man-made environments are a restricted subset of all clones in the species as a whole. PMID:4030689

  3. Human genetics: lessons from Quebec populations.

    PubMed

    Scriver, C R

    2001-01-01

    The population of Quebec, Canada (7.3 million) contains approximately 6 million French Canadians; they are the descendants of approximately 8500 permanent French settlers who colonized Nouvelle France between 1608 and 1759. Their well-documented settlements, internal migrations, and natural increase over four centuries in relative isolation (geographic, linguistic, etc.) contain important evidence of social transmission of demographic behavior that contributed to effective family size and population structure. This history is reflected in at least 22 Mendelian diseases, occurring at unusually high prevalence in its subpopulations. Immigration of non-French persons during the past 250 years has given the Quebec population further inhomogeneity, which is apparent in allelic diversity at various loci. The histories of Quebec's subpopulations are, to a great extent, the histories of their alleles. Rare pathogenic alleles with high penetrance and associated haplotypes at 10 loci (CFTR, FAH, HBB, HEXA, LDLR, LPL, PAH, PABP2, PDDR, and SACS) are expressed in probands with cystic fibrosis, tyrosinemia, beta-thalassemia, Tay-Sachs, familial hypercholesterolemia, hyperchylomicronemia, PKU, oculopharyngeal muscular dystrophy, pseudo vitamin D deficiency rickets, and spastic ataxia of Charlevoix-Saguenay, respectively) reveal the interpopulation and intrapopulation genetic diversity of Quebec. Inbreeding does not explain the clustering and prevalence of these genetic diseases; genealogical reconstructions buttressed by molecular evidence point to founder effects and genetic drift in multiple instances. Genealogical estimates of historical meioses and analysis of linkage disequilibrium show that sectors of this young population are suitable for linkage disequilibrium mapping of rare alleles. How the population benefits from what is being learned about its structure and how its uniqueness could facilitate construction of a genomic map of linkage disequilibrium are discussed

  4. Population genetics in the forensic DNA debate.

    PubMed Central

    Weir, B S

    1992-01-01

    The use of matching variable number of tandem repeat (VNTR) profiles to link suspects with crimes is potentially very powerful, but it has been quite controversial. Initial debate over laboratory procedures has largely given way to debate over the statistical and population genetic issues involved in calculating the frequency of a profile for a random member of a population. This frequency is used to weight the evidence of a match between suspect and crime scene material when the suspect denies responsibility for that material. A recent report from the National Research Council, intended to put to rest some of the issues, has instead raised further debate by advocating a procedure based on maximum frequencies of profile components over several different populations. PMID:1465380

  5. The paradoxical population genetics of Plasmodium falciparum.

    PubMed

    Hartl, Daniel L; Volkman, Sarah K; Nielsen, Kaare M; Barry, Alyssa E; Day, Karen P; Wirth, Dyann F; Winzeler, Elizabeth A

    2002-06-01

    Among the leading causes of death in African children is cerebral malaria caused by the parasitic protozoan Plasmodium falciparum. Endemic forms of this disease are thought to have originated in central Africa 5000-10000 years ago, coincident with the innovation of slash-and-burn agriculture and the diversification of the Anopheles gambiae complex of mosquito vectors. Population genetic studies of P. falciparum have yielded conflicting results. Some evidence suggests that today's population includes multiple ancient lineages pre-dating human speciation. Other evidence suggests that today's population derives from only one, or a small number, of these ancient lineages. Resolution of this issue is important for the evaluation of the long-term efficacy of drug and immunological control strategies. PMID:12036741

  6. Population genetics of purple saxifrage (Saxifraga oppositifolia) in the high Arctic archipelago of Svalbard

    PubMed Central

    Pietiläinen, Maria; Korpelainen, Helena

    2013-01-01

    We investigated patterns of genetic variability in Saxifraga oppositifolia in the isolated Arctic Svalbard archipelago. The genetic analysis included genotyping using nine polymorphic microsatellite markers and sequencing of the nuclear internal transcribed spacer region. Among populations, mean allele numbers per microsatellite locus ranged from 2.0 to 2.6, and 9 % of alleles were unique. Observed (HO) and expected (HE) heterozygosities averaged 0.522 and 0.445, respectively. Typically negative but non-significant FIS values (mean −0.173) were found in S. oppositifolia populations. FST values were relatively low (mean 0.123). The Bayesian structure analysis provided additional information on population genetic structures. Seven out of 11 studied populations, including populations located both near each other and far apart (distances 5–210 km), showed relatively homogeneous clustering patterns, while one population located on a slope in the main settlement of Longyearbyen possessed a unique genetic structure. The Mantel test proved that there is no significant correlation between genetic and geographical distances. Different growth habits (compact, trailing and intermediate) did not possess distinct genetic compositions based on microsatellite variation. Internal transcribed spacer sequencing revealed 12 polymorphic sites. Among 24 sequenced Svalbard samples, eight haplotypes were detected, none shared by the mainland samples. Population genetic structures of S. oppositifolia in Svalbard show that both genetic variation and differentiation levels are modest, outcrossing is the main mating system, and dispersal and gene flow are important, probably attributable to strong winds and human and animal vectors. PMID:23700503

  7. Negative effects of ocean acidification on two crustose coralline species using genetically homogeneous samples.

    PubMed

    Kato, Aki; Hikami, Mana; Kumagai, Naoki H; Suzuki, Atsushi; Nojiri, Yukihiro; Sakai, Kazuhiko

    2014-03-01

    We evaluated acidification effects on two crustose coralline algal species common to Pacific coral reefs, Lithophyllum kotschyanum and Hydrolithon samoense. We used genetically homogeneous samples of both species to eliminate misidentification of species. The growth rates and percent calcification of the walls of the epithallial cells (thallus surface cells) of both species decreased with increasing pCO₂. However, elevated pCO₂ more strongly inhibited the growth of L. kotschyanum versus H. samoense. The trend of decreasing percent calcification of the cell wall did not differ between these species, although intercellular calcification of the epithallial cells in L. kotschyanum was apparently reduced at elevated pCO₂, a result that might indicate that there are differences in the solubility or density of the calcite skeletons of these two species. These results can provide knowledge fundamental to future studies of the physiological and genetic mechanisms that underlie the response of crustose coralline algae to environmental stresses. PMID:24239067

  8. Genetic affinities of central China populations.

    PubMed

    Zhou, H Y; Wang, H W; Tan, S N; Chen, Y; Wang, W L; Tao, H X; Yin, Z C; Zou, Y H; Ouyang, S M; Ni, B

    2014-01-01

    Hunan locates in the south-central part of China, to the south of the middle reaches of the Yangtze River and south of Lake Dongting. According to the historical records, the peopling of Hunan by modern human ancestors can ascend to 40 thousand years ago. Thus, to trace the ancient maternal components can offer further insight into the origin of south-central China. In this study, we investigated the mitochondrial DNA of 114 individuals from Hunan Province (including 34 Han, 40 Tujia and 40 Miao). Hypervariable regions I and II of the mtDNA control region were sequenced, and the relative diagnostic variations in coding region according to the updated worldwide phylogeny tree were selected and typed by restriction fragment length polymorphism analysis or direct sequencing. All individuals were classified into specific (sub)haplogroups. By comparison with the surrounding populations, southern China-prevalent haplogroups were detected with relative higher frequency in the Tujia and Miao ethnic populations, such as haplogroup B, with more than 20%, lacking in the Han population, which illustrated its southern origin characters. In addition, we also detected northern of East Asia prevalent haplogroups with a relative higher frequency in Tujia populations than in the Miao and Yao ethnic groups, implying a gene flow from Han populations. However, the language-clustering tendency was supported by our principal component analysis and further genetic estimation results. Han and ethnic groups in central China exhibited specific ancestors related to their closer language affinity, although there was extensively genetic admixture between Han and ethnic groups. PMID:24615027

  9. Genetic structure of the Newfoundland and Labrador population: founder effects modulate variability.

    PubMed

    Zhai, Guangju; Zhou, Jiayi; Woods, Michael O; Green, Jane S; Parfrey, Patrick; Rahman, Proton; Green, Roger C

    2016-07-01

    The population of the province of Newfoundland and Labrador (NL) has been a resource for genetic studies because of its historical isolation and increased prevalence of several monogenic disorders. Controversy remains regarding the genetic substructure and the extent of genetic homogeneity, which have implications for disease gene mapping. Population substructure has been reported from other isolated populations such as Iceland, Finland and Sardinia. We undertook this study to further our understanding of the genetic architecture of the NL population. We enrolled 494 individuals randomly selected from NL. Genome-wide SNP data were analyzed together with that from 14 other populations including HapMap3, Ireland, Britain and Native American samples from the Human Genome Diversity Project. Using multidimensional scaling and admixture analysis, we observed that the genetic structure of the NL population resembles that of the British population but can be divided into three clusters that correspond to religious/ethnic origins: Protestant English, Roman Catholic Irish and North American aboriginals. We observed reduced heterozygosity and an increased inbreeding coefficient (mean=0.005), which corresponds to that expected in the offspring of third-cousin marriages. We also found that the NL population has a significantly higher number of runs of homozygosity (ROH) and longer lengths of ROH segments. These results are consistent with our understanding of the population history and indicate that the NL population may be ideal for identifying recessive variants for complex diseases that affect populations of European origin. PMID:26669659

  10. A screening on Specific Learning Disorders in an Italian speaking high genetic homogeneity area.

    PubMed

    Cappa, Claudia; Giulivi, Sara; Schilirò, Antonino; Bastiani, Luca; Muzio, Carlo; Meloni, Fabrizio

    2015-01-01

    The aim of the present research is to investigate the prevalence of Specific Learning Disorders (SLD) in Ogliastra, an area of the island of Sardinia, Italy. Having experienced centuries of isolation, Ogliastra has become a high genetic homogeneity area, and is considered particularly interesting for studies on different kinds of pathologies. Here we are going to describe the results of a screening carried out throughout 2 consecutive years in 49 second grade classes (24 considered in the first year and 25 in the second year of the study) of the Ogliastra region. A total of 610 pupils (average age 7.54 years; 293 female, 317 male) corresponding to 68.69% of all pupils who were attending second grade in the area, took part in the study. The tool used for the screening was "RSR-DSA. Questionnaire for the detection of learning difficulties and disorders", which allowed the identification of 83 subjects at risk (13.61% of the whole sample involved in the study). These subjects took part in an enhancement training program of about 6 months. After the program, pupils underwent assessment for reading, writing and calculation abilities, as well as cognitive assessment. According to the results of the assessment, the prevalence of SLDs is 6.06%. For what concerns dyslexia, 4.75% of the total sample manifested this disorder either in isolation or in comorbidity with other disorders. According to the first national epidemiological investigation carried out in Italy, the prevalence of dyslexia is 3.1-3.2%, which is lower than the prevalence obtained in the present study. Given the genetic basis of SLDs, this result, together with the presence of several cases of SLD in isolation (17.14%) and with a 3:1 ratio of males to females diagnosed with a SLD, was to be expected in a sample coming from a high genetic homogeneity area. PMID:26296080

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

    USGS Publications Warehouse

    Duda, T. F., Jr.

    1994-01-01

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

  12. Genetic diversity and differentiation of Mongolian and Russian yak populations.

    PubMed

    Xuebin, Q; Jianlin, H; Lkhagva, B; Chekarova, I; Badamdorj, D; Rege, J E O; Hanotte, O

    2005-04-01

    In this study we examined the genetic diversity of yak populations in the northernmost part of their current global distribution. Five Mongolian and one Russian yak populations as well as one Chinese yak population from the Qinghai-Tibetan Plateau, the putative centre of yak domestication, were analysed with 15 microsatellite loci to determine the level of genetic variation within populations as well as the genetic differentiation and relationship between populations. A total of 116 microsatellite alleles were identified. The mean number of alleles per locus (MNA) across populations was 7.73 +/- 1.98 and the mean expected heterozygosity (HE) was 0.696 +/- 0.026. The relative magnitude of gene differentiation (F(ST)) among populations was 4.1%, and all genetic differentiations (F(ST)) between populations were significant (p < 0.001). A significant inbreeding effect (F(IS)) was detected in the Hovsgol yak (p < 0.01). There was no indication of a recent bottleneck in any of the populations studied. The results showed that yak populations in Mongolia and Russia have maintained high genetic diversity within populations and a low, although significant, genetic differentiation between populations. Both phylogenetic and principal component analyses support a close genetic relationship between the Gobi Altai, south Gobi and north Hangai populations, and between the Hovsgol and Buryatia populations respectively. Our results indicate that these yak populations should be considered as distinct genetic entities in respect of conservation and breeding programmes. PMID:16130478

  13. New Nuclear SNP Markers Unravel the Genetic Structure and Effective Population Size of Albacore Tuna (Thunnus alalunga)

    PubMed Central

    Laconcha, Urtzi; Iriondo, Mikel; Arrizabalaga, Haritz; Manzano, Carmen; Markaide, Pablo; Montes, Iratxe; Zarraonaindia, Iratxe; Velado, Igor; Bilbao, Eider; Goñi, Nicolas; Santiago, Josu; Domingo, Andrés; Karakulak, Saadet; Oray, Işık; Estonba, Andone

    2015-01-01

    In the present study we have investigated the population genetic structure of albacore (Thunnus alalunga, Bonnaterre 1788) and assessed the loss of genetic diversity, likely due to overfishing, of albacore population in the North Atlantic Ocean. For this purpose, 1,331 individuals from 26 worldwide locations were analyzed by genotyping 75 novel nuclear SNPs. Our results indicated the existence of four genetically homogeneous populations delimited within the Mediterranean Sea, the Atlantic Ocean, the Indian Ocean and the Pacific Ocean. Current definition of stocks allows the sustainable management of albacore since no stock includes more than one genetic entity. In addition, short- and long-term effective population sizes were estimated for the North Atlantic Ocean albacore population, and results showed no historical decline for this population. Therefore, the genetic diversity and, consequently, the adaptive potential of this population have not been significantly affected by overfishing. PMID:26090851

  14. New Nuclear SNP Markers Unravel the Genetic Structure and Effective Population Size of Albacore Tuna (Thunnus alalunga).

    PubMed

    Laconcha, Urtzi; Iriondo, Mikel; Arrizabalaga, Haritz; Manzano, Carmen; Markaide, Pablo; Montes, Iratxe; Zarraonaindia, Iratxe; Velado, Igor; Bilbao, Eider; Goñi, Nicolas; Santiago, Josu; Domingo, Andrés; Karakulak, Saadet; Oray, Işık; Estonba, Andone

    2015-01-01

    In the present study we have investigated the population genetic structure of albacore (Thunnus alalunga, Bonnaterre 1788) and assessed the loss of genetic diversity, likely due to overfishing, of albacore population in the North Atlantic Ocean. For this purpose, 1,331 individuals from 26 worldwide locations were analyzed by genotyping 75 novel nuclear SNPs. Our results indicated the existence of four genetically homogeneous populations delimited within the Mediterranean Sea, the Atlantic Ocean, the Indian Ocean and the Pacific Ocean. Current definition of stocks allows the sustainable management of albacore since no stock includes more than one genetic entity. In addition, short- and long-term effective population sizes were estimated for the North Atlantic Ocean albacore population, and results showed no historical decline for this population. Therefore, the genetic diversity and, consequently, the adaptive potential of this population have not been significantly affected by overfishing. PMID:26090851

  15. [From population genetics to population genomics of forest trees: integrated population genomics approach].

    PubMed

    Krutovskiĭ, K V

    2006-10-01

    Early works by Altukhov and his associates on pine and spruce laid the foundation for Russian population genetic studies on tree species with the use of molecular genetic markers. In recent years, these species have become especially popular as nontraditional eukaryotic models for population and evolutionary genomic research. Tree species with large, cross-pollinating native populations, high genetic and phenotypic variation, growing in diverse environments and affected by environmental changes during hundreds of years of their individual development, are an ideal model for studying the molecular genetic basis of adaptation. The great advance in this field is due to the rapid development of population genomics in the last few years. In the broad sense, population genomics is a novel, fast-developing discipline, combining traditional population genetic approaches with the genomic level of analysis. Thousands of genes with known function and sometimes known genomic localization can be simultaneously studied in many individuals. This opens new prospects for obtaining statistical estimates for a great number of genes and segregating elements. Mating system, gene exchange, reproductive population size, population disequilibrium, interaction among populations, and many other traditional problems of population genetics can be now studied using data on variation in many genes. Moreover, population genomic analysis allows one to distinguish factors that affect individual genes, alleles, or nucleotides (such as, for example, natural selection) from factors affecting the entire genome (e.g., demography). This paper presents a brief review of traditional methods of studying genetic variation in forest tree species and introduces a new, integrated population genomics approach. The main stages of the latter are : (1) selection of genes, which are tentatively involved in variation of adaptive traits, by means of a detailed examination of the regulation and the expression of

  16. Genetic population structure and call variation in a passerine bird, the satin bowerbird, Ptilonorhynchus violaceus.

    PubMed

    Nicholls, J A; Austin, J J; Moritz, C; Goldizen, A W

    2006-06-01

    Geographic variation in vocalizations is widespread in passerine birds, but its origins and maintenance remain unclear. One hypothesis to explain this variation is that it is associated with geographic isolation among populations and therefore should follow a vicariant pattern similar to that typically found in neutral genetic markers. Alternatively, if environmental selection strongly influences vocalizations, then genetic divergence and vocal divergence may be disassociated. This study compared genetic divergence derived from 11 microsatellite markers with a metric of phenotypic divergence derived from male bower advertisement calls. Data were obtained from 16 populations throughout the entire distribution of the satin bowerbird, an Australian wet-forest-restricted passerine. There was no relationship between call divergence and genetic divergence, similar to most other studies on birds with learned vocalizations. Genetic divergence followed a vicariant model of evolution, with the differentiation of isolated populations and isolation-by-distance among continuous populations. Previous work on Ptilonorhynchus violaceus has shown that advertisement call structure is strongly influenced by the acoustic environment of different habitats. Divergence in vocalizations among genetically related populations in different habitats indicates that satin bowerbirds match their vocalizations to the environment in which they live, despite the homogenizing influence of gene flow. In combination with convergence of vocalizations among genetically divergent populations occurring in the same habitat, this shows the overriding importance that habitat-related selection can have on the establishment and maintenance of variation in vocalizations. PMID:16892977

  17. Genetic drift and the population history of the Irish travellers.

    PubMed

    Relethford, John H; Crawford, Michael H

    2013-02-01

    The Irish Travellers are an itinerant group in Ireland that has been socially isolated. Two hypotheses have been proposed concerning the genetic origin of the Travellers: (1) they are genetically related to Roma populations in Europe that share a nomadic lifestyle or (2) they are of Irish origin, and genetic differences from the rest of Ireland reflect genetic drift. These hypotheses were tested using data on 33 alleles from 12 red blood cell polymorphism loci. Comparison with other European, Roma, and Indian populations shows that the Travellers are genetically distinct from the Roma and Indian populations and most genetically similar to Ireland, in agreement with earlier genetic analyses of the Travellers. However, the Travellers are still genetically distinct from other Irish populations, which could reflect some external gene flow and/or the action of genetic drift in a small group that was descended from a small number of founders. In order to test the drift hypothesis, we analyzed genetic distances comparing the Travellers to four geographic regions in Ireland. These distances were then compared with adjusted distances that account for differential genetic drift using a method developed by Relethford (Hum Biol 68 (1996) 29-44). The unadjusted distances show the genetic distinctiveness of the Travellers. After adjustment for the expected effects of genetic drift, the Travellers are equidistant from the other Irish samples, showing their Irish origins and population history. The observed genetic differences are thus a reflection of genetic drift, and there is no evidence of any external gene flow. PMID:23180293

  18. Application of computer simulators in population genetics.

    PubMed

    Feng, Gao; Haipeng, Li

    2016-08-01

    The genomes of more and more organisms have been sequenced due to the advances in next-generation sequencing technologies. As a powerful tool, computer simulators play a critical role in studying the genome-wide DNA polymorphism pattern. Simulations can be performed both forwards-in-time and backwards-in-time, which complement each other and are suitable for meeting different needs, such as studying the effect of evolutionary dynamics, the estimation of parameters, and the validation of evolutionary hypotheses as well as new methods. In this review, we briefly introduced population genetics related theoretical framework and provided a detailed comparison of 32 simulators published over the last ten years. The future development of new simulators was also discussed. PMID:27531609

  19. Genetic population study of Y-chromosome markers in Benin and Ivory Coast ethnic groups.

    PubMed

    Fortes-Lima, Cesar; Brucato, Nicolas; Croze, Myriam; Bellis, Gil; Schiavinato, Stephanie; Massougbodji, Achille; Migot-Nabias, Florence; Dugoujon, Jean-Michel

    2015-11-01

    Ninety-six single nucleotide polymorphisms (SNPs) and seventeen short tandem repeat (STRs) were investigated on the Y-chromosome of 288 unrelated healthy individuals from populations in Benin (Bariba, Yoruba, and Fon) and the Ivory Coast (Ahizi and Yacouba). We performed a multidimensional scaling analysis based on FST and RST genetic distances using a large extensive database of sub-Saharan African populations. There is more genetic homogeneity in Ivory Coast populations compared with populations from Benin. Notably, the Beninese Yoruba are significantly differentiated from neighbouring groups, but also from the Yoruba from Nigeria (FST>0.05; P<0.01). The Y-chromosome dataset presented here provides new valuable data to understand the complex genetic diversity and human male demographic events in West Africa. PMID:26275614

  20. A Population Genetics Perspective on Geminivirus Infection

    PubMed Central

    Weigel, Karin; Pohl, Jens O.; Wege, Christina

    2015-01-01

    ABSTRACT The selective accumulation of both DNA components of a bipartite geminivirus, Abutilon mosaic virus, was recorded during early systemic infection of Nicotiana benthamiana plants. Purified nuclei were diagnosed for viral DNA using hybridization specific for DNA A or DNA B to detect these individual genome components either alone or both simultaneously by dual-color staining. Although this virus needs both components for symptomatic infection, DNA A alone was transported to upper leaves, where it was imported into phloem nuclei and replicated autonomously. The coinfection with DNA A and DNA B revealed an independent spread of both molecules, which resulted in a stochastic distribution of DNA A- and DNA A/B-infected nuclei. A population genetics evaluation of the respective frequencies was compared to a model computation. This elucidated a surprisingly simple relationship between the initial frequencies of the viral DNA components and the number of susceptible cells during the course of early systemic infection. IMPORTANCE For bipartite begomoviruses, DNA B-independent long-distance spread of DNA A has been described before, but it has never been shown whether viral DNA A alone invades nuclei of systemic tissues and replicates therein. This is demonstrated now for the first time. During infection with DNA A and DNA B, a similar solitary spread of DNA A can be recognized at early stages. We describe a population genetics model of how the hit probabilities of DNA A and DNA B for susceptible cells determine the relative frequencies of either genome component during the course of infection. PMID:26378173

  1. TRANSGENE ESCAPE MONITORING, POPULATION GENETICS, AND THE LAW

    EPA Science Inventory

    There has been little discussion about how to apply population genetics methods to monitor the spread of transgenes that are detected outside the agricultural populations where they are deployed. Population geneticists have developed tools for analyzing the genetic makeup of indi...

  2. Genetic structure of Tribolium castaneum (Coleptera: Tenebrionidae) populations in mills

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The red flour beetle, Tribolium castaneum, is primarily found associated with human structures such as wheat and rice mills, which are spatially isolated resource patches with apparently limited immigration that could produce genetically structured populations. We investigated genetic diversity and...

  3. Genetic diversity in Tunisian populations of faba bean (Vicia faba L.) based on morphological traits and molecular markers.

    PubMed

    Backouchi, I Z; Aouida, M; Khemiri, N; Jebara, M

    2015-01-01

    Genetic diversity within Vicia faba L. is key to the genetic improvement of this important species. In this study, morphological traits and RAPD molecular markers were used to assess the levels of polymorphism across 12 Tunisian populations, three major and nine minor from different locations. Analysis of morphological traits indicated that the three major populations showed significant differences and the nine minor populations exhibited considerable variation for most traits. The grain yield of the Alia population could be increased by inoculation. Of the seven primers tested, it was clear that the Cs12 primer would be recommend for genetic diversity analysis of V. faba.Within population genetic diversity exhibited 94% of total diversity. Intra-population genetic diversity (HS) was 0.16, which was clearly higher than between population genetic diversity (DST = 0.06) UPG-MA showed a high level of genetic variation between major and minor populations of V. faba L. Particularly the minor populations showed a high level of diversity and was divided into two subclusters. Ltaifia was separated from the other populations. In addition to a high grain yield, these populations showed the lowest Nei and Shannon indices (H = 0.08 and I = 0.13) justifying their homogeneity. For these reasons, these cultivars can be considered a selected population. However, the Takelsa population showed the highest Nei and Shannon indices (H = 0.13 and I = 0.21), indicating that this population was the most heterogeneous, which is interesting for breeding programs. PMID:26214437

  4. Viral load and clinicopathological features of chronic hepatitis C (1b) in a homogeneous patient population.

    PubMed

    Fanning, L; Kenny, E; Sheehan, M; Cannon, B; Whelton, M; O'Connell, J; Collins, J K; Shanahan, F

    1999-03-01

    Monitoring the progression of hepatitis C virus (HCV) includes clinical, biochemical, and histological parameters. Quantitation of viral load by reverse-transcription polymerase chain reaction (RT-PCR) may offer a more reliable marker of disease status. Conflicting reports on viral titers may reflect heterogeneity of patient population, mode of infection, and viral type/subtype. The aim of this study was to correlate quantitative serum viral load with alanine transaminase (ALT) and histological status in a homogenous population. The study population consisted of 77 Rhesus-negative women with chronic hepatitis C type 1b. Homogenous features of this study population included: same defined source of infection (contaminated anti-D immunoglobulin); same duration of disease (17 years at the time of study); same viral type/subtype; same ethnic origin; all healthy child-bearing females at the time of infection; and an absence of competing risk factors for infectious and other liver diseases. None of the patients had received antiviral treatment at the time of study. Liver biopsy was performed on all patients. All biopsies were scored by a single histopathologist who was blinded to the clinical and viral status of each patient. A weak, but statistically significant, correlation (rs =.26; P <.05) between serum viral load and the degree of inflammation (mean value: 3.87 +/- 2.17 [SD]) was found. There was no significant correlation between serum viral load and the degree of fibrosis (mean value: 0.84 +/- 0.8 [SD]; P =.06). There was no significant correlation between serum viral load and ALT, although there was a correlation between ALT and the degree of inflammation (rs =.241; P =.035). PMID:10051496

  5. Genetic studies of neuropsychiatric disorders in Costa Rica: a model for the use of isolated populations.

    PubMed

    Mathews, Carol A; Reus, Victor I; Bejarano, Julio; Escamilla, Michael A; Fournier, Eduardo; Herrera, Luis Diego; Lowe, Thomas L; McInnes, L Alison; Molina, Julio; Ophoff, Roel A; Raventos, Henrietta; Sandkuijl, Lodewijk A; Service, Susan K; Spesny, Mitzi; León, Pedro E; Freimer, Nelson B

    2004-03-01

    The importance of genetics in understanding the etiology of mental illness has become increasingly clear in recent years, as more evidence has mounted that almost all neuropsychiatric disorders have a genetic component. It has also become clear, however, that these disorders are etiologically complex, and multiple genetic and environmental factors contribute to their makeup. So far, traditional linkage mapping studies have not definitively identified specific disease genes for neuropsychiatric disorders, although some potential candidates have been identified via these methods (e.g. the dysbindin gene in schizophrenia; Straub et al., 2002; Schwab et al., 2003). For this reason, alternative approaches are being attempted, including studies in genetically isolated populations. Because isolated populations have a high degree of genetic homogeneity, their use may simplify the process of identifying disease genes in disorders where multiple genes may play a role. Several areas of Latin America contain genetically isolated populations that are well suited for the study of neuropsychiatric disorders. Genetic studies of several major psychiatric illnesses, including bipolar disorder, major depression, schizophrenia, Tourette Syndrome, alcohol dependence, attention deficit hyperactivity disorder, and obsessive-compulsive disorder, are currently underway in these regions. In this paper we highlight the studies currently being conducted by our groups in the Central Valley of Costa Rica to illustrate the potential advantages of this population for genetic studies. PMID:15091311

  6. Population genetic structure of the abyssal grenadier (Coryphaenoides armatus) around the mid-Atlantic ridge

    NASA Astrophysics Data System (ADS)

    Ritchie, H.; Cousins, N. J.; Cregeen, S. J.; Piertney, S. B.

    2013-12-01

    Understanding the factors that affect the levels and distribution of genetic diversity in oceanic and deep sea environments is a central focus in marine population genetics. Whilst it has been considered that the oceans represent a homogenous environment that would facilitate dispersal and minimise population structure, it is now clear that topographical features and current patterns can influence the extent of spatial gene flow and promote significant population genetic divergence even at local scales. Here we examine patterns of population genetic structure among N. Atlantic populations of the cosmopolitan abyssal grenadier Coryphaenoides armatus in relation to two hypothesised barriers to gene flow-the mid-Atlantic Ridge and the Charlie-Gibbs Fracture Zone/Sub-Polar Front. A suite of microsatellite markers were developed to examine the spatial pattern of allelic variation among 210 individuals from ten sampling locations encompassing sites east and west of the MAR and north and south of the CGFZ, plus a geographically distinct sample of individuals from the Crozet Islands in the Indian Ocean. Considerable genetic diversity was detected among individuals (na=5-13 and HO=0.46-0.69 across populations) but with an overall lack of genetic divergence between populations. Pairwise estimates of divergence among NE Atlantic samples were small and non-significant (max FST=0.04) and Structure-based Bayesian analysis of genetic clusters returned no distinct population structure. The only indication of genetic structure was between the Atlantic and Indian Oceans, with FST estimates of ca. 0.05. Patterns of genetic diversity and divergence are discussed in relation to what has been resolved in Coryphaenoides congeners, and what is known about the life history and ecology of C. armatus.

  7. Landscape structure and the genetic effects of a population collapse

    PubMed Central

    Caplins, Serena A.; Gilbert, Kimberly J.; Ciotir, Claudia; Roland, Jens; Matter, Stephen F.; Keyghobadi, Nusha

    2014-01-01

    Both landscape structure and population size fluctuations influence population genetics. While independent effects of these factors on genetic patterns and processes are well studied, a key challenge is to understand their interaction, as populations are simultaneously exposed to habitat fragmentation and climatic changes that increase variability in population size. In a population network of an alpine butterfly, abundance declined 60–100% in 2003 because of low over-winter survival. Across the network, mean microsatellite genetic diversity did not change. However, patch connectivity and local severity of the collapse interacted to determine allelic richness change within populations, indicating that patch connectivity can mediate genetic response to a demographic collapse. The collapse strongly affected spatial genetic structure, leading to a breakdown of isolation-by-distance and loss of landscape genetic pattern. Our study reveals important interactions between landscape structure and temporal demographic variability on the genetic diversity and genetic differentiation of populations. Projected future changes to both landscape and climate may lead to loss of genetic variability from the studied populations, and selection acting on adaptive variation will likely occur within the context of an increasing influence of genetic drift. PMID:25320176

  8. Population genetic studies in the genomic sequencing era

    PubMed Central

    CHEN, Hua

    2015-01-01

    Recent advances in high-throughput sequencing technologies have revolutionized the field of population genetics. Data now routinely contain genomic level polymorphism information, and the low cost of DNA sequencing enables researchers to investigate tens of thousands of subjects at a time. This provides an unprecedented opportunity to address fundamental evolutionary questions, while posing challenges on traditional population genetic theories and methods. This review provides an overview of the recent methodological developments in the field of population genetics, specifically methods used to infer ancient population history and investigate natural selection using large-sample, large-scale genetic data. Several open questions are also discussed at the end of the review. PMID:26228473

  9. Divergence genetics analysis reveals historical population genetic processes leading to contrasting phylogeographic patterns in co-distributed species.

    PubMed

    McGovern, Tamara M; Keever, Carson C; Saski, Christopher A; Hart, Michael W; Marko, Peter B

    2010-11-01

    Coalescent samplers are computational time machines for inferring the historical demographic genetic processes that have given rise to observable patterns of spatial genetic variation among contemporary populations. We have used traditional characterizations of population structure and coalescent-based inferences about demographic processes to reconstruct the population histories of two co-distributed marine species, the frilled dog whelk, Nucella lamellosa, and the bat star, Patiria miniata. Analyses of population structure were consistent with previous work in both species except that additional samples of N. lamellosa showed a larger regional genetic break on Vancouver Island (VI) rather than between the southern Alexander Archipelago as in P. miniata. Our understanding of the causes, rather than just the patterns, of spatial genetic variation was dramatically improved by coalescent analyses that emphasized variation in population divergence times. Overall, gene flow was greater in bat stars (planktonic development) than snails (benthic development) but spatially homogeneous within species. In both species, these large phylogeographic breaks corresponded to relatively ancient divergence times between populations rather than regionally restricted gene flow. Although only N. lamellosa shows a large break on VI, population separation times on VI are congruent between species, suggesting a similar response to late Pleistocene ice sheet expansion. The absence of a phylogeographic break in P. miniata on VI can be attributed to greater gene flow and larger effective population size in this species. Such insights put the relative significance of gene flow into a more comprehensive historical biogeographic context and have important implications for conservation and landscape genetic studies that emphasize the role of contemporary gene flow and connectivity in shaping patterns of population differentiation. PMID:21040048

  10. Using dense locality sampling resolves the subtle genetic population structure of the dispersive fish species Plecoglossus altivelis.

    PubMed

    Takeshima, Hirohiko; Iguchi, Kei'ichiro; Hashiguchi, Yasuyuki; Nishida, Mutsumi

    2016-07-01

    In dispersive species with continuous distributions, genetic differentiation between local populations is often absent or subtle and thus difficult to detect. To incorporate such subtle differentiation into management plans, it may be essential to analyse many samples from many localities using adequate numbers of high-resolution genetic markers. Here, we evaluated the usefulness of dense locality sampling in resolving genetic population structure in the ayu (Plecoglossus altivelis), a dispersive fish important in Japanese inland fisheries. Genetic variability in, and differentiation between, ayu populations around the Japan-Ryukyu Archipelago were investigated in 4746 individuals collected from 120 localities by genotyping 12 microsatellite markers. These individuals represented the two subspecies of ayu, namely the Ryukyuan subspecies (Plecoglossus altivelis ryukyuensis) and both amphidromous and landlocked forms of the nominotypical subspecies (P. a. altivelis) along the archipelago. We successfully detected an absence of genetic differentiation within the landlocked form and subtle but significant differentiation and clear geographic patterns of genetic variation among populations of the amphidromous form, which had been considered genetically homogeneous. This suggests that dense locality sampling effectively resolves subtle differences in genetic population structure, reducing stochastic deviation in the detection of genetic differentiation and geographic patterns in local populations of this dispersive species. Resampling analyses based on empirical data sets clearly demonstrate the effectiveness of increasing the number of locality samples for stable and reliable estimations of genetic fixation indices. The genetic population structure observed within the amphidromous form provides useful information for identifying management or conservation units in ayu. PMID:27085501

  11. Genetic control of mosquitoes: population suppression strategies.

    PubMed

    Wilke, André Barretto Bruno; Marrelli, Mauro Toledo

    2012-01-01

    Over the last two decades, morbidity and mortality from malaria and dengue fever among other pathogens are an increasing Public Health problem. The increase in the geographic distribution of vectors is accompanied by the emergence of viruses and diseases in new areas. There are insufficient specific therapeutic drugs available and there are no reliable vaccines for malaria or dengue, although some progress has been achieved, there is still a long way between its development and actual field use. Most mosquito control measures have failed to achieve their goals, mostly because of the mosquito's great reproductive capacity and genomic flexibility. Chemical control is increasingly restricted due to potential human toxicity, mortality in no target organisms, insecticide resistance, and other environmental impacts. Other strategies for mosquito control are desperately needed. The Sterile Insect Technique (SIT) is a species-specific and environmentally benign method for insect population suppression, it is based on mass rearing, radiation mediated sterilization, and release of a large number of male insects. Releasing of Insects carrying a dominant lethal gene (RIDL) offers a solution to many of the drawbacks of traditional SIT that have limited its application in mosquitoes while maintaining its environmentally friendly and species-specific utility. The self-limiting nature of sterile mosquitoes tends to make the issues related to field use of these somewhat less challenging than for self-spreading systems characteristic of population replacement strategies. They also are closer to field use, so might be appropriate to consider first. The prospect of genetic control methods against mosquito vectored human diseases is rapidly becoming a reality, many decisions will need to be made on a national, regional and international level regarding the biosafety, social, cultural and ethical aspects of the use and deployment of these vector control methods. PMID:22983293

  12. An Overview of the Genetic Structure within the Italian Population from Genome-Wide Data

    PubMed Central

    Di Gaetano, Cornelia; Voglino, Floriana; Guarrera, Simonetta; Fiorito, Giovanni; Rosa, Fabio; Di Blasio, Anna Maria; Manzini, Paola; Dianzani, Irma; Betti, Marta; Cusi, Daniele; Frau, Francesca; Barlassina, Cristina; Mirabelli, Dario; Magnani, Corrado; Glorioso, Nicola; Bonassi, Stefano; Piazza, Alberto; Matullo, Giuseppe

    2012-01-01

    In spite of the common belief of Europe as reasonably homogeneous at genetic level, advances in high-throughput genotyping technology have resolved several gradients which define different geographical areas with good precision. When Northern and Southern European groups were considered separately, there were clear genetic distinctions. Intra-country genetic differences were also evident, especially in Finland and, to a lesser extent, within other European populations. Here, we present the first analysis using the 125,799 genome-wide Single Nucleotide Polymorphisms (SNPs) data of 1,014 Italians with wide geographical coverage. We showed by using Principal Component analysis and model-based individual ancestry analysis, that the current population of Sardinia can be clearly differentiated genetically from mainland Italy and Sicily, and that a certain degree of genetic differentiation is detectable within the current Italian peninsula population. Pair-wise FST statistics Northern and Southern Italy amounts approximately to 0.001 between, and around 0.002 between Northern Italy and Utah residents with Northern and Western European ancestry (CEU). The Italian population also revealed a fine genetic substructure underscoring by the genomic inflation (Sardinia vs. Northern Italy = 3.040 and Northern Italy vs. CEU = 1.427), warning against confounding effects of hidden relatedness and population substructure in association studies. PMID:22984441

  13. Genetic diversity and population structure of the Guinea pig (Cavia porcellus, Rodentia, Caviidae) in Colombia

    PubMed Central

    Burgos-Paz, William; Cerón-Muñoz, Mario; Solarte-Portilla, Carlos

    2011-01-01

    The aim was to establish the genetic diversity and population structure of three guinea pig lines, from seven production zones located in Nariño, southwest Colombia. A total of 384 individuals were genotyped with six microsatellite markers. The measurement of intrapopulation diversity revealed allelic richness ranging from 3.0 to 6.56, and observed heterozygosity (Ho) from 0.33 to 0.60, with a deficit in heterozygous individuals. Although statistically significant (p < 0.05), genetic differentiation between population pairs was found to be low. Genetic distance, as well as clustering of guinea-pig lines and populations, coincided with the historical and geographical distribution of the populations. Likewise, high genetic identity between improved and native lines was established. An analysis of group probabilistic assignment revealed that each line should not be considered as a genetically homogeneous group. The findings corroborate the absorption of native genetic material into the improved line introduced into Colombia from Peru. It is necessary to establish conservation programs for native-line individuals in Nariño, and control genealogical and production records in order to reduce the inbreeding values in the populations. PMID:22215979

  14. Extreme genetic diversity in asexual grass thrips populations.

    PubMed

    Fontcuberta García-Cuenca, A; Dumas, Z; Schwander, T

    2016-05-01

    The continuous generation of genetic variation has been proposed as one of the main factors explaining the maintenance of sexual reproduction in nature. However, populations of asexual individuals may attain high levels of genetic diversity through within-lineage diversification, replicate transitions to asexuality from sexual ancestors and migration. How these mechanisms affect genetic variation in populations of closely related sexual and asexual taxa can therefore provide insights into the role of genetic diversity for the maintenance of sexual reproduction. Here, we evaluate patterns of intra- and interpopulation genetic diversity in sexual and asexual populations of Aptinothrips rufus grass thrips. Asexual A. rufus populations are found throughout the world, whereas sexual populations appear to be confined to few locations in the Mediterranean region. We found that asexual A. rufus populations are characterized by extremely high levels of genetic diversity, both in comparison with their sexual relatives and in comparison with other asexual species. Migration is extensive among asexual populations over large geographic distances, whereas close sexual populations are strongly isolated from each other. The combination of extensive migration with replicate evolution of asexual lineages, and a past demographic expansion in at least one of them, generated high local clone diversities in A. rufus. These high clone diversities in asexual populations may mimic certain benefits conferred by sex via genetic diversity and could help explain the extreme success of asexual A. rufus populations. PMID:26864612

  15. Population genetic diversity and fitness in multiple environments

    PubMed Central

    2010-01-01

    Background When a large number of alleles are lost from a population, increases in individual homozygosity may reduce individual fitness through inbreeding depression. Modest losses of allelic diversity may also negatively impact long-term population viability by reducing the capacity of populations to adapt to altered environments. However, it is not clear how much genetic diversity within populations may be lost before populations are put at significant risk. Development of tools to evaluate this relationship would be a valuable contribution to conservation biology. To address these issues, we have created an experimental system that uses laboratory populations of an estuarine crustacean, Americamysis bahia with experimentally manipulated levels of genetic diversity. We created replicate cultures with five distinct levels of genetic diversity and monitored them for 16 weeks in both permissive (ambient seawater) and stressful conditions (diluted seawater). The relationship between molecular genetic diversity at presumptive neutral loci and population vulnerability was assessed by AFLP analysis. Results Populations with very low genetic diversity demonstrated reduced fitness relative to high diversity populations even under permissive conditions. Population performance decreased in the stressful environment for all levels of genetic diversity relative to performance in the permissive environment. Twenty percent of the lowest diversity populations went extinct before the end of the study in permissive conditions, whereas 73% of the low diversity lines went extinct in the stressful environment. All high genetic diversity populations persisted for the duration of the study, although population sizes and reproduction were reduced under stressful environmental conditions. Levels of fitness varied more among replicate low diversity populations than among replicate populations with high genetic diversity. There was a significant correlation between AFLP diversity and

  16. Implications for health and disease in the genetic signature of the Ashkenazi Jewish population

    PubMed Central

    2012-01-01

    Background Relatively small, reproductively isolated populations with reduced genetic diversity may have advantages for genomewide association mapping in disease genetics. The Ashkenazi Jewish population represents a unique population for study based on its recent (< 1,000 year) history of a limited number of founders, population bottlenecks and tradition of marriage within the community. We genotyped more than 1,300 Ashkenazi Jewish healthy volunteers from the Hebrew University Genetic Resource with the Illumina HumanOmni1-Quad platform. Comparison of the genotyping data with that of neighboring European and Asian populations enabled the Ashkenazi Jewish-specific component of the variance to be characterized with respect to disease-relevant alleles and pathways. Results Using clustering, principal components, and pairwise genetic distance as converging approaches, we identified an Ashkenazi Jewish-specific genetic signature that differentiated these subjects from both European and Middle Eastern samples. Most notably, gene ontology analysis of the Ashkenazi Jewish genetic signature revealed an enrichment of genes functioning in transepithelial chloride transport, such as CFTR, and in equilibrioception, potentially shedding light on cystic fibrosis, Usher syndrome and other diseases over-represented in the Ashkenazi Jewish population. Results also impact risk profiles for autoimmune and metabolic disorders in this population. Finally, residual intra-Ashkenazi population structure was minimal, primarily determined by class 1 MHC alleles, and not related to host country of origin. Conclusions The Ashkenazi Jewish population is of potential utility in disease-mapping studies due to its relative homogeneity and distinct genomic signature. Results suggest that Ashkenazi-associated disease genes may be components of population-specific genomic differences in key functional pathways. PMID:22277159

  17. Uncovering the transmission dynamics of Plasmodium vivax using population genetics

    PubMed Central

    Barry, Alyssa E.; Waltmann, Andreea; Koepfli, Cristian; Barnadas, Celine; Mueller, Ivo

    2015-01-01

    Population genetic analysis of malaria parasites has the power to reveal key insights into malaria epidemiology and transmission dynamics with the potential to deliver tools to support control and elimination efforts. Analyses of parasite genetic diversity have suggested that Plasmodium vivax populations are more genetically diverse and less structured than those of Plasmodium falciparum indicating that P. vivax may be a more ancient parasite of humans and/or less susceptible to population bottlenecks, as well as more efficient at disseminating its genes. These population genetic insights into P. vivax transmission dynamics provide an explanation for its relative resilience to control efforts. Here, we describe current knowledge on P. vivax population genetic structure, its relevance to understanding transmission patterns and relapse and how this information can inform malaria control and elimination programmes. PMID:25891915

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

    PubMed Central

    Rosetti, Natalia; Remis, Maria Isabel

    2012-01-01

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

  19. Genetic structure of the world's polar bear populations

    USGS Publications Warehouse

    Paetkau, David; Amstrup, Steven C.; Born, E.W.; Calvert, W.; Derocher, A.E.; Garner, G.W.; Messier, F.; Stirling, I.; Taylor, M.K.; Wiig, O.; Strobeck, C.

    1999-01-01

    We studied genetic structure in polar bear (Ursus maritimus) populations by typing a sample of 473 individuals spanning the species distribution at 16 highly variable microsatellite loci. No genetic discontinuities were found that would be consistent with evolutionarily significant periods of isolation between groups. Direct comparison of movement data and genetic data from the Canadian Arctic revealed a highly significant correlation. Genetic data generally supported existing population (management unit) designations, although there were two cases where genetic data failed to differentiate between pairs of populations previously resolved by movement data. A sharp contrast was found between the minimal genetic structure observed among populations surrounding the polar basin and the presence of several marked genetic discontinuities in the Canadian Arctic. The discontinuities in the Canadian Arctic caused the appearance of four genetic clusters of polar bear populations. These clusters vary in total estimated population size from 100 to over 10 000, and the smallest may merit a relatively conservative management strategy in consideration of its apparent isolation. We suggest that the observed pattern of genetic discontinuities has developed in response to differences in the seasonal distribution and pattern of sea ice habitat and the effects of these differences on the distribution and abundance of seals.

  20. Genetic structure of the world's polar bear populations.

    PubMed

    Paetkau, D; Amstrup, S C; Born, E W; Calvert, W; Derocher, A E; Garner, G W; Messier, F; Stirling, I; Taylor, M K; Wiig, O; Strobeck, C

    1999-10-01

    We studied genetic structure in polar bear (Ursus maritimus) populations by typing a sample of 473 individuals spanning the species distribution at 16 highly variable microsatellite loci. No genetic discontinuities were found that would be consistent with evolutionarily significant periods of isolation between groups. Direct comparison of movement data and genetic data from the Canadian Arctic revealed a highly significant correlation. Genetic data generally supported existing population (management unit) designations, although there were two cases where genetic data failed to differentiate between pairs of populations previously resolved by movement data. A sharp contrast was found between the minimal genetic structure observed among populations surrounding the polar basin and the presence of several marked genetic discontinuities in the Canadian Arctic. The discontinuities in the Canadian Arctic caused the appearance of four genetic clusters of polar bear populations. These clusters vary in total estimated population size from 100 to over 10 000, and the smallest may merit a relatively conservative management strategy in consideration of its apparent isolation. We suggest that the observed pattern of genetic discontinuities has developed in response to differences in the seasonal distribution and pattern of sea ice habitat and the effects of these differences on the distribution and abundance of seals. PMID:10583821

  1. Reversible Switching of Liquid Crystalline Order Permits Synthesis of Homogeneous Populations of Dipolar Patchy Microparticles

    PubMed Central

    Wang, Xiaoguang; Miller, Daniel S.; de Pablo, Juan J.

    2014-01-01

    The spontaneous positioning of colloids on the surfaces of micrometer-sized liquid crystalline droplets and their subsequent polymerization offers the basis of a general and facile method for the synthesis of patchy microparticles. The existence of multiple local energetic minima, however, can generate kinetic traps for colloids on the surfaces of the liquid crystal (LC) droplets and result in heterogeneous populations of patchy microparticles. To address this issue, here we demonstrate that adsorbate-driven switching of the internal configurations of LC droplets can be used to sweep colloids to a single location on the LC droplet surfaces, thus resulting in the synthesis of homogeneous populations of patchy microparticles. The surface-driven switching of the LC can be triggered by addition of surfactant or salts, and permits the synthesis of dipolar microparticles as well as “Janus-like” microparticles. By using magnetic colloids, we illustrate the utility of the approach by synthesizing magnetically-responsive patchy microdroplets of LC with either dipolar or quadrupolar symmetry that exhibit distinct optical responses upon application of an external magnetic field. PMID:25484850

  2. Population size and time since island isolation determine genetic diversity loss in insular frog populations.

    PubMed

    Wang, Supen; Zhu, Wei; Gao, Xu; Li, Xianping; Yan, Shaofei; Liu, Xuan; Yang, Ji; Gao, Zengxiang; Li, Yiming

    2014-02-01

    Understanding the factors that contribute to loss of genetic diversity in fragmented populations is crucial for conservation measurements. Land-bridge archipelagoes offer ideal model systems for identifying the long-term effects of these factors on genetic variations in wild populations. In this study, we used nine microsatellite markers to quantify genetic diversity and differentiation of 810 pond frogs (Pelophylax nigromaculatus) from 24 islands of the Zhoushan Archipelago and three sites on nearby mainland China and estimated the effects of the island area, population size, time since island isolation, distance to the mainland and distance to the nearest larger island on reduced genetic diversity of insular populations. The mainland populations displayed higher genetic diversity than insular populations. Genetic differentiations and no obvious gene flow were detected among the frog populations on the islands. Hierarchical partitioning analysis showed that only time since island isolation (square-root-transformed) and population size (log-transformed) significantly contributed to insular genetic diversity. These results suggest that decreased genetic diversity and genetic differentiations among insular populations may have been caused by random genetic drift following isolation by rising sea levels during the Holocene. The results provide strong evidence for a relationship between retained genetic diversity and population size and time since island isolation for pond frogs on the islands, consistent with the prediction of the neutral theory for finite populations. Our study highlights the importance of the size and estimated isolation time of populations in understanding the mechanisms of genetic diversity loss and differentiation in fragmented wild populations. PMID:24351057

  3. Population Genetic History of Aristeus antennatus (Crustacea: Decapoda) in the Western and Central Mediterranean Sea

    PubMed Central

    Marra, Annamaria; Mona, Stefano; Sà, Rui M.; D’Onghia, Gianfranco; Maiorano, Porzia

    2015-01-01

    Aristeus antennatus is an ecologically and economically important deep-water species in the Mediterranean Sea. In this study we investigated the genetic variability of A. antennatus sampled from 10 sampling stations in the Western and Central Mediterranean. By comparing our new samples with available data from the Western area, we aim to identify potential genetic stocks of A. antennatus and to reconstruct its historical demography in the Mediterranean. We analyzed two regions of mitochondrial DNA in 319 individuals, namely COI and 16S. We found two main results: i) the genetic diversity values consistent with previous data within the Mediterranean and the absence of barriers to gene flow within the Mediterranean Sea; ii) a constant long-term effective population size in almost all demes but a strong signature of population expansion in the pooled sample about 50,000 years B.P./ago. We propose two explanation for our results. The first is based on the ecology of A. antennatus. We suggest the existence of a complex meta-population structured into two layers: a deeper-dwelling stock, not affected by fishing, which preserves the pattern of historical demography; and genetically homogeneous demes inhabiting the fishing grounds. The larval dispersal, adult migration and continuous movements of individuals from “virgin” deeper grounds not affected by fishing to upper fishing areas support an effective ‘rescue effect’ contributing to the recovery of the exploited stocks and explain their genetic homogeneity throughout the Mediterranean Sea. The second is based on the reproduction model of this shrimp: the high variance in offspring production calls for a careful interpretation of the data observed under classical population genetics and Kingman’s coalescent. In both cases, management policies for A. antennatus will therefore require careful evaluation of the meta-population dynamics of all stocks in the Mediterranean. In the future, it will be particularly

  4. Genetic Homogeneity Revealed Using SCoT, ISSR and RAPD Markers in Micropropagated Pittosporum eriocarpum Royle- An Endemic and Endangered Medicinal Plant

    PubMed Central

    Thakur, Julie; Dwivedi, Mayank D.; Sourabh, Pragya; Uniyal, Prem L.; Pandey, Arun K.

    2016-01-01

    Pittosporum eriocarpum Royle, a medicinally important taxon, is endemic to Uttarakhand region of Himalaya. It has become endangered due to over-collection and the loss of habitats. As raising plants through seeds in this plant is problematic, a reliable protocol for micropropagation using nodal explants has been developed. High shoot regeneration (95%) occurred in MS medium augmented with BA 0.4mg/l in combination IBA 0.6mg/l. In vitro regenerated shoots were rooted in MS medium supplemented with three auxins, of which 0.6 mg/l indole butyric acid proved to be the best for rooting (90%) with maximum number of roots per shoot. Thereafter, rooted plants were hardened and nearly 73% of rooted shoots were successfully acclimatized and established in the field. Start codon targeted (SCoT), inter simple sequence repeats (ISSR) and random amplified polymorphic DNA (RAPD) markers were used to validate the genetic homogeneity amongst nine in vitro raised plantlets with mother plant. DNA fingerprints of in vitro regenerated plantlets displayed monomorphic bands similar to mother plant, indicating homogeneity among the micropropagated plants with donor mother plant. The similarity values were calculated based on SCoT, ISSR and RAPD profiles which ranged from 0.89 to 1.00, 0.91 to 1.00 and 0.95 to 1.00 respectively. The dendrograms generated through Unweighted Pair Group Method with arithmetic mean (UPGMA) analysis revealed 97% similarity amongst micropropagated plants with donor mother plant, thus confirming genetic homogeneity of micropropagated clones. This is the first report on micropropagation and genetic homogeneity assessment of P. eriocarpum. The protocol would be useful for the conservation and large scale production of P. eriocarpum to meet the demand for medicinal formulations and also for the re-introduction of in vitro grown plants in the suitable natural habitats to restore the populations. PMID:27434060

  5. Population demographics and genetic diversity in remnant and translocated populations of sea otters

    USGS Publications Warehouse

    Bodkin, J.L.; Ballachey, B.E.; Cronin, M.A.; Scribner, K.T.

    1999-01-01

    The effects of small population size on genetic diversity and subsequent population recovery are theoretically predicted, but few empirical data are available to describe those relations. We use data from four remnant and three translocated sea otter (Enhydra lutris) populations to examine relations among magnitude and duration of minimum population size, population growth rates, and genetic variation. Metochondrial (mt)DNA haplotype diversity was correlated with the number of years at minimum population size (r = -0.741, p = 0.038) and minimum population size (r = 0.709, p = 0.054). We found no relation between population growth and haplotype diversity, altough growth was significantly greater in translocated than in remnant populations. Haplotype diversity in populations established from two sources was higher than in a population established from a single source and was higher than in the respective source populations. Haplotype frequencies in translocated populations of founding sizes of 4 and 28 differed from expected, indicating genetic drift and differential reproduction between source populations, whereas haplotype frequencies in a translocated population with a founding size of 150 did not. Relations between population demographics and genetic characteristics suggest that genetic sampling of source and translocated populations can provide valuable inferences about translocations.

  6. Use of Population Genetics to Assess the Ecology, Evolution, and Population Structure of Coccidioides

    PubMed Central

    Teixeira, Marcus M.

    2016-01-01

    During the past 20 years, a general picture of the genetic diversity and population structure of Coccidioides, the causal agent of coccidioidomycosis (Valley fever), has emerged. The genus consists of 2 genetically diverse species, C. immitis and C. posadasii, each of which contains 1 or more distinct populations with limited gene flow. Genotypic data indicate that C. immitis is divided into 2 subpopulations (central and southern California populations) and C. posadasii is divided into 3 subpopulations (Arizona, Mexico, and Texas/South America populations). However, admixture within and among these populations and the current paucity of environmental isolates limit our understanding of the population genetics of Coccidioides. We assessed population structure of Coccidioides in Arizona by analyzing 495 clinical and environmental isolates. Our findings confirm the population structure as previously described and indicate a finer scale population structure in Arizona. Environmental isolates appear to have higher genetic diversity than isolates from human patients. PMID:27191589

  7. Use of Population Genetics to Assess the Ecology, Evolution, and Population Structure of Coccidioides.

    PubMed

    Teixeira, Marcus M; Barker, Bridget M

    2016-06-01

    During the past 20 years, a general picture of the genetic diversity and population structure of Coccidioides, the causal agent of coccidioidomycosis (Valley fever), has emerged. The genus consists of 2 genetically diverse species, C. immitis and C. posadasii, each of which contains 1 or more distinct populations with limited gene flow. Genotypic data indicate that C. immitis is divided into 2 subpopulations (central and southern California populations) and C. posadasii is divided into 3 subpopulations (Arizona, Mexico, and Texas/South America populations). However, admixture within and among these populations and the current paucity of environmental isolates limit our understanding of the population genetics of Coccidioides. We assessed population structure of Coccidioides in Arizona by analyzing 495 clinical and environmental isolates. Our findings confirm the population structure as previously described and indicate a finer scale population structure in Arizona. Environmental isolates appear to have higher genetic diversity than isolates from human patients. PMID:27191589

  8. Genetic algorithms and MCML program for recovery of optical properties of homogeneous turbid media

    PubMed Central

    Morales Cruzado, Beatriz; y Montiel, Sergio Vázquez; Atencio, José Alberto Delgado

    2013-01-01

    In this paper, we present and validate a new method for optical properties recovery of turbid media with slab geometry. This method is an iterative method that compares diffuse reflectance and transmittance, measured using integrating spheres, with those obtained using the known algorithm MCML. The search procedure is based in the evolution of a population due to selection of the best individual, i.e., using a genetic algorithm. This new method includes several corrections such as non-linear effects in integrating spheres measurements and loss of light due to the finite size of the sample. As a potential application and proof-of-principle experiment of this new method, we use this new algorithm in the recovery of optical properties of blood samples at different degrees of coagulation. PMID:23504404

  9. Temporal distribution of genetically homogenous ‘free-living’ Hematodinium sp. in a Delmarva coastal ecosystem

    PubMed Central

    2012-01-01

    Background Significant damage to crustacean fisheries worldwide has been associated with Hematodinium sp. It has been postulated that Hematodinium sp. requires passage through the water column and/or intermediate hosts to complete its life cycle. Thus, an understanding of the prevalence and seasonality of Hematodinium sp. within environmentally-derived samples should yield insight into potential modes of disease transmission, and how these relate to infection cycles in hosts. Results We conducted a two year survey, from 2010–2011, in which 48 of 546 (8.8%) of environmental samples from the Maryland and Virginia coastal bays were positive for Hematodinium sp. between April and November, as based upon endpoint PCR analysis specific to blue crab isolates. Detection in both water and sediment was roughly equivalent, and there were no obvious seasonal patterns. However, there was a high detection in April water samples, which was unanticipated owing to the fact that crabs infected with Hematodinium sp. have not been observed in this early month of the seasonal disease cycle. Focusing on three sites of high prevalence (Sinnickson, VA; Tom’s Cove, VA; and Newport Bay, MD) Hematodinium sp. population diversity was analyzed using standard cloning methods. Of 131 clones, 109 (83.2%) were identical, 19 displayed a single nucleotide substitution, and 4 contain two nucleotide substitutions. Conclusions Our data suggests a continuous presence of Hematodinium sp. in both water and sediment of a combined Maryland and Virginia coastal bay ecosystem. The detection of Hematodinium sp. in the water column in April is an earlier manifestation of the parasite than predicted, pointing to an as yet unknown stage in its development prior to infection. That the population is relatively homogenous ranging from April to November, at three distinct sites, supports a hypothesis that one species of Hematodinium is responsible for infections within the ecosystem. PMID:22828185

  10. Genetic and morphological variation of three freshwater lake populations of Coilia ectenes (Engraulidae).

    PubMed

    Xie, J Y

    2012-10-01

    Population structure of the important commercial fish, Coilia ectenes, was investigated in samples from three freshwater lakes in the Eastern China using a multivariate approach of morphometrics and mitochondrial DNA control region sequencing. A total of eighteen morphological distances of truss method and eight morphometric variables were taken from each fish. Multivariate analyses of the morphometric data revealed significant morphological differences among the three lake populations, especially for those samples from Taihu Lake. Discriminant functions were used to compare sites, and these permitted an 83% success rate in distinguishing fish from the three sites. However, no obviously geographical differentiation was found among those populations of C. ectenes based on the genetic data. In the AMOVA analysis, only 2.2% genetic variability came from different populations, and most of them were present within the sub-populations. Experience a recent population expansion and some movement of fish among those areas, quite possibly enough to bring about relative genetic homogeneity, but there is insufficient to prevent the three populations from differing phenotypically. The diversified environmental factors may be playing an important role in shaping morphological variations among those populations. PMID:23270269

  11. A rangewide population genetic study of trumpeter swans

    USGS Publications Warehouse

    Oyler-McCance, S.J.; Ransler, F.A.; Berkman, L.K.; Quinn, T.W.

