WorldWideScience

Sample records for complex population genetic

  1. Genetic population structure of sympatric and allopatric populations of Baltic ciscoes (Coregonus albula complex, Teleostei, Coregonidae).

    Science.gov (United States)

    Mehner, Thomas; Pohlmann, Kirsten; Elkin, Che; Monaghan, Michael T; Nitz, Barbara; Freyhof, Jörg

    2010-03-29

    Teleost fishes of the Coregonidae are good model systems for studying postglacial evolution, adaptive radiation and ecological speciation. Of particular interest is whether the repeated occurrence of sympatric species pairs results from in-situ divergence from a single lineage or from multiple invasions of one or more different lineages. Here, we analysed the genetic structure of Baltic ciscoes (Coregonus albula complex), examining 271 individuals from 8 lakes in northern Germany using 1244 polymorphic AFLP loci. Six lakes had only one population of C. albula while the remaining two lakes had C. albula as well as a sympatric species (C. lucinensis or C. fontanae). AFLP demonstrated a significant population structure (Bayesian thetaB = 0.22). Lower differentiation between allopatric (thetaB = 0.028) than sympatric (0.063-0.083) populations contradicts the hypothesis of a sympatric origin of taxa, and there was little evidence for stocking or ongoing hybridization. Genome scans found only three loci that appeared to be under selection in both sympatric population pairs, suggesting a low probability of similar mechanisms of ecological segregation. However, removal of all non-neutral loci decreased the genetic distance between sympatric pairs, suggesting recent adaptive divergence at a few loci. Sympatric pairs in the two lakes were genetically distinct from the six other C. albula populations, suggesting introgression from another lineage may have influenced these two lakes. This was supported by an analysis of isolation-by-distance, where the drift-gene flow equilibrium observed among allopatric populations was disrupted when the sympatric pairs were included. While the population genetic data alone can not unambiguously uncover the mode of speciation, our data indicate that multiple lineages may be responsible for the complex patterns typically observed in Coregonus. Relative differences within and among lakes raises the possibility that multiple lineages may be

  2. The Impact of Evolutionary Driving Forces on Human Complex Diseases: A Population Genetics Approach

    Directory of Open Access Journals (Sweden)

    Amr T. M. Saeb

    2016-01-01

    Full Text Available Investigating the molecular evolution of human genome has paved the way to understand genetic adaptation of humans to the environmental changes and corresponding complex diseases. In this review, we discussed the historical origin of genetic diversity among human populations, the evolutionary driving forces that can affect genetic diversity among populations, and the effects of human movement into new environments and gene flow on population genetic diversity. Furthermore, we presented the role of natural selection on genetic diversity and complex diseases. Then we reviewed the disadvantageous consequences of historical selection events in modern time and their relation to the development of complex diseases. In addition, we discussed the effect of consanguinity on the incidence of complex diseases in human populations. Finally, we presented the latest information about the role of ancient genes acquired from interbreeding with ancient hominids in the development of complex diseases.

  3. Complex genetic origin of Indian populations and its implications

    Indian Academy of Sciences (India)

    2012-10-15

    Oct 15, 2012 ... statistical analyses, we predicted that the present-day. Indian populations .... of type 2 diabetes only amongst Indians (Metspalu et al. 2011). Our other ... A new variety of spondyloepi(meta)physeal dysplasia of the autosomal ...

  4. Genetic diversity and population genetic structure analysis of Echinococcus granulosus sensu stricto complex based on mitochondrial DNA signature.

    Directory of Open Access Journals (Sweden)

    Monika Sharma

    Full Text Available The genetic diversity and population genetics of the Echinococcus granulosus sensu stricto complex were investigated based on sequencing of mitochondrial DNA (mtDNA. Total 81 isolates of hydatid cyst collected from ungulate animals from different geographical areas of North India were identified by sequencing of cytochrome c oxidase subunit1 (coxi gene. Three genotypes belonging to E. granulosus sensu stricto complex were identified (G1, G2 and G3 genotypes. Further the nucleotide sequences (retrieved from GenBank for the coxi gene from seven populations of E. granulosus sensu stricto complex covering 6 continents, were compared with sequences of isolates analysed in this study. Molecular diversity indices represent overall high mitochondrial DNA diversity for these populations, but low nucleotide diversity between haplotypes. The neutrality tests were used to analyze signatures of historical demographic events. The Tajima's D test and Fu's FS test showed negative value, indicating deviations from neutrality and both suggested recent population expansion for the populations. Pairwise fixation index was significant for pairwise comparison of different populations (except between South America and East Asia, Middle East and Europe, South America and Europe, Africa and Australia, indicating genetic differentiation among populations. Based on the findings of the present study and those from earlier studies, we hypothesize that demographic expansion occurred in E. granulosus after the introduction of founder haplotype particular by anthropogenic movements.

  5. Genetic wealth, population health: Major histocompatibility complex variation in captive and wild ring-tailed lemurs (Lemur catta).

    Science.gov (United States)

    Grogan, Kathleen E; Sauther, Michelle L; Cuozzo, Frank P; Drea, Christine M

    2017-10-01

    Across species, diversity at the major histocompatibility complex (MHC) is critical to individual disease resistance and, hence, to population health; however, MHC diversity can be reduced in small, fragmented, or isolated populations. Given the need for comparative studies of functional genetic diversity, we investigated whether MHC diversity differs between populations which are open, that is experiencing gene flow, versus populations which are closed, that is isolated from other populations. Using the endangered ring-tailed lemur ( Lemur catta ) as a model, we compared two populations under long-term study: a relatively "open," wild population ( n  = 180) derived from Bezà Mahafaly Special Reserve, Madagascar (2003-2013) and a "closed," captive population ( n  = 121) derived from the Duke Lemur Center (DLC, 1980-2013) and from the Indianapolis and Cincinnati Zoos (2012). For all animals, we assessed MHC-DRB diversity and, across populations, we compared the number of unique MHC-DRB alleles and their distributions. Wild individuals possessed more MHC-DRB alleles than did captive individuals, and overall, the wild population had more unique MHC-DRB alleles that were more evenly distributed than did the captive population. Despite management efforts to maintain or increase genetic diversity in the DLC population, MHC diversity remained static from 1980 to 2010. Since 2010, however, captive-breeding efforts resulted in the MHC diversity of offspring increasing to a level commensurate with that found in wild individuals. Therefore, loss of genetic diversity in lemurs, owing to small founder populations or reduced gene flow, can be mitigated by managed breeding efforts. Quantifying MHC diversity within individuals and between populations is the necessary first step to identifying potential improvements to captive management and conservation plans.

  6. Genetic variability of Echinococcus granulosus complex in various geographical populations of Iran inferred by mitochondrial DNA sequences.

    Science.gov (United States)

    Spotin, Adel; Mahami-Oskouei, Mahmoud; Harandi, Majid Fasihi; Baratchian, Mehdi; Bordbar, Ali; Ahmadpour, Ehsan; Ebrahimi, Sahar

    2017-01-01

    To investigate the genetic variability and population structure of Echinococcus granulosus complex, 79 isolates were sequenced from different host species covering human, dog, camel, goat, sheep and cattle as of various geographical sub-populations of Iran (Northwestern, Northern, and Southeastern). In addition, 36 sequences of other geographical populations (Western, Southeastern and Central Iran), were directly retrieved from GenBank database for the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene. The confirmed isolates were grouped as G1 genotype (n=92), G6 genotype (n=14), G3 genotype (n=8) and G2 genotype (n=1). 50 unique haplotypes were identified based on the analyzed sequences of cox1. A parsimonious network of the sequence haplotypes displayed star-like features in the overall population containing IR23 (22: 19.1%) as the most common haplotype. According to the analysis of molecular variance (AMOVA) test, the high value of haplotype diversity of E. granulosus complex was shown the total genetic variability within populations while nucleotide diversity was low in all populations. Neutrality indices of the cox1 (Tajima's D and Fu's Fs tests) were shown negative values in Western-Northwestern, Northern and Southeastern populations which indicating significant divergence from neutrality and positive but not significant in Central isolates. A pairwise fixation index (Fst) as a degree of gene flow was generally low value for all populations (0.00647-0.15198). The statistically Fst values indicate that Echinococcus sensu stricto (genotype G1-G3) populations are not genetically well differentiated in various geographical regions of Iran. To appraise the hypothetical evolutionary scenario, further study is needed to analyze concatenated mitogenomes and as well a panel of single locus nuclear markers should be considered in wider areas of Iran and neighboring countries. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. Molecular Population Genetics.

    Science.gov (United States)

    Casillas, Sònia; Barbadilla, Antonio

    2017-03-01

    Molecular population genetics aims to explain genetic variation and molecular evolution from population genetics principles. The field was born 50 years ago with the first measures of genetic variation in allozyme loci, continued with the nucleotide sequencing era, and is currently in the era of population genomics. During this period, molecular population genetics has been revolutionized by progress in data acquisition and theoretical developments. The conceptual elegance of the neutral theory of molecular evolution or the footprint carved by natural selection on the patterns of genetic variation are two examples of the vast number of inspiring findings of population genetics research. Since the inception of the field, Drosophila has been the prominent model species: molecular variation in populations was first described in Drosophila and most of the population genetics hypotheses were tested in Drosophila species. In this review, we describe the main concepts, methods, and landmarks of molecular population genetics, using the Drosophila model as a reference. We describe the different genetic data sets made available by advances in molecular technologies, and the theoretical developments fostered by these data. Finally, we review the results and new insights provided by the population genomics approach, and conclude by enumerating challenges and new lines of inquiry posed by increasingly large population scale sequence data. Copyright © 2017 Casillas and Barbadilla.

  8. Genetic variation in populations of Culicoides variipennis complex in the six New England states, U.S.A.

    Science.gov (United States)

    Holbrook, F R; Tabachnick, W J; Brady, R

    1996-04-01

    We investigated the identity and distribution of members of the Culicoides variipennis complex in the six New England states of the U.S.A., a region where bluetongue transmission has not been detected. Analyses of seven polymorphic isozyme-encoding loci showed that only C.v.variipennis, not considered to be a vector of the bluetongue viruses, was present. The populations of C.v.variipennis were significantly more hetero-zygous than C.v.sonorensis and C.v.occidentalis populations from similar studies in the state of California. Estimates of genetic diversity among populations of C.v.variipennis in New England were similar to C.v.sonorensis in the state of Colorado, but were significantly more genetically divergent than California populations of C.v.occidentalis. The impact of these findings on the status of New England as a possible bluetongue-free region for the purpose of international trade in ruminant livestock and their germplasm is discussed.

  9. Genetics of complex diseases

    DEFF Research Database (Denmark)

    Mellerup, Erling; Møller, Gert Lykke; Koefoed, Pernille

    2012-01-01

    A complex disease with an inheritable component is polygenic, meaning that several different changes in DNA are the genetic basis for the disease. Such a disease may also be genetically heterogeneous, meaning that independent changes in DNA, i.e. various genotypes, can be the genetic basis...... for the disease. Each of these genotypes may be characterized by specific combinations of key genetic changes. It is suggested that even if all key changes are found in genes related to the biology of a certain disease, the number of combinations may be so large that the number of different genotypes may be close...... to the number of patients suffering from the disease. This hypothesis is based on a study of bipolar disorder....

  10. Genetic structure and contrasting selection pattern at two major histocompatibility complex genes in wild house mouse populations

    Czech Academy of Sciences Publication Activity Database

    Čížková, Dagmar; Goüy de Bellocq, J.; Baird, S. J. E.; Piálek, Jaroslav; Bryja, Josef

    2011-01-01

    Roč. 106, č. 5 (2011), s. 727-740 ISSN 0018-067X R&D Projects: GA AV ČR IAA600930608; GA ČR GA206/08/0640 Institutional research plan: CEZ:AV0Z60930519 Keywords : MHC * house mouse * selection * population structure * trans-species polymorphism Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.597, year: 2011

  11. Population-Wide Genetic Risk Prediction of Complex Diseases: A Pilot Feasibility Study in Macau Population for Precision Public Healthcare Planning

    OpenAIRE

    Tsui, Nancy B. Y.; Cheng, Gregory; Chung, Teresa; Lam, Christopher W. K.; Yee, Anita; Chung, Peter K. C.; Kwan, Tsz-Ki; Ko, Elaine; He, Daihai; Wong, Wing-Tak; Lau, Johnson Y. N.; Lau, Lok Ting; Fok, Manson

    2018-01-01

    The genetic bases of many common diseases have been identified through genome-wide association studies in the past decade. However, the application of this approach on public healthcare planning has not been well established. Using Macau with population of around 650,000 as a basis, we conducted a pilot study to evaluate the feasibility of population genomic research and its potential on public health decisions. By performing genome-wide SNP genotyping of over a thousand Macau individuals, we...

  12. Morphological and genetic evolution in eastern populations of the Macrhybopsis aestivalis complex (Cypriniformes: Cyprinidae), with the descriptions of four new species.

    Science.gov (United States)

    Gilbert, Carter R; Mayden, Richard L; Powers, Steven L

    2017-03-30

    For many years the North American cyprinid fish Macrhybopsis aestivalis (common name: Speckled Chub) was regarded as a single widespread and morphologically variable species, occurring in rivers throughout much of the Mississippi Valley and geographically adjacent eastern Gulf slope drainages, west to the Rio Grande basin in Texas, New Mexico, and Mexico. Eisenhour (1997) completed a morphological study of western populations of the Speckled Chub, the results of which appeared thereafter in published form (Eisenhour 1999, 2004). He demonstrated the existence of five valid species west of the Mississippi River (aestivalis, marconis, australis, tetranema, hyostoma), of which the name aestivalis was shown to be restricted to the population occurring in the Rio Grande and the geographically adjacent Rio San Fernando system, in northeastern Mexico. Eisenhour (2004) considered populations throughout the middle Mississippi Valley and its major tributaries to be a single morphologically variable species (hyostoma), and he also indicated that populations of Macrhybopsis from eastern Gulf slope drainages may represent a complex of species. Genetic confirmation of Eisenhour's conclusions regarding western species appeared in the publication by Underwood et al. (2003), who also showed that western populations of M. hyostoma, as presently recognized, are genetically much more complex than previously considered.     Meanwhile, the present authors were involved in a companion study of eastern populations of Macrhybopsis, for which a genetic summary of the eastern Gulf coast species was published by Mayden & Powers (2004). Based on their findings, four species were recognized from southeastern drainages (identified as species A-D), although no formal taxonomic descriptions were included. Their genetic data, in combination with meristic, morphometric and other morphological data presented herein, form the basis for a revised classification of eastern Macrhybopsis populations

  13. Genetic variability in Brazilian populations of Biomphalaria straminea complex detected by simple sequence repeat anchored polymerase chain reaction amplification

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    Caldeira Roberta L

    2001-01-01

    Full Text Available Biomphalaria glabrata, B. tenagophila and B. straminea are intermediate hosts of Schistosoma mansoni, in Brazil. The latter is of epidemiological importance in the northwest of Brazil and, due to morphological similarities, has been grouped with B. intermedia and B. kuhniana in a complex named B. straminea. In the current work, we have standardized the simple sequence repeat anchored polymerase chain reaction (SSR-PCR technique, using the primers (CA8RY and K7, to study the genetic variability of these species. The similarity level was calculated using the Dice coefficient and genetic distance using the Nei and Li coefficient. The trees were obtained by the UPGMA and neighbor-joining methods. We have observed that the most related individuals belong to the same species and locality and that individuals from different localities, but of the same species, present clear heterogeneity. The trees generated using both methods showed similar topologies. The SSR-PCR technique was shown to be very efficient in intrapopulational and intraspecific studies of the B. straminea complex snails.

  14. Population genetics and cryptic species

    International Nuclear Information System (INIS)

    McPheron, Bruce A.

    2000-01-01

    Does the definition of a species matter for pest management purposes? Taxonomists provide us with tools - usually morphological characters - to identify a group of organisms that we call a species. The implication of this identification is that all of the individuals that fit the provided description are members of the species in question. The taxonomists have considered the range of variation among individuals in defining the species, but this variation is often forgotten when we take the concept of species to the level of management. Just as there is morphological variation among individuals, there is also variation in practically any character we might imagine, which has implications for the short and long term success of our management tactics. The rich literature on insecticide resistance should be a constant reminder of the fact that the pressure on pest survival and reproduction applied by our management approaches frequently leads to evolutionary changes within the pest species. The degree of variation within a particular species is a defining characteristic of that species. This level of variability may have very important implications for successful management, so it is very important to measure variation and, whenever possible, the genetic basis of that variation, in a target species. Population genetic approaches can provide evidence of genetic structure (or lack thereof) among populations of a species. These types of data can be used to discuss the movement of pest populations on a local or global scale. In other cases, we may have a complex of species that share some, but not all, characteristics. Species complexes that share morphological characters (i.e., cannot be easily distinguished) but not biological characters are referred to as sibling or cryptic species

  15. Complex postglacial recolonization inferred from population genetic structure of mottled sculpin Cottus bairdii in tributaries of eastern Lake Michigan, U.S.A.

    Science.gov (United States)

    Homola, J J; Ruetz, C R; Kohler, S L; Thum, R A

    2016-11-01

    This study used analyses of the genetic structure of a non-game fish species, the mottled sculpin Cottus bairdii to hypothesize probable recolonization routes used by cottids and possibly other Laurentian Great Lakes fishes following glacial recession. Based on samples from 16 small streams in five major Lake Michigan, U.S.A., tributary basins, significant interpopulation differentiation was documented (overall F ST = 0·235). Differentiation was complex, however, with unexpectedly high genetic similarity among basins as well as occasionally strong differentiation within basins, despite relatively close geographic proximity of populations. Genetic dissimilarities were identified between eastern and western populations within river basins, with similarities existing between eastern and western populations across basins. Given such patterns, recolonization is hypothesized to have occurred on three occasions from more than one glacial refugium, with a secondary vicariant event resulting from reduction in the water level of ancestral Lake Michigan. By studying the phylogeography of a small, non-game fish species, this study provides insight into recolonization dynamics of the region that could be difficult to infer from game species that are often broadly dispersed by humans. © 2016 The Fisheries Society of the British Isles.

  16. Drainage isolation and climate change-driven population expansion shape the genetic structures of Tuber indicum complex in the Hengduan Mountains region.

    Science.gov (United States)

    Feng, Bang; Zhao, Qi; Xu, Jianping; Qin, Jiao; Yang, Zhu L

    2016-02-24

    The orogenesis of the Qinghai-Tibetan Plateau and the Quaternary climate changes have played key roles in driving the evolution of flora and fauna in Southwest China, but their effects on higher fungi are poorly addressed. In this study, we investigated the phylogeographic pattern of the Tuber indicum species complex, an economically important fungal group distributed in the Hengduan Mountains region. Our data confirmed the existence of two distinct lineages, T. indicum and T. himalayense, within this species complex. Three geographic groups (Groups W, N and C) were revealed within T. indicum, with Group W found in the paleo-Lancang River region, while Groups N and C corresponded to the two banks along the contemporary Jinsha River, suggesting that rivers have acted as barriers for gene flow among populations from different drainages. Historical range expansion resulted from climate changes was inferred in Group C, contributing to the observed gene flow among geographic populations within this group. Although no significant geographic structure was identified in T. himalayense, evidence of drainage isolation for this species was also detected. Our findings demonstrate that both topographic changes and Quaternary climate oscillations have played important roles in driving the genetic structures of the T. indicum species complex.

  17. Population genetics without intraspecific data

    DEFF Research Database (Denmark)

    Thorne, Jeffrey L; Choi, Sang Chul; Yu, Jiaye

    2007-01-01

    A central goal of computational biology is the prediction of phenotype from DNA and protein sequence data. Recent models of sequence change use in silico prediction systems to incorporate the effects of phenotype on evolutionary rates. These models have been designed for analyzing sequence data...... populations, and parameters of interspecific models should have population genetic interpretations. We show, with two examples, how population genetic interpretations can be assigned to evolutionary models. The first example considers the impact of RNA secondary structure on sequence change, and the second...... reflects the tendency for protein tertiary structure to influence nonsynonymous substitution rates. We argue that statistical fit to data should not be the sole criterion for assessing models of sequence change. A good interspecific model should also yield a clear and biologically plausible population...

  18. Genetic diversity and distribution patterns of diploid and polyploid hybrid water frog populations (Pelophylax esculentus complex) across Europe

    Czech Academy of Sciences Publication Activity Database

    Hoffmann, A.; Plötner, J.; Pruvost, N. B. M.; Christiansen, D. G.; Röthlisberger, S.; Choleva, Lukáš; Mikulíček, P.; Cogalniceanu, D.; Sas-Kovács, I.; Shabanov, D.; Morozov-Leonov, S.; Reyer, H. U.

    2015-01-01

    Roč. 24, č. 17 (2015), s. 4371-4391 ISSN 0962-1083 R&D Projects: GA ČR(CZ) GJ15-19947Y Institutional support: RVO:67985904 Keywords : all-hybrids populations * founder effects * geographic distribution Subject RIV: EG - Zoology Impact factor: 5.947, year: 2015

  19. CDPOP: A spatially explicit cost distance population genetics program

    Science.gov (United States)

    Erin L. Landguth; S. A. Cushman

    2010-01-01

    Spatially explicit simulation of gene flow in complex landscapes is essential to explain observed population responses and provide a foundation for landscape genetics. To address this need, we wrote a spatially explicit, individual-based population genetics model (CDPOP). The model implements individual-based population modelling with Mendelian inheritance and k-allele...

  20. Carney complex review: Genetic features.

    Science.gov (United States)

    Bosco Schamun, María Belén; Correa, Ricardo; Graffigna, Patricia; de Miguel, Valeria; Fainstein Day, Patricia

    2018-01-01

    Carney complex is a multiple neoplasia syndrome having endocrine and non-endocrine manifestations. Diagnostic criteria include myxoma, lentigines, and primary pigmented nodular adrenocortical disease, amongst other signs/symptoms. In most cases it is an autosomal dominant disease, and diagnosis therefore requires study and follow-up of the family members. Inactivating mutations of the PRKAR1A gene were identified as the main cause of the disease, although since 2015 other disease-related genes, including PRKACA and PRKACB activating mutations, have also been related with Carney complex. This review will address the genetic aspects related to Carney complex. Copyright © 2017 SEEN y SED. Publicado por Elsevier España, S.L.U. All rights reserved.

  1. Stochastic problems in population genetics

    CERN Document Server

    Maruyama, Takeo

    1977-01-01

    These are" notes based on courses in Theoretical Population Genetics given at the University of Texas at Houston during the winter quarter, 1974, and at the University of Wisconsin during the fall semester, 1976. These notes explore problems of population genetics and evolution involving stochastic processes. Biological models and various mathematical techniques are discussed. Special emphasis is given to the diffusion method and an attempt is made to emphasize the underlying unity of various problems based on the Kolmogorov backward equation. A particular effort was made to make the subject accessible to biology students who are not familiar with stochastic processes. The references are not exhaustive but were chosen to provide a starting point for the reader interested in pursuing the subject further. Acknowledgement I would like to use this opportunity to express my thanks to Drs. J. F. Crow, M. Nei and W. J. Schull for their hospitality during my stays at their universities. I am indebted to Dr. M. Kimura...

  2. Quantifying introgression risk with realistic population genetics.

    Science.gov (United States)

    Ghosh, Atiyo; Meirmans, Patrick G; Haccou, Patsy

    2012-12-07

    Introgression is the permanent incorporation of genes from the genome of one population into another. This can have severe consequences, such as extinction of endemic species, or the spread of transgenes. Quantification of the risk of introgression is an important component of genetically modified crop regulation. Most theoretical introgression studies aimed at such quantification disregard one or more of the most important factors concerning introgression: realistic genetical mechanisms, repeated invasions and stochasticity. In addition, the use of linkage as a risk mitigation strategy has not been studied properly yet with genetic introgression models. Current genetic introgression studies fail to take repeated invasions and demographic stochasticity into account properly, and use incorrect measures of introgression risk that can be manipulated by arbitrary choices. In this study, we present proper methods for risk quantification that overcome these difficulties. We generalize a probabilistic risk measure, the so-called hazard rate of introgression, for application to introgression models with complex genetics and small natural population sizes. We illustrate the method by studying the effects of linkage and recombination on transgene introgression risk at different population sizes.

  3. Sardinian Population (Italy): a Genetic Review

    African Journals Online (AJOL)

    thou

    , according to the classification suggested by Contini (1979). The genetic ... and to have maintained a genetic identity through their evolution: the cluster constituted ...... HLA class II haplotypes reveals that the Sardinian population is genetically.