    2007-01-01

    For management purposes, the range of naturally occurring trumpeter swans (Cygnus buccinator) has been divided into two populations, the Pacific Coast Population (PP) and the Rocky Mountain Population (RMP). Little is known about the distribution of genetic variation across the species' range despite increasing pressure to make difficult management decisions regarding the two populations and flocks within them. To address this issue, we used rapidly evolving genetic markers (mitochondrial DNA sequence and 17 nuclear microsatellite loci) to elucidate the underlying genetic structure of the species. Data from both markers revealed a significant difference between the PP and RMP with the Yukon Territory as a likely area of overlap. Additionally, we found that the two populations have somewhat similar levels of genetic diversity (PP is slightly higher) suggesting that the PP underwent a population bottleneck similar to a well-documented one in the RMP. Both genetic structure and diversity results reveal that the Tri-State flock, a suspected unique, non-migratory flock, is not genetically different from the Canadian flock of the RMP and need not be treated as a unique population from a genetic standpoint. Finally, trumpeter swans appear to have much lower mitochondrial DNA variability than other waterfowl studied thus far which may suggest a previous, species-wide bottleneck. ?? 2007 Springer Science+Business Media, Inc.

  12. Genetic variation and population structure in native Americans.

    PubMed

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

    2007-11-01

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

  13. Genetic Variation and Population Structure in Native Americans

    PubMed Central

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

    2007-01-01

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

  14. Mapping the genetic diversity of HLA haplotypes in the Japanese populations

    PubMed Central

    Saw, Woei-Yuh; Liu, Xuanyao; Khor, Chiea-Chuen; Takeuchi, Fumihiko; Katsuya, Tomohiro; Kimura, Ryosuke; Nabika, Toru; Ohkubo, Takayoshi; Tabara, Yasuharu; Yamamoto, Ken; Yokota, Mitsuhiro; Akiyama, Koichi; Asano, Hiroyuki; Asayama, Kei; Haga, Toshikazu; Hara, Azusa; Hirose, Takuo; Hosaka, Miki; Ichihara, Sahoko; Imai, Yutaka; Inoue, Ryusuke; Ishiguro, Aya; Isomura, Minoru; Isono, Masato; Kamide, Kei; Kato, Norihiro; Katsuya, Tomohiro; Kikuya, Masahiro; Kohara, Katsuhiko; Matsubara, Tatsuaki; Matsuda, Ayako; Metoki, Hirohito; Miki, Tetsuro; Murakami, Keiko; Nabika, Toru; Nakatochi, Masahiro; Ogihara, Toshio; Ohnaka, Keizo; Ohkubo, Takayoshi; Rakugi, Hiromi; Satoh, Michihiro; Shiwaku, Kunihiro; Sugimoto, Ken; Tabara, Yasuharu; Takami, Yoichi; Takayanagi, Ryoichi; Takeuchi, Fumihiko; Tsubota-Utsugi, Megumi; Yamamoto, Ken; Yamamoto, Koichi; Yamasaki, Masayuki; Yasui, Daisaku; Yokota, Mitsuhiro; Teo, Yik-Ying; Kato, Norihiro

    2015-01-01

    Japan has often been viewed as an Asian country that possesses a genetically homogenous community. The basis for partitioning the country into prefectures has largely been geographical, although cultural and linguistic differences still exist between some of the districts/prefectures, especially between Okinawa and the mainland prefectures. The Major Histocompatibility Complex (MHC) region has consistently emerged as the most polymorphic region in the human genome, harbouring numerous biologically important variants; nevertheless the presence of population-specific long haplotypes hinders the imputation of SNPs and classical HLA alleles. Here, we examined the extent of genetic variation at the MHC between eight Japanese populations sampled from Okinawa, and six other prefectures located in or close to the mainland of Japan, specifically focusing at the haplotypes observed within each population, and what the impact of any variation has on imputation. Our results indicated that Okinawa was genetically farther to the mainland Japanese than were Gujarati Indians from Tamil Indians, while the mainland Japanese from six prefectures were more homogeneous than between northern and southern Han Chinese. The distribution of haplotypes across Japan was similar, although imputation was most accurate for Okinawa and several mainland prefectures when population-specific panels were used as reference. PMID:26648100

  15. Genetic diversity and population differentiation in the cockle Cerastoderma edule estimated by microsatellite markers

    NASA Astrophysics Data System (ADS)

    Martínez, L.; Méndez, J.; Insua, A.; Arias-Pérez, A.; Freire, R.

    2013-03-01

    The edible cockle Cerastoderma edule is a marine bivalve commercially fished in several European countries that have lately suffered a significant decrease in production. Despite its commercial importance, genetic studies in this species are scarce. In this work, genetic diversity and population differentiation of C. edule has been assessed using 11 microsatellite markers in eight locations from the European Atlantic coast. All localities showed similar observed and expected heterozygosity values, but displayed differences in allelic richness, with lowest values obtained for localities situated farther north. Global Fst value revealed the existence of significant genetic structure; all but one locality from the Iberian Peninsula were genetically homogeneous, while more remote localities from France, The Netherlands, and Scotland were significantly different from all other localities. A combined effect of isolation by distance and the existence of barriers that limit gene flow may explain the differentiation observed.

  16. Isonymy and the genetic structure of Albanian populations.

    PubMed

    Mikerezi, Ilia; Pizzetti, Paola; Lucchetti, Enzo; Ekonomi, Milva

    2003-12-01

    It is well known that in systems of surname transmission through the paternal line, surnames simulate neutral gene alleles belonging to the Y chromosome. This property of surnames was used to analyze the genetic structure of Albanian populations. Two large samples of surnames belonging to two different periods of time were analyzed. The analysis of indicators of population structure showed that geographical distance has an important effect on surname distribution. It seems that isolation by distance and genetic drift have been still important factors in the determination of the genetic structure of the Albanian population. PMID:14746137

  17. Population Structure and Genetic Diversity of Native and Invasive Populations of Solanum rostratum (Solanaceae)

    PubMed Central

    Zhao, Jiali; Solís-Montero, Lislie; Lou, Anru; Vallejo-Marín, Mario

    2013-01-01

    Aims We investigate native and introduced populations of Solanum rostratum, an annual, self-compatible plant that has been introduced around the globe. This study is the first to compare the genetic diversity of Solanum rostratum between native and introduced populations. We aim to (1) determine the level of genetic diversity across the studied regions; (2) explore the likely origins of invasive populations in China; and (3) investigate whether there is the evidence of multiple introductions into China. Methods We genotyped 329 individuals at 10 microsatellite loci to determine the levels of genetic diversity and to investigate population structure of native and introduced populations of S. rostratum. We studied five populations in each of three regions across two continents: Mexico, the U.S.A. and China. Important Findings We found the highest genetic diversity among Mexican populations of S. rostratum. Genetic diversity was significantly lower in Chinese and U.S.A. populations, but we found no regional difference in inbreeding coefficients (FIS) or population differentiation (FST). Population structure analyses indicate that Chinese and U.S.A. populations are more closely related to each other than to sampled Mexican populations, revealing that introduced populations in China share an origin with the sampled U.S.A. populations. The distinctiveness between some introduced populations indicates multiple introductions of S. rostratum into China. PMID:24224008

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

    PubMed Central

    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

  19. 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

  20. Population genetic testing for cancer susceptibility: founder mutations to genomes.

    PubMed

    Foulkes, William D; Knoppers, Bartha Maria; Turnbull, Clare

    2016-01-01

    The current standard model for identifying carriers of high-risk mutations in cancer-susceptibility genes (CSGs) generally involves a process that is not amenable to population-based testing: access to genetic tests is typically regulated by health-care providers on the basis of a labour-intensive assessment of an individual's personal and family history of cancer, with face-to-face genetic counselling performed before mutation testing. Several studies have shown that application of these selection criteria results in a substantial proportion of mutation carriers being missed. Population-based genetic testing has been proposed as an alternative approach to determining cancer susceptibility, and aims for a more-comprehensive detection of mutation carriers. Herein, we review the existing data on population-based genetic testing, and consider some of the barriers, pitfalls, and challenges related to the possible expansion of this approach. We consider mechanisms by which population-based genetic testing for cancer susceptibility could be delivered, and suggest how such genetic testing might be integrated into existing and emerging health-care structures. The existing models of genetic testing (including issues relating to informed consent) will very likely require considerable alteration if the potential benefits of population-based genetic testing are to be fully realized. PMID:26483301

  1. Extensive genetic divergence among Diptychus maculatus populations in northwest China

    NASA Astrophysics Data System (ADS)

    Meng, Wei; Yang, Tianyan; Hai, Sa; Ma, Yanwu; Cai, Lingang; Ma, Xufa; Gao, Tianxiang; Guo, Yan

    2015-05-01

    D. maculates is a kind of specialized Schizothoracinae fish has been locally listed as a protected animal in Xinjiang Province, China. Ili River located in north of Tianshan Mountain and Tarim River located in north of Qinghai-Tibetan Plateau were two main distribution areas of this fish. To investigate the genetic diversity and genetic structure of D. maculates, four populations from Tarim River system and two populations from Ili River system were collected in this study. A 570-bp sequence of the control region was obtained for 105 specimens. Twenty-four haplotypes were detected from six populations, only Kunes River population and Kashi River population shared haplotypes with each other. For all the populations examined, the haplotype diversity ( h) was 0.904 8±0.012 6, nucleotide diversity (π) was 0.027 9±0.013 9, and the average number of pairwise nucleotide differences ( k) was 15.878 3±7.139 1. The analysis of molecular variance (AMOVA) showed that 86.31% of the total genetic variation was apportioned among populations, and the variation within sampled populations was 13.69%. Genetic differences among sampled populations were highly significant. F st statistical test indicated that all populations were significantly divergent from each other ( P<0.01). The largest F st value was between Yurungkash River population and Muzat River population, while the smallest F st value was between Kunes River population and Kashi River population. NJ phylogenetic tree of D-loop haplotypes revealed two main clades. The neutrality test and mismatch distribution analysis suggested that the fish had went through a recent population expansion. The uplift of Tianshan Mountain and movement of Qinghai-Tibetan Plateau might contribute to the wide genetic divergence of D. maculates in northwest China.

  2. High school students' understanding and problem solving in population genetics

    NASA Astrophysics Data System (ADS)

    Soderberg, Patti D.

    This study is an investigation of student understanding of population genetics and how students developed, used and revised conceptual models to solve problems. The students in this study participated in three rounds of problem solving. The first round involved the use of a population genetics model to predict the number of carriers in a population. The second round required them to revise their model of simple dominance population genetics to make inferences about populations containing three phenotype variations. The third round of problem solving required the students to revise their model of population genetics to explain anomalous data where the proportions of males and females with a trait varied significantly. As the students solved problems, they were involved in basic scientific processes as they observed population phenomena, constructed explanatory models to explain the data they observed, and attempted to persuade their peers as to the adequacy of their models. In this study, the students produced new knowledge about the genetics of a trait in a population through the revision and use of explanatory population genetics models using reasoning that was similar to what scientists do. The students learned, used and revised a model of Hardy-Weinberg equilibrium to generate and test hypotheses about the genetics of phenotypes given only population data. Students were also interviewed prior to and following instruction. This study suggests that a commonly held intuitive belief about the predominance of a dominant variation in populations is resistant to change, despite instruction and interferes with a student's ability to understand Hardy-Weinberg equilibrium and microevolution.

  3. The genetic structure of a relict population of wood frogs

    USGS Publications Warehouse

    Scherer, Rick; Muths, Erin; Noon, Barry; Oyler-McCance, Sara

    2012-01-01

    Habitat fragmentation and the associated reduction in connectivity between habitat patches are commonly cited causes of genetic differentiation and reduced genetic variation in animal populations. We used eight microsatellite markers to investigate genetic structure and levels of genetic diversity in a relict population of wood frogs (Lithobates sylvatica) in Rocky Mountain National Park, Colorado, where recent disturbances have altered hydrologic processes and fragmented amphibian habitat. We also estimated migration rates among subpopulations, tested for a pattern of isolation-by-distance, and looked for evidence of a recent population bottleneck. The results from the clustering algorithm in Program STRUCTURE indicated the population is partitioned into two genetic clusters (subpopulations), and this result was further supported by factorial component analysis. In addition, an estimate of FST (FST = 0.0675, P value \\0.0001) supported the genetic differentiation of the two clusters. Estimates of migration rates among the two subpopulations were low, as were estimates of genetic variability. Conservation of the population of wood frogs may be improved by increasing the spatial distribution of the population and improving gene flow between the subpopulations. Construction or restoration of wetlands in the landscape between the clusters has the potential to address each of these objectives.

  4. Noninvasive genetics provides insights into the population size and genetic diversity of an Amur tiger population in China.

    PubMed

    Wang, Dan; Hu, Yibo; Ma, Tianxiao; Nie, Yonggang; Xie, Yan; Wei, Fuwen

    2016-01-01

    Understanding population size and genetic diversity is critical for effective conservation of endangered species. The Amur tiger (Panthera tigris altaica) is the largest felid and a flagship species for wildlife conservation. Due to habitat loss and human activities, available habitat and population size are continuously shrinking. However, little is known about the true population size and genetic diversity of wild tiger populations in China. In this study, we collected 55 fecal samples and 1 hair sample to investigate the population size and genetic diversity of wild Amur tigers in Hunchun National Nature Reserve, Jilin Province, China. From the samples, we determined that 23 fecal samples and 1 hair sample were from 7 Amur tigers: 2 males, 4 females and 1 individual of unknown sex. Interestingly, 2 fecal samples that were presumed to be from tigers were from Amur leopards, highlighting the significant advantages of noninvasive genetics over traditional methods in studying rare and elusive animals. Analyses from this sample suggested that the genetic diversity of wild Amur tigers is much lower than that of Bengal tigers, consistent with previous findings. Furthermore, the genetic diversity of this Hunchun population in China was lower than that of the adjoining subpopulation in southwest Primorye Russia, likely due to sampling bias. Considering the small population size and relatively low genetic diversity, it is urgent to protect this endangered local subpopulation in China. PMID:26663614

  5. Experimental Population Genetics in the Introductory Genetics Laboratory Using "Drosophila" as a Model Organism

    ERIC Educational Resources Information Center

    Johnson, Ronald; Kennon, Tillman

    2009-01-01

    Hypotheses of population genetics are derived and tested by students in the introductory genetics laboratory classroom as they explore the effects of biotic variables (physical traits of fruit flies) and abiotic variables (island size and distance) on fruit fly populations. In addition to this hypothesis-driven experiment, the development of…

  6. Surprisingly little population genetic structure in a fungus-associated beetle despite its exploitation of multiple hosts

    PubMed Central

    Wood, Corlett W; Donald, Hannah M; Formica, Vincent A; Brodie, Edmund D

    2013-01-01

    In heterogeneous environments, landscape features directly affect the structure of genetic variation among populations by functioning as barriers to gene flow. Resource-associated population genetic structure, in which populations that use different resources (e.g., host plants) are genetically distinct, is a well-studied example of how environmental heterogeneity structures populations. However, the pattern that emerges in a given landscape should depend on its particular combination of resources. If resources constitute barriers to gene flow, population differentiation should be lowest in homogeneous landscapes, and highest where resources exist in equal proportions. In this study, we tested whether host community diversity affects population genetic structure in a beetle (Bolitotherus cornutus) that exploits three sympatric host fungi. We collected B. cornutus from plots containing the three host fungi in different proportions and quantified population genetic structure in each plot using a panel of microsatellite loci. We found no relationship between host community diversity and population differentiation in this species; however, we also found no evidence of resource-associated differentiation, suggesting that host fungi are not substantial barriers to gene flow. Moreover, we detected no genetic differentiation among B. cornutus populations separated by several kilometers, even though a previous study demonstrated moderate genetic structure on the scale of a few hundred meters. Although we found no effect of community diversity on population genetic structure in this study, the role of host communities in the structuring of genetic variation in heterogeneous landscapes should be further explored in a species that exhibits resource-associated population genetic structure. PMID:23789061

  7. Genetic Structure of Daphnia galeata Populations in Eastern China

    PubMed Central

    Wolinska, Justyna; Ma, Xiaolin; Yang, Zhong; Hu, Wei; Yin, Mingbo

    2015-01-01

    This study presents the first examination of the genetic structure of Daphnia longispina complex populations in Eastern China. Only one species, D. galeata, was present across the eight investigated lakes; as identified by taxon assignment using allelic variation at 15 microsatellite loci. Three genetically differentiated D. galeata subgroups emerged independent of the type of statistical analysis applied. Thus, Bayesian clustering, discriminant analysis based on results from factorial correspondence analysis, and UPGMA clustering consistently showed that populations from two neighbouring lakes were genetically separated from a mixture of genotypes found in other lakes, which formed another two subgroups. Clonal diversity was high in all D. galeata populations, and most samples showed no deviation from Hardy-Weinberg equilibrium, indicating that clonal selection had little effect on the genetic diversity. Overall, populations did not cluster by geographical origin. Further studies will show if the observed pattern can be explained by natural colonization processes or by recent anthropogenic impact on predominantly artificial lakes. PMID:25768727

  8. Genetic structure of Daphnia galeata populations in Eastern China.

    PubMed

    Wei, Wenzhi; Gießler, Sabine; Wolinska, Justyna; Ma, Xiaolin; Yang, Zhong; Hu, Wei; Yin, Mingbo

    2015-01-01

    This study presents the first examination of the genetic structure of Daphnia longispina complex populations in Eastern China. Only one species, D. galeata, was present across the eight investigated lakes; as identified by taxon assignment using allelic variation at 15 microsatellite loci. Three genetically differentiated D. galeata subgroups emerged independent of the type of statistical analysis applied. Thus, Bayesian clustering, discriminant analysis based on results from factorial correspondence analysis, and UPGMA clustering consistently showed that populations from two neighbouring lakes were genetically separated from a mixture of genotypes found in other lakes, which formed another two subgroups. Clonal diversity was high in all D. galeata populations, and most samples showed no deviation from Hardy-Weinberg equilibrium, indicating that clonal selection had little effect on the genetic diversity. Overall, populations did not cluster by geographical origin. Further studies will show if the observed pattern can be explained by natural colonization processes or by recent anthropogenic impact on predominantly artificial lakes. PMID:25768727

  9. Genetic Diversity and Population Structure of the Rare and Endangered Plant Species Pulsatilla patens (L.) Mill in East Central Europe

    PubMed Central

    Szczecińska, Monika; Sramko, Gabor; Wołosz, Katarzyna; Sawicki, Jakub

    2016-01-01

    Pulsatilla patens s.s. is a one of the most endangered plant species in Europe. The present range of this species in Europe is highly fragmented and the size of the populations has been dramatically reduced in the past 50 years. The rapid disappearance of P. patens localities in Europe has prompted the European Commission to initiate active protection of this critically endangered species. The aim of this study was to estimate the degree and distribution of genetic diversity within European populations of this endangered species. We screened 29 populations of P. patens using a set of six microsatellite primers. The results of our study indicate that the analyzed populations are characterized by low levels of genetic diversity (Ho = 0.005) and very high levels of inbreeding (FIS = 0.90). These results suggest that genetic erosion could be partially responsible for the lower fitness in smaller populations of this species. Private allelic richness was very low, being as low as 0.00 for most populations. Average genetic diversity over loci and mean number of alleles in P. patens populations were significantly correlated with population size, suggesting severe genetic drift. The results of AMOVA point to higher levels of variation within populations than between populations.The results of Structure and PCoA analyses suggest that the genetic structure of the studied P. patens populations fall into three clusters corresponding to geographical regions. The most isolated populations (mostly from Romania) formed a separate group with a homogeneous gene pool located at the southern, steppic part of the distribution range. Baltic, mostly Polish, populations fall into two genetic groups which were not fully compatible with their geographic distribution.Our results indicate the serious genetic depauperation of P. patens in the western part of its range, even hinting at an ongoing extinction vortex. Therefore, special conservation attention is required to maintain the populations

  10. Genetic Diversity and Population Structure of the Rare and Endangered Plant Species Pulsatilla patens (L.) Mill in East Central Europe.

    PubMed

    Szczecińska, Monika; Sramko, Gabor; Wołosz, Katarzyna; Sawicki, Jakub

    2016-01-01

    Pulsatilla patens s.s. is a one of the most endangered plant species in Europe. The present range of this species in Europe is highly fragmented and the size of the populations has been dramatically reduced in the past 50 years. The rapid disappearance of P. patens localities in Europe has prompted the European Commission to initiate active protection of this critically endangered species. The aim of this study was to estimate the degree and distribution of genetic diversity within European populations of this endangered species. We screened 29 populations of P. patens using a set of six microsatellite primers. The results of our study indicate that the analyzed populations are characterized by low levels of genetic diversity (Ho = 0.005) and very high levels of inbreeding (FIS = 0.90). These results suggest that genetic erosion could be partially responsible for the lower fitness in smaller populations of this species. Private allelic richness was very low, being as low as 0.00 for most populations. Average genetic diversity over loci and mean number of alleles in P. patens populations were significantly correlated with population size, suggesting severe genetic drift. The results of AMOVA point to higher levels of variation within populations than between populations.The results of Structure and PCoA analyses suggest that the genetic structure of the studied P. patens populations fall into three clusters corresponding to geographical regions. The most isolated populations (mostly from Romania) formed a separate group with a homogeneous gene pool located at the southern, steppic part of the distribution range. Baltic, mostly Polish, populations fall into two genetic groups which were not fully compatible with their geographic distribution.Our results indicate the serious genetic depauperation of P. patens in the western part of its range, even hinting at an ongoing extinction vortex. Therefore, special conservation attention is required to maintain the populations

  11. [Genetic subdivision of the Buryat population].

    PubMed

    2014-03-01

    The results of an estimation of the level of subdivision in the Buryat ethnos (obtained oh the basis of data published by a number of research teams) are given. Altogether, information about 34 loci, including 25 diallelic loci and 9 STR loci, was analyzed. The results of the analysis, both for the diallelic polymorphic variants in genes predisposed to multifactorial diseases and for neutral STR markers, indicate the subdivision of the genetic structure of the different territorial groups of Buryats. The peculiarities of the ethnogenesis and heterogeneity of the settlement of Buryat tribes on the territory of residence are considered as one possible (but not the sole) explanation of the genetic heterogeneity of different territorial groups of Buryats. It is indicated that it is important to take into account information about the territorial, ethnic, and tribal affiliation of individuals (included in the studied groups) when planning studies aiming to establish a genetic component of the determination of pathological states in humans. PMID:25508085

  12. [Genetic subdivision of the Buryat population].

    PubMed

    Babushkina, N P; Eremina, E R; Kucher, A N

    2014-03-01

    The results of an estimation of the level of subdivision in the Buryat ethnos (obtained oh the basis of data published by a number of research teams) are given. Altogether, information about 34 loci, including 25 diallelic loci and 9 STR loci, was analyzed. The results of the analysis, both for the diallelic polymorphic variants in genes predisposed to multifactorial diseases and for neutral STR markers, indicate the subdivision of the genetic structure of the different territorial groups of Buryats. The peculiarities of the ethnogenesis and heterogeneity of the settlement of Buryat tribes on the territory of residence are considered as one possible (but not the sole) explanation of the genetic heterogeneity of different territorial groups of Buryats. It is indicated that it is important to take into account information about the territorial, ethnic, and tribal affiliation of individuals (included in the studied groups) when planning studies aiming to establish a genetic component of the determination of pathological states in humans. PMID:25438554

  13. TEMPORAL CHANGES OF GENETIC DIVERSITY IN SUGARCANE BREEDING POPULATIONS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Concerns about decline of genetic diversity in sugarcane (Saccharum spp.) breeding programs need be addressed to define better breeding strategies aimed at achieving greater genetic gains. The objectives of this study were to reconstruct the divergence in the Canal Point breeding populations as temp...

  14. Thirty years of tick population genetics: a comprehensive review.

    PubMed

    Araya-Anchetta, Ana; Busch, Joseph D; Scoles, Glen A; Wagner, David M

    2015-01-01

    Population genetic studies provide insights into the basic biology of arthropod disease vectors by estimating dispersal patterns and their potential to spread pathogens. In wingless vectors, such as ticks, gene flow will be defined in large part by the mobility of their hosts. However, tick behaviors and life cycle strategies can limit their dispersal even on highly mobile hosts and lead to an increase in genetic structure. In this review we synthesize the published literature from three decades of tick population genetic studies. Based on studies from 22 tick species (including representatives from Amblyomma, Bothriocroton, Dermacentor, Ixodes, Ornithodoros, and Rhipicephalus), observed levels of population genetic structure in ticks varied from no structure to very high levels. In about half of the species (including representatives from Amblyomma, Bothriocroton, Dermacentor, and Ornithodoros), tick genetic structure appeared to be determined primarily by the movement capacity of hosts, with low gene flow observed in ticks that use smaller bodied less mobile hosts and high gene flow in ticks using highly mobile hosts. In a number of other species (primarily from Ixodes, Ornithodoros, and Rhipicephalus), behavioral limitations to gene flow appeared to result in greater genetic structure than expected based upon host movement capability alone. We also discuss the strengths and limitations of genetic markers and their applicability to ticks and suggest possible analyses when planning population genetic studies for ticks. PMID:25461844

  15. The Evolutionary Biology and Population Genetics Underlying Fungal Strain Typing

    PubMed Central

    Taylor, John W.; Geiser, David M.; Burt, Austin; Koufopanou, Vassiliki

    1999-01-01

    Strain typing of medically important fungi and fungal population genetics have been stimulated by new methods of tapping DNA variation. The aim of this contribution is to show how awareness of fungal population genetics can increase the utility of strain typing to better serve the interests of medical mycology. Knowing two basic features of fungal population biology, the mode of reproduction and genetic differentiation or isolation, can give medical mycologists information about the intraspecific groups that are worth identifying and the number and type of markers that would be needed to do so. The same evolutionary information can be just as valuable for the selection of fungi for development and testing of pharmaceuticals or vaccines. The many methods of analyzing DNA variation are evaluated in light of the need for polymorphic loci that are well characterized, simple, independent, and stable. Traditional population genetic and new phylogenetic methods for analyzing mode of reproduction, genetic differentiation, and isolation are reviewed. Strain typing and population genetic reports are examined for six medically important species: Coccidioides immitis, Histoplasma capsulatum, Candida albicans, Cryptococcus neoformans, Aspergillus fumigatus, and A. flavus. Research opportunities in the areas of genomics, correlation of clinical variation with genetic variation, amount of recombination, and standardization of approach are suggested. PMID:9880478

  16. Genetic diversity and population structure in contemporary house sparrow populations along an urbanization gradient

    PubMed Central

    Vangestel, C; Mergeay, J; Dawson, D A; Callens, T; Vandomme, V; Lens, L

    2012-01-01

    House sparrow (Passer domesticus) populations have suffered major declines in urban as well as rural areas, while remaining relatively stable in suburban ones. Yet, to date no exhaustive attempt has been made to examine how, and to what extent, spatial variation in population demography is reflected in genetic population structuring along contemporary urbanization gradients. Here we use putatively neutral microsatellite loci to study if and how genetic variation can be partitioned in a hierarchical way among different urbanization classes. Principal coordinate analyses did not support the hypothesis that urban/suburban and rural populations comprise two distinct genetic clusters. Comparison of FST values at different hierarchical scales revealed drift as an important force of population differentiation. Redundancy analyses revealed that genetic structure was strongly affected by both spatial variation and level of urbanization. The results shown here can be used as baseline information for future genetic monitoring programmes and provide additional insights into contemporary house sparrow dynamics along urbanization gradients. PMID:22588131

  17. Global Population Genetic Structure of Caenorhabditis remanei Reveals Incipient Speciation

    PubMed Central

    Dey, Alivia; Jeon, Yong; Wang, Guo-Xiu; Cutter, Asher D.

    2012-01-01

    Mating system transitions dramatically alter the evolutionary trajectories of genomes that can be revealed by contrasts of species with disparate modes of reproduction. For such transitions in Caenorhabditis nematodes, some major causes of genome variation in selfing species have been discerned. And yet, we have only limited understanding of species-wide population genetic processes for their outcrossing relatives, which represent the reproductive state of the progenitors of selfing species. Multilocus–multipopulation sequence polymorphism data provide a powerful means to uncover the historical demography and evolutionary processes that shape genomes. Here we survey nucleotide polymorphism across the X chromosome for three populations of the outcrossing nematode Caenorhabditis remanei and demonstrate its divergence from a fourth population describing a closely related new species from China, C. sp. 23. We find high genetic variation globally and within each local population sample. Despite geographic barriers and moderate genetic differentiation between Europe and North America, considerable gene flow connects C. remanei populations. We discovered C. sp. 23 while investigating C. remanei, observing strong genetic differentiation characteristic of reproductive isolation that was confirmed by substantial F2 hybrid breakdown in interspecific crosses. That C. sp. 23 represents a distinct biological species provides a cautionary example of how standard practice can fail for mating tests of species identity in this group. This species pair permits full application of divergence population genetic methods to obligately outcrossing species of Caenorhabditis and also presents a new focus for interrogation of the genetics and evolution of speciation with the Caenorhabditis model system. PMID:22649079

  18. Genetic Evaluations for Mixed-Breed Populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An all-breed animal model was developed for routine genetic evaluations of US dairy cattle. Data sets from individual breeds were combined, and records from crossbred cows were included. About 1% of recent cows were first generation crossbreds. Numbers of cows with records since 1960 ranged from 10 ...

  19. Genetics of Type 2 Diabetes: the Power of Isolated Populations.

    PubMed

    Andersen, Mette Korre; Pedersen, Casper-Emil Tingskov; Moltke, Ida; Hansen, Torben; Albrechtsen, Anders; Grarup, Niels

    2016-07-01

    Type 2 diabetes (T2D) affects millions of people worldwide. Improving the understanding of the underlying mechanisms and ultimately improving the treatment strategies are, thus, of great interest. To achieve this, identification of genetic variation predisposing to T2D is important. A large number of variants have been identified in large outbred populations, mainly from Europe and Asia. However, to elucidate additional variation, isolated populations have a number of advantageous properties, including increased amounts of linkage disequilibrium, and increased probability for presence of high frequency disease-associated variants due to genetic drift. Collectively, this increases the statistical power to detect association signals in isolated populations compared to large outbred populations. In this review, we elaborate on why isolated populations are a powerful resource for the identification of complex disease variants and describe their contributions to the understanding of the genetics of T2D. PMID:27189761

  20. Population Genetic Structure of Aedes fluviatilis (Diptera: Culicidae).

    PubMed

    Multini, Laura Cristina; Wilke, André Barretto Bruno; Suesdek, Lincoln; Marrelli, Mauro Toledo

    2016-01-01

    Although Aedes fluviatilis is an anthropophilic mosquito found abundantly in urban environments, its biology, epidemiological potential and genetic characteristics are poorly understood. Climate change and urbanization processes that result in environmental modifications benefit certain anthropophilic mosquito species such as Ae. fluviatilis, greatly increasing their abundance in urban areas. To gain a better understanding of whether urbanization processes modulate the genetic structure of this species in the city of São Paulo, we used eight microsatellite loci to genetically characterize Ae. fluviatilis populations collected in nine urban parks in the city of São Paulo. Our results show that there is high gene flow among the populations of this species, heterozygosity deficiency and low genetic structure and that the species may have undergone a recent population expansion. There are two main hypotheses to explain these findings: (i) Ae. fluviatilis populations have undergone a population expansion as a result of urbanization; and (ii) as urbanization of the city of São Paulo occurred recently and was quite intense, the structuring of these populations cannot be observed yet, apart from in the populations of Ibirapuera and Piqueri parks, where the first signs of structuring have appeared. We believe that the expansion found in Ae. fluviatilis populations is probably correlated with the unplanned urbanization of the city of São Paulo, which transformed green areas into urbanized areas, as well as the increasing population density in the city. PMID:27598889

  1. Host genetics and population structure effects on parasitic disease

    PubMed Central

    Williams-Blangero, Sarah; Criscione, Charles D.; VandeBerg, John L.; Correa-Oliveira, Rodrigo; Williams, Kimberly D.; Subedi, Janardan; Kent, Jack W.; Williams, Jeff; Kumar, Satish; Blangero, John

    2012-01-01

    Host genetic factors exert significant influences on differential susceptibility to many infectious diseases. In addition, population structure of both host and parasite may influence disease distribution patterns. In this study, we assess the effects of population structure on infectious disease in two populations in which host genetic factors influencing susceptibility to parasitic disease have been extensively studied. The first population is the Jirel population of eastern Nepal that has been the subject of research on the determinants of differential susceptibility to soil-transmitted helminth infections. The second group is a Brazilian population residing in an area endemic for Trypanosoma cruzi infection that has been assessed for genetic influences on differential disease progression in Chagas disease. For measures of Ascaris worm burden, within-population host genetic effects are generally more important than host population structure factors in determining patterns of infectious disease. No significant influences of population structure on measures associated with progression of cardiac disease in individuals who were seropositive for T. cruzi infection were found. PMID:22312056

  2. Genetic characterization of northeastern Italian population isolates in the context of broader European genetic diversity

    PubMed Central

    Esko, Tõnu; Mezzavilla, Massimo; Nelis, Mari; Borel, Christelle; Debniak, Tadeusz; Jakkula, Eveliina; Julia, Antonio; Karachanak, Sena; Khrunin, Andrey; Kisfali, Peter; Krulisova, Veronika; Aušrelé Kučinskiené, Zita; Rehnström, Karola; Traglia, Michela; Nikitina-Zake, Liene; Zimprich, Fritz; Antonarakis, Stylianos E; Estivill, Xavier; Glavač, Damjan; Gut, Ivo; Klovins, Janis; Krawczak, Michael; Kučinskas, Vaidutis; Lathrop, Mark; Macek, Milan; Marsal, Sara; Meitinger, Thomas; Melegh, Béla; Limborska, Svetlana; Lubinski, Jan; Paolotie, Aarno; Schreiber, Stefan; Toncheva, Draga; Toniolo, Daniela; Wichmann, H-Erich; Zimprich, Alexander; Metspalu, Mait; Gasparini, Paolo; Metspalu, Andres; D'Adamo, Pio

    2013-01-01

    Population genetic studies on European populations have highlighted Italy as one of genetically most diverse regions. This is possibly due to the country's complex demographic history and large variability in terrain throughout the territory. This is the reason why Italy is enriched for population isolates, Sardinia being the best-known example. As the population isolates have a great potential in disease-causing genetic variants identification, we aimed to genetically characterize a region from northeastern Italy, which is known for isolated communities. Total of 1310 samples, collected from six geographically isolated villages, were genotyped at >145 000 single-nucleotide polymorphism positions. Newly genotyped data were analyzed jointly with the available genome-wide data sets of individuals of European descent, including several population isolates. Despite the linguistic differences and geographical isolation the village populations still show the greatest genetic similarity to other Italian samples. The genetic isolation and small effective population size of the village populations is manifested by higher levels of genomic homozygosity and elevated linkage disequilibrium. These estimates become even more striking when the detected substructure is taken into account. The observed level of genetic isolation in Friuli-Venezia Giulia region is more extreme according to several measures of isolation compared with Sardinians, French Basques and northern Finns, thus proving the status of an isolate. PMID:23249956

  3. Genetic characterization of northeastern Italian population isolates in the context of broader European genetic diversity.

    PubMed

    Esko, Tõnu; Mezzavilla, Massimo; Nelis, Mari; Borel, Christelle; Debniak, Tadeusz; Jakkula, Eveliina; Julia, Antonio; Karachanak, Sena; Khrunin, Andrey; Kisfali, Peter; Krulisova, Veronika; Aušrelé Kučinskiené, Zita; Rehnström, Karola; Traglia, Michela; Nikitina-Zake, Liene; Zimprich, Fritz; Antonarakis, Stylianos E; Estivill, Xavier; Glavač, Damjan; Gut, Ivo; Klovins, Janis; Krawczak, Michael; Kučinskas, Vaidutis; Lathrop, Mark; Macek, Milan; Marsal, Sara; Meitinger, Thomas; Melegh, Béla; Limborska, Svetlana; Lubinski, Jan; Paolotie, Aarno; Schreiber, Stefan; Toncheva, Draga; Toniolo, Daniela; Wichmann, H-Erich; Zimprich, Alexander; Metspalu, Mait; Gasparini, Paolo; Metspalu, Andres; D'Adamo, Pio

    2013-06-01

    Population genetic studies on European populations have highlighted Italy as one of genetically most diverse regions. This is possibly due to the country's complex demographic history and large variability in terrain throughout the territory. This is the reason why Italy is enriched for population isolates, Sardinia being the best-known example. As the population isolates have a great potential in disease-causing genetic variants identification, we aimed to genetically characterize a region from northeastern Italy, which is known for isolated communities. Total of 1310 samples, collected from six geographically isolated villages, were genotyped at >145000 single-nucleotide polymorphism positions. Newly genotyped data were analyzed jointly with the available genome-wide data sets of individuals of European descent, including several population isolates. Despite the linguistic differences and geographical isolation the village populations still show the greatest genetic similarity to other Italian samples. The genetic isolation and small effective population size of the village populations is manifested by higher levels of genomic homozygosity and elevated linkage disequilibrium. These estimates become even more striking when the detected substructure is taken into account. The observed level of genetic isolation in Friuli-Venezia Giulia region is more extreme according to several measures of isolation compared with Sardinians, French Basques and northern Finns, thus proving the status of an isolate. PMID:23249956

  4. Microsatellite analysis of genetic diversity and population structure of Arabian horse populations.

    PubMed

    Khanshour, Anas; Conant, Eleanore; Juras, Rytis; Cothran, Ernest Gus

    2013-01-01

    The Arabian horse ignites imagination throughout the world. Populations of this breed exist in many countries, and recent genetic work has examined the diversity and ancestry of a few of these populations in isolation. Here, we explore 7 different populations of Arabians represented by 682 horses. Three of these are Middle Eastern populations from near the historical origin of the breed, including Syrian, Persian, and Saudi Arabian. The remaining Western populations are found in Europe (the Shagya Arabian and Polish Arabian) and in America (American Arabian). Analysis of genetic structure was carried out using 15 microsatellite loci. Genetic distances, analysis of molecular variance, factorial correspondence analysis, and a Bayesian method were applied. The results consistently show higher level of diversity within the Middle Eastern populations than the Western populations. The Western Arabian populations were the main source among population variation. Genetic differentiation was not strong among all Middle Eastern populations, but all American Arabians showed differentiation from Middle Eastern populations and were somewhat uniform among themselves. Here, we explore the diversities of many different populations of Arabian horses and find that populations not from the Middle East have noticeably lower levels of diversity, which may adversely affect the health of these populations. PMID:23450090

  5. Mortality Rates in a Genetically Heterogeneous Population of Caenorhabditis elegans

    NASA Astrophysics Data System (ADS)

    Brooks, Anne; Lithgow, Gordon J.; Johnson, Thomas E.

    1994-02-01

    Age-specific mortality rates in isogenic populations of the nematode Caenorhabditis elegans increase exponentially throughout life. In genetically heterogeneous populations, age-specific mortality increases exponentially until about 17 days and then remains constant until the last death occurs at about 60 days. This period of constant age-specific mortality results from genetic heterogeneity. Subpopulations differ in mean life-span, but they all exhibit near exponential, albeit different, rates of increase in age-specific mortality. Thus, much of the observed heterogeneity in mortality rates later in life could result from genetic heterogeneity and not from an inherent effect of aging.

  6. 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

  7. Evolutionary genetics in wild primates: combining genetic approaches with field studies of natural populations

    PubMed Central

    Tung, Jenny; Alberts, Susan C; Wray, Gregory A

    2010-01-01

    Ecological and evolutionary studies of wild primates hold important keys to understanding both the shared characteristics of primate biology and the genetic and phenotypic differences that make specific lineages, including our own, unique. Although complementary genetic research on nonhuman primates has long been of interest, recent technological and methodological advances now enable functional and population genetic studies in an unprecedented manner. In the past several years, novel genetic data sets have revealed new information about the demographic history of primate populations and the genetics of adaptively important traits. In combination with the rich history of behavioral, ecological, and physiological work on natural primate populations, genetic approaches promise to provide a compelling picture of primate evolution in the past and in the present day. PMID:20580115

  8. Alphaviruses: Population genetics and determinants of emergence

    PubMed Central

    Weaver, Scott C.; Winegar, Richard; Manger, Ian D.; Forrester, Naomi L.

    2013-01-01

    Alphaviruses are responsible for several medically important emerging diseases and are also significant veterinary pathogens. Due to the aerosol infectivity of some alphaviruses and their ability to cause severe, sometimes fatal neurologic diseases, they are also of biodefense importance. This review discusses the ecology, epidemiology and molecular virology of the alphaviruses, then focuses on three of the most important members of the genus: Venezuelan and eastern equine encephalitis and chikungunya viruses, with emphasis on their genetics and emergence mechanisms, and how current knowledge as well as gaps influence our ability to detect and determine the source of both natural outbreaks and potential use for bioterrorism. This article is one of a series in Antiviral Research on the genetic diversity of emerging viruses. PMID:22522323

  9. Genetic variation in natural honeybee populations, Apis mellifera capensis

    NASA Astrophysics Data System (ADS)

    Hepburn, Randall; Neumann, Peter; Radloff, Sarah E.

    2004-09-01

    Genetic variation in honeybee, Apis mellifera, populations can be considerably influenced by breeding and commercial introductions, especially in areas with abundant beekeeping. However, in southern Africa apiculture is based on the capture of wild swarms, and queen rearing is virtually absent. Moreover, the introduction of European subspecies constantly failed in the Cape region. We therefore hypothesize a low human impact on genetic variation in populations of Cape honeybees, Apis mellifera capensis. A novel solution to studying genetic variation in honeybee populations based on thelytokous worker reproduction is applied to test this hypothesis. Environmental effects on metrical morphological characters of the phenotype are separated to obtain a genetic residual component. The genetic residuals are then re-calculated as coefficients of genetic variation. Characters measured included hair length on the abdomen, width and length of wax plate, and three wing angles. The data show for the first time that genetic variation in Cape honeybee populations is independent of beekeeping density and probably reflects naturally occurring processes such as gene flow due to topographic and climatic variation on a microscale.

  10. Genetic relationships of the Portuguese Lidia bovine populations

    PubMed Central

    Correia, P; Baron, E; da Silva, J. M; Cortés, O

    2014-01-01

    To clarify the genetic relationships among the Lidia breed lineages and two main Portuguese Lidia bovine populations, Casta Portuguesa and Brava dos Açores, 24 autosomal microsatellites were analyzed in 120 samples. Brava dos Açores showed the highest observed and expected heterozygosity (0.73 and 0.70, respectively) while Casta Portuguesa showed the lowest observed and expected heterozygosity (0.51 and 0.50, respectively). The results of this study were compared with the previous microsatellites data from the main Lidia bovine lineages. Casta Portuguesa was the most genetically isolated Lidia bovine population as revealed by the average FST genetic distance value with respect to the other lineages (32%). All the populations of Portuguese Lidia had negative FIS values. The Neighbour-joining dendrogram grouped Casta Portuguesa in the same branch with Miura, which was supported by the STRUCTURE software. The results evidenced low levels of genetic diversity and high levels of genetic differentiation in Casta Portuguesa and high levels of genetic diversity in Brava dos Açores populations, probably due to the crossbreeding of different bovine lineages at origin, and genetic flow among herds. PMID:27175132

  11. Translating Population Difference: The Use and Re-Use of Genetic Ancestry in Brazilian Cancer Genetics

    PubMed Central

    Gibbon, Sahra

    2016-01-01

    ABSTRACT In the past ten years, there has been an expansion of scientific interest in population genetics linked to both understanding histories of human migration and the way that population difference and diversity may account for and/or be implicated in health and disease. In this article, I examine how particular aspects of a globalizing research agenda related to population differences and genetic ancestry are taken up in locally variant ways in the nascent field of Brazilian cancer genetics. Drawing on a broad range of ethnographic data from clinical and nonclinical contexts in the south of Brazil, I examine the ambiguities that attention to genetic ancestry generates, so revealing the disjunctured and diverse ways a global research agenda increasingly orientated to questions of population difference and genetic ancestry is being used and reused. PMID:26452039

  12. Translating Population Difference: The Use and Re-Use of Genetic Ancestry in Brazilian Cancer Genetics.

    PubMed

    Gibbon, Sahra

    2016-01-01

    In the past ten years, there has been an expansion of scientific interest in population genetics linked to both understanding histories of human migration and the way that population difference and diversity may account for and/or be implicated in health and disease. In this article, I examine how particular aspects of a globalizing research agenda related to population differences and genetic ancestry are taken up in locally variant ways in the nascent field of Brazilian cancer genetics. Drawing on a broad range of ethnographic data from clinical and nonclinical contexts in the south of Brazil, I examine the ambiguities that attention to genetic ancestry generates, so revealing the disjunctured and diverse ways a global research agenda increasingly orientated to questions of population difference and genetic ancestry is being used and reused. PMID:26452039

  13. Genetic diversity and population genetics of large lungworms (Dictyocaulus, Nematoda) in wild deer in Hungary.

    PubMed

    Ács, Zoltán; Hayward, Alexander; Sugár, László

    2016-09-01

    Dictyocaulus nematode worms live as parasites in the lower airways of ungulates and can cause significant disease in both wild and farmed hosts. This study represents the first population genetic analysis of large lungworms in wildlife. Specifically, we quantify genetic variation in Dictyocaulus lungworms from wild deer (red deer, fallow deer and roe deer) in Hungary, based on mitochondrial cytochrome c oxidase subunit 1 (cox1) sequence data, using population genetic and phylogenetic analyses. The studied Dictyocaulus taxa display considerable genetic diversity. At least one cryptic species and a new parasite-host relationship are revealed by our molecular study. Population genetic analyses for Dictyocaulus eckerti revealed high gene flow amongst weakly structured spatial populations that utilise the three host deer species considered here. Our results suggest that D. eckerti is a widespread generalist parasite in ungulates, with a diverse genetic backround and high evolutionary potential. In contrast, evidence of cryptic genetic structure at regional geographic scales was observed for Dictyocaulus capreolus, which infects just one host species, suggesting it is a specialist within the studied area. D. capreolus displayed lower genetic diversity overall, with only moderate gene flow compared to the closely related D. eckerti. We suggest that the differing vagility and dispersal behaviour of hosts are important contributing factors to the population structure of lungworms, and possibly other nematode parasites with single-host life cycles. Our findings are of relevance for the management of lungworms in deer farms and wild deer populations. PMID:27150969

  14. Genetic diversity within and between natural populations of Rattus norvegicus.

    PubMed

    Cramer, D V; Chakravarti, A; Arenas, O; Humprieres, J; Mowery, P A

    1988-01-01

    The levels of gene diversity for 17 polymorphic loci in natural populations of wild rats were examined for three separate locations in North and South America. The level of gene diversity in the total sample for the RT1.A locus, the dominant class I histocompatibility locus in the major histocompatibility (RT1) complex of the rat, was 0.807. The degree of gene diversity for nonalloantigenic loci scattered throughout the rat genome was 0.215, a level comparable to, if not slightly higher than, that for other mammalian species. The large and consistent levels of diversity for individuals within each population suggest that significant deviations from random mating have occurred within each group. Conclusions from analyzing genetic distance and the index of genetic differentiation between the three populations are consistent with these populations' geographic isolation and small effective population size. Assuming that the separation of the North and South American groups has existed for approximately 300 years, the effective size of these populations is estimated to be approximately 1,500 individuals. Apparent differences in the distribution of the number and frequency of alleles in the major histocompatibility complexes of mice and rats and the level of genetic differentiation among separate rat populations may be due to the effects of genetic drift in small populations. PMID:3183358

  15. Population genetics of Thamnaconus hypargyreus (Tetraodontiformes: Monacanthidae) in the South China Sea.

    PubMed

    Li, Yufang; Chen, Guobao; Yu, Jie; Wu, Shuiqing; Xiong, Dan; Li, Xia; Cui, Ke; Li, Yongzhen

    2016-01-01

    Knowledge of population structure is particularly important for long-term fisheries management and conservation. Lesser-spotted leatherjacket Thamnaconus hypargyreus is an economically important fish species in the South China Sea. Fish specimens (totally 158 individuals) used in this study were collected from five geographical locations in the north of the South China Sea and the southwestern Nansha Islands. The results were as follows: a total of 636 nucleotides of the mitochondrial DNA (mtDNA) control region (CR) of T. hypargyreus were amplified by polymerase chain reaction (PCR) technology. Both 103 mutations of nucleotide acids without inserting or deleting one and 91 haplotypes were found among the examined CR fragment. High haplotype diversity (0.9419 ± 0.0151) and nucleotide diversity (0.0095 ± 0.00506) relatively together with a recent and sudden population expansion which characterizes the genetic population structure of this species. Analysis of molecular variance (AMOVA) and the fixation indices (Fst) of five groups showed that the genetic variance mainly came from individuals within groups, and there was no genetic differentiation between groups. The phylogenetic trees including maximum likelihood (ML) and Bayesian inference (BI) proved no phylogeographic differentiation structure in five groups. The mtDNA marker suggested the five groups should be genetic homogeneity, which implied T. hypargyreus in the north and southwest continental shelf of the South China Sea belongs to one population. PMID:24865897

  16. Population genetic structure of traditional populations in the Peruvian Central Andes and implications for South American population history.

    PubMed

    Cabana, Graciela S; Lewis, Cecil M; Tito, Raúl Y; Covey, R Alan; Cáceres, Angela M; Cruz, Augusto F De La; Durand, Diana; Housman, Genevieve; Hulsey, Brannon I; Iannacone, Gian Carlo; López, Paul W; Martínez, Rolando; Medina, Ángel; Dávila, Olimpio Ortega; Pinto, Karla Paloma Osorio; Santillán, Susan I Polo; Domínguez, Percy Rojas; Rubel, Meagan; Smith, Heather F; Smith, Silvia E; Massa, Verónica Rubín de Celis; Lizárraga, Beatriz; Stone, Anne C

    2014-01-01

    Molecular-based characterizations of Andean peoples are traditionally conducted in the service of elucidating continent-level evolutionary processes in South America. Consequently, genetic variation among "western" Andean populations is often represented in relation to variation among "eastern" Amazon and Orinoco River Basin populations. This west-east contrast in patterns of population genetic variation is typically attributed to large-scale phenomena, such as dual founder colonization events or differing long-term microevolutionary histories. However, alternative explanations that consider the nature and causes of population genetic diversity within the Andean region remain underexplored. Here we examine population genetic diversity in the Peruvian Central Andes using data from the mtDNA first hypervariable region and Y-chromosome short tandem repeats among 17 newly sampled populations and 15 published samples. Using this geographically comprehensive data set, we first reassessed the currently accepted pattern of western versus eastern population genetic structure, which our results ultimately reject: mtDNA population diversities were lower, rather than higher, within Andean versus eastern populations, and only highland Y-chromosomes exhibited significantly higher within-population diversities compared with eastern groups. Multiple populations, including several highland samples, exhibited low genetic diversities for both genetic systems. Second, we explored whether the implementation of Inca state and Spanish colonial policies starting at about ad 1400 could have substantially restructured population genetic variation and consequently constitute a primary explanation for the extant pattern of population diversity in the Peruvian Central Andes. Our results suggest that Peruvian Central Andean population structure cannot be parsimoniously explained as the sole outcome of combined Inca and Spanish policies on the region's population demography: highland populations

  17. Wilhelm Ludwig and his contributions to population genetics.

    PubMed

    Antonovics, J

    1990-03-01

    This article reviews the life and work of the German biologist Wilhelm Ludwig (1901-1959), whose contributions to population genetics have been largely ignored. Ludwig's work was a rich tapestry of population biology, spanning investigations into population growth, biological asymmetries, sex ratio, and paternity analysis. He was ahead of his time in explicitly combining the theory of population ecology and population genetics. His classic paper on annidation showed the possibility of population differentiation in the face of gene flow, and his early studies demonstrated the importance of selection in evolutionary change. Much of his work spanned the period of the Second World War in Germany, and interesting questions remain about his life during this turbulent period. PMID:21232329

  18. Matching Strategies for Genetic Association Studies in Structured Populations

    PubMed Central

    Hinds, David A.; Stokowski, Renee P.; Patil, Nila; Konvicka, Karel; Kershenobich, David; Cox, David R.; Ballinger, Dennis G.

    2004-01-01

    Association studies in populations that are genetically heterogeneous can yield large numbers of spurious associations if population subgroups are unequally represented among cases and controls. This problem is particularly acute for studies involving pooled genotyping of very large numbers of single-nucleotide–polymorphism (SNP) markers, because most methods for analysis of association in structured populations require individual genotyping data. In this study, we present several strategies for matching case and control pools to have similar genetic compositions, based on ancestry information inferred from genotype data for ∼300 SNPs tiled on an oligonucleotide-based genotyping array. We also discuss methods for measuring the impact of population stratification on an association study. Results for an admixed population and a phenotype strongly confounded with ancestry show that these simple matching strategies can effectively mitigate the impact of population stratification. PMID:14740319

  19. Some Consequences of Demographic Stochasticity in Population Genetics

    PubMed Central

    Parsons, Todd L.; Quince, Christopher; Plotkin, Joshua B.

    2010-01-01

    Much of population genetics is based on the diffusion limit of the Wright–Fisher model, which assumes a fixed population size. This assumption is violated in most natural populations, particularly for microbes. Here we study a more realistic model that decouples birth and death events and allows for a stochastically varying population size. Under this model, classical quantities such as the probability of and time before fixation of a mutant allele can differ dramatically from their Wright–Fisher expectations. Moreover, inferences about natural selection based on Wright–Fisher assumptions can yield erroneous and even contradictory conclusions: at small population densities one allele will appear superior, whereas at large densities the other allele will dominate. Consequently, competition assays in laboratory conditions may not reflect the outcome of long-term evolution in the field. These results highlight the importance of incorporating demographic stochasticity into basic models of population genetics. PMID:20457879

  20. Molecular Population Genetic Structure in the Piping Plover

    USGS Publications Warehouse

    Miller, Mark P.; Haig, Susan M.; Gratto-Trevor, Cheri L.; Mullins, Thomas D.

    2009-01-01

    The Piping Plover (Charadrius melodus) is a migratory shorebird currently listed as Endangered in Canada and the U.S. Great Lakes, and threatened throughout the remainder of its U.S. breeding and winter range. In this study, we undertook the first comprehensive molecular genetic-based investigation of Piping Plovers. Our primary goals were to (1) address higher level subspecific taxonomic issues, (2) characterize population genetic structure, and (3) make inferences regarding past bottlenecks or population expansions that have occurred within this species. Our analyses included samples of individuals from 23 U.S. States and Canadian Provinces, and were based on mitochondrial DNA sequences (580 bp, n = 245 individuals) and eight nuclear microsatellite loci (n = 229 individuals). Our findings illustrate strong support for separate Atlantic and Interior Piping Plover subspecies (C. m. melodus and C. m. circumcinctus, respectively). Birds from the Great Lakes region were allied with the Interior subspecies group and should be taxonomically referred to as C. m. circumcinctus. Population genetic analyses suggested that genetic structure was stronger among Atlantic birds relative to the Interior group. This pattern indicates that natal and breeding site fidelity may be reduced among Interior birds. Furthermore, analyses suggested that Interior birds have previously experienced genetic bottlenecks, whereas no evidence for such patterns existed among the Atlantic subspecies. Likewise, genetic analyses indicated that the Great Lakes region has experienced a population expansion. This finding may be interpreted as population growth following a previous bottleneck event. No genetic evidence for population expansions was found for Atlantic, Prairie Canada, or U.S. Northern Great Plains individuals. We interpret our population history insights in light of 25 years of Piping Plover census data. Overall, differences observed between Interior and Atlantic birds may reflect

  1. Lack of population genetic differentiation of a marine ovoviviparous fish Sebastes schlegelii in Northwestern Pacific.

    PubMed

    Zhang, Hui; Yanagimoto, Takashi; Zhang, Xiumei; Song, Na; Gao, Tianxiang

    2016-05-01

    Sebastes schlegelii is one of the fishes that aggregate around drifting seaweed during early development. To examine the population genetic structure of S. schlegelii, a 452-bp fragment of the mtDNA control region was sequenced and used to interpret life history characteristics and larval dispersal strategy. Two-hundred and twenty-one individuals from 13 sites across the entire range of S. schlegelii in China, Japan and Korea were analyzed. A neighbor-joining tree and network showed that there were no significant genealogical structures corresponding to sampling locations. AMOVA, pair-wise FST and exact test revealed no significant genetic differentiation among locations. The migration rate among locations was high based on the result of LAMARC. We conclude that larval dispersal with drifting seaweed and the current environmental factors may play an important role in shaping the contemporary phylogeographic pattern and genetic homogeneity of S. schlegelii. PMID:25269000

  2. Genetics in geographically structured populations: defining, estimating and interpreting FST

    PubMed Central

    Holsinger, Kent E.; Weir, Bruce S.

    2015-01-01

    Wright’s F-statistics, and especially FST, provide important insights into the evolutionary processes that influence the structure of genetic variation within and among populations, and they are among the most widely used descriptive statistics in population and evolutionary genetics. Estimates of FST can identify regions of the genome that have been the target of selection, and comparisons of FST from different parts of the genome can provide insights into the demographic history of populations. For these reasons and others, FST has a central role in population and evolutionary genetics and has wide applications in fields that range from disease association mapping to forensic science. This Review clarifies how FST is defined, how it should be estimated, how it is related to similar statistics and how estimates of FST should be interpreted. PMID:19687804

  3. Medical Genetics and the First Studies of the Genetics of Populations in Mexico.

    PubMed

    Barahona, Ana

    2016-09-01

    Following World War II (WWII), there was a new emphasis within genetics on studying the genetic composition of populations. This probably had a dual source in the growing strength of evolutionary biology and the new international interest in understanding the effects of radiation on human populations, following the atomic bombings in Japan. These global concerns were shared by Mexican physicians. Indeed, Mexico was one of the leading centers of this trend in human genetics. Three leading players in this story were Mario Salazar Mallén, Adolfo Karl, and Rubén Lisker. Their trajectories and the international networks in human genetics that were established after WWII, paved the way for the establishment of medical and population genetics in Mexico. Salazar Mallén's studies on the distribution and characterization of ABO blood groups in indigenous populations were the starting point while Karl's studies on the distribution of abnormal hemoglobin in Mexican indigenous populations showed the relationships observed in other laboratories at the time. It was Lisker's studies, however, that were instrumental in the development of population genetics in the context of national public policies for extending health care services to the Mexican population. In particular, he conducted studies on Mexican indigenous groups contributing to the knowledge of the biological diversity of human populations according to international trends that focused on the variability of human populations in terms of genetic frequencies. From the start, however, Lisker was as committed to the reconstruction of shared languages and practices as he was to building networks of collaboration in order to guarantee the necessary groundwork for establishing the study of the genetics of human populations in Mexico. This study also allows us to place Mexican science within a global context in which connected narratives describe the interplay between global trends and national contexts. PMID:27601615

  4. Population screening for genetic susceptibility to disease.

    PubMed Central

    Clarke, A.

    1995-01-01

    Genetic screening for susceptibility to common diseases, such as the common cancers, cardiovascular disease, and diabetes, may soon be technically feasible. Commercial interests should not be allowed to introduce such screening before proper evaluation or without adequate counselling and support. The evaluation of such testing should include psychosocial and medical outcomes and outcomes for those given low risks as well as high risks. These tests may distract attention away from environmental factors contributing to disease, for which social and political measures may be more appropriate than individualised susceptibility screening and lifestyle modification. PMID:7613325

  5. Genetic analysis in the Collaborative Cross breeding population

    SciTech Connect

    Philip, Vivek; Sokoloff, Greta; Ackert-Bicknell, Cheryl; Striz, Martin; Branstetter, Lisa R; Beckmann, Melissa; Spence, Jason S; Jackson, Barbara L; Galloway, Leslie D; Barker, Gene; Wymore, Ann M; Hunsicker, Patricia R; Durtschi, David W; Shaw, Ginger S; Shinpock, Sarah G; Manly, Kenneth F; Miller, Darla R; Donahue, Kevin; Culiat, Cymbeline T; Churchill, Gary A; Lariviere, William R; Palmer, Abraham; O'Hara, Bruce; Voy, Brynn H; Chesler, Elissa J

    2011-01-01

    Genetic reference populations in model organisms are critical resources for systems genetic analysis of disease related phenotypes. The breeding history of these inbred panels may influence detectable allelic and phenotypic diversity. The existing panel of common inbred strains reflects historical selection biases, and existing recombinant inbred panels have low allelic diversity. All such populations may be subject to consequences of inbreeding depression. The Collaborative Cross (CC) is a mouse reference population with high allelic diversity that is being constructed using a randomized breeding design that systematically outcrosses eight founder strains, followed by inbreeding to obtain new recombinant inbred strains. Five of the eight founders are common laboratory strains, and three are wild-derived. Since its inception, the partially inbred CC has been characterized for physiological, morphological, and behavioral traits. The construction of this population provided a unique opportunity to observe phenotypic variation as new allelic combinations arose through intercrossing and inbreeding to create new stable genetic combinations. Processes including inbreeding depression and its impact on allelic and phenotypic diversity were assessed. Phenotypic variation in the CC breeding population exceeds that of existing mouse genetic reference populations due to both high founder genetic diversity and novel epistatic combinations. However, some focal evidence of allele purging was detected including a suggestive QTL for litter size in a location of changing allele frequency. Despite these inescapable pressures, high diversity and precision for genetic mapping remain. These results demonstrate the potential of the CC population once completed and highlight implications for development of related populations. Supplementary material consists of Supplementary Table 1 Phenotypic means, variances, ranges and heritabilities for all traits and generations, Supplementary Table

  6. Disease and freeways drive genetic change in urban bobcat populations

    PubMed Central

    Serieys, Laurel E K; Lea, Amanda; Pollinger, John P; Riley, Seth P D; Wayne, Robert K

    2015-01-01

    Urbanization profoundly impacts animal populations by causing isolation, increased susceptibility to disease, and exposure to toxicants. Genetic effects include reduced effective population size, increased population substructure, and decreased adaptive potential. We investigated the influence that urbanization and a disease epizootic had on the population genetics of bobcats (Lynx rufus) distributed across a highly fragmented urban landscape. We genotyped more than 300 bobcats, sampled from 1996 to 2012, for variation at nine neutral and seven immune gene-linked microsatellite loci. We found that two freeways are significant barriers to gene flow. Further, a 3-year disease epizootic, associated with secondary anticoagulant rodenticide exposure, caused a population bottleneck that led to significant genetic differentiation between pre- and post-disease populations that was greater than that between populations separated by major freeways for >60 years. However, balancing selection acted on immune-linked loci during the epizootic, maintaining variation at functional regions. Conservation assessments need to assay loci that are potentially under selection to better preserve the adaptive potential of populations at the urban–wildland interface. Further, interconnected regions that contain appropriate habitat for wildlife will be critical to the long-term viability of animal populations in urban landscapes. PMID:25667604

  7. Disease and freeways drive genetic change in urban bobcat populations.

    PubMed

    Serieys, Laurel E K; Lea, Amanda; Pollinger, John P; Riley, Seth P D; Wayne, Robert K

    2015-01-01

    Urbanization profoundly impacts animal populations by causing isolation, increased susceptibility to disease, and exposure to toxicants. Genetic effects include reduced effective population size, increased population substructure, and decreased adaptive potential. We investigated the influence that urbanization and a disease epizootic had on the population genetics of bobcats (Lynx rufus) distributed across a highly fragmented urban landscape. We genotyped more than 300 bobcats, sampled from 1996 to 2012, for variation at nine neutral and seven immune gene-linked microsatellite loci. We found that two freeways are significant barriers to gene flow. Further, a 3-year disease epizootic, associated with secondary anticoagulant rodenticide exposure, caused a population bottleneck that led to significant genetic differentiation between pre- and post-disease populations that was greater than that between populations separated by major freeways for >60 years. However, balancing selection acted on immune-linked loci during the epizootic, maintaining variation at functional regions. Conservation assessments need to assay loci that are potentially under selection to better preserve the adaptive potential of populations at the urban-wildland interface. Further, interconnected regions that contain appropriate habitat for wildlife will be critical to the long-term viability of animal populations in urban landscapes. PMID:25667604

  8. Iberia: population genetics, anthropology, and linguistics.

    PubMed

    Arnaiz-Villena, A; Martínez-Laso, J; Alonso-García, J

    1999-10-01

    Basques, Portuguese, Spaniards, and Algerians have been studied for HLA and mitochondrial DNA markers, and the data analysis suggests that pre-Neolithic gene flow into Iberia came from ancient white North Africans (Hamites). The Basque language has also been used to translate the Iberian-Tartesian language and also Etruscan and Minoan Linear A. Physical anthropometry of Iberian Mesolithic and Neolithic skeletons does not support the demic replacement in Iberia of preexisting Mesolithic people by Neolithic people bearing new farming technologies from Europe and the Middle East. Also, the presence of cardial impressed pottery in western Mediterranean Europe and across the Maghreb (North Africa) coasts at the beginning of the Neolithic provides good evidence of pre-Neolithic circum-Mediterranean contacts by sea. In addition, pre-dynastic Egyptian El-Badari culture (4,500 years ago) is similar to southern Iberian Neolithic settlements with regard to pottery and animal domestication. Taking the genetic, linguistic, anthropological, and archeological evidence together with the documented Saharan area desiccation starting about 10,000 years ago, we believe that it is possible that a genetic and cultural pre-Neolithic flow coming from southern Mediterranean coasts existed toward northern Mediterranean areas, including at least Iberia and some Mediterranean islands. This model would substitute for the demic diffusion model put forward to explain Neolithic innovations in Western Europe. PMID:10510567

  9. Genetic Diversity and Population Structure of Teosinte

    PubMed Central

    Fukunaga, Kenji; Hill, Jason; Vigouroux, Yves; Matsuoka, Yoshihiro; Sanchez G., Jesus; Liu, Kejun; Buckler, Edward S.; Doebley, John

    2005-01-01

    The teosintes, the closest wild relatives of maize, are important resources for the study of maize genetics and evolution and for plant breeding. We genotyped 237 individual teosinte plants for 93 microsatellites. Phylogenetic relationships among species and subspecific taxa were largely consistent with prior analyses for other types of molecular markers. Plants of all species formed monophyletic clades, although relationships among species were not fully resolved. Phylogenetic analysis indicated that the Mexican annual teosintes divide into two clusters that largely correspond to the previously defined subspecies, Z. mays ssp. parviglumis and ssp. mexicana, although there are a few samples that represent either evolutionary intermediates or hybrids between these two subspecies. The Mexican annual teosintes show genetic substructuring along geographic lines. Hybridization or introgression between some teosintes and maize occurs at a low level and appears most common with Z. mays ssp. mexicana. Phylogeographic and phylogenetic analyses of the Mexican annual teosintes indicated that ssp. parviglumis diversified in the eastern part of its distribution and spread from east to west and that ssp. mexicana diversified in the Central Plateau of Mexico and spread along multiple paths to the north and east. We defined core sets of collections of Z. mays ssp. mexicana and ssp. parviglumis that attempt to capture the maximum number of microsatellite alleles for given sample sizes. PMID:15687282

  10. GENETIC CHARACTERIZATION OF AN ALGERIAN POPULATION OF MYCOSPHAERELLA GRAMINICOLA WITH MICROSATELLITE MARKERS.

    PubMed

    Allioui, N; Siah, A; Randoux, B; Brinis, L; Reignault, Ph; Halama, P

    2015-01-01

    Mycosphaerella graminicola (anamorph: Zymoseptoria tritici, formerly Septoria tritici), the responsible for Septoria tritici blotch, is the most frequently occurring disease on wheat crops worldwide. The populations of this pathogen were previously characterized in several areas around the world, but not in Algeria so far. The present study aims thus at investigating the genetic diversity and population structure of M. graminicola in this country. One hundred and twenty monoconidial isolates of this fungus (60 from bread wheat and 60 from durum wheat) were collected during the 2012 growing season from five distinct geographical locations in Algeria. They were then fingerprinted using eight microsatellite markers. The number of alleles per locus ranged from 2 to 11, with an average of 6.25 alleles per locus. We found out a moderate gene diversity, a high genotype diversity (72% of unique haplotypes) and a low population differentiation within the population. Further analyses using both UPGMA and Bayesian clustering methods confirmed the lack of genetic structuration irrespective of geographical locations and host species. These findings are likely due to the frequent occurrence of sexual reproduction in the field, leading to genetic diversification and allele homogenization via wind born ascospores within the population. PMID:27141757

  11. Genetic Structure in Dwarf Bamboo (Bashania fangiana) Clonal Populations with Different Genet Ages

    PubMed Central

    Ma, Qing-qing; Song, Hui-xing; Zhou, Shi-qiang; Yang, Wan-qin; Li, De-sheng; Chen, Jin-song

    2013-01-01

    Amplified fragment length polymorphism (AFLP) fingerprints were used to reveal genotypic diversity of dwarf bamboo (Bashania fangiana) clonal populations with two different genet ages (≤30 years versus >70 years) at Wolong National Natural Reserve, Sichuan province, China. We generated AFLP fingerprints for 96 leaf samples, collected at 30 m intervals in the two populations, using ten selective primer pairs. A total of 92 genotypes were identified from the both populations. The mean proportion of distinguishable genotypes (G/N) was 0.9583 (0.9375 to 0.9792) and Simpson's index of diversity (D) was 0.9982 (0.9973 to 0.9991). So, two B. fangiana populations were multiclonal and highly diverse. The largest single clone may occur over a distance of about 30 m. Our results demonstrated that the genotypic diversity and genet density of B. fangiana clonal population did not change significantly (47 versus 45) with genet aging and low partitioned genetic differentiation was between the two populations (Gst = 0.0571). The analysis of molecular variance consistently showed that a large proportion of the genetic variation (87.79%) existed among the individuals within populations, whereas only 12.21% were found among populations. In addition, the high level of genotypic diversity in the two populations implies that the further works were needed to investigate the reasons for the poor seed set in B. fangiana after flowering. PMID:24244360

  12. Population status and population genetics of northern leopard frogs in Arizona

    USGS Publications Warehouse

    Theimer, Tad C.; Drost, Charles A.; O'Donnell, Ryan P.; Mock, Karen E.

    2011-01-01

    Increasing isolation of populations by habitat fragmentation threatens the persistence of many species, both from stochastic loss of small isolated populations, and from inbreeding effects in populations that have become genetically isolated. In the southwestern United States, amphibian habitat is naturally patchy in occurrence because of the prevailing aridity of the region. Streams, rivers, and other wetlands are important both as habitat and as corridors that connect populations. However, populations of some species have become more fragmented and isolated by habitat degradation and loss. Northern leopard frogs (Rana pipiens) have experienced serious declines in the Southwest. We conducted an extensive survey across the known range of northern leopard frogs in Arizona to determine the current distribution and abundance of the species. From a range that once spanned much of the northern and central part of the State, northern leopard frogs have been reduced to three or four widely separated populations, near Lyman Lake in east-central Arizona, in the Stoneman Lake area south of Flagstaff, along Truxton Wash near Peach Springs, and a population of uncertain extent on Navajo Nation lands. The Lyman Lake and Truxton Wash populations are small and extremely isolated. The Stoneman Lake population, however, is an extensive metapopulation spread across several stream drainages, including numerous ponds, wetlands, and artificial tanks. This is the only population in Arizona that is increasing in extent and numbers, but there is concern about the apparent introduction of nonnative genetic stock from eastern North America into this area. We analyzed genetic diversity within and genetic divergence among populations of northern leopard frogs, across both extant and recently extirpated populations in Arizona. We also analyzed mitochondrial DNA to place these populations into a larger phylogenetic framework and to determine whether any populations contained genetic material

  13. Population genetic structure and connectivity of the harmful dinoflagellate Alexandrium minutum in the Mediterranean Sea

    PubMed Central

    Casabianca, Silvia; Penna, Antonella; Pecchioli, Elena; Jordi, Antoni; Basterretxea, Gotzon; Vernesi, Cristiano

    2012-01-01

    The toxin-producing microbial species Alexandrium minutum has a wide distribution in the Mediterranean Sea and causes high biomass blooms with consequences on the environment, human health and coastal-related economic activities. Comprehension of algal genetic differences and associated connectivity is fundamental to understand the geographical scale of adaptation and dispersal pathways of harmful microalgal species. In the present study, we combine A. minutum population genetic analyses based on microsatellites with indirect connectivity (Ci) estimations derived from a general circulation model of the Mediterranean sea. Our results show that four major clusters of genetically homogeneous groups can be identified, loosely corresponding to four regional seas: Adriatic, Ionian, Tyrrhenian and Catalan. Each of the four clusters included a small fraction of mixed and allochthonous genotypes from other Mediterranean areas, but the assignment to one of the four clusters was sufficiently robust as proved by the high ancestry coefficient values displayed by most of the individuals (>84%). The population structure of A. minutum on this scale can be explained by microalgal dispersion following the main regional circulation patterns over successive generations. We hypothesize that limited connectivity among the A. minutum populations results in low gene flow but not in the erosion of variability within the population, as indicated by the high gene diversity values. This study represents a first and new integrated approach, combining both genetic and numerical methods, to characterize and interpret the population structure of a toxic microalgal species. This approach of characterizing genetic population structure and connectivity at a regional scale holds promise for the control and management of the harmful algal bloom events in the Mediterranean Sea. PMID:21593032

  14. Population genetic structure and connectivity of the harmful dinoflagellate Alexandrium minutum in the Mediterranean Sea.

    PubMed

    Casabianca, Silvia; Penna, Antonella; Pecchioli, Elena; Jordi, Antoni; Basterretxea, Gotzon; Vernesi, Cristiano

    2012-01-01

    The toxin-producing microbial species Alexandrium minutum has a wide distribution in the Mediterranean Sea and causes high biomass blooms with consequences on the environment, human health and coastal-related economic activities. Comprehension of algal genetic differences and associated connectivity is fundamental to understand the geographical scale of adaptation and dispersal pathways of harmful microalgal species. In the present study, we combine A. minutum population genetic analyses based on microsatellites with indirect connectivity (C(i)) estimations derived from a general circulation model of the Mediterranean sea. Our results show that four major clusters of genetically homogeneous groups can be identified, loosely corresponding to four regional seas: Adriatic, Ionian, Tyrrhenian and Catalan. Each of the four clusters included a small fraction of mixed and allochthonous genotypes from other Mediterranean areas, but the assignment to one of the four clusters was sufficiently robust as proved by the high ancestry coefficient values displayed by most of the individuals (>84%). The population structure of A. minutum on this scale can be explained by microalgal dispersion following the main regional circulation patterns over successive generations. We hypothesize that limited connectivity among the A. minutum populations results in low gene flow but not in the erosion of variability within the population, as indicated by the high gene diversity values. This study represents a first and new integrated approach, combining both genetic and numerical methods, to characterize and interpret the population structure of a toxic microalgal species. This approach of characterizing genetic population structure and connectivity at a regional scale holds promise for the control and management of the harmful algal bloom events in the Mediterranean Sea. PMID:21593032

  15. Genetic diversity and conservation in a small endangered horse population.

    PubMed

    Janova, Eva; Futas, Jan; Klumplerova, Marie; Putnova, Lenka; Vrtkova, Irena; Vyskocil, Mirko; Frolkova, Petra; Horin, Petr

    2013-08-01

    The Old Kladruber horses arose in the 17th century as a breed used for ceremonial purposes. Currently, grey and black coat colour varieties exist as two sub-populations with different recent breeding history. As the population underwent historical bottlenecks and intensive inbreeding, loss of genetic variation is considered as the major threat. Therefore, genetic diversity in neutral and non-neutral molecular markers was examined in the current nucleus population. Fifty microsatellites, 13 single nucleotide polymorphisms (SNPs) in immunity-related genes, three mutations in coat colour genes and one major histocompatibility (MHC-DRA) gene were studied for assessing genetic diversity after 15 years of conservation. The results were compared to values obtained in a similar study 13 years ago. The extent of genetic diversity of the current population was comparable to other breeds, despite its small size and isolation. The comparison between 1997 and 2010 did not show differences in the extent of genetic diversity and no loss of allele richness and/or heterozygosity was observed. Genetic differences identified between the black and grey sub-populations observed 13 years ago persisted. Deviations from the Hardy-Weinberg equilibrium found in 19 microsatellite loci and in five SNP loci are probably due to selective breeding. No differences between neutral and immunity-related markers were found. No changes in the frequencies of markers associated with two diseases, melanoma and insect bite hypersensitivity, were observed, due probably to the short interval of time between comparisons. It, thus, seems that, despite its small size, previous bottlenecks and inbreeding, the molecular variation of Old Kladruber horses is comparable to other horse breeds and that the current breeding policy does not compromise genetic variation of this endangered population. PMID:23649723

  16. Genetic structure and phylogeography of European catfish (Silurus glanis) populations.

    PubMed

    Triantafyllidis, A; Krieg, F; Cottin, C; Abatzopoulos, T J; Triantaphyllidis, C; Guyomard, R

    2002-06-01

    The genetic structure of Silurus glanis (Europe's largest freshwater fish species) across most of its natural distribution was investigated using 10 microsatellite loci. The revealed levels of genetic diversity were much higher than previous allozyme and restriction fragment length polymorphism mitochondrial DNA analyses had shown; relative levels of variability among populations were however, in good agreement with the previous studies. Populations from large basins (Volga and Danube rivers) were the most polymorphic, while samples from the smaller Greek rivers, which are more prone to genetic bottleneck, exhibited the lowest levels of genetic diversity. Microsatellite multilocus genotyping permitted the assignment of individual fish to their population of origin with a score as high as 98.3%. Despite the great genetic differentiation of S. glanis populations, no consistent pattern of geographical structuring was revealed, in contrast to previous studies of European freshwater fish species. A model of isolation by distance seems more probable and a hypothesis of recent dispersion from only one glacial refugium is proposed. The discovery of the highest levels of microsatellite and mitochondrial diversity in the Volga sample and the presence of river connections, during the Pleistocene, between this area and all major areas of the present catfish distribution, place this refugium around the Ponto-Caspian region. Combining these data with those from previous studies, a number of markers are now available to monitor wild and hatchery populations even at the individual level. PMID:12030981

  17. Genetic structure of a lotic population of Burkholderia (Pseudomonas) cepacia

    SciTech Connect

    Wise, M.G.; Shimkets, L.J.; McArthur, J.V.

    1995-05-01

    The genetic structure of a population of Burkholderia (Pseudomonas) cepacia isolated from a southeastern blackwater stream was investigated by using multilocus enzyme electrophoresis to examine the allelic variation in eight structural gene loci. Overall, 213 isolates were collected at transect points along the stream continuum, from both the sediments along the bank and the water column. Multilocus enzyme electrophoresis analysis revealed 164 distinct electrophoretic types, and the mean genetic diversity of the entire population was 0.574. Genetic diversity values did not vary spatially along the stream continuum. From a canonical discriminant analysis, Mahalonobis distances (measurements of genetic similarity between populations) revealed significant differences among the subpopulations at the sediment sampling points, suggesting bacterial adaptation to a heterogeneous (or patchy) microgeographical environment. Multilocus linkage disequilibrium analysis of the isolates revealed only limited association between alleles, suggesting frequent recombination, relative to binary fission, in this population. Furthermore, the dendrogram created from the data of this study and the allele mismatch distribution are typical of a population characterized by extensive genetic mixing. We suggest that B. cepacia be added to the growing list of bacteria that are not obligatorily clonal. 41 refs., 5 figs., 3 tabs.

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

    PubMed Central

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

    2009-01-01

    Background and Aims Gene flow and genetic variability within and among alpine plant populations can be greatly influenced by the steep environmental gradients and heterogeneous topography of alpine landscapes. In this study, the effects are examined of natural isolation of alpine habitats on genetic diversity and geographic structure in populations of C. thyrsoides, a rare and isolated European Alpine monocarpic perennial with limited seed dispersal capacity. Methods Molecular diversity was analysed for 736 individuals from 32 populations in the Swiss Alps and adjacent Jura mountains using five polymorphic microsatellite loci. Pollen flow was estimated using pollen grain-sized fluorescent powder. In addition, individual-based Bayesian approaches were applied to examine population structure. Key Results High within-population genetic diversity (HE = 0·76) and a relatively low inbreeding coefficient (FIS = 0·022) were found. Genetic differentiation among populations measured with a standardized measure was considerable (G′ST = 0·53). A significant isolation-by-distance relationship was found (r = 0·62, P < 0·001) and a significant geographic sub-structure, coinciding with proposed postglacial migration patterns. Altitudinal location and size of populations did not influence molecular variation. Direct measures of pollen flow revealed that insect-mediated pollen dispersal was restricted to short distances within a population. Conclusions The natural isolation of suitable habitats for C. thyrsoides restricts gene flow among the populations as expected for a monocarpic species with very limited seed dispersal capacities. The observed high within-population genetic diversity in this rare monocarpic perennial is best explained by its outcrossing behaviour, long-lived individuals and overlapping generations. Despite the high within-population genetic diversity, the considerable genetic differentiation and the clear western–eastern differentiation in this species

  19. Genetic differentiation among North Atlantic killer whale populations.

    PubMed

    Foote, Andrew D; Vilstrup, Julia T; De Stephanis, Renaud; Verborgh, Philippe; Abel Nielsen, Sandra C; Deaville, Robert; Kleivane, Lars; Martín, Vidal; Miller, Patrick J O; Oien, Nils; Pérez-Gil, Monica; Rasmussen, Morten; Reid, Robert J; Robertson, Kelly M; Rogan, Emer; Similä, Tiu; Tejedor, Maria L; Vester, Heike; Víkingsson, Gísli A; Willerslev, Eske; Gilbert, M Thomas P; Piertney, Stuart B

    2011-02-01

    Population genetic structure of North Atlantic killer whale samples was resolved from differences in allele frequencies of 17 microsatellite loci, mtDNA control region haplotype frequencies and for a subset of samples, using complete mitogenome sequences. Three significantly differentiated populations were identified. Differentiation based on microsatellite allele frequencies was greater between the two allopatric populations than between the two pairs of partially sympatric populations. Spatial clustering of individuals within each of these populations overlaps with the distribution of particular prey resources: herring, mackerel and tuna, which each population has been seen predating. Phylogenetic analyses using complete mitogenomes suggested two populations could have resulted from single founding events and subsequent matrilineal expansion. The third population, which was sampled at lower latitudes and lower density, consisted of maternal lineages from three highly divergent clades. Pairwise population differentiation was greater for estimates based on mtDNA control region haplotype frequencies than for estimates based on microsatellite allele frequencies, and there were no mitogenome haplotypes shared among populations. This suggests low or no female migration and that gene flow was primarily male mediated when populations spatially and temporally overlap. These results demonstrate that genetic differentiation can arise through resource specialization in the absence of physical barriers to gene flow. PMID:21241391

  20. Genetic population structure of the blister beetle, Gnathium minimum: core and peripheral populations.

    PubMed

    Marschalek, Daniel A; Berres, Mark E

    2014-01-01

    Populations on the periphery of a species' range tend to contain lower genetic variation and increased genetic differentiation compared to populations at the core of a species range, although some exceptions to this generalization occur. The blister beetle Gnathium minimum (Say) exhibits a wide-ranging distribution in the western United States but has peripheral or disjunct populations in Mexico, Florida, and Wisconsin. We used amplified fragment length polymorphism (AFLP) to compare the genetic variation and magnitude of genetic differentiation of the Wisconsin peripheral population to western core populations (Colorado, Kansas, New Mexico, and Texas). The proportion of polymorphic loci was 53.6 and 54.3, and expected heterozygosity 0.1864 and 0.1933 for the Kansas/Colorado (n = 87) and New Mexico/Texas (n = 35) regions, respectively. Specimens from Wisconsin (n = 121) had a lower proportion of polymorphic loci (38.4) and expected heterozygosity (0.1475). Genetic cluster estimation with GENELAND and F ST values showed greater genetic differentiation among the sampling locations within Wisconsin compared to core regions. Significant isolation-by-distance (IBD) was also observed in Wisconsin but not within the core regions. Lower genetic variation and increased isolation may reduce the Wisconsin population's ability to respond to change, thereby increasing their susceptibility to extinction. PMID:25160848

  1. Population structure and genetic diversity in natural populations of Theobroma speciosum Willd. Ex Spreng (Malvaceae).

    PubMed

    Giustina, L D; Luz, L N; Vieira, F S; Rossi, F S; Soares-Lopes, C R A; Pereira, T N S; Rossi, A A B

    2014-01-01

    The genus Theobroma found in the Amazon region is composed of 22 species, including Theobroma speciosum, better known as cacauí. These species are constantly threatened by forest fragmentation caused by human activities and require conservation strategies and management aimed at preserving them in their natural environments. The main objective of this study was to analyze the population structure and genetic diversity within and between natural populations of T. speciosum by using ISSR molecular markers to understand the population structure of the species. Four natural populations belonging to the Amazon rainforest (BAC, CRO, FLA, and PNA), located in the State of Mato Grosso, were selected. Amplification reactions were performed using 15 ISSR primers. A total of 101 loci were found, of which 54.46% were polymorphic at the species level. The BAC population showed higher genetic diversity (H=0.095 and I=0.144) and higher percentage of polymorphism (28.71%). The populations showed an FST value of 0.604, indicating marked genetic differentiation. The highest genetic variation was found between populations. Gene flow was low between populations, indicating genetic isolation between populations. PMID:24615108

  2. Population connectivity and genetic structure of burbot (Lota lota) populations in the Wind River Basin, Wyoming

    USGS Publications Warehouse

    Underwood, Zachary E.; Mandeville, Elizabeth G.; Walters, Annika W.

    2016-01-01

    Burbot (Lota lota) occur in the Wind River Basin in central Wyoming, USA, at the southwestern extreme of the species’ native range in North America. The most stable and successful of these populations occur in six glacially carved mountain lakes on three different tributary streams and one large main stem impoundment (Boysen Reservoir) downstream from the tributary populations. Burbot are rarely found in connecting streams and rivers, which are relatively small and high gradient, with a variety of potential barriers to upstream movement of fish. We used high-throughput genomic sequence data for 11,197 SNPs to characterize the genetic diversity, population structure, and connectivity among burbot populations on the Wind River system. Fish from Boysen Reservoir and lower basin tributary populations were genetically differentiated from those in the upper basin tributary populations. In addition, fish within the same tributary streams fell within the same genetic clusters, suggesting there is movement of fish between lakes on the same tributaries but that populations within each tributary system are isolated and genetically distinct from other populations. Observed genetic differentiation corresponded to natural and anthropogenic barriers, highlighting the importance of barriers to fish population connectivity and gene flow in human-altered linked lake-stream habitats.

  3. Generalized population models and the nature of genetic drift.

    PubMed

    Der, Ricky; Epstein, Charles L; Plotkin, Joshua B

    2011-09-01

    The Wright-Fisher model of allele dynamics forms the basis for most theoretical and applied research in population genetics. Our understanding of genetic drift, and its role in suppressing the deterministic forces of Darwinian selection has relied on the specific form of sampling inherent to the Wright-Fisher model and its diffusion limit. Here we introduce and analyze a broad class of forward-time population models that share the same mean and variance as the Wright-Fisher model, but may otherwise differ. The proposed class unifies and further generalizes a number of population-genetic processes of recent interest, including the Λ and Cannings processes. Even though these models all have the same variance effective population size, they encode a rich diversity of alternative forms of genetic drift, with significant consequences for allele dynamics. We characterize in detail the behavior of standard population-genetic quantities across this family of generalized models. Some quantities, such as heterozygosity, remain unchanged; but others, such as neutral absorption times and fixation probabilities under selection, deviate by orders of magnitude from the Wright-Fisher model. We show that generalized population models can produce startling phenomena that differ qualitatively from classical behavior - such as assured fixation of a new mutant despite the presence of genetic drift. We derive the forward-time continuum limits of the generalized processes, analogous to Kimura's diffusion limit of the Wright-Fisher process, and we discuss their relationships to the Kingman and non-Kingman coalescents. Finally, we demonstrate that some non-diffusive, generalized models are more likely, in certain respects, than the Wright-Fisher model itself, given empirical data from Drosophila populations. PMID:21718713

  4. Evaluation of genetic variation among wild rice populations in Cambodia

    PubMed Central

    Orn, Chhourn; Shishido, Rieko; Akimoto, Masahiro; Ishikawa, Ryo; Htun, Than Myint; Nonomura, Ken-Ichi; Koide, Yohei; Sarom, Men; Vang, Seng; Sophany, Sakhan; Makara, Ouk; Ishii, Takashige

    2015-01-01

    A total of 448 samples in five natural populations of wild rice (Oryza rufipogon) were collected in Cambodia. They were examined using 12 SSR and two chloroplast markers to evaluate the degree of variation among populations and the genetic structure within populations. In the two annual populations, the number of plants with homozygous alleles at all 12 SSR loci were high (66.3% and 79.5%), suggesting that these plants propagate mainly through self-pollination. In the three perennial populations, no individuals had all homozygous genotypes, but redundant genotypes resulted from clonal propagation were observed. Percentages of the redundant genotypes were highly varied (3.6%, 29.2% and 86.0%). This may be due to the different stable levels of environmental conditions. As for chloroplast genome, most of the wild plants showed the same chloroplast types as most Indica-type cultivars have. However, plants with different chloroplast types were maintained, even in the same population. In tropical Asian countries, many wild rice populations were observed under similar ecological conditions examined in this study. Therefore, the present results concerning population structure will be important to further elucidate genetic features of wild rice, and will also give strong clues to utilize and conserve wild natural genetic resources. PMID:26719746

  5. A model agreement for genetic research in socially identifiable populations.

    PubMed

    Foster, M W; Bernsten, D; Carter, T H

    1998-09-01

    Genetic research increasingly focuses on population-specific human genetic diversity. However, the naming of a human population in public databases and scientific publications entails collective risks for its members. Those collective risks can be evaluated and protections can be put in place by the establishment of a dialogue with the subject population, before a research study is initiated. Here we describe an agreement to undertake genetic research with a Native American tribe. We identified the culturally appropriate public and private social units within which community members are accustomed to make decisions about health. We then engaged those units in a process of communal discourse. In their discourses about our proposed study, community members expressed most concern about culturally specific implications. We also found that, in this population, private social units were more influential in communal decision making than were public authorities. An agreement was reached that defined the scope of research, provided options for naming the population in publications (including anonymity), and addressed the distribution of royalties from intellectual property, the future use of archival samples, and specific cultural concerns. We found that informed consent by individuals could not fully address these collective issues. This approach may serve as a general model for the undertaking of population-specific genetic studies. PMID:9718343

  6. Genetic Diversity among Ancient Nordic Populations

    PubMed Central

    Melchior, Linea; Lynnerup, Niels; Siegismund, Hans R.; Kivisild, Toomas; Dissing, Jørgen

    2010-01-01

    Using established criteria for work with fossil DNA we have analysed mitochondrial DNA from 92 individuals from 18 locations in Denmark ranging in time from the Mesolithic to the Medieval Age. Unequivocal assignment of mtDNA haplotypes was possible for 56 of the ancient individuals; however, the success rate varied substantially between sites; the highest rates were obtained with untouched, freshly excavated material, whereas heavy handling, archeological preservation and storage for many years influenced the ability to obtain authentic endogenic DNA. While the nucleotide diversity at two locations was similar to that among extant Danes, the diversity at four sites was considerably higher. This supports previous observations for ancient Britons. The overall occurrence of haplogroups did not deviate from extant Scandinavians, however, haplogroup I was significantly more frequent among the ancient Danes (average 13%) than among extant Danes and Scandinavians (∼2.5%) as well as among other ancient population samples reported. Haplogroup I could therefore have been an ancient Southern Scandinavian type “diluted” by later immigration events. Interestingly, the two Neolithic samples (4,200 YBP, Bell Beaker culture) that were typed were haplogroup U4 and U5a, respectively, and the single Bronze Age sample (3,300–3,500 YBP) was haplogroup U4. These two haplogroups have been associated with the Mesolithic populations of Central and Northern Europe. Therefore, at least for Southern Scandinavia, our findings do not support a possible replacement of a haplogroup U dominated hunter-gatherer population by a more haplogroup diverse Neolithic Culture. PMID:20689597

  7. Inter-chromosomal variation in the pattern of human population genetic structure.

    PubMed

    Baye, Tesfaye M

    2011-05-01

    Emerging technologies now make it possible to genotype hundreds of thousands of genetic variations in individuals, across the genome. The study of loci at finer scales will facilitate the understanding of genetic variation at genomic and geographic levels. We examined global and chromosomal variations across HapMap populations using 3.7 million single nucleotide polymorphisms to search for the most stratified genomic regions of human populations and linked these regions to ontological annotation and functional network analysis. To achieve this, we used five complementary statistical and genetic network procedures: principal component (PC), cluster, discriminant, fixation index (FST) and network/pathway analyses. At the global level, the first two PC scores were sufficient to account for major population structure; however, chromosomal level analysis detected subtle forms of population structure within continental populations, and as many as 31 PCs were required to classify individuals into homogeneous groups. Using recommended population ancestry differentiation measures, a total of 126 regions of the genome were catalogued. Gene ontology and networks analyses revealed that these regions included the genes encoding oculocutaneous albinism II (OCA2), hect domain and RLD 2 (HERC2), ectodysplasin A receptor (EDAR) and solute carrier family 45, member 2 (SLC45A2). These genes are associated with melanin production, which is involved in the development of skin and hair colour, skin cancer and eye pigmentation. We also identified the genes encoding interferon-γ (IFNG) and death-associated protein kinase 1 (DAPK1), which are associated with cell death, inflammatory and immunological diseases. An in-depth understanding of these genomic regions may help to explain variations in adaptation to different environments. Our approach offers a comprehensive strategy for analysing chromosome-based population structure and differentiation, and demonstrates the application of

  8. RESEARCH ON GENETIC SEXING AND POPULATION GENETICS OF SCREWWORM AT LINCOLN, NEBRASKA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The following technical abstract refers to an invited oral presentation given at the IAEA/FAO sponsored Consultants Meeting on Genetic Sexing and Population Genetics of the Screwworm, August 2000. Responsibility for screwworm research at the USDA-ARS-Midwest Livestock Insects Research Unit (MLIRU) ...

  9. Population genetic structure and genetic diversity of soybean aphids from USA, Korea and Japan

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Following its recent invasion of North America, the soybean aphid (Aphis glycines Matsumura) has become the number one insect pest of soybean (Glycine max L. Merr.) in the north central states of USA. Very little is known about the population genetic structure and genetic diversity of the soybean ap...

  10. Population genetic structure of Theileria parva field isolates from indigenous cattle populations of Uganda.

    PubMed

    Muwanika, Vincent; Kabi, Fredrick; Masembe, Charles

    2016-03-01

    Theileria parva causes East Coast Fever (ECF) a protozoan infection which manifests as a non-symptomatic syndrome among endemically stable indigenous cattle populations. Knowledge of the current genetic diversity and population structure of T. parva is critical for predicting pathogen evolutionary trends to inform development of effective control strategies. In this study the population genetic structure of 78 field isolates of T. parva from indigenous cattle (Ankole, n=41 and East African shorthorn Zebu (EASZ), n=37) sampled from the different agro ecological zones (AEZs) of Uganda was investigated. A total of eight mini- and micro-satellite markers encompassing the four chromosomes of T. parva were used to genotype the study field isolates. The genetic diversity of the surveyed T. parva populations was observed to range from 0.643±0.55 to 0.663±0.41 among the Central and Western AEZs respectively. The overall Wright's F index showed significant genetic variation between the surveyed T. parva populations based on the different AEZs and indigenous cattle breeds (FST=0.133, p<0.01) and (FST=0.101, p<0.01) respectively. Significant pairwise population genetic differentiations (p<0.05) were observed with FST values ranging from 0.048 to 0.173 between the eastern and northern, eastern and western populations respectively. The principal component analysis (PCA) showed a high level of genetic and geographic sub-structuring among populations. Linkage disequilibrium was observed when populations from all the study AEZs were treated as a single population and when analysed separately. On the overall, the significant genetic diversity and geographic sub-structuring exhibited among the study T. parva isolates has critical implications for ECF control. PMID:26613662

  11. Molecular population genetic analysis of emerged bacterial pathogens: selected insights.

    PubMed Central

    Musser, J. M.

    1996-01-01

    Research in bacterial population genetics has increased in the last 10 years. Population genetic theory and tools and related strategies have been used to investigate bacterial pathogens that have contributed to recent episodes of temporal variation in disease frequency and severity. A common theme demonstrated by these analyses is that distinct bacterial clones are responsible for disease outbreaks and increases in infection frequency. Many of these clones are characterized by unique combinations of virulence genes or alleles of virulence genes. Because substantial interclonal variance exists in relative virulence, molecular population genetic studies have led to the concept that the unit of bacterial pathogenicity is the clone or cell line. Continued new insights into host parasite interactions at the molecular level will be achieved by combining clonal analysis of bacterial pathogens with large-scale comparative sequencing of virulence genes. PMID:8903193

  12. gPGA: GPU Accelerated Population Genetics Analyses

    PubMed Central

    Zhou, Chunbao; Lang, Xianyu; Wang, Yangang; Zhu, Chaodong

    2015-01-01

    Background The isolation with migration (IM) model is important for studies in population genetics and phylogeography. IM program applies the IM model to genetic data drawn from a pair of closely related populations or species based on Markov chain Monte Carlo (MCMC) simulations of gene genealogies. But computational burden of IM program has placed limits on its application. Methodology With strong computational power, Graphics Processing Unit (GPU) has been widely used in many fields. In this article, we present an effective implementation of IM program on one GPU based on Compute Unified Device Architecture (CUDA), which we call gPGA. Conclusions Compared with IM program, gPGA can achieve up to 52.30X speedup on one GPU. The evaluation results demonstrate that it allows datasets to be analyzed effectively and rapidly for research on divergence population genetics. The software is freely available with source code at https://github.com/chunbaozhou/gPGA. PMID:26248314

  13. Quasispecies theory in the context of population genetics

    PubMed Central

    Wilke, Claus O

    2005-01-01

    Background A number of recent papers have cast doubt on the applicability of the quasispecies concept to virus evolution, and have argued that population genetics is a more appropriate framework to describe virus evolution than quasispecies theory. Results I review the pertinent literature, and demonstrate for a number of cases that the quasispecies concept is equivalent to the concept of mutation-selection balance developed in population genetics, and that there is no disagreement between the population genetics of haploid, asexually-replicating organisms and quasispecies theory. Conclusion Since quasispecies theory and mutation-selection balance are two sides of the same medal, the discussion about which is more appropriate to describe virus evolution is moot. In future work on virus evolution, we would do good to focus on the important questions, such as whether we can develop accurate, quantitative models of virus evolution, and to leave aside discussions about the relative merits of perfectly equivalent concepts. PMID:16107214

  14. Population structure and genetic diversity of moose in Alaska.

    PubMed

    Schmidt, Jennifer I; Hundertmark, Kris J; Bowyer, R Terry; McCracken, Kevin G

    2009-01-01

    Moose (Alces alces) are highly mobile mammals that occur across arboreal regions of North America, Europe, and Asia. Alaskan moose (Alces alces gigas) range across much of Alaska and are primary herbivore consumers, exerting a prominent influence on ecosystem structure and functioning. Increased knowledge gained from population genetics provides insights into their population dynamics, history, and dispersal of these unique large herbivores and can aid in conservation efforts. We examined the genetic diversity and population structure of moose (n = 141) with 8 polymorphic microsatellites from 6 regions spanning much of Alaska. Expected heterozygosity was moderate (H(E) = 0.483-0.612), and private alleles ranged from 0 to 6. Both F(ST) and R(ST) indicated significant population structure (P < 0.001) with F(ST) < 0.109 and R(ST) < 0.125. Results of analyses from STRUCTURE indicated 2 prominent population groups, a mix of moose from the Yakutat and Tetlin regions versus all other moose, with slight substructure observed among the second population. Estimates of dispersal differed between analytical approaches, indicating a high level of historical or current gene flow. Mantel tests indicated that isolation-by-distance partially explained observed structure among moose populations (R(2) = 0.45, P < 0.01). Finally, there was no evidence of bottlenecks either at the population level or overall. We conclude that weak population structure occurs among moose in Alaska with population expansion from interior Alaska westward toward the coast. PMID:18836148

  15. Genetic causes of monogenic familial hypercholesterolemia in the Greek population: Lessons, mistakes, and the way forward.

    PubMed

    Mollaki, Vasiliki; Drogari, Euridiki

    2016-01-01

    Familial hypercholesterolemia (FH) is a leading cause of premature atherosclerosis. Genetic defects in the LDLR, APOB and PCSK9 genes cause FH, and confirmation of a gene defect is essential for an indisputable diagnosis of the disease. FH is underdiagnosed and we aimed to revise the genetic defects that have been characterized in FH patients of Greek origin and define an effective, future strategy for genetic studies. A literature search was performed in MEDLINE and EMBASE on genetic studies with FH patients of Greek origin. To date, no APOB and PCSK9 mutations have been found in the Greek population. It must be noted however, that only a small number of patients has been screened for PCSK9 mutations. In total, 41 LDLR defects have been characterized, with 6 common mutations c.1646G>A (p.Gly546Asp), c.858C>A (p.Ser286Arg), c.81C>G (p.Cys27Trp), c.1285G>A (p.Val429Met), c.517T>C (p.Cys173Arg), and c.1775G>A (p.Gly592Glu) that account for >80% of all mutations. Due to geographic isolation, ​founder mutations exist in a subpopulation in North West Greece and the Greek Cypriot population but not in the general population. Genetic testing should focus primarily on LDLR, and subsequently on PCSK9 and APOB. The Greek population is genetically homogeneous, which allows for a quick molecular diagnosis of the disease. Cascade screening is feasible and will certainly facilitate the identification of additional patients. PMID:27578104

  16. The population genetics of synthetic lethals.

    PubMed

    Phillips, P C; Johnson, N A

    1998-09-01

    Synthetic lethals are variants at different loci that have little or no effect on viability singly but cause lethality in combination. The importance of synthetic lethals and, more generally, of synthetic deleterious loci (SDL) has been controversial. Here, we derive the expected frequencies for SDL under a mutation-selection balance for the complete haploid model and selected cases of the diploid model. We have also obtained simple approximations that demonstrate good fit to exact solutions based on numerical iterations. In the haploid case, equilibrium frequencies of carrier haplotypes (individuals with only a single mutation) are comparable to analogous single-locus results, after allowing for the effects of linkage. Frequencies in the diploid case, however, are much higher and more comparable to the square root of the single-locus results. In particular, when selection operates only on the double-mutant homozygote and linkage is not too tight, the expected frequency of the carriers is approximately the quartic root of the ratio between the mutation rate and the selection coefficient of the synthetics. For a reasonably wide set of models, the frequencies of carriers can be on the order of a few percent. The equilibrium frequencies of these deleterious alleles can be relatively high because, with SDL, both dominance and epistasis act to shield carriers from exposure to selection. We also discuss the possible role of SDL in maintaining genetic variation and in hybrid breakdown. PMID:9725860

  17. The ancient Yakuts: a population genetic enigma

    PubMed Central

    Keyser, Christine; Hollard, Clémence; Gonzalez, Angela; Fausser, Jean-Luc; Rivals, Eric; Alexeev, Anatoly Nikolayevich; Riberon, Alexandre; Crubézy, Eric; Ludes, Bertrand

    2015-01-01

    This study is part of an ongoing project aiming at determining the ethnogenesis of an eastern Siberian ethnic group, the Yakuts, on the basis of archaeological excavations carried out over a period of 10 years in three regions of Yakutia: Central Yakutia, the Vilyuy River basin and the Verkhoyansk area. In this study, genetic analyses were carried out on skeletal remains from 130 individuals of unknown ancestry dated mainly from the fifteenth to the nineteenth century AD. Kinship studies were conducted using sets of commercially available autosomal and Y-chromosomal short tandem repeats (STRs) along with hypervariable region I sequences of the mitochondrial DNA. An unexpected and intriguing finding of this work was that the uniparental marker systems did not always corroborate results from autosomal DNA analyses; in some cases, false-positive relationships were observed. These discrepancies revealed that 15 autosomal STR loci are not sufficient to discriminate between first degree relatives and more distantly related individuals in our ancient Yakut sample. The Y-STR analyses led to similar conclusions, because the current Y-STR panels provided the limited resolution of the paternal lineages. PMID:25487336

  18. The ancient Yakuts: a population genetic enigma.

    PubMed

    Keyser, Christine; Hollard, Clémence; Gonzalez, Angela; Fausser, Jean-Luc; Rivals, Eric; Alexeev, Anatoly Nikolayevich; Riberon, Alexandre; Crubézy, Eric; Ludes, Bertrand

    2015-01-19

    This study is part of an ongoing project aiming at determining the ethnogenesis of an eastern Siberian ethnic group, the Yakuts, on the basis of archaeological excavations carried out over a period of 10 years in three regions of Yakutia: Central Yakutia, the Vilyuy River basin and the Verkhoyansk area. In this study, genetic analyses were carried out on skeletal remains from 130 individuals of unknown ancestry dated mainly from the fifteenth to the nineteenth century AD. Kinship studies were conducted using sets of commercially available autosomal and Y-chromosomal short tandem repeats (STRs) along with hypervariable region I sequences of the mitochondrial DNA. An unexpected and intriguing finding of this work was that the uniparental marker systems did not always corroborate results from autosomal DNA analyses; in some cases, false-positive relationships were observed. These discrepancies revealed that 15 autosomal STR loci are not sufficient to discriminate between first degree relatives and more distantly related individuals in our ancient Yakut sample. The Y-STR analyses led to similar conclusions, because the current Y-STR panels provided the limited resolution of the paternal lineages. PMID:25487336

  19. Genetic Diversity and Population Structure of Theileria annulata in Oman

    PubMed Central

    Al-Hamidhi, Salama; H. Tageldin, Mohammed.; Weir, William; Al-Fahdi, Amira; Johnson, Eugene H.; Bobade, Patrick; Alqamashoui, Badar; Beja-Pereira, Albano; Thompson, Joanne; Kinnaird, Jane; Shiels, Brian; Tait, Andy; Babiker, Hamza

    2015-01-01

    Background Theileriosis, caused by a number of species within the genus Theileria, is a common disease of livestock in Oman. It is a major constraint to the development of the livestock industry due to a high rate of morbidity and mortality in both cattle and sheep. Since little is currently known about the genetic diversity of the parasites causing theileriosis in Oman, the present study was designed to address this issue with specific regard to T. annulata in cattle. Methods Blood samples were collected from cattle from four geographically distinct regions in Oman for genetic analysis of the Theileria annulata population. Ten genetic markers (micro- and mini-satellites) representing all four chromosomes of T. annulata were applied to these samples using a combination of PCR amplification and fragment analysis. The resultant genetic data was analysed to provide a first insight into the structure of the T. annulata population in Oman. Results We applied ten micro- and mini-satellite markers to a total of 310 samples obtained from different regions (174 [56%] from Dhofar, 68 [22%] from Dhira, 44 [14.5%] from Batinah and 24 [8%] from Sharqia). A high degree of allelic diversity was observed among the four parasite populations. Expected heterozygosity for each site ranged from 0.816 to 0.854. A high multiplicity of infection was observed in individual hosts, with an average of 3.3 to 3.4 alleles per locus, in samples derived from Batinah, Dhofar and Sharqia regions. In samples from Dhira region, an average of 2.9 alleles per locus was observed. Mild but statistically significant linkage disequilibrium between pairs of markers was observed in populations from three of the four regions. In contrast, when the analysis was performed at farm level, no significant linkage disequilibrium was observed. Finally, no significant genetic differentiation was seen between the four populations, with most pair-wise FST values being less than 0.03. Slightly higher FST values (GST

  20. Genetic Determinants of Pubertal Timing in the General Population

    PubMed Central

    Gajdos, Zofia K.Z.; Henderson, Katherine D.; Hirschhorn, Joel N.

    2010-01-01

    Puberty is an important developmental stage during which reproductive capacity is attained. The timing of puberty varies greatly among healthy individuals in the general population and is influenced by both genetic and environmental factors. Although genetic variation is known to influence the normal spectrum of pubertal timing, the specific genes involved remain largely unknown. Genetic analyses have identified a number of genes responsible for rare disorders of pubertal timing such as hypogonadotropic hypogonadism and Kallmann syndrome. Recently, the first loci with common variation reproducibly associated with population variation in the timing of puberty were identified at 6q21 in or near LIN28B and at 9q31.2. However, these two loci explain only a small fraction of the genetic contribution to population variation in pubertal timing, suggesting the need to continue to consider other loci and other types of variants. Here we provide an update of the genes implicated in disorders of puberty, discuss genes and pathways that may be involved in the timing of normal puberty, and suggest additional avenues of investigation to identify genetic regulators of puberty in the general population. PMID:20144687

  1. FINE-SCALE GENETIC DIFFERENTIATION BETWEEN CONTAMINANT-TOLERANT AND CONTAMINANT SENSITIVE FISH POPULATIONS

    EPA Science Inventory

    Studies have suggested that environmental contaminants can act as selective forces on exposed populations of wildlife species. Chronically exposed populations have shown reduced genetic diversity and/or demonstrated other genetic changes. We evaluated the genetic structure of pop...

  2. Population amalgamation and genetic variation: observations on artificially agglomerated tribal populations of Central and South America.

    PubMed

    Chakraborty, R; Smouse, P E; Neel, J V

    1988-11-01

    The interpretation of data on genetic variation with regard to the relative roles of different evolutionary factors that produce and maintain genetic variation depends critically on our assumptions concerning effective population size and the level of migration between neighboring populations. In humans, recent population growth and movements of specific ethnic groups across wide geographic areas mean that any theory based on assumptions of constant population size and absence of substructure is generally untenable. We examine the effects of population subdivision on the pattern of protein genetic variation in a total sample drawn from an artificial agglomerate of 12 tribal populations of Central and South America, analyzing the pooled sample as though it were a single population. Several striking findings emerge. (1) Mean heterozygosity is not sensitive to agglomeration, but the number of different alleles (allele count) is inflated, relative to neutral mutation/drift/equilibrium expectation. (2) The inflation is most serious for rare alleles, especially those which originally occurred as tribally restricted "private" polymorphisms. (3) The degree of inflation is an increasing function of both the number of populations encompassed by the sample and of the genetic divergence among them. (4) Treating an agglomerated population as though it were a panmictic unit of long standing can lead to serious biases in estimates of mutation rates, selection pressures, and effective population sizes. Current DNA studies indicate the presence of numerous genetic variants in human populations. The findings and conclusions of this paper are all fully applicable to the study of genetic variation at the DNA level as well. PMID:3189334

  3. Temporal genetic stability of Stegomyia aegypti (= Aedes aegypti) populations.

    PubMed

    Gloria-Soria, A; Kellner, D A; Brown, J E; Gonzalez-Acosta, C; Kamgang, B; Lutwama, J; Powell, J R

    2016-06-01

    The mosquito Stegomyia aegypti (= Aedes aegypti) (Diptera: Culicidae) is the primary vector of viruses that cause yellow fever, dengue and Chikungunya fever. In the absence of effective vaccines, the reduction of these diseases relies on vector control strategies. The success of these strategies is tightly linked to the population dynamics of target populations. In the present study, 14 collections from St. aegypti populations separated by periods of 1-13 years were analysed to determine their temporal genetic stability. Although temporal structure is discernible in most populations, the degree of temporal differentiation is dependent on the population and does not obscure the geographic structure of the various populations. The results suggest that performing detailed studies in the years prior to and after population reduction- or modification-based control interventions at each target field site may be useful in assessing the probability of success. PMID:26744174

  4. High genetic load in an old isolated butterfly population.

    PubMed

    Mattila, Anniina L K; Duplouy, Anne; Kirjokangas, Malla; Lehtonen, Rainer; Rastas, Pasi; Hanski, Ilkka

    2012-09-11

    We investigated inbreeding depression and genetic load in a small (N(e) ∼ 100) population of the Glanville fritillary butterfly (Melitaea cinxia), which has been completely isolated on a small island [Pikku Tytärsaari (PT)] in the Baltic Sea for at least 75 y. As a reference, we studied conspecific populations from the well-studied metapopulation in the Åland Islands (ÅL), 400 km away. A large population in Saaremaa, Estonia, was used as a reference for estimating genetic diversity and N(e). We investigated 58 traits related to behavior, development, morphology, reproductive performance, and metabolism. The PT population exhibited high genetic load (L = 1 - W(PT)/W(ÅL)) in a range of fitness-related traits including adult weight (L = 0.12), flight metabolic rate (L = 0.53), egg viability (L = 0.37), and lifetime production of eggs in an outdoor population cage (L = 0.70). These results imply extensive fixation of deleterious recessive mutations, supported by greatly reduced diversity in microsatellite markers and immediate recovery (heterosis) of egg viability and flight metabolic rate in crosses with other populations. There was no significant inbreeding depression in most traits due to one generation of full-sib mating. Resting metabolic rate was significantly elevated in PT males, which may be related to their short lifespan (L = 0.25). The demographic history and the effective size of the PT population place it in the part of the parameter space in which models predict mutation accumulation. This population exemplifies the increasingly common situation in fragmented landscapes, in which small and completely isolated populations are vulnerable to extinction due to high genetic load. PMID:22908265

  5. Genetic structure of the indigenous populations of Siberia.

    PubMed

    Crawford, M H; Williams, J T; Duggirala, R

    1997-10-01

    This study explores the genetic structure of Siberian indigenous populations on the basis of standard blood group and protein markers and DNA variable number of tandem repeats (VNTR) variation. Four analytical methods were utilized in this study: Harpending and Jenkin's R-matrix; Harpending and Ward's method of correlating genetic heterozygosity (H) to the distance from the centroid of the gene frequency array (rii); spatial autocorrelation, and Mantel tests. Because of the underlying assumptions of the various methods, the numbers of populations used in the analyses varied from 15 to 62. Since spatial autocorrelation is based upon separate correlations between alleles, a larger number of standard blood markers and populations were used. Fewest Siberian populations have been sampled for VNTRs, thus, only a limited comparison was possible. The four analytical procedures employed in this study yielded complementary results suggestive of the effects of unique historical events, evolutionary forces, and geography on the distribution of alleles in Siberian indigenous populations. The principal components analysis of the R-matrix demonstrated the presence of populational clusters that reflect their phylogenetic relationship. Mantel comparisons of matrices indicate that an intimate relationship exists between geography, languages, and genetics of Siberian populations. Spatial autocorrelation patterns reflect the isolation-by-distance model of Malecot and the possible effects of long-distance migration. PMID:9386825

  6. Genetic affinities of the Jewish populations of India.

    PubMed

    Chaubey, Gyaneshwer; Singh, Manvendra; Rai, Niraj; Kariappa, Mini; Singh, Kamayani; Singh, Ashish; Pratap Singh, Deepankar; Tamang, Rakesh; Selvi Rani, Deepa; Reddy, Alla G; Kumar Singh, Vijay; Singh, Lalji; Thangaraj, Kumarasamy

    2016-01-01

    Due to the lack of written records or inscription, the origin and affiliation of Indian Jewish populations with other world populations remain contentious. Previous genetic studies have found evidence for a minor shared ancestry of Indian Jewish with Middle Eastern (Jewish) populations. However, these studies (relied on limited individuals), haven't explored the detailed temporal and spatial admixture process of Indian Jewish populations with the local Indian populations. Here, using large sample size with combination of high resolution biparental (autosomal) and uniparental markers (Y chromosome and mitochondrial DNA), we reconstructed genetic history of Indian Jewish by investigating the patterns of genetic diversity. Consistent with the previous observations, we detected minor Middle Eastern specific ancestry component among Indian Jewish communities, but virtually negligible in their local neighbouring Indian populations. The temporal test of admixture suggested that the first admixture of migrant Jewish populations from Middle East to South India (Cochin) occurred during fifth century. Overall, we concluded that the Jewish migration and admixture in India left a record in their genomes, which can link them to the 'Jewish Diaspora'. PMID:26759184

  7. Genetic affinities of the Jewish populations of India

    PubMed Central

    Chaubey, Gyaneshwer; Singh, Manvendra; Rai, Niraj; Kariappa, Mini; Singh, Kamayani; Singh, Ashish; Pratap Singh, Deepankar; Tamang, Rakesh; Selvi Rani, Deepa; Reddy, Alla G.; Kumar Singh, Vijay; Singh, Lalji; Thangaraj, Kumarasamy

    2016-01-01

    Due to the lack of written records or inscription, the origin and affiliation of Indian Jewish populations with other world populations remain contentious. Previous genetic studies have found evidence for a minor shared ancestry of Indian Jewish with Middle Eastern (Jewish) populations. However, these studies (relied on limited individuals), haven’t explored the detailed temporal and spatial admixture process of Indian Jewish populations with the local Indian populations. Here, using large sample size with combination of high resolution biparental (autosomal) and uniparental markers (Y chromosome and mitochondrial DNA), we reconstructed genetic history of Indian Jewish by investigating the patterns of genetic diversity. Consistent with the previous observations, we detected minor Middle Eastern specific ancestry component among Indian Jewish communities, but virtually negligible in their local neighbouring Indian populations. The temporal test of admixture suggested that the first admixture of migrant Jewish populations from Middle East to South India (Cochin) occurred during fifth century. Overall, we concluded that the Jewish migration and admixture in India left a record in their genomes, which can link them to the ‘Jewish Diaspora’. PMID:26759184

  8. Genetic diversity and differentiation of Kermode bear populations.

    PubMed

    Marshall, H D; Ritland, K

    2002-04-01

    The Kermode bear is a white phase of the North American black bear that occurs in low to moderate frequency on British Columbia's mid-coast. To investigate the genetic uniqueness of populations containing the white phase, and to ascertain levels of gene flow among populations, we surveyed 10 highly polymorphic microsatellite loci, assayed from trapped bear hairs. A total of 216 unique bear genotypes, 18 of which were white, was sampled among 12 localities. Island populations, where Kermodes are most frequent, show approximately 4% less diversity than mainland populations, and the island richest in white bears (Gribbell) exhibited substantial genetic isolation, with a mean pairwise FST of 0.14 with other localities. Among all localities, FST for the molecular variant underlying the coat-colour difference (A893G) was 0.223, which falls into the 95th percentile of the distribution of FST values among microsatellite alleles, suggestive of greater differentiation for coat colour than expected under neutrality. Control-region sequences confirm that Kermode bears are part of a coastal or western lineage of black bears whose existence predates the Wisconsin glaciation, but microsatellite variation gave no evidence of past population expansion. We conclude that Kermodism was established and is maintained in populations by a combination of genetic isolation and somewhat reduced population sizes in insular habitat, with the possible contribution of selective pressure and/or nonrandom mating. PMID:11972757

  9. Methods for the survey and genetic analysis of populations

    DOEpatents

    Ashby, Matthew

    2003-09-02

    The present invention relates to methods for performing surveys of the genetic diversity of a population. The invention also relates to methods for performing genetic analyses of a population. The invention further relates to methods for the creation of databases comprising the survey information and the databases created by these methods. The invention also relates to methods for analyzing the information to correlate the presence of nucleic acid markers with desired parameters in a sample. These methods have application in the fields of geochemical exploration, agriculture, bioremediation, environmental analysis, clinical microbiology, forensic science and medicine.