  4. Assessing population genetic structure via the maximisation of genetic distance

    Directory of Open Access Journals (Sweden)

    Toro Miguel A

    2009-11-01

    Full Text Available Abstract Background The inference of the hidden structure of a population is an essential issue in population genetics. Recently, several methods have been proposed to infer population structure in population genetics. Methods In this study, a new method to infer the number of clusters and to assign individuals to the inferred populations is proposed. This approach does not make any assumption on Hardy-Weinberg and linkage equilibrium. The implemented criterion is the maximisation (via a simulated annealing algorithm of the averaged genetic distance between a predefined number of clusters. The performance of this method is compared with two Bayesian approaches: STRUCTURE and BAPS, using simulated data and also a real human data set. Results The simulations show that with a reduced number of markers, BAPS overestimates the number of clusters and presents a reduced proportion of correct groupings. The accuracy of the new method is approximately the same as for STRUCTURE. Also, in Hardy-Weinberg and linkage disequilibrium cases, BAPS performs incorrectly. In these situations, STRUCTURE and the new method show an equivalent behaviour with respect to the number of inferred clusters, although the proportion of correct groupings is slightly better with the new method. Re-establishing equilibrium with the randomisation procedures improves the precision of the Bayesian approaches. All methods have a good precision for FST ≥ 0.03, but only STRUCTURE estimates the correct number of clusters for FST as low as 0.01. In situations with a high number of clusters or a more complex population structure, MGD performs better than STRUCTURE and BAPS. The results for a human data set analysed with the new method are congruent with the geographical regions previously found. Conclusion This new method used to infer the hidden structure in a population, based on the maximisation of the genetic distance and not taking into consideration any assumption about Hardy

  5. Complex genetics controls natural variation among seed quality phenotypes in a recombinant inbred population of an interspecific cross between Solanum lycopersicum × Solanum pimpinellifolium

    NARCIS (Netherlands)

    Kazmi, R.H.; Khan, N.; Willems, L.A.J.; Heusden, van A.W.; Ligterink, J.W.; Hilhorst, H.W.M.

    2012-01-01

    Seed quality in tomato is associated with many complex physiological and genetic traits. While plant processes are frequently controlled by the action of small- to large-effect genes that follow classic Mendelian inheritance, our study suggests that seed quality is primarily quantitative and

  6. Deep Learning for Population Genetic Inference.

    Science.gov (United States)

    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.

  7. Deep Learning for Population Genetic Inference.

    Directory of Open Access Journals (Sweden)

    Sara Sheehan

    2016-03-01

    Full Text Available 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.

  8. Deep Learning for Population Genetic Inference

    Science.gov (United States)

    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

  9. Microsatellite data analysis for population genetics

    Science.gov (United States)

    Theories and analytical tools of population genetics have been widely applied for addressing various questions in the fields of ecological genetics, conservation biology, and any context where the role of dispersal or gene flow is important. Underlying much of population genetics is the analysis of ...

  10. Genetics Home Reference: tuberous sclerosis complex

    Science.gov (United States)

    ... 42. Citation on PubMed Northrup H, Koenig MK, Pearson DA, Au KS. Tuberous Sclerosis Complex. 1999 Jul ... Tuberous sclerosis complex: advances in diagnosis, genetics, and management. J Am Acad Dermatol. 2007 Aug;57(2): ...

  11. [Genetic structure of natural populations

    International Nuclear Information System (INIS)

    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

  12. Bacterial Population Genetics in a Forensic Context

    Energy Technology Data Exchange (ETDEWEB)

    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

  13. Genetic structure of Potentilla acaulis (Rosaceae) populations ...

    African Journals Online (AJOL)

    Jane

    2011-07-18

    Jul 18, 2011 ... populations based on randomly amplified polymorphic. DNA (RAPD) in habitat ..... the correlation between ΦST values and genetic distances was highly ... Propagule recruitment from genets of perennial clonal plants could ...

  14. Biochemical genetic variation between four populations of ...

    African Journals Online (AJOL)

    system) to 0.093 in the Spekboom River population (Limpopo River system). The genetic distance, FST and NEM values, as well as pair-wise contingency c2 analyses indicate a lack of gene flow between populations, as expected for isolated fish. Evidence of foreign genetic material in one population was also observed.

  15. Conservation genetics of managed ungulate populations

    Science.gov (United States)

    Scribner, Kim T.

    1993-01-01

    Natural populations of many species are increasingly impacted by human activities. Perturbations are particularly pronunced for large ungulates due in part to sport and commercial harvest, to reductions and fragmentation of native habitat, and as the result of reintroductions. These perturbations affect population size, sex and age composition, and population breeding structure, and as a consequence affect the levels and partitioning of genetic variation. Three case histories highlighting long-term ecological genetic research on mule deer Odocoileus hemionus (Rafinesque, 1817), white-tailed deer O. virginianus (Zimmermann, 1780), and Alpine ibex Capra i. ibex Linnaeus, 1758 are presented. Joint examinations of population ecological and genetic data from several populations of each species reveal: (1) that populations are not in genetic equilibrium, but that allele frequencies and heterozygosity change dramatically over time and among cohorts produced in successive years, (2) populations are genetically structured over short and large geographic distances reflecting local breeding structure and patterns of gene flow, respectively; however, this structure is quite dynamic over time, due in part to population exploitation, and (3) restocking programs are often undertaken with small numbers of founding individuals resulting in dramatic declines in levels of genetic variability and increasing levels of genetic differentiation among populations due to genetic drift. Genetic characteristics have and will continue to provide valuable indirect sources of information relating enviromental and human perturbations to changes in population processes.

  16. Studying the Genetics of Complex Disease With Ancestry-Specific Human Phenotype Networks: The Case of Type 2 Diabetes in East Asian Populations.

    Science.gov (United States)

    Qiu, Jingya; Moore, Jason H; Darabos, Christian

    2016-05-01

    Genome-wide association studies (GWAS) have led to the discovery of over 200 single nucleotide polymorphisms (SNPs) associated with type 2 diabetes mellitus (T2DM). Additionally, East Asians develop T2DM at a higher rate, younger age, and lower body mass index than their European ancestry counterparts. The reason behind this occurrence remains elusive. With comprehensive searches through the National Human Genome Research Institute (NHGRI) GWAS catalog literature, we compiled a database of 2,800 ancestry-specific SNPs associated with T2DM and 70 other related traits. Manual data extraction was necessary because the GWAS catalog reports statistics such as odds ratio and P-value, but does not consistently include ancestry information. Currently, many statistics are derived by combining initial and replication samples from study populations of mixed ancestry. Analysis of all-inclusive data can be misleading, as not all SNPs are transferable across diverse populations. We used ancestry data to construct ancestry-specific human phenotype networks (HPN) centered on T2DM. Quantitative and visual analysis of network models reveal the genetic disparities between ancestry groups. Of the 27 phenotypes in the East Asian HPN, six phenotypes were unique to the network, revealing the underlying ancestry-specific nature of some SNPs associated with T2DM. We studied the relationship between T2DM and five phenotypes unique to the East Asian HPN to generate new interaction hypotheses in a clinical context. The genetic differences found in our ancestry-specific HPNs suggest different pathways are involved in the pathogenesis of T2DM among different populations. Our study underlines the importance of ancestry in the development of T2DM and its implications in pharmocogenetics and personalized medicine. © 2016 The Authors. *Genetic Epidemiology Published by Wiley Periodicals, Inc.

  17. Genetic analysis of Mexican Criollo cattle populations.

    Science.gov (United States)

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

    2008-10-01

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

  18. GENETIC AND MORPHOLOGICAL VARIATION OF POPULATIONS BELONGING TO THE BULINUS TRUNCATUS/TROPICUS COMPLEX (GASTROPODA; PLANORBIDAE) IN SOUTH WESTERN ZIMBABWE

    DEFF Research Database (Denmark)

    Mukaratirwa, S.; Kristensen, Thomas K.; Siegismund, Hans Redlef

    1998-01-01

    , in respect of allozyme variation (5 polymorphic loci), shell morphology (9 variables), copulatory organ and chromosome number. Comparative data were obtained from snails from north western Zimbabwe identified definitely as B. tropicus. Analysis of the genetic structure revealed a high degree of polymorphism...... (P) ranging from 0.29-0.80 among populations from Plumtree and expected heterozygosity (He) from 0.02-0.22. No enzymatic diagnostic loci were found which could differentiate the different morphs or populations and discriminant function analysis on the morphological data showed an overlap of morphs...

  19. Genetic basis of a cognitive complexity metric.

    Directory of Open Access Journals (Sweden)

    Narelle K Hansell

    Full Text Available Relational complexity (RC is a metric reflecting capacity limitation in relational processing. It plays a crucial role in higher cognitive processes and is an endophenotype for several disorders. However, the genetic underpinnings of complex relational processing have not been investigated. Using the classical twin model, we estimated the heritability of RC and genetic overlap with intelligence (IQ, reasoning, and working memory in a twin and sibling sample aged 15-29 years (N = 787. Further, in an exploratory search for genetic loci contributing to RC, we examined associated genetic markers and genes in our Discovery sample and selected loci for replication in four independent samples (ALSPAC, LBC1936, NTR, NCNG, followed by meta-analysis (N>6500 at the single marker level. Twin modelling showed RC is highly heritable (67%, has considerable genetic overlap with IQ (59%, and is a major component of genetic covariation between reasoning and working memory (72%. At the molecular level, we found preliminary support for four single-marker loci (one in the gene DGKB, and at a gene-based level for the NPS gene, having influence on cognition. These results indicate that genetic sources influencing relational processing are a key component of the genetic architecture of broader cognitive abilities. Further, they suggest a genetic cascade, whereby genetic factors influencing capacity limitation in relational processing have a flow-on effect to more complex cognitive traits, including reasoning and working memory, and ultimately, IQ.

  20. Genetic variation between ecotypic populations of Chloris ...

    African Journals Online (AJOL)

    Genetic variation between ecotypic populations of Chloris roxburghiana grass detected through RAPD analysis. ... frequency indicated that the four populations of C. roxburghiana were genetically distinct, probably as a result of variation in soil fertility, geographical isolation and socio-ecological history of the study sites.

  1. What Use Is Population Genetics?

    Science.gov (United States)

    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. Copyright © 2015 by the Genetics Society of America.

  2. Refining and defining riverscape genetics: How rivers influence population genetic structure

    Science.gov (United States)

    Chanté D. Davis; Clinton W. Epps; Rebecca L. Flitcroft; Michael A. Banks

    2018-01-01

    Traditional analysis in population genetics evaluates differences among groups of individuals and, in some cases, considers the effects of distance or potential barriers to gene flow. Genetic variation of organisms in complex landscapes, seascapes, or riverine systems, however, may be shaped by many forces. Recent research has linked habitat heterogeneity and landscape...

  3. Multi-population Genomic Relationships for Estimating Current Genetic Variances Within and Genetic Correlations Between Populations.

    Science.gov (United States)

    Wientjes, Yvonne C J; Bijma, Piter; Vandenplas, Jérémie; Calus, Mario P L

    2017-10-01

    Different methods are available to calculate multi-population genomic relationship matrices. Since those matrices differ in base population, it is anticipated that the method used to calculate genomic relationships affects the estimate of genetic variances, covariances, and correlations. The aim of this article is to define the multi-population genomic relationship matrix to estimate current genetic variances within and genetic correlations between populations. The genomic relationship matrix containing two populations consists of four blocks, one block for population 1, one block for population 2, and two blocks for relationships between the populations. It is known, based on literature, that by using current allele frequencies to calculate genomic relationships within a population, current genetic variances are estimated. In this article, we theoretically derived the properties of the genomic relationship matrix to estimate genetic correlations between populations and validated it using simulations. When the scaling factor of across-population genomic relationships is equal to the product of the square roots of the scaling factors for within-population genomic relationships, the genetic correlation is estimated unbiasedly even though estimated genetic variances do not necessarily refer to the current population. When this property is not met, the correlation based on estimated variances should be multiplied by a correction factor based on the scaling factors. In this study, we present a genomic relationship matrix which directly estimates current genetic variances as well as genetic correlations between populations. Copyright © 2017 by the Genetics Society of America.

  4. Genetics Home Reference: Carney complex

    Science.gov (United States)

    ... cortisol (hypercortisolism) can lead to the development of Cushing syndrome. This syndrome causes weight gain in the face ... Institute of Diabetes and Digestive and Kidney Diseases: Cushing's Syndrome Educational Resources (6 links) Disease InfoSearch: Carney Complex ...

  5. Genetic changeover in Drosophila populations

    International Nuclear Information System (INIS)

    Wallace, B.

    1986-01-01

    Three populations of Drosophila melanogaster that were daughter populations of two others with histories of high, continuous radiation exposure [population 5 (irradiated, small population size) gave rise to populations 17 (small) and 18 (large); population 6 (irradiated, large population size) gave rise to population 19 (large)] were maintained for 1 year with no radiation exposure. The frequency with which random combinations of second chromosomes taken from population 19 proved to be lethal changed abruptly after about 8 months, thus revealing the origin of a selectively favored element in that population. (This element may or may not have been the cause of the lethality.) A comparison of the loss of lethals in populations 17 and 18 with a loss that occurred concurrently in the still-irradiated population 5 suggests that a second, selectively favored element had arisen in that population just before populations 17 and 18 were split off. This element was on a nonlethal chromosome. The result in population 5 was the elimination of many lethals from that population, followed by a subsequent increase as mutations occurred in the favored nonlethal chromosome. Populations 17 and 18, with no radiation exposure, underwent a loss of lethals with no subsequent increase. The events described here, as well as others to be described elsewhere, suggest that populations may be subject to episodic periods of rapid gene frequency changes that occur under intense selection pressure. In the instances in which the changeover was revealed by the elimination of preexisting lethals, earlier lethal frequencies were reduced by approximately one-half; the selectively favored elements appear, then, to be favored in the heterozygous--not homozygous--condition

  6. Genetic basis of a cognitive complexity metric

    NARCIS (Netherlands)

    Hansell, Narelle K; Halford, Graeme S; Andrews, Glenda; Shum, David H K; Harris, Sarah E; Davies, Gail; Franic, Sanja; Christoforou, Andrea; Zietsch, Brendan; Painter, Jodie; Medland, Sarah E; Ehli, Erik A; Davies, Gareth E; Steen, Vidar M; Lundervold, Astri J; Reinvang, Ivar; Montgomery, Grant W; Espeseth, Thomas; Hulshoff Pol, Hilleke E; Starr, John M; Martin, Nicholas G; Le Hellard, Stephanie; Boomsma, Dorret I; Deary, Ian J; Wright, Margaret J

    2015-01-01

    Relational complexity (RC) is a metric reflecting capacity limitation in relational processing. It plays a crucial role in higher cognitive processes and is an endophenotype for several disorders. However, the genetic underpinnings of complex relational processing have not been investigated. Using

  7. Genetic Basis of a Cognitive Complexity Metric

    NARCIS (Netherlands)

    Hansell, N.K.; Halford, G.S.; Andrews, G.; Shum, D.H.K.; Harris, S.E.; Davies, G.; Franic, S.; Christoforou, A.; Zietsch, B.; Painter, J.; Medland, S.E.; Ehli, E.A.; Davies, G.E.; Steen, V.M.; Lundervold, A.J.; Reinvang, I.; Montgomery, G.W.; Espeseth, T.; Hulshoff Pol, H.E.; Starr, J.M.; Martin, N.G.; Le Hellard, S.; Boomsma, D.I.; Deary, I.J.; Wright, M.J.

    2015-01-01

    Relational complexity (RC) is a metric reflecting capacity limitation in relational processing. It plays a crucial role in higher cognitive processes and is an endophenotype for several disorders. However, the genetic underpinnings of complex relational processing have not been investigated. Using

  8. Genetic composition of captive panda population.

    Science.gov (United States)

    Yang, Jiandong; Shen, Fujun; Hou, Rong; Da, Yang

    2016-10-03

    A major function of the captive panda population is to preserve the genetic diversity of wild panda populations in their natural habitats. Understanding the genetic composition of the captive panda population in terms of genetic contributions from the wild panda populations provides necessary knowledge for breeding plans to preserve the genetic diversity of the wild panda populations. The genetic contributions from different wild populations to the captive panda population were highly unbalanced, with Qionglai accounting for 52.2 % of the captive panda gene pool, followed by Minshan with 21.5 %, Qinling with 10.6 %, Liangshan with 8.2 %, and Xiaoxiangling with 3.6 %, whereas Daxiangling, which had similar population size as Xiaoxiangling, had no genetic representation in the captive population. The current breeding recommendations may increase the contribution of some small wild populations at the expense of decreasing the contributions of other small wild populations, i.e., increasing the Xiaoxiangling contribution while decreasing the contribution of Liangshan, or sharply increasing the Qinling contribution while decreasing the contributions of Xiaoxiangling and Liangshan, which were two of the three smallest wild populations and were already severely under-represented in the captive population. We developed three habitat-controlled breeding plans that could increase the genetic contributions from the smallest wild populations to 6.7-11.2 % for Xiaoxiangling, 11.5-12.3 % for Liangshan and 12.9-20.0 % for Qinling among the offspring of one breeding season while reducing the risk of hidden inbreeding due to related founders from the same habitat undetectable by pedigree data. The three smallest wild panda populations of Daxiangling, Xiaoxiangling and Liangshan either had no representation or were severely unrepresented in the current captive panda population. By incorporating the breeding goal of increasing the genetic contributions from the smallest wild

  9. Genetic diversity of disease-associated loci in Turkish population.

    Science.gov (United States)

    Karaca, Sefayet; Cesuroglu, Tomris; Karaca, Mehmet; Erge, Sema; Polimanti, Renato

    2015-04-01

    Many consortia and international projects have investigated the human genetic variation of a large number of ethno-geographic groups. However, populations with peculiar genetic features, such as the Turkish population, are still absent in publically available datasets. To explore the genetic predisposition to health-related traits of the Turkish population, we analyzed 34 genes associated with different health-related traits (for example, lipid metabolism, cardio-vascular diseases, hormone metabolism, cellular detoxification, aging and energy metabolism). We observed relevant differences between the Turkish population and populations with non-European ancestries (that is, Africa and East Asia) in some of the investigated genes (that is, AGT, APOE, CYP1B1, GNB3, IL10, IL6, LIPC and PON1). As most complex traits are highly polygenic, we developed polygenic scores associated with different health-related traits to explore the genetic diversity of the Turkish population with respect to other human groups. This approach showed significant differences between the Turkish population and populations with non-European ancestries, as well as between Turkish and Northern European individuals. This last finding is in agreement with the genetic structure of European and Middle East populations, and may also agree with epidemiological evidences about the health disparities of Turkish communities in Northern European countries.

  10. Advances in the genetically complex autoinflammatory diseases.

    Science.gov (United States)

    Ombrello, Michael J

    2015-07-01

    Monogenic diseases usually demonstrate Mendelian inheritance and are caused by highly penetrant genetic variants of a single gene. In contrast, genetically complex diseases arise from a combination of multiple genetic and environmental factors. The concept of autoinflammation originally emerged from the identification of individual, activating lesions of the innate immune system as the molecular basis of the hereditary periodic fever syndromes. In addition to these rare, monogenic forms of autoinflammation, genetically complex autoinflammatory diseases like the periodic fever, aphthous stomatitis, pharyngitis, and cervical adenitis (PFAPA) syndrome, chronic recurrent multifocal osteomyelitis (CRMO), Behçet's disease, and systemic arthritis also fulfill the definition of autoinflammatory diseases-namely, the development of apparently unprovoked episodes of inflammation without identifiable exogenous triggers and in the absence of autoimmunity. Interestingly, investigations of these genetically complex autoinflammatory diseases have implicated both innate and adaptive immune abnormalities, blurring the line between autoinflammation and autoimmunity. This reinforces the paradigm of concerted innate and adaptive immune dysfunction leading to genetically complex autoinflammatory phenotypes.

  11. Population genetics of African ungulates

    DEFF Research Database (Denmark)

    Lorenzen, Eline

    -specific data sets, which are used to elucidate evolutionary processes of importance to the savannah ungulate community. Patterns of DNA variation were analyzed to assess the genetic signatures of Pleistocene refugia and investigate aspects of speciation, intraspecific structuring, hybridization, and historic...

  12. Population Genetics of Phytophthora infestans

    DEFF Research Database (Denmark)

    Montes, Melanie Sarah

    a high diversity of lineages, with different strains appearing from field to field. Different strains were also tested for their resistance to the fungicide metalaxyl, and it was shown that there is potential for linking genetic markers to resistance. In a pilot study it was then tested whether P...

  13. Wolf population genetics in Europe

    DEFF Research Database (Denmark)

    Hindrikson, Maris; Remm, Jaanus; Pilot, Malgorzata

    2017-01-01

    genetic studies in Europe, covering major studies from the ‘pre-genomic era’ and the first insights of the ‘genomics era’. We analyse, summarize and discuss findings derived from analyses of three compartments of the mammalian genome with different inheritance modes: maternal (mitochondrial DNA), paternal...

  14. Genetic disorders from an endogamous population

    African Journals Online (AJOL)

    Abdulbari Bener

    b Dept. of Evidence for Population Health Unit, School of Epidemiology and Health Sciences, University of Manchester, Manchester, UK ... genetics counseling and screening for the hereditary diseases programme. Results: The ..... Elementary.

  15. Highlighting nonlinear patterns in population genetics datasets

    KAUST Repository

    Alanis Lobato, Gregorio; Cannistraci, Carlo Vittorio; Eriksson, Anders; Manica, Andrea; Ravasi, Timothy

    2015-01-01

    Detecting structure in population genetics and case-control studies is important, as it exposes phenomena such as ecoclines, admixture and stratification. Principal Component Analysis (PCA) is a linear dimension-reduction technique commonly used for this purpose, but it struggles to reveal complex, nonlinear data patterns. In this paper we introduce non-centred Minimum Curvilinear Embedding (ncMCE), a nonlinear method to overcome this problem. Our analyses show that ncMCE can separate individuals into ethnic groups in cases in which PCA fails to reveal any clear structure. This increased discrimination power arises from ncMCE's ability to better capture the phylogenetic signal in the samples, whereas PCA better reflects their geographic relation. We also demonstrate how ncMCE can discover interesting patterns, even when the data has been poorly pre-processed. The juxtaposition of PCA and ncMCE visualisations provides a new standard of analysis with utility for discovering and validating significant linear/nonlinear complementary patterns in genetic data.

  16. Highlighting nonlinear patterns in population genetics datasets

    KAUST Repository

    Alanis Lobato, Gregorio

    2015-01-30

    Detecting structure in population genetics and case-control studies is important, as it exposes phenomena such as ecoclines, admixture and stratification. Principal Component Analysis (PCA) is a linear dimension-reduction technique commonly used for this purpose, but it struggles to reveal complex, nonlinear data patterns. In this paper we introduce non-centred Minimum Curvilinear Embedding (ncMCE), a nonlinear method to overcome this problem. Our analyses show that ncMCE can separate individuals into ethnic groups in cases in which PCA fails to reveal any clear structure. This increased discrimination power arises from ncMCE\\'s ability to better capture the phylogenetic signal in the samples, whereas PCA better reflects their geographic relation. We also demonstrate how ncMCE can discover interesting patterns, even when the data has been poorly pre-processed. The juxtaposition of PCA and ncMCE visualisations provides a new standard of analysis with utility for discovering and validating significant linear/nonlinear complementary patterns in genetic data.

  17. Pronounced fixation, strong population differentiation and complex population history in the Canary Islands blue tit subspecies complex.

    Science.gov (United States)

    Hansson, Bengt; Ljungqvist, Marcus; Illera, Juan-Carlos; Kvist, Laura

    2014-01-01

    Evolutionary molecular studies of island radiations may lead to insights in the role of vicariance, founder events, population size and drift in the processes of population differentiation. We evaluate the degree of population genetic differentiation and fixation of the Canary Islands blue tit subspecies complex using microsatellite markers and aim to get insights in the population history using coalescence based methods. The Canary Island populations were strongly genetically differentiated and had reduced diversity with pronounced fixation including many private alleles. In population structure models, the relationship between the central island populations (La Gomera, Tenerife and Gran Canaria) and El Hierro was difficult to disentangle whereas the two European populations showed consistent clustering, the two eastern islands (Fuerteventura and Lanzarote) and Morocco weak clustering, and La Palma a consistent unique lineage. Coalescence based models suggested that the European mainland forms an outgroup to the Afrocanarian population, a split between the western island group (La Palma and El Hierro) and the central island group, and recent splits between the three central islands, and between the two eastern islands and Morocco, respectively. It is clear that strong genetic drift and low level of concurrent gene flow among populations have shaped complex allelic patterns of fixation and skewed frequencies over the archipelago. However, understanding the population history remains challenging; in particular, the pattern of extreme divergence with low genetic diversity and yet unique genetic material in the Canary Island system requires an explanation. A potential scenario is population contractions of a historically large and genetically variable Afrocanarian population, with vicariance and drift following in the wake. The suggestion from sequence-based analyses of a Pleistocene extinction of a substantial part of North Africa and a Pleistocene/Holocene eastward

  18. Pronounced fixation, strong population differentiation and complex population history in the Canary Islands blue tit subspecies complex.