  10. The fine-scale genetic structure of the British population.

    PubMed

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

    2015-03-19

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

  11. Genetic scores of smoking behaviour in a Chinese population

    PubMed Central

    Yang, Shanshan; He, Yao; Wang, Jianhua; Wang, Yiyan; Wu, Lei; Zeng, Jing; Liu, Miao; Zhang, Di; Jiang, Bin; Li, Xiaoying

    2016-01-01

    This study sought to structure a genetic score for smoking behaviour in a Chinese population. Single-nucleotide polymorphisms (SNPs) from genome-wide association studies (GWAS) were evaluated in a community-representative sample (N = 3,553) of Beijing, China. The candidate SNPs were tested in four genetic models (dominance model, recessive model, heterogeneous codominant model and additive model), and 7 SNPs were selected to structure a genetic score. A total of 3,553 participants (1,477 males and 2,076 females) completed the survey. Using the unweighted score, we found that participants with a high genetic score had a 34% higher risk of trying smoking and a 43% higher risk of SI at ≤18 years of age after adjusting for age, gender, education, occupation, ethnicity, body mass index (BMI) and sports activity time. The unweighted genetic scores were chosen to best extrapolate and understand these results. Importantly, genetic score was significantly associated with smoking behaviour (smoking status and SI at ≤18 years of age). These results have the potential to guide relevant health education for individuals with high genetic scores and promote the process of smoking control to improve the health of the population. PMID:26948517

  12. The fine scale genetic structure of the British population

    PubMed Central

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

    2015-01-01

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

  13. The genetic consequences of selection in natural populations.

    PubMed

    Thurman, Timothy J; Barrett, Rowan D H

    2016-04-01

    The selection coefficient, s, quantifies the strength of selection acting on a genetic variant. Despite this parameter's central importance to population genetic models, until recently we have known relatively little about the value of s in natural populations. With the development of molecular genetic techniques in the late 20th century and the sequencing technologies that followed, biologists are now able to identify genetic variants and directly relate them to organismal fitness. We reviewed the literature for published estimates of natural selection acting at the genetic level and found over 3000 estimates of selection coefficients from 79 studies. Selection coefficients were roughly exponentially distributed, suggesting that the impact of selection at the genetic level is generally weak but can occasionally be quite strong. We used both nonparametric statistics and formal random-effects meta-analysis to determine how selection varies across biological and methodological categories. Selection was stronger when measured over shorter timescales, with the mean magnitude of s greatest for studies that measured selection within a single generation. Our analyses found conflicting trends when considering how selection varies with the genetic scale (e.g., SNPs or haplotypes) at which it is measured, suggesting a need for further research. Besides these quantitative conclusions, we highlight key issues in the calculation, interpretation, and reporting of selection coefficients and provide recommendations for future research. PMID:26836758

  14. CCAST: a model-based gating strategy to isolate homogeneous subpopulations in a heterogeneous population of single cells.

    PubMed

    Anchang, Benedict; Do, Mary T; Zhao, Xi; Plevritis, Sylvia K

    2014-07-01

    A model-based gating strategy is developed for sorting cells and analyzing populations of single cells. The strategy, named CCAST, for Clustering, Classification and Sorting Tree, identifies a gating strategy for isolating homogeneous subpopulations from a heterogeneous population of single cells using a data-derived decision tree representation that can be applied to cell sorting. Because CCAST does not rely on expert knowledge, it removes human bias and variability when determining the gating strategy. It combines any clustering algorithm with silhouette measures to identify underlying homogeneous subpopulations, then applies recursive partitioning techniques to generate a decision tree that defines the gating strategy. CCAST produces an optimal strategy for cell sorting by automating the selection of gating markers, the corresponding gating thresholds and gating sequence; all of these parameters are typically manually defined. Even though CCAST is optimized for cell sorting, it can be applied for the identification and analysis of homogeneous subpopulations among heterogeneous single cell data. We apply CCAST on single cell data from both breast cancer cell lines and normal human bone marrow. On the SUM159 breast cancer cell line data, CCAST indicates at least five distinct cell states based on two surface markers (CD24 and EPCAM) and provides a gating sorting strategy that produces more homogeneous subpopulations than previously reported. When applied to normal bone marrow data, CCAST reveals an efficient strategy for gating T-cells without prior knowledge of the major T-cell subtypes and the markers that best define them. On the normal bone marrow data, CCAST also reveals two major mature B-cell subtypes, namely CD123+ and CD123- cells, which were not revealed by manual gating but show distinct intracellular signaling responses. More generally, the CCAST framework could be used on other biological and non-biological high dimensional data types that are

  15. Population genetic structure of Bombus terrestris in Europe: Isolation and genetic differentiation of Irish and British populations.

    PubMed

    Moreira, António S; Horgan, Finbarr G; Murray, Tomás E; Kakouli-Duarte, Thomais

    2015-07-01

    The genetic structure of the earth bumblebee (Bombus terrestris L.) was examined across 22 wild populations and two commercially reared populations using eight microsatellite loci and two mitochondrial genes. Our study included wild bumblebee samples from six populations in Ireland, one from the Isle of Man, four from Britain and 11 from mainland Europe. A further sample was acquired from New Zealand. Observed levels of genetic variability and heterozygosity were low in Ireland and the Isle of Man, but relatively high in continental Europe and among commercial populations. Estimates of Fst revealed significant genetic differentiation among populations. Bayesian cluster analysis indicated that Irish populations were highly differentiated from British and continental populations, the latter two showing higher levels of admixture. The data suggest that the Irish Sea and prevailing south westerly winds act as a considerable geographical barrier to gene flow between populations in Ireland and Britain; however, some immigration from the Isle of Man to Ireland was detected. The results are discussed in the context of the recent commercialization of bumblebees for the European horticultural industry. PMID:25958977

  16. A Global Population Genetic Study of Pantala flavescens

    PubMed Central

    Troast, Daniel; Suhling, Frank; Jinguji, Hiroshi; Sahlén, Göran; Ware, Jessica

    2016-01-01

    Among terrestrial arthropods, the dragonfly species Pantala flavescens is remarkable due to their nearly global distribution and extensive migratory ranges; the largest of any known insect. Capable of migrating across oceans, the potential for high rates of gene flow among geographically distant populations is significant. It has been hypothesized that P. flavescens may be a global panmictic population but no sufficient genetic evidence has been collected thus far. Through a population genetic analysis of P. flavescens samples from North America, South America, and Asia, the current study aimed to examine the extent at which gene flow is occurring on a global scale and discusses the implications of the genetic patterns we uncovered on population structure and genetic diversity of the species. This was accomplished using PCR-amplified cytochrome oxidase one (CO1) mitochondrial DNA data to reconstruct phylogenetic trees, a haplotype network, and perform molecular variance analyses. Our results suggested high rates of gene flow are occurring among all included geographic regions; providing the first significant evidence that Pantala flavescens should be considered a global panmictic population. PMID:26934181

  17. A Global Population Genetic Study of Pantala flavescens.

    PubMed

    Troast, Daniel; Suhling, Frank; Jinguji, Hiroshi; Sahlén, Göran; Ware, Jessica

    2016-01-01

    Among terrestrial arthropods, the dragonfly species Pantala flavescens is remarkable due to their nearly global distribution and extensive migratory ranges; the largest of any known insect. Capable of migrating across oceans, the potential for high rates of gene flow among geographically distant populations is significant. It has been hypothesized that P. flavescens may be a global panmictic population but no sufficient genetic evidence has been collected thus far. Through a population genetic analysis of P. flavescens samples from North America, South America, and Asia, the current study aimed to examine the extent at which gene flow is occurring on a global scale and discusses the implications of the genetic patterns we uncovered on population structure and genetic diversity of the species. This was accomplished using PCR-amplified cytochrome oxidase one (CO1) mitochondrial DNA data to reconstruct phylogenetic trees, a haplotype network, and perform molecular variance analyses. Our results suggested high rates of gene flow are occurring among all included geographic regions; providing the first significant evidence that Pantala flavescens should be considered a global panmictic population. PMID:26934181

  18. Genetic population structure of local populations of the endangered saltmarsh sesarmid crab Clistocoeloma sinense in Japan.

    PubMed

    Yuhara, Takeshi; Kawane, Masako; Furota, Toshio

    2014-01-01

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

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

    PubMed Central

    Yuhara, Takeshi; Kawane, Masako; Furota, Toshio

    2014-01-01

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

  20. Plasmodium vivax Populations Are More Genetically Diverse and Less Structured than Sympatric Plasmodium falciparum Populations

    PubMed Central

    Jennison, Charlie; Arnott, Alicia; Tessier, Natacha; Tavul, Livingstone; Koepfli, Cristian; Felger, Ingrid; Siba, Peter M.; Reeder, John C.; Bahlo, Melanie; Mueller, Ivo; Barry, Alyssa E.

    2015-01-01

    Introduction The human malaria parasite, Plasmodium vivax, is proving more difficult to control and eliminate than Plasmodium falciparum in areas of co-transmission. Comparisons of the genetic structure of sympatric parasite populations may provide insight into the mechanisms underlying the resilience of P. vivax and can help guide malaria control programs. Methodology/Principle findings P. vivax isolates representing the parasite populations of four areas on the north coast of Papua New Guinea (PNG) were genotyped using microsatellite markers and compared with previously published microsatellite data from sympatric P. falciparum isolates. The genetic diversity of P. vivax (He = 0.83–0.85) was higher than that of P. falciparum (He = 0.64–0.77) in all four populations. Moderate levels of genetic differentiation were found between P. falciparum populations, even over relatively short distances (less than 50 km), with 21–28% private alleles and clear geospatial genetic clustering. Conversely, very low population differentiation was found between P. vivax catchments, with less than 5% private alleles and no genetic clustering observed. In addition, the effective population size of P. vivax (30353; 13043–69142) was larger than that of P. falciparum (18871; 8109–42986). Conclusions/Significance Despite comparably high prevalence, P. vivax had higher diversity and a panmictic population structure compared to sympatric P. falciparum populations, which were fragmented into subpopulations. The results suggest that in comparison to P. falciparum, P. vivax has had a long-term large effective population size, consistent with more intense and stable transmission, and limited impact of past control and elimination efforts. This underlines suggestions that more intensive and sustained interventions will be needed to control and eventually eliminate P. vivax. This research clearly demonstrates how population genetic analyses can reveal deeper insight into transmission

  1. Population genetics of Setaria viridis, a new model system.

    PubMed

    Huang, Pu; Feldman, Maximilian; Schroder, Stephan; Bahri, Bochra A; Diao, Xianmin; Zhi, Hui; Estep, Matt; Baxter, Ivan; Devos, Katrien M; Kellogg, Elizabeth A

    2014-10-01

    An extensive survey of the standing genetic variation in natural populations is among the priority steps in developing a species into a model system. In recent years, green foxtail (Setaria viridis), along with its domesticated form foxtail millet (S. italica), has rapidly become a promising new model system for C4 grasses and bioenergy crops, due to its rapid life cycle, large amount of seed production and small diploid genome, among other characters. However, remarkably little is known about the genetic diversity in natural populations of this species. In this study, we survey the genetic diversity of a worldwide sample of more than 200 S. viridis accessions, using the genotyping-by-sequencing technique. Two distinct genetic groups in S. viridis and a third group resembling S. italica were identified, with considerable admixture among the three groups. We find the genetic variation of North American S. viridis correlates with both geography and climate and is representative of the total genetic diversity in this species. This pattern may reflect several introduction/dispersal events of S. viridis into North America. We also modelled demographic history and show signal of recent population decline in one subgroup. Finally, we show linkage disequilibrium decay is rapid (<45 kb) in our total sample and slow in genetic subgroups. These results together provide an in-depth understanding of the pattern of genetic diversity of this new model species on a broad geographic scale. They also provide key guidelines for on-going and future work including germplasm preservation, local adaptation, crossing designs and genomewide association studies. PMID:25185718

  2. Genetic Structure of Atriplex halimus Populations in the Mediterranean Basin

    PubMed Central

    ORTÍZ-DORDA, J.; MARTÍNEZ-MORA, C.; CORREAL, E.; SIMÓN, B.; CENIS, J. L.

    2005-01-01

    • Background and Aims The saltbush Atriplex halimus is a chenopodiaceous plant well adapted to dry saline habitats and widely distributed in the Mediterranean Basin. A study was carried out to analyse the genetic diversity of A. halimus at the level of the Mediterranean Basin. • Methods To assess the intra- and interpopulational variation of A. halimus a total of 51 populations and six plants per populations was analysed with the RAPD-PCR technique. For the study of the phylogeny of the populations, 21 samples of A. halimus and seven samples of other species of Atriplex were analysed by the sequencing of the ITS (internal transcribed spacer) region of the ribosomal DNA. • Key Results The AMOVA analysis of the RAPD results showed that populations were divided into two discrete genetic groups, as the variation among groups accounted for 54·36 % of the total variance of the collection. At the same time, the intrapopulational diversity was high, as 301 out of 306 plants analysed constituted an individual RAPD haplotype. The sequencing of the ITS region also showed a significant separation of the two genetic groups, with a genetic distance of 0·023 nucleotide substitutions per site. Using A. breweri, A. canescens, A. glauca and A. prostrata as outgroups in the phylogenetic analysis, A. breweri and A. canescens are the species closest to A. halimus from this group, while A. prostrata is the most distant. • Conclusions The present work indicates that two genetic groups of A. halimus can be distinguished after analysing the genetic diversity of 51 populations from ten countries in the Mediterranean Basin. PMID:15713783

  3. Genomic evidence for ecological divergence against a background of population homogeneity in the marine snail Chlorostoma funebralis.

    PubMed

    Gleason, Lani U; Burton, Ronald S

    2016-08-01

    The balance between natural selection, gene flow and genetic drift is difficult to resolve in marine invertebrates with extensive dispersal and fluctuating population sizes. The intertidal snail Chlorostoma funebralis has planktonic larvae and previous work using mtDNA polymorphism reported no genetic population structure. Nevertheless, recent studies have documented differences in thermal tolerance and transcriptomic responses to heat stress between northern and southern California, USA, populations. To gain insight into the dynamics influencing adaptive divergence, we used double-digest restriction site-associated DNA (ddRAD) sequencing to identify 1861 genomewide, quality-filtered single-nucleotide polymorphism (SNP) loci for C. funebralis collected from three northern and three southern California sites (15 individuals per population). Considering all SNPs, there was no evidence for genetic differentiation among populations or regions (average FST  = 0.0042). However, outlier tests revealed 34 loci putatively under divergent selection between northern and southern populations, and structure and SNP tree analyses based on these outliers show clear genetic differentiation between geographic regions. Three of these outliers are known or hypothesized to be involved in stress granule formation, a response to environmental stress such as heat. Combined with previous work that found thermally tolerant southern populations show high baseline expression of stress response genes, these results further suggest that thermal stress is a strong selective pressure across C. funebralis populations. Overall, this study increases our understanding of the factors constraining local adaptation in marine organisms, while suggesting that ecologically driven, strong differentiation can occur at relevant loci in a species with planktonic larvae. PMID:27199218

  4. Contrasting patterns of genetic variation in core and peripheral populations of highly outcrossing and wind pollinated forest tree species

    PubMed Central

    Wójkiewicz, Błażej; Litkowiec, Monika; Wachowiak, Witold

    2016-01-01

    Gene flow tends to have a homogenising effect on a species’ background genetic variation over large geographical areas. However, it is usually unknown to what extent the genetic structure of populations is influenced by gene exchange between core and peripheral populations that may represent stands of different evolutionary and demographic history. In this study, we looked at the patterns of population differentiation in Scots pine—a highly outcrossing and wind pollinated conifer species that forms large ecosystems of great ecological and economic importance in Europe and Asia. A set of 13 polymorphic nuclear microsatellite loci was analysed to infer the genetic relationships among 24 populations (676 individuals) from Europe and Asia Minor. The study included specimens from the primary continuous range and from isolated, marginal stands that are considered to be autochthonous populations representative of the species’ putative refugial areas. Despite their presumably different histories, a similar level of genetic variation and no evidence of a population bottleneck was found across the populations. Differentiation among populations was relatively low (average FST = 0.035); however, the population structure was not homogenous, which was clearly evident from the allelic frequency spectra and Bayesian assignment analysis. Significant differentiation over short geographical distances was observed between isolated populations within the Iberian and Anatolian Peninsulas (Asia Minor), which contrasted with the absence of genetic differentiation observed between distant populations e.g., between central and northern Europe. The analysed populations were assigned to several groups that corresponded to the geographical regions of their occurrence. These results will be useful in genetics studies in Scots pine that aim to link nucleotide and phenotypic variation across the species distribution range and for development of sustainable breeding and management

  5. Contrasting patterns of genetic variation in core and peripheral populations of highly outcrossing and wind pollinated forest tree species.

    PubMed

    Wójkiewicz, Błażej; Litkowiec, Monika; Wachowiak, Witold

    2016-01-01

    Gene flow tends to have a homogenising effect on a species' background genetic variation over large geographical areas. However, it is usually unknown to what extent the genetic structure of populations is influenced by gene exchange between core and peripheral populations that may represent stands of different evolutionary and demographic history. In this study, we looked at the patterns of population differentiation in Scots pine-a highly outcrossing and wind pollinated conifer species that forms large ecosystems of great ecological and economic importance in Europe and Asia. A set of 13 polymorphic nuclear microsatellite loci was analysed to infer the genetic relationships among 24 populations (676 individuals) from Europe and Asia Minor. The study included specimens from the primary continuous range and from isolated, marginal stands that are considered to be autochthonous populations representative of the species' putative refugial areas. Despite their presumably different histories, a similar level of genetic variation and no evidence of a population bottleneck was found across the populations. Differentiation among populations was relatively low (average FST = 0.035); however, the population structure was not homogenous, which was clearly evident from the allelic frequency spectra and Bayesian assignment analysis. Significant differentiation over short geographical distances was observed between isolated populations within the Iberian and Anatolian Peninsulas (Asia Minor), which contrasted with the absence of genetic differentiation observed between distant populations e.g., between central and northern Europe. The analysed populations were assigned to several groups that corresponded to the geographical regions of their occurrence. These results will be useful in genetics studies in Scots pine that aim to link nucleotide and phenotypic variation across the species distribution range and for development of sustainable breeding and management programs

  6. Genetic population structure and contemporary dispersal patterns of a recent European invader, the Chinese mitten crab, Eriocheir sinensis.

    PubMed

    Herborg, Leif-Matthias; Weetman, David; van Oosterhout, Cock; Hänfling, Bernd

    2007-01-01

    Genetic studies of recently established populations are challenging because the assumption of equilibrium underlying many analyses is likely to be violated. Using microsatellites, we investigated determinants of genetic structure and migration among invasive European-Chinese mitten crab populations, applying a combination of traditional population genetic analyses and nonequilibrium Bayesian methods. Consistent with their recent history, invasive populations showed much lower levels of genetic diversity than a native Chinese population, indicative of recent bottlenecks. Population differentiation was generally low but significant and especially pronounced among recently established populations. Significant differentiation among cohorts from the same geographical location (River Thames) suggests the low effective population size and associated strong genetic drift that would be anticipated from a very recent colonization. An isolation-by-distance pattern appears to be driven by an underlying correlation between geographical distance and population age, suggesting that cumulative homogenizing gene flow reduces founder bottleneck-associated genetic differentiation between longer-established populations. This hypothesis was supported by a coalescent analysis, which supported a drift + gene flow model as more likely than a model excluding gene flow. Furthermore, admixture analysis identified several recent migrants between the UK and Continental European population clusters. Admixture proportions were significantly predicted by the volume of shipping between sites, indicating that human-mediated transport remains a significant factor for dispersal of mitten crabs after the initial establishment of populations. Our study highlights the value of nonequilibrium methods for the study of invasive species, and also the importance of evaluating nonequilibrium explanations for isolation by distance patterns. PMID:17217341

  7. Study of population genetic polymorphism and gene flow rate in Indian snow trout, Schizothorax richardsonii fish of Himalaya, India.

    PubMed

    Sivaraman, G K; Barat, A; Ali, S; Mahanta, P C

    2014-11-01

    The genetic polymorphism and gene flow rate among the Indian snow trout fish population S. richadsonii from three different locations viz., Chirapani stream of Champawat district, Kosi and Gola river of Nainital district, Uttarakhand State, India were assessed by employing twenty numbers of Randomly Amplified Polymorphic DNA (RAPD) markers. The overall percent polymorphisms among these three populations were 14.76 with 6.56, 4.92 and 3.28 in Chirapani, Kosi and Gola river population, respectively. Chirapani population had higher proportion of polymorphic loci as compared to the Kosi and Gola. The higher value of genetic distance (0.1565) was obtained between Chirapani and Gola population and the lower value of genetic distance was observed between Chirapani and Kosi (0.1058) river population. The cluster analysis revealed that in the formation of two clusters, one consisted of Chirapani and Kosi and the other was Gola fish population. Gst estimates among these populations showed some extent of homogeneity with lower genetic differentiation rate between populations and further suggested that higher tolerance to mutation, as expected that RAPD bands, arose from both coding and non-coding DNA regions. The findings revealed that the rate of gene flow in three populations seemed very low i.e. highly conserved its genetic diversity in their natural waterbodies and indicative of little migration among populations (geographically isolated and not the possibilities man made interventions/introduction of similar kind of fish species). It is further concluded that the Chirapani, Kosi and Gola river populations of S. richardsonii were being conserved naturally in their habitat and the species actual genetic potential were being maintained (adaptation to local climatic conditions, reproduction, production traits and disease resistance trait etc) in their natural habitat. PMID:25522514

  8. Genetic substructure of Kuwaiti population reveals migration history.

    PubMed

    Alsmadi, Osama; Thareja, Gaurav; Alkayal, Fadi; Rajagopalan, Ramakrishnan; John, Sumi Elsa; Hebbar, Prashantha; Behbehani, Kazem; Thanaraj, Thangavel Alphonse

    2013-01-01

    The State of Kuwait is characterized by settlers from Saudi Arabia, Iran, and other regions of the Arabian Peninsula. The settlements and subsequent admixtures have shaped the genetics of Kuwait. High prevalence of recessive disorders and metabolic syndromes (that increase risk of diabetes) is seen in the peninsula. Understanding the genetic structure of its population will aid studies designed to decipher the underlying causes of these disorders. In this study, we analyzed 572,366 SNP markers from 273 Kuwaiti natives genotyped using the illumina HumanOmniExpress BeadChip. Model-based clustering identified three genetic subgroups with different levels of admixture. A high level of concordance (Mantel test, p=0.0001 for 9999 repeats) was observed between the derived genetic clusters and the surname-based ancestries. Use of Human Genome Diversity Project (HGDP) data to understand admixtures in each group reveals the following: the first group (Kuwait P) is largely of West Asian ancestry, representing Persians with European admixture; the second group (Kuwait S) is predominantly of city-dwelling Saudi Arabian tribe ancestry, and the third group (Kuwait B) includes most of the tent-dwelling Bedouin surnames and is characterized by the presence of 17% African ancestry. Identity by Descent and Homozygosity analyses find Kuwait's population to be heterogeneous (placed between populations that have large amount of ROH and the ones with low ROH) with Kuwait S as highly endogamous, and Kuwait B as diverse. Population differentiation FST estimates place Kuwait P near Asian populations, Kuwait S near Negev Bedouin tribes, and Kuwait B near the Mozabite population. FST distances between the groups are in the range of 0.005 to 0.008; distances of this magnitude are known to cause false positives in disease association studies. Results of analysis for genetic features such as linkage disequilibrium decay patterns conform to Kuwait's geographical location at the nexus of Africa

  9. Small population size and extremely low levels of genetic diversity in island populations of the platypus, Ornithorhynchus anatinus

    PubMed Central

    Furlan, Elise; Stoklosa, J; Griffiths, J; Gust, N; Ellis, R; Huggins, R M; Weeks, A R

    2012-01-01

    Genetic diversity generally underpins population resilience and persistence. Reductions in population size and absence of gene flow can lead to reductions in genetic diversity, reproductive fitness, and a limited ability to adapt to environmental change increasing the risk of extinction. Island populations are typically small and isolated, and as a result, inbreeding and reduced genetic diversity elevate their extinction risk. Two island populations of the platypus, Ornithorhynchus anatinus, exist; a naturally occurring population on King Island in Bass Strait and a recently introduced population on Kangaroo Island off the coast of South Australia. Here we assessed the genetic diversity within these two island populations and contrasted these patterns with genetic diversity estimates in areas from which the populations are likely to have been founded. On Kangaroo Island, we also modeled live capture data to determine estimates of population size. Levels of genetic diversity in King Island platypuses are perilously low, with eight of 13 microsatellite loci fixed, likely reflecting their small population size and prolonged isolation. Estimates of heterozygosity detected by microsatellites (HE= 0.032) are among the lowest level of genetic diversity recorded by this method in a naturally outbreeding vertebrate population. In contrast, estimates of genetic diversity on Kangaroo Island are somewhat higher. However, estimates of small population size and the limited founders combined with genetic isolation are likely to lead to further losses of genetic diversity through time for the Kangaroo Island platypus population. Implications for the future of these and similarly isolated or genetically depauperate populations are discussed. PMID:22837830

  10. Interplay of population genetics and dynamics in the genetic control of mosquitoes

    PubMed Central

    Alphey, Nina; Bonsall, Michael B.

    2014-01-01

    Some proposed genetics-based vector control methods aim to suppress or eliminate a mosquito population in a similar manner to the sterile insect technique. One approach under development in Anopheles mosquitoes uses homing endonuclease genes (HEGs)—selfish genetic elements (inherited at greater than Mendelian rate) that can spread rapidly through a population even if they reduce fitness. HEGs have potential to drive introduced traits through a population without large-scale sustained releases. The population genetics of HEG-based systems has been established using discrete-time mathematical models. However, several ecologically important aspects remain unexplored. We formulate a new continuous-time (overlapping generations) combined population dynamic and genetic model and apply it to a HEG that targets and knocks out a gene that is important for survival. We explore the effects of density dependence ranging from undercompensating to overcompensating larval competition, occurring before or after HEG fitness effects, and consider differences in competitive effect between genotypes (wild-type, heterozygotes and HEG homozygotes). We show that population outcomes—elimination, suppression or loss of the HEG—depend crucially on the interaction between these ecological aspects and genetics, and explain how the HEG fitness properties, the homing rate (drive) and the insect's life-history parameters influence those outcomes. PMID:24522781

  11. Prediction of monthly rainfall on homogeneous monsoon regions of India based on large scale circulation patterns using Genetic Programming

    NASA Astrophysics Data System (ADS)

    Kashid, Satishkumar S.; Maity, Rajib

    2012-08-01

    SummaryPrediction of Indian Summer Monsoon Rainfall (ISMR) is of vital importance for Indian economy, and it has been remained a great challenge for hydro-meteorologists due to inherent complexities in the climatic systems. The Large-scale atmospheric circulation patterns from tropical Pacific Ocean (ENSO) and those from tropical Indian Ocean (EQUINOO) are established to influence the Indian Summer Monsoon Rainfall. The information of these two large scale atmospheric circulation patterns in terms of their indices is used to model the complex relationship between Indian Summer Monsoon Rainfall and the ENSO as well as EQUINOO indices. However, extracting the signal from such large-scale indices for modeling such complex systems is significantly difficult. Rainfall predictions have been done for 'All India' as one unit, as well as for five 'homogeneous monsoon regions of India', defined by Indian Institute of Tropical Meteorology. Recent 'Artificial Intelligence' tool 'Genetic Programming' (GP) has been employed for modeling such problem. The Genetic Programming approach is found to capture the complex relationship between the monthly Indian Summer Monsoon Rainfall and large scale atmospheric circulation pattern indices - ENSO and EQUINOO. Research findings of this study indicate that GP-derived monthly rainfall forecasting models, that use large-scale atmospheric circulation information are successful in prediction of All India Summer Monsoon Rainfall with correlation coefficient as good as 0.866, which may appears attractive for such a complex system. A separate analysis is carried out for All India Summer Monsoon rainfall for India as one unit, and five homogeneous monsoon regions, based on ENSO and EQUINOO indices of months of March, April and May only, performed at end of month of May. In this case, All India Summer Monsoon Rainfall could be predicted with 0.70 as correlation coefficient with somewhat lesser Correlation Coefficient (C.C.) values for different

  12. Population Genetic and Admixture Analyses of Culex pipiens Complex (Diptera: Culicidae) Populations in California, United States

    PubMed Central

    Kothera, Linda; Nelms, Brittany M.; Reisen, William K.; Savage, Harry M.

    2013-01-01

    Microsatellite markers were used to genetically characterize 19 Culex pipiens complex populations from California. Two populations showed characteristics of earlier genetic bottlenecks. The overall FST value and a neighbor-joining tree suggested moderate amounts of genetic differentiation. Analyses using Structure indicated K = 4 genetic clusters: Cx. pipiens form pipiens L., Cx. quinquefasciatus Say, Cx. pipiens form molestus Forskäl, and a group of genetically similar individuals of hybrid origin. A Discriminant Analysis of Principal Components indicated that the latter group is a mixture of the other three taxa, with form pipiens and form molestus contributing somewhat more ancestry than Cx. quinquefasciatus. Characterization of 56 morphologically autogenous individuals classified most as Cx. pipiens form molestus, and none as Cx. pipiens form pipiens or Cx. quinquefasciatus. Comparison of California microsatellite data with those of Cx. pipiens pallens Coquillett from Japan indicated the latter does not contribute significantly to genotypes in California. PMID:23958909

  13. Genetic diversity and population differentiation of natural populations of Sclerotinia sclerotiorum on lentils in eastern Washington.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic diversity and population differentiation of natural populations of Sclerotinia sclerotiorum on lentils in eastern Washington. X. Wang and W. Chen. Washington State University, Pullman, WA, and USDA-ARS, Pullman, WA 99163 Sclerotinia sclerotiorum is the causal agent of white mold on lentils....

  14. Genetic Characterization of Human Populations: From ABO to a Genetic Map of the British People

    PubMed Central

    Bodmer, Walter

    2015-01-01

    From 1900, when Landsteiner first described the ABO blood groups, to the present, the methods used to characterize the genetics of human populations have undergone a remarkable development. Concomitantly, our understanding of the history and spread of human populations across the earth has become much more detailed. As has often been said, a better understanding of the genetic relationships among the peoples of the world is one of the best antidotes to racial prejudices. Such an understanding provides us with a fascinating, improved insight into our origins as well as with valuable information about population differences that are of medical relevance. The study of genetic polymorphisms has been essential to the analysis of the relationships between human populations. The evolution of methods used to study human polymorphisms and the resulting contributions to our understanding of human health and history is the subject of this Perspectives. PMID:25657345

  15. Source population characteristics affect heterosis following genetic rescue of fragmented plant populations

    PubMed Central

    Pickup, M.; Field, D. L.; Rowell, D. M.; Young, A. G.

    2013-01-01

    Understanding the relative importance of heterosis and outbreeding depression over multiple generations is a key question in evolutionary biology and is essential for identifying appropriate genetic sources for population and ecosystem restoration. Here we use 2455 experimental crosses between 12 population pairs of the rare perennial plant Rutidosis leptorrhynchoides (Asteraceae) to investigate the multi-generational (F1, F2, F3) fitness outcomes of inter-population hybridization. We detected no evidence of outbreeding depression, with inter-population hybrids and backcrosses showing either similar fitness or significant heterosis for fitness components across the three generations. Variation in heterosis among population pairs was best explained by characteristics of the foreign source or home population, and was greatest when the source population was large, with high genetic diversity and low inbreeding, and the home population was small and inbred. Our results indicate that the primary consideration for maximizing progeny fitness following population augmentation or restoration is the use of seed from large, genetically diverse populations. PMID:23173202

  16. Analyzing Population Genetics Data: A Comparison of the Software

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Choosing a software program for analyzing population genetic data can be a challenge without prior knowledge of the methods used by each program. There are numerous web sites listing programs by type of data analyzed, type of analyses performed, or other criteria. Even with programs categorized in ...

  17. Population genetics related to adaptation in elite oat germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Six hundred thirty five oat lines and 2,635 SNP loci were used to evaluate population structure, linkage disequilibrium (LD) and genotype-phenotype association with heading date. The first five principal components (PC) accounted for 25.3% of genetic variation. Neither the eigenvalues of the first 2...

  18. Involving study populations in the review of genetic research.

    PubMed

    Sharp, R R; Foster, M W

    2000-01-01

    Genetic research can present risks to all members of a study population, not just those who choose to participate in research. The authors suggest that community-based reviews of research protocols can help identify and minimize such research-related risks. PMID:11067631

  19. Population genetics of Setaria viridis, a new model system

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An extensive survey of the standing genetic variation in natural populations is among the priority steps in developing a species into a model system. In recent years, green foxtail (Setaria viridis), along with its domesticated form foxtail millet (S. italica), has rapidly become a promising new mod...

  20. Genetic structure of Tribolium castaneum populations in mills

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We investigated the genetic diversity and differentiation among nine populations of T. castaneum using eight polymorphic loci, including microsatellites and other insertion-deletion polymorphisms (=”indels”). Samples were collected in food processing/storage facilities located in Kansas, Nebraska, ...

  1. Population genetic diversity and hybrid detection in captive zebras

    PubMed Central

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

    2015-01-01

    Zebras are members of the horse family. There are three species of zebras: the plains zebra Equus quagga, the Grevy’s zebra E. grevyi and the mountain zebra E. zebra. The Grevy’s zebra and the mountain zebra are endangered, and hybridization between the Grevy’s zebra and the plains zebra has been documented, leading to a requirement for conservation genetic management within and between the species. We characterized 28 microsatellite markers in Grevy’s zebra and assessed cross-amplification in plains zebra and two of its subspecies, as well as mountain zebra. A range of standard indices were employed to examine population genetic diversity and hybrid populations between Grevy’s and plains zebra were simulated to investigate subspecies and hybrid detection. Microsatellite marker polymorphism was conserved across species with sufficient variation to enable individual identification in all populations. Comparative diversity estimates indicated greater genetic variation in plains zebra and its subspecies than Grevy’s zebra, despite potential ascertainment bias. Species and subspecies differentiation were clearly demonstrated and F1 and F2 hybrids were correctly identified. These findings provide insights into captive population genetic diversity in zebras and support the use of these markers for identifying hybrids, including the known hybrid issue in the endangered Grevy’s zebra. PMID:26294133

  2. Genetic Studies of Stuttering in a Founder Population

    ERIC Educational Resources Information Center

    Wittke-Thompson, Jacqueline K.; Ambrose, Nicoline; Yairi, Ehud; Roe, Cheryl; Cook, Edwin H.; Ober, Carole; Cox, Nancy J.

    2007-01-01

    Genome-wide linkage and association analyses were conducted to identify genetic determinants of stuttering in a founder population in which 48 individuals affected with stuttering are connected in a single 232-person genealogy. A novel approach was devised to account for all necessary relationships to enable multipoint linkage analysis. Regions…

  3. Genetic disorders in children and young adults: a population study.

    PubMed Central

    Baird, P A; Anderson, T W; Newcombe, H B; Lowry, R B

    1988-01-01

    The data base of an ongoing population-based registry with multiple sources of ascertainment was used to estimate the present population load from genetic disease in more than 1 million consecutive live births. It was found that, before approximately age 25 years, greater than or equal to 53/1,000 live-born individuals can be expected to have diseases with an important genetic component. This total was composed of single-gene disorders (3.6/1,000), consisting of autosomal dominant (1.4/1,000), autosomal recessive (1.7/1,000), and X-linked recessive disorders (0.5/1,000). Chromosomal anomalies accounted for 1.8/1,000, multifactorial disorders (including those present at birth and those of onset before age 25 years) accounted for 46.4/1,000, and cases of genetic etiology in which the precise mechanism was not identified accounted for 1.2/1,000. Previous studies have usually considered all congenital anomalies (ICD 740-759) as part of the genetic load, but only those judged to fit into one of the above categories were included in the present study. Data for congenital anomalies are therefore also presented separately, to facilitate comparison with earlier studies. If all congenital anomalies are considered as part of the genetic load, then greater than or equal to 79/1,000 live-born individuals have been identified as having one or other genetic disorder before approximately age 25 years. These new data represent a better estimate of the genetic load in the population than do previous studies. PMID:3358420

  4. Genetic drift in an infinite population. The pseudohitchhiking model.

    PubMed Central

    Gillespie, J H

    2000-01-01

    Selected substitutions at one locus can induce stochastic dynamics that resemble genetic drift at a closely linked neutral locus. The pseudohitchhiking model is a one-locus model that approximates these effects and can be used to describe the major consequences of linked selection. As the changes in neutral allele frequencies when hitchhiking are rapid, diffusion theory is not appropriate for studying neutral dynamics. A stationary distribution and some results on substitution processes are presented that use the theory of continuous-time Markov processes with discontinuous sample paths. The coalescent of the pseudohitchhiking model is shown to have a random number of branches at each node, which leads to a frequency spectrum that is different from that of the equilibrium neutral model. If genetic draft, the name given to these induced stochastic effects, is a more important stochastic force than genetic drift, then a number of paradoxes that have plagued population genetics disappear. PMID:10835409

  5. Spread of pedigree versus genetic ancestry in spatially distributed populations.

    PubMed

    Kelleher, J; Etheridge, A M; Véber, A; Barton, N H

    2016-04-01

    Ancestral processes are fundamental to modern population genetics and spatial structure has been the subject of intense interest for many years. Despite this interest, almost nothing is known about the distribution of the locations of pedigree or genetic ancestors. Using both spatially continuous and stepping-stone models, we show that the distribution of pedigree ancestors approaches a travelling wave, for which we develop two alternative approximations. The speed and width of the wave are sensitive to the local details of the model. After a short time, genetic ancestors spread far more slowly than pedigree ancestors, ultimately diffusing out with radius ∼ t rather than spreading at constant speed. In contrast to the wave of pedigree ancestors, the spread of genetic ancestry is insensitive to the local details of the models. PMID:26546979

  6. Population genetics and evaluation of genetic evidence for subspecies in the Semipalmated Sandpiper (Calidris pusilla)

    USGS Publications Warehouse

    Miller, Mark P.; Gratto-Trevor, Cheri; Haig, Susan M.; Mizrahi, David S.; Mitchell, Melanie M.; Mullins, Thomas D.

    2013-01-01

    Semipalmated Sandpipers (Calidris pusilla) are among the most common North American shorebirds. Breeding in Arctic North America, this species displays regional differences in migratory pathways and possesses longitudinal bill length variation. Previous investigations suggested that genetic structure may occur within Semipalmated Sandpipers and that three subspecies corresponding to western, central, and eastern breeding groups exist. In this study, mitochondrial control region sequences and nuclear microsatellite loci were used to analyze DNA of birds (microsatellites: n = 120; mtDNA: n = 114) sampled from seven North American locations. Analyses designed to quantify genetic structure and diversity patterns, evaluate genetic evidence for population size changes, and determine if genetic data support the existence of Semipalmated Sandpiper subspecies were performed. Genetic structure based only on the mtDNA data was observed, whereas the microsatellite loci provided no evidence of genetic differentiation. Differentiation among locations and regions reflected allele frequency differences rather than separate phylogenetic groups, and similar levels of genetic diversity were noted. Combined, the two data sets provided no evidence to support the existence of subspecies and were not useful for determining migratory connectivity between breeding sites and wintering grounds. Birds from western and central groups displayed signatures of population expansions, whereas the eastern group was more consistent with a stable overall population. Results of this analysis suggest that the eastern group was the source of individuals that colonized the central and western regions currently utilized by Semipalmated Sandpipers.

  7. Comparing G: multivariate analysis of genetic variation in multiple populations.

    PubMed

    Aguirre, J D; Hine, E; McGuigan, K; Blows, M W

    2014-01-01

    The additive genetic variance-covariance matrix (G) summarizes the multivariate genetic relationships among a set of traits. The geometry of G describes the distribution of multivariate genetic variance, and generates genetic constraints that bias the direction of evolution. Determining if and how the multivariate genetic variance evolves has been limited by a number of analytical challenges in comparing G-matrices. Current methods for the comparison of G typically share several drawbacks: metrics that lack a direct relationship to evolutionary theory, the inability to be applied in conjunction with complex experimental designs, difficulties with determining statistical confidence in inferred differences and an inherently pair-wise focus. Here, we present a cohesive and general analytical framework for the comparative analysis of G that addresses these issues, and that incorporates and extends current methods with a strong geometrical basis. We describe the application of random skewers, common subspace analysis, the 4th-order genetic covariance tensor and the decomposition of the multivariate breeders equation, all within a Bayesian framework. We illustrate these methods using data from an artificial selection experiment on eight traits in Drosophila serrata, where a multi-generational pedigree was available to estimate G in each of six populations. One method, the tensor, elegantly captures all of the variation in genetic variance among populations, and allows the identification of the trait combinations that differ most in genetic variance. The tensor approach is likely to be the most generally applicable method to the comparison of G-matrices from any sampling or experimental design. PMID:23486079

  8. Population genetic screening programmes: principles, techniques, practices, and policies.

    PubMed

    Godard, Béatrice; ten Kate, Leo; Evers-Kiebooms, Gerry; Aymé, Ségolène

    2003-12-01

    This paper examines the professional and scientific views on the principles, techniques, practices, and policies that impact on the population genetic screening programmes in Europe. This paper focuses on the issues surrounding potential screening programmes, which require further discussion before their introduction. It aims to increase, among the health-care professions and health policy-makers, awareness of the potential screening programmes as an issue of increasing concern to public health. The methods comprised primarily the review of the existing professional guidelines, regulatory frameworks and other documents related to population genetic screening programmes in Europe. Then, the questions that need debate, in regard to different types of genetic screening before and after birth, were examined. Screening for conditions such as cystic fibrosis, Duchenne muscular dystrophy, familial hypercholesterolemia, fragile X syndrome, hemochromatosis, and cancer susceptibility was discussed. Special issues related to genetic screening were also examined, such as informed consent, family aspects, commercialization, the players on the scene and monitoring genetic screening programmes. Afterwards, these questions were debated by 51 experts from 15 European countries during an international workshop organized by the European Society of Human Genetics Public and Professional Policy Committee in Amsterdam, The Netherlands, 19-20, November, 1999. Arguments for and against starting screening programmes have been put forward. It has been questioned whether genetic screening differs from other types of screening and testing in terms of ethical issues. The general impression on the future of genetic screening is that one wants to 'proceed with caution', with more active impetus from the side of patients' organizations and more reluctance from the policy-makers. The latter try to obviate the potential problems about the abortion and eugenics issues that might be perceived as a

  9. Genetic redundancy in evolving populations of simulated robots.

    PubMed

    Miglino, Orazio; Walker, Richard

    2002-01-01

    A number of authors have argued that redundancy in biological organisms contributes to their evolvability. We investigate this hypothesis via the experimental manipulation of genetic redundancy in evolving populations of simulated robots controlled by artificial neural networks. A genetic algorithm is used to simulate the evolution of robots with the ability to perform a previously studied task. Redundancy is measured using systematic lesioning. In our experiments, populations of robots with larger genotypes achieve systematically higher fitness than populations whose genotypes are smaller. It is shown that, in principle, robots with smaller genotypes have enough computational power to achieve optimal fitness. Populations with larger (redundant) genotypes appear, however, to be more evolvable and display significantly higher diversity. It is argued that this enhanced evolvability is a direct effect of genetic redundancy, which allows populations of redundant robots to explore neutral networks spanning large areas of genotype space. We conjecture that, where cost considerations allow, redundancy in functional or potentially functional components of the genome may make a valuable contribution to evolution in artificial and perhaps in biological systems. The methods described in the article provide a practical way of testing this hypothesis for the artificial case. PMID:12537686

  10. Microsatellite Analysis of the Population Genetic Structure of Anolis carolinensis Introduced to the Ogasawara Islands.

    PubMed

    Sugawara, Hirotaka; Takahashi, Hiroo; Hayashi, Fumio

    2015-01-01

    DNA analysis can reveal the origins and dispersal patterns of invasive species. The green anole Anolis carolinensis is one such alien animal, which has been dispersed widely by humans from its native North America to many Pacific Ocean islands. In the Ogasawara (Bonin) Islands, this anole was recorded from Chichi-jima at the end of the 1960s, and then from Haha-jima in the early 1980s. These two islands are inhabited. In 2013, it was also found on the uninhabited Ani-jima, close to Chichi-jima. Humans are thought to have introduced the anole to Haha-jima, while the mode of introduction to Ani-jima is unknown. To clarify its dispersal patterns within and among these three islands, we assessed the fine-scale population genetic structure using five microsatellite loci. The results show a homogeneous genetic structure within islands, but different genetic structures among islands, suggesting that limited gene flow occurs between islands. The recently established Ani-jima population may have originated from several individuals simultaneously, or by repeated immigration from Chichi-jima. We must consider frequent incursions among these islands to control these invasive lizard populations and prevent their negative impact on native biodiversity. PMID:25660696

  11. The 20th century Danish facial cleft population--epidemiological and genetic-epidemiological studies.

    PubMed

    Christensen, K

    1999-03-01

    Since Dr. Fogh-Andersen's legendary 1942 thesis, the Danish facial cleft population has been one of the most extensively studied in terms of epidemiology and genetic-epidemiology. The etiology of cleft lip and/or palate (CLP) is still largely an enigma, and different results concerning environmental and genetic risk factors are obtained in different countries and regions. This may be due to etiological heterogeneity between settings. Therefore, an in-depth studied area with an ethnically homogeneous population, such as Denmark, has provided one of the best opportunities for progress in CLP etiological research. The present review summarizes epidemiological and genetic-epidemiological studies conducted in the 20th century Danish facial cleft population. Furthermore, analyses of sex differences, time trends and seasonality for more than 7000 CLP cases born in Denmark in the period 1936 to 1987 are presented. The review also points toward the excellent opportunities for continued etiological CLP research in Denmark in the 21st century using already established resources and an on-going prospective cohort study of 100,000 pregnant women. PMID:10213053

  12. Microsatellite diversity and genetic structure of fragmented populations of the rare, fire-dependent shrub Grevillea macleayana.

    PubMed

    England, Phillip R; Usher, Annette V; Whelan, Robert J; Ayre, David J

    2002-06-01

    Recent habitat loss and fragmentation superimposed upon ancient patterns of population subdivision are likely to have produced low levels of neutral genetic diversity and marked genetic structure in many plant species. The genetic effects of habitat fragmentation may be most pronounced in species that form small populations, are fully self-compatible and have limited seed dispersal. However, long-lived seed banks, mobile pollinators and long adult lifespans may prevent or delay the accumulation of genetic effects. We studied a rare Australian shrub species, Grevillea macleayana (Proteaceae), that occurs in many small populations, is self-compatible and has restricted seed dispersal. However, it has a relatively long adult lifespan (c. 30 years), a long-lived seed bank that germinates after fire and is pollinated by birds that are numerous and highly mobile. These latter characteristics raise the possibility that populations in the past may have been effectively large and genetically homogeneous. Using six microsatellites, we found that G. macleayana may have relatively low within-population diversity (3.2-4.2 alleles/locus; Hexp = 0.420-0.530), significant population differentiation and moderate genetic structure (FST = 0.218) showing isolation by distance, consistent with historically low gene flow. The frequency distribution of allele sizes suggest that this geographical differentiation is being driven by mutation. We found a lack mutation-drift equilibrium in some populations that is indicative of population bottlenecks. Combined with evidence for large spatiotemporal variation of selfing rates, this suggests that fluctuating population sizes characterize the demography in this species, promoting genetic drift. We argue that natural patterns of pollen and seed dispersal, coupled with the patchy, fire-shaped distribution, may have restricted long-distance gene flow in the past. PMID:12030976

  13. Fragmentation, Fusion, and Genetic Homogeneity in a Calcareous Sponge (Porifera, Calcarea).

    PubMed

    Padua, André; Leocorny, Pedro; Custódio, Márcio Reis; Klautau, Michelle

    2016-06-01

    Sessile marine invertebrates living on hard substrata usually present strategies such as size variations, longer life spans, fragmentation and fusion to occupy and compete for space. Calcareous sponges are usually small and short-lived, and some species are known to undergo frequent fragmentation and fusion events. However, whether fusion occurs only between genetically identical individuals remains unclear. We investigated the occurrence of chimaeras in the calcareous sponge Clathrina aurea by following the dynamics of fragmentation and fusion of 66 individuals in the field for up to 18 months and determined size variations and the life span of each individual. Microsatellites were used to determine whether fusion events occur among genetically different individuals. Growth and shrinkage of individuals were frequently observed, showing that size cannot be associated with age in C. aurea. The life span of the species ranged from 1 to 16 months (mean: 4.7 months). Short life spans and variable growth rates have been observed in other species of the class Calcarea. Fragmentation and fusion events were observed, but fusion events always occurred between genetically identical individuals, as has been suggested by graft experiments in adult Demospongiae and other Calcarea. These results suggest that at least C. aurea adults may have some mechanism to avoid chimaerism. PMID:27194182

  14. How Obstacles Perturb Population Fronts and Alter Their Genetic Structure.

    PubMed

    Möbius, Wolfram; Murray, Andrew W; Nelson, David R

    2015-12-01

    As populations spread into new territory, environmental heterogeneities can shape the population front and genetic composition. We focus here on the effects of an important building block of heterogeneous environments, isolated obstacles. With a combination of experiments, theory, and simulation, we show how isolated obstacles both create long-lived distortions of the front shape and amplify the effect of genetic drift. A system of bacteriophage T7 spreading on a spatially heterogeneous Escherichia coli lawn serves as an experimental model system to study population expansions. Using an inkjet printer, we create well-defined replicates of the lawn and quantitatively study the population expansion of phage T7. The transient perturbations of the population front found in the experiments are well described by a model in which the front moves with constant speed. Independent of the precise details of the expansion, we show that obstacles create a kink in the front that persists over large distances and is insensitive to the details of the obstacle's shape. The small deviations between experimental findings and the predictions of the constant speed model can be understood with a more general reaction-diffusion model, which reduces to the constant speed model when the obstacle size is large compared to the front width. Using this framework, we demonstrate that frontier genotypes just grazing the side of an isolated obstacle increase in abundance, a phenomenon we call 'geometry-enhanced genetic drift', complementary to the founder effect associated with spatial bottlenecks. Bacterial range expansions around nutrient-poor barriers and stochastic simulations confirm this prediction. The effect of the obstacle on the genealogy of individuals at the front is characterized by simulations and rationalized using the constant speed model. Lastly, we consider the effect of two obstacles on front shape and genetic composition of the population illuminating the effects expected from

  15. Population genetic analysis of Enterocytozoon bieneusi in humans.

    PubMed

    Li, Wei; Cama, Vitaliano; Feng, Yaoyu; Gilman, Robert H; Bern, Caryn; Zhang, Xichen; Xiao, Lihua

    2012-01-01

    Genotyping based on sequence analysis of the ribosomal internal transcribed spacer has revealed significant genetic diversity in Enterocytozoonbieneusi. Thus far, the population genetics of E. bieneusi and its significance in the epidemiology of microsporidiosis have not been examined. In this study, a multilocus sequence typing of E. bieneusi in AIDS patients in Lima, Peru was conducted, using 72 specimens previously genotyped as A, D, IV, EbpC, WL11, Peru7, Peru8, Peru10 and Peru11 at the internal transcribed spacer locus. Altogether, 39 multilocus genotypes were identified among the 72 specimens. The observation of strong intragenic linkage disequilibria and limited genetic recombination among markers were indicative of an overall clonal population structure of E. bieneusi. Measures of pair-wise intergenic linkage disequilibria and a standardised index of association (IAS) based on allelic profile data further supported this conclusion. Both sequence-based and allelic profile-based phylogenetic analyses showed the presence of two genetically isolated groups in the study population, one (group 1) containing isolates of the anthroponotic internal transcribed spacer genotype A, and the other (group 2) containing isolates of multiple internal transcribed spacer genotypes (mainly genotypes D and IV) with zoonotic potential. The measurement of linkage disequilibria and recombination indicated group 2 had a clonal population structure, whereas group 1 had an epidemic population structure. The formation of the two sub-populations was confirmed by STRUCTURE and Wright's fixation index (FST) analyses. The data highlight the power of MLST in understanding the epidemiology of E. bieneusi. PMID:22534008

  16. How Obstacles Perturb Population Fronts and Alter Their Genetic Structure

    PubMed Central

    Möbius, Wolfram; Murray, Andrew W.; Nelson, David R.

    2015-01-01

    As populations spread into new territory, environmental heterogeneities can shape the population front and genetic composition. We focus here on the effects of an important building block of heterogeneous environments, isolated obstacles. With a combination of experiments, theory, and simulation, we show how isolated obstacles both create long-lived distortions of the front shape and amplify the effect of genetic drift. A system of bacteriophage T7 spreading on a spatially heterogeneous Escherichia coli lawn serves as an experimental model system to study population expansions. Using an inkjet printer, we create well-defined replicates of the lawn and quantitatively study the population expansion of phage T7. The transient perturbations of the population front found in the experiments are well described by a model in which the front moves with constant speed. Independent of the precise details of the expansion, we show that obstacles create a kink in the front that persists over large distances and is insensitive to the details of the obstacle’s shape. The small deviations between experimental findings and the predictions of the constant speed model can be understood with a more general reaction-diffusion model, which reduces to the constant speed model when the obstacle size is large compared to the front width. Using this framework, we demonstrate that frontier genotypes just grazing the side of an isolated obstacle increase in abundance, a phenomenon we call ‘geometry-enhanced genetic drift’, complementary to the founder effect associated with spatial bottlenecks. Bacterial range expansions around nutrient-poor barriers and stochastic simulations confirm this prediction. The effect of the obstacle on the genealogy of individuals at the front is characterized by simulations and rationalized using the constant speed model. Lastly, we consider the effect of two obstacles on front shape and genetic composition of the population illuminating the effects

  17. Loss of genetic variability in social spiders: genetic and phylogenetic consequences of population subdivision and inbreeding

    PubMed Central

    Agnarsson, I; Avilés, L; Maddison, W P

    2013-01-01

    The consequences of population subdivision and inbreeding have been studied in many organisms, particularly in plants. However, most studies focus on the short-term consequences, such as inbreeding depression. To investigate the consequences of both population fragmentation and inbreeding for genetic variability in the longer term, we here make use of a natural inbreeding experiment in spiders, where sociality and accompanying population subdivision and inbreeding have evolved repeatedly. We use mitochondrial and nuclear data to infer phylogenetic relationships among 170 individuals of Anelosimus spiders representing 23 species. We then compare relative mitochondrial and nuclear genetic variability of the inbred social species and their outbred relatives. We focus on four independently derived social species and four subsocial species, including two outbred–inbred sister species pairs. We find that social species have 50% reduced mitochondrial sequence divergence. As inbreeding is not expected to reduce genetic variability in the maternally inherited mitochondrial genome, this suggests the loss of variation due to strong population subdivision, founder effects, small effective population sizes (colonies as individuals) and lineage turnover. Social species have < 10% of the nuclear genetic variability of the outbred species, also suggesting the loss of genetic variability through founder effects and/or inbreeding. Inbred sociality hence may result in reduction in variability through various processes. Sociality in most Anelosimus species probably arose relatively recently (0.1–2 mya), with even the oldest social lineages having failed to diversify. This is consistent with the hypothesis that inbred spider sociality represents an evolutionary dead end. Heterosis underlies a species potential to respond to environmental change and/or disease. Inbreeding and loss of genetic variability may thus limit diversification in social Anelosimus lineages and similarly pose

  18. Genetic differentiation of Puccinia triticina populations in the Middle East and genetic similarity with populations in Central Asia

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Leaf rust of wheat, caused by Puccinia triticina is a common and widespread disease in the Middle East. The objective of this study was to determine if genetically differentiated groups of P. triticina are present in the Middle East region and to compare the population from the Middle East with the ...

  19. Population Genetics of Euphydryas Butterflies. I. Genetic Variation and the Neutrality Hypothesis

    PubMed Central

    McKechnie, Stephen W.; Ehrlich, Paul R.; White, Raymond R.

    1975-01-01

    Twenty-one populations of the checkerspot butterfly, Euphydryas editha, and ten populations of Euphydryas chalcedona were sampled for genetic variation at eight polymorphic enzyme loci. Both species possessed loci that were highly variable from population to population and loci that were virtually identical across all populations sampled. Our data indicate that the neutrality hypothesis is untenable for the loci studied, and therefore selection is indicated as the major factor responsible for producing these patterns. Thorough ecological work allowed gene flow to be ruled out (in almost all instances) as a factor maintaining similar gene frequencies across populations. The Lewontin-Krakauer test indicated magnitudes of heterogeneity among standardized variances of gene frequencies inconsistent with the neutrality hypothesis. The question of whether or not to correct this statistic for sample size is discussed. Observed equitability of gene frequencies of multiple allelic loci was found to be greater than that predicted under the neutrality hypothesis. Genetic differentiation presisting through two generations was found between the one pair of populations known to exchange significant numbers of individuals per generation. Two matrices of genetic distance between populations, based on the eight loci sampled, were found to be significantly correlated with a matrix of environmental distance, based on measures of fourteen environmental parameters. Correlations between gene frequencies and environmental parameters, results of multiple regression analysis, and results of principle component analysis showed strong patterns of association and of "explained" variation. The correlation analyses suggest which factors might be further investigated as proximate selective agents. PMID:1205135

  20. An Ancient Mediterranean Melting Pot: Investigating the Uniparental Genetic Structure and Population History of Sicily and Southern Italy

    PubMed Central

    Sarno, Stefania; Boattini, Alessio; Carta, Marilisa; Ferri, Gianmarco; Alù, Milena; Yao, Daniele Yang; Ciani, Graziella; Pettener, Davide; Luiselli, Donata

    2014-01-01

    Due to their strategic geographic location between three different continents, Sicily and Southern Italy have long represented a major Mediterranean crossroad where different peoples and cultures came together over time. However, its multi-layered history of migration pathways and cultural exchanges, has made the reconstruction of its genetic history and population structure extremely controversial and widely debated. To address this debate, we surveyed the genetic variability of 326 accurately selected individuals from 8 different provinces of Sicily and Southern Italy, through a comprehensive evaluation of both Y-chromosome and mtDNA genomes. The main goal was to investigate the structuring of maternal and paternal genetic pools within Sicily and Southern Italy, and to examine their degrees of interaction with other Mediterranean populations. Our findings show high levels of within-population variability, coupled with the lack of significant genetic sub-structures both within Sicily, as well as between Sicily and Southern Italy. When Sicilian and Southern Italian populations were contextualized within the Euro-Mediterranean genetic space, we observed different historical dynamics for maternal and paternal inheritances. Y-chromosome results highlight a significant genetic differentiation between the North-Western and South-Eastern part of the Mediterranean, the Italian Peninsula occupying an intermediate position therein. In particular, Sicily and Southern Italy reveal a shared paternal genetic background with the Balkan Peninsula and the time estimates of main Y-chromosome lineages signal paternal genetic traces of Neolithic and post-Neolithic migration events. On the contrary, despite showing some correspondence with its paternal counterpart, mtDNA reveals a substantially homogeneous genetic landscape, which may reflect older population events or different demographic dynamics between males and females. Overall, both uniparental genetic structures and TMRCA

  1. Paternal genetic affinity between western Austronesians and Daic populations

    PubMed Central

    2008-01-01

    Background Austronesian is a linguistic family spread in most areas of the Southeast Asia, the Pacific Ocean, and the Indian Ocean. Based on their linguistic similarity, this linguistic family included Malayo-Polynesians and Taiwan aborigines. The linguistic similarity also led to the controversial hypothesis that Taiwan is the homeland of all the Malayo-Polynesians, a hypothesis that has been debated by ethnologists, linguists, archaeologists, and geneticists. It is well accepted that the Eastern Austronesians (Micronesians and Polynesians) derived from the Western Austronesians (Island Southeast Asians and Taiwanese), and that the Daic populations on the mainland are supposed to be the headstream of all the Austronesian populations. Results In this report, we studied 20 SNPs and 7 STRs in the non-recombining region of the 1,509 Y chromosomes from 30 China Daic populations, 23 Indonesian and Vietnam Malayo-Polynesian populations, and 11 Taiwan aboriginal populations. These three groups show many resemblances in paternal lineages. Admixture analyses demonstrated that the Daic populations are hardly influenced by Han Chinese genetically, and that they make up the largest proportion of Indonesians. Most of the population samples contain a high frequency of haplogroup O1a-M119, which is nearly absent in other ethnic families. The STR network of haplogroup O1a* illustrated that Indonesian lineages did not derive from Taiwan aborigines as linguistic studies suggest, but from Daic populations. Conclusion We show that, in contrast to the Taiwan homeland hypothesis, the Island Southeast Asians do not have a Taiwan origin based on their paternal lineages. Furthermore, we show that both Taiwan aborigines and Indonesians likely derived from the Daic populations based on their paternal lineages. These two populations seem to have evolved independently of each other. Our results indicate that a super-phylum, which includes Taiwan aborigines, Daic, and Malayo-Polynesians, is

  2. Population and forensic genetic analyses of mitochondrial DNA control region variation from six major provinces in the Korean population.