    Directory of Open Access Journals (Sweden)

    Bengt Hansson

    Full Text Available Evolutionary molecular studies of island radiations may lead to insights in the role of vicariance, founder events, population size and drift in the processes of population differentiation. We evaluate the degree of population genetic differentiation and fixation of the Canary Islands blue tit subspecies complex using microsatellite markers and aim to get insights in the population history using coalescence based methods. The Canary Island populations were strongly genetically differentiated and had reduced diversity with pronounced fixation including many private alleles. In population structure models, the relationship between the central island populations (La Gomera, Tenerife and Gran Canaria and El Hierro was difficult to disentangle whereas the two European populations showed consistent clustering, the two eastern islands (Fuerteventura and Lanzarote and Morocco weak clustering, and La Palma a consistent unique lineage. Coalescence based models suggested that the European mainland forms an outgroup to the Afrocanarian population, a split between the western island group (La Palma and El Hierro and the central island group, and recent splits between the three central islands, and between the two eastern islands and Morocco, respectively. It is clear that strong genetic drift and low level of concurrent gene flow among populations have shaped complex allelic patterns of fixation and skewed frequencies over the archipelago. However, understanding the population history remains challenging; in particular, the pattern of extreme divergence with low genetic diversity and yet unique genetic material in the Canary Island system requires an explanation. A potential scenario is population contractions of a historically large and genetically variable Afrocanarian population, with vicariance and drift following in the wake. The suggestion from sequence-based analyses of a Pleistocene extinction of a substantial part of North Africa and a Pleistocene

  19. A Genetic Study of Wild Populations and Evolution A Genetic Study of Wild Populations and Evolution

    Directory of Open Access Journals (Sweden)

    Hovanitz William

    1944-06-01

    Full Text Available The determination of the scientific basis of heredity within the last two decades and the verification of the principal conclusions in many different plants and animals has made possible the application of analytical methods in the study of variations in wild populations. As with the physical and chemical sciences, genetics has been enabled to make use of mathematics to compound (often theoretically out of simple units, the genes, the complexity known as an organism, much in the same way as a chemist compounds molecules with atoms and the physicist compounds atoms with protons and electrons. The determination of the scientific basis of heredity within the last two decades and the verification of the principal conclusions in many different plants and animals has made possible the application of analytical methods in the study of variations in wild populations. As with the physical and chemical sciences, genetics has been enabled to make use of mathematics to compound (often theoretically out of simple units, the genes, the complexity known as an organism, much in the same way as a chemist compounds molecules with atoms and the physicist compounds atoms with protons and electrons.

  20. The geometry of population genetics

    CERN Document Server

    Akin, Ethan

    1979-01-01

    The differential equations which model the action of selection and recombination are nonlinear equations which are impossible to It is even difficult to describe in general the solve explicitly. Recently, Shahshahani began using qualitative behavior of solutions. differential geometry to study these equations [28]. with this mono­ graph I hope to show that his ideas illuminate many aspects of pop­ ulation genetics. Among these are his proof and clarification of Fisher's Fundamental Theorem of Natural Selection and Kimura's Maximum Principle and also the effect of recombination on entropy. We also discover the relationship between two classic measures of 2 genetic distance: the x measure and the arc-cosine measure. There are two large applications. The first is a precise definition of the biological concept of degree of epistasis which applies to general (i.e. frequency dependent) forms of selection. The second is the unexpected appearance of cycling. We show that cycles can occur in the two-locus-two-allele...

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

    Science.gov (United States)

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

    2014-10-01

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

  2. Population Genetic Aspects of Pollinator Decline

    Directory of Open Access Journals (Sweden)

    Laurence Packer

    2001-06-01

    Full Text Available We reviewed the theory of conservation genetics, with special emphasis on the influence of haplodiploidy and other aspects of bee biology upon conservation genetic parameters. We then investigated the possibility that pollinator decline can be addressed in this way, using two meta-analytical approaches on genetic data from the Hymenoptera and the Lepidoptera. First, we compared levels of heterozygosity between the orders. As has been found previously, the haplodiploid Hymenoptera had markedly lower levels of genetic variation than the Lepidoptera. Bees had even lower levels, and bumble bees, in particular, often seemed almost monomorphic genetically. However, the statistically confounding effects of phylogeny render detailed interpretation of such data difficult. Second, we investigated patterns of gene flow among populations of these insects. Hymenoptera were far more likely to show genetic effects of population fragmentation than are Lepidoptera, even at similar geographic distances between populations. The reduced effective population sizes resulting from haplodiploidy probably contributed to this result. The proportion of species with low levels of gene flow did not vary among the different taxonomic groups within the Hymenoptera.

  3. Genetic population structure of muskellunge in the Great Lakes

    Science.gov (United States)

    Kapuscinski, Kevin L.; Sloss, Brian L.; Farrell, John M.

    2013-01-01

    We quantified genetic relationships among Muskellunge Esox masquinongy from 15 locations in the Great Lakes to determine the extent and distribution of measurable population structure and to identify appropriate spatial scales for fishery management and genetic conservation. We hypothesized that Muskellunge from each area represented genetically distinct populations, which would be evident from analyses of genotype data. A total of 691 Muskellunge were sampled (n = 10–127/site) and genetic data were collected at 13 microsatellite loci. Results from a suite of analyses (including pairwise genetic differentiation, Bayesian admixture prediction, analysis of molecular variance, and tests of isolation by distance) indicated the presence of nine distinct genetic groups, including two that were approximately 50 km apart. Geographic proximity and low habitat complexity seemed to facilitate genetic similarity among areas, whereas Muskellunge from areas of greater habitat heterogeneity exhibited high differentiation. Muskellunge from most areas contained private alleles, and mean within-area genetic variation was similar to that reported for other freshwater fishes. Management programs aimed at conserving the broader diversity and long-term sustainability of Muskellunge could benefit by considering the genetically distinct groups as independent fisheries, and individual spawning and nursery habitats could subsequently be protected to conserve the evolutionary potential of Muskellunge.

  4. Migraine genetics : from monogenic to complex forms

    NARCIS (Netherlands)

    Vanmolkot, Kaate Raymond Josepha

    2008-01-01

    Migraine has a strong genetic component, but the identification of these factors has proven difficult mainly because of the complex interaction of multiple loci and environmental factors. Unraveling its molecular basis and deciphering pathways leading to migraine attacks will help identifying novel

  5. Philosophy of race meets population genetics.

    Science.gov (United States)

    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. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. Quantifying introgression risk with realistic population genetics

    OpenAIRE

    Ghosh, Atiyo; Meirmans, Patrick G.; Haccou, Patsy

    2012-01-01

    Introgression is the permanent incorporation of genes from the genome of one population into another. This can have severe consequences, such as extinction of endemic species, or the spread of transgenes. Quantification of the risk of introgression is an important component of genetically modified crop regulation. Most theoretical introgression studies aimed at such quantification disregard one or more of the most important factors concerning introgression: realistic genetical mechanisms, rep...

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

    DEFF Research Database (Denmark)

    Andersen, Mette Korre; Pedersen, Casper-Emil Tingskov; Moltke, Ida

    2016-01-01

    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 complex disease variants and describe their contributions to the understanding of the genetics of T2D. © 2016, Springer Science+Business Media New York....... 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...

  8. Genetic history of the African Sahelian populations.

    Science.gov (United States)

    Černý, V; Kulichová, I; Poloni, E S; Nunes, J M; Pereira, L; Mayor, A; Sanchez-Mazas, A

    2018-03-01

    From a biogeographic perspective, Africa is subdivided into distinct horizontal belts. Human populations living along the Sahel/Savannah belt south of the Sahara desert have often been overshadowed by extensive studies focusing on other African populations such as hunter-gatherers or Bantu in particular. However, the Sahel together with the Savannah bordering it in the south is a challenging region where people had and still have to cope with harsh climatic conditions and show resilient behaviours. Besides exponentially growing urban populations, several local groups leading various lifestyles and speaking languages belonging to three main linguistic families still live in rural localities across that region today. Thanks to several years of consistent population sampling throughout this area, the genetic history of the African Sahelian populations has been largely reconstructed and a deeper knowledge has been acquired regarding their adaptation to peculiar environments and/or subsistence modes. Distinct exposures to pathogens-in particular, malaria-likely contributed to their genetic differentiation for HLA genes. In addition, although food-producing strategies spread within the Sahel/Savannah belt relatively recently, during the last five millennia according to recent archaeological and archaeobotanical studies, remarkable amounts of genetic differences are also observed between sedentary farmers and more mobile pastoralists at multiple neutral and selected loci, reflecting both demographic effects and genetic adaptations to distinct cultural traits, such as dietary habits. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  9. Quantifying introgression risk with realistic population genetics

    NARCIS (Netherlands)

    Ghosh, A.; Meirmans, P.G.; Haccou, P.

    2012-01-01

    Introgression is the permanent incorporation of genes from the genome of one population into another. This can have severe consequences, such as extinction of endemic species, or the spread of transgenes. Quantification of the risk of introgression is an important component of genetically modified

  10. Great ape genetic diversity and population history

    DEFF Research Database (Denmark)

    Prado-Martinez, Javier; Sudmant, Peter H; Kidd, Jeffrey M

    2013-01-01

    Most great ape genetic variation remains uncharacterized; however, its study is critical for understanding population history, recombination, selection and susceptibility to disease. Here we sequence to high coverage a total of 79 wild- and captive-born individuals representing all six great ape...

  11. Loss of genetic diversity in Maculinea populations over 10 years

    DEFF Research Database (Denmark)

    Nash, David Richard; Lomborg, Andreas Eg

    I will present the results of research on the population genetics of Maculinea alcon and M. arion in Southern scandinavia, which shows a strong decrease in genetic diversity in most populations, even if those populations are apparently otherwise healthy....

  12. Complex and unexpected dynamics in simple genetic regulatory networks

    Science.gov (United States)

    Borg, Yanika; Ullner, Ekkehard; Alagha, Afnan; Alsaedi, Ahmed; Nesbeth, Darren; Zaikin, Alexey

    2014-03-01

    One aim of synthetic biology is to construct increasingly complex genetic networks from interconnected simpler ones to address challenges in medicine and biotechnology. However, as systems increase in size and complexity, emergent properties lead to unexpected and complex dynamics due to nonlinear and nonequilibrium properties from component interactions. We focus on four different studies of biological systems which exhibit complex and unexpected dynamics. Using simple synthetic genetic networks, small and large populations of phase-coupled quorum sensing repressilators, Goodwin oscillators, and bistable switches, we review how coupled and stochastic components can result in clustering, chaos, noise-induced coherence and speed-dependent decision making. A system of repressilators exhibits oscillations, limit cycles, steady states or chaos depending on the nature and strength of the coupling mechanism. In large repressilator networks, rich dynamics can also be exhibited, such as clustering and chaos. In populations of Goodwin oscillators, noise can induce coherent oscillations. In bistable systems, the speed with which incoming external signals reach steady state can bias the network towards particular attractors. These studies showcase the range of dynamical behavior that simple synthetic genetic networks can exhibit. In addition, they demonstrate the ability of mathematical modeling to analyze nonlinearity and inhomogeneity within these systems.

  13. PGG.Population: a database for understanding the genomic diversity and genetic ancestry of human populations.

    Science.gov (United States)

    Zhang, Chao; Gao, Yang; Liu, Jiaojiao; Xue, Zhe; Lu, Yan; Deng, Lian; Tian, Lei; Feng, Qidi; Xu, Shuhua

    2018-01-04

    There are a growing number of studies focusing on delineating genetic variations that are associated with complex human traits and diseases due to recent advances in next-generation sequencing technologies. However, identifying and prioritizing disease-associated causal variants relies on understanding the distribution of genetic variations within and among populations. The PGG.Population database documents 7122 genomes representing 356 global populations from 107 countries and provides essential information for researchers to understand human genomic diversity and genetic ancestry. These data and information can facilitate the design of research studies and the interpretation of results of both evolutionary and medical studies involving human populations. The database is carefully maintained and constantly updated when new data are available. We included miscellaneous functions and a user-friendly graphical interface for visualization of genomic diversity, population relationships (genetic affinity), ancestral makeup, footprints of natural selection, and population history etc. Moreover, PGG.Population provides a useful feature for users to analyze data and visualize results in a dynamic style via online illustration. The long-term ambition of the PGG.Population, together with the joint efforts from other researchers who contribute their data to our database, is to create a comprehensive depository of geographic and ethnic variation of human genome, as well as a platform bringing influence on future practitioners of medicine and clinical investigators. PGG.Population is available at https://www.pggpopulation.org. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. Genetic classification of populations using supervised learning.

    Directory of Open Access Journals (Sweden)

    Michael Bridges

    2011-05-01

    Full Text Available There are many instances in genetics in which we wish to determine whether two candidate populations are distinguishable on the basis of their genetic structure. Examples include populations which are geographically separated, case-control studies and quality control (when participants in a study have been genotyped at different laboratories. This latter application is of particular importance in the era of large scale genome wide association studies, when collections of individuals genotyped at different locations are being merged to provide increased power. The traditional method for detecting structure within a population is some form of exploratory technique such as principal components analysis. Such methods, which do not utilise our prior knowledge of the membership of the candidate populations. are termed unsupervised. Supervised methods, on the other hand are able to utilise this prior knowledge when it is available.In this paper we demonstrate that in such cases modern supervised approaches are a more appropriate tool for detecting genetic differences between populations. We apply two such methods, (neural networks and support vector machines to the classification of three populations (two from Scotland and one from Bulgaria. The sensitivity exhibited by both these methods is considerably higher than that attained by principal components analysis and in fact comfortably exceeds a recently conjectured theoretical limit on the sensitivity of unsupervised methods. In particular, our methods can distinguish between the two Scottish populations, where principal components analysis cannot. We suggest, on the basis of our results that a supervised learning approach should be the method of choice when classifying individuals into pre-defined populations, particularly in quality control for large scale genome wide association studies.

  15. Genetic classification of populations using supervised learning.

    LENUS (Irish Health Repository)

    Bridges, Michael

    2011-01-01

    There are many instances in genetics in which we wish to determine whether two candidate populations are distinguishable on the basis of their genetic structure. Examples include populations which are geographically separated, case-control studies and quality control (when participants in a study have been genotyped at different laboratories). This latter application is of particular importance in the era of large scale genome wide association studies, when collections of individuals genotyped at different locations are being merged to provide increased power. The traditional method for detecting structure within a population is some form of exploratory technique such as principal components analysis. Such methods, which do not utilise our prior knowledge of the membership of the candidate populations. are termed unsupervised. Supervised methods, on the other hand are able to utilise this prior knowledge when it is available.In this paper we demonstrate that in such cases modern supervised approaches are a more appropriate tool for detecting genetic differences between populations. We apply two such methods, (neural networks and support vector machines) to the classification of three populations (two from Scotland and one from Bulgaria). The sensitivity exhibited by both these methods is considerably higher than that attained by principal components analysis and in fact comfortably exceeds a recently conjectured theoretical limit on the sensitivity of unsupervised methods. In particular, our methods can distinguish between the two Scottish populations, where principal components analysis cannot. We suggest, on the basis of our results that a supervised learning approach should be the method of choice when classifying individuals into pre-defined populations, particularly in quality control for large scale genome wide association studies.

  16. Effects of complex life cycles on genetic diversity: cyclical parthenogenesis.

    Science.gov (United States)

    Rouger, R; Reichel, K; Malrieu, F; Masson, J P; Stoeckel, S

    2016-11-01

    Neutral patterns of population genetic diversity in species with complex life cycles are difficult to anticipate. Cyclical parthenogenesis (CP), in which organisms undergo several rounds of clonal reproduction followed by a sexual event, is one such life cycle. Many species, including crop pests (aphids), human parasites (trematodes) or models used in evolutionary science (Daphnia), are cyclical parthenogens. It is therefore crucial to understand the impact of such a life cycle on neutral genetic diversity. In this paper, we describe distributions of genetic diversity under conditions of CP with various clonal phase lengths. Using a Markov chain model of CP for a single locus and individual-based simulations for two loci, our analysis first demonstrates that strong departures from full sexuality are observed after only a few generations of clonality. The convergence towards predictions made under conditions of full clonality during the clonal phase depends on the balance between mutations and genetic drift. Second, the sexual event of CP usually resets the genetic diversity at a single locus towards predictions made under full sexuality. However, this single recombination event is insufficient to reshuffle gametic phases towards full-sexuality predictions. Finally, for similar levels of clonality, CP and acyclic partial clonality (wherein a fixed proportion of individuals are clonally produced within each generation) differentially affect the distribution of genetic diversity. Overall, this work provides solid predictions of neutral genetic diversity that may serve as a null model in detecting the action of common evolutionary or demographic processes in cyclical parthenogens (for example, selection or bottlenecks).

  17. Population genetics models of local ancestry.

    Science.gov (United States)

    Gravel, Simon

    2012-06-01

    Migrations have played an important role in shaping the genetic diversity of human populations. Understanding genomic data thus requires careful modeling of historical gene flow. Here we consider the effect of relatively recent population structure and gene flow and interpret genomes of individuals that have ancestry from multiple source populations as mosaics of segments originating from each population. This article describes general and tractable models for local ancestry patterns with a focus on the length distribution of continuous ancestry tracts and the variance in total ancestry proportions among individuals. The models offer improved agreement with Wright-Fisher simulation data when compared to the state-of-the art and can be used to infer time-dependent migration rates from multiple populations. Considering HapMap African-American (ASW) data, we find that a model with two distinct phases of "European" gene flow significantly improves the modeling of both tract lengths and ancestry variances.

  18. Extensive population genetic structure in the giraffe

    Directory of Open Access Journals (Sweden)

    Grether Gregory F

    2007-12-01

    Full Text Available Abstract Background A central question in the evolutionary diversification of large, widespread, mobile mammals is how substantial differentiation can arise, particularly in the absence of topographic or habitat barriers to dispersal. All extant giraffes (Giraffa camelopardalis are currently considered to represent a single species classified into multiple subspecies. However, geographic variation in traits such as pelage pattern is clearly evident across the range in sub-Saharan Africa and abrupt transition zones between different pelage types are typically not associated with extrinsic barriers to gene flow, suggesting reproductive isolation. Results By analyzing mitochondrial DNA sequences and nuclear microsatellite loci, we show that there are at least six genealogically distinct lineages of giraffe in Africa, with little evidence of interbreeding between them. Some of these lineages appear to be maintained in the absence of contemporary barriers to gene flow, possibly by differences in reproductive timing or pelage-based assortative mating, suggesting that populations usually recognized as subspecies have a long history of reproductive isolation. Further, five of the six putative lineages also contain genetically discrete populations, yielding at least 11 genetically distinct populations. Conclusion Such extreme genetic subdivision within a large vertebrate with high dispersal capabilities is unprecedented and exceeds that of any other large African mammal. Our results have significant implications for giraffe conservation, and imply separate in situ and ex situ management, not only of pelage morphs, but also of local populations.

  19. Population Genetics of Three Dimensional Range Expansions

    Science.gov (United States)

    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.

  20. Spatial and population genetic structure of microsatellites in white pine

    Science.gov (United States)

    Paula E. Marquardt; Bryan K. Epperson

    2004-01-01

    We evaluated the population genetic structure of seven microsatellite loci for old growth and second growth populations of eastern white pine (Pinus strobus). From each population, located within Hartwick Pines State Park, Grayling, Michigan, USA, 120-122 contiguous trees were sampled for genetic analysis. Within each population, genetic diversity...

  1. Population genetic analysis of ascertained SNP data

    Directory of Open Access Journals (Sweden)

    Nielsen Rasmus

    2004-03-01

    Full Text Available Abstract The large single nucleotide polymorphism (SNP typing projects have provided an invaluable data resource for human population geneticists. Almost all of the available SNP loci, however, have been identified through a SNP discovery protocol that will influence the allelic distributions in the sampled loci. Standard methods for population genetic analysis based on the available SNP data will, therefore, be biased. This paper discusses the effect of this ascertainment bias on allelic distributions and on methods for quantifying linkage disequilibrium and estimating demographic parameters. Several recently developed methods for correcting for the ascertainment bias will also be discussed.

  2. Estimating the contribution of genetic variants to difference in incidence of disease between population groups.

    Science.gov (United States)

    Moonesinghe, Ramal; Ioannidis, John P A; Flanders, W Dana; Yang, Quanhe; Truman, Benedict I; Khoury, Muin J

    2012-08-01

    Genome-wide association studies have identified multiple genetic susceptibility variants to several complex human diseases. However, risk-genotype frequency at loci showing robust associations might differ substantially among different populations. In this paper, we present methods to assess the contribution of genetic variants to the difference in the incidence of disease between different population groups for different scenarios. We derive expressions for the contribution of a single genetic variant, multiple genetic variants, and the contribution of the joint effect of a genetic variant and an environmental factor to the difference in the incidence of disease. The contribution of genetic variants to the difference in incidence increases with increasing difference in risk-genotype frequency, but declines with increasing difference in incidence between the two populations. The contribution of genetic variants also increases with increasing relative risk and the contribution of joint effect of genetic and environmental factors increases with increasing relative risk of the gene-environmental interaction. The contribution of genetic variants to the difference in incidence between two populations can be expressed as a function of the population attributable risks of the genetic variants in the two populations. The contribution of a group of genetic variants to the disparity in incidence of disease could change considerably by adding one more genetic variant to the group. Any estimate of genetic contribution to the disparity in incidence of disease between two populations at this stage seems to be an elusive goal.

  3. Estimating the contribution of genetic variants to difference in incidence of disease between population groups

    Science.gov (United States)

    Moonesinghe, Ramal; Ioannidis, John PA; Flanders, W Dana; Yang, Quanhe; Truman, Benedict I; Khoury, Muin J

    2012-01-01

    Genome-wide association studies have identified multiple genetic susceptibility variants to several complex human diseases. However, risk-genotype frequency at loci showing robust associations might differ substantially among different populations. In this paper, we present methods to assess the contribution of genetic variants to the difference in the incidence of disease between different population groups for different scenarios. We derive expressions for the contribution of a single genetic variant, multiple genetic variants, and the contribution of the joint effect of a genetic variant and an environmental factor to the difference in the incidence of disease. The contribution of genetic variants to the difference in incidence increases with increasing difference in risk-genotype frequency, but declines with increasing difference in incidence between the two populations. The contribution of genetic variants also increases with increasing relative risk and the contribution of joint effect of genetic and environmental factors increases with increasing relative risk of the gene–environmental interaction. The contribution of genetic variants to the difference in incidence between two populations can be expressed as a function of the population attributable risks of the genetic variants in the two populations. The contribution of a group of genetic variants to the disparity in incidence of disease could change considerably by adding one more genetic variant to the group. Any estimate of genetic contribution to the disparity in incidence of disease between two populations at this stage seems to be an elusive goal. PMID:22333905

  4. Reliability of genetic bottleneck tests for detecting recent population declines

    NARCIS (Netherlands)

    Peery, M. Zachariah; Kirby, Rebecca; Reid, Brendan N.; Stoelting, Ricka; Doucet-Beer, Elena; Robinson, Stacie; Vasquez-Carrillo, Catalina; Pauli, Jonathan N.; Palsboll, Per J.

    The identification of population bottlenecks is critical in conservation because populations that have experienced significant reductions in abundance are subject to a variety of genetic and demographic processes that can hasten extinction. Genetic bottleneck tests constitute an appealing and

  5. Parâmetros genéticos da resistência ao complexo da queima-das-folhas em populações de cenoura Genetic parameters of the resistance to the leaf blight disease complex in carrot populations

    Directory of Open Access Journals (Sweden)

    Giovani O Silva

    2009-09-01

    Full Text Available Os parâmetros genéticos vinculados ao complexo de patógenos causadores da queima-das-folhas de cenoura foram determinados utilizando famílias de meio-irmãos oriundas de populações do grupo varietal 'Brasília'. Ainda, verificou-se quais populações eram capazes de proporcionar maior ganho para este caráter. O experimento foi conduzido em Brasília entre novembro/06 e fevereiro/07. Foram avaliadas cinco populações em fase final de melhoramento (processamento 1 (P1, processamento 2 (P2, mesa 3 (M3, mesa 4 (M4 e mesa 5 (M5, utilizando delineamento em blocos ao acaso com duas repetições (parcelas de 2 m². A avaliação da severidade da queima-das-folhas foi feita aos 90 dias após semeio e os dados foram submetidos à análise de variância para estimar os parâmetros genéticos e o ganho direto esperado com a seleção. O caráter resistência à queima-das-folhas apresentou-se significativo em diferenciar as populações. A população P1 mostrou os maiores valores dos parâmetros genéticos e ganhos esperados com a seleção, ao passo que a população M3 mostrou-se a menos promissora na obtenção de ganhos para níveis mais elevados de resistência. Os valores da relação entre os coeficientes de variação genética e ambiental e de herdabilidade foram baixos. Estes dados podem ser explicados pela ausência de variabilidade genética nas populações, mas também podem indicar a necessidade de um maior refinamento nos processos de avaliação e de inoculação em condições de campo, de forma a garantir o estabelecimento de epidemias mais uniformes da queima-das-folhas nas parcelas experimentais.The genetic parameters associated with resistance to the carrot leaf blight disease complex were evaluated using half-sib families derived from the varietal group 'Brasília'. We also evaluated which populations would provide larger gains for this character. Field assay was carried out in Brasília during the summer season (from

  6. Population Genetic Structure of the People of Qatar

    Science.gov (United States)

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

    2010-01-01

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

  7. Restoration of coral populations in light of genetic diversity estimates

    Science.gov (United States)

    Shearer, T. L.; Porto, I.; Zubillaga, A. L.

    2009-09-01

    Due to the importance of preserving the genetic integrity of populations, strategies to restore damaged coral reefs should attempt to retain the allelic diversity of the disturbed population; however, genetic diversity estimates are not available for most coral populations. To provide a generalized estimate of genetic diversity (in terms of allelic richness) of scleractinian coral populations, the literature was surveyed for studies describing the genetic structure of coral populations using microsatellites. The mean number of alleles per locus across 72 surveyed scleractinian coral populations was 8.27 (±0.75 SE). In addition, population genetic datasets from four species ( Acropora palmata, Montastraea cavernosa, Montastraea faveolata and Pocillopora damicornis) were analyzed to assess the minimum number of donor colonies required to retain specific proportions of the genetic diversity of the population. Rarefaction analysis of the population genetic datasets indicated that using 10 donor colonies randomly sampled from the original population would retain >50% of the allelic diversity, while 35 colonies would retain >90% of the original diversity. In general, scleractinian coral populations are genetically diverse and restoration methods utilizing few clonal genotypes to re-populate a reef will diminish the genetic integrity of the population. Coral restoration strategies using 10-35 randomly selected local donor colonies will retain at least 50-90% of the genetic diversity of the original population.