    PubMed

    Hong, Seung Beom; Kim, Ki Cheol; Kim, Wook

    2015-07-01

    We generated complete mitochondrial DNA (mtDNA) control region sequences from 704 unrelated individuals residing in six major provinces in Korea. In addition to our earlier survey of the distribution of mtDNA haplogroup variation, a total of 560 different haplotypes characterized by 271 polymorphic sites were identified, of which 473 haplotypes were unique. The gene diversity and random match probability were 0.9989 and 0.0025, respectively. According to the pairwise comparison of the 704 control region sequences, the mean number of pairwise differences between individuals was 13.47±6.06. Based on the result of mtDNA control region sequences, pairwise FST genetic distances revealed genetic homogeneity of the Korean provinces on a peninsular level, except in samples from Jeju Island. This result indicates there may be a need to formulate a local mtDNA database for Jeju Island, to avoid bias in forensic parameter estimates caused by genetic heterogeneity of the population. Thus, the present data may help not only in personal identification but also in determining maternal lineages to provide an expanded and reliable Korean mtDNA database. These data will be available on the EMPOP database via accession number EMP00661. PMID:25900647

  3. Genetic Affinities of the Central Indian Tribal Populations

    PubMed Central

    Singh, Vipin Kumar; Shah, Anish M.; Anugula, Sharath; Rani, Deepa Selvi; Reddy, Alla G.; Eaaswarkhanth, Muthukrishnan; Chaubey, Gyaneshwer; Singh, Lalji; Thangaraj, Kumarasamy

    2012-01-01

    Background The central Indian state Madhya Pradesh is often called as ‘heart of India’ and has always been an important region functioning as a trinexus belt for three major language families (Indo-European, Dravidian and Austroasiatic). There are less detailed genetic studies on the populations inhabited in this region. Therefore, this study is an attempt for extensive characterization of genetic ancestries of three tribal populations, namely; Bharia, Bhil and Sahariya, inhabiting this region using haploid and diploid DNA markers. Methodology/Principal Findings Mitochondrial DNA analysis showed high diversity, including some of the older sublineages of M haplogroup and prominent R lineages in all the three tribes. Y-chromosomal biallelic markers revealed high frequency of Austroasiatic-specific M95-O2a haplogroup in Bharia and Sahariya, M82-H1a in Bhil and M17-R1a in Bhil and Sahariya. The results obtained by haploid as well as diploid genetic markers revealed strong genetic affinity of Bharia (a Dravidian speaking tribe) with the Austroasiatic (Munda) group. The gene flow from Austroasiatic group is further confirmed by their Y-STRs haplotype sharing analysis, where we determined their founder haplotype from the North Munda speaking tribe, while, autosomal analysis was largely in concordant with the haploid DNA results. Conclusions/Significance Bhil exhibited largely Indo-European specific ancestry, while Sahariya and Bharia showed admixed genetic package of Indo-European and Austroasiatic populations. Hence, in a landscape like India, linguistic label doesn't unequivocally follow the genetic footprints. PMID:22393414

  4. Genetic management of the Göttingen Minipig population.

    PubMed

    Simianer, Henner; Köhn, Friederike

    2010-01-01

    The Göttingen Minipig is a laboratory animal of worldwide importance. The breed was developed in the 1960's at the University of Göttingen, Germany, using the founder breeds Minnesota Minipigs, Vietnamese Potbelly Pig and German Landrace. After the initial period under free range conditions the population was stocked under high hygienic standards. In 1992 an exclusive licence contract was made between Ellegaard Göttingen Minipigs ApS in Denmark and the University of Göttingen. Since 2002 the production and marketing of Göttingen Minipigs in the USA is managed by Marshall Farms, Inc. under licence from Ellegaard Göttingen Minipigs A/S. Today, there are three Danish, one American and one German population. The genetic management for all populations is provided by the University of Göttingen. The main focus is the maintenance and reduction of inbreeding and genetic drift, the maintenance of a high degree of uniformity and genetic progress in the main selection traits. The main selection trait in the past was the number of piglets born alive. By producing many piglets per sow and year, a fast genetic exchange of breeding animals could be achieved leading to a minimised inbreeding in the populations. To satisfy the market demands of a small and easy to handle minipig and to overcome the problem of an antagonistic relationship between litter size and body weight, the trait body weight reduction was included in the selection scheme using a restricted selection index. It is planned for the future to include temperament traits in the breeding scheme. Due to fast developments in genome-based breeding applications, these new methods can soon be implemented for an efficient control of genetic drift and inbreeding or even for genome-based selection. PMID:20570747

  5. Genetic structure among continental and island populations of gyrfalcons.

    PubMed

    Johnson, Jeff A; Burnham, Kurt K; Burnham, William A; Mindell, David P

    2007-08-01

    Little is known about the possible influence that past glacial events have had on the phylogeography and population structure of avian predators in the Arctic and sub-Arctic. In this study, we use microsatellite and mitochondrial control region DNA variation to investigate the population genetic structure of gyrfalcons (Falco rusticolus) throughout a large portion of their circumpolar distribution. In most locations sampled, the mtDNA data revealed little geographic structure; however, five out of eight mtDNA haplotypes were unique to a particular geographic area (Greenland, Iceland, or Alaska) and the Iceland population differed from others based on haplotype frequency differences (F(ST)). With the microsatellite results, significant population structure (F(ST), principal components analysis, and cluster analysis) was observed identifying Greenland and Iceland as separate populations, while Norway, Alaska and Canada were identified as a single population consistent with contemporary gene flow across Russia. Within Greenland, differing levels of gene flow between western and eastern sampling locations was indicated with apparent asymmetric dispersal in western Greenland from north to south. This dispersal bias is in agreement with the distribution of plumage colour variants with white gyrfalcons in much higher proportion in northern Greenland. Lastly, because the mtDNA control region sequence differed by only one to four nucleotides from a common haplotype among all gyrfalcons, we infer that the observed microsatellite population genetic structure has developed since the last glacial maximum. This conclusion is further supported by our finding that a closely related species, the saker falcon (Falco cherrug), has greater genetic heterogeneity, including mtDNA haplotypes differing by 1-16 nucleotide substitutions from a common gyrfalcon haplotype. This is consistent with gyrfalcons having expanded rapidly from a single glacial-age refugium to their current

  6. The population genetics of clonal and partially clonal diploids.

    PubMed Central

    Balloux, François; Lehmann, Laurent; de Meeûs, Thierry

    2003-01-01

    The consequences of variable rates of clonal reproduction on the population genetics of neutral markers are explored in diploid organisms within a subdivided population (island model). We use both analytical and stochastic simulation approaches. High rates of clonal reproduction will positively affect heterozygosity. As a consequence, nearly twice as many alleles per locus can be maintained and population differentiation estimated as F(ST) value is strongly decreased in purely clonal populations as compared to purely sexual ones. With increasing clonal reproduction, effective population size first slowly increases and then points toward extreme values when the reproductive system tends toward strict clonality. This reflects the fact that polymorphism is protected within individuals due to fixed heterozygosity. Contrarily, genotypic diversity smoothly decreases with increasing rates of clonal reproduction. Asexual populations thus maintain higher genetic diversity at each single locus but a lower number of different genotypes. Mixed clonal/sexual reproduction is nearly indistinguishable from strict sexual reproduction as long as the proportion of clonal reproduction is not strongly predominant for all quantities investigated, except for genotypic diversities (both at individual loci and over multiple loci). PMID:12930767

  7. Exhaustive search for conservation networks of populations representing genetic diversity.

    PubMed

    Diniz-Filho, J A F; Diniz, J V B P L; Telles, M P C

    2016-01-01

    Conservation strategies routinely use optimization methods to identify the smallest number of units required to represent a set of features that need to be conserved, including biomes, species, and populations. In this study, we provide R scripts to facilitate exhaustive search for solutions that represent all of the alleles in networks with the smallest possible number of populations. The script also allows other variables to be added to describe the populations, thereby providing the basis for multi-objective optimization and the construction of Pareto curves by averaging the values in the solutions. We applied this algorithm to an empirical dataset that comprised 23 populations of Eugenia dysenterica, which is a tree species with a widespread distribution in the Cerrado biome. We observed that 15 populations would be necessary to represent all 249 alleles based on 11 microsatellite loci, and that the likelihood of representing all of the alleles with random networks is less than 0.0001. We selected the solution (from two with the smallest number of populations) obtained for the populations with a higher level of climatic stability as the best strategy for in situ conservation of genetic diversity of E. dysenterica. The scripts provided in this study are a simple and efficient alternative to more complex optimization methods, especially when the number of populations is relatively small (i.e., <25 populations). PMID:26909939

  8. Genetic Diversity and Genetic Structure of Different Types of Natural Populations in Osmanthus fragrans Lour. and the Relationships with Sex Ratio, Population Structure, and Geographic Isolation

    PubMed Central

    Hu, Shaoqing; Wu, Shuai; Wang, Yiguang; Zhang, Yuanyan

    2014-01-01

    Osmanthus fragrans Lour., an evergreen small tree, has the rare sexual system of androdioecy (coexistence of males and hermaphrodites), once with wide-spread natural distribution in the areas of the South Yangzi river basin. However, due to excessive human utilization, natural distribution became fragmented and the number and size of natural populations reduced sharply. With four different types of natural populations from the same region as research object, we aim to provide a comparative analysis on the relationships among genetic diversity, sexual system, population structure and size, and geographic isolation by ISSR. In genetic parameters of Ne, He, and I, the LQGC population had the highest value and the LQZGQ population had the lowest value. These indicated that LQGC population showed the highest genetic diversity, followed by QDH and JN population, and LQZGQ population exhibited the lowest genetic diversity. Genetic diversity in populations is closely related to population structure, reproduction mode, and sex ratio. However, there seems to be no obvious correlation between genetic diversity and population size. The results of AMOVA showed that genetic variations mostly occurred within populations. It indicates that no significant genetic differentiation among populations occurs, and geographic isolation has no significant effect on genetic diversity. PMID:25436228

  9. Genetic diversity and genetic structure of different types of natural populations in Osmanthus fragrans Lour. and the relationships with sex ratio, population structure, and geographic isolation.

    PubMed

    Hu, Shaoqing; Wu, Shuai; Wang, Yiguang; Zhao, Hongbo; Zhang, Yuanyan

    2014-01-01

    Osmanthus fragrans Lour., an evergreen small tree, has the rare sexual system of androdioecy (coexistence of males and hermaphrodites), once with wide-spread natural distribution in the areas of the South Yangzi river basin. However, due to excessive human utilization, natural distribution became fragmented and the number and size of natural populations reduced sharply. With four different types of natural populations from the same region as research object, we aim to provide a comparative analysis on the relationships among genetic diversity, sexual system, population structure and size, and geographic isolation by ISSR. In genetic parameters of N e , H e , and I, the LQGC population had the highest value and the LQZGQ population had the lowest value. These indicated that LQGC population showed the highest genetic diversity, followed by QDH and JN population, and LQZGQ population exhibited the lowest genetic diversity. Genetic diversity in populations is closely related to population structure, reproduction mode, and sex ratio. However, there seems to be no obvious correlation between genetic diversity and population size. The results of AMOVA showed that genetic variations mostly occurred within populations. It indicates that no significant genetic differentiation among populations occurs, and geographic isolation has no significant effect on genetic diversity. PMID:25436228

  10. Demography and genetic structure of a recovering grizzly bear population

    USGS Publications Warehouse

    Kendall, K.C.; Stetz, J.B.; Boulanger, J.; Macleod, A.C.; Paetkau, David; White, Gary C.

    2009-01-01

    Grizzly bears (brown bears; Ursus arctos) are imperiled in the southern extent of their range worldwide. The threatened population in northwestern Montana, USA, has been managed for recovery since 1975; yet, no rigorous data were available to monitor program success. We used data from a large noninvasive genetic sampling effort conducted in 2004 and 33 years of physical captures to assess abundance, distribution, and genetic health of this population. We combined data from our 3 sampling methods (hair trap, bear rub, and physical capture) to construct individual bear encounter histories for use in Huggins-Pledger closed mark-recapture models. Our population estimate, N?? = 765 (95% CI = 715-831) was more than double the existing estimate derived from sightings of females with young. Based on our results, the estimated known, human-caused mortality rate in 2004 was 4.6% (95% CI = 4.2-4.9%), slightly above the 4% considered sustainable; however, the high proportion of female mortalities raises concern. We used location data from telemetry, confirmed sightings, and genetic sampling to estimate occupied habitat. We found that grizzly bears occupied 33,480 km2 in the Northern Continental Divide Ecosystem (NCDE) during 1994-2007, including 10,340 km beyond the Recovery Zone. We used factorial correspondence analysis to identify potential barriers to gene flow within this population. Our results suggested that genetic interchange recently increased in areas with low gene flow in the past; however, we also detected evidence of incipient fragmentation across the major transportation corridor in this ecosystem. Our results suggest that the NCDE population is faring better than previously thought, and they highlight the need for a more rigorous monitoring program.

  11. Identification of genetic and epigenetic marks involved in population structure.

    PubMed

    Liu, Jingyu; Hutchison, Kent; Perrone-Bizzozero, Nora; Morgan, Marilee; Sui, Jing; Calhoun, Vince

    2010-01-01

    Population structure is well known as a prevalent and important factor in genetic studies, but its relevance in epigenetics is unclear. Very little is known about the affected epigenetic markers and their connections with genetics. In this study we assessed the impact of population diversity on genome wide single nucleotide polymorphisms (SNPs) and DNA methylation levels in 196 participants from five ethnic groups, using principle and independent component analyses. Three population stratification factors (PSFs) were identified in the genomic SNP dataset, accounting for a relatively large portion of total variance (6%). In contrast, only one PSF was identified in genomic methylation dataset accounting for 0.2% of total variance. This methylation PSF, however, was significantly correlated with the largest SNP PSF (r = 0.72, p<1E-23). We then investigated the top contributing markers in these two linked PSFs. The SNP PSF predominantly consists of 8 SNPs from three genes, SLC45A2, HERC2 and CTNNA2, known to encode skin/hair/eye color. The methylation PSF includes 48 methylated sites in 44 genes coding for basic molecular functions, including transcription regulation, DNA binding, cytokine, and transferase activity. Among them, 8 sites are either hypo- or hyper-methylated correlating to minor alleles of SNPs in the SNP PSF. We found that the genes in SNP and methylation PSFs share common biological processes including sexual/multicellular organism reproduction, cell-cell signaling and cytoskeleton organization. We further investigated the transcription regulatory network operating at these genes and identified that most of genes closely interact with ID2, which encodes for a helix-loop-helix inhibitor of DNA binding. Overall, our results show a significant correlation between genetic and epigenetic population stratification, and suggest that the interrelationship between genetic and epigenetic population structure is mediated via complex multiple gene interactions

  12. [Genetic diversity in two populations of the snail Strombus gigas (Gastropoda: Strombidae) from Yucatan, Mexico, using microsatellite].

    PubMed

    Zamora-Bustillos, Roberto; Rodríguez-Canul, Rossanna; García de León, Francisco J; Tello Cetina, Jorge

    2011-09-01

    The pink conch Strombus gigas is an important fisheries resource in the Caribbean region, including the Yucatán Peninsula. We analyzed the genetic diversity and genetic structure of two populations (Alacranes Reef and Chinchorro Bank) with the use of five microsatellite molecular markers. The results indicate that the two populations are in the same rank of genetic diversity (He), from 0.613 to 0.692. Significant deviation from H-WE was observed in the both populations due to deficit to heterozygotes, this was attributed to inbreeding as a consequence of over-fishing; nevertheless, other possible causes considered are mixing of individuals from two or more populations, and the existence of null alleles. Levels of genetic differentiation indicated the existence of a single homogenous population in the Yucatan Peninsula (F(ST) de 0.003, p = 0.49), which fits with highest levels of gene flow is significant (2.3 individuals) between both populations. Results from this study support the hypothesis that S. gigas is part of a single panmictic population in the Yucatan Peninsula; therefore, this fishery resource should be regulated the same way for both areas. PMID:22017119

  13. The population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens.

    PubMed

    Wilson, Benjamin A; Garud, Nandita R; Feder, Alison F; Assaf, Zoe J; Pennings, Pleuni S

    2016-01-01

    Drug resistance is a costly consequence of pathogen evolution and a major concern in public health. In this review, we show how population genetics can be used to study the evolution of drug resistance and also how drug resistance evolution is informative as an evolutionary model system. We highlight five examples from diverse organisms with particular focus on: (i) identifying drug resistance loci in the malaria parasite Plasmodium falciparum using the genomic signatures of selective sweeps, (ii) determining the role of epistasis in drug resistance evolution in influenza, (iii) quantifying the role of standing genetic variation in the evolution of drug resistance in HIV, (iv) using drug resistance mutations to study clonal interference dynamics in tuberculosis and (v) analysing the population structure of the core and accessory genome of Staphylococcus aureus to understand the spread of methicillin resistance. Throughout this review, we discuss the uses of sequence data and population genetic theory in studying the evolution of drug resistance. PMID:26578204

  14. Bucking the trend: genetic analysis reveals high diversity, large population size and low differentiation in a deep ocean cetacean.

    PubMed

    Thompson, K F; Patel, S; Baker, C S; Constantine, R; Millar, C D

    2016-03-01

    Understanding the genetic structure of a population is essential to its conservation and management. We report the level of genetic diversity and determine the population structure of a cryptic deep ocean cetacean, the Gray's beaked whale (Mesoplodon grayi). We analysed 530 bp of mitochondrial control region and 12 microsatellite loci from 94 individuals stranded around New Zealand and Australia. The samples cover a large area of the species distribution (~6000 km) and were collected over a 22-year period. We show high genetic diversity (h=0.933-0.987, π=0.763-0.996% and Rs=4.22-4.37, He=0.624-0.675), and, in contrast to other cetaceans, we found a complete lack of genetic structure in both maternally and biparentally inherited markers. The oceanic habitats around New Zealand are diverse with extremely deep waters, seamounts and submarine canyons that are suitable for Gray's beaked whales and their prey. We propose that the abundance of this rich habitat has promoted genetic homogeneity in this species. Furthermore, it has been suggested that the lack of beaked whale sightings is the result of their low abundance, but this is in contrast to our estimates of female effective population size based on mitochondrial data. In conclusion, the high diversity and lack of genetic structure can be explained by a historically large population size, in combination with no known exploitation, few apparent behavioural barriers and abundant habitat. PMID:26626574

  15. Genetically distinct coelacanth population off the northern Tanzanian coast

    PubMed Central

    Nikaido, Masato; Sasaki, Takeshi; Emerson, J. J.; Aibara, Mitsuto; Mzighani, Semvua I.; Budeba, Yohana L.; Ngatunga, Benjamin P.; Iwata, Masamitsu; Abe, Yoshitaka; Li, Wen-Hsiung; Okada, Norihiro

    2011-01-01

    Since the sensational discovery of a living coelacanth off the east coast of South Africa, the geographic distribution of viable coelacanth populations has been a subject of debate. In the past, the coelacanths off the African mainland were thought to be strays from the Comoros because most coelacanths captured were caught in the waters surrounding the Comoros archipelagos. However, in recent years, a large number of coelacanths were captured off the coast of Tanzania, including nine living specimens observed in a remotely operated vehicles survey. Thus, it is possible that there is a reproducing population inhabiting waters off the Tanzania coast. We have sequenced the complete mitochondrial genomes of 21 Tanzanian and 2 Comoran coelacanths and analyzed these sequences together with two additional full mitochondrial genomes and 47 d-loop sequences from the literature. We found that the coelacanth population off the northern Tanzanian coast is genetically differentiated from those of the southern Tanzania coast and the Comoros, whereas no significant genetic differentiation occurs between the latter two localities. The differentiation between the northern and southern Tanzanian coast populations is consistent with the hypothesis that the existence of northward-flowing ocean current along the Tanzanian coast may reduce or prevent gene flow from the northern to the southern population. Finally, we estimated that the population localized to the southern Tanzanian coast and the Comoros diverged from other coelacanths at least 200,000 y ago. These results indicate that the coelacanths off the northern Tanzania coast are not strays but a genetically distinct group. Our study provides important information for the conservation of this threatened “living fossil.” PMID:22025696

  16. Genetic variation in natural populations of Populus tremuloide

    SciTech Connect

    Cheliak, W.M.

    1980-01-01

    Vegetative reproduction results in a mosaic of clones throughout the extensive natural range of this species. An electrophoretic survey of 26 loci in 222 trees from seven natural populations in Alberta demonstrated great variability. Average observed population heterozygosity was 0.52 with an average of 2.3 alleles per locus; 84% of the loci were polymorphic. A model (for a finite population with neutral alleles) was developed to investigate the effects of partial vegetative reproduction on the amount of variation in a population. Results of the survey conformed to those predicted by the model for a population with a rate of sexual establishment greater than 1/N, where N is the population size. The model states that under these conditions, vegetative reproduction has no effect on the population. Therefore, the high level of observed variation is not an artifact of the mode of natural reproduction. These results support conclusions about high population variability based on phenotypic measurements and also suggest a genetic basis for this variation, rather than simply phenotypic plasticity.

  17. Genetic Admixture and Flavor Preferences: Androstenone Sensitivity in Malagasy Populations.

    PubMed

    Razafindrazaka, Harilanto; Monnereau, Aurore; Razafindrazaka, Dina; Tonasso, Laure; Schiavinato, Stephanie; Rakotoarisoa, Jean-Aimé; Radimilahy, Chantal; Letellier, Thierry; Pierron, Denis

    2015-01-01

    The genetic basis of androstenone anosmia has been well studied due to androstenone's putative role as a human sex pheromone and its presence in pork meat. Polymorphisms have been identified on the olfactory receptor gene OR7D4, which significantly affect perception of androstenone pleasantness and intensity in several Western populations. This study aims to investigate androstenone sensitivity and the influence of OR7D4 polymorphisms in non-Western populations. Androstenone perception was tested in 132 individuals from Madagascar using a double three-alternative choice test with two concentrations of androstenone (0.17 and 1.7 µg/ml). We found that Malagasy populations described this molecule in a similar way to European populations, and 21% of the sample was not able to smell androstenone. In contrast to previous studies, there was no significant evidence of the influence of rs61729907: C>T (R88W) and rs5020278: C>T polymorphisms (T133M) on androstenone sensitivity in Malagasy populations. We found, however, a significant effect of the polymorphism rs61732668 (P79L) and a significant difference in androstenone perception between populations in different locations across Madagascar. This study indicates the existence of population-specific factors in androstenone sensitivity, suggesting that population history has a role in shaping an individual's smell and flavor preferences and food preferences in general. PMID:26416322

  18. Genetics in Population Health Science: Strategies and Opportunities

    PubMed Central

    Moffitt, Terrie E.; Caspi, Avshalom

    2013-01-01

    Translational research is needed to leverage discoveries from the frontiers of genome science to improve public health. So far, public health researchers have largely ignored genetic discoveries, and geneticists have ignored important aspects of population health science. This mutual neglect should end. In this article, we discuss 3 areas where public health researchers can help to advance translation: (1) risk assessment: investigate genetic profiles as components in composite risk assessments; (2) targeted intervention: conduct life-course longitudinal studies to understand when genetic risks manifest in development and whether intervention during sensitive periods can have lasting effects; and (3) improved understanding of environmental causation: collaborate with geneticists on gene–environment interaction research. We illustrate with examples from our own research on obesity and smoking. PMID:23927511

  19. Genetics in population health science: strategies and opportunities.

    PubMed

    Belsky, Daniel W; Moffitt, Terrie E; Caspi, Avshalom

    2013-10-01

    Translational research is needed to leverage discoveries from the frontiers of genome science to improve public health. So far, public health researchers have largely ignored genetic discoveries, and geneticists have ignored important aspects of population health science. This mutual neglect should end. In this article, we discuss 3 areas where public health researchers can help to advance translation: (1) risk assessment: investigate genetic profiles as components in composite risk assessments; (2) targeted intervention: conduct life-course longitudinal studies to understand when genetic risks manifest in development and whether intervention during sensitive periods can have lasting effects; and (3) improved understanding of environmental causation: collaborate with geneticists on gene-environment interaction research. We illustrate with examples from our own research on obesity and smoking. PMID:23927511

  20. Genetic Diversity and Population Structure of Haemonchus contortus.

    PubMed

    Gilleard, J S; Redman, E

    2016-01-01

    Haemonchus contortus is one of the most successful and problematic livestock parasites worldwide. From its apparent evolutionary origins in sub-Saharan Africa, it is now found in small ruminants in almost all regions of the globe, and can infect a range of different domestic and wildlife artiodactyl hosts. It has a remarkably high propensity to develop resistance to anthelmintic drugs, making control increasingly difficult. The success of this parasite is, at least in part, due to its extremely high levels of genetic diversity that, in turn, provide a high adaptive capacity. Understanding this genetic diversity is important for many areas of research including anthelmintic resistance, epidemiology, control, drug/vaccine development and molecular diagnostics. In this article, we review the current knowledge of H. contortus genetic diversity and population structure for both field isolates and laboratory strains. We highlight the practical relevance of this knowledge with a particular emphasis on anthelmintic resistance research. PMID:27238002

  1. Distribution and population genetics of walleye and sauger

    USGS Publications Warehouse

    Haponski, Amanda E.; Sloss, Brian L.

    2014-01-01

    Conserving genetic diversity and local adaptations are management priorities for wild populations of exploited species, which increasingly are subject to climate change, habitat loss, and pollution. These constitute growing concerns for the walleye Sander vitreus, an ecologically and economically valuable North American temperate fish with large Laurentian Great Lakes' fisheries. This study compares genetic diversity and divergence patterns across its widespread native range using mitochondrial (mt) DNA control region sequences and nine nuclear DNA microsatellite (μsat) loci, examining historic and contemporary influences. We analyze the genetic and morphological characters of a putative endemic variant– “blue pike” S. v. “glaucus” –described from Lakes Erie and Ontario, which became extinct. Walleye with turquoise-colored mucus also are evaluated, since some have questioned whether these are related to the “blue pike”.

  2. Genetic map of Triticum turgidum based on a hexaploid wheat population without genetic recombination for D genome

    PubMed Central

    2012-01-01

    Background A synthetic doubled-haploid hexaploid wheat population, SynDH1, derived from the spontaneous chromosome doubling of triploid F1 hybrid plants obtained from the cross of hybrids Triticum turgidum ssp. durum line Langdon (LDN) and ssp. turgidum line AS313, with Aegilops tauschii ssp. tauschii accession AS60, was previously constructed. SynDH1 is a tetraploidization-hexaploid doubled haploid (DH) population because it contains recombinant A and B chromosomes from two different T. turgidum genotypes, while all the D chromosomes from Ae. tauschii are homogenous across the whole population. This paper reports the construction of a genetic map using this population. Results Of the 606 markers used to assemble the genetic map, 588 (97%) were assigned to linkage groups. These included 513 Diversity Arrays Technology (DArT) markers, 72 simple sequence repeat (SSR), one insertion site-based polymorphism (ISBP), and two high-molecular-weight glutenin subunit (HMW-GS) markers. These markers were assigned to the 14 chromosomes, covering 2048.79 cM, with a mean distance of 3.48 cM between adjacent markers. This map showed good coverage of the A and B genome chromosomes, apart from 3A, 5A, 6A, and 4B. Compared with previously reported maps, most shared markers showed highly consistent orders. This map was successfully used to identify five quantitative trait loci (QTL), including two for spikelet number on chromosomes 7A and 5B, two for spike length on 7A and 3B, and one for 1000-grain weight on 4B. However, differences in crossability QTL between the two T. turgidum parents may explain the segregation distortion regions on chromosomes 1A, 3B, and 6B. Conclusions A genetic map of T. turgidum including 588 markers was constructed using a synthetic doubled haploid (SynDH) hexaploid wheat population. Five QTLs for three agronomic traits were identified from this population. However, more markers are needed to increase the density and resolution of this map in the

  3. Restoration of genetic connectivity among Northern Rockies wolf populations.

    PubMed

    Hebblewhite, Mark; Musiani, Marco; Mills, L Scott

    2010-10-01

    Probably no conservation genetics issue is currently more controversial than the question of whether grey wolves (Canis lupus) in the Northern Rockies have recovered to genetically effective levels. Following the dispersal-based recolonization of Northwestern Montana from Canada, and reintroductions to Yellowstone and Central Idaho, wolves have vastly exceeded population recovery goals of 300 wolves distributed in at least 10 breeding pairs in each of Wyoming, Idaho and Montana. With >1700 wolves currently, efforts to delist wolves from endangered status have become mired in legal battles over the distinct population segment (DPS) clause of the Endangered Species Act (ESA), and whether subpopulations within the DPS were genetically isolated. An earlier study by vonHoldt et al. (2008) suggested Yellowstone National Park wolves were indeed isolated and was used against delisting in 2008. Since then, wolves were temporarily delisted, and a first controversial hunting season occurred in fall of 2009. Yet, concerns over the genetic recovery of wolves in the Northern Rockies remain, and upcoming District court rulings in the summer of 2010 will probably include consideration of gene flow between subpopulations. In this issue of Molecular Ecology, vonHoldt et al. (2010) conduct the largest analysis of gene flow and population structure of the Northern Rockies wolves to date. Using an impressive sampling design and novel analytic methods, vonHoldt et al. (2010) show substantial levels of gene flow between three identified subpopulations of wolves within the Northern Rockies, clarifying previous analyses and convincingly showing genetic recovery. PMID:21040035

  4. Reconstructing the population genetic history of the Caribbean.

    PubMed

    Moreno-Estrada, Andrés; Gravel, Simon; Zakharia, Fouad; McCauley, Jacob L; Byrnes, Jake K; Gignoux, Christopher R; Ortiz-Tello, Patricia A; Martínez, Ricardo J; Hedges, Dale J; Morris, Richard W; Eng, Celeste; Sandoval, Karla; Acevedo-Acevedo, Suehelay; Norman, Paul J; Layrisse, Zulay; Parham, Peter; Martínez-Cruzado, Juan Carlos; Burchard, Esteban González; Cuccaro, Michael L; Martin, Eden R; Bustamante, Carlos D

    2013-11-01

    The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, we investigate the population genetic history of this region by characterizing patterns of genome-wide variation among 330 individuals from three of the Greater Antilles (Cuba, Puerto Rico, Hispaniola), two mainland (Honduras, Colombia), and three Native South American (Yukpa, Bari, and Warao) populations. We combine these data with a unique database of genomic variation in over 3,000 individuals from diverse European, African, and Native American populations. We use local ancestry inference and tract length distributions to test different demographic scenarios for the pre- and post-colonial history of the region. We develop a novel ancestry-specific PCA (ASPCA) method to reconstruct the sub-continental origin of Native American, European, and African haplotypes from admixed genomes. We find that the most likely source of the indigenous ancestry in Caribbean islanders is a Native South American component shared among inland Amazonian tribes, Central America, and the Yucatan peninsula, suggesting extensive gene flow across the Caribbean in pre-Columbian times. We find evidence of two pulses of African migration. The first pulse--which today is reflected by shorter, older ancestry tracts--consists of a genetic component more similar to coastal West African regions involved in early stages of the trans-Atlantic slave trade. The second pulse--reflected by longer, younger tracts--is more similar to present-day West-Central African populations, supporting historical records of later transatlantic deportation. Surprisingly, we also identify a Latino-specific European component that has significantly diverged from its parental Iberian source populations, presumably as a result of small European founder population size. We demonstrate that the ancestral components in admixed genomes can be traced back to distinct sub-continental source

  5. Reconstructing the Population Genetic History of the Caribbean

    PubMed Central

    Moreno-Estrada, Andrés; Gravel, Simon; Zakharia, Fouad; McCauley, Jacob L.; Byrnes, Jake K.; Gignoux, Christopher R.; Ortiz-Tello, Patricia A.; Martínez, Ricardo J.; Hedges, Dale J.; Morris, Richard W.; Eng, Celeste; Sandoval, Karla; Acevedo-Acevedo, Suehelay; Norman, Paul J.; Layrisse, Zulay; Parham, Peter; Martínez-Cruzado, Juan Carlos; Burchard, Esteban González; Cuccaro, Michael L.; Martin, Eden R.; Bustamante, Carlos D.

    2013-01-01

    The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, we investigate the population genetic history of this region by characterizing patterns of genome-wide variation among 330 individuals from three of the Greater Antilles (Cuba, Puerto Rico, Hispaniola), two mainland (Honduras, Colombia), and three Native South American (Yukpa, Bari, and Warao) populations. We combine these data with a unique database of genomic variation in over 3,000 individuals from diverse European, African, and Native American populations. We use local ancestry inference and tract length distributions to test different demographic scenarios for the pre- and post-colonial history of the region. We develop a novel ancestry-specific PCA (ASPCA) method to reconstruct the sub-continental origin of Native American, European, and African haplotypes from admixed genomes. We find that the most likely source of the indigenous ancestry in Caribbean islanders is a Native South American component shared among inland Amazonian tribes, Central America, and the Yucatan peninsula, suggesting extensive gene flow across the Caribbean in pre-Columbian times. We find evidence of two pulses of African migration. The first pulse—which today is reflected by shorter, older ancestry tracts—consists of a genetic component more similar to coastal West African regions involved in early stages of the trans-Atlantic slave trade. The second pulse—reflected by longer, younger tracts—is more similar to present-day West-Central African populations, supporting historical records of later transatlantic deportation. Surprisingly, we also identify a Latino-specific European component that has significantly diverged from its parental Iberian source populations, presumably as a result of small European founder population size. We demonstrate that the ancestral components in admixed genomes can be traced back to distinct sub

  6. Factors affecting levels of genetic diversity in natural populations.

    PubMed Central

    Amos, W; Harwood, J

    1998-01-01

    Genetic variability is the clay of evolution, providing the base material on which adaptation and speciation depend. It is often assumed that most interspecific differences in variability are due primarily to population size effects, with bottlenecked populations carrying less variability than those of stable size. However, we show that population bottlenecks are unlikely to be the only factor, even in classic case studies such as the northern elephant seal and the cheetah, where genetic polymorphism is virtually absent. Instead, we suggest that the low levels of variability observed in endangered populations are more likely to result from a combination of publication biases, which tend to inflate the level of variability which is considered 'normal', and inbreeding effects, which may hasten loss of variability due to drift. To account for species with large population sizes but low variability we advance three hypotheses. First, it is known that certain metapopulation structures can result in effective population sizes far below the census size. Second, there is increasing evidence that heterozygous sites mutate more frequently than equivalent homozygous sites, plausibly because mismatch repair between homologous chromosomes during meiosis provides extra opportunities to mutate. Such a mechanism would undermine the simple relationship between heterozygosity and effective population size. Third, the fact that related species that differ greatly in variability implies that large amounts of variability can be gained or lost rapidly. We argue that such cases are best explained by rapid loss through a genome-wide selective sweep, and suggest a mechanism by which this could come about, based on forced changes to a control gene inducing coevolution in the genes it controls. Our model, based on meiotic drive in mammals, but easily extended to other systems, would tend to facilitate population isolation by generating molecular incompatabilities. Circumstances can even be

  7. APOL1 Kidney Risk Alleles: Population Genetics and Disease Associations

    PubMed Central

    Limou, Sophie; Nelson, George W.; Kopp, Jeffrey B.; Winkler, Cheryl A.

    2014-01-01

    APOL1 kidney disease is a unique case in the field of the genetics of common disease: 2 variants (termed G1 and G2) with high population frequency have been repeatedly associated with nondiabetic CKDs, with very strong effect size (odds ratios 3–29) in populations of sub-Saharan African descent. This review provides an update on the spectrum of APOL1 kidney disease and on the worldwide distribution of these kidney risk variants. We also summarize the proper way to run a recessive analysis on joint and independent effects of APOL1 G1 and G2 kidney risk variants. PMID:25168832

  8. [Application of population genetics in the field of medicine].

    PubMed

    Octavio-Aguilar, Pablo; Ramos-Frías, Josefina

    2014-01-01

    Human populations follow the same evolutionary principles as other organisms, although mixed with social and cultural elements, which can result in a high prevalence of certain diseases within specific ethnic groups. In this work, the Hardy-Weinberg principle is analyzed from a medical, social and biological viewpoint to understand the evolutionary processes of autosomal recessive diseases. It can be concluded that the incidence of these diseases is inversely related to the levels of genetic variability within populations, which depends on colonization, recolonization and migration events, as well as on social conventions such as racism, social stratification and segregation. PMID:24967923

  9. Adapting populations in space: clonal interference and genetic diversity

    NASA Astrophysics Data System (ADS)

    Weissman, Daniel; Barton, Nick

    Most species inhabit ranges much larger than the scales over which individuals interact. How does this spatial structure interact with adaptive evolution? We consider a simple model of a spatially-extended, adapting population and show that, while clonal interference severely limits the adaptation of purely asexual populations, even rare recombination is enough to allow adaptation at rates approaching those of well-mixed populations. We also find that the genetic hitchhiking produced by the adaptive alleles sweeping through the population has strange effects on the patterns of genetic diversity. In large spatial ranges, even low rates of adaptation cause all individuals in the population to rapidly trace their ancestry back to individuals living in a small region in the center of the range. The probability of fixation of an allele is thus strongly dependent on the allele's spatial location, with alleles from the center favored. Surprisingly, these effects are seen genome-wide (instead of being localized to the regions of the genome undergoing the sweeps). The spatial concentration of ancestry produces a power-law dependence of relatedness on distance, so that even individuals sampled far apart are likely to be fairly closely related, masking the underlying spatial structure.

  10. Into the depth of population genetics: pattern of structuring in mesophotic red coral populations

    NASA Astrophysics Data System (ADS)

    Costantini, Federica; Abbiati, Marco

    2016-03-01

    Deep-sea reef-building corals are among the most conspicuous invertebrates inhabiting the hard-bottom habitats worldwide and are particularly susceptible to human threats. The precious red coral ( Corallium rubrum, L. 1758) has a wide bathymetric distribution, from shallow up to 800 m depth, and represents a key species in the Mediterranean mesophotic reefs. Several studies have investigated genetic variability in shallow-water red coral populations, while geographic patterns in mesophotic habitats are largely unknown. This study investigated genetic variability of C. rubrum populations dwelling between 55 and 120 m depth, from the Ligurian to the Ionian Sea along about 1500 km of coastline. A total of 18 deep rocky banks were sampled. Colonies were analyzed by means of a set of microsatellite loci and the putative control region of the mitochondrial DNA. Collected data were compared with previous studies. Both types of molecular markers showed high genetic similarity between populations within the northern (Ligurian Sea and Tuscan Archipelago) and the southern (Tyrrhenian and Ionian seas) study areas. Variability in habitat features between the sampling sites did not affect the genetic variability of the populations. Conversely, the patchy distribution of suitable habitats affected populations' connectivity within and among deep coral banks. Based on these results and due to the emphasis on red coral protection in the Mediterranean Sea by international institutions, red coral could be promoted as a `focal species' to develop management plans for the conservation of deep coralligenous reefs, a reservoir of marine biodiversity.

  11. Population genetic segmentation of MHC-correlated perfume preferences.

    PubMed

    Hämmerli, A; Schweisgut, C; Kaegi, M

    2012-04-01

    It has become difficult to find a matching perfume. An overwhelming number of 300 new perfumes launch each year, and marketing campaigns target pre-defined groups based on gender, age or income rather than on individual preferences. Recent evidence for a genetic basis of perfume preferences, however, could be the starting point for a novel population genetic approach to better match perfumes with people's preferences. With a total of 116 participants genotyped for alleles of three loci of the major histocompatibility complex (MHC), the aim of this study was to test whether common MHC alleles could be used as genetic markers to segment a given population into preference types. Significant deviations from random expectations for a set of 10 common perfume ingredients indicate how such segmentation could be achieved. In addition, preference patterns of participants confronted with images that contained a sexual communication context significantly differed in their ratings for some of the scents compared with participants confronted with images of perfume bottles. This strongly supports the assumption that genetically correlated perfume preferences evolved in the context of sexual communication. The results are discussed in the light of perfume customization. PMID:22084926

  12. Spontaneous genetic clustering in populations of competing organisms.

    PubMed

    Rogers, Tim; McKane, Alan J; Rossberg, Axel G

    2012-12-01

    We introduce and analyse an individual-based evolutionary model, in which a population of genetically diverse organisms compete with each other for limited resources. Through theoretical analysis and stochastic simulations, we show that the model exhibits a pattern-forming instability which is highly amplified by the effects of demographic noise, leading to the spontaneous formation of genotypic clusters. This mechanism supports the thesis that stochasticity has a central role in the formation and coherence of species. PMID:23114226

  13. Ecological and Genetic Barriers Differentiate Natural Populations of Saccharomyces cerevisiae.

    PubMed

    Clowers, Katie J; Heilberger, Justin; Piotrowski, Jeff S; Will, Jessica L; Gasch, Audrey P

    2015-09-01

    How populations that inhabit the same geographical area become genetically differentiated is not clear. To investigate this, we characterized phenotypic and genetic differences between two populations of Saccharomyces cerevisiae that in some cases inhabit the same environment but show relatively little gene flow. We profiled stress sensitivity in a group of vineyard isolates and a group of oak-soil strains and found several niche-related phenotypes that distinguish the populations. We performed bulk-segregant mapping on two of the distinguishing traits: The vineyard-specific ability to grow in grape juice and oak-specific tolerance to the cell wall damaging drug Congo red. To implicate causal genes, we also performed a chemical genomic screen in the lab-strain deletion collection and identified many important genes that fell under quantitative trait loci peaks. One gene important for growth in grape juice and identified by both the mapping and the screen was SSU1, a sulfite-nitrite pump implicated in wine fermentations. The beneficial allele is generated by a known translocation that we reasoned may also serve as a genetic barrier. We found that the translocation is prevalent in vineyard strains, but absent in oak strains, and presents a postzygotic barrier to spore viability. Furthermore, the translocation was associated with a fitness cost to the rapid growth rate seen in oak-soil strains. Our results reveal the translocation as a dual-function locus that enforces ecological differentiation while producing a genetic barrier to gene flow in these sympatric populations. PMID:25953281

  14. Ecological and Genetic Barriers Differentiate Natural Populations of Saccharomyces cerevisiae

    PubMed Central

    Clowers, Katie J.; Heilberger, Justin; Piotrowski, Jeff S.; Will, Jessica L.; Gasch, Audrey P.

    2015-01-01

    How populations that inhabit the same geographical area become genetically differentiated is not clear. To investigate this, we characterized phenotypic and genetic differences between two populations of Saccharomyces cerevisiae that in some cases inhabit the same environment but show relatively little gene flow. We profiled stress sensitivity in a group of vineyard isolates and a group of oak-soil strains and found several niche-related phenotypes that distinguish the populations. We performed bulk-segregant mapping on two of the distinguishing traits: The vineyard-specific ability to grow in grape juice and oak-specific tolerance to the cell wall damaging drug Congo red. To implicate causal genes, we also performed a chemical genomic screen in the lab-strain deletion collection and identified many important genes that fell under quantitative trait loci peaks. One gene important for growth in grape juice and identified by both the mapping and the screen was SSU1, a sulfite-nitrite pump implicated in wine fermentations. The beneficial allele is generated by a known translocation that we reasoned may also serve as a genetic barrier. We found that the translocation is prevalent in vineyard strains, but absent in oak strains, and presents a postzygotic barrier to spore viability. Furthermore, the translocation was associated with a fitness cost to the rapid growth rate seen in oak-soil strains. Our results reveal the translocation as a dual-function locus that enforces ecological differentiation while producing a genetic barrier to gene flow in these sympatric populations. PMID:25953281

  15. The phylogeography of Fagus hayatae (Fagaceae): genetic isolation among populations.

    PubMed

    Ying, Ling-Xiao; Zhang, Ting-Ting; Chiu, Ching-An; Chen, Tze-Ying; Luo, Shu-Jin; Chen, Xiao-Yong; Shen, Ze-Hao

    2016-05-01

    The beech species Fagus hayatae is an important relict tree species in subtropical China, whose biogeographical patterns may reflect floral responses to climate change in this region during the Quaternary. Previous studies have revealed phylogeography for three of the four Fagus species in China, but study on F. hayatae, the most sparsely distributed of these species, is still lacking. Here, molecular methods based on eight simple sequence repeat (SSR) loci of nuclear DNA (nDNA) and three chloroplast DNA (cpDNA) sequences were applied for analyses of genetic diversity and structure in 375 samples from 14 F. hayatae populations across its whole range. Both nDNA and cpDNA indicated a high level of genetic diversity in this species. Significant fixation indexes and departures from the Hardy-Weinberg equilibrium, with a genetic differentiation parameter of R st of 0.233, were detected in nDNA SSR loci among populations, especially those on Taiwan Island, indicating strong geographic partitioning. The populations were classified into two clusters, without a prominent signal of isolation-by-distance. For the 15 haplotypes detected in the cpDNA sequence fragments, there was a high genetic differentiation parameter (G st = 0.712) among populations. A high G st of 0.829 was also detected outside but not within the Sichuan Basin. Consistent with other Fagus species in China, no recent population expansion was detected from tests of neutrality and mismatch distribution analysis. Overall, genetic isolation with limited gene flow was prominent for this species and significant phylogeographic structures existed across its range except for those inside the Sichuan Basin. Our study suggested long-term geographic isolation in F. hayatae with limited population admixture and the existence of multiple refugia in the mountainous regions of the Sichuan Basin and southeast China during the Quaternary. These results may provide useful information critical for the conservation of F

  16. Boosting forward-time population genetic simulators through genotype compression

    PubMed Central

    2013-01-01

    Background Forward-time population genetic simulations play a central role in deriving and testing evolutionary hypotheses. Such simulations may be data-intensive, depending on the settings to the various parameters controlling them. In particular, for certain settings, the data footprint may quickly exceed the memory of a single compute node. Results We develop a novel and general method for addressing the memory issue inherent in forward-time simulations by compressing and decompressing, in real-time, active and ancestral genotypes, while carefully accounting for the time overhead. We propose a general graph data structure for compressing the genotype space explored during a simulation run, along with efficient algorithms for constructing and updating compressed genotypes which support both mutation and recombination. We tested the performance of our method in very large-scale simulations. Results show that our method not only scales well, but that it also overcomes memory issues that would cripple existing tools. Conclusions As evolutionary analyses are being increasingly performed on genomes, pathways, and networks, particularly in the era of systems biology, scaling population genetic simulators to handle large-scale simulations is crucial. We believe our method offers a significant step in that direction. Further, the techniques we provide are generic and can be integrated with existing population genetic simulators to boost their performance in terms of memory usage. PMID:23763838

  17. Utilization of RAPD markers to assess genetic diversity of wild populations of North American ginseng (Panax quinquefolium).

    PubMed

    Lim, Wansang; Mudge, Kenneth W; Weston, Leslie A

    2007-01-01

    The Catskill Mountains of New York State are an important source of wild-collected American ginseng (Panax quinquefolium) and, increasingly, of woods-cultivated ginseng. The objective of this study was to assess genetic diversity among 9 different wild ginseng populations in and adjacent to the Catskill Mountain region of New York State and to compare these to wild populations from other states including Kentucky, Tennessee, North Carolina, Pennsylvania, and Virginia, and one cultivated population from Wisconsin. Randomly amplified polymorphic DNA (RAPD) markers were used to estimate the genetic distance among samples from the 15 populations. Pooled DNA from 10 plants of each of 8 New York populations was initially screened with 64 random primers; subsequently, the 15 primers that exhibited the greatest number of reproducible polymorphic markers were selected for further experimentation. Gel electrophoresis with the selected 15 primers produced 124 highly reproducible polymorphic bands. The ratio of discordant bands to total bands scored was used to estimate the genetic distance within and among populations. Multidimensional scaling (MDS) of the relation matrix showed distinctly separate clusters between New York and non-New York populations, indicating separation between these two groupings. The MDS analysis was confirmed using pooled chi-square tests for fragment homogeneity. This study shows that RAPD markers can be used as population-specific markers for Panax quinquefolium, and may eventually be utilized as markers for ginsenoside assessment. PMID:17315311

  18. Contemporary paternal genetic landscape of Polish and German populations: from early medieval Slavic expansion to post-World War II resettlements.

    PubMed

    Rębała, Krzysztof; Martínez-Cruz, Begoña; Tönjes, Anke; Kovacs, Peter; Stumvoll, Michael; Lindner, Iris; Büttner, Andreas; Wichmann, H-Erich; Siváková, Daniela; Soták, Miroslav; Quintana-Murci, Lluís; Szczerkowska, Zofia; Comas, David

    2013-04-01

    Homogeneous Proto-Slavic genetic substrate and/or extensive mixing after World War II were suggested to explain homogeneity of contemporary Polish paternal lineages. Alternatively, Polish local populations might have displayed pre-war genetic heterogeneity owing to genetic drift and/or gene flow with neighbouring populations. Although sharp genetic discontinuity along the political border between Poland and Germany indisputably results from war-mediated resettlements and homogenisation, it remained unknown whether Y-chromosomal diversity in ethnically/linguistically defined populations was clinal or discontinuous before the war. In order to answer these questions and elucidate early Slavic migrations, 1156 individuals from several Slavic and German populations were analysed, including Polish pre-war regional populations and an autochthonous Slavic population from Germany. Y chromosomes were assigned to 39 haplogroups and genotyped for 19 STRs. Genetic distances revealed similar degree of differentiation of Slavic-speaking pre-war populations from German populations irrespective of duration and intensity of contacts with German speakers. Admixture estimates showed minor Slavic paternal ancestry (~20%) in modern eastern Germans and hardly detectable German paternal ancestry in Slavs neighbouring German populations for centuries. BATWING analysis of isolated Slavic populations revealed that their divergence was preceded by rapid demographic growth, undermining theory that Slavic expansion was primarily linguistic rather than population spread. Polish pre-war regional populations showed within-group heterogeneity and lower STR variation within R-M17 subclades compared with modern populations, which might have been homogenised by war resettlements. Our results suggest that genetic studies on early human history in the Vistula and Oder basins should rely on reconstructed pre-war rather than modern populations. PMID:22968131

  19. Expanding the population genetic perspective of cnidarian-Symbiodinium symbioses.

    PubMed

    Santos, Scott R

    2014-09-01

    The modern synthesis was a seminal period in the biological sciences, establishing many of the core principles of evolutionary biology that we know today. Significant catalysts were the contributions of R.A. Fisher, J.B.S. Haldane and Sewall Wright (and others) developing the theoretical underpinning of population genetics, thus demonstrating adaptive evolution resulted from the interplay of forces such as natural selection and mutation within groups of individuals occupying the same space and time (i.e. a population). Given its importance, it is surprising that detailed population genetic data remain lacking for numerous organisms vital to many ecosystems. For example, the coral reef ecosystem is well recognized for its high biodiversity and productivity, numerous ecological services and significant economic and societal values (Moberg & Folke 1999;Cinner 2014). Many coral reef invertebrates form symbiotic relationships with single-celled dinoflagellates within the genus Symbiodinium Freudenthal (Taylor 1974), with hosts providing these (typically) intracellular symbionts with by-products of metabolism and in turn receiving photosynthetically fixed carbon capable of meeting hosts' respiratory demands (Falkowski et al. 1984; Muscatine et al. 1984). Unfortunately, the health and integrity of the coral reef ecosystem has been significantly and negatively impacted by onslaughts like anthropogenic eutrophication and disease in addition to global climate change, with increased incidences of 'bleaching' events (characterized as the loss of photosynthetic pigments from the algal cell or massive reduction of Symbiodinium density from hosts' tissue) and host mortality leading to staggering declines in geographic coverage (Bruno & Selig 2007) that have raised questions on the viability of this ecosystem as we know it (Bellwood et al. 2004; Parmesan 2006). One avenue towards anticipating the future of the coral reef ecosystem is by developing a broader and deeper

  20. High Spatial Genetic Structure and Genetic Diversity in Chinese Populations of Sitobion miscanthi (Hemiptera: Aphididae).

    PubMed

    Wang, Yongmo; Hereward, James P; Zhang, Guoan

    2016-02-01

    The wheat aphid, Sitobion miscanthi Takahashi, a serious wheat pest, was previously considered to be highly migratory and anholocyclic in China. We recorded 69 alleles and 346 multilocus genotypes among 708 aphid individuals from 12 populations in China using 5 microsatellite loci. This genotypic diversity indicates that at least some holocyclic lineages exist. Bayesian clustering analysis revealed that there are two differentiated genetic groups of S. misanthi, one northern and one southern, in China. Principal coordinates analysis of population genetic distance, pairwise F(ST)'s, and network analysis of individual minimum spanning distance also supported the division. Low levels of migration were detected between the northern and southern sampling sites, but the high genetic differentiation does not support the hypothesis S. miscanthi overwinters in the south and migrates to the north in the spring annually. PMID:26487744

  1. GEOGRAPHIC AND ENVIRONMENTAL CORRELATES OR REGIONAL POPULATION GENETIC STRUCTURE IN THE CENTRAL STONEROLLER (CAMPOSTOMA ANOMALUM)

    EPA Science Inventory

    Environmental factors that impact population sizes, migration rates, mutation rates or selective forces can leave lasting genetic imprints on patterns of intraspecific genetic variation. This suggests that measures of genetic diversity may be useful indicators of the condition o...

  2. Chromosomal Rearrangements as Barriers to Genetic Homogenization between Archaic and Modern Humans.

    PubMed

    Rogers, Rebekah L

    2015-12-01

    Chromosomal rearrangements, which shuffle DNA throughout the genome, are an important source of divergence across taxa. Using a paired-end read approach with Illumina sequence data for archaic humans, I identify changes in genome structure that occurred recently in human evolution. Hundreds of rearrangements indicate genomic trafficking between the sex chromosomes and autosomes, raising the possibility of sex-specific changes. Additionally, genes adjacent to genome structure changes in Neanderthals are associated with testis-specific expression, consistent with evolutionary theory that new genes commonly form with expression in the testes. I identify one case of new-gene creation through transposition from the Y chromosome to chromosome 10 that combines the 5'-end of the testis-specific gene Fank1 with previously untranscribed sequence. This new transcript experienced copy number expansion in archaic genomes, indicating rapid genomic change. Among rearrangements identified in Neanderthals, 13% are transposition of selfish genetic elements, whereas 32% appear to be ectopic exchange between repeats. In Denisovan, the pattern is similar but numbers are significantly higher with 18% of rearrangements reflecting transposition and 40% ectopic exchange between distantly related repeats. There is an excess of divergent rearrangements relative to polymorphism in Denisovan, which might result from nonuniform rates of mutation, possibly reflecting a burst of transposable element activity in the lineage that led to Denisovan. Finally, loci containing genome structure changes show diminished rates of introgression from Neanderthals into modern humans, consistent with the hypothesis that rearrangements serve as barriers to gene flow during hybridization. Together, these results suggest that this previously unidentified source of genomic variation has important biological consequences in human evolution. PMID:26399483

  3. DEVELOPMENT OF A DNA ARCHIVE FOR GENETIC MONITORING OF FISH POPULATIONS

    EPA Science Inventory

    Analysis of intraspecific genetic diversity provides a potentially powerful tool to estimate the impacts of environmental stressors on populations. Genetic responses of populations to novel stressors include dramatic shifts in genotype frequencies at loci under selection (i.e. ad...

  4. EFFECTS OF CHEMICAL CONTAMINANTS ON GENETIC DIVERSITY IN NATURAL POPULATIONS: IMPLICATIONS FOR BIOMONITORING AND ECOTOXICOLOGY

    EPA Science Inventory

    The conservation of genetic diversity has emerged as one of the central issues in conservation biology. Although researchers in the areas of evolutionary biology, population management, and conservation biology routinely investigate genetic variability in natural populations, onl...

  5. Genetic divergence between Melipona quadrifasciata Lepeletier (Hymenoptera, Apidae) populations

    PubMed Central

    Tavares, Mara Garcia; Pietrani, Nathalia Teixeira; de Castro Durvale, Maxwell; Resende, Helder Canto; de Oliveira Campos, Lucio Antonio

    2013-01-01

    Melipona quadrifasciata is a stingless bee widely found throughout the Brazilian territory, with two recognized subspecies, M. quadrifasciata anthidioides, that exhibits interrupted metasomal stripes, and M. quadrifasciata quadrifasciata, with continuous metasomal stripes. This study aimed to estimate the genetic variability of these subspecies. For this purpose, 127 colonies from 15 Brazilian localities were analyzed, using nine species-specific microsatellite primers. At these loci, the number of alleles ranged from three to 15 (mean: 7.2), and the observed heterozygosity (Ho) ranged from 0.03–0.21, while the expected heterozygosity (He) ranged from 0.23–0.47. The genetic distances among populations ranged from 0.03–0.45. The FST multilocus value (0.23) indicated that the populations sampled were structured, and the clustering analysis showed the formation of two subgroups and two more distant populations. The first group contained the subspecies M. quadrifasciata quadrifasciata, and the other, the subspecies M. quadrifasciata anthidioides and the two M. quadrifasciata populations with continuous metasomal stripes from northern Minas Gerais. These results confirmed that the yellow metasomal stripes alone are not a good means for correctly identifying the different subspecies of M. quadrifasciata. PMID:23569416

  6. Whole mitochondrial genome genetic diversity in an Estonian population sample.

    PubMed

    Stoljarova, Monika; King, Jonathan L; Takahashi, Maiko; Aaspõllu, Anu; Budowle, Bruce

    2016-01-01

    Mitochondrial DNA is a useful marker for population studies, human identification, and forensic analysis. Commonly used hypervariable regions I and II (HVI/HVII) were reported to contain as little as 25% of mitochondrial DNA variants and therefore the majority of power of discrimination of mitochondrial DNA resides in the coding region. Massively parallel sequencing technology enables entire mitochondrial genome sequencing. In this study, buccal swabs were collected from 114 unrelated Estonians and whole mitochondrial genome sequences were generated using the Illumina MiSeq system. The results are concordant with previous mtDNA control region reports of high haplogroup HV and U frequencies (47.4 and 23.7% in this study, respectively) in the Estonian population. One sample with the Northern Asian haplogroup D was detected. The genetic diversity of the Estonian population sample was estimated to be 99.67 and 95.85%, for mtGenome and HVI/HVII data, respectively. The random match probability for mtGenome data was 1.20 versus 4.99% for HVI/HVII. The nucleotide mean pairwise difference was 27 ± 11 for mtGenome and 7 ± 3 for HVI/HVII data. These data describe the genetic diversity of the Estonian population sample and emphasize the power of discrimination of the entire mitochondrial genome over the hypervariable regions. PMID:26289416

  7. Argentine Population Genetic Structure: Large Variance in Amerindian Contribution

    PubMed Central

    Seldin, Michael F.; Tian, Chao; Shigeta, Russell; Scherbarth, Hugo R.; Silva, Gabriel; Belmont, John W.; Kittles, Rick; Gamron, Susana; Allevi, Alberto; Palatnik, Simon A.; Alvarellos, Alejandro; Paira, Sergio; Caprarulo, Cesar; Guillerón, Carolina; Catoggio, Luis J.; Prigione, Cristina; Berbotto, Guillermo A.; García, Mercedes A.; Perandones, Carlos E.; Pons-Estel, Bernardo A.; Alarcon-Riquelme, Marta E.

    2011-01-01

    Argentine population genetic structure was examined using a set of 78 ancestry informative markers (AIMs) to assess the contributions of European, Amerindian, and African ancestry in 94 individuals members of this population. Using the Bayesian clustering algorithm STRUCTURE, the mean European contribution was 78%, the Amerindian contribution was 19.4%, and the African contribution was 2.5%. Similar results were found using weighted least mean square method: European, 80.2%; Amerindian, 18.1%; and African, 1.7%. Consistent with previous studies the current results showed very few individuals (four of 94) with greater than 10% African admixture. Notably, when individual admixture was examined, the Amerindian and European admixture showed a very large variance and individual Amerindian contribution ranged from 1.5 to 84.5% in the 94 individual Argentine subjects. These results indicate that admixture must be considered when clinical epidemiology or case control genetic analyses are studied in this population. Moreover, the current study provides a set of informative SNPs that can be used to ascertain or control for this potentially hidden stratification. In addition, the large variance in admixture proportions in individual Argentine subjects shown by this study suggests that this population is appropriate for future admixture mapping studies. PMID:17177183

  8. The Relevance of HLA Sequencing in Population Genetics Studies

    PubMed Central

    Sanchez-Mazas, Alicia

    2014-01-01

    Next generation sequencing (NGS) is currently being adapted by different biotechnological platforms to the standard typing method for HLA polymorphism, the huge diversity of which makes this initiative particularly challenging. Boosting the molecular characterization of the HLA genes through efficient, rapid, and low-cost technologies is expected to amplify the success of tissue transplantation by enabling us to find donor-recipient matching for rare phenotypes. But the application of NGS technologies to the molecular mapping of the MHC region also anticipates essential changes in population genetic studies. Huge amounts of HLA sequence data will be available in the next years for different populations, with the potential to change our understanding of HLA variation in humans. In this review, we first explain how HLA sequencing allows a better assessment of the HLA diversity in human populations, taking also into account the methodological difficulties it introduces at the statistical level; secondly, we show how analyzing HLA sequence variation may improve our comprehension of population genetic relationships by facilitating the identification of demographic events that marked human evolution; finally, we discuss the interest of both HLA and genome-wide sequencing and genotyping in detecting functionally significant SNPs in the MHC region, the latter having also contributed to the makeup of the HLA molecular diversity observed today. PMID:25126587

  9. Differentiation with drift: a spatio-temporal genetic analysis of Galapagos mockingbird populations (Mimus spp.).

    PubMed

    Hoeck, Paquita E A; Bollmer, Jennifer L; Parker, Patricia G; Keller, Lukas F

    2010-04-12

    Small and isolated island populations provide ideal systems to study the effects of limited population size, genetic drift and gene flow on genetic diversity. We assessed genetic diversity within and differentiation among 19 mockingbird populations on 15 Galápagos islands, covering all four endemic species, using 16 microsatellite loci. We tested for signs of drift and gene flow, and used historic specimens to assess genetic change over the last century and to estimate effective population sizes. Within-population genetic diversity and effective population sizes varied substantially among island populations and correlated strongly with island size, suggesting that island size serves as a good predictor for effective population size. Genetic differentiation among populations was pronounced and increased with geographical distance. A century of genetic drift did not change genetic diversity on an archipelago-wide scale, but genetic drift led to loss of genetic diversity in small populations, especially in one of the two remaining populations of the endangered Floreana mockingbird. Unlike in other Galápagos bird species such as the Darwin's finches, gene flow among mockingbird populations was low. The clear pattern of genetically distinct populations reflects the effects of genetic drift and suggests that Galápagos mockingbirds are evolving in relative isolation. PMID:20194174

  10. MORPHOLOGICAL AND GENETIC VARIATION IN THE POPULATIONS OF SARGASSUM HEMIPHYLLUM (PHAEOPHYCEAE) IN THE NORTHWESTERN PACIFIC(1).

    PubMed

    Cheang, Chi Chiu; Chu, Ka Hou; Ang, Put O

    2008-08-01

    Difficulty in species identification of Sargassum (Sargassaceae, Fucales) is partly attributed to the high polymorphism among its individuals and populations. This study aimed at assessing morphological and genetic variations in two varieties, var. hemiphyllum J. Agardh and var. chinense J. Agardh, of Sargassum hemiphyllum (Turner) C. Agardh, a widely distributed species in the northwestern Pacific. We investigated 26 measurable, five numerical, and 33 categorical morphological parameters associated with different branching levels of specimens from each of six localities within its distribution range using cluster analysis (CA) and principal coordinate analysis (PCoA). Leaf size of the primary and secondary branching levels and the vesicle size of the secondary branches of the specimens examined were determined to be the most important morphological parameters that were significantly different among populations. Change in leaf and vesicle length of individuals among the six populations followed a latitudinal gradient, with smaller leaves and vesicles associated with northern populations and larger ones in the southern populations. The possible influence of the gradual change in sea surface temperatures (SSTs) along this gradient in the northwestern Pacific on leaf and vesicle morphologies of this species was suggested. PCR-RFLP analysis of the RUBISCO spacer in the chloroplast genome revealed two distinct and highly homogenous clades, a China clade and a Japan-Korea clade, which corresponded to var. chinense and var. hemiphyllum, respectively. The formation of refugia along the "Paleo-coast" in the East China Sea during glacial periods is suggested to have led to the vicariance of ancestral populations of S. hemiphyllum and thus to have promoted genetic differentiation. The massive freshwater outflow of the Yellow and Yangtze rivers may continue to act as a barrier, prolonging the allopatric distribution of the two varieties. PMID:27041602

  11. Homogeneous Population of the Brown Alga Sargassum polycystum in Southeast Asia: Possible Role of Recent Expansion and Asexual Propagation

    PubMed Central

    Chan, Sze Wai; Cheang, Chi Chiu; Chirapart, Anong; Gerung, Grevo; Tharith, Chea; Ang, Put

    2013-01-01

    Southeast Asia has been known as one of the biodiversity hotspots in the world. Repeated glacial cycles during Pleistocene were believed to cause isolation of marine taxa in refugia, resulting in diversification among lineages. Recently, ocean current was also found to be another factor affecting gene flow by restricting larval dispersal in animals. Macroalgae are unique in having mode of reproduction that differs from that of animals. Our study on the phylogeographical pattern of the brown macroalga Sargassum polycystum using nuclear Internal Transcribed Spacer 2 (ITS2), plastidal RuBisCO spacer (Rub spacer) and mitochondrial cytochrome oxidase subunit-III (Cox3) as molecular markers revealed genetic homogeneity across 27 sites in Southeast Asia and western Pacific, in sharp contrast to that revealed from most animal studies. Our data suggested that S. polycystum persisted in single refugium during Pleistocene in a panmixia pattern. Expansion occurred more recently after the Last Glacial Maximum and recolonization of the newly flooded Sunda Shelf could have involved asexual propagation of the species. High dispersal ability through floating fronds carrying developing germlings may also contribute to the low genetic diversity of the species. PMID:24147050

  12. Multiple Stellar Populations of Globular Clusters from Homogeneous Ca by Photometry. I. M22 (NGC 6656)

    NASA Astrophysics Data System (ADS)

    Lee, Jae-Woo

    2015-07-01

    We investigate the multiple stellar populations in one of the peculiar globular clusters (GCs), M22, using new ground-based wide-field Ca by and Hubble Space Telescope Wide-Field Camera 3 photometry with equivalent passbands, confirming our previous result that M22 has a distinctive red giant branch (RGB) split mainly due to the difference in metal abundances. We also make use of radial velocity measurements by others of the large number of cluster membership stars. Our main results are the following. (1) The RGB and the subgiant branch number ratios show that the calcium-weak (Ca-w) group is the dominant population of the cluster. However, an irreconcilable difference can be seen in the rather simple classification into two horizontal branches by others. (2) Each group has its own CN-CH anticorrelation. However, the alleged CN-CH positive correlation is likely illusory. (3) The location of the RGB bump of the calcium-strong (Ca-s) group is significantly fainter, which may pose a challenge to the helium enhancement scenario in the Ca-s group. (4) The positions of the centers are similar. (5) The Ca-w group is slightly more centrally concentrated, whereas the Ca-s is more elongated at larger radii. (6) The mean radial velocities for both groups are similar, but the Ca-s group has a larger velocity dispersion. (7) The Ca-s group rotates faster. The plausible scenario for the formation of M22 is that it formed via a merger of two GCs in a dwarf galaxy environment and accreted later to our Galaxy. Partially based on observations made with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated by AURA, Inc., under NASA contract NAS 5-26555.

  13. Small population size and extremely low levels of genetic diversity in island populations of the platypus, Ornithorhynchus anatinus.

    PubMed

    Furlan, Elise; Stoklosa, J; Griffiths, J; Gust, N; Ellis, R; Huggins, R M; Weeks, A R

    2012-04-01

    Genetic diversity generally underpins population resilience and persistence. Reductions in population size and absence of gene flow can lead to reductions in genetic diversity, reproductive fitness, and a limited ability to adapt to environmental change increasing the risk of extinction. Island populations are typically small and isolated, and as a result, inbreeding and reduced genetic diversity elevate their extinction risk. Two island populations of the platypus, Ornithorhynchus anatinus, exist; a naturally occurring population on King Island in Bass Strait and a recently introduced population on Kangaroo Island off the coast of South Australia. Here we assessed the genetic diversity within these two island populations and contrasted these patterns with genetic diversity estimates in areas from which the populations are likely to have been founded. On Kangaroo Island, we also modeled live capture data to determine estimates of population size. Levels of genetic diversity in King Island platypuses are perilously low, with eight of 13 microsatellite loci fixed, likely reflecting their small population size and prolonged isolation. Estimates of heterozygosity detected by microsatellites (H(E)= 0.032) are among the lowest level of genetic diversity recorded by this method in a naturally outbreeding vertebrate population. In contrast, estimates of genetic diversity on Kangaroo Island are somewhat higher. However, estimates of small population size and the limited founders combined with genetic isolation are likely to lead to further losses of genetic diversity through time for the Kangaroo Island platypus population. Implications for the future of these and similarly isolated or genetically depauperate populations are discussed. PMID:22837830

  14. Local genetic structure in a white-bearded manakin population.

    PubMed

    Höglund, Jacob; Shorey, Lisa

    2003-09-01

    Local genetic structure was studied in lekking white-bearded manakins in a study area on northern Trinidad, West Indies. The study population consisted of nine leks, at which a total of 238 birds were caught. By genotyping the individuals at eight polymorphic microsatellite loci we inferred some males on leks to be related (r = 0.25) as we found an average number of 14.8 half-sib relationships and two full-sib relationships per lek. We found that the sampled birds belonged to one genetic population that was slightly inbred (FIS and FIT = 0.02). Kinship coefficients decreased with increasing geographical distance, indicating that related birds displayed at the same or nearby leks. However, leks did not consist of only one family group because the average genetic distance (aij) between males within leks was higher than when comparing males on leks within close proximity. These patterns suggest limited male dispersal, that some type of kin recognition process between individuals may exist in this species and that males on leks may be more likely to establish themselves as territory-holding birds if a relative is already present. PMID:12919483

  15. [Genetic, population and phenotypic characteristics of patients with Hirschsprung disease].

    PubMed

    Ruiz Aja, E; Vega Hernández, L; Martínez Ezquerra, N; De Diego García, E; Pérez Marrodan, A; Alvarez-Buhilla, P López

    2012-07-01

    Hirschsprung disease (HSCR) is caused by the absence of ganglion cells in the intestine due to defects in the migration of enteric nervous system cells during embryologic development. The incidence is one in every 5000 births, more common in men than women. There are two main phenotypes according to the aganglionic segment length: Short (S-HSCR, (80% of patients) and Long (L-HSCR, 20%). Variations have been detected in the coding sequence of the RET proto-oncogene in patients with HSCR, suggesting a genetic predisposition to the disease. Our aim is to find and analyze polymorphisms (SNPs) associated with the disease. We are interested also in stablish an association between sex and type of aganglionic segment. We analyzed the RET promoter as well a polymorphism in exon 13 strongly associated to the disease. The populations for the study were a group of 56 patients with sporadic HSCR and 178 healthy controls. The results obtained show that the disease is more common in men than in women (3:1). The RET genotype shows that alleles A and G of the promoter (c.-200A > G and c.-196C > A) and G of exon 13 (c.2307T > G) are associated with the affected population. Our data suggest neither association between the disease phenotype and the distribution of the polymorphisms analyzed nor with the sex of the patients. The presence of certain polymorphisms in the RET sequence indicates a genetic predisposition (combined with other genetic or environmental factors) to the disease. PMID:23480009

  16. Multilocus genotypic data reveal high genetic diversity and low population genetic structure of Iranian indigenous sheep.

    PubMed

    Vahidi, S M F; Faruque, M O; Falahati Anbaran, M; Afraz, F; Mousavi, S M; Boettcher, P; Joost, S; Han, J L; Colli, L; Periasamy, K; Negrini, R; Ajmone-Marsan, P

    2016-08-01

    Iranian livestock diversity is still largely unexplored, in spite of the interest in the populations historically reared in this country located near the Fertile Crescent, a major livestock domestication centre. In this investigation, the genetic diversity and differentiation of 10 Iranian indigenous fat-tailed sheep breeds were investigated using 18 microsatellite markers. Iranian breeds were found to host a high level of diversity. This conclusion is substantiated by the large number of alleles observed across loci (average 13.83, range 7-22) and by the high within-breed expected heterozygosity (average 0.75, range 0.72-0.76). Iranian sheep have a low level of genetic differentiation, as indicated by the analysis of molecular variance, which allocated a very small proportion (1.67%) of total variation to the between-population component, and by the small fixation index (FST  = 0.02). Both Bayesian clustering and principal coordinates analysis revealed the absence of a detectable genetic structure. Also, no isolation by distance was observed through comparison of genetic and geographical distances. In spite of high within-breed variation, signatures of inbreeding were detected by the FIS indices, which were positive in all and statistically significant in three breeds. Possible factors explaining the patterns observed, such as considerable gene flow and inbreeding probably due to anthropogenic activities in the light of population management and conservation programmes, are discussed. PMID:26953226

  17. Genetic variation and structure of house sparrow populations: is there an island effect?

    PubMed

    Jensen, Henrik; Moe, Rune; Hagen, Ingerid Julie; Holand, Anna Marie; Kekkonen, Jaana; Tufto, Jarle; Saether, Bernt-Erik

    2013-04-01

    Population genetic structure and intrapopulation levels of genetic variation have important implications for population dynamics and evolutionary processes. Habitat fragmentation is one of the major threats to biodiversity. It leads to smaller population sizes and reduced gene flow between populations and will thus also affect genetic structure. We use a natural system of island and mainland populations of house sparrows along the coast of Norway to characterize the different population genetic properties of fragmented populations. We genotyped 636 individuals distributed across 14 populations at 15 microsatellite loci. The level of genetic differentiation was estimated using F-statistics and specially designed Mantel tests were conducted to study the influence of population type (i.e. mainland or island) and geographic distance on the genetic population structure. Furthermore, the effects of population type, population size and latitude on the level of genetic variation within populations were examined. Our results suggest that genetic processes on islands and mainland differed in two important ways. First, the intrapopulation level of genetic variation tended to be lower and the occurrence of population bottlenecks more frequent on islands than the mainland. Second, although the general level of genetic differentiation was low to moderate, it was higher between island populations than between mainland populations. However, differentiation increased in mainland populations somewhat faster with geographical distance. These results suggest that population bottleneck events and genetic drift have been more important in shaping the genetic composition of island populations compared with populations on the mainland. Such knowledge is relevant for a better understanding of evolutionary processes and conservation of threatened populations. PMID:23379682

  18. Population Genetics of Plasmodium vivax in the Peruvian Amazon

    PubMed Central

    Delgado-Ratto, Christopher; Gamboa, Dionicia; Soto-Calle, Veronica E.; Van den Eede, Peter; Torres, Eliana; Sánchez-Martínez, Luis; Contreras-Mancilla, Juan; Rosanas-Urgell, Anna; Rodriguez Ferrucci, Hugo; Llanos-Cuentas, Alejandro; Erhart, Annette

    2016-01-01

    Background Characterizing the parasite dynamics and population structure provides useful information to understand the dynamic of transmission and to better target control interventions. Despite considerable efforts for its control, vivax malaria remains a major health problem in Peru. In this study, we have explored the population genetics of Plasmodium vivax isolates from Iquitos, the main city in the Peruvian Amazon, and 25 neighbouring peri-urban as well as rural villages along the Iquitos-Nauta Road. Methodology/ Results From April to December 2008, 292 P. vivax isolates were collected and successfully genotyped using 14 neutral microsatellites. Analysis of the molecular data revealed a similar proportion of monoclonal and polyclonal infections in urban areas, while in rural areas monoclonal infections were predominant (p = 0.002). Multiplicity of infection was higher in urban (MOI = 1.5–2) compared to rural areas (MOI = 1) (p = 0.003). The level of genetic diversity was similar in all areas (He = 0.66–0.76, p = 0.32) though genetic differentiation between areas was substantial (PHIPT = 0.17, p<0.0001). Principal coordinate analysis showed a marked differentiation between parasites from urban and rural areas. Linkage disequilibrium was detected in all the areas (IAs = 0.08–0.49, for all p<0.0001). Gene flow among the areas was stablished through Bayesian analysis of migration models. Recent bottleneck events were detected in 4 areas and a recent parasite expansion in one of the isolated areas. In total, 87 unique haplotypes grouped in 2 or 3 genetic clusters described a sub-structured parasite population. Conclusion/Significance Our study shows a sub-structured parasite population with clonal propagation, with most of its components recently affected by bottleneck events. Iquitos city is the main source of parasite spreading for all the peripheral study areas. The routes of transmission and gene flow and the reduction of the parasite population described

  19. Automated Quantification of DNA Demethylation Effects in Cells via 3D Mapping of Nuclear Signatures and Population Homogeneity Assessment1

    PubMed Central

    Gertych, Arkadiusz; Wawrowsky, Kolja A.; Lindsley, Erik; Vishnevsky, Eugene; Farkas, Daniel L.; Tajbakhsh, Jian

    2009-01-01

    Background Today’s advanced microscopic imaging applies to the preclinical stages of drug discovery that employ high-throughput and high-content three-dimensional (3D) analysis of cells to more efficiently screen candidate compounds. Drug efficacy can be assessed by measuring response homogeneity to treatment within a cell population. In this study topologically quantified nuclear patterns of methylated cytosine and global nuclear DNA are utilized as signatures of cellular response to the treatment of cultured cells with the demethylating anti-cancer agents: 5-azacytidine (5-AZA) and octreotide (OCT). Methods Mouse pituitary folliculostellate TtT-GF cells treated with 5-AZA and OCT for 48 hours, and untreated populations, were studied by immunofluorescence with a specific antibody against 5-methylcytosine (MeC), and 4,6-diamidino-2-phenylindole (DAPI) for delineation of methylated sites and global DNA in nuclei (n=163). Cell images were processed utilizing an automated 3D analysis software that we developed by combining seeded watershed segmentation to extract nuclear shells with measurements of Kullback-Leibler’s (K-L) divergence to analyze cell population homogeneity in the relative nuclear distribution patterns of MeC versus DAPI stained sites. Each cell was assigned to one of the four classes: similar, likely similar, unlikely similar and dissimilar. Results Evaluation of the different cell groups revealed a significantly higher number of cells with similar or likely similar MeC/DAPI patterns among untreated cells (~100%), 5-AZA-treated cells (90%), and a lower degree of same type of cells (64%) in the OCT-treated population. The latter group contained (28%) of unlikely similar or dissimilar (7%) cells. Conclusion Our approach was successful in the assessment of cellular behavior relevant to the biological impact of the applied drugs, i.e. the reorganization of MeC/DAPI distribution by demethylation. In a comparison with other metrics, K-L divergence has

  20. NAT2 genetic variations among South Indian populations.

    PubMed

    Lakkakula, Saikrishna; Mohan Pathapati, Ram; Chaubey, Gyaneshwer; Munirajan, Arasambattu Kannan; Lakkakula, Bhaskar Vks; Maram, Rajasekhar

    2014-01-01

    The N-acetyltransferases (NATs) are xenobiotic-metabolizing enzymes involved in the metabolism of drugs, environmental toxins and the aromatic amine carcinogens present in cigarette smoke. Genetic variations in NAT2 have long been recognized as the cause of variable enzymatic activity or stability, leading to slow or rapid acetylation. In the present study, we genotyped three single-nucleotide polymorphisms (SNPs) from the NAT2 gene (rs1799929, rs1799930 and rs1799931), using TaqMan allelic discrimination, among 212 individuals from six major South Indian populations and compared the results with other available Indian and worldwide data. All three of the markers followed Hardy-Weinberg equilibrium and were highly polymorphic in the studied populations. The constructed haplotypes showed a high level of heterozygosity. All of the populations in the present study commonly shared only four haplotypes out of the eight possible three-site haplotypes. The haplotypes exhibited fairly high frequencies across multiple populations, where three haplotypes were shared by all six populations with a cumulative frequency ranging from 88.2% (Madiga) to 97.0% (Balija). We also observed a tribal-specific haplotype. A strong linkage disequilibrium (LD) between rs1799929 and rs1799930 was consistent in all of the studied populations, with the exception of the Madiga. A comparison of the genomic regions 20-kb up- and downstream of rs1799930 in a large number of worldwide samples showed a strong LD of this SNP with another NAT2 SNP, rs1112005, among the majority of the populations. Moreover, our lifestyle test (hunter-gatherer versus agriculturist) in comparison with the NAT2 variant suggested that two of the studied populations (Balija and Madiga) have likely shifted their diet more recently. PMID:27081506

  1. On the dynamics of neutral mutations in a mathematical model for a homogeneous stem cell population

    PubMed Central

    Traulsen, Arne; Lenaerts, Tom; Pacheco, Jorge M.; Dingli, David

    2013-01-01

    The theory of the clonal origin of cancer states that a tumour arises from one cell that acquires mutation(s) leading to the malignant phenotype. It is the current belief that many of these mutations give a fitness advantage to the mutant population allowing it to expand, eventually leading to disease. However, mutations that lead to such a clonal expansion need not give a fitness advantage and may in fact be neutral—or almost neutral—with respect to fitness. Such mutant clones can be eliminated or expand stochastically, leading to a malignant phenotype (disease). Mutations in haematopoietic stem cells give rise to diseases such as chronic myeloid leukaemia (CML) and paroxysmal nocturnal haemoglobinuria (PNH). Although neutral drift often leads to clonal extinction, disease is still possible, and in this case, it has important implications both for the incidence of disease and for therapy, as it may be more difficult to eliminate neutral mutations with therapy. We illustrate the consequences of such dynamics, using CML and PNH as examples. These considerations have implications for many other tumours as well. PMID:23221988

  2. Genetic Diversity of Eight Domestic Goat Populations Raised in Turkey

    PubMed Central

    Bulut, Zafer; Kurar, Ercan; Ozsensoy, Yusuf; Altunok, Vahdettin; Nizamlioglu, Mehmet

    2016-01-01

    The objective of this study was to determine the intra- and intergenetic diversities of eight different goat populations in Turkey including Hair, Angora, Kilis, Yayladag, Shami, Honamli, Saanen, and Alpine. A total of 244 DNA samples were genotyped using 11 microsatellites loci. The genetic differentiation between breeds was considerable as a result of the statistically significant (P < 0.001) pairwise FST values of each pair of breeds. Exceptionally, FST values calculated for Honamli and Hair breeds were statistically nonsignificant (P > 0.05). Heterozygosity values ranged between 0.62 and 0.73. According to the structure and assignment test, Angora and Yayladag goats were assigned to the breed they belong to, while other breeds were assigned to two or more different groups. Because this study for the first time presented genetic data on the Yayladag goat, results of structure analysis and assigned test suggest that further analyses are needed using additional and different molecular markers. PMID:27092309

  3. Adoption of a High-Impact Innovation in a Homogeneous Population

    NASA Astrophysics Data System (ADS)

    Weiss, Curtis H.; Poncela-Casasnovas, Julia; Glaser, Joshua I.; Pah, Adam R.; Persell, Stephen D.; Baker, David W.; Wunderink, Richard G.; Nunes Amaral, Luís A.

    2014-10-01

    Adoption of innovations, whether new ideas, technologies, or products, is crucially important to knowledge societies. The landmark studies of adoption dealt with innovations having great societal impact (such as antibiotics or hybrid crops) but where determining the utility of the innovation was straightforward (such as fewer side effects or greater yield). Recent large-scale studies of adoption were conducted within heterogeneous populations and focused on products with little societal impact. Here, we focus on a case with great practical significance: adoption by small groups of highly trained individuals of innovations with large societal impact but for which it is impractical to determine the true utility of the innovation. Specifically, we study experimentally the adoption by critical care physicians of a diagnostic assay that complements current protocols for the diagnosis of life-threatening bacterial infections and for which a physician cannot estimate the true accuracy of the assay based on personal experience. We show through computational modeling of the experiment that infection-spreading models—which have been formalized as generalized contagion processes—are not consistent with the experimental data, while a model inspired by opinion models is able to reproduce the empirical data. Our modeling approach enables us to investigate the efficacy of different intervention schemes on the rate and robustness of innovation adoption in the real world. While our study is focused on critical care physicians, our findings have implications for other settings in education, research, and business, where small groups of highly qualified peers make decisions about the adoption of innovations whose utility is difficult if not impossible to gauge.

  4. Adoption of a High-Impact Innovation in a Homogeneous Population.

    PubMed

    Weiss, Curtis H; Poncela-Casasnovas, Julia; Glaser, Joshua I; Pah, Adam R; Persell, Stephen D; Baker, David W; Wunderink, Richard G; Nunes Amaral, Luís A

    2014-10-15

    Adoption of innovations, whether new ideas, technologies, or products, is crucially important to knowledge societies. The landmark studies of adoption dealt with innovations having great societal impact (such as antibiotics or hybrid crops) but where determining the utility of the innovation was straightforward (such as fewer side effects or greater yield). Recent large-scale studies of adoption were conducted within heterogeneous populations and focused on products with little societal impact. Here, we focus on a case with great practical significance: adoption by small groups of highly trained individuals of innovations with large societal impact but for which it is impractical to determine the true utility of the innovation. Specifically, we study experimentally the adoption by critical care physicians of a diagnostic assay that complements current protocols for the diagnosis of life-threatening bacterial infections and for which a physician cannot estimate the true accuracy of the assay based on personal experience. We show through computational modeling of the experiment that infection-spreading models-which have been formalized as generalized contagion processes-are not consistent with the experimental data, while a model inspired by opinion models is able to reproduce the empirical data. Our modeling approach enables us to investigate the efficacy of different intervention schemes on the rate and robustness of innovation adoption in the real world. While our study is focused on critical care physicians, our findings have implications for other settings in education, research, and business, where small groups of highly qualified peers make decisions about the adoption of innovations whose utility is difficult if not impossible to gauge. PMID:25392742

  5. Patients With First-Episode Psychosis are Not a Homogeneous Population: Implications for Treatment

    PubMed Central

    Cocchi, Angelo; Cerati, Giorgio; Lora, Antonio; Meneghelli, Anna; Monzani, Emiliano; Percudani, Mauro; Petrovich, Lorenzo; Mirabella, Fiorino; Picardi, Angelo; Preti, Antonio

    2014-01-01

    Objective: This study aimed at defining the characteristics of a population of patients diagnosed with first-episode psychosis (FEP), and accessing for the first time a center for early intervention in psychosis in the health district of Milan and its surroundings. Methods: Patients were included in the study from January 2007 to December 2008; criteria: first contact with any public mental health service of the catchment area for a first episode of schizophrenia or related syndromes according to the ICD-10 criteria. Cluster analysis was used to divide patients into groups based on the main socio-demographic and clinical characteristics at presentation. Results: Overall, 91 FEP patients were enrolled in the study. Two clusters were identified, which differed principally by symptom profile. Patients in cluster 1 (n=36) had severe agitation, and a history of alcohol and/or substance abuse at presentation more often than those in cluster 2 (n=55), who were more likely to suffer at presentation from severe depression or apathy, anxiety, poor self-care, functional or work impairment and severe social withdrawal. After six months of treatment patients improved on almost all symptomatic dimensions on the Health of the Nation Outcome Scale and the Brief Psychiatric Rating Scale, with greater improvement in cluster 1 than in cluster 2. Conclusions: The findings of this study need replication in larger samples and on a wider severity scale. Nevertheless, the heterogeneity of patients with FEP might impact on treatment. Policymakers should recognize the importance of the diagnostic and outcome assessment in the treatment of severe mental disorders. PMID:24600479

  6. Stochasticity in space, persistence in time: genetic heterogeneity in harbour populations of the introduced ascidian Styela plicata

    PubMed Central

    Pineda, Mari-Carmen; Lorente, Beatriz; López-Legentil, Susanna; Palacín, Creu

    2016-01-01

    Spatio-temporal changes in genetic structure among populations provide crucial information on the dynamics of secondary spread for introduced marine species. However, temporal components have rarely been taken into consideration when studying the population genetics of non-indigenous species. This study analysed the genetic structure of Styela plicata, a solitary ascidian introduced in harbours and marinas of tropical and temperate waters, across spatial and temporal scales. A fragment of the mitochondrial gene Cytochrome Oxidase subunit I (COI) was sequenced from 395 individuals collected at 9 harbours along the NW Mediterranean coast and adjacent Atlantic waters (> 1,200 km range) at two time points 5 years apart (2009 and 2014). The levels of gene diversity were relatively low for all 9 locations in both years. Analyses of genetic differentiation and distribution of molecular variance revealed strong genetic structure, with significant differences among many populations, but no significant differences among years. A weak and marginally significant correlation between geographic distance and gene differentiation was found. Our results revealed spatial structure and temporal genetic homogeneity in S. plicata, suggesting a limited role of recurrent, vessel-mediated transport of organisms among small to medium-size harbours. Our study area is representative of many highly urbanized coasts with dense harbours. In these environments, the episodic chance arrival of colonisers appears to determine the genetic structure of harbour populations and the genetic composition of these early colonising individuals persists in the respective harbours, at least over moderate time frames (five years) that encompass ca. 20 generations of S. plicata. PMID:27366653

  7. Stochasticity in space, persistence in time: genetic heterogeneity in harbour populations of the introduced ascidian Styela plicata.

    PubMed

    Pineda, Mari-Carmen; Lorente, Beatriz; López-Legentil, Susanna; Palacín, Creu; Turon, Xavier

    2016-01-01

    Spatio-temporal changes in genetic structure among populations provide crucial information on the dynamics of secondary spread for introduced marine species. However, temporal components have rarely been taken into consideration when studying the population genetics of non-indigenous species. This study analysed the genetic structure of Styela plicata, a solitary ascidian introduced in harbours and marinas of tropical and temperate waters, across spatial and temporal scales. A fragment of the mitochondrial gene Cytochrome Oxidase subunit I (COI) was sequenced from 395 individuals collected at 9 harbours along the NW Mediterranean coast and adjacent Atlantic waters (> 1,200 km range) at two time points 5 years apart (2009 and 2014). The levels of gene diversity were relatively low for all 9 locations in both years. Analyses of genetic differentiation and distribution of molecular variance revealed strong genetic structure, with significant differences among many populations, but no significant differences among years. A weak and marginally significant correlation between geographic distance and gene differentiation was found. Our results revealed spatial structure and temporal genetic homogeneity in S. plicata, suggesting a limited role of recurrent, vessel-mediated transport of organisms among small to medium-size harbours. Our study area is representative of many highly urbanized coasts with dense harbours. In these environments, the episodic chance arrival of colonisers appears to determine the genetic structure of harbour populations and the genetic composition of these early colonising individuals persists in the respective harbours, at least over moderate time frames (five years) that encompass ca. 20 generations of S. plicata. PMID:27366653

  8. Genetic homogeneity of Pelizaeus-Merzbacher disease: Tight linkage to the proteolipoprotein locus in 16 affected families

    SciTech Connect

    Boespflug-Tanguy, O.; Mimault, C.; Cavagna, A.; Giraud, G.; Dastugue, B.; Melki, J.; Dinh, D.P.; Dautigny, A.

    1994-09-01

    Among the numerous leukodystrophies that have an early onset and no biochemical markers, Pelizaeus-Merzbacher disease (PMD) is one that can be identified using strict clinical criteria and demonstrating an abnormal formation of myelin that is restricted to the CNS in electrophysiological studies and brain magnetic resonance imaging (MRI). In PMD, 12 different base substitutions and one total deletion of the genomic region containing the PLP gene have been reported, but, despite extensive analysis, PLP exon mutations have been found in only 10%-25% of the families analyzed. To test the genetic homogeneity of this disease, the authors have carried out linkage analysis with polymorphic markers of the PLP genomic region in 16 families selected on strict diagnostic criteria of PMD. They observed a tight linkage of the PMD locus with markers of the PLP gene (cDNA PLP, exon IV polymorphism) and of the Xq22 region (DXS17, DXS94, and DXS287), whereas the markers located more proximally (DXYS1X and DXS3) or distally (DXS11) were not linked to the PMD locus. Multipoint analysis gave a maximal location score for the PMD locus (13.98) and the PLP gene (8.32) in the same interval between DXS94 and DXS287, suggesting that in all families PMD is linked to the PLP locus. Mutations of the extraexonic PLP gene sequences or of another unknown close gene could be involved in PMD. In an attempt to identify molecular defects of this genomic region that are responsible for PMD, these results meant that RFLP analysis could be used to improve genetic counseling for the numerous affected families in which a PLP exon mutation could not be demonstrated. 39 refs., 2 figs., 2 tabs.

  9. Population genetic studies in the Balkans. I. Serum proteins.

    PubMed

    Scheil, H G; Scheffrahn, W; Schmidt, H D; Huckenbeck, W; Efremovska, L; Xirotiris, N

    2001-09-01

    Within a study of the genetics of Southeastern European populations seven serum protein polymorphisms (AMY2, BF, C3, CP, GC, HPA, TF) were examined in three samples of Aromuns (Albania: the village of Andon Poci, province Gjirocaster, Republic of Macedonia: Stip region, Romania: the village Kogalniceanu, province Dobruja) and four reference samples (Albanians: Tirana, Romanians: Constanta and Ploiesti as well as Greeks (Northeastern Greece)). The Aromun samples from Albania and Romania form one separate cluster and the reference samples together with the Aromuns from Macedonia (Stip region) form a second one. PMID:11591047

  10. Population admixture may appear to mask, change or reverse genetic effects of genes underlying complex traits.

    PubMed Central

    Deng, H W

    2001-01-01

    Association studies using random population samples are increasingly being applied in the identification and inference of genetic effects of genes underlying complex traits. It is well recognized that population admixture may yield false-positive identification of genetic effects for complex traits. However, it is less well appreciated that population admixture can appear to mask, change, or reverse true genetic effects for genes underlying complex traits. By employing a simple population genetics model, we explore the effects and the conditions of population admixture in masking, changing, or even reversing true genetic effects of genes underlying complex traits. PMID:11729172

  11. Genetically distinct populations of northern shrimp, Pandalus borealis, in the North Atlantic: adaptation to different temperatures as an isolation factor.

    PubMed

    Jorde, Per Erik; Søvik, Guldborg; Westgaard, Jon-Ivar; Albretsen, Jon; André, Carl; Hvingel, Carsten; Johansen, Torild; Sandvik, Anne Dagrun; Kingsley, Michael; Jørstad, Knut Eirik

    2015-04-01

    The large-scale population genetic structure of northern shrimp, Pandalus borealis, was investigated over the species' range in the North Atlantic, identifying multiple genetically distinct groups. Genetic divergence among sample localities varied among 10 microsatellite loci (range: FST = -0.0002 to 0.0475) with a highly significant average (FST = 0.0149; P < 0.0001). In contrast, little or no genetic differences were observed among temporal replicates from the same localities (FST = 0.0004; P = 0.33). Spatial genetic patterns were compared to geographic distances, patterns of larval drift obtained through oceanographic modelling, and temperature differences, within a multiple linear regression framework. The best-fit model included all three factors and explained approximately 29% of all spatial genetic divergence. However, geographic distance and larval drift alone had only minor effects (2.5-4.7%) on large-scale genetic differentiation patterns, whereas bottom temperature differences explained most (26%). Larval drift was found to promote genetic homogeneity in parts of the study area with strong currents, but appeared ineffective across large temperature gradients. These findings highlight the breakdown of gene flow in a species with a long pelagic larval phase (up to 3 months) and indicate a role for local adaptation to temperature conditions in promoting evolutionary diversification and speciation in the marine environment. PMID:25782085

  12. Historical and anthropogenic factors affecting the population genetic structure of Ontario's inland lake populations of Walleye (Sander vitreus).

    PubMed

    Walter, Ryan P; Cena, Christopher J; Morgan, George E; Heath, Daniel D

    2012-01-01

    Populations existing in formerly glaciated areas often display composite historical and contemporary patterns of genetic structure. For Canadian freshwater fishes, population genetic structure is largely reflective of dispersal from glacial refugia and isolation within drainage basins across a range of scales. Enhancement of sport fisheries via hatchery stocking programs and other means has the potential to alter signatures of natural evolutionary processes. Using 11 microsatellite loci genotyped from 2182 individuals, we analyzed the genetic structure of 46 inland lake walleye (Sander vitreus) populations spanning five major drainage basins within the province of Ontario, Canada. Population genetic analyses coupled with genotype assignment allowed us to: 1) characterize broad- and fine-scale genetic structure among Ontario walleye populations; and 2) determine if the observed population divergence is primarily due to natural or historical processes, or recent anthropogenic events. The partitioning of genetic variation revealed higher genetic divergence among lakes than among drainage basins or proposed ancestries-indicative of relatively high isolation among lakes, study-wide. Walleye genotypes were clustered into three major groups, likely reflective of Missourian, Mississippian, and Atlantic glacial refugial ancestry. Despite detectable genetic signatures indicative of anthropogenic influences, province-wide spatial genetic structure remains consistent with the hypothesis of dispersal from distinct glacial refugia and subsequent isolation of lakes within primary drainage basins. Our results provide a novel example of minimal impacts from fishery enhancement to the broad-scale genetic structure of inland fish populations. PMID:23125407

  13. Genetic Evidence for Recent Population Mixture in India

    PubMed Central

    Moorjani, Priya; Thangaraj, Kumarasamy; Patterson, Nick; Lipson, Mark; Loh, Po-Ru; Govindaraj, Periyasamy; Berger, Bonnie; Reich, David; Singh, Lalji

    2013-01-01

    Most Indian groups descend from a mixture of two genetically divergent populations: Ancestral North Indians (ANI) related to Central Asians, Middle Easterners, Caucasians, and Europeans; and Ancestral South Indians (ASI) not closely related to groups outside the subcontinent. The date of mixture is unknown but has implications for understanding Indian history. We report genome-wide data from 73 groups from the Indian subcontinent and analyze linkage disequilibrium to estimate ANI-ASI mixture dates ranging from about 1,900 to 4,200 years ago. In a subset of groups, 100% of the mixture is consistent with having occurred during this period. These results show that India experienced a demographic transformation several thousand years ago, from a region in which major population mixture was common to one in which mixture even between closely related groups became rare because of a shift to endogamy. PMID:23932107

  14. Multi-locus genetic risk score predicts risk for Crohn’s disease in Slovenian population

    PubMed Central

    Zupančič, Katarina; Skok, Kristijan; Repnik, Katja; Weersma, Rinse K; Potočnik, Uroš; Skok, Pavel

    2016-01-01

    AIM: To develop a risk model for Crohn’s disease (CD) based on homogeneous population. METHODS: In our study were included 160 CD patients and 209 healthy individuals from Slovenia. The association study was performed for 112 single nucleotide polymorphisms (SNPs). We generated genetic risk scores (GRS) based on the number of risk alleles using weighted additive model. Discriminatory accuracy was measured by area under ROC curve (AUC). For risk evaluation, we divided individuals according to positive and negative likelihood ratios (LR) of a test, with LR > 5 for high risk group and LR < 0.20 for low risk group. RESULTS: The highest accuracy, AUC of 0.78 was achieved with GRS combining 33 SNPs with optimal sensitivity and specificity of 75.0% and 72.7%, respectively. Individuals with the highest risk (GRS > 5.54) showed significantly increased odds of developing CD (OR = 26.65, 95%CI: 11.25-63.15) compared to the individuals with the lowest risk (GRS < 4.57) which is a considerably greater risk captured than in one SNP with the highest effect size (OR = 3.24). When more than 33 SNPs were included in GRS, discriminatory ability was not improved significantly; AUC of all 74 SNPs was 0.76. CONCLUSION: The authors proved the possibility of building accurate genetic risk score based on 33 risk variants on Slovenian CD patients which may serve as a screening tool in the targeted population. PMID:27076762

  15. Genetic and phenotypic differentiation of an Andean intermediate altitude population

    PubMed Central

    Eichstaedt, Christina A; Antão, Tiago; Cardona, Alexia; Pagani, Luca; Kivisild, Toomas; Mormina, Maru

    2015-01-01

    Highland populations living permanently under hypobaric hypoxia have been subject of extensive research because of the relevance of their physiological adaptations for the understanding of human health and disease. In this context, what is considered high altitude is a matter of interpretation and while the adaptive processes at high altitude (above 3000 m) are well documented, the effects of moderate altitude (below 3000 m) on the phenotype are less well established. In this study, we compare physiological and anthropometric characteristics as well as genetic variations in two Andean populations: the Calchaquíes (2300 m) and neighboring Collas (3500 m). We compare their phenotype and genotype to the sea-level Wichí population. We measured physiological (heart rate, oxygen saturation, respiration rate, and lung function) as well as anthropometric traits (height, sitting height, weight, forearm, and tibia length). We conducted genome-wide genotyping on a subset of the sample (n = 74) and performed various scans for positive selection. At the phenotypic level (n = 179), increased lung capacity stood out in both Andean groups, whereas a growth reduction in distal limbs was only observed at high altitude. At the genome level, Calchaquíes revealed strong signals around PRKG1, suggesting that the nitric oxide pathway may be a target of selection. PRKG1 was highlighted by one of four selection tests among the top five genes using the population branch statistic. Selection tests results of Collas were reported previously. Overall, our study shows that some phenotypic and genetic differentiation occurs at intermediate altitude in response to moderate lifelong selection pressures. PMID:25948820

  16. Genetic Similarity of Island Populations of Tent Caterpillars during Successive Outbreaks

    PubMed Central

    Franklin, Michelle T.; Myers, Judith H.; Cory, Jenny S.

    2014-01-01

    Cyclic or fluctuating populations experience regular periods of low population density. Genetic bottlenecks during these periods could give rise to temporal or spatial genetic differentiation of populations. High levels of movement among increasing populations, however, could ameliorate any differences and could also synchronize the dynamics of geographically separated populations. We use microsatellite markers to investigate the genetic differentiation of four island and one mainland population of western tent caterpillars, Malacosoma californicum pluviale, in two periods of peak or pre-peak density separated by 8 years. Populations showed high levels of genetic variation and little genetic differentiation either temporally between peaks or spatially among sites. Mitochondrial haplotypes were also shared between one island population and one mainland population in the two years studied. An isolation-by-distance analysis showed the FST values of the two geographically closest populations to have the highest level of differentiation in both years. We conclude that high levels of dispersal among populations maintain both synchrony of population dynamics and override potential genetic differentiation that might occur during population troughs. As far we are aware, this is the first time that genetic similarity between temporally separated population outbreaks in insects has been investigated. A review of genetic data for both vertebrate and invertebrate species of cyclic animals shows that a lack of spatial genetic differentiation is typical, and may result from high levels of dispersal associated with fluctuating dynamics. PMID:24858905

  17. The population genetics of pharmacogenomics VIP variants in the Sherpa population.

    PubMed

    Wang, Li; Ren, Yongchao; Shi, Xugang; Yuan, Dongya; Liu, Kai; Geng, Tingting; Li, Gang; Kang, Longli; Jin, Tian-bo

    2016-02-01

    Polymorphic distributions of pharmacogenes among some ethnicities are under-represented in current pharmacogenetic research. Particularly, there is a paucity of pharmacogenetic information in the Sherpa population in Tibet. We used the Sequenom MassARRAY single nucleotide polymorphism (SNP) genotyping technology to detect 86 very important pharmacogene (VIP) variants in Sherpas and compared the genotypic frequencies of these variants with HapMap populations. Overall, 59 of the 60 previously reported variants in the HapMap populations were found in our study. We found minimal differences between populations of Sherpas and Chinese Han in Beijing (CHB), Chinese in Metropolitan Denver, Colorado (CHD), Japanese in Tokyo, Japan (JPT), and Mexicans in Los Angeles, California (MEX) after a strict Bonferroni correction. Only 8, 4, 5, 4 VIP genotypes, respectively, were different in these groups. Additionally, pairwise FST values and clustering analyses showed that the VIP variants in the Sherpa population exhibited a close genetic affinity with the CHB and JPT populations, but they were most similar to the CHD population. Our results contribute to a better understanding of the molecular basis underlying ethnic differences in drug response, which may potentially benefit the development of personalized medicine for the Sherpa population. PMID:26825850

  18. Genetic variation and population genetic structure of Rhizophora apiculata (Rhizophoraceae) in the Greater Sunda Islands, Indonesia using microsatellite markers.

    PubMed

    Yahya, Andi Fadly; Hyun, Jung Oh; Lee, Jae Ho; Kim, Yong Yul; Lee, Kyung Mi; Hong, Kyung Nak; Kim, Seung-Chul

    2014-03-01

    Genetic variations within and among Rhizophora apiculata populations in the Greater Sunda Islands of Indonesia were studied using microsatellite markers. The study found 38 alleles on five loci in 15 populations. The observed (H(o)) and expected (H(e)) heterozygosity values are 0.338 and 0.378, respectively. Inbreeding effect from self-pollination might explain its heterozygote deficiency. Population genetic differentiation (F(ST) = 0.381) was similar to other mangrove species. The genetic diversity of R. apiculata populations along the coastline inside the archipelago (e.g., Buleleng, Donggala, Mamuju, and Takalar) was higher than those of population along the coastline outside the archipelago, especially northern Sumatra populations (i.e., Langkat, Tapanuli Tengah, Dumai, and Padang). The isolation by distances and sea currents directions as well as their connectivity might affect the gene flow and genetic exchange. The more isolated with fewer connections by sea currents, the smaller gene flow and genetic exchange observed between populations. The higher genetic exchange, on the contrary, occurred when population location was closer to the meeting point of the sea currents. The study also showed that the patterns of sea current movement seemed to have influence genetic clustering of populations which fell into three main groups (Sunda Shelf Mangroves) and one isolated population (New Guinea Mangroves). PMID:24323307

  19. Genetic structure of natural populations: Final technical report

    SciTech Connect

    Ayala, F.J.

    1987-12-31

    We determined the LD/sub 50/ for individuals with any one of four genetic constitutions. The LD/sub 50/ was in kR units (S and F refer to the two common alleles found in natural populations and N is a mull allele) S/S 5.31, F/F 4.61, S/F 4.19, N/N 3.16. These results are as expected under the hypothesis the SOD is involved in radio-resistance and the degree of protection is a function of SOD specific activity. S codes for an allozyme that has the highest in vitro specific activity while N reduces the amount of enzyme to 3.5% of the normal level. Natural selection experiments in population cages were carried out for 13 generations. In control populations, the frequency of the S allele decreases from the initial frequency of 0.50 to an equilibrium value 0.1 to 0.2 in about 10 generations. In populations with the larvae receiving 4 KR in each generation, s reaches an equilibrium frequency of 0.6; when the irradiation was no longer applied, the frequency of S started declining, eventually reaching 0.1 to 0.2. These results corroborate the hypothesis that SOD protects against irradiation and that the degree of protection is correlated by the in vitro specific activity of the allozymes. 29 refs., 4 tabs.

  20. Genetic variability of inflammatory genes in the Brazilian population.

    PubMed

    dos Santos, Marcelo; Stur, Elaine; Maia, Lucas Lima; Agostini, Lidiane Pignaton; Peterle, Gabriela Tonini; Mendes, Suzanny Oliveira; Tajara, Eloiza Helena; de Carvalho, Marcos Brasilino; Louro, Iúri Drumond; Silva-Conforti, Adriana Madeira Álvares

    2013-11-01

    Inflammatory gene variants have been associated with several diseases, including cancer, diabetes, vascular diseases, neurodegenerative diseases, arthritis, and others. Therefore, determining the population genetic composition of inflammation-related genes can be useful for the determination of general risk, prognostic and therapeutic strategies to prevent or cure specific diseases. We have aimed to identify polymorphism genotype frequencies in genes related to the inflammatory response in the Brazilian population, namely, IκBL -62AT, IκBL -262CT, tumor necrosis factors alpha (TNFa) -238GA, TNFa -308GA, lymphotoxin-alpha (LTa) +80AC, LTa +252AG, FAS -670AG, and FASL -844TC, considering the white, black, and Pardo ethnicities of the São Paulo State. Our results suggest that the Brazilian population is under a miscegenation process at the current time, since some genotypes are not in the Hardy-Weinberg equilibrium. In addition, we conclude that the Pardo ethnicity is derived from a complex mixture of ethnicities, including the native Indian population. PMID:23909556

  1. Genetic architecture of prostate cancer in the Ashkenazi Jewish population

    PubMed Central

    Vijai, J; Kirchhoff, T; Gallagher, D; Hamel, N; Guha, S; Darvasi, A; Lencz, T; Foulkes, W D; Offit, K; Klein, R J

    2011-01-01

    Background: Recently, numerous prostate cancer risk loci have been identified, some of which show association in specific populations. No study has yet investigated whether these single nucleotide polymorphisms (SNPs) are associated with prostate cancer in the Ashkenazi Jewish (AJ) population. Methods: A total of 29 known prostate cancer risk SNPs were genotyped in 963 prostate cancer cases and 613 controls of AJ ancestry. These data were combined with data from 1241 additional Ashkenazi controls and tested for association with prostate cancer. Correction for multiple testing was performed using the false discovery rate procedure. Results: Ten of twenty-three SNPs that passed quality control procedures were associated with prostate cancer risk at a false discovery rate of 5%. Of these, nine were originally discovered in studies of individuals of European ancestry. Based on power calculations, the number of significant associations observed is not surprising. Conclusion: We see no convincing evidence that the genetic architecture of prostate cancer in the AJ population is substantively different from that observed in other populations of European ancestry. PMID:21829199

  2. Genetic Variability of Inflammatory Genes in the Brazilian Population

    PubMed Central

    dos Santos, Marcelo; Stur, Elaine; Maia, Lucas Lima; Agostini, Lidiane Pignaton; Peterle, Gabriela Tonini; Mendes, Suzanny Oliveira; Tajara, Eloiza Helena; de Carvalho, Marcos Brasilino; Louro, Iúri Drumond

    2013-01-01

    Inflammatory gene variants have been associated with several diseases, including cancer, diabetes, vascular diseases, neurodegenerative diseases, arthritis, and others. Therefore, determining the population genetic composition of inflammation-related genes can be useful for the determination of general risk, prognostic and therapeutic strategies to prevent or cure specific diseases. We have aimed to identify polymorphism genotype frequencies in genes related to the inflammatory response in the Brazilian population, namely, IκBL −62AT, IκBL −262CT, tumor necrosis factors alpha (TNFa) −238GA, TNFa −308GA, lymphotoxin-alpha (LTa) +80AC, LTa +252AG, FAS −670AG, and FASL −844TC, considering the white, black, and Pardo ethnicities of the São Paulo State. Our results suggest that the Brazilian population is under a miscegenation process at the current time, since some genotypes are not in the Hardy–Weinberg equilibrium. In addition, we conclude that the Pardo ethnicity is derived from a complex mixture of ethnicities, including the native Indian population. PMID:23909556

  3. Population Structure, Genetic Variation, and Linkage Disequilibrium in Perennial Ryegrass Populations Divergently Selected for Freezing Tolerance

    PubMed Central

    Kovi, Mallikarjuna Rao; Fjellheim, Siri; Sandve, Simen R.; Larsen, Arild; Rudi, Heidi; Asp, Torben; Kent, Matthew Peter; Rognli, Odd Arne

    2015-01-01

    Low temperature is one of the abiotic stresses seriously affecting the growth of perennial ryegrass (Lolium perenne L.), and freezing tolerance is a complex trait of major agronomical importance in northern and central Europe. Understanding the genetic control of freezing tolerance would aid in the development of cultivars of perennial ryegrass with improved adaptation to frost. The plant material investigated in this study was an experimental synthetic population derived from pair-crosses among five European perennial ryegrass genotypes, representing adaptations to a range of climatic conditions across Europe. A total number of 80 individuals (24 of High frost [HF]; 29 of Low frost [LF], and 27 of Unselected [US]) from the second generation of the two divergently selected populations and an unselected (US) control population were genotyped using 278 genome-wide SNPs derived from perennial ryegrass transcriptome sequences. Our studies investigated the genetic diversity among the three experimental populations by analysis of molecular variance and population structure, and determined that the HF and LF populations are very divergent after selection for freezing tolerance, whereas the HF and US populations are more similar. Linkage disequilibrium (LD) decay varied across the seven chromosomes and the conspicuous pattern of LD between the HF and LF population confirmed their divergence in freezing tolerance. Furthermore, two Fst outlier methods; finite island model (fdist) by LOSITAN and hierarchical structure model using ARLEQUIN, both detected six loci under directional selection. These outlier loci are most probably linked to genes involved in freezing tolerance, cold adaptation, and abiotic stress. These six candidate loci under directional selection for freezing tolerance might be potential marker resources for breeding perennial ryegrass cultivars with improved freezing tolerance. PMID:26617611

  4. Continuous Influx of Genetic Material from Host to Virus Populations

    PubMed Central

    Gilbert, Clément; Peccoud, Jean; Chateigner, Aurélien; Moumen, Bouziane

    2016-01-01

    Many genes of large double-stranded DNA viruses have a cellular origin, suggesting that host-to-virus horizontal transfer (HT) of DNA is recurrent. Yet, the frequency of these transfers has never been assessed in viral populations. Here we used ultra-deep DNA sequencing of 21 baculovirus populations extracted from two moth species to show that a large diversity of moth DNA sequences (n = 86) can integrate into viral genomes during the course of a viral infection. The majority of the 86 different moth DNA sequences are transposable elements (TEs, n = 69) belonging to 10 superfamilies of DNA transposons and three superfamilies of retrotransposons. The remaining 17 sequences are moth sequences of unknown nature. In addition to bona fide DNA transposition, we uncover microhomology-mediated recombination as a mechanism explaining integration of moth sequences into viral genomes. Many sequences integrated multiple times at multiple positions along the viral genome. We detected a total of 27,504 insertions of moth sequences in the 21 viral populations and we calculate that on average, 4.8% of viruses harbor at least one moth sequence in these populations. Despite this substantial proportion, no insertion of moth DNA was maintained in any viral population after 10 successive infection cycles. Hence, there is a constant turnover of host DNA inserted into viral genomes each time the virus infects a moth. Finally, we found that at least 21 of the moth TEs integrated into viral genomes underwent repeated horizontal transfers between various insect species, including some lepidopterans susceptible to baculoviruses. Our results identify host DNA influx as a potent source of genetic diversity in viral populations. They also support a role for baculoviruses as vectors of DNA HT between insects, and call for an evaluation of possible gene or TE spread when using viruses as biopesticides or gene delivery vectors. PMID:26829124

  5. Genetic signature of anthropogenic population collapse in orang-utans.

    PubMed

    Goossens, Benoît; Chikhi, Lounès; Ancrenaz, Marc; Lackman-Ancrenaz, Isabelle; Andau, Patrick; Bruford, Michael W

    2006-02-01

    Great ape populations are undergoing a dramatic decline, which is predicted to result in their extinction in the wild from entire regions in the near future. Recent findings have particularly focused on African apes, and have implicated multiple factors contributing to this decline, such as deforestation, hunting, and disease. Less well-publicised, but equally dramatic, has been the decline in orang-utans, whose distribution is limited to parts of Sumatra and Borneo. Using the largest-ever genetic sample from wild orang-utan populations, we show strong evidence for a recent demographic collapse in North Eastern Borneo and demonstrate that this signature is independent of the mutation and demographic models used. This is the first demonstration that genetic data can detect and quantify the effect of recent, human-induced deforestation and habitat fragmentation on an endangered species. Because current demographic collapses are usually confounded by ancient events, this suggests a much more dramatic decline than demographic data alone and emphasises the need for major conservation efforts. PMID:16417405

  6. Genetic variability and viral seroconversion in an outcrossing vertebrate population

    PubMed Central

    Gompper, Matthew E.; Monello, Ryan J.; Eggert, Lori S.