  8. The Etruscans: a population-genetic study

    DEFF Research Database (Denmark)

    Vernesi, Cristiano; Caramelli, David; Dupanloup, Isabelle

    2004-01-01

    The origins of the Etruscans, a non-Indo-European population of preclassical Italy, are unclear. There is broad agreement that their culture developed locally, but the Etruscans' evolutionary and migrational relationships are largely unknown. In this study, we determined mitochondrial DNA sequences...... a culture but also a mitochondrial gene pool. Genetic distances and sequence comparisons show closer evolutionary relationships with the eastern Mediterranean shores for the Etruscans than for modern Italian populations. All mitochondrial lineages observed among the Etruscans appear typically European...... or West Asian, but only a few haplotypes were found to have an exact match in a modern mitochondrial database, raising new questions about the Etruscans' fate after their assimilation into the Roman state....

  9. Controlling complexity: the clinical relevance of mouse complex genetics

    Czech Academy of Sciences Publication Activity Database

    Forejt, Jiří

    2013-01-01

    Roč. 21, č. 11 (2013), s. 1191-1196 ISSN 1018-4813 Institutional support: RVO:68378050 Keywords : Mouse model * Forward genetics * Rewiev Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Genetics and heredity (medical genetics to be 3) Impact factor: 4.225, year: 2013

  10. Familial clustering and genetic risk for dementia in a genetically isolated Dutch population.

    NARCIS (Netherlands)

    K. Sleegers (Kristel); F. Forey; J. Theuns (Jessie); Y.S. Aulchenko (Yurii); S. Rademakers (Suzanne); M. Cruts (Marc); W.A. van Gool (Willem); P. Heutink (Peter); B.A. Oostra (Ben); J.C. van Swieten (John); C.M. van Duijn (Cornelia); C. van Broeckhoven (Christine)

    2004-01-01

    textabstractDespite advances in elucidating the genetic epidemiology of Alzheimer's disease and frontotemporal dementia, the aetiology for most patients with dementia remains unclear. We examined the genetic epidemiology of dementia in a recent genetically isolated Dutch population founded around

  11. Familial clustering and genetic risk for dementia in a genetically isolated Dutch population

    NARCIS (Netherlands)

    Sleegers, K.; Roks, G.; Theuns, J.; Aulchenko, Y. S.; Rademakers, R.; Cruts, M.; van Gool, W. A.; van Broeckhoven, C.; Heutink, P.; Oostra, B. A.; van Swieten, J. C.; van Duijn, C. M.

    2004-01-01

    Despite advances in elucidating the genetic epidemiology of Alzheimer's disease and frontotemporal dementia, the aetiology for most patients with dementia remains unclear. We examined the genetic epidemiology of dementia in a recent genetically isolated Dutch population founded around 1750. The

  12. Human population genetics and “ancestrality” business

    OpenAIRE

    André Langaney

    2009-01-01

    Following the foundation of theoretical population genetics by Wright, Fischer, Haldane and Malécot, in the first half of the 20th century, applied human population genetics developed with great success with the improvement and accumulation of new technologies to measure genetic polymorphism, first through protein polymorphisms since the 1960’s, then through DNA typing and sequencing since the 1980’s. The field of population genetics and biological anthropology was developed by a handful of d...

  13. Capacities for population-genetic variation and ecological adaptations

    Directory of Open Access Journals (Sweden)

    Marinković Dragoslav

    2007-01-01

    Full Text Available In contemporary science of population genetics it is equally complex and important to visualize how adaptive limits of individual variation are determined, as well as to describe the amount and sort of this variation. Almost all century the scientists devoted their efforts to explain the principles and structure of biological variation (genetic, developmental, environmental, interactive, etc., basing its maintenance within existing limits mostly on equilibria proclaimed by Hardy-Weinberg rules. Among numerous model-organisms that have been used to prove these rules and demonstrate new variants within mentioned concepts, Drosophila melanogaster is a kind of queen that is used in thousands of experiments for almost exactly 100 years (CARPENTER 1905, with which numerous discoveries and principles were determined that later turned out to be applicable to all other organisms. It is both, in nature and in laboratory, that Drosophilids were used to demonstrate the basic principles of population-genetic variation that was later applied to other species of animals. In ecological-genetic variation their richness in different environments could be used as an exact indicator of the status of a determined habitat, and its population-genetic structure may definitely point out to a possibility that specific resources of the environment start to be in danger to deteriorate, or to disappear in the near future. This paper shows clear-cut differences among environmental habitats, when populations of Drosophilidae are quantitatively observed in different wild, semi-domestic and domestic environments, demonstrating a highly expressed mutual dependence of these two parameters. A crucial approach is how to estimate the causes that determine the limits of biological, i.e. of individual and population-genetic variation. The realized, i.e. adaptive variation, is much lesser than a total possible variation of a polygenic trait, and in this study, using a moderately

  14. Population genetic structure of the people of Qatar.

    Science.gov (United States)

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

    2010-07-09

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

  15. Complexity in a population of Artemia

    Energy Technology Data Exchange (ETDEWEB)

    Ali, A.A., E-mail: abduladem1@yahoo.co [Electrical Engineering Department, University of Basrah (Iraq); Fortuna, L., E-mail: lfortuna@diees.unict.i [DIEEI, Faculty of Engineering, University of Catania (Italy); Frasca, M., E-mail: mfrasca@diees.unict.i [DIEEI, Faculty of Engineering, University of Catania (Italy); Rashid, M.T., E-mail: mofid76@yahoo.co [Electrical Engineering Department, University of Basrah (Iraq); Xibilia, M.G., E-mail: mxibilia@ingegneria.unime.i [DiSIA, Faculty of Engineering, University of Messina (Italy)

    2011-04-15

    Highlights: Experiments on collective motion of populations of animals (Artemia salina). Design of low-cost experimental setup for complex systems. Control of collective motion of populations of Artemia. Models of collective motion of populations of Artemia. - Abstract: Artemia salina belongs to a genus of very primordial crustaceans, whose behavior is not widely investigated in literature. Their collective behavior is studied in this paper both experimentally and theoretically. Different experiments have been designed to control the direction of motion of an Artemia population by exploiting their sensitivity to light and to measure the response of the population to light at different wavelengths. Mathematical models have been also derived, explaining the mechanisms underlying Artemia flocking formation when a light spot is applied to the system. The results obtained allow to develop new strategies for distributed control of agents and to test them in a simple and low cost experimental setup.

  16. Complexity in a population of Artemia

    International Nuclear Information System (INIS)

    Ali, A.A.; Fortuna, L.; Frasca, M.; Rashid, M.T.; Xibilia, M.G.

    2011-01-01

    Highlights: → Experiments on collective motion of populations of animals (Artemia salina). → Design of low-cost experimental setup for complex systems. → Control of collective motion of populations of Artemia. → Models of collective motion of populations of Artemia. - Abstract: Artemia salina belongs to a genus of very primordial crustaceans, whose behavior is not widely investigated in literature. Their collective behavior is studied in this paper both experimentally and theoretically. Different experiments have been designed to control the direction of motion of an Artemia population by exploiting their sensitivity to light and to measure the response of the population to light at different wavelengths. Mathematical models have been also derived, explaining the mechanisms underlying Artemia flocking formation when a light spot is applied to the system. The results obtained allow to develop new strategies for distributed control of agents and to test them in a simple and low cost experimental setup.

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

    Science.gov (United States)

    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. © 2011 The Authors. ICS © 2011 Society of Cosmetic Scientists and the Société Française de Cosmétologie.

  18. Endocrine autoimmune disease: genetics become complex.

    Science.gov (United States)

    Wiebolt, Janneke; Koeleman, Bobby P C; van Haeften, Timon W

    2010-12-01

    The endocrine system is a frequent target in pathogenic autoimmune responses. Type 1 diabetes and autoimmune thyroid disease are the prevailing examples. When several diseases cluster together in one individual, the phenomenon is called autoimmune polyglandular syndrome. Progress has been made in understanding the genetic factors involved in endocrine autoimmune diseases. Studies on monogenic autoimmune diseases such as autoimmune polyglandular syndrome type 1, immunodysregulation, polyendocrinopathy, enteropathy, X-linked and primary immune deficiencies helped uncover the role of key regulators in the preservation of immune tolerance. Alleles of the major histocompatibility complex have been known to contribute to the susceptibility to most forms of autoimmunity for more than 3 decades. Furthermore, sequencing studies revealed three non-major histocompatibility complex loci and some disease specific loci, which control T lymphocyte activation or signalling. Recent genome-wide association studies (GWAS) have enabled acceleration in the identification of novel (non-HLA) loci and hence other relevant immune response pathways. Interestingly, several loci are shared between autoimmune diseases, and surprisingly some work in opposite direction. This means that the same allele which predisposes to a certain autoimmune disease can be protective in another. Well powered GWAS in type 1 diabetes has led to the uncovering of a significant number of risk variants with modest effect. These studies showed that the innate immune system may also play a role in addition to the adaptive immune system. It is anticipated that next generation sequencing techniques will uncover other (rare) variants. For other autoimmune disease (such as autoimmune thyroid disease) GWAS are clearly needed. © 2010 The Authors. European Journal of Clinical Investigation © 2010 Stichting European Society for Clinical Investigation Journal Foundation.

  19. Population Genetics of Identifiler System in Malaysia.

    Science.gov (United States)

    Nakamura, Yasutaka; Samejima, Michinaga; Minaguchi, Kiyoshi; Nambiar, Phrabhakaran

    2016-01-01

    Short tandem repeat (STR) polymorphisms were investigated in 341 unrelated Malay individuals (218 males and 123 females) living in or around Kuala Lumpur by using a forensic analysts kit. The following STRs were targeted: D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, and FGA. The purpose of this study was to elucidate population genetics in Malaysia and calculate statistical parameters for forensic and anthropological research. Data on these STRs in the target population were obtained and subjected to statistical analysis. Accordance with the Hardy-Weinberg equilibrium was proven for all the loci targeted. The combined power of discrimination was greater than 0.9999999999, indicating that this multiplex system is an excellent tool for forensic casework. The allele frequency in the data were weighed against that in four other local populations (Chinese, Iranian, Belgian, and African). The average coefficient of correlation was strongest in the order of Africa (0.092522), Belgium (0.264822), Iran (0.404363), and China (0.706661). These results are consistent with what is known about the anthropological history of and prehistoric human migration in the Malay region. We believe that these data offer a valuable anthropological resource, being applicable to the statistical evaluation of DNA evidence in human identification, as well as the determination of ethnicity in healthy populations.

  20. Genetic variation and population structure of interleukin genes ...

    Indian Academy of Sciences (India)

    ... phylogenetic analysis based on genetic distances between populations agreed with known social and cultural data ... thus, impact on community genetics (Bittles 2001, 2002). ... reflect an interaction between evolutionary and demographic.

  1. Empirical complexities in the genetic foundations of lethal mutagenesis.

    Science.gov (United States)

    Bull, James J; Joyce, Paul; Gladstone, Eric; Molineux, Ian J

    2013-10-01

    From population genetics theory, elevating the mutation rate of a large population should progressively reduce average fitness. If the fitness decline is large enough, the population will go extinct in a process known as lethal mutagenesis. Lethal mutagenesis has been endorsed in the virology literature as a promising approach to viral treatment, and several in vitro studies have forced viral extinction with high doses of mutagenic drugs. Yet only one empirical study has tested the genetic models underlying lethal mutagenesis, and the theory failed on even a qualitative level. Here we provide a new level of analysis of lethal mutagenesis by developing and evaluating models specifically tailored to empirical systems that may be used to test the theory. We first quantify a bias in the estimation of a critical parameter and consider whether that bias underlies the previously observed lack of concordance between theory and experiment. We then consider a seemingly ideal protocol that avoids this bias-mutagenesis of virions-but find that it is hampered by other problems. Finally, results that reveal difficulties in the mere interpretation of mutations assayed from double-strand genomes are derived. Our analyses expose unanticipated complexities in testing the theory. Nevertheless, the previous failure of the theory to predict experimental outcomes appears to reside in evolutionary mechanisms neglected by the theory (e.g., beneficial mutations) rather than from a mismatch between the empirical setup and model assumptions. This interpretation raises the specter that naive attempts at lethal mutagenesis may augment adaptation rather than retard it.

  2. Population Genetic Structure and Gene Flow Among Nigerian Goats ...

    African Journals Online (AJOL)

    Population Genetic structure in 200 indigenous goats sampled across four states from the South-Western and South Southern region of Nigeria was assessed using 7 microsatellite DNA markers. Observed Analysis of molecular genetic variation (AMOVA) was higher within populations (3.47) than among populations (1.84) ...

  3. Adaptive major histocompatibility complex (MHC) and neutral genetic variation in two native Baltic Sea fishes (perch Perca fluviatilis and zander Sander lucioperca) with comparisons to an introduced and disease susceptible population in Australia (P. fluviatilis): assessing the risk of disease epidemics.

    Science.gov (United States)

    Faulks, L K; Östman, Ö

    2016-04-01

    This study assessed the major histocompatibility complex (MHC) and neutral genetic variation and structure in two percid species, perch Perca fluviatilis and zander Sander lucioperca, in a unique brackish ecosystem, the Baltic Sea. In addition, to assess the importance of MHC diversity to disease susceptibility in these populations, comparisons were made to an introduced, disease susceptible, P. fluviatilis population in Australia. Eighty-three MHC class II B exon 2 variants were amplified: 71 variants from 92 P. fluviatilis samples, and 12 variants from 82 S. lucioperca samples. Microsatellite and MHC data revealed strong spatial genetic structure in S. lucioperca, but not P. fluviatilis, across the Baltic Sea. Both microsatellite and MHC data showed higher levels of genetic diversity in P. fluviatilis from the Baltic Sea compared to Australia, which may have facilitated the spread of an endemic virus, EHNV in the Australian population. The relatively high levels of genetic variation in the Baltic Sea populations, together with spatial genetic structure, however, suggest that there currently seems to be little risk of disease epidemics in this system. To ensure this remains the case in the face of ongoing environmental changes, fisheries and habitat disturbance, the conservation of local-scale genetic variation is recommended. © 2016 The Fisheries Society of the British Isles.

  4. Population genetics of reef coral endosymbionts (Symbiodinium, Dinophyceae).

    Science.gov (United States)

    Thornhill, D J; Howells, E J; Wham, D C; Steury, T D; Santos, S R

    2017-05-01

    Symbiodinium is a diverse genus of unicellular dinoflagellate symbionts associating with various marine protists and invertebrates. Although the broadscale diversity and phylogenetics of the Symbiodinium complex is well established, there have been surprisingly few data on fine-scale population structure and biogeography of these dinoflagellates. Yet population-level processes contribute strongly to the biology of Symbiodinium, including how anthropogenic-driven global climate change impacts these symbionts and their host associations. Here, we present a synthesis of population-level characteristics for Symbiodinium, with an emphasis on how phylogenetic affinities, dynamics within and among host individuals, and a propensity towards clonality shape patterns on and across reefs. Major inferences include the following: (i) Symbiodinium populations within individual hosts are comprised mainly of cells belonging to a single or few genetic clones. (ii) Symbiont populations exhibit a mixed mode of reproduction, wherein at least one sexual recombination event occurs in the genealogy between most genotypes, but clonal propagation predominates overall. (iii) Mutualistic Symbiodinium do not perpetually persist outside their hosts, instead undergoing turnover and replacement via the continuous shedding of viable clonal cells from host individuals. (iv) Symbiont populations living in the same host, but on different reefs, are often genetically subdivided, suggesting low connectivity, adaptation to local conditions, or prolific asexual reproduction and low effective population sizes leading to disproportionate success within and among hosts. Overall, this synthesis forms a basis for future investigations of coral symbiosis ecology and evolution as well as delimitation of species boundaries in Symbiodinium and other eukaryotic microorganisms. © 2017 John Wiley & Sons Ltd.

  5. Comparison of association mapping methods in a complex pedigreed population

    DEFF Research Database (Denmark)

    Sahana, Goutam; Guldbrandtsen, Bernt; Janss, Luc

    2010-01-01

    to collect SNP signals in intervals, to avoid the scattering of a QTL signal over multiple neighboring SNPs. Methods not accounting for genetic background (full pedigree information) performed worse, and methods using haplotypes were considerably worse with a high false-positive rate, probably due...... to the presence of low-frequency haplotypes. It was necessary to account for full relationships among individuals to avoid excess false discovery. Although the methods were tested on a cattle pedigree, the results are applicable to any population with a complex pedigree structure...

  6. Genetic variability in the population of the endemic bee Anthophora ...

    African Journals Online (AJOL)

    The genetic diversity and spatial genetic population structure of the solitary bee Anthophora pauperata Walker 1871, a species endemic to St Katherine Protectorate, were studied by RAPD markers in seven wadis in the St Katherine Protectorate, South Sinai, Egypt. High levels of genetic diversity were found, mostly within ...

  7. Genetic determinants of circulating sphingolipid concentrations in European populations.

    Directory of Open Access Journals (Sweden)

    Andrew A Hicks

    2009-10-01

    Full Text Available 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 beta-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 9.08x10(-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

  8. Population Genetics and Natural Selection in Rheumatic Disease.

    Science.gov (United States)

    Ramos, Paula S

    2017-08-01

    Human genetic diversity is the result of population genetic forces. This genetic variation influences disease risk and contributes to health disparities. Natural selection is an important influence on human genetic variation. Because immune and inflammatory function genes are enriched for signals of positive selection, the prevalence of rheumatic disease-risk alleles seen in different populations is partially the result of differing selective pressures (eg, due to pathogens). This review summarizes the genetic regions associated with susceptibility to different rheumatic diseases and concomitant evidence for natural selection, including known agents of selection exerting selective pressure in these regions. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Population genetic structure of the sidespot barb, Barbus neefi, from ...

    African Journals Online (AJOL)

    Allozyme analysis was used to determine patterns of genetic variation within and between populations of Barbus neefi. The products of 29 loci were analysed, with 17 loci being monomorphic in all populations. The genetic variability estimates compared well with values reported in the literature. The percentage of ...

  10. Genetic structure of populations and differentiation in forest trees

    Science.gov (United States)

    Raymond P. Guries; F. Thomas Ledig

    1981-01-01

    Electrophoretic techniques permit population biologists to analyze genetic structure of natural populations by using large numbers of allozyme loci. Several methods of analysis have been applied to allozyme data, including chi-square contingency tests, F-statistics, and genetic distance. This paper compares such statistics for pitch pine (Pinus rigida...

  11. Mitochondrial DNA genetic variations among four horse populations in Egypt

    Directory of Open Access Journals (Sweden)

    Othman E. Othman

    2017-12-01

    It is concluded that sequence analysis of mtDNA control region is still the most informative tool for the identification of genetic biodiversity and phylogeny of different horse breeds and populations. The horse populations reared in Egypt possess low genetic diversity and all of them are belonged to Equus caballus breed.

  12. Genetic diversity analysis in the Hypericum perforatum populations ...

    African Journals Online (AJOL)

    Assessment of genetic variability among the Hypericum perforatum populations is critical to the development of effective conservation strategies in the Kashmir valley. To obtain accurate estimates of genetic diversity among and within populations of H. perforatum, inter-simple sequence repeats (ISSR) markers were used.

  13. Genetic diversity and population structure of sweet cassava using ...

    African Journals Online (AJOL)

    The objective of this study was to evaluate the population structure and genetic diversity among 66 sweet cassava (Manihot esculenta Crantz) traditional accessions collected in Maringa, Parana, Brazil, using microsatellite molecular markers. Population structure was analyzed by means of genetic distances and ...

  14. Genetic diversity and population structure of Chinese honeybees ...

    African Journals Online (AJOL)

    Genetic diversity and population structure of Chinese honeybees (Apis cerana) under microsatellite markers. T Ji, L Yin, G Chen. Abstract. Using 21 microsatellite markers and PCR method, the polymorphisms of 20 Apis cerana honeybee populations across China was investigated and the genetic structure and diversity of ...

  15. AMOVA-based clustering of population genetic data

    NARCIS (Netherlands)

    Meirmans, P.G.

    2012-01-01

    Determining the genetic structure of populations is becoming an increasingly important aspect of genetic studies. One of the most frequently used methods is the calculation of F-statistics using an Analysis of Molecular Variance (AMOVA). However, this has the drawback that the population hierarchy

  16. Identification of management units using population genetic data

    NARCIS (Netherlands)

    Palsboll, Per J.; Berube, Martine; Allendorf, Fred W.

    The identification of management units (MUs) is central to the management of natural populations and is crucial for monitoring the effects of human activity upon species abundance. Here, we propose that the identification of MUs from population genetic data should be based upon the amount of genetic

  17. Population genetic diversity and fitness in multiple environments

    Directory of Open Access Journals (Sweden)

    McGreevy Thomas J

    2010-07-01

    Full Text Available Abstract 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

  18. Landscape attributes and life history variability shape genetic structure of trout populations in a stream network

    Science.gov (United States)

    Neville, H.M.; Dunham, J.B.; Peacock, M.M.

    2006-01-01

    Spatial and temporal landscape patterns have long been recognized to influence biological processes, but these processes often operate at scales that are difficult to study by conventional means. Inferences from genetic markers can overcome some of these limitations. We used a landscape genetics approach to test hypotheses concerning landscape processes influencing the demography of Lahontan cutthroat trout in a complex stream network in the Great Basin desert of the western US. Predictions were tested with population- and individual-based analyses of microsatellite DNA variation, reflecting patterns of dispersal, population stability, and local effective population sizes. Complementary genetic inferences suggested samples from migratory corridors housed a mixture of fish from tributaries, as predicted based on assumed migratory life histories in those habitats. Also as predicted, populations presumed to have greater proportions of migratory fish or from physically connected, large, or high quality habitats had higher genetic variability and reduced genetic differentiation from other populations. Populations thought to contain largely non-migratory individuals generally showed the opposite pattern, suggesting behavioral isolation. Estimated effective sizes were small, and we identified significant and severe genetic bottlenecks in several populations that were isolated, recently founded, or that inhabit streams that desiccate frequently. Overall, this work suggested that Lahontan cutthroat trout populations in stream networks are affected by a combination of landscape and metapopulation processes. Results also demonstrated that genetic patterns can reveal unexpected processes, even within a system that is well studied from a conventional ecological perspective. ?? Springer 2006.

  19. How Ebola impacts genetics of Western lowland gorilla populations.

    Science.gov (United States)

    Le Gouar, Pascaline J; Vallet, Dominique; David, Laetitia; Bermejo, Magdalena; Gatti, Sylvain; Levréro, Florence; Petit, Eric J; Ménard, Nelly

    2009-12-18

    Emerging infectious diseases in wildlife are major threats for both human health and biodiversity conservation. Infectious diseases can have serious consequences for the genetic diversity of populations, which could enhance the species' extinction probability. The Ebola epizootic in western and central Africa induced more than 90% mortality in Western lowland gorilla population. Although mortality rates are very high, the impacts of Ebola on genetic diversity of Western lowland gorilla have never been assessed. We carried out long term studies of three populations of Western lowland gorilla in the Republic of the Congo (Odzala-Kokoua National Park, Lossi gorilla sanctuary both affected by Ebola and Lossi's periphery not affected). Using 17 microsatellite loci, we compared genetic diversity and structure of the populations and estimate their effective size before and after Ebola outbreaks. Despite the effective size decline in both populations, we did not detect loss in genetic diversity after the epizootic. We revealed temporal changes in allele frequencies in the smallest population. Immigration and short time elapsed since outbreaks could explain the conservation of genetic diversity after the demographic crash. Temporal changes in allele frequencies could not be explained by genetic drift or random sampling. Immigration from genetically differentiated populations and a non random mortality induced by Ebola, i.e., selective pressure and cost of sociality, are alternative hypotheses. Understanding the influence of Ebola on gorilla genetic dynamics is of paramount importance for human health, primate evolution and conservation biology.

  20. How Ebola impacts genetics of Western lowland gorilla populations.

    Directory of Open Access Journals (Sweden)

    Pascaline J Le Gouar

    2009-12-01

    Full Text Available Emerging infectious diseases in wildlife are major threats for both human health and biodiversity conservation. Infectious diseases can have serious consequences for the genetic diversity of populations, which could enhance the species' extinction probability. The Ebola epizootic in western and central Africa induced more than 90% mortality in Western lowland gorilla population. Although mortality rates are very high, the impacts of Ebola on genetic diversity of Western lowland gorilla have never been assessed.We carried out long term studies of three populations of Western lowland gorilla in the Republic of the Congo (Odzala-Kokoua National Park, Lossi gorilla sanctuary both affected by Ebola and Lossi's periphery not affected. Using 17 microsatellite loci, we compared genetic diversity and structure of the populations and estimate their effective size before and after Ebola outbreaks. Despite the effective size decline in both populations, we did not detect loss in genetic diversity after the epizootic. We revealed temporal changes in allele frequencies in the smallest population.Immigration and short time elapsed since outbreaks could explain the conservation of genetic diversity after the demographic crash. Temporal changes in allele frequencies could not be explained by genetic drift or random sampling. Immigration from genetically differentiated populations and a non random mortality induced by Ebola, i.e., selective pressure and cost of sociality, are alternative hypotheses. Understanding the influence of Ebola on gorilla genetic dynamics is of paramount importance for human health, primate evolution and conservation biology.

  1. Genetic complexity underlying hybrid male sterility in Drosophila.

    OpenAIRE

    Sawamura, Kyoichi; Roote, John; Wu, Chung-I; Yamamoto, Masa-Toshi

    2004-01-01

    Recent genetic analyses of closely related species of Drosophila have indicated that hybrid male sterility is the consequence of highly complex synergistic effects among multiple genes, both conspecific and heterospecific. On the contrary, much evidence suggests the presence of major genes causing hybrid female sterility and inviability in the less-related species, D. melanogaster and D. simulans. Does this contrast reflect the genetic distance between species? Or, generally, is the genetic b...

  2. Genetics Home Reference: mitochondrial complex III deficiency

    Science.gov (United States)

    ... the energy from food into a form that cells can use. Complex III is one of several complexes that ... in mtDNA. Because egg cells, but not sperm cells, contribute mitochondria to the ... from their mother. These disorders can appear in every generation of ...

  3. Worms under stress: unravelling genetic complex traits through perturbation

    NARCIS (Netherlands)

    Rodriguez Sanchez, M.

    2014-01-01

    The genetic architecture of an organism could be considered ‘the most amazing piece of engineering’ existing in nature. Looking from a certain distance, the genetic complexity of an organism could be described as an immense jigsaw puzzle. As in a real jigsaw, the connection between two pieces

  4. Detailed genetic structure of European bitterling populations in Central Europe

    Directory of Open Access Journals (Sweden)

    Veronika Bartáková

    2015-11-01

    Full Text Available The European bitterling (Rhodeus amarus is a small cyprinid fish whose populations declined markedly between 1950 and 1980. However, its range currently expands, partly due to human-assisted introductions. We determined the genetic variability and detailed spatial structure among bitterling populations in Central Europe and tested alternative hypotheses about colonization of this area. Twelve polymorphic microsatellite loci on a large sample of 688 individuals had been used to analyse genetic variability and population structure. Samples originated from 27 localities with emphasis on area of the Czech Republic where three major sea drainages (Black, Baltic, and Northern Sea meet. Highly variable level of intrapopulation genetic variability had generally been detected and a recent decrease in numbers (“bottleneck” had been indicated by genetic data among six populations. High level of interpopulation differentiation was identified even within the basins. There was a significant role of genetic drift and indications of low dispersal ability of R. amarus. Surprisingly, the Odra River was inhabited by two distinct populations without any genetic signatures of a secondary contact. Czech part of the Odra (Baltic basin was colonized from the Danubian refugium (similarly to adjacent Danubian basin rivers including the Morava, while Polish part of the Odra was genetically similar to the populations in the Vistula River (Baltic basin, that has been colonized by a different (Eastern phylogeographic lineage of R. amarus. Most Czech R. amarus populations were colonized from the Danubian refugium, suggesting potential for a human-mediated colonization of the Odra or Elbe Rivers by R. amarus. One Elbe basin population was genetically mixed from the two (Danubian and Eastern phylogeographic lineages. In general the Czech populations of R. amarus were genetically stable except for a single population which has probably been recently introduced. This research

  5. A rangewide population genetic study of trumpeter swans

    Science.gov (United States)

    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.

  6. Role of population genetics in the sterile insect technique

    International Nuclear Information System (INIS)

    Krafsur, E.S.

    2005-01-01

    The detection and analysis of genetic variation in natural and laboratory populations are reviewed. The application of population genetic methods and theory can help to plan and evaluate the implementation of area-wide integrated pest management (AW-IPM) programmes that use the sterile insect technique (SIT). Population genetic studies can play an important role in estimating dispersal rates and thus gene flow among target populations, determining if sibling species exist, establishing the origin of outbreaks or reintroductions, and supporting the quality control of mass-reared colonies. The target's population history may be examined, in terms of 'bottlenecks', range fragmentations, and expansions. Genetic methods can be helpful in distinguishing wild insects from released sterile or substerile ones, and in ascertaining, together with mating cross-compatibility studies, the compatibility of mass-reared colonies with target wild insects. (author)

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

    Directory of Open Access Journals (Sweden)

    Jian-Wei Zong

    Full Text Available 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

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

    Science.gov (United States)

    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

  9. Population genetic structure analysis in endangered Hordeum ...

    African Journals Online (AJOL)

    Administrator

    2011-09-07

    Sep 7, 2011 ... populations are grown by few local farmers in low-input farming systems. Based on 117 random ... Triticeae of the Poaceae (Graminae) family found throughout the ... populations and phylogeography is made easy by the.

  10. Population genetic structure in wild and aquaculture populations of Hemibarbus maculates inferred from microsatellites markers

    Directory of Open Access Journals (Sweden)

    Linlin Li

    2017-03-01

    Full Text Available The objective of this study was to investigate 4 aquaculture populations Shanghai (SH, Hangzhou (HZ, Kaihua (KH and Xianju (XJ and one wild population Yingshan (YS of spotted barbell (Hemibarbus maculates to assess their genetic diversity level and investigate the genetic structure of the populations. The dendrogram and STRUCTURE revealed that the populations XJ, KH, and HZ jointly formed one cluster, to which the populations SH and YS were sequentially adhered. The genetic diversity of the cultured populations maintained better, possible due to favourable hatchery conditions that decreased the effect of environmental selection present in wild populations. The results of the present study will contribute to the management of spotted barbell genetic resources, but also demonstrates how the genetic diversity of freshwater species is vulnerable to human activity.

  11. Predictors for reproductive isolation in a ring species complex following genetic and ecological divergence.

    Science.gov (United States)

    Pereira, Ricardo J; Monahan, William B; Wake, David B

    2011-07-06

    Reproductive isolation (RI) is widely accepted as an important "check point" in the diversification process, since it defines irreversible evolutionary trajectories. Much less consensus exists about the processes that might drive RI. Here, we employ a formal quantitative analysis of genetic interactions at several stages of divergence within the ring species complex Ensatina eschscholtzii in order to assess the relative contribution of genetic and ecological divergence for the development of RI. By augmenting previous genetic datasets and adding new ecological data, we quantify levels of genetic and ecological divergence between populations and test how they correlate with a restriction of genetic admixture upon secondary contact. Our results indicate that the isolated effect of ecological divergence between parental populations does not result in reproductively isolated taxa, even when genetic transitions between parental taxa are narrow. Instead, processes associated with overall genetic divergence are the best predictors of reproductive isolation, and when parental taxa diverge in nuclear markers we observe a complete cessation of hybridization, even to sympatric occurrence of distinct evolutionary lineages. Although every parental population has diverged in mitochondrial DNA, its degree of divergence does not predict the extent of RI. These results show that in Ensatina, the evolutionary outcomes of ecological divergence differ from those of genetic divergence. While evident properties of taxa may emerge via ecological divergence, such as adaptation to local environment, RI is likely to be a byproduct of processes that contribute to overall genetic divergence, such as time in geographic isolation, rather than being a direct outcome of local adaptation.

  12. Genetic population structure of the vulnerable bog fritillary butterfly.

    Science.gov (United States)

    Vandewoestijne, S; Baguette, M

    2004-01-01

    Populations of the bog fritillary butterfly Proclossiana eunomia (Lepidoptera, Nymphalidae) occur in patchy habitat in central and western Europe. P. eunomia is a vulnerable species in the Belgian Ardennes and the number of occupied sites has significantly decreased in this region since the 1960s. RAPD (random amplified polymorphic DNA) markers were used to study the consequences of habitat loss and fragmentation on the genetic population structure of this species. Gene diversity was lower in populations with smaller population sizes. Genetic subdivision was high (Fst=0.0887) considering the small spatial scale of this study (150 km2). The most geographically isolated population was also the most genetically differentiated one. The genetic population structure and genetic differentiation detected in this study were explained by (1) differences in altitude of the sampled locations and, (2) lower dispersal propensity and dispersal rate in fragmented landscapes versus continuous landscapes. Results from the RAPD analyses were compared with a previous allozyme based study on the same populations. The results of this study suggest that increased fragmentation has lead to a greater genetic differentiation between remaining P. eunomia populations.

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

    Science.gov (United States)

    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.

  14. Genetic Investigations Using Immuno-biochemical Markers in a Maramureş Brown Cattle Population

    Directory of Open Access Journals (Sweden)

    Nicoleta Isfan

    2011-05-01

    Full Text Available The study of the genetic markers and identifying new markers involves an increasing number of research projects in the fields of genetics of immunology, biochemical genetics, molecular genetics, quantity genetics and the genetic improvement of animals. Some studies on genes frequency determining the red cells specificity and for whey hemoglobin are approached in the present report. In this way, some blood factors, most of them belonging to B system (the most complex system in cattle have been evidenced. The lowest gene frequency was present in K factor (7%, and highest one in, O1, G’ , W and F1 (100%. In addition to basic importance on knowledge and determination of cattle population genetic structure for studied protein loci, another theme proposed to correlate hemoglobin type with some traits of economical importance: milk yield, fat and protein content, fat and protein yield. Higher performance was recorded by HbA/HbA individuals.

  15. Population structure and genetic diversity of Sudanese native chickens

    African Journals Online (AJOL)

    The objectives of this study were to analyze genetic diversity and population structure of Sudanese native chicken breeds involved in a conservation program. Five Sudanese native chicken breeds were compared with populations studied previously, which included six purebred lines, six African populations and one ...

  16. Assessment of genetic variation among four populations of Small ...

    African Journals Online (AJOL)

    From the findings, it can be concluded that the SEA goats in this study showed high in population genetic variation, which implies that there is good scope for their further improvement through selection within populations. The Sukuma population, which has fairly high inbreeding, is moderately differentiated from Pare, Sonjo ...

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

    Science.gov (United States)

    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…

  18. Molecular genetic diversity and genetic structure of Vietnamese indigenous pig populations

    DEFF Research Database (Denmark)

    Pham, L. D.; Do, Duy Ngoc; Nam, L. Q.

    2014-01-01

    The study characterized genetic diversity and genetic structure of five indigenous pig populations (Ha Lang, Muong Te, Mong Cai, Lung and Lung Pu), two wild pig populations (Vietnamese and Thai wild pigs) and an exotic pig breed (Yorkshire) using FAO/ISAG recommended 16 microsatellite markers...

  19. Genetic parameters in a Swine Population

    Directory of Open Access Journals (Sweden)

    Dana Popa

    2010-05-01

    Full Text Available The estimation of the variance-covariance components is a very important step in animal breeding because these components are necessary for: estimation of the genetic parameters, prediction of the breeding value and design of animal breeding programs. The estimation of genetic parameters is the first step in the development of a swine breeding program, using artificial insemination. Various procedures exist for estimation of heritability. There are three major procedures used for estimating heritability: analysis of variance (ANOVA, parents-offspring regression and restricted maximum likelihood (REML. By using ANOVA methodology or regression method it is possible to obtain aberrant values of genetic parameters (negative or over unit value of heritability coefficient, for example which can not be interpreting because is out of biological limits.

  20. Genetic diversity of six populations of red hybrid tilapia, using microsatellites genetic markers

    Directory of Open Access Journals (Sweden)

    Boris Briñez R.

    2011-05-01

    Full Text Available Objective. To determine and evaluate the genetic diversity of six populations of red hybrid tilapia, with the purpose to assess the potential benefit of a future breeding program conducted at the Research Center for Aquaculture (Ceniacua, Colombia. Material and methods. A total of 300 individuals, representing a wide genetic variability, were genotyped using a fluorescent microsatellite marker set of 5 gene-based SSRs in 6 different farms belonging to 4 States of Colombia. Results. The result showed that the mean number of alleles per locus per population was 8.367. The population 5 had the highest mean number of alleles with 9.6 alleles, followed by population 4 with 9.4 alleles, population 2 with 9.2, population 3 with 8.0, population 1 with 7.2 and population 6 with 6.8 alleles. The analysis of the distribution of genetic variation was (17.32% among population, while among individuals within populations was (28.55% and within individuals was high (54.12%. The standard diversity indices showed that population 4 was the more variable (mean He=0.837 followed by population 1 (mean He=0.728, population 3 (mean He=0.721, population 5 (mean He=0.705, population 2 (mean He=0.690, population 6 (mean He=0.586. Highly significant deviations from Hardy–Weinberg, exhibited all of the populations, mostly due to deficits of heterozygotes. Genotype frequencies at loci UNH 106 of population 5 and loci UNH 172 of population 6 were Hardy-Weinberg equilibrium (HWE. Conclusions. The results of this study, contribute to the genetic breeding program of Tilapia, conduced by the Research Center for Aquaculture. The Fst distance showed that the samples are differentiated genetically and it is possible to use at the beginning of the genetic program. However, it is recommended to introduce others individuals to the crossbreeding program.

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

    Science.gov (United States)

    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. © 2015 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.

  2. Genetics Home Reference: mitochondrial complex I deficiency

    Science.gov (United States)

    ... the energy from food into a form that cells can use. Complex I is the first of five mitochondrial ... maternal inheritance. Because egg cells, but not sperm cells, contribute ... only from their mother. These disorders can appear in every generation of ...

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

    Science.gov (United States)

    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.

  4. Genetic diversity in wild populations of Paulownia fortune.

    Science.gov (United States)

    Li, H Y; Ru, G X; Zhang, J; Lu, Y Y

    2014-11-01

    The genetic diversities of 16 Paulownia fortunei populations involving 143 individuals collected from 6 provinces in China were analyzed using amplified fragment length polymorphism (AFLP). A total of 9 primer pairs with 1169 polymorphic loci were screened out, and each pair possessed 132 bands on average. The percentage of polymorphic bands (98.57%), the effective number of alleles (1.2138-1.2726), Nei's genetic diversity (0.1566-0.1887), and Shannon's information index (0.2692-0.3117) indicated a plentiful genetic diversity and different among Paulownia fortunei populations. The genetic differentiation coefficient between populations was 0.2386, while the gene flow was 1.0954, and the low gene exchange promoted genetic differentiation. Analysis of variance indicated that genetic variation mainly occurred within populations (81.62% of total variation) rather than among populations (18.38%). The 16 populations were divided by unweighted pair-group method with arithmetic means (UPGMA) into 4 groups with obvious regionalism, in which the populations with close geographical locations (latitude) were clustered together.

  5. Population genetic characteristics of horse chestnut in Serbia

    Directory of Open Access Journals (Sweden)

    Ocokoljić Mirjana

    2013-01-01

    Full Text Available The general population genetic characteristics of cultivated horse chestnut trees excelling in growth, phenotype characteristics, type of inflorescence, productivity and resistance to the leafminer Cameraria ohridella Deschka and Dimić were analyzed in Serbia. The analyzed population genetic parameters point to fundamental differences in the genetic structure among the cultivated populations in Serbia. The study shows the variability in all properties among the populations and inter-individual variability within the populations. The variability and differential characteristics were assessed using statistical parameters, taking into account the satisfactory reflection of the hereditary potential. The assessed differences in the vitality and evolution potential of different populations can determine the methods of horse chestnut gene pool collection, reconstruction and improvement. [Projekat Ministarstva nauke Republike Srbije, br. 31041: Establishment of Wood Plantations Intended for a forestation of Serbia

  6. Molecular species identification and population genetics of ...

    African Journals Online (AJOL)

    Molecular genetic techniques, such as DNA barcoding and genotyping, are increasingly being used to assist with the conservation and management of chondrichthyans worldwide. Southern Africa is a shark biodiversity hotspot, with a large number of endemic species. According to the IUCN Red List, a quarter of South ...

  7. Genetic disorders from an endogamous population

    African Journals Online (AJOL)

    Background: Marriage between close relatives has been practised globally since the early existence of human society. The role of consanguinity and inbreeding affecting human health is a topic of great interest in medical genetics. Objective: The objective of the study was to investigate the extent of consanguinity and its ...

  8. Genetic diversity in coastal and inland desert populations of ...

    African Journals Online (AJOL)

    ajl yemi

    2011-11-14

    Nov 14, 2011 ... 0.00196 showed low degree of differentiation among populations. .... number of amplification products per primer varied from 6 to 14, and these ..... strategies on genetic diversity estimates obtained with RAPD markers in ...

  9. Review: Genetic diversity and population structure of cotton ...

    African Journals Online (AJOL)

    Cotton (Gossypium spp.) is the world's leading natural fiber crop and is cultivated in diverse temperate and tropical areas. In this sense, molecular markers are important tools for polymorphism identification in genetic diversity analyses. The objective of this study was to evaluate genetic diversity and population structure in ...

  10. Analysis of genetic structure in Melia volkensii (Gurke.) populations ...

    African Journals Online (AJOL)

    Administrator

    2Farm Forestry Programme, Kenya Forestry Research Institute, P. O. Box 20412, Nairobi, Kenya. Accepted 5 ... were used to estimate genetic distances between populations and for construction of neighbour-joining phenograms. Analysis of Molecular Variance (AMOVA) indicated significant genetic differentiation between ...

  11. Genetic diversity, population structure and marker trait associations ...

    Indian Academy of Sciences (India)

    Supplementary data: Genetic diversity, population structure and marker trait associations for seed quality traits in cotton (Gossypium hirsutum). Ashok Badigannavar and Gerald O. Myers. J. Genet. 94, 87–94. Table 1. List of cotton germplasm lines used in this study. Germplasm no. Cultivar. Region. Germplasm no. Cultivar.

  12. Genetic diversity and population structure of maize landraces from ...

    African Journals Online (AJOL)

    Genetic diversity and population structure of maize landraces from Côte ... However, no study on the genetic diversity of the species has been performed to date. ... The cross between two individuals from different groups might help exploit the ...

  13. Low genetic diversity of Phytophthora infestans population in potato ...

    African Journals Online (AJOL)

    AJL

    genetic diversity of P. infestans and geographical origin. These results provided a foundation for making integrated control measures in the future. Key words: Phytophthora infestans, population genetics, simple-sequence repeat (SSR), potato late blight. INTRODUCTION. Phytophthora infestans (Mont.) de Bary, causing the ...

  14. Population structure and genetic diversity of native and invasive populations of Solanum rostratum (Solanaceae.

    Directory of Open Access Journals (Sweden)

    Jiali Zhao

    Full Text Available 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.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.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 (F IS or population differentiation (F ST. 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.

  15. MONITORING OF GENETIC DIVERSITY IN FARMED DEER POPULATIONS USING MICROSATELLITE MARKERS

    Directory of Open Access Journals (Sweden)

    Pavol Bajzík

    2011-12-01

    Full Text Available Deer (Cervidaei belong to the most important species used as farmed animals. We focused on assesing the genetic diversity among five deer populations. Analysis has been performed on a total of 183 animals originating from Czech Republic, Hungary, New Zealand, Poland and Slovak Republic. Genetic variability were investigated using 8 microsatellite markers used in deer. Statistical data of all populations we obtained on the basis of Nei statistics, using by POWERMARKER 3.23 programme. Graphical view of relationships among populations and individuals in the populations was obtained using the Dendroscope software. Molecular genetic data combinated with evaluation in statistical programmes could lead to a complex view of populations and diffrences among them.doi:10.5219/172

  16. Genetic assessment of captive red panda (Ailurus fulgens) population.

    Science.gov (United States)

    Kumar, Arun; Rai, Upashna; Roka, Bhupen; Jha, Alankar K; Reddy, P Anuradha

    2016-01-01

    Red panda (Ailurus fulgens) is threatened across its range by detrimental human activities and rapid habitat changes necessitating captive breeding programs in various zoos globally to save this flagship species from extinction. One of the ultimate aims of ex situ conservation is reintroduction of endangered animals into their natural habitats while maintaining 90 % of the founder genetic diversity. Advances in molecular genetics and microsatellite genotyping techniques make it possible to accurately estimate genetic diversity of captive animals of unknown ancestry. Here we assess genetic diversity of the red panda population in Padmaja Naidu Himalayan Zoological Park, Darjeeling, which plays a pivotal role in ex situ conservation of red panda in India. We generated microsatellite genotypes of fifteen red pandas with a set of fourteen loci. This population is genetically diverse with 68 % observed heterozygosity (H O ) and mean inbreeding (F IS ) coefficient of 0.05. However population viability analysis reveals that this population has a very low survival probability (<2 %) and will rapidly loose its genetic diversity to 37 % mainly due to small population size and skewed male-biased sex ratio. Regular supplementation with a pair of adult individuals every five years will increase survival probability and genetic diversity to 99 and 61 % respectively and will also support future harvesting of individuals for reintroduction into the wild and exchange with other zoos.

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

    Science.gov (United States)

    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. Copyright © 2016 by

  18. Population genetic differentiation of height and body mass index across Europe

    DEFF Research Database (Denmark)

    Robinson, Matthew R.; Hemani, Gibran; Medina-Gomez, Carolina

    2015-01-01

    Across-nation differences in the mean values for complex traits are common(1-8), but the reasons for these differences are unknown. Here we find that many independent loci contribute to population genetic differences in height and body mass index (BMI) in 9,416 individuals across 14 European...... countries. Using discovery data on over 250,000 individuals and unbiased effect size estimates from 17,500 sibling pairs, we estimate that 24% (95% credible interval (CI) = 9%, 41%) and 8% (95% CI = 4%, 16%) of the captured additive genetic variance for height and BMI, respectively, reflect population...... genetic differences. Population genetic divergence differed significantly from that in a null model (height, P

  19. Inferring genetic connectivity in real populations, exemplified by coastal and oceanic Atlantic cod.

    Science.gov (United States)

    Spies, Ingrid; Hauser, Lorenz; Jorde, Per Erik; Knutsen, Halvor; Punt, André E; Rogers, Lauren A; Stenseth, Nils Chr

    2018-04-19

    Genetic data are commonly used to estimate connectivity between putative populations, but translating them to demographic dispersal rates is complicated. Theoretical equations that infer a migration rate based on the genetic estimator F ST , such as Wright's equation, F ST ≈ 1/(4 N e m + 1), make assumptions that do not apply to most real populations. How complexities inherent to real populations affect migration was exemplified by Atlantic cod in the North Sea and Skagerrak and was examined within an age-structured model that incorporated genetic markers. Migration was determined under various scenarios by varying the number of simulated migrants until the mean simulated level of genetic differentiation matched a fixed level of genetic differentiation equal to empirical estimates. Parameters that decreased the N e / N t ratio (where N e is the effective and N t is the total population size), such as high fishing mortality and high fishing gear selectivity, increased the number of migrants required to achieve empirical levels of genetic differentiation. Higher maturity-at-age and lower selectivity increased N e / N t and decreased migration when genetic differentiation was fixed. Changes in natural mortality, fishing gear selectivity, and maturity-at-age within expected limits had a moderate effect on migration when genetic differentiation was held constant. Changes in population size had the greatest effect on the number of migrants to achieve fixed levels of F ST , particularly when genetic differentiation was low, F ST ≈ 10 -3 Highly variable migration patterns, compared with constant migration, resulted in higher variance in genetic differentiation and higher extreme values. Results are compared with and provide insight into the use of theoretical equations to estimate migration among real populations. Copyright © 2018 the Author(s). Published by PNAS.

  20. Toward a Better Understanding of Population Genetics: Pop!World--A Virtual, Inquiry-Based Tool for Teaching Population Genetics

    Science.gov (United States)

    Poulin, Jessica; Ramamurthy, Bina; Dittmar, Katharina

    2013-01-01

    Population genetics is fundamental to understanding evolutionary theory, and is taught in most introductory biology/evolution courses. Many students are unaware that understanding this topic requires pertinent knowledge

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

    Science.gov (United States)

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

    2012-09-01

    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.

  2. Population-genetic analysis of seven qualitative traits in the population of the municipality Maglaj (Bosnia and Herzegovina

    Directory of Open Access Journals (Sweden)

    Mrehić Elma

    2015-01-01

    Full Text Available On the basis of the complex seven monogenic qualitative characteristics (shape of the earlobes, hairiness of middle phalange, flexibility of lateral tongue edges, the extensiveness of the distal and proximal joint of the thumb and the flexibility of the distal phalanx of the little finger and one sexually conditioned property (digital index we analyzed the genetic structure of four populations of rural municipality Maglaj: Kosova, Novi Šeher, Jablanica, Moševac, then one isolated local population Ravna and one urban population area called Maglaj. The survey covered a total of 440 students (213 girls and 227 boys aged 11-18 years. According to the degree of genetic heterogeneity, values of Wahlund variance that are obtained for each trait belong in the category of low genetic differentiation. The maximum value of Wahlund variance was identified for the property shape of the earlobes (by Cavalli - Sforza, Bodmer = 0.0452, and the lowest for phenotypic system flexibility of lateral tongue edges (by Cavalli - Sforza, Bodmer = 0.0000. Studied set of population is the most heterogeneous according to the frequency of recessive allelogene for phenotypic characteristic shape of the earlobes, and the most homogeneous for the phenotypic trait flexibility of lateral tongue edge. Based on the analysis of genetic distance for seven phenotypic traits in populations of municipality Maglaj we established the minimum genetic distance between populations of Kosova and Maglaj (fθ = 0.0007, and the largest genetic distance between populations of Jablanica and Moševac (fθ = 0.0144. It was noted that the lowest average coefficient of kinship has a local population of Kosova (fθ = 0.0028, while the highest average coefficient of kinship has a population Moševac (fθ = 0.0081. The greatest characteristic has a population of Moševac (fθs = 0.7556, and the lowest characteristic has a population of Novi Šeher (fθs = -0.0795. Based on the obtained values of

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

    Science.gov (United States)

    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.