    2011-01-01

    Inverse correlations between genetic variability and parasitism are important concerns for conservation biologists. We examined correlations between neutral genetic variability and the presence of antibodies to canine distemper virus (CDV) and feline parvovirus (FPV) in a free-ranging population of raccoons. Over 3 years there was a strong relationship between age and seroprevalence rates. Most young animals were seronegative to CDV and FPV, but the oldest age class was greater than 80 per cent seropositive to both viruses. CDV-seropositive animals had greater heterozygosity and lower measures of inbreeding compared with CDV-seronegative animals. This relationship was strongest among the youngest animals and did not occur during a 1 year CDV epidemic. In contrast, FPV-seropositive animals only had significantly lower measures of inbreeding in 1 year, perhaps because FPV-associated mortality is relatively low or primarily occurs among very young individuals that were under-represented in our sampling. These results suggest that even in large outcrossing populations, animals with lower heterozygosity and higher measures of inbreeding are less likely to successfully mount an immune response when challenged by highly pathogenic parasites. PMID:20667873

  7. Population genetics of the wild yeast Saccharomyces paradoxus.

    PubMed Central

    Johnson, Louise J; Koufopanou, Vassiliki; Goddard, Matthew R; Hetherington, Richard; Schäfer, Stefanie M; Burt, Austin

    2004-01-01

    Saccharomyces paradoxus is the closest known relative of the well-known S. cerevisiae and an attractive model organism for population genetic and genomic studies. Here we characterize a set of 28 wild isolates from a 10-km(2) sampling area in southern England. All 28 isolates are homothallic (capable of mating-type switching) and wild type with respect to nutrient requirements. Nine wild isolates and two lab strains of S. paradoxus were surveyed for sequence variation at six loci totaling 7 kb, and all 28 wild isolates were then genotyped at seven polymorphic loci. These data were used to calculate nucleotide diversity and number of segregating sites in S. paradoxus and to investigate geographic differentiation, population structure, and linkage disequilibrium. Synonymous site diversity is approximately 0.3%. Extensive incompatibilities between gene genealogies indicate frequent recombination between unlinked loci, but there is no evidence of recombination within genes. Some localized clonal growth is apparent. The frequency of outcrossing relative to inbreeding is estimated at 1.1% on the basis of heterozygosity. Thus, all three modes of reproduction known in the lab (clonal replication, inbreeding, and outcrossing) have been important in molding genetic variation in this species. PMID:15020405

  8. Population genetic consequences of the Allee effect and the role of offspring-number variation.

    PubMed

    Wittmann, Meike J; Gabriel, Wilfried; Metzler, Dirk

    2014-09-01

    A strong demographic Allee effect in which the expected population growth rate is negative below a certain critical population size can cause high extinction probabilities in small introduced populations. But many species are repeatedly introduced to the same location and eventually one population may overcome the Allee effect by chance. With the help of stochastic models, we investigate how much genetic diversity such successful populations harbor on average and how this depends on offspring-number variation, an important source of stochastic variability in population size. We find that with increasing variability, the Allee effect increasingly promotes genetic diversity in successful populations. Successful Allee-effect populations with highly variable population dynamics escape rapidly from the region of small population sizes and do not linger around the critical population size. Therefore, they are exposed to relatively little genetic drift. It is also conceivable, however, that an Allee effect itself leads to an increase in offspring-number variation. In this case, successful populations with an Allee effect can exhibit less genetic diversity despite growing faster at small population sizes. Unlike in many classical population genetics models, the role of offspring-number variation for the population genetic consequences of the Allee effect cannot be accounted for by an effective-population-size correction. Thus, our results highlight the importance of detailed biological knowledge, in this case on the probability distribution of family sizes, when predicting the evolutionary potential of newly founded populations or when using genetic data to reconstruct their demographic history. PMID:25009148

  9. Loss of genetic integrity in wild lake trout populations following stocking: insights from an exhaustive study of 72 lakes from Québec, Canada.

    PubMed

    Valiquette, Eliane; Perrier, Charles; Thibault, Isabel; Bernatchez, Louis

    2014-06-01

    Stocking represents the most important management tool worldwide to increase and sustain commercial and recreational fisheries in a context of overexploitation. Genetic impacts of this practice have been investigated in many studies, which examined population and individual admixture, but few have investigated determinants of these processes. Here, we addressed these questions from the genotyping at 19 microsatellite loci of 3341 adult lake trout (Salvelinus namaycush) from 72 unstocked and stocked lakes. Results showed an increase in genetic diversity and a twofold decrease in the extent of genetic differentiation among stocked populations when compared to unstocked. Stocked populations were characterized by significant admixture at both population and individual levels. Moreover, levels of admixture in stocked populations were strongly correlated with stocking intensity and a threshold value of total homogenization between source and stocked populations was identified. Our results also suggest that under certain scenarios, the genetic impacts of stocking could be of short duration. Overall, our study emphasizes the important alteration of the genetic integrity of stocked populations and the need to better understand determinants of admixture to optimize stocking strategies and to conserve the genetic integrity of wild populations. PMID:25067947

  10. Loss of genetic integrity in wild lake trout populations following stocking: insights from an exhaustive study of 72 lakes from Québec, Canada

    PubMed Central

    Valiquette, Eliane; Perrier, Charles; Thibault, Isabel; Bernatchez, Louis

    2014-01-01

    Stocking represents the most important management tool worldwide to increase and sustain commercial and recreational fisheries in a context of overexploitation. Genetic impacts of this practice have been investigated in many studies, which examined population and individual admixture, but few have investigated determinants of these processes. Here, we addressed these questions from the genotyping at 19 microsatellite loci of 3341 adult lake trout (Salvelinus namaycush) from 72 unstocked and stocked lakes. Results showed an increase in genetic diversity and a twofold decrease in the extent of genetic differentiation among stocked populations when compared to unstocked. Stocked populations were characterized by significant admixture at both population and individual levels. Moreover, levels of admixture in stocked populations were strongly correlated with stocking intensity and a threshold value of total homogenization between source and stocked populations was identified. Our results also suggest that under certain scenarios, the genetic impacts of stocking could be of short duration. Overall, our study emphasizes the important alteration of the genetic integrity of stocked populations and the need to better understand determinants of admixture to optimize stocking strategies and to conserve the genetic integrity of wild populations. PMID:25067947

  11. Genetic Determinants of Circulating Sphingolipid Concentrations in European Populations

    PubMed Central

    Pramstaller, Peter P.; Rudan, Igor; Franklin, Christopher S.; Liebisch, Gerhard; Erdmann, Jeanette; Jonasson, Inger; Zorkoltseva, Irina V.; Pattaro, Cristian; Hayward, Caroline; Isaacs, Aaron; Hengstenberg, Christian; Campbell, Susan; Gnewuch, Carsten; Janssens, A. CecileJ.W.; Kirichenko, Anatoly V.; König, Inke R.; Marroni, Fabio; Polasek, Ozren; Demirkan, Ayse; Kolcic, Ivana; Schwienbacher, Christine; Igl, Wilmar; Biloglav, Zrinka; Witteman, Jacqueline C. M.; Pichler, Irene; Zaboli, Ghazal; Axenovich, Tatiana I.; Peters, Annette; Schreiber, Stefan; Wichmann, H.-Erich; Schunkert, Heribert; Hastie, Nick; Oostra, Ben A.; Wild, Sarah H.; Meitinger, Thomas; Gyllensten, Ulf; van Duijn, Cornelia M.; Wilson, James F.; Wright, Alan; Schmitz, Gerd; Campbell, Harry

    2009-01-01

    Sphingolipids have essential roles as structural components of cell membranes and in cell signalling, and disruption of their metabolism causes several diseases, with diverse neurological, psychiatric, and metabolic consequences. Increasingly, variants within a few of the genes that encode enzymes involved in sphingolipid metabolism are being associated with complex disease phenotypes. Direct experimental evidence supports a role of specific sphingolipid species in several common complex chronic disease processes including atherosclerotic plaque formation, myocardial infarction (MI), cardiomyopathy, pancreatic β-cell failure, insulin resistance, and type 2 diabetes mellitus. Therefore, sphingolipids represent novel and important intermediate phenotypes for genetic analysis, yet little is known about the major genetic variants that influence their circulating levels in the general population. We performed a genome-wide association study (GWAS) between 318,237 single-nucleotide polymorphisms (SNPs) and levels of circulating sphingomyelin (SM), dihydrosphingomyelin (Dih-SM), ceramide (Cer), and glucosylceramide (GluCer) single lipid species (33 traits); and 43 matched metabolite ratios measured in 4,400 subjects from five diverse European populations. Associated variants (32) in five genomic regions were identified with genome-wide significant corrected p-values ranging down to 9.08×10−66. The strongest associations were observed in or near 7 genes functionally involved in ceramide biosynthesis and trafficking: SPTLC3, LASS4, SGPP1, ATP10D, and FADS1–3. Variants in 3 loci (ATP10D, FADS3, and SPTLC3) associate with MI in a series of three German MI studies. An additional 70 variants across 23 candidate genes involved in sphingolipid-metabolizing pathways also demonstrate association (p = 10−4 or less). Circulating concentrations of several key components in sphingolipid metabolism are thus under strong genetic control, and variants in these loci can be

  12. Population Genetics of Anopheles coluzzii Immune Pathways and Genes

    PubMed Central

    Rottschaefer, Susan M.; Crawford, Jacob E.; Riehle, Michelle M.; Guelbeogo, Wamdaogo M.; Gneme, Awa; Sagnon, N’Fale; Vernick, Kenneth D.; Lazzaro, Brian P.

    2014-01-01

    Natural selection is expected to drive adaptive evolution in genes involved in host–pathogen interactions. In this study, we use molecular population genetic analyses to understand how natural selection operates on the immune system of Anopheles coluzzii (formerly A. gambiae “M form”). We analyzed patterns of intraspecific and interspecific genetic variation in 20 immune-related genes and 17 nonimmune genes from a wild population of A. coluzzii and asked if patterns of genetic variation in the immune genes are consistent with pathogen-driven selection shaping the evolution of defense. We found evidence of a balanced polymorphism in CTLMA2, which encodes a C-type lectin involved in regulation of the melanization response. The two CTLMA2 haplotypes, which are distinguished by fixed amino acid differences near the predicted peptide cleavage site, are also segregating in the sister species A. gambiae (“S form”) and A. arabiensis. Comparison of the two haplotypes between species indicates that they were not shared among the species through introgression, but rather that they arose before the species divergence and have been adaptively maintained as a balanced polymorphism in all three species. We additionally found that STAT-B, a retroduplicate of STAT-A, shows strong evidence of adaptive evolution that is consistent with neofunctionalization after duplication. In contrast to the striking patterns of adaptive evolution observed in these Anopheles-specific immune genes, we found no evidence of adaptive evolution in the Toll and Imd innate immune pathways that are orthologously conserved throughout insects. Genes encoding the Imd pathway exhibit high rates of amino acid divergence between Anopheles species but also display elevated amino acid diversity that is consistent with relaxed purifying selection. These results indicate that adaptive coevolution between A. coluzzii and its pathogens is more likely to involve novel or lineage-specific molecular mechanisms

  13. Population genetic structure, linkage disequilibrium and effective population size of conserved and extensively raised village chicken populations of Southern Africa

    PubMed Central

    Khanyile, Khulekani S.; Dzomba, Edgar F.; Muchadeyi, Farai C.

    2015-01-01

    Extensively raised village chickens are considered a valuable source of biodiversity, with genetic variability developed over thousands of years that ought to be characterized and utilized. Surveys that can reveal a population's genetic structure and provide an insight into its demographic history will give valuable information that can be used to manage and conserve important indigenous animal genetic resources. This study reports population diversity and structure, linkage disequilibrium and effective population sizes of Southern African village chickens and conservation flocks from South Africa. DNA samples from 312 chickens from South African village and conservation flocks (n = 146), Malawi (n = 30) and Zimbabwe (n = 136) were genotyped using the Illumina iSelect chicken SNP60K BeadChip. Population genetic structure analysis distinguished the four conservation flocks from the village chicken populations. Of the four flocks, the Ovambo clustered closer to the village chickens particularly those sampled from South Africa. Clustering of the village chickens followed a geographic gradient whereby South African chickens were closer to those from Zimbabwe than to chickens from Malawi. Different conservation flocks seemed to have maintained different components of the ancestral genomes with a higher proportion of village chicken diversity found in the Ovambo population. Overall population LD averaged over chromosomes ranged from 0.03 ± 0.07 to 0.58 ± 0.41 and averaged 0.15 ± 0.16. Higher LD, ranging from 0.29 to 0.36, was observed between SNP markers that were less than 10 kb apart in the conservation flocks. LD in the conservation flocks steadily decreased to 0.15 (PK) and 0.24 (VD) at SNP marker interval of 500 kb. Genomewide LD decay in the village chickens from Malawi, Zimbabwe and South Africa followed a similar trend as the conservation flocks although the mean LD values for the investigated SNP intervals were lower. The results suggest low effective

  14. Gingival recession and associated factors in a homogeneous Mexican adult male population: A cross-sectional study

    PubMed Central

    Minaya-Sánchez, Mirna; Medina-Solís, Carlo E.; Vallejos-Sánchez, Ana A.; Marquez-Corona, Maria L.; Pontigo-Loyola, América P.; Islas-Granillo, Horacio; Maupomé, Gerardo

    2012-01-01

    Background: Diverse variables are implicated in the pathogenesis of gingival recession; more detailed knowledge about the relationship between the clinical presentation of gingival recession and assorted risk indicators may lead to improved patient monitoring, early intervention, and subsequent prevention. The objective was to evaluate clinically gingival recession in a homogeneous Mexican adult male population and to determine the strength of association with related factors. Method: A cross-sectional study was carried out in a largely homogeneous group in terms of ethnic background, socioeconomic status, gender, occupation, and medical/dental insurance, in Campeche, Mexico. Periodontal examinations were undertaken to determine diverse clinical dental variables. All periodontal clinical examinations were assessed using the Florida Probe System, a dental chair and one examiner. Questionnaires were used to collect diverse risk indicators. Statistical analyses were undertaken with negative binomial regression models. Results: The mean number of sites with gingival recession per subject was 6.73±5.81; the prevalence was 87.6%. In the negative binomial regression model we observed that for (i) each year of age, and (ii) each percentage unit of increase in sites with plaque, and (iii) with suppuration, mean sites with gingival recession increased 2.9%, 1.0% and 13.0%, respectively. Having a spouse was associated with gingival recession. Conclusions: We observed association between gingival recession, and sociodemographic and clinical parameters. Patients need to be educated about risk indicators for gingival recession as well as the preventive maneuvers that may be implemented to minimize its occurrence. The potential of improved oral self-care to prevent a largely benign condition such as gingival recession is important, given the associated disorders that may ensue root exposure, such as root caries and root hypersensitivity. Key words:Oral health, periodontal health

  15. Temporal changes in genetic variation of boll weevil (Coleoptera: Curculionidae) populations, and implications for population assignment in eradication zones

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic differentiation among 10 populations of boll weevil, Anthonomus grandis grandis, sampled in 2009, in Texas and Mexico, was determined using ten microsatellite loci. In addition, temporal changes in genetic composition were examined in the eight populations for which samples were available fr...

  16. [Genetic demography of populations of three megalopolises in relation to the problem of creating genetic databases].

    PubMed

    Kurbatova, O L; Pobedonostseva, E Iu; Veremeĭchik, V M; Prudnikova, A S; Atramentova, L A; Tsybovskiĭ, I S; Udina, I G

    2013-04-01

    Based on data collected from urban residents by questionnaire, the basic parameters of the genetic-demographic structure of populations of the three megalopolises, i.e., Moscow, Kharkov, and Minsk, have been calculated, including the migration coefficients and their dynamics in generations, the radius of the cities migration attraction, the parameters of marriage structure (the proportion ofinterethnic marriages, the level of intraethnic assortative mating, the marital distances), and the gene flow between the ethnic groups. It is shown that the representatives of the most numerous ethnic groups in each megalopolis have considerable amount of admixture. For Russians of Moscow, Ukrainians of Kharkov, and Belarusians of Minsk, the proportion of individuals whose ancestors were all born in the given city for at least three generations and belonged to the same nationality turned out to be very low (4.75% in Moscow, 1.83% in Kharkov, and 3.13% in Minsk). This finding questions the formation of a reference population in the megalopolis as a sampling of aboriginals of certain ethnic origins. In the paper, we justify principles of creating genetic databases for the population of the megalopolis taking into account the complexity and dynamism of its population structure. PMID:23866628

  17. Population genetic structure and long-distance dispersal among seabird populations: implications for colony persistence.

    PubMed

    Bicknell, A W J; Knight, M E; Bilton, D; Reid, J B; Burke, T; Votier, S C

    2012-06-01

    Dramatic local population decline brought about by anthropogenic-driven change is an increasingly common threat to biodiversity. Seabird life history traits make them particularly vulnerable to such change; therefore, understanding population connectivity and dispersal dynamics is vital for successful management. Our study used a 357-base pair mitochondrial control region locus sequenced for 103 individuals and 18 nuclear microsatellite loci genotyped for 245 individuals to investigate population structure in the Atlantic and Pacific populations of the pelagic seabird, Leach's storm-petrel Oceanodroma leucorhoa leucorhoa. This species is under intense predation pressure at one regionally important colony on St Kilda, Scotland, where a disparity between population decline and predation rates hints at immigration from other large colonies. AMOVA, F(ST), Φ(ST) and Bayesian cluster analyses revealed no genetic structure among Atlantic colonies (Global Φ(ST) = -0.02 P > 0.05, Global F(ST) = 0.003, P > 0.05, STRUCTURE K = 1), consistent with either contemporary gene flow or strong historical association within the ocean basin. The Pacific and Atlantic populations are genetically distinct (Global Φ(ST) = 0.32 P < 0.0001, Global F(ST) = 0.04, P < 0.0001, STRUCTURE K = 2), but evidence for interocean exchange was found with individual exclusion/assignment and population coalescent analyses. These findings highlight the importance of conserving multiple colonies at a number of different sites and suggest that management of this seabird may be best viewed at an oceanic scale. Moreover, our study provides an illustration of how long-distance movement may ameliorate the potentially deleterious impacts of localized environmental change, although direct measures of dispersal are still required to better understand this process. PMID:22548276

  18. Simple phenotypic sweeps hide complex genetic changes in populations.

    PubMed

    Maharjan, Ram P; Liu, Bin; Feng, Lu; Ferenci, Thomas; Wang, Lei

    2015-02-01

    Changes in allele frequencies and the fixation of beneficial mutations are central to evolution. The precise relationship between mutational and phenotypic sweeps is poorly described however, especially when multiple alleles are involved. Here, we investigate these relationships in a bacterial population over 60 days in a glucose-limited chemostat in a large population. High coverage metagenomic analysis revealed a disconnection between smooth phenotypic sweeps and the complexity of genetic changes in the population. Phenotypic adaptation was due to convergent evolution and involved soft sweeps by 7-26 highly represented alleles of several genes in different combinations. Allele combinations spread from undetectably low baselines, indicating that minor subpopulations provide the basis of most innovations. A hard sweep was also observed, involving a single combination of rpoS, mglD, malE, sdhC, and malT mutations sweeping to greater than 95% of the population. Other mutant genes persisted but at lower abundance, including hfq, consistent with its demonstrated frequency-dependent fitness under glucose limitation. Other persistent, newly identified low-frequency mutations were in the aceF, galF, ribD and asm genes, in noncoding regulatory regions, three large indels and a tandem duplication; these were less affected by fluctuations involving more dominant mutations indicating separate evolutionary paths. Our results indicate a dynamic subpopulation structure with a minimum of 42 detectable mutations maintained over 60 days. We also conclude that the massive population-level mutation supply in combination with clonal interference leads to the soft sweeps observed, but not to the exclusion of an occasional hard sweep. PMID:25589261

  19. Differences in genetic variation in antigen-processing machinery components and association with cervical carcinoma risk in two Indonesian populations.

    PubMed

    Mehta, Akash M; Spaans, Vivian M; Mahendra, Nyoman Bayu; Osse, Elisabeth M; Vet, Jessica N I; Purwoto, Gatot; Surya, I G D; Cornian, Santoso; Peters, Alexander A; Fleuren, Gert J; Jordanova, Ekaterina S

    2015-06-01

    Genetic variation of antigen-processing machinery (APM) components has been shown to be associated with cervical carcinoma risk and outcome in a genetically homogeneous Dutch population. However, the role of APM component single nucleotide polymorphisms (SNPs) in genetically heterogeneous populations with different distributions of human papillomavirus (HPV) subtypes remains unclear. Eleven non-synonymous, coding SNPs in the TAP1, TAP2, LMP2, LMP7 and ERAP1 genes were genotyped in cervical carcinoma patients and healthy controls from two distinct Indonesian populations (Balinese and Javanese). Individual genotype and allele distributions were investigated using single-marker analysis, and combined SNP effects were assessed by haplotype construction and haplotype interaction analysis. Allele distribution patterns in Bali and Java differed in relation to cervical carcinoma risk, with four ERAP1 SNPs and one TAP2 SNP in the Javanese population showing significant association with cervical carcinoma risk, while in the Balinese population, only one TAP2 SNP showed this association. Multimarker analysis demonstrated that in the Javanese patients, one specific haplotype, consisting of the ERAP1-575 locus on chromosome 5 and the TAP2-379 and TAP2-651 loci on chromosome 6, was significantly associated with cervical carcinoma risk (global P = 0.008); no significant haplotype associations were found in the Balinese population. These data indicate not only that genetic variation in APM component genes is associated with cervical carcinoma risk in Indonesia but also that the patterns of association differ depending on background genetic composition and possibly on differences in HPV type distribution. PMID:25796583

  20. Combined analyses of kinship and FST suggest potential drivers of chaotic genetic patchiness in high gene-flow populations

    PubMed Central

    Iacchei, Matthew; Ben-Horin, Tal; Selkoe, Kimberly A; Bird, Christopher E; García-Rodríguez, Francisco J; Toonen, Robert J

    2013-01-01

    We combine kinship estimates with traditional F-statistics to explain contemporary drivers of population genetic differentiation despite high gene flow. We investigate range-wide population genetic structure of the California spiny (or red rock) lobster (Panulirus interruptus) and find slight, but significant global population differentiation in mtDNA (ΦST = 0.006, P = 0.001; Dest_Chao = 0.025) and seven nuclear microsatellites (FST = 0.004, P < 0.001; Dest_Chao = 0.03), despite the species’ 240- to 330-day pelagic larval duration. Significant population structure does not correlate with distance between sampling locations, and pairwise FST between adjacent sites often exceeds that among geographically distant locations. This result would typically be interpreted as unexplainable, chaotic genetic patchiness. However, kinship levels differ significantly among sites (pseudo-F16,988 = 1.39, P = 0.001), and ten of 17 sample sites have significantly greater numbers of kin than expected by chance (P < 0.05). Moreover, a higher proportion of kin within sites strongly correlates with greater genetic differentiation among sites (Dest_Chao, R2 = 0.66, P < 0.005). Sites with elevated mean kinship were geographically proximate to regions of high upwelling intensity (R2 = 0.41, P = 0.0009). These results indicate that P. interruptus does not maintain a single homogenous population, despite extreme dispersal potential. Instead, these lobsters appear to either have substantial localized recruitment or maintain planktonic larval cohesiveness whereby siblings more likely settle together than disperse across sites. More broadly, our results contribute to a growing number of studies showing that low FST and high family structure across populations can coexist, illuminating the foundations of cryptic genetic patterns and the nature of marine dispersal. PMID:23802550

  1. Combined analyses of kinship and FST suggest potential drivers of chaotic genetic patchiness in high gene-flow populations.

    PubMed

    Iacchei, Matthew; Ben-Horin, Tal; Selkoe, Kimberly A; Bird, Christopher E; García-Rodríguez, Francisco J; Toonen, Robert J

    2013-07-01

    We combine kinship estimates with traditional F-statistics to explain contemporary drivers of population genetic differentiation despite high gene flow. We investigate range-wide population genetic structure of the California spiny (or red rock) lobster (Panulirus interruptus) and find slight, but significant global population differentiation in mtDNA (ΦST = 0.006, P = 0.001; D(est_Chao) = 0.025) and seven nuclear microsatellites (F(ST) = 0.004, P < 0.001; D(est_Chao) = 0.03), despite the species' 240- to 330-day pelagic larval duration. Significant population structure does not correlate with distance between sampling locations, and pairwise FST between adjacent sites often exceeds that among geographically distant locations. This result would typically be interpreted as unexplainable, chaotic genetic patchiness. However, kinship levels differ significantly among sites (pseudo-F(16,988) = 1.39, P = 0.001), and ten of 17 sample sites have significantly greater numbers of kin than expected by chance (P < 0.05). Moreover, a higher proportion of kin within sites strongly correlates with greater genetic differentiation among sites (D(est_Chao), R(2) = 0.66, P < 0.005). Sites with elevated mean kinship were geographically proximate to regions of high upwelling intensity (R(2) = 0.41, P = 0.0009). These results indicate that P. interruptus does not maintain a single homogenous population, despite extreme dispersal potential. Instead, these lobsters appear to either have substantial localized recruitment or maintain planktonic larval cohesiveness whereby siblings more likely settle together than disperse across sites. More broadly, our results contribute to a growing number of studies showing that low F(ST) and high family structure across populations can coexist, illuminating the foundations of cryptic genetic patterns and the nature of marine dispersal. PMID:23802550

  2. Genetic analysis of Indian tasar silkmoth (Antheraea mylitta) populations.

    PubMed

    Chakraborty, Saikat; Muthulakshmi, M; Vardhini, Deena; Jayaprakash, P; Nagaraju, J; Arunkumar, K P

    2015-01-01

    Indian tasar silkmoth, Antheraea mylitta is an economically important wild silkmoth species distributed across India. A number of morphologically and ethologically well-defined ecotypes are known for this species that differ in their primary food plant specificity. Most of these ecotypes do not interbreed in nature, but are able to produce offspring under captive conditions. Microsatellite markers were developed for A. mylitta, and out of these, ten well-behaved microsatellite loci were used to analyze the population structure of different ecoraces. A total of 154 individual moths belonging to eight different ecoraces, were screened at each locus. Hierarchical analysis of population structure using Analysis of MOlecular VAriance (AMOVA) revealed significant structuring (FST = 0.154) and considerable inbreeding (FIS = 0.505). A significant isolation by distance was also observed. The number of possible population clusters was investigated using distance method, Bayesian algorithm and self organization maps (SOM). The first two methods revealed two distinct clusters, whereas the SOM showed the different ecoraces not to be clearly differentiated. These results suggest that although there is a large degree of phenotypic variation among the different ecoraces of A. mylitta, genetically they are not very different, and the phenotypic differences may largely be a result of their respective ecology. PMID:26510465

  3. Genetic analysis of Indian tasar silkmoth (Antheraea mylitta) populations

    PubMed Central

    Chakraborty, Saikat; Muthulakshmi, M; Vardhini, Deena; Jayaprakash, P; Nagaraju, J; Arunkumar, K. P.

    2015-01-01

    Indian tasar silkmoth, Antheraea mylitta is an economically important wild silkmoth species distributed across India. A number of morphologically and ethologically well-defined ecotypes are known for this species that differ in their primary food plant specificity. Most of these ecotypes do not interbreed in nature, but are able to produce offspring under captive conditions. Microsatellite markers were developed for A. mylitta, and out of these, ten well-behaved microsatellite loci were used to analyze the population structure of different ecoraces. A total of 154 individual moths belonging to eight different ecoraces, were screened at each locus. Hierarchical analysis of population structure using Analysis of MOlecular VAriance (AMOVA) revealed significant structuring (FST = 0.154) and considerable inbreeding (FIS = 0.505). A significant isolation by distance was also observed. The number of possible population clusters was investigated using distance method, Bayesian algorithm and self organization maps (SOM). The first two methods revealed two distinct clusters, whereas the SOM showed the different ecoraces not to be clearly differentiated. These results suggest that although there is a large degree of phenotypic variation among the different ecoraces of A. mylitta, genetically they are not very different, and the phenotypic differences may largely be a result of their respective ecology. PMID:26510465

  4. Peach genetic resources: diversity, population structure and linkage disequilibrium

    PubMed Central

    2013-01-01

    was considerable LD extension while no variation of LD with physical distance was observed in the landraces. From the first STRUCTURE result, LG1 had the greatest proportion of alleles in LD within all three subpopulations. Conclusions Our study demonstrates a high level of genetic diversity and relatively fast decay of LD in the Oriental peach breeding program. Inclusion of Chinese landraces will have a greater effect on increasing genetic diversity in Occidental breeding programs. Fingerprinting with genotype data for all 658 cultivars will be used for accession management in different germplasms. A higher density of markers are needed for association mapping in Oriental germplasm due to the low extension of LD. Population structure and evaluation of LD provides valuable information for GWAS experiment design in peach. PMID:24041442

  5. Detection of genetic polymorphism in the populations of brinjal shoot and fruit borer, Leucinodes orbonalis (Guenee).

    PubMed

    Karthikeyan, K A M; Vijayakumar, I; Murali, P; Suresh, P; Janarthanan, S

    2005-06-01

    In the present study six different populations of L. orbonalis were collected and subjected to analysis of genetic variability in terms of carboxylesterase isozyme pattern and DNA polymorphism using RAPD-PCR. Pattern of carboxylesterase revealed a similar isozyme cluster in the populations namely, sivaganga (population-3), dindigal (population-4), virudhunagar (population-5) and coimbatore (population-6). Similarly, the populations of L. orbonalis recorded 3 distinct randomly amplified polymorphic DNA markers in all populations grouped above. This pattern of genetic variability in the populations was also supported by the analysis of the similarity indices and UPGMA dendrogram. PMID:15991581

  6. [Population genetic variation and structure analysis on five populations of mirror carp Cyprinus carpio L. using microsatellites].

    PubMed

    Quan, Ying-Chun; Li, Da-Yu; Cao, Ding-Chen; Sun, Xiao-Wen; Liang, Li-Qun

    2006-12-01

    In this paper, population genetic variability and genetic structure of five populations of an important cultivation species, mirror carp (Cyprinus carpio L.) were analyzed using 30 microsatellite loci. The observed (Ho) and expected (He) heterozygosity values, polymorphic information content (PIC) and number of effective alleles (Ae) were all determined. The genetic similarity coefficient and Nei's standard genetic distance were computed based on the allele frequencies. The Hardy-Weinberg equilibrium was checked by chi2 test. Genetic differentiation and hierarchical partition of genetic diversity were evaluated by FST and Nm. A dendrogram was constructed based on UPGMA methods using PHYLIP software package supported by a bootstrap value of 91.0%. Totally 7,083 fragments were procured. Their lengths were from 102 bp to 446 bp. For each locus, 1-16 alleles were amplified, adding up to 356 alleles in all the 5 populations. We found the genetic variability level was relatively high in all five populations, as shown by Ae = 1.07-2.30, He= 0.70-0.78 and PIC=0.69-0.75, respectively. The genetic similarity coefficients were all above 0.52, indicating their close genetic relationships. The UPGMA phylogenetic tree showed mirror carps sampled from Donggang, Fengcheng and Liaozhong were clustered into one group and the other two populations, both collected from Songpu, were grouped together. There were obvious relations between genetic distances and geographical distributions of the five populations. No fragments were amplified from some loci of EST-SSRs, which may suggest the loss of these loci in mirror carp genome or sequence divergence at the primer binding sites. These null alleles may result from selection because functional genes are under more selection pressure than non-encoding loci. Overall, population genetic variation is high for each of the five mirror carp, and the differentiations are also significant among populations. PMID:17138540

  7. Biotinidase deficiency: a treatable genetic disorder in the Saudi population.

    PubMed

    Joshi, S; al-Essa, M A; Archibald, A; Ozand, P T

    1999-11-01

    Biotinidase deficiency is an autosomal recessive genetic disorder which is not uncommon in the Saudi population. Biotinidase is responsible for biotin recycling and biotin is an essential cofactor for activation of the carboxylase enzymes. Absence of biotinidase leads to infantile or early childhood encephalopathy, seizure disorder, dermatitis, alopecia, neural deafness and optic atrophy. The disease can be diagnosed by simple fluorometric enzyme assay. Treatment with biotin is both cheap and simple, resulting in rewarding clinical recovery and normalization of the biochemical, neuroradiological and neurophysiological parameters. If neglected, however, a patient may die of acute metabolic acidosis or may suffer from permanent neural deafness and optic atrophy, with mental and motor handicap. We describe the detection and treatment of 20 cases of biotinidase deficiency in our hospital and recommend the introduction of a neonatal screening programme for this disorder. PMID:11924114

  8. Examination of genetic variants influencing lipid traits in pediatric populations

    PubMed Central

    Wang, Kai; Zhang, Haitao; Mentch, Frank D.; Bradfield, Jonathan P.; Glessner, Joseph T.; Qiu, Haijun; Guo, Yiran; Hou, Cuiping; Frackelton, Edward C.; Thomas, Kelly; Bender, Amber; Albano, Anthony; Otieno, George; Garris, Maria; Seidler, Kallyn; Moy, Alexander; Kim, Cecilia E.; Keating, Brendan; Chiavacci, Rosetta M.; Grundmeier, Robert; Sleiman, Patrick A.; Grant, Struan F.A.; Hakonarson, Hakon

    2012-01-01

    Previous large-scale genome-wide association studies in adult populations have implicated ∽100 loci in determining high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol, or triglyceride levels. However, whether these loci also contribute to variations of lipid traits in pediatric populations remain unknown. Here we assayed a population of Philadelphia children by high-density single nucleotide polymorphism arrays, and performed association analysis on lipid traits ascertained from lipid measurements stored in electronic medical records. We examined previously reported lipid trait associations, and found that most of them show identical direction of association in our pediatric cohorts, including genome-wide significant association on cholesteryl ester transfer protein with HDL-C levels (rs3764261, P = 2.1 × 10−8) and other significant associations on oxysterol-binding protein-like protein 7, low-density lipoprotein receptor-related protein 4 and low-density lipoprotein receptor-related protein 1. Additionally, we identified suggestive association on low-density lipoprotein receptor-related protein 1B with HDL-C levels (rs17736712, P = 2.1 × 10−7), but this signal is not supported by previous meta-analysis on adult cohorts. Finally, we examined rare copy number variants and identified deletions encompassing tetratricopeptide repeat domain 39B in two children with extreme lipid measures. Our results highlight the commonalities and differences of genetic components in determining lipid traits in pediatric versus adult populations. Furthermore, our study demonstrates the unique utility of automated information retrieval from electronic medical records in facilitating the identification of genotype-phenotype associations.

  9. Molecular epidemiology, population genetics, and pathogenic role of Helicobacter pylori

    PubMed Central

    Suzuki, Rumiko; Shiota, Seiji; Yamaoka, Yoshio

    2012-01-01

    Helicobacter pylori infection is linked to various gastroduodenal diseases; however, only approximately 20% of infected individuals develop severe diseases. Despite the high prevalence of H. pylori infection in Africa and South Asia, the incidence of gastric cancer in these areas is much lower than in other countries. Furthermore, the incidence of gastric cancer tends to decrease from north to south in East Asia. Such geographic differences in the pathology can be explained, at least in part, by the presence of different types of H. pylori virulence factors, especially cagA, vacA, and the right end of the cag pathogenicity island. The genotype of the virulence genes is also useful as a tool to track human migration utilizing the high genetic diversity and frequent recombination between different H. pylori strains. Multilocus sequence typing (MLST) analysis using 7 housekeeping genes can also help predict the history of human migrations. Population structure analysis based on MLST has revealed 7 modern population types of H. pylori, which derived from 6 ancestral populations. Interestingly, the incidence of gastric cancer is closely related to the distribution of H. pylori populations. The different incidence of gastric cancer can be partly attributed to the different genotypes of H. pylori circulating in different geographic areas. Although approaches by MLST and virulence factors are effective, these methods focus on a small number of genes and may miss information conveyed by the rest of the genome. Genome-wide analyses using DNA microarray or whole-genome sequencing technology give a broad view on the genome of H. pylori. In particular, next-generation sequencers, which can read DNA sequences in less time and at lower costs than Sanger sequencing, enabled us to efficiently investigate not only the evolution of H. pylori, but also novel virulence factors and genomic changes related to drug resistance. PMID:22197766

  10. The congruence between matrilineal genetic (mtDNA) and geographic diversity of Iranians and the territorial populations

    PubMed Central

    Bahmanimehr, Ardeshir; Eskandari, Ghafar; Nikmanesh, Fatemeh

    2015-01-01

    Objective(s): From the ancient era, emergence of Agriculture in the connecting region of Mesopotamia and the Iranian plateau at the foothills of the Zagros Mountains, made Iranian gene pool as an important source of populating the region. It has differentiated the population spread and different language groups. In order to trace the maternal genetic affinity between Iranians and other populations of the area and to establish the place of Iranians in a broad framework of ethnically and linguistically diverse groups of Middle Eastern and South Asian populations, a comparative study of territorial groups was designed and used in the population statistical analysis. Materials and Methods: Mix of 616 samples was sequenced for complete mtDNA or hyper variable regions in this study. A published dataset of neighboring populations was used as a comparison in the Iranian matrilineal lineage study based on mtDNA haplogroups. Results: Statistical analyses data, demonstrate a close genetic structure of all Iranian populations, thus suggesting their origin from a common maternal ancestral gene pool and show that the diverse maternal genetic structure does not reflect population differentiation in the region in their language. Conclusion: In the aggregate of the eastward spreads of proto-Elamo-Dravidian language from the Southwest region of Iran, the Elam province, a reasonable degree of homogeneity has been observed among Iranians in this study. The approach will facilitate our perception of the more detailed relationship of the ethnic groups living in Iran with the other ancient peoples of the area, testing linguistic hypothesis and population movements. PMID:25810873

  11. Facial asymmetry and genetic ancestry in Latin American admixed populations.

    PubMed

    Quinto-Sánchez, Mirsha; Adhikari, Kaustubh; Acuña-Alonzo, Victor; Cintas, Celia; Silva de Cerqueira, Caio Cesar; Ramallo, Virginia; Castillo, Lucia; Farrera, Arodi; Jaramillo, Claudia; Arias, Williams; Fuentes, Macarena; Everardo, Paola; de Avila, Francisco; Gomez-Valdés, Jorge; Hünemeier, Tábita; Gibbon, Shara; Gallo, Carla; Poletti, Giovanni; Rosique, Javier; Bortolini, Maria Cátira; Canizales-Quinteros, Samuel; Rothhammer, Francisco; Bedoya, Gabriel; Ruiz-Linares, Andres; González-José, Rolando

    2015-05-01

    Fluctuating and directional asymmetry are aspects of morphological variation widely used to infer environmental and genetic factors affecting facial phenotypes. However, the genetic basis and environmental determinants of both asymmetry types is far from being completely known. The analysis of facial asymmetries in admixed individuals can be of help to characterize the impact of a genome's heterozygosity on the developmental basis of both fluctuating and directional asymmetries. Here we characterize the association between genetic ancestry and individual asymmetry on a sample of Latin-American admixed populations. To do so, three-dimensional (3D) facial shape attributes were explored on a sample of 4,104 volunteers aged between 18 and 85 years. Individual ancestry and heterozygosity was estimated using more than 730,000 genome-wide markers. Multivariate techniques applied to geometric morphometric data were used to evaluate the magnitude and significance of directional and fluctuating asymmetry (FA), as well as correlations and multiple regressions aimed to estimate the relationship between facial FA scores and heterozygosity and a set of covariates. Results indicate that directional and FA are both significant, the former being the strongest expression of asymmetry in this sample. In addition, our analyses suggest that there are some specific patterns of facial asymmetries characterizing the different ancestry groups. Finally, we find that more heterozygous individuals exhibit lower levels of asymmetry. Our results highlight the importance of including ancestry-admixture estimators, especially when the analyses are aimed to compare levels of asymmetries on groups differing on socioeconomic levels, as a proxy to estimate developmental noise. PMID:25582401

  12. Estimating Meiotic Gene Conversion Rates From Population Genetic Data

    PubMed Central

    Gay, J.; Myers, S.; McVean, G.

    2007-01-01

    Gene conversion plays an important part in shaping genetic diversity in populations, yet estimating the rate at which it occurs is difficult because of the short lengths of DNA involved. We have developed a new statistical approach to estimating gene conversion rates from genetic variation, by extending an existing model for haplotype data in the presence of crossover events. We show, by simulation, that when the rate of gene conversion events is at least comparable to the rate of crossover events, the method provides a powerful approach to the detection of gene conversion and estimation of its rate. Application of the method to data from the telomeric X chromosome of Drosophila melanogaster, in which crossover activity is suppressed, indicates that gene conversion occurs ∼400 times more often than crossover events. We also extend the method to estimating variable crossover and gene conversion rates and estimate the rate of gene conversion to be ∼1.5 times higher than the crossover rate in a region of human chromosome 1 with known recombination hotspots. PMID:17660532

  13. Population Genetic Analysis Infers Migration Pathways of Phytophthora ramorum in U.S. Nurseries

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recently introduced, exotic plant pathogens may exhibit low genetic diversity and be limited to clonal reproduction. However, rapidly mutating molecular markers such as microsatellites can reveal genetic variation within these populations and be used to model putative migration patterns. Phytophthor...

  14. Genetic diversity and population differentiation of Sclerotinia sclerotiorum collected from canola in China and in USA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic and phenotypic diversity and population differentiation of Sclerotinia sclerotiorum isolates infecting canola from China and the United States were investigated. Genetic diversity was assessed with eight microsatellite markers and mycelial compatibility groups (MCGs). Phenotypic diversity wa...

  15. Update on the Comparative Assessment of Genetic Diversity Between Accessible and Remote Potato Populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There is limited information on the organization of potato genetic diversity (GD) in natural habitats. Answering questions on that topic has significant implications for germplasm conservation -- for example, targeting habitats and populations with greater genetic richness or distinctiveness for col...

  16. Genetic population structure of the endemic fourline wrasse (Larabicus quadrilineatus) suggests limited larval dispersal distances in the Red Sea.

    PubMed

    Froukh, Tawfiq; Kochzius, Marc

    2007-04-01

    The connectivity among marine populations is determined by the dispersal capabilities of adults as well as their eggs and larvae. Dispersal distances and directions have a profound effect on gene flow and genetic differentiation within species. Genetic homogeneity over large areas is a common feature of coral reef fishes and can reflect high dispersal capability resulting in high levels of gene flow. If fish larvae return to their parental reef, gene flow would be restricted and genetic differentiation could occur. Larabicus quadrilineatus (Labridae) is considered as an endemic fish species of the Red Sea and Gulf of Aden. The juveniles of this species are cleaner fish that feed on ectoparasites of other fishes. Here, we investigated the genetic population structure and gene flow in L. quadrilineatus among five locations in the Red Sea to infer connectivity among them. To estimate genetic diversity, we analysed 369 bp of 237 mitochondrial DNA control region sequences. Haplotype and nucleotide diversities were higher in the southern than in the northern Red Sea. Analysis of molecular variance (amova) detected the highest significant genetic variation between northern and central/southern populations (Phi(CT) = 0.01; P < 0.001). Migration analysis revealed a several fold higher northward than southward migration, which could be explained by oceanographic conditions and spawning season. Even though the Phi(ST) value of 0.01 is rather low and implies a long larval dispersal distance, estimates based on the isolation-by-distance model show a very low mean larval dispersal distance (0.44-5.1 km) compared to other studies. In order to enable a sustainable ornamental fishery on the fourline wrasse, the results of this study suggest that populations in the northern and southern Red Sea should be managed separately as two different stocks. The rather low larval dispersal distance of about 5 km needs to be considered in the design of marine protected areas to enable

  17. [A comparative study on genetic polymorphism and genetic relationship of 13 SNPs in three Chinese populations].

    PubMed

    Wang, Rui-Heng; Liu, Li-Min; Zhao, Jin-Ling

    2009-03-01

    Using the fluorescence labeled capillary electrophoresis of multi-PCR technique, the single nucleotide polymorphism (SNP) typing system of fragment length discrepant allele specific fluorescence labeled multi-PCR technique is established based on the principle of allele-specific PCR. The typing of the 13 SNP loci can be completed simultaneously according to the length of PCR products and the number of product peaks. It appears a single product peak when the SNP is homozygous, and two product peaks with 4 bp differences will appear when it is heterozygous. By using this system, we conducted population census about allele frequencies for 13 autosomal SNP loci in Southern Liaoning Han samples, Mongolian samples in Inner Mongolia and Zhuang samples in Guangxi area, and got the allele frequencies of the 13 SNP loci in the three populations, then preliminarily discussed their genetic relationship by comparing their differences in allelic polymorphism. The results indicate that the allelic distributions of the 13 SNP loci in the three populations are polymorphic, and the difference is significant in some SNP loci (P< or =0.01). The sampling survey shows that the result is consistent with Hardy-Weinberg equilibrium, and Han population in southern Liaoning has relatively closer relationship with Mongolian in Inner Mongolia than with Zhuang population in Guangxi by origin. PMID:19273440

  18. Experimental separation of genetic and demographic factors on extinction risk in wild populations.

    PubMed

    Wootton, J Timothy; Pfister, Catherine A

    2013-10-01

    When populations reach small size, an extinction risk vortex may arise from genetic (inbreeding depression, genetic drift) and ecological (demographic stochasticity, Allee effects, environmental fluctuation) processes. The relative contribution of these processes to extinction in wild populations is unknown, but important for conserving endangered species. In experimental field populations of a harvested kelp (Postelsia palmaeformis), in which we independently varied initial genetic diversity (completely inbred, control, outbred) and population size, ecological processes dominated the risk of extinction, whereas the contribution of genetic diversity was slight. Our results match theoretical predictions that demographic processes will generally doom small populations to extinction before genetic effects act strongly, prioritize detailed ecological analysis over descriptions of genetic structure in assessing conservation of at-risk species, and highlight the need for field experiments manipulating both demographics and genetic structure on long-term extinction risk. PMID:24358695

  19. The genetic structure of wild Orobanche cumana Wallr. (Orobanchaceae) populations in eastern Bulgaria reflects introgressions from weedy populations.

    PubMed

    Pineda-Martos, Rocío; Pujadas-Salvà, Antonio J; Fernández-Martínez, José M; Stoyanov, Kiril; Velasco, Leonardo; Pérez-Vich, Begoña

    2014-01-01

    Orobanche cumana is a holoparasitic plant naturally distributed from central Asia to south-eastern Europe, where it parasitizes wild Asteraceae species. It is also an important parasitic weed of sunflower crops. The objective of this research was to investigate genetic diversity, population structure, and virulence on sunflower of O. cumana populations parasitizing wild plants in eastern Bulgaria. Fresh tissue of eight O. cumana populations and mature seeds of four of them were collected in situ on wild hosts. Genetic diversity and population structure were studied with SSR markers and compared to weedy populations. Two main gene pools were identified in Bulgarian populations, with most of the populations having intermediate characteristics. Cross-inoculation experiments revealed that O. cumana populations collected on wild species possessed similar ability to parasitize sunflower to those collected on sunflower. The results were explained on the basis of an effective genetic exchange between populations parasitizing sunflower crops and those parasitizing wild species. The occurrence of bidirectional gene flow may have an impact on wild populations, as new physiological races continuously emerge in weedy populations. Also, genetic variability of wild populations may favour the ability of weedy populations to overcome sunflower resistance mechanisms. PMID:25143963

  20. Population dynamics of a natural red deer population over 200 years detected via substantial changes of genetic variation.

    PubMed

    Hoffmann, Gunther Sebastian; Johannesen, Jes; Griebeler, Eva Maria

    2016-05-01

    Most large mammals have constantly been exposed to anthropogenic influence over decades or even centuries. Because of their long generation times and lack of sampling material, inferences of past population genetic dynamics, including anthropogenic impacts, have only relied on the analysis of the structure of extant populations. Here, we investigate for the first time the change in the genetic constitution of a natural red deer population over two centuries, using up to 200-year-old antlers (30 generations) stored in trophy collections. To the best of our knowledge, this is the oldest DNA source ever used for microsatellite population genetic analyses. We demonstrate that government policy and hunting laws may have strong impacts on populations that can lead to unexpectedly rapid changes in the genetic constitution of a large mammal population. A high ancestral individual polymorphism seen in an outbreeding population (1813-1861) was strongly reduced in descendants (1923-1940) during the mid-19th and early 20th century by genetic bottlenecks. Today (2011), individual polymorphism and variance among individuals is increasing in a constant-sized (managed) population. Differentiation was high among periods (F ST > ***); consequently, assignment tests assigned individuals to their own period with >85% probability. In contrast to the high variance observed at nuclear microsatellite loci, mtDNA (D-loop) was monomorphic through time, suggesting that male immigration dominates the genetic evolution in this population. PMID:27096075

  1. Genetic diversity, population structure and relationships in indigenous cattle populations of Ethiopia and Korean Hanwoo breeds using SNP markers

    PubMed Central

    Edea, Zewdu; Dadi, Hailu; Kim, Sang-Wook; Dessie, Tadelle; Lee, Taeheon; Kim, Heebal; Kim, Jong-Joo; Kim, Kwan-Suk

    2013-01-01

    In total, 166 individuals from five indigenous Ethiopian cattle populations – Ambo (n = 27), Borana (n = 35), Arsi (n = 30), Horro (n = 36), and Danakil (n = 38) – were genotyped for 8773 single nucleotide polymorphism (SNP) markers to assess genetic diversity, population structure, and relationships. As a representative of taurine breeds, Hanwoo cattle (n = 40) were also included in the study for reference. Among Ethiopian cattle populations, the proportion of SNPs with minor allele frequencies (MAFs) ≥0.05 ranged from 81.63% in Borana to 85.30% in Ambo, with a mean of 83.96% across all populations. The Hanwoo breed showed the highest proportion of polymorphism, with MAFs ≥0.05, accounting for 95.21% of total SNPs. The mean expected heterozygosity varied from 0.370 in Danakil to 0.410 in Hanwoo. The mean genetic differentiation (FST; 1%) in Ethiopian cattle revealed that within individual variation accounted for approximately 99% of the total genetic variation. As expected, FST and Reynold genetic distance were greatest between Hanwoo and Ethiopian cattle populations, with average values of 17.62 and 18.50, respectively. The first and second principal components explained approximately 78.33% of the total variation and supported the clustering of the populations according to their historical origins. At K = 2 and 3, a considerable source of variation among cattle is the clustering of the populations into Hanwoo (taurine) and Ethiopian cattle populations. The low estimate of genetic differentiation (FST) among Ethiopian cattle populations indicated that differentiation among these populations is low, possibly owing to a common historical origin and high gene flow. Genetic distance, phylogenic tree, principal component analysis, and population structure analyses clearly differentiated the cattle population according to their historical origins, and confirmed that Ethiopian cattle populations are genetically distinct from the Hanwoo breed. PMID:23518904

  2. Global diversity and genetic contributions of chicken populations from African, Asian and European regions.

    PubMed

    Lyimo, C M; Weigend, A; Msoffe, P L; Eding, H; Simianer, H; Weigend, S

    2014-12-01

    Genetic diversity and population structure of 113 chicken populations from Africa, Asia and Europe were studied using 29 microsatellite markers. Among these, three populations of wild chickens and nine commercial purebreds were used as reference populations for comparison. Compared to commercial lines and chickens sampled from the European region, high mean numbers of alleles and a high degree of heterozygosity were found in Asian and African chickens as well as in Red Junglefowl. Population differentiation (FST ) was higher among European breeds and commercial lines than among African, Asian and Red Junglefowl populations. Neighbour-Net genetic clustering and structure analysis revealed two main groups of Asian and north-west European breeds, whereas African populations overlap with other breeds from Eastern Europe and the Mediterranean region. Broilers and brown egg layers were situated between the Asian and north-west European clusters. structure analysis confirmed a lower degree of population stratification in African and Asian chickens than in European breeds. High genetic differentiation and low genetic contributions to global diversity have been observed for single European breeds. Populations with low genetic variability have also shown a low genetic contribution to a core set of diversity in attaining maximum genetic variation present from the total populations. This may indicate that conservation measures in Europe should pay special attention to preserving as many single chicken breeds as possible to maintain maximum genetic diversity given that higher genetic variations come from differentiation between breeds. PMID:25315897

  3. Joint effects of population size and isolation on genetic erosion in fragmented populations: finding fragmentation thresholds for management

    PubMed Central

    Méndez, María; Vögeli, Matthias; Tella, José L; Godoy, José A

    2014-01-01

    Size and isolation of local populations are main parameters of interest when assessing the genetic consequences of habitat fragmentation. However, their relative influence on the genetic erosion of local populations remains unclear. In this study, we first analysed how size and isolation of habitat patches influence the genetic variation of local populations of the Dupont's lark (Chersophilus duponti), an endangered songbird. An information-theoretic approach to model selection allowed us to address the importance of interactions between habitat variables, an aspect seldom considered in fragmentation studies, but which explained up to 65% of the variance in genetic parameters. Genetic diversity and inbreeding were influenced by the size of local populations depending on their degree of isolation, and genetic differentiation was positively related to isolation. We then identified a minimum local population of 19 male territories and a maximum distance of 30 km to the nearest population as thresholds from which genetic erosion becomes apparent. Our results alert on possibly misleading conclusions and suboptimal management recommendations when only additive effects are taken into account and encourage the use of most explanatory but easy-to-measure variables for the evaluation of genetic risks in conservation programmes. PMID:24822084

  4. Beyond race: towards a whole-genome perspective on human populations and genetic variation.

    PubMed

    Foster, Morris W; Sharp, Richard R

    2004-10-01

    The renewed emphasis on population-specific genetic variation, exemplified most prominently by the International HapMap Project, is complicated by a longstanding, uncritical reliance on existing population categories in genetic research. Race and other pre-existing population definitions (ethnicity, religion, language, nationality, culture and so on) tend to be contentious concepts that have polarized discussions about the ethics and science of research into population-specific human genetic variation. By contrast, a broader consideration of the multiple historical sources of genetic variation provides a whole-genome perspective on the ways i n which existing population definitions do, and do not, account for how genetic variation is distributed among individuals. Although genetics will continue to rely on analytical tools that make use of particular population histories, it is important to interpret findings in a broader genomic context. PMID:15510170

  5. The Population Reference Sample, POPRES: A Resource for Population, Disease, and Pharmacological Genetics Research

    PubMed Central

    Nelson, Matthew R.; Bryc, Katarzyna; King, Karen S.; Indap, Amit; Boyko, Adam R.; Novembre, John; Briley, Linda P.; Maruyama, Yuka; Waterworth, Dawn M.; Waeber, Gérard; Vollenweider, Peter; Oksenberg, Jorge R.; Hauser, Stephen L.; Stirnadel, Heide A.; Kooner, Jaspal S.; Chambers, John C.; Jones, Brendan; Mooser, Vincent; Bustamante, Carlos D.; Roses, Allen D.; Burns, Daniel K.; Ehm, Margaret G.; Lai, Eric H.

    2008-01-01

    Technological and scientific advances, stemming in large part from the Human Genome and HapMap projects, have made large-scale, genome-wide investigations feasible and cost effective. These advances have the potential to dramatically impact drug discovery and development by identifying genetic factors that contribute to variation in disease risk as well as drug pharmacokinetics, treatment efficacy, and adverse drug reactions. In spite of the technological advancements, successful application in biomedical research would be limited without access to suitable sample collections. To facilitate exploratory genetics research, we have assembled a DNA resource from a large number of subjects participating in multiple studies throughout the world. This growing resource was initially genotyped with a commercially available genome-wide 500,000 single-nucleotide polymorphism panel. This project includes nearly 6,000 subjects of African-American, East Asian, South Asian, Mexican, and European origin. Seven informative axes of variation identified via principal-component analysis (PCA) of these data confirm the overall integrity of the data and highlight important features of the genetic structure of diverse populations. The potential value of such extensively genotyped collections is illustrated by selection of genetically matched population controls in a genome-wide analysis of abacavir-associated hypersensitivity reaction. We find that matching based on country of origin, identity-by-state distance, and multidimensional PCA do similarly well to control the type I error rate. The genotype and demographic data from this reference sample are freely available through the NCBI database of Genotypes and Phenotypes (dbGaP). PMID:18760391

  6. Genealogical data in population medical genetics: Field guidelines

    PubMed Central

    Poletta, Fernando A.; Orioli, Ieda M.; Castilla, Eduardo E.

    2014-01-01

    This is a guide for fieldwork in Population Medical Genetics research projects. Data collection, handling, and analysis from large pedigrees require the use of specific tools and methods not widely familiar to human geneticists, unfortunately leading to ineffective graphic pedigrees. Initially, the objective of the pedigree must be decided, and the available information sources need to be identified and validated. Data collection and recording by the tabulated method is advocated, and the involved techniques are presented. Genealogical and personal information are the two main components of pedigree data. While the latter is unique to each investigation project, the former is solely represented by gametic links between persons. The triad of a given pedigree member and its two parents constitutes the building unit of a genealogy. Likewise, three ID numbers representing those three elements of the triad is the record field required for any pedigree analysis. Pedigree construction, as well as pedigree and population data analysis, varies according to the pre-established objectives, the existing information, and the available resources. PMID:24764752

  7. Genetic Predisposition for Dermal Problems in Hexavalent Chromium Exposed Population

    PubMed Central

    Sharma, Priti; Bihari, Vipin; Agarwal, Sudhir K.; Goel, Sudhir K.

    2012-01-01

    We studied the effect of genetic susceptibility on hexavalent chromium induced dermal adversities. The health status of population was examined from the areas of Kanpur (India) having the elevated hexavalent chromium levels in groundwater. Blood samples were collected for DNA isolation to conduct polymorphic determination of genes, namely: NQO1 (C609T), hOGG1 (C1245G), GSTT1, and GSTM1 (deletion). Symptomatic exposed subjects (n = 38) were compared with asymptomatic exposed subjects (n = 108) along with asymptomatic controls (n = 148) from a non contaminated reference community. Exposed symptomatic group consisted of 36.8% subjects who were GSTM1 null genotyped as compared to asymptomatic where only 19.4% subjects were null. The exposed subjects with GSTM1 null genotype were more susceptible to dermal adversities in comparison with wild genotyped subjects (OR = 2.42; 95% CI = 1.071–5.451). Age, smoking, gender or duration of residence were not found to have any confounding effect towards this association. Association with other genes was not statistically significant, nonetheless, possible contribution by these genes cannot be ruled out. In conclusion, variation in the polymorphic status of GSTM1 gene may influence dermal outcomes among residents from Cr(VI) contaminated areas. Further studies are therefore, needed to examine these observations among different population groups. PMID:22919465

  8. The Druze: A Population Genetic Refugium of the Near East

    PubMed Central

    Shlush, Liran I.; Behar, Doron M.; Yudkovsky, Guennady; Templeton, Alan; Hadid, Yarin; Basis, Fuad; Hammer, Michael; Itzkovitz, Shalev; Skorecki, Karl

    2008-01-01

    Background Phylogenetic mitochondrial DNA haplogroups are highly partitioned across global geographic regions. A unique exception is the X haplogroup, which has a widespread global distribution without major regions of distinct localization. Principal Findings We have examined mitochondrial DNA sequence variation together with Y-chromosome-based haplogroup structure among the Druze, a religious minority with a unique socio-demographic history residing in the Near East. We observed a striking overall pattern of heterogeneous parental origins, consistent with Druze oral tradition, together with both a high frequency and a high diversity of the mitochondrial DNA (mtDNA) X haplogroup within a confined regional subpopulation. Furthermore demographic modeling indicated low migration rates with nearby populations. Conclusions These findings were enabled through the use of a paternal kindred based sampling approach, and suggest that the Galilee Druze represent a population isolate, and that the combination of a high frequency and diversity of the mtDNA X haplogroup signifies a phylogenetic refugium, providing a sample snapshot of the genetic landscape of the Near East prior to the modern age. PMID:18461126

  9. Genetic evidence for two founding populations of the Americas

    PubMed Central

    Skoglund, Pontus; Mallick, Swapan; Bortolini, Maria Cátira; Chennagiri, Niru; Hünemeier, Tábita; Petzl-Erler, Maria Luiza; Salzano, Francisco Mauro; Patterson, Nick; Reich, David

    2015-01-01

    Genetic studies have been consistent with a single common origin of Native American groups from Central and South America1-4. However, some morphological studies have suggested a more complex picture, whereby the northeast Asian affinities of present-day Native Americans contrast with a distinctive morphology seen in some of the earliest American skeletons, which share traits with present-day Australasians (indigenous groups in Australia, Melanesia, and island southeast Asia)5-8. Here we analyze genome-wide data to show that some Amazonian Native Americans descend partly from a Native American founding population that carried ancestry more closely related to indigenous Australians, New Guineans and Andaman Islanders than to any present-day Eurasians or Native Americans. This signature is not present to the same extent or at all in present-day Northern and Central Americans or a ~12,600 year old Clovis genome, suggesting a more diverse set of founding populations of the Americas than previously accepted. PMID:26196601

  10. Genetic evidence for two founding populations of the Americas.

    PubMed

    Skoglund, Pontus; Mallick, Swapan; Bortolini, Maria Cátira; Chennagiri, Niru; Hünemeier, Tábita; Petzl-Erler, Maria Luiza; Salzano, Francisco Mauro; Patterson, Nick; Reich, David

    2015-09-01

    Genetic studies have consistently indicated a single common origin of Native American groups from Central and South America. However, some morphological studies have suggested a more complex picture, whereby the northeast Asian affinities of present-day Native Americans contrast with a distinctive morphology seen in some of the earliest American skeletons, which share traits with present-day Australasians (indigenous groups in Australia, Melanesia, and island Southeast Asia). Here we analyse genome-wide data to show that some Amazonian Native Americans descend partly from a Native American founding population that carried ancestry more closely related to indigenous Australians, New Guineans and Andaman Islanders than to any present-day Eurasians or Native Americans. This signature is not present to the same extent, or at all, in present-day Northern and Central Americans or in a ∼12,600-year-old Clovis-associated genome, suggesting a more diverse set of founding populations of the Americas than previously accepted. PMID:26196601

  11. Population-genetic influences on genomic estimates of the inbreeding coefficient: a global perspective

    PubMed Central

    Pemberton, Trevor J.; Rosenberg, Noah A.