  4. Population genetic analysis of cat populations from Mexico ...

    Indian Academy of Sciences (India)

    Unknown

    Facultad de Ciencias, Pontificia Universidad Javeriana, Cra 7A No 43-82, Bogotá DC, Colombia. 2Department of ... (Amazonas) and Northern Brazilian populations are very different ..... tama, Santa Cruz, La Paz, and Santo Domingo cat popu-.

  5. The heterogeneous HLA genetic makeup of the Swiss population.

    Science.gov (United States)

    Buhler, Stéphane; Nunes, José Manuel; Nicoloso, Grazia; Tiercy, Jean-Marie; Sanchez-Mazas, Alicia

    2012-01-01

    This study aims at investigating the HLA molecular variation across Switzerland in order to determine possible regional differences, which would be highly relevant to several purposes: optimizing donor recruitment strategies in hematopoietic stem cell transplantation (HSCT), providing reliable reference data in HLA and disease association studies, and understanding the population genetic background(s) of this culturally heterogeneous country. HLA molecular data of more than 20,000 HSCT donors from 9-13 recruitment centers of the whole country were analyzed. Allele and haplotype frequencies were estimated by using new computer tools adapted to the heterogeneity and ambiguity of the data. Non-parametric and resampling statistical tests were performed to assess Hardy-Weinberg equilibrium, selective neutrality and linkage disequilibrium among different loci, both in each recruitment center and in the whole national registry. Genetic variation was explored through genetic distance and hierarchical analysis of variance taking into account both geographic and linguistic subdivisions in Switzerland. The results indicate a heterogeneous genetic makeup of the Swiss population: first, allele frequencies estimated on the whole national registry strongly deviate from Hardy-Weinberg equilibrium, by contrast with the results obtained for individual centers; second, a pronounced differentiation is observed for Ticino, Graubünden, and, to a lesser extent, Wallis, suggesting that the Alps represent(ed) a barrier to gene flow; finally, although cultural (linguistic) boundaries do not represent a main genetic differentiation factor in Switzerland, the genetic relatedness between population from south-eastern Switzerland and Italy agrees with historical and linguistic data. Overall, this study justifies the maintenance of a decentralized donor recruitment structure in Switzerland allowing increasing the genetic diversity of the national--and hence global--donor registry. It also

  6. Genetic diversity in India and the inference of Eurasian population expansion.

    Science.gov (United States)

    Xing, Jinchuan; Watkins, W Scott; Hu, Ya; Huff, Chad D; Sabo, Aniko; Muzny, Donna M; Bamshad, Michael J; Gibbs, Richard A; Jorde, Lynn B; Yu, Fuli

    2010-01-01

    Genetic studies of populations from the Indian subcontinent are of great interest because of India's large population size, complex demographic history, and unique social structure. Despite recent large-scale efforts in discovering human genetic variation, India's vast reservoir of genetic diversity remains largely unexplored. To analyze an unbiased sample of genetic diversity in India and to investigate human migration history in Eurasia, we resequenced one 100-kb ENCODE region in 92 samples collected from three castes and one tribal group from the state of Andhra Pradesh in south India. Analyses of the four Indian populations, along with eight HapMap populations (692 samples), showed that 30% of all SNPs in the south Indian populations are not seen in HapMap populations. Several Indian populations, such as the Yadava, Mala/Madiga, and Irula, have nucleotide diversity levels as high as those of HapMap African populations. Using unbiased allele-frequency spectra, we investigated the expansion of human populations into Eurasia. The divergence time estimates among the major population groups suggest that Eurasian populations in this study diverged from Africans during the same time frame (approximately 90 to 110 thousand years ago). The divergence among different Eurasian populations occurred more than 40,000 years after their divergence with Africans. Our results show that Indian populations harbor large amounts of genetic variation that have not been surveyed adequately by public SNP discovery efforts. Our data also support a delayed expansion hypothesis in which an ancestral Eurasian founding population remained isolated long after the out-of-Africa diaspora, before expanding throughout Eurasia. © 2010 Xing et al.; licensee BioMed Central Ltd.

  7. Genetic diversity, population structure, and traditional culture of Camellia reticulata.

    Science.gov (United States)

    Xin, Tong; Huang, Weijuan; De Riek, Jan; Zhang, Shuang; Ahmed, Selena; Van Huylenbroeck, Johan; Long, Chunlin

    2017-11-01

    Camellia reticulata is an arbor tree that has been cultivated in southwestern China by various sociolinguistic groups for esthetic purposes as well as to derive an edible seed oil. This study examined the influence of management, socio-economic factors, and religion on the genetic diversity patterns of Camellia reticulata utilizing a combination of ethnobotanical and molecular genetic approaches. Semi-structured interviews and key informant interviews were carried out with local communities in China's Yunnan Province. We collected plant material ( n  = 190 individuals) from five populations at study sites using single-dose AFLP markers in order to access the genetic diversity within and between populations. A total of 387 DNA fragments were produced by four AFLP primer sets. All DNA fragments were found to be polymorphic (100%). A relatively high level of genetic diversity was revealed in C. reticulata samples at both the species ( H sp  = 0.3397, I sp  = 0.5236) and population (percentage of polymorphic loci = 85.63%, H pop  = 0.2937, I pop  = 0.4421) levels. Findings further revealed a relatively high degree of genetic diversity within C. reticulata populations (Analysis of Molecular Variance = 96.31%). The higher genetic diversity within populations than among populations of C. reticulata from different geographies is likely due to the cultural and social influences associated with its long cultivation history for esthetic and culinary purposes by diverse sociolinguistic groups. This study highlights the influence of human management, socio-economic factors, and other cultural variables on the genetic and morphological diversity of C. reticulata at a regional level. Findings emphasize the important role of traditional culture on the conservation and utilization of plant genetic diversity.

  8. Genetic population structure of Shoal Bass within their native range

    Science.gov (United States)

    Taylor, Andrew T.; Tringali, Michael D.; Sammons, Steven M.; Ingram, Travis R.; O'Rouke, Patrick M.; Peterson, Douglas L.; Long, James M.

    2018-01-01

    Endemic to the Apalachicola River basin of the southeastern USA, the Shoal Bass Micropterus cataractae is a fluvial‐specialist sport fish that is imperiled because of anthropogenic habitat alteration. To counter population declines, restorative stocking efforts are becoming an increasingly relevant management strategy. However, population genetic structure within the species is currently unknown, but it could influence management decisions, such as brood source location. Leveraging a collaborative effort to collect and genotype specimens with 16 microsatellite loci, our objective was to characterize hierarchical population structure and genetic differentiation of the Shoal Bass across its native range, including an examination of structuring mechanisms, such as relatedness and inbreeding levels. Specimens identified as Shoal Bass were collected from 13 distinct sites (N ranged from 17 to 209 per location) and were then taxonomically screened to remove nonnative congeners and hybrids (pure Shoal Bass N ranged from 13 to 183 per location). Our results revealed appreciable population structure, with five distinct Shoal Bass populations identifiable at the uppermost hierarchical level that generally corresponded with natural geographic features and anthropogenic barriers. Substructure was recovered within several of these populations, wherein differences appeared related to spatial isolation and local population dynamics. An analysis of molecular variance revealed that 3.6% of the variation in our data set was accounted for among three larger river drainages, but substructure within each river drainage also explained an additional 8.9% of genetic variation, demonstrating that management at a scale lower than the river drainage level would likely best conserve genetic diversity. Results provide a population genetic framework that can inform future management decisions, such as brood source location, so that genetic diversity within and among populations is

  9. Genetic diversity and population structure of leaf-nosed bat ...

    African Journals Online (AJOL)

    Genetic variation and population structure of the leaf-nosed bat Hipposideros speoris were estimated using 16S rRNA sequence and microsatellite analysis. Twenty seven distinct mitochondrial haplotypes were identified from 186 individuals, sampled from eleven populations. FST test revealed significant variations ...

  10. Uncovering the Genetic History of the Present Day Greenlandic Population

    DEFF Research Database (Denmark)

    Moltke, Ida; Fumagalli, Matteo; Korneliussen, Thorfinn S

    2015-01-01

    Because of past limitations in samples and genotyping technologies, important questions about the history of the present-day Greenlandic population remain unanswered. In an effort to answer these questions and in general investigate the genetic history of the Greenlandic population, we analyzed...

  11. Ecological and population genetics of locally rare plants: A review

    Science.gov (United States)

    Simon A. Lei

    2001-01-01

    Plant species with limited dispersal ability, narrow geographical and physiological tolerance ranges, as well as with specific habitat and ecological requirements are likely to be rare. Small and isolated populations and species contain low levels of within-population genetic variation in many plant species. The gene pool of plants is a product of phenotype-environment...

  12. Population Genetic Status of the Western Indian Ocean

    African Journals Online (AJOL)

    Abstract—Population genetics offers a useful technique for studying the population structure of marine organisms and has relevance to both systematics and the conservation of biodiversity. The Western Indian Ocean (WIO) is faced with increasing evidence of degradation and effective management initiatives are needed to ...

  13. Recolonization after habitat restoration leads to decreased genetic variation in populations of a terrestrial orchid.

    Science.gov (United States)

    Vandepitte, K; Gristina, A S; De Hert, K; Meekers, T; Roldán-Ruiz, I; Honnay, O

    2012-09-01

    Colonization is crucial to habitat restoration projects that rely on the spontaneous regeneration of the original vegetation. However, as a previously declining plant species spreads again, the likelihood of founder effects increases through recurrent population founding and associated serial bottlenecks. We related Amplified Fragment Length Polymorphism markers genetic variation and fitness to colonization history for all extant populations of the outcrossing terrestrial orchid Dactylorhiza incarnata in an isolated coastal dune complex. Around 1970, D. incarnata suffered a severe bottleneck yet ultimately persisted and gradually spread throughout the spatially segregated dune slacks, aided by the restoration of an open vegetation. Genetic assignment demonstrated dispersal to vacant sites from few nearby extant populations and very limited inflow from outside the spatially isolated reserve. Results further indicated that recurrent founding from few local sources resulted in the loss of genetic diversity and promoted genetic divergence (F(ST) = 0.35) among populations, but did not influence population fitness. The few source populations initially available and the limited inflow of genes from outside the study reserve, as a consequence of habitat degradation and spatial isolation, may have magnified the genetic effects of recurrent population founding. © 2012 Blackwell Publishing Ltd.

  14. Teaching Genetic Counseling Skills: Incorporating a Genetic Counseling Adaptation Continuum Model to Address Psychosocial Complexity.

    Science.gov (United States)

    Shugar, Andrea

    2017-04-01

    Genetic counselors are trained health care professionals who effectively integrate both psychosocial counseling and information-giving into their practice. Preparing genetic counseling students for clinical practice is a challenging task, particularly when helping them develop effective and active counseling skills. Resistance to incorporating these skills may stem from decreased confidence, fear of causing harm or a lack of clarity of psycho-social goals. The author reflects on the personal challenges experienced in teaching genetic counselling students to work with psychological and social complexity, and proposes a Genetic Counseling Adaptation Continuum model and methodology to guide students in the use of advanced counseling skills.

  15. Genetic evidence for a Paleolithic human population expansion in Africa

    Science.gov (United States)

    Reich, David E.; Goldstein, David B.

    1998-01-01

    Human populations have undergone dramatic expansions in size, but other than the growth associated with agriculture, the dates and magnitudes of those expansions have never been resolved. Here, we introduce two new statistical tests for population expansion, which use variation at a number of unlinked genetic markers to study the demographic histories of natural populations. By analyzing genetic variation in various aboriginal populations from throughout the world, we show highly significant evidence for a major human population expansion in Africa, but no evidence of expansion outside of Africa. The inferred African expansion is estimated to have occurred between 49,000 and 640,000 years ago, certainly before the Neolithic expansions, and probably before the splitting of African and non-African populations. In showing a significant difference between African and non-African populations, our analysis supports the unique role of Africa in human evolutionary history, as has been suggested by most other genetic work. In addition, the missing signal in non-African populations may be the result of a population bottleneck associated with the emergence of these populations from Africa, as postulated in the “Out of Africa” model of modern human origins. PMID:9653150

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

    OpenAIRE

    Vangestel, C; Mergeay, Joachim; 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 hierar...

  17. Molecular taxonomic, epidemiological and population genetic ...

    African Journals Online (AJOL)

    Admin

    with yam anthracnose, as well the population biology of C. gloeosporioides on yam. Sexual ..... evolution of the ascomycetes, and indicates that the ..... of Colletotrichum gloeosporioides Penz. from yam (Dioscorea spp.) in. Nigeria. In: Akoroda AO, Ngeve JM (eds) Root crops in the 21st century. Proceedings of the 7th.

  18. Population genetic structure in natural and reintroduced beaver (Castor fiber populations in Central Europe

    Directory of Open Access Journals (Sweden)

    Kautenburger, R.

    2008-12-01

    Full Text Available Castor fiber Linnaeus, 1758 is the only indigenous species of the genus Castor in Europe and Asia. Due to extensive hunting until the beginning of the 20th century, the distribution of the formerly widespread Eurasian beaver was dramatically reduced. Only a few populations remained and these were in isolated locations, such as the region of the German Elbe River. The loss of genetic diversity in small or captive populations throughgenetic drift and inbreeding is a severe conservation problem. However, the reintroduction of beaver populations from several regions in Europe has shown high viability and populations today are growing fast. In the present study we analysed the population genetic structure of a natural and two reintroduced beaver populations in Germany and Austria. Furthermore, we studied the genetic differentiation between two beaver species, C. fiber and the American beaver (C. canadensis, using RAPD (Random Amplified Polymorphic DNA as a genetic marker. The reintroduced beaver populations of different origins and the autochthonous population of the Elbe River showed a similar low genetic heterogeneity. There was an overall high genetic similarity in the species C. fiber, and no evidence was found for a clear subspecific structure in the populations studied.

  19. The value of some Corsican sub-populations for genetic association studies

    Directory of Open Access Journals (Sweden)

    Vona Giuseppe

    2008-07-01

    Full Text Available Abstract Background Genetic isolates with a history of a small founder population, long-lasting isolation and population bottlenecks represent exceptional resources in the identification of disease genes. In these populations the disease allele reveals Linkage Disequilibrium (LD with markers over significant genetic intervals, therefore facilitating disease locus identification. In a previous study we examined the LD extension on the Xq13 region in three Corsican sub-populations from the inner mountainous region of the island. On the basis of those previous results we have proposed a multistep procedure to carry out studies aimed at the identification of genes involved in complex diseases in Corsica. A prerequisite to carry out the proposed multi-step procedure was the presence of different degrees of LD on the island and a common genetic derivation of the different Corsican sub-populations. In order to evaluate the existence of these conditions in the present paper we extended the analysis to the Corsican coastal populations. Methods Samples were analyzed using seven dinucleotide microsatellite markers on chromosome Xq13-21: DXS983, DXS986, DXS8092, DXS8082, DXS1225, DXS8037 and DXS995 spanning approximately 4.0 cM (13.3 Mb. We have also investigated the distribution of the DXS1225-DXS8082 haplotype which has been recently proposed as a good marker of population genetic history due to its low recombination rate. Results the results obtained indicate a decrease of LD on the island from the central mountainous toward the coastal sub-populations. In addition the analysis of the DXS1225-DXS8082 haplotype revealed: 1 the presence of a particular haplotype with high frequency; 2 the derivation from a common genetic pool of the sub-populations examined in the present study. Conclusion These results indicate the Corsican sub-populations useful for the fine mapping of genes contributing to complex diseases.

  20. The geography of malaria genetics in the Democratic Republic of Congo: A complex and fragmented landscape

    Science.gov (United States)

    Carrel, Margaret; Patel, Jaymin; Taylor, Steve M.; Janko, Mark; Mwandagalirwa, Melchior Kashamuka; Tshefu, Antoinette K.; Escalante, Ananias A.; McCollum, Andrea; Alam, Md Tauqeer; Udhayakumar, Venkatachalam; Meshnick, Steven; Emch, Michael

    2014-01-01

    Understanding how malaria parasites move between populations is important, particularly given the potential for malaria to be reintroduced into areas where it was previously eliminated. We examine the distribution of malaria genetics across seven sites within the Democratic Republic of Congo (DRC) and two nearby countries, Ghana and Kenya, in order to understand how the relatedness of malaria parasites varies across space, and whether there are barriers to the flow of malaria parasites within the DRC or across borders. Parasite DNA was retrieved from dried blood spots from 7 Demographic and Health Survey sample clusters in the DRC. Malaria genetic characteristics of parasites from Ghana and Kenya were also obtained. For each of 9 geographic sites (7 DRC, 1 Ghana and 1 Kenya), a pair-wise RST statistic was calculated, indicating the genetic distance between malaria parasites found in those locations. Mapping genetics across the spatial extent of the study area indicates a complex genetic landscape, where relatedness between two proximal sites may be relatively high (RST > 0.64) or low (RST < 0.05), and where distal sites also exhibit both high and low genetic similarity. Mantel’s tests suggest that malaria genetics differ as geographic distances increase. Principal Coordinate Analysis suggests that genetically related samples are not co-located. Barrier analysis reveals no significant barriers to gene flow between locations. Malaria genetics in the DRC have a complex and fragmented landscape. Limited exchange of genes across space is reflected in greater genetic distance between malaria parasites isolated at greater geographic distances. There is, however, evidence for close genetic ties between distally located sample locations, indicating that movement of malaria parasites and flow of genes is being driven by factors other than distance decay. This research demonstrates the contributions that spatial disease ecology and landscape genetics can make to

  1. Genetic diversity in Chilean populations of rainbow trout, Oncorhynchus mykiss

    Directory of Open Access Journals (Sweden)

    Claudia B Cárcamo

    2015-03-01

    Full Text Available The rainbow trout Oncorhynchus mykiss, was first introduced in Chile between 1905 and 1920 and is currently widely distributed in Chile from Antofagasta (23°S to Patagonia (55°S. The broad range of the geographic and climatic distributions of this species in Chile offers a unique opportunity to study the effect of naturalization of an introduced species on its genetic variability. It is of particular importance to observe the genetic variability of populations in the northern range of this species distribution, in a transition zone where a Mediterranean-type climate changes to an arid climate. The present study analyzed allozymic variability and distribution within and between populations of O. mykiss from the river basins of Elqui and Limari rivers, and six culture strains, using starch-gel protein electrophoresis. Populations were found to be in Hardy-Weinberg equilibrium and the average values of He (0.045, polymorphism (13.9% and allele per locus (1.19 are similar to rainbow trout in its native distributional range. About 77.8% of the genetic variability was within population, similar to the variability reported for wild populations in the northern hemisphere. However, a marked genetic differentiation between wild populations was also found. This is likely to be the consequence of initial founder effects followed by subsequent introgression of resident populations caused by reseeding with trout of different origins in both basins.

  2. Genetic diversity among ancient Nordic populations

    DEFF Research Database (Denmark)

    Melchior, Linea Cecilie; Lynnerup, Niels; Siegismund, Hans Redlef

    2010-01-01

    , 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...... the ancient Danes (average 13%) than among extant Danes and Scandinavians ( approximately 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...

  3. Genetic diversity and relatedness among seven red deer (Cervus elaphus populations

    Directory of Open Access Journals (Sweden)

    Lenka Maršálková

    2014-02-01

    Full Text Available Deer (Cervidae recently belongs to the most important species. The aim of presenting study was evaluation of genetic diversity and relationship within and among seven red deer populations from different origins - Czech Republic, Hungary, hybrids Hungary x New Zealand, Lithuania, New Zealand, Poland and Slovak Republic. This study was conducted to determine the levels of genetic variability and relationships among deer populations from a total of 637 animals originating from seven countries Czech Republic (50, Hungary (35, Hungary x New Zealand hybrids (67, Lithuania (26, New Zealand (82, Poland (347 and Slovak Republic (30.  We used the hair bulbs as a source of DNA.  In total, 213 alleles were observed from the 10 loci surveyed. The number of alleles per locus ranged from 11 (IOBT965 to 35 (T156, RT13. Genetic diversity and relatedness among red deer populations has been performed on a total of 637 animals. A panel of 10 microsatellite markers used in deer were optimized. On the basis of this panel of microsatellites we were investigated genetic variability and relationships by using statistical and graphical programmes. We evaluated how close populations are to each other and their genetic admixture. Molecular genetic data combined with evaluation in statistical programmes could lead to a complex view of populations

  4. The ethics of complexity. Genetics and autism, a literature review.

    Science.gov (United States)

    Hens, Kristien; Peeters, Hilde; Dierickx, Kris

    2016-04-01

    It is commonly believed that the etiology of autism is at least partly explained through genetics. Given the complexity of autism and the variability of the autistic phenotype, genetic research and counseling in this field are also complex and associated with specific ethical questions. Although the ethics of autism genetics, especially with regard to reproductive choices, has been widely discussed on the public fora, an in depth philosophical or bioethical reflection on all aspects of the theme seems to be missing. With this literature review we wanted to map the basic questions and answers that exist in the bioethical literature on autism genetics, research, counseling and reproduction, and provide suggestions as to how the discussion can proceed. We found 19 papers that fitted the description of "bioethics literature focusing on autism genetics," and analyzed their content to distill arguments and themes. We concluded that because of the complexity of autism, and the uncertainty with regard to its status, more ethical reflection is needed before definite conclusions and recommendations can be drawn. Moreover, there is a dearth of bioethical empirical studies querying the opinions of all parties, including people with autism themselves. Such empirical bioethical studies should be urgently done before bioethical conclusions regarding the aims and desirability of research into autism genes can be done. Also, fundamental philosophical reflection on concepts of disease should accompany research into the etiology of autism. © 2016 Wiley Periodicals, Inc.

  5. Enabling complex genetic circuits to respond to extrinsic environmental signals.

    Science.gov (United States)

    Hoynes-O'Connor, Allison; Shopera, Tatenda; Hinman, Kristina; Creamer, John Philip; Moon, Tae Seok

    2017-07-01

    Genetic circuits have the potential to improve a broad range of metabolic engineering processes and address a variety of medical and environmental challenges. However, in order to engineer genetic circuits that can meet the needs of these real-world applications, genetic sensors that respond to relevant extrinsic and intrinsic signals must be implemented in complex genetic circuits. In this work, we construct the first AND and NAND gates that respond to temperature and pH, two signals that have relevance in a variety of real-world applications. A previously identified pH-responsive promoter and a temperature-responsive promoter were extracted from the E. coli genome, characterized, and modified to suit the needs of the genetic circuits. These promoters were combined with components of the type III secretion system in Salmonella typhimurium and used to construct a set of AND gates with up to 23-fold change. Next, an antisense RNA was integrated into the circuit architecture to invert the logic of the AND gate and generate a set of NAND gates with up to 1168-fold change. These circuits provide the first demonstration of complex pH- and temperature-responsive genetic circuits, and lay the groundwork for the use of similar circuits in real-world applications. Biotechnol. Bioeng. 2017;114: 1626-1631. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  6. Population genetics of the Mediterranean fruit fly, Ceratitis capitata (Wied.)

    International Nuclear Information System (INIS)

    Kourti, A.; Loukas, M.; Economopoulos, A.P.

    1990-01-01

    The genetic structure of 15 wild populations of Mediterranean fruit fly (medfly), Ceratitis capitata (Wiedemann), sampled from different geographical areas and different host fruit tree species, has been studied. Each population was analysed for 25 enzyme systems detected electrophoretically. All the Mediterranean populations proved to be highly monomorphic (H-bar=0.053) whereas those from South Africa and Reunion were highly heteromorphic (H-bar=0.234 and 0.153 respectively). As the urea denaturation method was used, no hidden genetic variability caused by the usual electrophoretic conditions was detected. The most probable explanation of the low genetic variability observed in the introduced populations of the medfly seems to be the historical reasons, namely the time elapsed since colonization and the number of individuals of the founder population. Experiments in the field and in the laboratory failed to detect any pattern of preference for oviposition sites in the medfly populations. More specifically, the differences in allele frequencies for the polymorphic loci among these populations do not seem to be correlated either with the taxonomic status of the host fruit or with the size of the fruit. It is concluded that the medfly as a fine grained species may utilize many alternative food resources without an apparent action of selection (or at least one that is detectable by the methods used). By estimating the genetic distances between the populations and/or by using the allozymes as genetic markers the route(s) of dispersion of the fly from its geographic centre of origin, which is placed in Africa, could be roughly traced. Finally, no systematic changes in allele frequencies were observed in populations reared on artificial substrate. (author). 43 refs, 2 figs, 9 tabs

  7. Complexity theory and genetics: The computational power of crossing over

    Czech Academy of Sciences Publication Activity Database

    Pudlák, Pavel

    2001-01-01

    Roč. 171, č. 1 (2001), s. 201-223 ISSN 0890-5401 R&D Projects: GA AV ČR IAA1019901 Institutional research plan: CEZ:AV0Z1019905; CEZ:AV0Z1019905 Keywords : complexity * genetics * croning over Subject RIV: BA - General Mathematics Impact factor: 0.571, year: 2001

  8. Genetic and epidemiological aspect of Complex Regional Pain Syndrome

    NARCIS (Netherlands)

    Rooij, Annetje Monique de

    2010-01-01

    Complex Regional Pain Syndrome (CRPS) is a painful disorder affecting one or more extremities. CRPS is characterized by various combinations of sensory, autonomic and motor disturbances. Genetic factors are suggested to play a role in CRPS, but this has not been extensively studied. Therefore the

  9. Alu polymorphic insertions reveal genetic structure of north Indian populations.

    Science.gov (United States)

    Tripathi, Manorama; Tripathi, Piyush; Chauhan, Ugam Kumari; Herrera, Rene J; Agrawal, Suraksha

    2008-10-01

    The Indian subcontinent is characterized by the ancestral and cultural diversity of its people. Genetic input from several unique source populations and from the unique social architecture provided by the caste system has shaped the current genetic landscape of India. In the present study 200 individuals each from three upper-caste and four middle-caste Hindu groups and from two Muslim populations in North India were examined for 10 polymorphic Alu insertions (PAIs). The investigated PAIs exhibit high levels of polymorphism and average heterozygosity. Limited interpopulation variance and genetic flow in the present study suggest admixture. The results of this study demonstrate that, contrary to common belief, the caste system has not provided an impermeable barrier to genetic exchange among Indian groups.