    2014-01-01

    Background/Aims Culturally-driven marital practices provide a key instance of an interaction between social and genetic processes in shaping patterns of human genetic variation, producing, for example, increased identity by descent through consanguineous marriage. A commonly used measure to quantify identity by descent in an individual is the inbreeding coefficient, a quantity that reflects not only consanguinity, but also other aspects of kinship in the population to which the individual belongs. Here, in populations worldwide, we examine the relationship between genomic estimates of the inbreeding coefficient and population patterns in genetic variation. Methods Using genotypes at 645 microsatellites, we compare inbreeding coefficients from 5,043 individuals representing 237 worldwide populations to demographic consanguinity frequency estimates available for 26 populations, as well as to other quantities that can illuminate population-genetic influences on inbreeding coefficients. Results We observe higher inbreeding coefficient estimates in populations and geographic regions with known high levels of consanguinity or genetic isolation, and in populations with an increased effect of genetic drift and decreased genetic diversity with increasing distance from Africa. For the small number of populations with specific consanguinity estimates, we find a correlation between inbreeding coefficients and consanguinity frequency (r=0.349, P=0.040). Conclusions The results emphasize the importance of both consanguinity and population-genetic factors in influencing variation in inbreeding coefficients, and they provide insight into factors useful for assessing the effect of consanguinity on genomic patterns in different populations. PMID:25060268

  12. Does population size affect genetic diversity? A test with sympatric lizard species.

    PubMed

    Hague, M T J; Routman, E J

    2016-01-01

    Genetic diversity is a fundamental requirement for evolution and adaptation. Nonetheless, the forces that maintain patterns of genetic variation in wild populations are not completely understood. Neutral theory posits that genetic diversity will increase with a larger effective population size and the decreasing effects of drift. However, the lack of compelling evidence for a relationship between genetic diversity and population size in comparative studies has generated some skepticism over the degree that neutral sequence evolution drives overall patterns of diversity. The goal of this study was to measure genetic diversity among sympatric populations of related lizard species that differ in population size and other ecological factors. By sampling related species from a single geographic location, we aimed to reduce nuisance variance in genetic diversity owing to species differences, for example, in mutation rates or historical biogeography. We compared populations of zebra-tailed lizards and western banded geckos, which are abundant and short-lived, to chuckwallas and desert iguanas, which are less common and long-lived. We assessed population genetic diversity at three protein-coding loci for each species. Our results were consistent with the predictions of neutral theory, as the abundant species almost always had higher levels of haplotype diversity than the less common species. Higher population genetic diversity in the abundant species is likely due to a combination of demographic factors, including larger local population sizes (and presumably effective population sizes), faster generation times and high rates of gene flow with other populations. PMID:26306730

  13. Urban habitat fragmentation and genetic population structure of bobcats in coastal southern California

    USGS Publications Warehouse

    Ruell, E.W.; Riley, S.P.D.; Douglas, M.R.; Antolin, M.F.; Pollinger, J.R.; Tracey, J.A.; Lyren, L.M.; Boydston, E.E.; Fisher, R.N.; Crooks, K.R.

    2012-01-01

    Although habitat fragmentation is recognized as a primary threat to biodiversity, the effects of urban development on genetic population structure vary among species and landscapes and are not yet well understood. Here we use non-invasive genetic sampling to compare the effects of fragmentation by major roads and urban development on levels of dispersal, genetic diversity, and relatedness between paired bobcat populations in replicate landscapes in coastal southern California. We hypothesized that bobcat populations in sites surrounded by urbanization would experience reduced functional connectivity relative to less isolated nearby populations. Our results show that bobcat genetic population structure is affected by roads and development but not always as predicted by the degree that these landscape features surround fragments. Instead, we suggest that urban development may affect functional connectivity between bobcat populations more by limiting the number and genetic diversity of source populations of migrants than by creating impermeable barriers to dispersal.

  14. Temporal population genetic instability in range-edge western toads, Anaxyrus boreas.

    PubMed

    Holmes, Iris

    2015-01-01

    In this article, we address the temporal stability of population genetic structure in a range-edge population that is undergoing continual, short-distance colonization events. We sampled western toad, Anaxyrus boreas, breeding populations over 2 seasons near their northern range limit in southeast Alaska. We sampled 20 ponds each during the summers of 2008 and 2009, with 14 ponds sampled in both summers. We found considerable turnover in the population genetic relationships among ponds in those 2 seasons, as well as biologically meaningful genetic differentiation between years within some ponds. We found relatively consistent relationships between major population centers, whereas the relationships between the central ponds and smaller, outlying populations differed year to year. This finding indicates that multiple years of genetic sampling may be important for understanding the genetic landscape of some populations. PMID:25433082

  15. Alu repeats as markers for human population genetics

    SciTech Connect

    Batzer, M.A.; Alegria-Hartman, M.; Bazan, H.

    1993-09-01

    The Human-Specific (HS) subfamily of Alu sequences is comprised of a group of 500 nearly identical members which are almost exclusively restricted to the human genome. Individual subfamily members share an average of 97.9% nucleotide identity with each other and an average of 98.9% nucleotide identity with the HS subfamily consensus sequence. HS Alu family members are thought to be derived from a single source ``master`` gene, and have an average age of 2.8 million years. We have developed a Polymerase Chain Reaction (PCR) based assay using primers complementary to the 5 in. and 3 in. unique flanking DNA sequences from each HS Alu that allows the locus to be assayed for the presence or absence of an Alu repeat. Individual HS Alu sequences were found to be either monomorphic or dimorphic for the presence or absence of each repeat. The monomorphic HS Alu family members inserted in the human genome after the human/great ape divergence (which is thought to have occurred 4--6 million years ago), but before the radiation of modem man. The dimorphic HS Alu sequences inserted in the human genome after the radiation of modem man (within the last 200,000-one million years) and represent a unique source of information for human population genetics and forensic DNA analyses. These sites can be developed into Dimorphic Alu Sequence Tagged Sites (DASTS) for the Human Genome Project as well. HS Alu family member insertion dimorphism differs from other types of polymorphism (e.g. Variable Number of Tandem Repeat [VNTR] or Restriction Fragment Length Polymorphism [RFLP]) because individuals share HS Alu family member insertions based upon identity by descent from a common ancestor as a result of a single event which occurred one time within the human population. The VNTR and RFLP polymorphisms may arise multiple times within a population and are identical by state only.

  16. Spatial genetic structure of Long-tailed Ducks (Clangula hyemalis) among Alaskan, Canadian, and Russian breeding populations

    USGS Publications Warehouse

    Wilson, Robert E.; Gust, J R; Petersen, Margaret; Talbot, Sandra

    2016-01-01

    Arctic ecosystems are changing at an unprecedented rate. How Arctic species are able to respond to such environmental change is partially dependent on the connections between local and broadly distributed populations. For species like the Long-tailed Duck (Clangula hyemalis), we have limited telemetry and band-recovery information from which to infer population structure and migratory connectivity; however, genetic analyses can offer additional insights. To examine population structure in the Long-tailed Duck, we characterized variation at mtDNA control region and microsatellite loci among four breeding areas in Alaska, Canada, and Russia. We observed significant differences in the variance of mtDNA haplotype frequencies between the Yukon-Kuskokwim Delta (YKD) and the three Arctic locations (Arctic Coastal Plain in Alaska, eastern Siberia, and central Canadian Arctic). However, like most sea duck genetic assessments, our study found no evidence of population structure based on autosomal microsatellite loci. Long-tailed Ducks use multiple wintering areas where pair formation occurs with some populations using both the Pacific and Atlantic Oceans. This situation provides a greater opportunity for admixture across breeding locales, which would likely homogenize the nuclear genome even in the presence of female philopatry. The observed mtDNA differentiation was largely due to the presence of two divergent clades: (A) a clade showing signs of admixture among all breeding locales and (B) a clade primarily composed of YKD samples. We hypothesize that the pattern of mtDNA differentiation reflects some degree of philopatry to the YKD and isolation of two refugial populations with subsequent expansion and admixture. We recommend additional genetic assessments throughout the circumpolar range of Long-tailed Ducks to further quantify aspects of genetic diversity and migratory connectivity in this species.

  17. Genetic Diversity and Structure of Brazilian Populations of Diatraea saccharalis (Lepidoptera: Crambidae): Implications for Pest Management.

    PubMed

    Silva-Brandão, Karina L; Santos, Thiago V; Cônsoli, Fernando L; Omoto, Celso

    2015-02-01

    The sugarcane borer, Diatraea saccharalis (F.), is the main pest of sugarcane in Brazil. Genetic variability and gene flow among 13 Brazilian populations of the species were evaluated based on mitochondrial DNA sequences to estimate the exchange of genetic information within and among populations. We found high genetic structure among sampled localities (ΦST=0.50923), and pairwise genetic distances were significantly correlated to geographic distances. Demographic analysis and genealogical network of mitochondrial sequences indicate population growth and admixture of D. saccharalis populations, events likely related to the sequential expansion of the corn and sugarcane crops in Brazil. The implications of these findings for pest management are discussed. PMID:26470135

  18. POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans.

    PubMed

    Raghavan, Maanasa; Steinrücken, Matthias; Harris, Kelley; Schiffels, Stephan; Rasmussen, Simon; DeGiorgio, Michael; Albrechtsen, Anders; Valdiosera, Cristina; Ávila-Arcos, María C; Malaspinas, Anna-Sapfo; Eriksson, Anders; Moltke, Ida; Metspalu, Mait; Homburger, Julian R; Wall, Jeff; Cornejo, Omar E; Moreno-Mayar, J Víctor; Korneliussen, Thorfinn S; Pierre, Tracey; Rasmussen, Morten; Campos, Paula F; Damgaard, Peter de Barros; Allentoft, Morten E; Lindo, John; Metspalu, Ene; Rodríguez-Varela, Ricardo; Mansilla, Josefina; Henrickson, Celeste; Seguin-Orlando, Andaine; Malmström, Helena; Stafford, Thomas; Shringarpure, Suyash S; Moreno-Estrada, Andrés; Karmin, Monika; Tambets, Kristiina; Bergström, Anders; Xue, Yali; Warmuth, Vera; Friend, Andrew D; Singarayer, Joy; Valdes, Paul; Balloux, Francois; Leboreiro, Ilán; Vera, Jose Luis; Rangel-Villalobos, Hector; Pettener, Davide; Luiselli, Donata; Davis, Loren G; Heyer, Evelyne; Zollikofer, Christoph P E; Ponce de León, Marcia S; Smith, Colin I; Grimes, Vaughan; Pike, Kelly-Anne; Deal, Michael; Fuller, Benjamin T; Arriaza, Bernardo; Standen, Vivien; Luz, Maria F; Ricaut, Francois; Guidon, Niede; Osipova, Ludmila; Voevoda, Mikhail I; Posukh, Olga L; Balanovsky, Oleg; Lavryashina, Maria; Bogunov, Yuri; Khusnutdinova, Elza; Gubina, Marina; Balanovska, Elena; Fedorova, Sardana; Litvinov, Sergey; Malyarchuk, Boris; Derenko, Miroslava; Mosher, M J; Archer, David; Cybulski, Jerome; Petzelt, Barbara; Mitchell, Joycelynn; Worl, Rosita; Norman, Paul J; Parham, Peter; Kemp, Brian M; Kivisild, Toomas; Tyler-Smith, Chris; Sandhu, Manjinder S; Crawford, Michael; Villems, Richard; Smith, David Glenn; Waters, Michael R; Goebel, Ted; Johnson, John R; Malhi, Ripan S; Jakobsson, Mattias; Meltzer, David J; Manica, Andrea; Durbin, Richard; Bustamante, Carlos D; Song, Yun S; Nielsen, Rasmus; Willerslev, Eske

    2015-08-21

    How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year isolation period in Beringia. After their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 ka, one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative "Paleoamerican" relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model. PMID:26198033

  19. Population Genetic Structure of the Cotton Bollworm Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) in India as Inferred from EPIC-PCR DNA Markers

    PubMed Central

    Behere, Gajanan Tryambak; Tay, Wee Tek; Russell, Derek Alan; Kranthi, Keshav Raj; Batterham, Philip

    2013-01-01

    Helicoverpa armigera is an important pest of cotton and other agricultural crops in the Old World. Its wide host range, high mobility and fecundity, and the ability to adapt and develop resistance against all common groups of insecticides used for its management have exacerbated its pest status. An understanding of the population genetic structure in H. armigera under Indian agricultural conditions will help ascertain gene flow patterns across different agricultural zones. This study inferred the population genetic structure of Indian H. armigera using five Exon-Primed Intron-Crossing (EPIC)-PCR markers. Nested alternative EPIC markers detected moderate null allele frequencies (4.3% to 9.4%) in loci used to infer population genetic structure but the apparently genome-wide heterozygote deficit suggests in-breeding or a Wahlund effect rather than a null allele effect. Population genetic analysis of the 26 populations suggested significant genetic differentiation within India but especially in cotton-feeding populations in the 2006–07 cropping season. In contrast, overall pair-wise FST estimates from populations feeding on food crops indicated no significant population substructure irrespective of cropping seasons. A Baysian cluster analysis was used to assign the genetic make-up of individuals to likely membership of population clusters. Some evidence was found for four major clusters with individuals in two populations from cotton in one year (from two populations in northern India) showing especially high homogeneity. Taken as a whole, this study found evidence of population substructure at host crop, temporal and spatial levels in Indian H. armigera, without, however, a clear biological rationale for these structures being evident. PMID:23326431

  20. Genetic structure of introduced populations: 120-year-old DNA footprint of historic introduction in an insular small mammal population

    PubMed Central

    Simpson, Siobhan; Blampied, Nick; Peniche, Gabriela; Dozières, Anne; Blackett, Tiffany; Coleman, Stephen; Cornish, Nina; Groombridge, Jim J

    2013-01-01

    Wildlife populations have been introduced to new areas by people for centuries, but this human-mediated movement can disrupt natural patterns of genetic structure by altering patterns of gene flow. Insular populations are particularly prone to these influences due to limited opportunities for natural dispersal onto islands. Consequently, understanding how genetic patterns develop in island populations is important, particularly given that islands are frequently havens for protected wildlife. We examined the evolutionary origins and extent of genetic structure within the introduced island population of red squirrels (Sciurus vulgaris) on the Channel Island of Jersey using mitochondrial DNA (mtDNA) control region sequence and nuclear microsatellite genotypes. Our findings reveal two different genetic origins and a genetic architecture reflective of the introductions 120 years ago. Genetic structure is marked within the maternally inherited mtDNA, indicating slow dispersal of female squirrels. However, nuclear markers detected only weak genetic structure, indicating substantially greater male dispersal. Data from both mitochondrial and nuclear markers support historic records that squirrels from England were introduced to the west of the island and those from mainland Europe to the east. Although some level of dispersal and introgression across the island between the two introductions is evident, there has not yet been sufficient gene flow to erase this historic genetic “footprint.” We also investigated if inbreeding has contributed to high observed levels of disease, but found no association. Genetic footprints of introductions can persist for considerable periods of time and beyond traditional timeframes of wildlife management. PMID:23532702

  1. Influence of genetic composition of test-animal populations on chronic toxicity studies used for risk estimation.

    PubMed

    Littlefield, N A; Wolff, G L; Nelson, C J

    1985-01-01

    A lifespan exposure of mice to benzidine dihydrochloride was conducted for 33 m using both sexes of two populations of mice with the same gene pool. One population was the genetically homogeneous F1 hybrid produced by crossing BALB/cStCrlC3Hf/Nctr males with C57BL/6jfC3Hf/Nctr females. The second population consisted of genetically heterogenous monohybrid cross (MC) offspring produced by mating the F1 hybrids inter se. Data comparisons were made to determine if gene distribution among members of a population affects the response to a toxic insult. Endpoints tested consisted of mortality, liver tumor incidence and time of tumor onset, mortality from reticulum-cell sarcoma, and body weights. In most instances it was noted that among animals not dosed (controls), the F1 population had lower background incidence of lesions and lived longer than the MC population. However, among the dosed animals, the F1 mice were generally more susceptible to the toxic agent and developed higher incidences of the chemically induced lesions than did the MC population. The F1 hybrid population gave a more conservative estimate of risk than did the MC population. The calculation of the liver tumor risk for these two populations showed that lifespan exposure to benzidine would be predicted to result in a larger number (higher risk) when using the F1 data. A 4.5-fold difference in the toxic response was observed between the F1 females and the MC males. This emphasizes the importance of gene distribution in risk estimation studies. PMID:4032486

  2. Influence of genetic composition of test-animal populations on chronic toxicity studies used for risk estimation

    SciTech Connect

    Littlefield, N.A.; Wolff, G.L.; Nelson, C.J.

    1985-01-01

    A lifespan exposure of mice to benzidine dihydrochloride was conducted for 33 m using both sexes of two populations of mice with the same gene pool. One population was the genetically homogeneous F/sub 1/ hybrid produced by crossing BALB/cStCrlC3Hf/Nctr males with C57BL/6JfC3Hf/Nctr females. The second population consisted of genetically heterogenous monohybrid cross (MC) offspring produced by mating the F/sub 1/ hybrids inter se. Data comparisons were made to determine if gene distribution among members of a population affects the response to a toxic insult. Endpoints tested consisted of mortality, liver tumor incidence and time of tumor onset, mortality from reticulum-cell sarcoma, and body weights. In most instances it was noted that among animals not dosed (controls), the F/sub 1/ population has lower background incidence of lesions and lived longer than the MC population. However, among the dosed animals, the F/sub 1/ mice were generally more susceptible to the toxic agent and developed higher incidences of the chemically induced lesions than did the MC population. The F/sub 1/ hybrid population gave a more conservative estimate of risk than did the MC population. The calculation of the liver tumor risk for these two populations showed that lifespan, exposure to benzidine would be predicted to result in a larger number (higher risk) when using the F/sub 1/ data. A 4.5-fold difference in the toxic response was observed between the F/sub 1/ females and the MC males. This emphasizes the importance of gene distribution in risk estimation studies.

  3. Genetic Diversity and Population Structure of Sitodiplosis mosellana in Northern China

    PubMed Central

    Duan, Yun; Wu, Yu-qing; Luo, Li-zhi; Miao, Jin; Gong, Zhong-jun; Jiang, Yue-li; Li, Tong

    2013-01-01

    The wheat midge, Sitodiplosis mosellana, is an important pest in Northern China. We tested the hypothesis that the population structure of this species arises during a range expansion over the past 30 years. This study used microsatellite and mitochondrial loci to conduct population genetic analysis of S. mosellana across its distribution range in China. We found strong genetic structure among the 16 studied populations, including two genetically distinct groups (the eastern and western groups), broadly consistent with the geography and habitat fragmentation. These results underline the importance of natural barriers in impeding dispersal and gene flow of S. mosellana populations. Low to moderate genetic diversity among the populations and moderate genetic differentiation (FST = 0.117) between the two groups were also found. The populations in the western group had lower genetic diversity, higher genetic differentiation and lower gene flow (FST = 0.116, Nm = 1.89) than those in the eastern group (FST = 0.049, Nm = 4.91). Genetic distance between populations was positively and significantly correlated with geographic distance (r = 0.56, P<0.001). The population history of this species provided no evidence for population expansion or bottlenecks in any of these populations. Our data suggest that the distribution of genetic diversity, genetic differentiation and population structure of S. mosellana have resulted from a historical event, reflecting its adaptation to diverse habitats and forming two different gene pools. These results may be the outcome of a combination of restricted gene flow due to geographical and environmental factors, population history, random processes of genetic drift and individual dispersal patterns. Given the current risk status of this species in China, this study can offer useful information for forecasting outbreaks and designing effective pest management programs. PMID:24265688

  4. Population Bottlenecks and Nonequilibrium Models in Population Genetics. III. Genic Homozygosity in Populations Which Experience Periodic Bottlenecks

    PubMed Central

    Maruyama, Takeo; Fuerst, Paul A.

    1985-01-01

    The amount of variability in a population that experiences repeated restrictions in population size has been calculated. The restrictions in size occur cyclically with a fixed cycle length. Analytical formulas for describing the gene identity at any specific time in the expanded and restricted phases of the cycle, and for the average and second moment of the gene identity, have been derived. It is shown that the level of genetic diversity depends critically on the two parameters that account for the population size, mutation rate and the time of duration for each of the two phases in the cycle. If one or both of these composite parameters are small, the gene diversity will be much reduced, and population gene diversity will then be predictable from knowledge of the harmonic mean population size over the entire cycle. If these parameters take on intermediate values, diversity changes constantly during the cycle, fluctuating steadily from a high to a low value and back again. If these parameters are large, gene diversity will fluctuate rapidly between extreme values and will stay at the extremes for long periods of time. PMID:4054613

  5. Population Bottlenecks and Nonequilibrium Models in Population Genetics. I. Allele Numbers When Populations Evolve from Zero Variability

    PubMed Central

    Maruyama, Takeo; Fuerst, Paul A.

    1984-01-01

    A simple numerical method was developed for the mean number and average age of alleles in a population that was initiated with no genetic variation following a sudden population expansion. The methods are used to examine the question of whether allele numbers are elevated compared with values seen in equilibrium populations having equivalent gene diversity. Excess allele numbers in expanding populations were found to be the rule. This was true whether the population began with zero variation or with low levels of variation in either of two initial distributions (initially an equilibrium allele frequency distribution or initially with loci occurring in only two classes of variation). Although the increase of alleles may persist for only a short time, when compared with the time which is required for approach to final equilibrium, the increase may be long when measured in absolute generation numbers. The pattern of increase in very rare alleles (those present only once in a sample) and the persistence of the original allele were also investigated. PMID:6500263

  6. Population genetic structure of Anopheles gambiae mosquitoes on Lake Victoria islands, west Kenya

    PubMed Central

    Chen, Hong; Minakawa, Noboru; Beier, John; Yan, Guiyun

    2004-01-01

    Background Understanding the genetic structure of island Anopheles gambiae populations is important for the current tactics in mosquito control and for the proposed strategy using genetically-modified mosquitoes (GMM). Genetically-isolated mosquito populations on islands are a potential site for testing GMM. The objective of this study was to determine the genetic structure of A. gambiae populations on the islands in Lake Victoria, western Kenya. Methods The genetic diversity and the population genetic structures of 13 A. gambiae populations from five islands on Lake Victoria and six villages from the surrounding mainland area in the Suba District were examined using six microsatellite markers. The distance range of sampling sites varied between 2.5 and 35.1 km. Results A similar level of genetic diversity between island mosquito populations and adjacent mainland populations was found. The average number of alleles per locus was 7.3 for the island populations and 6.8 for the mainland populations. The average observed heterozygosity was 0.32 and 0.28 for the island and mainland populations, respectively. A low but statistically significant genetic structure was detected among the island populations (FST = 0.019) and between the island and mainland populations (FST = 0.003). A total of 12 private alleles were found, and nine of them were from the island populations. Conclusion A level of genetic differentiation between the island and mainland populations was found. Large extent of gene flow between the island and mainland mosquito populations may result from wind- or human-assisted dispersal. Should the islands on Lake Victoria be used as a trial site for the release program of GMM, mosquito dispersal between the islands and between the island and the mainland should be vigorously monitored. PMID:15581429

  7. Population genetic evidence for cold adaptation in European Drosophila melanogaster populations.

    PubMed

    Božičević, Vedran; Hutter, Stephan; Stephan, Wolfgang; Wollstein, Andreas

    2016-03-01

    We studied Drosophila melanogaster populations from Europe (the Netherlands and France) and Africa (Rwanda and Zambia) to uncover genetic evidence of adaptation to cold. We present here four lines of evidence for genes involved in cold adaptation from four perspectives: (i) the frequency of SNPs at genes previously known to be associated with chill-coma recovery time (CCRT), startle reflex (SR) and resistance to starvation stress (RSS) vary along environmental gradients and therefore among populations; (ii) SNPs of genes that correlate significantly with latitude and altitude in African and European populations overlap with SNPs that correlate with a latitudinal cline from North America; (iii) at the genomewide level, the top candidate genes are enriched in gene ontology (GO) terms that are related to cold tolerance; (iv) GO enriched terms from North American clinal genes overlap significantly with those from Africa and Europe. Each SNP was tested in 10 independent runs of Bayenv2, using the median Bayes factors to ascertain candidate genes. None of the candidate genes were found close to the breakpoints of cosmopolitan inversions, and only four candidate genes were linked to QTLs related to CCRT. To overcome the limitation that we used only four populations to test correlations with environmental gradients, we performed simulations to estimate the power of our approach for detecting selection. Based on our results, we propose a novel network of genes that is involved in cold adaptation. PMID:26558479

  8. Genetic Studies of Stuttering in a Founder Population

    PubMed Central

    Wittke-Thompson, Jacqueline K.; Ambrose, Nicoline; Yairi, Ehud; Roe, Cheryl; Cook, Edwin H.; Ober, Carole; Cox, Nancy J.

    2007-01-01

    Genome-wide linkage and association analyses were conducted to identify genetic determinants of stuttering in a founder population in which 48 individuals affected with stuttering are connected in a single 232-person genealogy. A novel approach was devised to account for all necessary relationships to enable multipoint linkage analysis. Regions with nominal evidence for linkage were found on chromosomes 3 (P=0.013, 208.8 centiMorgans (cM)), 13 (P=0.012, 52.6 cM), and 15 (P=0.02, 100 cM). Regions with nominal evidence for association with stuttering that overlapped with a linkage signal are located on chromosomes 3 (P=0.0047, 195 cM), 9 (P=0.0067, 46.5 cM), and 13 (P=0.0055, 52.6 cM). We also conducted the first meta-analysis for stuttering using results from linkage studies in the Hutterites and The Illinois International Genetics of Stuttering Project and identified regions with nominal evidence for linkage on chromosomes 2 (P=0.013, 180–195 cM) and 5 (P=0.0051, 105–120 cM; P=0.015, 120–135 cM). None of the linkage signals detected in the Hutterite sample alone, or in the meta-analysis, meet genome-wide criteria for significance, although some of the stronger signals overlap linkage mapping signals previously reported for other speech and language disorders. PMID:17276504

  9. Correlation analysis of genetic diversity and population structure of Houttuynia cordata Thunb with regard to environment.

    PubMed

    Zhong, J; Wu, F-C; Qiu, P; Dai, L-J

    2016-01-01

    To study the levels of genetic diversity, and population structure, of Houttuynia cordata Thunb, the genetic background and relationships of populations were analyzed in terms of environmental factors. The genetic diversity and population structure of H. cordata were investigated using sequence-related amplified polymorphisms and correlation with environmental factors was analyzed using the SPSS software. Two thousand one hundred sixty-three sites were amplified from 41 pairs of primers, 1825 of which were polymorphic, and the percentage of polymorphic loci was 84.37%; the percentage of polymorphic sites was 72.14 and 67.77% at the species and population level, respectively. The observed number of alleles was 1.52 and 1.30 at species and population level, respectively. The effective number of alleles was 1.38 and 1.24 at species and population level, respectively. The Nei's diversity was 0.26 and 0.15 at species and population level, respectively. The Shannon's information index was 0.87 and 0.63 at species and population level, respectively. The genetic differentiation coefficient of populations was 0.51, and 12 populations were divided into three classes based on D = 0.20; the genetic diversities of different populations are correlated at different significance levels (P < 0.05) with environmental factors. Genetic differentiation existed among populations and the populations exhibited heteroplasmy. PMID:27525953

  10. Genetic variability and bottleneck detection of four Tricholoma matsutake populations from northeastern and southwestern China.

    PubMed

    Zeng, Dong-Fang; Chen, Bin

    2015-08-01

    The excessive commercial collection of matsutake mushrooms can lead to extreme reduction of population size, which may cause genetic bottleneck and decrease genetic diversity of Tricholoma matsutake. Here, six polymorphic microsatellite loci markers were used to examine the genetic diversity of four natural T. matsutake populations from two main producing regions of China. The minimum combinations of four loci were able to discriminate total 86 sampled individuals with distinctive multilocus genotypes. Our analysis of molecular variance (AMOVA) revealed that about 80% and 20% of the overall genetic variation were respectively partitioned within and among populations. The principal-coordinate analyses (PCA) distinguished the four tested populations into three genetic clusters, each of which was correlated with respective endemic host plants on a geographical basis. The AMOVA, PCA and pairwise population FST estimates consistently displayed the same genetic divergence patterns and spatial structure of T. matsutake mediated by host plants in China. The significant heterozygosity excesses demonstrated that a recent genetic bottleneck occurred in each population tested. The complementary M-ratio test indicated past genetic bottleneck events over longer periods. Only four individuals were identified as putative first generation migrants within northeastern China, which implies restricted interpopulation gene flow in T. matsutake. We discuss that the significant genetic differentiation among populations of T. matsutake is most likely a function of host adaptation, host specificity, genetic bottleneck, limited dispersal and habitat fragmentation. PMID:25682708

  11. DEVELOPMENT OF AQUATIC MODELS FOR TESTING THE RELATIONSHIP BETWEEN GENETIC DIVERSITY AND POPULATION EXTINCTION RISK

    EPA Science Inventory

    The relationship between population adaptive potential and extinction risk in a changing environment is not well understood. Although the expectation is that genetic diversity is directly related to the capacity of populations to adapt, the statistical and predictive aspects of ...

  12. Genetics driven interventions for ex situ conservation of red junglefowl (Gallus gallus murghi) populations in India.

    PubMed

    Mukesh; Fernandes, Merwyn; Han, Jianlin; Sathyakumar, Sambandam

    2013-01-01

    Genetics driven interventions (GDI) are imperative for ex situ conservation to exhort long-term sustenance of small and isolated populations in captivity as they are more prone to an increased extinction risk due to inbreeding and genetic drift. We investigated constitutive genetic attributes of four captive Red Junglefowl (RJF) populations in India, to facilitate the prioritization of the birds to formulate an effective breeding action plan. All the four RJF populations were found to be evident of significant inbreeding but none of them had exhibited any signature of bottleneck footprints in the recent past. Bayesian cluster analysis revealed three distinct groups among the four captive RJF populations. Interestingly, birds of Kufri population were assigned together with Gopalpur as well as with Morni populations, indicating their shared genetic ancestry. Among the four populations, Morni population displayed the richest genetic attributes and was therefore presumed as a key source of genetic variation. Nine birds of Morni population were relatively pure (q-value >0.98) and carried about 50% of the total private alleles of Morni population. Thus, being the foremost reservoir of allelic diversity, these nine birds may be selected for launching alien alleles to other RJF populations to rescue their loss of genetic diversity arising from inbreeding. PMID:23813667

  13. Unexpected genetic heterogeneity for primary ciliary dyskinesia in the Irish Traveller population.

    PubMed

    Casey, Jillian P; McGettigan, Paul A; Healy, Fiona; Hogg, Claire; Reynolds, Alison; Kennedy, Breandan N; Ennis, Sean; Slattery, Dubhfeasa; Lynch, Sally A

    2015-02-01

    We present a study of five children from three unrelated Irish Traveller families presenting with primary ciliary dyskinesia (PCD). As previously characterized disorders in the Irish Traveller population are caused by common homozygous mutations, we hypothesised that all three PCD families shared the same recessive mutation. However, exome sequencing showed that there was no pathogenic homozygous mutation common to all families. This finding was supported by histology, which showed that each family has a different type of ciliary defect; transposition defect (family A), nude epithelium (family B) and absence of inner and outer dynein arms (family C). Therefore, each family was analysed independently using homozygosity mapping and exome sequencing. The affected siblings in family A share a novel 1 bp duplication in RSPH4A (NM_001161664.1:c.166dup; p.Arg56Profs*11), a radial-spoke head protein involved in ciliary movement. In family B, we identified three candidate genes (CCNO, KCNN3 and CDKN1C), with a 5-bp duplication in CCNO (NM_021147.3:c.258_262dup; p.Gln88Argfs*8) being the most likely cause of ciliary aplasia. This is the first study to implicate CCNO, a DNA repair gene reported to be involved in multiciliogenesis, in PCD. In family C, we identified a ∼3.5-kb deletion in DYX1C1, a neuronal migration gene previously associated with PCD. This is the first report of a disorder in the relatively small Irish Traveller population to be caused by >1 disease gene. Our study identified at least three different PCD genes in the Irish Traveller population, highlighting that one cannot always assume genetic homogeneity, even in small consanguineous populations. PMID:24824133

  14. Historical data refute recent range contraction as cause of low genetic diversity in isolated frog populations.

    PubMed

    Hoffman, Eric A; Blouin, Michael S

    2004-02-01

    This study tested whether low genetic diversity in remnant populations of a declining amphibian is best explained by recent bottlenecks or by a history of being peripheral. We compared diversity from eight microsatellite loci in historical and extant populations from the interior and former periphery of the species' range. We found that historic peripheral populations already had reduced levels of genetic variation before the range contraction. Therefore, low diversity in remnants could not be ascribed to recent range contractions. This study shows that a common conservation strategy for rescuing genetically depauperate populations, artificial gene flow, may often be unwarranted and detrimental to evolutionarily important peripheral populations. PMID:14717886

  15. Population genetic structure of urban malaria vector Anopheles stephensi in India.

    PubMed

    Sharma, Richa; Sharma, Arvind; Kumar, Ashwani; Dube, Madhulika; Gakhar, S K

    2016-04-01

    Malaria is a major public health problem in India because climatic condition and geography of India provide an ideal environment for development of malaria vector. Anopheles stephensi is a major urban malaria vector in India and its control has been hampered by insecticide resistance. In present study population genetic structure of A. stephensi is analyzed at macro geographic level using 13 microsatellite markers. Significantly high genetic differentiation was found in all studied populations with differentiation values (FST) ranging from 0.0398 to 0.1808. The geographic distance was found to be playing a major role in genetic differentiation between different populations. Overall three genetic pools were observed and population of central India was found to be coexisting in two genetic pools. High effective population size (Ne) was found in all the studied populations. PMID:26777030

  16. Genetic Consequence of Restricted Habitat and Population Decline in Endangered Isoetes sinensis (Isoetaceae)

    PubMed Central

    KANG, MING; YE, QIGANG; HUANG, HONGWEN

    2005-01-01

    • Background and Aims Isoetes sinensis (Isoeteaceae) is a critically endangered aquatic quillwort in eastern China. Rapid decline of extant population size and local population extinction have occurred in recent years and have raised great concerns among conservationists. • Methods Amplified fragment length polymorphisms (AFLPs) were used to investigate the genetic variation and population structure of seven extant populations of the species. • Key Results Eight primer combinations produced a total of 343 unambiguous bands of which 210 (61·2 %) were polymorphic. Isoetes sinensis exhibited a high level of intra-population genetic diversity (HE = 0·118; hs = 0·147; I = 0·192; P = 35·2 %). The genetic variation within each of the populations was not positively correlated with their size, suggesting recent population decline, which is well in accordance with field data of demographic surveys. Moreover, a high degree of genetic differentiation (FST = 0·535; GST = 0·608; θB = 0·607) was detected among populations and no correlation was found between geographical and genetic distance, suggesting that populations were in disequilibrium of migration-drift. Genetic drift played a more important role than gene flow in the current population genetic structure of I. sinensis because migration of I. sinensis is predominantly water-mediated and habitat range was highly influenced by environment changes. • Conclusions Genetic information obtained in the present study provides useful baseline data for formulating conservation strategies. Conservation management, including both reinforcement for in situ populations and ex situ conservation programmes should be carefully designed to avoid the potential risk of outbreeding depression by admixture of individuals from different regions. However, translocation within the same regional population should be considered as a measure of genetic enhancement to rehabilitate local populations. An ex situ conservation

  17. The Population Genetics of Cultivation: Domestication of a Traditional Chinese Medicine, Scrophularia ningpoensis Hemsl. (Scrophulariaceae)

    PubMed Central

    Chen, Chuan; Li, Pan; Wang, Rui-Hong; Schaal, Barbara A.; Fu, Cheng-Xin

    2014-01-01

    Background Domestic cultivation of medicinal plants is an important strategy for protecting these species from over harvesting. Some species of medicinal plants have been brought into cultivation for more than hundreds years. Concerns about severe loss of genetic diversity and sustainable cultivation can potentially limit future use of these valuable plants. Genetic studies with comprehensive sampling of multiple medicinal species by molecular markers will allow for assessment and management of these species. Here we examine the population genetic consequences of cultivation and domestication in Scrophularia ningpoensis Hemsl. We used chloroplast DNA and genomic AFLP markers to clarify not only the effects of domestication on genetic diversity, but also determine the geographic origins of cultivars and their genetic divergence from native populations. These results will allow both better management of cultivated populations, but also provide insights for crop improvement. Results Twenty-one cpDNA haplotypes of S. ningpoensis were identified. Wild populations contain all haplotypes, whereas only three haplotypes were found in cultivated populations with wild populations having twice the haplotype diversity of cultivated populations. Genetic differentiation between cultivated populations and wild populations was significant. Genomic AFLP markers revealed similar genetic diversity patterns. Furthermore, Structure analysis grouped all wild populations into two gene pools; two of which shared the same gene pool with cultivated S. ningpoensis. The result of Neighbor-Joining analysis was consistent with the structure analysis. In principal coordinate analysis, three cultivated populations from Zhejiang Province grouped together and were separated from other cultivated populations. Conclusions These results suggest that cultivated S. ningpoensis has experienced dramatic loss of genetic diversity under anthropogenic influence. We postulate that strong artificial selection

  18. Genetic structure of Mesoamerican populations of Big-leaf mahogany (Swietenia macrophylla) inferred from microsatellite analysis.

    PubMed

    Novick, Rachel Roth; Dick, Christopher W; Lemes, Maristerra R; Navarro, Carlos; Caccone, Adalgisa; Bermingham, Eldredge

    2003-11-01

    While microsatellites have been used to examine genetic structure in local populations of Neotropical trees, genetic studies based on such high-resolution markers have not been carried out for Mesoamerica as a whole. Here we assess the genetic structure of the Mesoamerican mahogany Swietenia macrophylla King (big-leaf mahogany), a Neotropical tree species recently listed as endangered in CITES which is commercially extinct through much of its native range. We used seven variable microsatellite loci to assess genetic diversity and population structure in eight naturally established mahogany populations from six Mesoamerican countries. Measures of genetic differentiation (FST and RST) indicated significant differences between most populations. Unrooted dendrograms based on genetic distances between populations provide evidence of strong phylogeographic structure in Mesoamerican mahogany. The two populations on the Pacific coasts of Costa Rica and Panama were genetically distant from all the others, and from one another. The remaining populations formed two clusters, one comprised of the northern populations of Mexico, Belize and Guatemala and the other containing the southern Atlantic populations of Nicaragua and Costa Rica. Significant correlation was found between geographical distance and all pairwise measures of genetic divergence, suggesting the importance of regional biogeography and isolation by distance in Mesoamerican mahogany. The results of this study demonstrate greater phylogeographic structure than has been found across Amazon basin S. macrophylla. Our findings suggest a relatively complex Mesoamerican biogeographic history and lead to the prediction that other Central American trees will show similar patterns of regional differentiation. PMID:14629370

  19. Microsatellite markers reveal genetic divergence among wild and cultured populations of Chinese sucker Myxocyprinus asiaticus.

    PubMed

    Cheng, W W; Wang, D Q; Wang, C Y; Du, H; Wei, Q W

    2016-01-01

    Studies of genetic diversity and genetic population structure are critical for the conservation and management of endangered species. The Chinese sucker Myxocyprinus asiaticus is a vulnerable monotypic species in China, which is at a risk of decline owing to fluctuations in effective population size and other demographic and environmental factors. We screened 11 microsatellite loci in 214 individuals to assess genetic differentiation in both wild and cultured populations. The single extant wild population had a higher number of alleles (13) than the cultured populations (average 7.3). High levels of genetic diversity, expressed as observed and expected heterozygosity (HO = 0.771, HE = 0.748, respectively), were found in both wild and cultured populations. We also report significant differentiation among wild and cultured populations (global FST = 0.023, P < 0.001). Both STRUCTURE analysis and neighbor-joining tree revealed three moderately divergent primary genetic clusters: the wild Yangtze population and the Sichuan population were each identified as an individual cluster, with the remaining populations clustered together. Twenty-two samples collected from the Yangtze River were assigned to the cultured population, demonstrating the efficacy of artificial propagation to avoid drastic reduction in the population size of M. asiaticus. These genetic data support the endangered status of the M. asiaticus and have implications for conservation management planning. PMID:27173283

  20. Population size is weakly related to quantitative genetic variation and trait differentiation in a stream fish.

    PubMed

    Wood, Jacquelyn L A; Tezel, Defne; Joyal, Destin; Fraser, Dylan J

    2015-09-01

    How population size influences quantitative genetic variation and differentiation among natural, fragmented populations remains unresolved. Small, isolated populations might occupy poor quality habitats and lose genetic variation more rapidly due to genetic drift than large populations. Genetic drift might furthermore overcome selection as population size decreases. Collectively, this might result in directional changes in additive genetic variation (VA ) and trait differentiation (QST ) from small to large population size. Alternatively, small populations might exhibit larger variation in VA and QST if habitat fragmentation increases variability in habitat types. We explored these alternatives by investigating VA and QST using nine fragmented populations of brook trout varying 50-fold in census size N (179-8416) and 10-fold in effective number of breeders, Nb (18-135). Across 15 traits, no evidence was found for consistent differences in VA and QST with population size and almost no evidence for increased variability of VA or QST estimates at small population size. This suggests that (i) small populations of some species may retain adaptive potential according to commonly adopted quantitative genetic measures and (ii) populations of varying sizes experience a variety of environmental conditions in nature, however extremely large studies are likely required before any firm conclusions can be made. PMID:26207947

  1. Population structure and genetic diversity of black redhorse (Moxostoma duquesnei) in a highly fragmented watershed

    USGS Publications Warehouse

    Reid, S.M.; Wilson, C.C.; Mandrak, N.E.; Carl, L.M.

    2008-01-01

    Dams have the potential to affect population size and connectivity, reduce genetic diversity, and increase genetic differences among isolated riverine fish populations. Previous research has reported adverse effects on the distribution and demographics of black redhorse (Moxostoma duquesnei), a threatened fish species in Canada. However, effects on genetic diversity and population structure are unknown. We used microsatellite DNA markers to assess the number of genetic populations in the Grand River (Ontario) and to test whether dams have resulted in a loss of genetic diversity and increased genetic differentiation among populations. Three hundred and seventy-seven individuals from eight Grand River sites were genotyped at eight microsatellite loci. Measures of genetic diversity were moderately high and not significantly different among populations; strong evidence of recent population bottlenecks was not detected. Pairwise FST and exact tests identified weak (global FST = 0.011) but statistically significant population structure, although little population structuring was detected using either genetic distances or an individual-based clustering method. Neither geographic distance nor the number of intervening dams were correlated with pairwise differences among populations. Tests for regional equilibrium indicate that Grand River populations were either in equilibrium between gene flow and genetic drift or that gene flow is more influential than drift. While studies on other species have identified strong dam-related effects on genetic diversity and population structure, this study suggests that barrier permeability, river fragment length and the ecological characteristics of affected species can counterbalance dam-related effects. ?? 2007 Springer Science+Business Media B.V.

  2. MOLECULAR GENETIC APPROACHES TO PEST AND NONTARGET POPULATION MONITORING

    EPA Science Inventory

    The U.S. Environmental Protection Agency has interest in a number of applications of genetic monitoring methodologies. Genetic monitoring in agroecosystems can provide valuable environmental information regarding both traditional and novel pesticides. One group of pesticides of...

  3. Genetic variability and population structure of Plasmodium falciparum parasite populations from different malaria ecological regions of Kenya.

    PubMed

    Ingasia, Luicer A; Cheruiyot, Jelagat; Okoth, Sheila Akinyi; Andagalu, Ben; Kamau, Edwin

    2016-04-01

    Transmission intensity, movement of human and vector hosts, biogeographical features, and malaria control measures are some of the important factors that determine Plasmodium falciparum parasite genetic variability and population structure. Kenya has different malaria ecologies which might require different disease intervention methods. Refined parasite population genetic studies are critical for informing malaria control and elimination strategies. This study describes the genetic diversity and population structure of P. falciparum parasites from the different malaria ecological zones in Kenya. Twelve multi-locus microsatellite (MS) loci previously described were genotyped in 225 P. falciparum isolates collected between 2012 and 2013 from five sites; three in lowland endemic regions (Kisumu, Kombewa, and Malindi) and two in highland, epidemic regions (Kisii and Kericho). Parasites from the lowland endemic and highland epidemic regions of western Kenya had high genetic diversity compared to coastal lowland endemic region of Kenya [Malindi]. The Kenyan parasites had a mean genetic differentiation index (FST) of 0.072 (p=0.011). The multi-locus genetic analysis of the 12 MS revealed all the parasites had unique haplotypes. Significant linkage disequilibrium (LD) was observed in all the five parasite populations. Kisumu had the most significant index of association values (0.16; p<0.0001) whereas Kisii had the least significant index of association values (0.03; p<0.0001). Our data suggest high genetic diversity in Kenyan parasite population with the exception of parasite from Malindi where malaria has been on the decline. The presence of significant LD suggests that there is occurrence of inbreeding in the parasite population. Parasite populations from Kisii showed the strongest evidence for epidemic population structure whereas the rest of the regions showed panmixia. Defining the genetic diversity of the parasites in different ecological regions of Kenya after

  4. Population structure and genetic diversity among eelgrass (Zostera marina) beds and depths in San Francisco Bay.

    PubMed

    Ort, Brian S; Cohen, C Sarah; Boyer, Katharyn E; Wyllie-Echeverria, Sandy

    2012-07-01

    The seagrass Zostera marina is widely distributed in coastal regions throughout much of the northern hemisphere, forms the foundation of an important ecological habitat, and is suffering population declines. Studies in the Atlantic and Pacific oceans indicate that the degree of population genetic differentiation is location dependent. San Francisco Bay, California, USA, is a high-current, high-wind environment where rafting of seed-bearing shoots has the potential to enhance genetic connectivity among Z. marina populations. We tested Z. marina from six locations, including one annual population, within the bay to assess population differentiation and to compare levels of within-population genetic diversity. Using 7 microsatellite loci, we found significant differentiation among all populations. The annual population had significantly higher clonal diversity than the others but showed no detectible differences in heterozygosity or allelic richness. There appears to be sufficient input of genetic variation through sexual reproduction or immigration into the perennial populations to prevent significant declines in the number and frequency of alleles. In additional depth comparisons, we found differentiation among deep and shallow portions in 1 of 3 beds evaluated. Genetic drift, sweepstakes recruitment, dispersal limitation, and possibly natural selection may have combined to produce genetic differentiation over a spatial scale of 3-30 km in Z. marina. This implies that the scale of genetic differentiation may be smaller than expected for seagrasses in other locations too. We suggest that populations in close proximity may not be interchangeable for use as restoration material. PMID:22577191

  5. Genetic structure of lake whitefish, Coregonus clupeaformis, populations in the northern main basin of Lake Huron

    USGS Publications Warehouse

    Stott, Wendylee; Ebener, Mark P.; Mohr, Lloyd; Schaeffer, Jeff; Roseman, Edward F.; Harford, William J.; Johnson, James E.; Fietsch, Cherie-Lee

    2012-01-01

    Genetic analysis of spawning lake whitefish (Coregonus clupeaformis) from six sites in the main basin of Lake Huron was conducted to determine population structure. Samples from fisheryindependent assessment surveys in the northwest main basin were analyzed to determine the relative contributions of lake whitefish genetic populations. Genetic population structure was identified using data from seven microsatellite DNA loci. One population was identified at Manitoulin Island, one to two were observed in the east-central main basin (Fishing Island and Douglas Point), and one to two populations were found in the northwest (Thunder Bay and Duncan Bay). The genetic identity of collections from Duncan Bay and Thunder Bay was not consistent among methods used to analyze population structure. Low genetic distances suggested that they comprised one population, but genic differences indicated that they may constitute separate populations. Simulated data indicated that the genetic origins of samples from a mixed-fishery could be accurately identified, but accuracy could be improved by incorporating additional microsatellite loci. Mixture analysis and individual assignment tests performed on mixed-stock samples collected from the western main basin suggested that genetic populations from the east-central main basin contributed less than those from the western main basin and that the proportional contribution of each baseline population was similar in each assessment sample. Analysis of additional microsatellite DNA loci may be useful to help improve the precision of the estimates, thus increasing our ability to manage and protect this valuable resource.

  6. Surname distribution in population genetics and in statistical physics

    NASA Astrophysics Data System (ADS)

    Rossi, Paolo

    2013-12-01

    Surnames tend to behave like neutral genes, and their distribution has attracted a growing attention from genetists and physicists. We review the century-long history of surname studies and discuss the most recent developments. Isonymy has been regarded as a tool for the measurement of consanguinity of individuals and populations and has been applied to the analysis of migrations. The analogy between patrilineal surname transmission and the propagation of Y chromosomes has been exploited for the genetic characterization of families, communities and control groups. Surname distribution is the result of a stochastic dynamics, which has been studied either as a Yule process or as a branching phenomenon: both approaches predict the asymptotic power-law behavior which has been observed in many empirical researches. Models of neutral evolution based on the theory of disordered systems have suggested the application of field-theoretical techniques, and in particular the Renormalization Group, to describe the dynamics leading to scale-invariant distributions and to compute the related (critical) exponents.

  7. Genetic diversity and population structure of cucumber (Cucumis sativus L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Understanding genetic variation in germplasm collection is essential for the conservation and their efficient use in plant breeding. Cucumber is an important vegetable crop worldwide. Previous studies revealed a low genetic diversity in cucumber, but detailed insights into the crop’s genetic structu...

  8. The power of genetic monitoring for studying demography, ecology and genetics of a reintroduced brown bear population.

    PubMed

    De Barba, M; Waits, L P; Garton, E O; Genovesi, P; Randi, E; Mustoni, A; Groff, C

    2010-09-01

    Genetic monitoring has rarely been used for wildlife translocations despite the potential benefits this approach offers, compared to traditional field-based methods. We applied genetic monitoring to the reintroduced brown bear population in northern Italy. From 2002 to 2008, 2781 hair and faecal samples collected noninvasively plus 12 samples obtained from captured or dead bears were used to follow the demographic and geographical expansion and changes in genetic composition. Individual genotypes were used to reconstruct the wild pedigree and revealed that the population increased rapidly, from nine founders to >27 individuals in 2008 (lambda=1.17-1.19). Spatial mapping of bear samples indicated that most bears were distributed in the region surrounding the translocation site; however, individual bears were found up to 163 km away. Genetic diversity in the population was high, with expected heterozygosity of 0.74-0.79 and allelic richness of 4.55-5.41. However, multi-year genetic monitoring data showed that mortality rates were elevated, immigration did not occur, one dominant male sired all cubs born from 2002 to 2005, genetic diversity declined, relatedness increased, inbreeding occurred, and the effective population size was extremely small (Ne=3.03, ecological method). The comprehensive information collected through genetic monitoring is critical for implementing future conservation plans for the brown bear population in the Italian Alps. This study provides a model for other reintroduction programmes by demonstrating how genetic monitoring can be implemented to uncover aspects of the demography, ecology and genetics of small and reintroduced populations that will advance our understanding of the processes influencing their viability, evolution, and successful restoration. PMID:20735733

  9. Environmental heterogeneity explains the genetic structure of Continental and Mediterranean populations of Fraxinus angustifolia Vahl.

    PubMed

    Temunović, Martina; Franjić, Jozo; Satovic, Zlatko; Grgurev, Marin; Frascaria-Lacoste, Nathalie; Fernández-Manjarrés, Juan F

    2012-01-01

    Tree species with wide distributions often exhibit different levels of genetic structuring correlated to their environment. However, understanding how environmental heterogeneity influences genetic variation is difficult because the effects of gene flow, drift and selection are confounded. We investigated the genetic variation and its ecological correlates in a wind-pollinated Mediterranean tree species, Fraxinus angustifolia Vahl, within a recognised glacial refugium in Croatia. We sampled 11 populations from environmentally divergent habitats within the Continental and Mediterranean biogeographical regions. We combined genetic data analyses based on nuclear microsatellite loci, multivariate statistics on environmental data and ecological niche modelling (ENM). We identified a geographic structure with a high genetic diversity and low differentiation in the Continental region, which contrasted with the significantly lower genetic diversity and higher population divergence in the Mediterranean region. The positive and significant correlation between environmental and genetic distances after controlling for geographic distance suggests an important influence of ecological divergence of the sites in shaping genetic variation. The ENM provided support for niche differentiation between the populations from the Continental and Mediterranean regions, suggesting that contemporary populations may represent two divergent ecotypes. Ecotype differentiation was also supported by multivariate environmental and genetic distance analyses. Our results suggest that despite extensive gene flow in continental areas, long-term stability of heterogeneous environments have likely promoted genetic divergence of ashes in this region and can explain the present-day genetic variation patterns of these ancient populations. PMID:22905171

  10. Environmental Heterogeneity Explains the Genetic Structure of Continental and Mediterranean Populations of Fraxinus angustifolia Vahl

    PubMed Central

    Temunović, Martina; Franjić, Jozo; Satovic, Zlatko; Grgurev, Marin; Frascaria-Lacoste, Nathalie; Fernández-Manjarrés, Juan F.

    2012-01-01

    Tree species with wide distributions often exhibit different levels of genetic structuring correlated to their environment. However, understanding how environmental heterogeneity influences genetic variation is difficult because the effects of gene flow, drift and selection are confounded. We investigated the genetic variation and its ecological correlates in a wind-pollinated Mediterranean tree species, Fraxinus angustifolia Vahl, within a recognised glacial refugium in Croatia. We sampled 11 populations from environmentally divergent habitats within the Continental and Mediterranean biogeographical regions. We combined genetic data analyses based on nuclear microsatellite loci, multivariate statistics on environmental data and ecological niche modelling (ENM). We identified a geographic structure with a high genetic diversity and low differentiation in the Continental region, which contrasted with the significantly lower genetic diversity and higher population divergence in the Mediterranean region. The positive and significant correlation between environmental and genetic distances after controlling for geographic distance suggests an important influence of ecological divergence of the sites in shaping genetic variation. The ENM provided support for niche differentiation between the populations from the Continental and Mediterranean regions, suggesting that contemporary populations may represent two divergent ecotypes. Ecotype differentiation was also supported by multivariate environmental and genetic distance analyses. Our results suggest that despite extensive gene flow in continental areas, long-term stability of heterogeneous environments have likely promoted genetic divergence of ashes in this region and can explain the present-day genetic variation patterns of these ancient populations. PMID:22905171

  11. Spatio-temporal variation in the genetic composition of wild populations of pearl oyster (Pinctada margaritifera cumingii) in French Polynesia following 10 years of juvenile translocation.

    PubMed

    Arnaud-Haond, S; Vonau, V; Bonhomme, F; Boudry, P; Blanc, F; Prou, J; Seaman, T; Goyard, E

    2004-07-01

    Abstract The genetic impact of the cultural practice of spat collection and translocation between genetically distinct stocks of black-lipped pearl oyster, Pinctada margaritifera cumingii, was studied by comparing samples collected in the 1980s and 2000s from seven atolls in French Polynesia. An amova revealed homogenization of the previously genetically distinct wild stocks of Tuamotu-Gambier and Society archipelagos (the indices of genetic differentiation among archipelagos and among populations within archipelagos, respectively, Phi(CT) and Phi(ST), decreased from 0.032* and 0.025*, respectively, to 0.006(NS) and 0.007(NS)). These results suggest high success of spontaneous reproduction in farms, probably due to the very high density of cultivated pearl oysters, and underline the importance of genetic monitoring of future hatchery produced stocks. PMID:15189220

  12. Genetic structure of Mugil cephalus L. populations from the northern coast of Egypt

    PubMed Central

    Magdy, Mahmoud; Eshak, Mariam Gergis; Rashed, Mohamed Abdel-Salam

    2016-01-01

    Aim: The gray mullet, Mugil cephalus, has been farmed in semi-intensive ponds with tilapia and carps in Egypt for years. The current study used the fluorescent amplified fragment length polymorphism (F-AFLP) technique to search for genetic differences between the populations of M. cephalus in the northern region of Egypt and to detect the gene flow between sampled locations and the homogeneity within M. cephalus genetic pool in Egypt. Materials and Methods: To fulfill the study objectives 60 (15/location) samples were collected from four northern coast governorates of Egypt (Alexandria “sea,” Kafr El-Sheikh “farm,” Damietta “farm” and Port Said “sea”). Three replicates of bulked DNA (5 samples/replicate) for each location were successfully amplified using the standard AFLP protocol using fluorescent primers. DNA polymorphism, genetic diversity, and population structure were assessed while positive outlier loci were successfully detected among the sampled locations. Based on the geographical distribution of sampling sites, the gene flow, the genetic differentiation, and correlations to sampling locations were estimated. Results: A total of 1890 polymorphic bands were scored for all locations, where 765, 1054, 673, and 751 polymorphic bands were scored between samples from Alexandria, Kafr El-Sheikh, Damietta and Port Said, respectively. The effective number of alleles (ne) for all bulked samples combined together was 1.42. The expected heterozygosity under Hardy–Weinberg assumption (He) for all bulked samples combined together was 0.28. Bulked samples from Damietta yielded the lowest ne (1.35) and the lowest He (0.23) when inbreeding coefficient (FIS) = 1. Bulked samples from Kafr El-Sheikh scored the highest ne (1.55) and the highest He (0.37). Bulked samples from Alexandria scored 1.40 for ne and 0.26 for He, while bulked samples from Port Said scored 1.39 for ne and 0.26 for He. The observed bulked samples formed three sub-population groups

  13. Genetic diversity and the conservation priority of Glycine soja populations from Northern China.

    PubMed

    Niu, Y L; Guo, W Y; Bai, L R; Zhao, J C

    2015-01-01

    Knowledge of the spatial patterns of genetic variation in wild populations has significant implications for in situ conservation and the determination of conservation order. To study the levels of genetic diversity, spatial genetic structures, and genetic distances in Glycine soja, 11 natural populations in northern China were analyzed by estimating genetic coefficients using inter-simple sequence repeat (ISSR) fingerprints via mixed sampling strategies. Sixteen ISSR primers generated 98 reproducible polymorphic amplification banding patterns of 172 scored, accounting for 56.98% of the polymorphisms among the populations. The dendrogram based on Nei's genetic distance showed that distinct genetic differentiation occurred in G. soja. The Unweighted Pair-Group Method with Arithmetic Mean cluster analysis indicated two broad groups, and one contained all of the populations except three from Chengde, which formed the smaller second group. The spatial genetic structure evident in the wild soybean populations may be attributed to restricted seed dispersal and the dominant breeding system of this species. The detection of genetic structures in wild soybean populations could be a significant index for the effective conservation of many wild populations, and it could be exploited by soybean breeding programs to increase production. PMID:26681007

  14. High genetic differentiation and cross-shelf patterns of genetic diversity among Great Barrier Reef populations of Symbiodinium

    NASA Astrophysics Data System (ADS)

    Howells, E. J.; van Oppen, M. J. H.; Willis, B. L.

    2009-03-01

    The resilience of Symbiodinium harboured by corals is dependent on the genetic diversity and extent of connectivity among reef populations. This study presents genetic analyses of Great Barrier Reef (GBR) populations of clade C Symbiodinium hosted by the alcyonacean coral,