  10. Genetical pressures and social organization in small mammal populations

    International Nuclear Information System (INIS)

    Berry, R.J.

    1978-01-01

    Inherited variation is often useful for detecting and measuring ecological pressures in natural populations. For example, changes in allele and genotypic frequencies at the gene locus controlling the haemoglobin β chain in Mus musculus samples trapped on an isolated Welsh island have provided information about different mechanisms of death at different times of year and about the influence of social structure on genetical constitution. Notwithstanding, considerable caution has to be exercised in interpreting genetical changes, since detectable varients are often no more than linked markers of physiologically important gene loci, while habitat, deme, or ageing differences may be obscured in pooled data, such as are represented by concepts like overall allozymic heterozygosity. For these reasons, genetical studies on wild populations are likely to be most profitable when the contribution of individual genes to physiological or behavioral traits can be analyzed; it is at this level that genetics and ecology properly complement each other

  11. Genetic affinities between endogamous and inbreeding populations of Uttar Pradesh.

    Science.gov (United States)

    Khan, Faisal; Pandey, Atul Kumar; Tripathi, Manorma; Talwar, Sudha; Bisen, Prakash S; Borkar, Minal; Agrawal, Suraksha

    2007-04-07

    India has experienced several waves of migration since the Middle Paleolithic. It is believed that the initial demic movement into India was from Africa along the southern coastal route, approximately 60,000-85,000 years before present (ybp). It has also been reported that there were two other major colonization which included eastward diffusion of Neolithic farmers (Elamo Dravidians) from Middle East sometime between 10,000 and 7,000 ybp and a southern dispersal of Indo Europeans from Central Asia 3,000 ybp. Mongol entry during the thirteenth century A.D. as well as some possible minor incursions from South China 50,000 to 60,000 ybp may have also contributed to cultural, linguistic and genetic diversity in India. Therefore, the genetic affinity and relationship of Indians with other world populations and also within India are often contested. In the present study, we have attempted to offer a fresh and immaculate interpretation on the genetic relationships of different North Indian populations with other Indian and world populations. We have first genotyped 20 tetra-nucleotide STR markers among 1800 north Indian samples of nine endogamous populations belonging to three different socio-cultural strata. Genetic distances (Nei's DA and Reynold's Fst) were calculated among the nine studied populations, Caucasians and East Asians. This analysis was based upon the allelic profile of 20 STR markers to assess the genetic similarity and differences of the north Indian populations. North Indians showed a stronger genetic relationship with the Europeans (DA 0.0341 and Fst 0.0119) as compared to the Asians (DA 0.1694 and Fst - 0.0718). The upper caste Brahmins and Muslims were closest to Caucasians while middle caste populations were closer to Asians. Finally, three phylogenetic assessments based on two different NJ and ML phylogenetic methods and PC plot analysis were carried out using the same panel of 20 STR markers and 20 geo-ethnic populations. The three phylogenetic

  12. Genetic affinities between endogamous and inbreeding populations of Uttar Pradesh

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    Borkar Minal

    2007-04-01

    Full Text Available Abstract Background India has experienced several waves of migration since the Middle Paleolithic. It is believed that the initial demic movement into India was from Africa along the southern coastal route, approximately 60,000–85,000 years before present (ybp. It has also been reported that there were two other major colonization which included eastward diffusion of Neolithic farmers (Elamo Dravidians from Middle East sometime between 10,000 and 7,000 ybp and a southern dispersal of Indo Europeans from Central Asia 3,000 ybp. Mongol entry during the thirteenth century A.D. as well as some possible minor incursions from South China 50,000 to 60,000 ybp may have also contributed to cultural, linguistic and genetic diversity in India. Therefore, the genetic affinity and relationship of Indians with other world populations and also within India are often contested. In the present study, we have attempted to offer a fresh and immaculate interpretation on the genetic relationships of different North Indian populations with other Indian and world populations. Results We have first genotyped 20 tetra-nucleotide STR markers among 1800 north Indian samples of nine endogamous populations belonging to three different socio-cultural strata. Genetic distances (Nei's DA and Reynold's Fst were calculated among the nine studied populations, Caucasians and East Asians. This analysis was based upon the allelic profile of 20 STR markers to assess the genetic similarity and differences of the north Indian populations. North Indians showed a stronger genetic relationship with the Europeans (DA 0.0341 and Fst 0.0119 as compared to the Asians (DA 0.1694 and Fst – 0.0718. The upper caste Brahmins and Muslims were closest to Caucasians while middle caste populations were closer to Asians. Finally, three phylogenetic assessments based on two different NJ and ML phylogenetic methods and PC plot analysis were carried out using the same panel of 20 STR markers and 20

  13. gPGA: GPU Accelerated Population Genetics Analyses.

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    Chunbao Zhou

    Full Text Available 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.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.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.

  14. Quasispecies theory in the context of population genetics

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    Wilke Claus O

    2005-08-01

    Full Text Available Abstract 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.

  15. Use of genetic data to infer population-specific ecological and phenotypic traits from mixed aggregations.

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    Paul Moran

    Full Text Available Many applications in ecological genetics involve sampling individuals from a mixture of multiple biological populations and subsequently associating those individuals with the populations from which they arose. Analytical methods that assign individuals to their putative population of origin have utility in both basic and applied research, providing information about population-specific life history and habitat use, ecotoxins, pathogen and parasite loads, and many other non-genetic ecological, or phenotypic traits. Although the question is initially directed at the origin of individuals, in most cases the ultimate desire is to investigate the distribution of some trait among populations. Current practice is to assign individuals to a population of origin and study properties of the trait among individuals within population strata as if they constituted independent samples. It seemed that approach might bias population-specific trait inference. In this study we made trait inferences directly through modeling, bypassing individual assignment. We extended a Bayesian model for population mixture analysis to incorporate parameters for the phenotypic trait and compared its performance to that of individual assignment with a minimum probability threshold for assignment. The Bayesian mixture model outperformed individual assignment under some trait inference conditions. However, by discarding individuals whose origins are most uncertain, the individual assignment method provided a less complex analytical technique whose performance may be adequate for some common trait inference problems. Our results provide specific guidance for method selection under various genetic relationships among populations with different trait distributions.

  16. Use of genetic data to infer population-specific ecological and phenotypic traits from mixed aggregations

    Science.gov (United States)

    Moran, Paul; Bromaghin, Jeffrey F.; Masuda, Michele

    2014-01-01

    Many applications in ecological genetics involve sampling individuals from a mixture of multiple biological populations and subsequently associating those individuals with the populations from which they arose. Analytical methods that assign individuals to their putative population of origin have utility in both basic and applied research, providing information about population-specific life history and habitat use, ecotoxins, pathogen and parasite loads, and many other non-genetic ecological, or phenotypic traits. Although the question is initially directed at the origin of individuals, in most cases the ultimate desire is to investigate the distribution of some trait among populations. Current practice is to assign individuals to a population of origin and study properties of the trait among individuals within population strata as if they constituted independent samples. It seemed that approach might bias population-specific trait inference. In this study we made trait inferences directly through modeling, bypassing individual assignment. We extended a Bayesian model for population mixture analysis to incorporate parameters for the phenotypic trait and compared its performance to that of individual assignment with a minimum probability threshold for assignment. The Bayesian mixture model outperformed individual assignment under some trait inference conditions. However, by discarding individuals whose origins are most uncertain, the individual assignment method provided a less complex analytical technique whose performance may be adequate for some common trait inference problems. Our results provide specific guidance for method selection under various genetic relationships among populations with different trait distributions.

  17. The genetic consequences of selection in natural populations.

    Science.gov (United States)

    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. © 2016 John Wiley & Sons Ltd.

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

    Science.gov (United States)

    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

    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. 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. 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' = 0.075, θ = 0.07) were

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

    Directory of Open Access Journals (Sweden)

    Salama Al-Hamidhi

    Full Text Available 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.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.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' = 0.075,

  20. POPULATION GENETICS OF Atta sexdens rubropilosa (HYMENOPTERA: FORMICIDAE

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    Liriana Belizário Cantagalli

    2013-01-01

    Full Text Available The genetic variability of Atta sexdens rubropilosa leaf-cutting ants collected from five brazilian localities was evaluated with PCR-RAPD technique. We used 15 primers producing 148 fragments of which 123 (83,11 % contained polymorphisms. The estimated Shannon index was 0.3836 ± 0.2335 showing that these ants possess high genetic diversity. The GST value was 0,2372 and PT = 0,184, indicating that the analyzed populations are moderately differentiated and 82 % of the variation obtained occur within populations. Although Mantel’s test had shown correlation between genetic distances and geographic was observed that Ivatuba and Itambé (33,8 km have the small geographical distance and the largest genetic distance. The lower genetic distance was estimated for Maringá and Ivatuba but this localities have a small geographic distance (42,3 km, indicating that there are no barriers for mating among reproducers in these populations. The high degree of polymorphism (83,11 % and the ability to cross among the populations in the studied regions indicate that this species of leaf-cutting ant is well adapted to the region; therefore, integrated control programs can be developed.

  1. Population genetics of Atta sexdens rubropilosa (Hymenoptera: Formicidae)

    International Nuclear Information System (INIS)

    Belizario Cantagalli, Liriana; Aparecida Mangolin, Claudete; Colla Ruvolo Takasusuki, Maria Claudia

    2013-01-01

    The genetic variability of Atta sexdens rubropilosa leaf-cutting ants collected from five Brazilian localities was evaluated with PCR-RAPD technique. we used 15 primers producing 148 fragments of which 123 (83.11 %) contained polymorphisms. the estimated Shannon index was 0.3836 ± 0.2335 showing that these ants possess high genetic diversity. the G S T value was 0.2372 and Φ p t = 0.184, indicating that the analyzed populations are moderately differentiated and 82 % of the variation obtained occur within populations. although mantel's test had shown correlation between genetic distances and geographic was observed that Ivatuba and Itambe (33.8 km) have the small geographical distance and the largest genetic distance. the lower genetic distance was estimated for Maringa and Ivatuba but this localities have a small geographic distance (42.3 km), indicating that there are no barriers for mating among reproducers in these populations. the high degree of polymorphism (83.11 %) and the ability to cross among the populations in the studied regions indicate that this species of leaf-cutting ant is well adapted to the region; therefore, integrated control programs can be developed.

  2. Microsatellite variability reveals high genetic diversity and low genetic differentiation in a critical giant panda population

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    Jiandong YANG, Zhihe ZHANG, Fujun SHEN, Xuyu YANG, Liang ZHANG, Limin CHEN, Wenping ZHANG, Qing ZHU, Rong HOU

    2011-12-01

    Full Text Available Understanding present patterns of genetic diversity is critical in order to design effective conservation and management strategies for endangered species. Tangjiahe Nature Reserve (NR is one of the most important national reserves for giant pandas Ailuropoda melanoleuca in China. Previous studies have shown that giant pandas in Tangjiahe NR may be threatened by population decline and fragmentation. Here we used 10 microsatellite DNA markers to assess the genetic variability in the Tangjiahe population. The results indicate a low level of genetic differentiation between the Hongshihe and Motianling subpopulations in the reserve. Assignment tests using the Bayesian clustering method in STRUCTURE identified one genetic cluster from 42 individuals of the two subpopulations. All individuals from the same subpopulation were assigned to one cluster. This indicates high gene flow between subpopulations. F statistic analyses revealed a low FIS-value of 0.024 in the total population and implies a randomly mating population in Tangjiahe NR. Additionally, our data show a high level of genetic diversity for the Tangjiahe population. Mean allele number (A, Allelic richness (AR and mean expected heterozygosity (HE for the Tangjiahe population was 5.9, 5.173 and 0.703, respectively. This wild giant panda population can be restored through concerted effort [Current Zoology 57 (6: 717–724, 2011].

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

    Science.gov (United States)

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

    2017-06-01

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

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

    Science.gov (United States)

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

    2011-01-01

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

  5. Genetic structure of seven Mexican indigenous populations based on five polymarker loci.

    Science.gov (United States)

    Buentello-Malo, Leonora; Peñaloza-Espinosa, Rosenda I; Loeza, Francisco; Salamanca-Gomez, Fabio; Cerda-Flores, Ricardo M

    2003-01-01

    This descriptive study investigates the genetic structure of seven Mexican indigenous populations (Mixteca Alta, Mixteca Baja, Otomies, Purepecha, Nahuas-Guerrero, Nahuas-Xochimilco, and Tzeltales) on the basis of five PCR-based polymorphic DNA loci: LDLR, GYPA, HBGG, D7S8, and GC. Genetic distance and diversity analyses indicate that these Mexican indigenous are similar and that more than 96% of the total gene diversity (H(T)) can be attributed to individual variation within populations. Mixteca-Alta, Mixteca-Baja, and Nahuas-Xochimilco show indications of higher admixture with European-derived persons. The demonstration of a relative genetic homogeneity of Mexican Indians for the markers studied suggests that this population is suitable for studying disease-marker associations in the search for candidate genes of complex diseases. Copyright 2002 Wiley-Liss, Inc.

  6. Patterns of genetic diversity of local pig populations in the State of Pernambuco, Brazil

    Directory of Open Access Journals (Sweden)

    Elizabete Cristina da Silva

    2011-08-01

    Full Text Available This study estimated the genetic diversity and structure of 12 genetic groups (GG of locally adapted and specialized pigs in the state of Pernambuco using 22 microsatellite markers. Nine locally adapted breeds (Baé, Caruncho, Canastra, Canastrão, Mamelado, Moura, Nilo, Piau and UDB (Undefined Breed and 3 specialized breeds (Duroc, Landrace and Large White, totaling 190 animals, were analyzed. The Analysis of Molecular Variance (AMOVA showed that 3.2% of the total variation was due to differences between genetic groups, and 3.6% to differences between local and commercial pigs. One hundred and ninety eight alleles were identified and apart from the Large White breed, all GG presented Hardy-Weinberg Equilibrium deviations for some loci. The total and effective allele means were lower for Duroc (3.65 and 3.01 and higher for UDB (8.89 and 4.53 and Canastra (8.61 and 4.58. Using Nei's standard genetic distance and the UPGMA method, it was possible to observe that the Landrace breed was grouped with the local genetic groups Canastra, Moura, Canastrão, Baé and Caruncho. Due to the complex admixture pattern, the genetic variability of the 12 genetic groups can be analyzed by distributing the individuals into two populations as demonstrated by a Bayesian analysis, corroborating the results from AMOVA, which revealed a low level of genetic differentiation between the inferred populations.

  7. Genetic aspects of pathological gambling: a complex disorder with shared genetic vulnerabilities.

    Science.gov (United States)

    Lobo, Daniela S S; Kennedy, James L

    2009-09-01

    To summarize and discuss findings from genetic studies conducted on pathological gambling (PG). Searches were conducted on PubMed and PsychInfo databases using the keywords: 'gambling and genes', 'gambling and family' and 'gambling and genetics', yielding 18 original research articles investigating the genetics of PG. Twin studies using the Vietnam Era Twin Registry have found that: (i) the heritability of PG is estimated to be 50-60%; (ii) PG and subclinical PG are a continuum of the same disorder; (iii) PG shares genetic vulnerability factors with antisocial behaviours, alcohol dependence and major depressive disorder; (iv) genetic factors underlie the association between exposure to traumatic life-events and PG. Molecular genetic investigations on PG are at an early stage and published studies have reported associations with genes involved in the brain's reward and impulse control systems. Despite the paucity of studies in this area, published studies have provided considerable evidence of the influence of genetic factors on PG and its complex interaction with other psychiatric disorders and environmental factors. The next step would be to investigate the association and interaction of these variables in larger molecular genetic studies with subphenotypes that underlie PG. Results from family and genetic investigations corroborate further the importance of understanding the biological underpinnings of PG in the development of more specific treatment and prevention strategies.

  8. Genetic complexity underlying hybrid male sterility in Drosophila.

    Science.gov (United States)

    Sawamura, Kyoichi; Roote, John; Wu, Chung-I; Yamamoto, Masa-Toshi

    2004-02-01

    Recent genetic analyses of closely related species of Drosophila have indicated that hybrid male sterility is the consequence of highly complex synergistic effects among multiple genes, both conspecific and heterospecific. On the contrary, much evidence suggests the presence of major genes causing hybrid female sterility and inviability in the less-related species, D. melanogaster and D. simulans. Does this contrast reflect the genetic distance between species? Or, generally, is the genetic basis of hybrid male sterility more complex than that of hybrid female sterility and inviability? To clarify this point, the D. simulans introgression of the cytological region 34D-36A to the D. melanogaster genome, which causes recessive male sterility, was dissected by recombination, deficiency, and complementation mapping. The 450-kb region between two genes, Suppressor of Hairless and snail, exhibited a strong effect on the sterility. Males are (semi-)sterile if this region of the introgression is made homozygous or hemizygous. But no genes in the region singly cause the sterility; this region has at least two genes, which in combination result in male sterility. Further, the males are less fertile when heterozygous with a larger introgression, which suggests that dominant modifiers enhance the effects of recessive genes of male sterility. Such an epistatic view, even in the less-related species, suggests that the genetic complexity is special to hybrid male sterility.

  9. Genetic distances between the Utah Mormons and related populations.

    Science.gov (United States)

    McLellan, T; Jorde, L B; Skolnick, M H

    1984-01-01

    Gene frequency data, consisting of six red cell antigen loci, nine electrophoretic systems, and HLA-A and -B are reported for the Utah Mormon population. These are compared statistically to gene frequencies from at U.S. population, 13 European populations, and seven populations from three religious isolates. The Mormon gene frequencies are similar to those of their northern European ancestors. This is explained by the large founding size of the Mormon population and high rates of gene flow. In contrast, the religious isolates (Amish, Hutterites, and Mennonites) show marked divergence from their ancestral populations and each other, due to isolation and random genetic drift. The HLA loci and electrophoretic loci presented here yield sets of genetic distances that are highly correlated (r = .734) and that both correspond closely to the actual geographic distances among the European populations. The genetic distances based on red cell antigen loci correspond less closely to the geographic distances and exhibit lower correlations with both the HLA and electrophoretic loci (r = .524 and r = .565, respectively). PMID:6591796

  10. The evolution of RNA viruses: A population genetics view

    Science.gov (United States)

    Moya, Andrés; Elena, Santiago F.; Bracho, Alma; Miralles, Rosario; Barrio, Eladio

    2000-01-01

    RNA viruses are excellent experimental models for studying evolution under the theoretical framework of population genetics. For a proper justification of this thesis we have introduced some properties of RNA viruses that are relevant for studying evolution. On the other hand, population genetics is a reductionistic theory of evolution. It does not consider or make simplistic assumptions on the transformation laws within and between genotypic and phenotypic spaces. However, such laws are minimized in the case of RNA viruses because the phenotypic space maps onto the genotypic space in a much more linear way than on higher DNA-based organisms. Under experimental conditions, we have tested the role of deleterious and beneficial mutations in the degree of adaptation of vesicular stomatitis virus (VSV), a nonsegmented virus of negative strand. We also have studied how effective population size, initial genetic variability in populations, and environmental heterogeneity shapes the impact of mutations in the evolution of vesicular stomatitis virus. Finally, in an integrative attempt, we discuss pros and cons of the quasispecies theory compared with classic population genetics models for haploid organisms to explain the evolution of RNA viruses. PMID:10860958

  11. Enclaves of genetic diversity resisted Inca impacts on population history.

    Science.gov (United States)

    Barbieri, Chiara; Sandoval, José R; Valqui, Jairo; Shimelman, Aviva; Ziemendorff, Stefan; Schröder, Roland; Geppert, Maria; Roewer, Lutz; Gray, Russell; Stoneking, Mark; Fujita, Ricardo; Heggarty, Paul

    2017-12-12

    The Inca Empire is claimed to have driven massive population movements in western South America, and to have spread Quechua, the most widely-spoken language family of the indigenous Americas. A test-case is the Chachapoyas region of northern Peru, reported as a focal point of Inca population displacements. Chachapoyas also spans the environmental, cultural and demographic divides between Amazonia and the Andes, and stands along the lowest-altitude corridor from the rainforest to the Pacific coast. Following a sampling strategy informed by linguistic data, we collected 119 samples, analysed for full mtDNA genomes and Y-chromosome STRs. We report a high indigenous component, which stands apart from the network of intense genetic exchange in the core central zone of Andean civilization, and is also distinct from neighbouring populations. This unique genetic profile challenges the routine assumption of large-scale population relocations by the Incas. Furthermore, speakers of Chachapoyas Quechua are found to share no particular genetic similarity or gene-flow with Quechua speakers elsewhere, suggesting that here the language spread primarily by cultural diffusion, not migration. Our results demonstrate how population genetics, when fully guided by the archaeological, historical and linguistic records, can inform multiple disciplines within anthropology.

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

    Science.gov (United States)

    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. © 2014 John Wiley & Sons Ltd.

  13. Genetic diversity and population genetic structure of the only population of Aoluguya Reindeer (Rangifer tarandus) in China.

    Science.gov (United States)

    Ju, Yan; Liu, Huamiao; Rong, Min; Zhang, Ranran; Dong, Yimeng; Zhou, Yongna; Xing, Xiumei

    2018-04-16

    Aoluguya Reindeer is the only reindeer species in China and currently approximately 1000 Aoluguya Reindeer remain semi-domesticated. A relative low diversity estimate was found by investigating genetic variability and demographic history of its population. Mismatch distribution curve of its nucleotide sequences and neutral test indicate its population has not experienced expansion. Genetic diversity and population structure were also analysed by using its mtDNA and microsatellites technology. Statistical results of these analyses showed there were varying degrees of population inbreeding and suggested that gene flow existed among its populations at one time. Three mutation models were also used to detect the bottleneck effect of reindeer population. The genetic variation of eight populations is relatively small. In addition, the clustering program STRUCTURE was used to analyse Aoluguya Reindeer population structure, to determine its optimal K and first time to analyse the phylogenetic status of Aoluguya Reindeer among other reindeer subspecies. It is recommended that the government establish a natural conservation area in Aoluguya Reindeer growing geography, forbade the trade and hunting of Aoluguya Reindeer, and strengthen the protection of this endangered species.

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

    Science.gov (United States)

    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. © 2016 The Royal Entomological Society.

  15. Analysis of genetic diversity in Bolivian llama populations using microsatellites.

    Science.gov (United States)

    Barreta, J; Gutiérrez-Gil, B; Iñiguez, V; Romero, F; Saavedra, V; Chiri, R; Rodríguez, T; Arranz, J J

    2013-08-01

    South American camelids (SACs) have a major role in the maintenance and potential future of rural Andean human populations. More than 60% of the 3.7 million llamas living worldwide are found in Bolivia. Due to the lack of studies focusing on genetic diversity in Bolivian llamas, this analysis investigates both the genetic diversity and structure of 12 regional groups of llamas that span the greater part of the range of distribution for this species in Bolivia. The analysis of 42 microsatellite markers in the considered regional groups showed that, in general, there were high levels of polymorphism (a total of 506 detected alleles; average PIC across per marker: 0.66), which are comparable with those reported for other populations of domestic SACs. The estimated diversity parameters indicated that there was high intrapopulational genetic variation (average number of alleles and average expected heterozygosity per marker: 12.04 and 0.68, respectively) and weak genetic differentiation among populations (FST range: 0.003-0.052). In agreement with these estimates, Bolivian llamas showed a weak genetic structure and an intense gene flow between all the studied regional groups, which is due to the exchange of reproductive males between the different flocks. Interestingly, the groups for which the largest pairwise FST estimates were observed, Sud Lípez and Nor Lípez, showed a certain level of genetic differentiation that is probably due to the pattern of geographic isolation and limited communication infrastructures of these southern localities. Overall, the population parameters reported here may serve as a reference when establishing conservation policies that address Bolivian llama populations. © 2012 Blackwell Verlag GmbH.

  16. Genomic patterns in Acropora cervicornis show extensive population structure and variable genetic diversity.

    Science.gov (United States)

    Drury, Crawford; Schopmeyer, Stephanie; Goergen, Elizabeth; Bartels, Erich; Nedimyer, Ken; Johnson, Meaghan; Maxwell, Kerry; Galvan, Victor; Manfrino, Carrie; Lirman, Diego

    2017-08-01

    Threatened Caribbean coral communities can benefit from high-resolution genetic data used to inform management and conservation action. We use Genotyping by Sequencing (GBS) to investigate genetic patterns in the threatened coral, Acropora cervicornis , across the Florida Reef Tract (FRT) and the western Caribbean. Results show extensive population structure at regional scales and resolve previously unknown structure within the FRT. Different regions also exhibit up to threefold differences in genetic diversity (He), suggesting targeted management based on the goals and resources of each population is needed. Patterns of genetic diversity have a strong spatial component, and our results show Broward and the Lower Keys are among the most diverse populations in Florida. The genetic diversity of Caribbean staghorn coral is concentrated within populations and within individual reefs (AMOVA), highlighting the complex mosaic of population structure. This variance structure is similar over regional and local scales, which suggests that in situ nurseries are adequately capturing natural patterns of diversity, representing a resource that can replicate the average diversity of wild assemblages, serving to increase intraspecific diversity and potentially leading to improved biodiversity and ecosystem function. Results presented here can be translated into specific goals for the recovery of A. cervicornis , including active focus on low diversity areas, protection of high diversity and connectivity, and practical thresholds for responsible restoration.

  17. Supervised Machine Learning for Population Genetics: A New Paradigm

    Science.gov (United States)

    Schrider, Daniel R.; Kern, Andrew D.

    2018-01-01

    As population genomic datasets grow in size, researchers are faced with the daunting task of making sense of a flood of information. To keep pace with this explosion of data, computational methodologies for population genetic inference are rapidly being developed to best utilize genomic sequence data. In this review we discuss a new paradigm that has emerged in computational population genomics: that of supervised machine learning (ML). We review the fundamentals of ML, discuss recent applications of supervised ML to population genetics that outperform competing methods, and describe promising future directions in this area. Ultimately, we argue that supervised ML is an important and underutilized tool that has considerable potential for the world of evolutionary genomics. PMID:29331490

  18. Genetics of simple and complex host-parasite interactions

    International Nuclear Information System (INIS)

    Sidhu, G.S.; Webster, J.M.

    1977-01-01

    In nature a host plant can be viewed as a miniature replica of an ecological system where true and incidental parasites share the same habitat. Consequently, they influence each other's presence directly by interspecific interaction, and indirectly by inducing changes in the host's physiology and so form disease complexes. Since all physiological phenomena have their counterpart in the respective genetic systems of interacting organisms, valuable genetic information can be derived from the analysis of complex parasitic systems. Disease complexes may be classified according to the nature of interaction between various parasites on the same host. One parasite may nullify the host's resistance to another (e.g. Tomato - Meloidogyne incognita + Fusarium oxysporum lycopersici system). Conversely, a parasite may invoke resistance in the host against another parasite (e.g. Tomato - Fusarium oxysporum lycopersici + Verticillium albo atrum system). From the study of simple parasitic systems we know that resistance versus susceptibility against a single parasite is normally monogenically controlled. However, when more than one parasite interacts to invoke or nullify each other's responses on the same host plant, the genetic results suggest epistatic ratios. Nevertheless, epistatic ratios have been obtained also from simple parasitic systems owing to gene interaction. The epistatic ratios obtained from complex and simple parasitic systems are contrasted and compared. It is suggested that epistatic ratios obtained from simple parasitic systems may, in fact, be artifacts resulting from complex parasitic associations that often occur in nature. Polygenic inheritance and the longevity of a cultivar is also discussed briefly in relation to complex parasitic associations. Induced mutations can play a significant role in the study of complex parasitic associations, and thus can be very useful in controlling plant diseases

  19. An alternative covariance estimator to investigate genetic heterogeneity in populations.

    Science.gov (United States)

    Heslot, Nicolas; Jannink, Jean-Luc

    2015-11-26

    For genomic prediction and genome-wide association studies (GWAS) using mixed models, covariance between individuals is estimated using molecular markers. Based on the properties of mixed models, using available molecular data for prediction is optimal if this covariance is known. Under this assumption, adding individuals to the analysis should never be detrimental. However, some empirical studies showed that increasing training population size decreased prediction accuracy. Recently, results from theoretical models indicated that even if marker density is high and the genetic architecture of traits is controlled by many loci with small additive effects, the covariance between individuals, which depends on relationships at causal loci, is not always well estimated by the whole-genome kinship. We propose an alternative covariance estimator named K-kernel, to account for potential genetic heterogeneity between populations that is characterized by a lack of genetic correlation, and to limit the information flow between a priori unknown populations in a trait-specific manner. This is similar to a multi-trait model and parameters are estimated by REML and, in extreme cases, it can allow for an independent genetic architecture between populations. As such, K-kernel is useful to study the problem of the design of training populations. K-kernel was compared to other covariance estimators or kernels to examine its fit to the data, cross-validated accuracy and suitability for GWAS on several datasets. It provides a significantly better fit to the data than the genomic best linear unbiased prediction model and, in some cases it performs better than other kernels such as the Gaussian kernel, as shown by an empirical null distribution. In GWAS simulations, alternative kernels control type I errors as well as or better than the classical whole-genome kinship and increase statistical power. No or small gains were observed in cross-validated prediction accuracy. This alternative

  20. Rapid genetic erosion in pollutant-exposed experimental chironomid populations

    Energy Technology Data Exchange (ETDEWEB)

    Nowak, Carsten [Abteilung Okologie und Evolution, Institut fuer Okologie, Evolution und Diversitaet, J. W. Goethe-Universitaet Frankfurt am Main, Siesmayerstrasse 70, 60054 Frankfurt am Main (Germany)], E-mail: cnowak@senckenberg.de; Vogt, Christian [Abteilung Aquatische Okotoxikologie, Institut fuer Okologie, Evolution und Diversitaet, J. W. Goethe-Universitaet Frankfurt am Main, Siesmayerstrasse 70, 60054 Frankfurt am Main (Germany)], E-mail: vogt@bio.uni-frankfurt.de; Pfenninger, Markus [Abteilung Okologie und Evolution, Institut fuer Okologie, Evolution und Diversitaet, J. W. Goethe-Universitaet Frankfurt am Main, Siesmayerstrasse 70, 60054 Frankfurt am Main (Germany)], E-mail: pfenninger@bio.uni-frankfurt.de; Schwenk, Klaus [Abteilung Okologie und Evolution, Institut fuer Okologie, Evolution und Diversitaet, J. W. Goethe-Universitaet Frankfurt am Main, Siesmayerstrasse 70, 60054 Frankfurt am Main (Germany)], E-mail: k.schwenk@bio.uni-frankfurt.de; Oehlmann, Joerg [Abteilung Aquatische Okotoxikologie, Institut fuer Okologie, Evolution und Diversitaet, J. W. Goethe-Universitaet Frankfurt am Main, Siesmayerstrasse 70, 60054 Frankfurt am Main (Germany)], E-mail: oehlmann@bio.uni-frankfurt.de; Streit, Bruno [Abteilung Okologie und Evolution, Institut fuer Okologie, Evolution und Diversitaet, J. W. Goethe-Universitaet Frankfurt am Main, Siesmayerstrasse 70, 60054 Frankfurt am Main (Germany)], E-mail: streit@bio.uni-frankfurt.de; Oetken, Matthias [Abteilung Aquatische Okotoxikologie, Institut fuer Okologie, Evolution und Diversitaet, J. W. Goethe-Universitaet Frankfurt am Main, Siesmayerstrasse 70, 60054 Frankfurt am Main (Germany)], E-mail: oetken@bio.uni-frankfurt.de

    2009-03-15

    Few studies have evaluated how effectively environmental contamination may reduce genetic diversity of a population. Here, we chose a laboratory approach in order to test if tributyltin (TBT) exposure at environmentally relevant concentrations leads to reduced genetic variation in the midge Chironomus riparius. Two TBT-exposed and two unexposed experimental populations were reared simultaneously in the laboratory for 12 generations. We recorded several life-history traits in each generation and monitored genetic variation over time using five variable microsatellite markers. TBT-exposed strains showed increased larval mortality (treatments: 43.8%; controls: 27.8%), slightly reduced reproductive output, and delayed larval development. Reduction of genetic variation was strongest and only significant in the TBT-exposed strains (treatments: -45.9%, controls: -24.4% of initial heterozygosity) after 12 generations. Our findings document that chemical pollution may lead to a rapid decrease in genetic diversity, which has important implications for conservation strategies and ecological management in polluted environments. - Chronic TBT exposure reduces allelic variation at five variable microsatellite loci in experimental populations of Chironomus riparius.

  1. Rapid genetic erosion in pollutant-exposed experimental chironomid populations

    International Nuclear Information System (INIS)

    Nowak, Carsten; Vogt, Christian; Pfenninger, Markus; Schwenk, Klaus; Oehlmann, Joerg; Streit, Bruno; Oetken, Matthias

    2009-01-01

    Few studies have evaluated how effectively environmental contamination may reduce genetic diversity of a population. Here, we chose a laboratory approach in order to test if tributyltin (TBT) exposure at environmentally relevant concentrations leads to reduced genetic variation in the midge Chironomus riparius. Two TBT-exposed and two unexposed experimental populations were reared simultaneously in the laboratory for 12 generations. We recorded several life-history traits in each generation and monitored genetic variation over time using five variable microsatellite markers. TBT-exposed strains showed increased larval mortality (treatments: 43.8%; controls: 27.8%), slightly reduced reproductive output, and delayed larval development. Reduction of genetic variation was strongest and only significant in the TBT-exposed strains (treatments: -45.9%, controls: -24.4% of initial heterozygosity) after 12 generations. Our findings document that chemical pollution may lead to a rapid decrease in genetic diversity, which has important implications for conservation strategies and ecological management in polluted environments. - Chronic TBT exposure reduces allelic variation at five variable microsatellite loci in experimental populations of Chironomus riparius

  2. RAPD analysis for genetic diversity of two populations of Mystus ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-09-01

    Sep 1, 2009 ... and other aquatic ecosystem and the ecological complexes. ... is a property at the population level while the functional diversity concept ... warm water fish species, which are distributed all over the world. ..... Phylogenetic.

  3. Population genetic structure and demographic history of small ...

    African Journals Online (AJOL)

    Population genetic structure and demographic history of small yellow croaker, ... diversity (0.0112 ± 0.0061 to 0.0141 ± 0.0075) were detected in the species. ... into two closely related clades, but did not appear to have any geographic ...

  4. Genetic diversity of Annona senegalensis Pers. populations as ...

    African Journals Online (AJOL)

    Annona senegalensis Pers. is one of the wild fruit tree for domestication in southern Africa. An assessment of the genetic diversity in A. senegalensis would assist in planning for future germplasm collection, conservation and fruit domestication programmes. During 2004 to 2006 nine populations were collected from different ...

  5. Genetic structure of Balearic honeybee populations based on microsatellite polymorphism

    Directory of Open Access Journals (Sweden)

    Moritz Robin FA

    2003-05-01

    Full Text Available Abstract The genetic variation of honeybee colonies collected in 22 localities on the Balearic Islands (Spain was analysed using eight polymorphic microsatellite loci. Previous studies have demonstrated that these colonies belong either to the African or west European evolutionary lineages. These populations display low variability estimated from both the number of alleles and heterozygosity values, as expected for the honeybee island populations. Although genetic differentiation within the islands is low, significant heterozygote deficiency is present, indicating a subpopulation genetic structure. According to the genetic differentiation test, the honeybee populations of the Balearic Islands cluster into two groups: Gimnesias (Mallorca and Menorca and Pitiusas (Ibiza and Formentera, which agrees with the biogeography postulated for this archipelago. The phylogenetic analysis suggests an Iberian origin of the Balearic honeybees, thus confirming the postulated evolutionary scenario for Apis mellifera in the Mediterranean basin. The microsatellite data from Formentera, Ibiza and Menorca show that ancestral populations are threatened by queen importations, indicating that adequate conservation measures should be developed for protecting Balearic bees.

  6. Genetic structure and diversity within and among six populations of ...

    African Journals Online (AJOL)

    Yomi

    2010-04-24

    Apr 24, 2010 ... Genetic structure and diversity within and among six populations of .... Lyopholized samples were ground to a fine powder. DNA extraction ..... 22(3): 287-292. Pei YL, Zou, YP, Yin Z, Wang XQ, Zhang ZX, Hong DY (1995).

  7. Population genetic structure of coral reef species Plectorhinchus ...

    African Journals Online (AJOL)

    The population genetic structure and the dispersal ability of Plectorhinchus flavomaculatus from South China Sea were examined with a 464 bp segment of mtDNA control region. A total of 116 individuals were collected from 12 coral reefs in Xisha, Zhongsha and Nansha archipelagos and 22 haplotypes were obtained.

  8. Population structure and genetic trends for indigenous African beef ...

    African Journals Online (AJOL)

    The aim of this study was to investigate population structure and genetic trends based on pedigree and performance records of five indigenous African beef cattle breeds (Afrikaner, Boran, Drakensberger, Nguni and Tuli) in South Africa. Pedigree completeness over six generations was higher than 88.5% in the first ...

  9. Genetic assessment of captive elephant (Elephas maximus) populations in Thailand

    NARCIS (Netherlands)

    Thitaram, Chatchote; Somgird, Chaleamchart; Mahasawangkul, Sittidet; Angkavanich, Taweepoke; Roongsri, Ronnachit; Thongtip, Nikorn; Colenbrander, Ben; van Steenbeek, Frank G.; Lenstra, Johannes A.

    2010-01-01

    The genetic diversity and population structure of 136 captive Thai elephants (Elephas maximus) with known region of origin were investigated by analysis of 14 highly polymorphic microsatellite loci. We did not detect significant indications of inbreeding and only a low differentiation of elephants

  10. Population genetic diversity and hybrid detection in captive zebras.

    Science.gov (United States)

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

    2015-08-21

    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.

  11. RAPD analysis for genetic diversity of two populations of Mystus ...

    African Journals Online (AJOL)

    ) was applied to analyze the genetic variation of the 2 populations of Mystus vittatus (Bloch) of Madhya Pradesh, India. 10 random 10-mer primers were primarily scored in 3 individuals from each of the 2 locations. Five primers, which gave ...

  12. Genetic diversity of endangered populations of Butia capitata ...

    African Journals Online (AJOL)

    The flora and fauna of the Cerrado biome in central Brazil both show great diversity and high levels of endemism. Butia capitata is a palm native to this biome that has significant economic, social, and environmental value. We sought to identify and quantify the genetic diversity of four fragmented populations of B. capitata ...

  13. Genetic variability and structure of an isolated population of ...

    Indian Academy of Sciences (India)

    Rosa-Laura Heredia-Bobadilla

    2017-11-15

    Nov 15, 2017 ... Journal of Genetics, Vol. 96, No. 6, December 2017 ... or international status of protection. The mole ... populations by a matrix of agriculture and urbanization, can be considered ...... BioScience 38, 471–479. Lemos-Espinal ...

  14. Genetic diversity in Kenyan populations of Acacia senegal (L.) willd ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-07-18

    Jul 18, 2008 ... species grows to 2-15 m tall with a flat or rounded crown. (Maundu et al., 1999). ... Our knowledge on the structure of genetic diversity of. A. senegal in Kenya ..... conclusion that spatial organization of local populations and the ...

  15. Genetic and metabolite diversity of Sardinian populations of Helichrysum italicum.

    Science.gov (United States)

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

    2013-01-01

    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. 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. 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. 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.

  16. Genetic and metabolite diversity of Sardinian populations of Helichrysum italicum.

    Directory of Open Access Journals (Sweden)

    Sara Melito

    Full Text Available 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.

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

    Science.gov (United States)

    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 ...

  18. Genetic diversity of Jatropha curcas L. populations in Kenya using ...

    African Journals Online (AJOL)

    Jatropha curcas L is an economically potential tree species gaining interest globally because of its feasible contribution towards production of commercial biofuel. Little is known however, of its genetic variation patterns within Kenyan accessions for maximum exploitation. Eight populations covering most of its distribution ...

  19. Intertidal population genetic dynamics at a microgeographic seascape scale.

    Science.gov (United States)

    Hu, Zi-Min

    2013-06-01

    The intertidal community is among the most physically harsh niches on earth, with highly heterogeneous environmental and biological factors that impose strong habitat selection on population abundance, genetic connectivity and ecological adaptation of organisms in nature. However, most genetic studies to date have concentrated on the influence of basin-wide or regional marine environments (e.g. habitat discontinuities, oceanic currents and fronts, and geographic barriers) on spatiotemporal distribution and composition of intertidal invertebrates having planktonic stages or long-distance dispersal capability. Little is known about sessile marine organisms (e.g. seaweeds) in the context of topographic tidal gradients and reproductive traits at the microgeographic scale. In this issue of Molecular Ecology, Krueger-Hadfield et al. () implemented an elaborate sampling strategy with red seaweed (Chondrus crispus) from a 90-m transect stand near Roscoff and comprehensively detected genome-scale genetic differentiation and biases in ploidy level. This study not only revealed that tidal height resulted in genetic differentiation between high- and low-shore stands and restricted the genetic exchange within the high-shore habitat, but also demonstrated that intergametophytic nonrandom fertilization in C. crispus can cause significant deviation from Hardy-Weinberg equilibrium. Such new genetic insights highlight the importance of microgeographic genetic dynamics and life history characteristics for better understanding the evolutionary processes of speciation and diversification of intertidal marine organisms. © 2013 John Wiley & Sons Ltd.

  20. Local environment but not genetic differentiation influences biparental care in ten plover populations.

    Directory of Open Access Journals (Sweden)

    Orsolya Vincze

    Full Text Available Social behaviours are highly variable between species, populations and individuals. However, it is contentious whether behavioural variations are primarily moulded by the environment, caused by genetic differences, or a combination of both. Here we establish that biparental care, a complex social behaviour that involves rearing of young by both parents, differs between closely related populations, and then test two potential sources of variation in parental behaviour between populations: ambient environment and genetic differentiation. We use 2904 hours behavioural data from 10 geographically distinct Kentish (Charadrius alexandrinus and snowy plover (C. nivosus populations in America, Europe, the Middle East and North Africa to test these two sources of behavioural variation. We show that local ambient temperature has a significant influence on parental care: with extreme heat (above 40 °C total incubation (i.e. % of time the male or female incubated the nest increased, and female share (% female share of incubation decreased. By contrast, neither genetic differences between populations, nor geographic distances predicted total incubation or female's share of incubation. These results suggest that the local environment has a stronger influence on a social behaviour than genetic differentiation, at least between populations of closely related species.

  1. Detection of expression quantitative trait Loci in complex mouse crosses: impact and alleviation of data quality and complex population substructure.

    Science.gov (United States)

    Iancu, Ovidiu D; Darakjian, Priscila; Kawane, Sunita; Bottomly, Daniel; Hitzemann, Robert; McWeeney, Shannon

    2012-01-01

    Complex Mus musculus crosses, e.g., heterogeneous stock (HS), provide increased resolution for quantitative trait loci detection. However, increased genetic complexity challenges detection methods, with discordant results due to low data quality or complex genetic architecture. We quantified the impact of theses factors across three mouse crosses and two different detection methods, identifying procedures that greatly improve detection quality. Importantly, HS populations have complex genetic architectures not fully captured by the whole genome kinship matrix, calling for incorporating chromosome specific relatedness information. We analyze three increasingly complex crosses, using gene expression levels as quantitative traits. The three crosses were an F(2) intercross, a HS formed by crossing four inbred strains (HS4), and a HS (HS-CC) derived from the eight lines found in the collaborative cross. Brain (striatum) gene expression and genotype data were obtained using the Illumina platform. We found large disparities between methods, with concordance varying as genetic complexity increased; this problem was more acute for probes with distant regulatory elements (trans). A suite of data filtering steps resulted in substantial increases in reproducibility. Genetic relatedness between samples generated overabundance of detected eQTLs; an adjustment procedure that includes the kinship matrix attenuates this problem. However, we find that relatedness between individuals is not evenly distributed across the genome; information from distinct chromosomes results in relatedness structure different from the whole genome kinship matrix. Shared polymorphisms from distinct chromosomes collectively affect expression levels, confounding eQTL detection. We suggest that considering chromosome specific relatedness can result in improved eQTL detection.

  2. Population genetics of Trypanosoma brucei rhodesiense: clonality and diversity within and between foci.

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    Craig W Duffy

    2013-11-01

    Full Text Available African trypanosomes are unusual among pathogenic protozoa in that they can undergo their complete morphological life cycle in the tsetse fly vector with mating as a non-obligatory part of this development. Trypanosoma brucei rhodesiense, which infects humans and livestock in East and Southern Africa, has classically been described as a host-range variant of the non-human infective Trypanosoma brucei that occurs as stable clonal lineages. We have examined T. b. rhodesiense populations from East (Uganda and Southern (Malawi Africa using a panel of microsatellite markers, incorporating both spatial and temporal analyses. Our data demonstrate that Ugandan T. b. rhodesiense existed as clonal populations, with a small number of highly related genotypes and substantial linkage disequilibrium between pairs of loci. However, these populations were not stable as the dominant genotypes changed and the genetic diversity also reduced over time. Thus these populations do not conform to one of the criteria for strict clonality, namely stability of predominant genotypes over time, and our results show that, in a period in the mid 1990s, the previously predominant genotypes were not detected but were replaced by a novel clonal population with limited genetic relationship to the original population present between 1970 and 1990. In contrast, the Malawi T. b. rhodesiense population demonstrated significantly greater diversity and evidence for frequent genetic exchange. Therefore, the population genetics of T. b. rhodesiense is more complex than previously described. This has important implications for the spread of the single copy T. b. rhodesiense gene that allows human infectivity, and therefore the epidemiology of the human disease, as well as suggesting that these parasites represent an important organism to study the influence of optional recombination upon population genetic dynamics.

  3. Sex differences in genetic architecture of complex phenotypes?

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    Jacqueline M Vink

    Full Text Available We examined sex differences in familial resemblance for a broad range of behavioral, psychiatric and health related phenotypes (122 complex traits in children and adults. There is a renewed interest in the importance of genotype by sex interaction in, for example, genome-wide association (GWA studies of complex phenotypes. If different genes play a role across sex, GWA studies should consider the effect of genetic variants separately in men and women, which affects statistical power. Twin and family studies offer an opportunity to compare resemblance between opposite-sex family members to the resemblance between same-sex relatives, thereby presenting a test of quantitative and qualitative sex differences in the genetic architecture of complex traits. We analyzed data on lifestyle, personality, psychiatric disorder, health, growth, development and metabolic traits in dizygotic (DZ same-sex and opposite-sex twins, as these siblings are perfectly matched for age and prenatal exposures. Sample size varied from slightly over 300 subjects for measures of brain function such as EEG power to over 30,000 subjects for childhood psychopathology and birth weight. For most phenotypes, sample sizes were large, with an average sample size of 9027 individuals. By testing whether the resemblance in DZ opposite-sex pairs is the same as in DZ same-sex pairs, we obtain evidence for genetic qualitative sex-differences in the genetic architecture of complex traits for 4% of phenotypes. We conclude that for most traits that were examined, the current evidence is that same the genes are operating in men and women.

  4. Population genetics of non-genetic traits: Evolutionary roles of stochasticity in gene expression

    KAUST Repository

    Mineta, Katsuhiko; Matsumoto, Tomotaka; Osada, Naoki; Araki, Hitoshi

    2015-01-01

    The role of stochasticity in evolutionary genetics has long been debated. To date, however, the potential roles of non-genetic traits in evolutionary processes have been largely neglected. In molecular biology, growing evidence suggests that stochasticity in gene expression (SGE) is common and that SGE has major impacts on phenotypes and fitness. Here, we provide a general overview of the potential effects of SGE on population genetic parameters, arguing that SGE can indeed have a profound effect on evolutionary processes. Our analyses suggest that SGE potentially alters the fate of mutations by influencing effective population size and fixation probability. In addition, a genetic control of SGE magnitude could evolve under certain conditions, if the fitness of the less-fit individual increases due to SGE and environmental fluctuation. Although empirical evidence for our arguments is yet to come, methodological developments for precisely measuring SGE in living organisms will further advance our understanding of SGE-driven evolution.

  5. Population genetics of non-genetic traits: Evolutionary roles of stochasticity in gene expression

    KAUST Repository

    Mineta, Katsuhiko

    2015-05-01

    The role of stochasticity in evolutionary genetics has long been debated. To date, however, the potential roles of non-genetic traits in evolutionary processes have been largely neglected. In molecular biology, growing evidence suggests that stochasticity in gene expression (SGE) is common and that SGE has major impacts on phenotypes and fitness. Here, we provide a general overview of the potential effects of SGE on population genetic parameters, arguing that SGE can indeed have a profound effect on evolutionary processes. Our analyses suggest that SGE potentially alters the fate of mutations by influencing effective population size and fixation probability. In addition, a genetic control of SGE magnitude could evolve under certain conditions, if the fitness of the less-fit individual increases due to SGE and environmental fluctuation. Although empirical evidence for our arguments is yet to come, methodological developments for precisely measuring SGE in living organisms will further advance our understanding of SGE-driven evolution.

  6. Genetic effects at pleiotropic loci are context-dependent with consequences for the maintenance of genetic variation in populations.

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    Heather A Lawson

    2011-09-01

    Full Text Available Context-dependent genetic effects, including genotype-by-environment and genotype-by-sex interactions, are a potential mechanism by which genetic variation of complex traits is maintained in populations. Pleiotropic genetic effects are also thought to play an important role in evolution, reflecting functional and developmental relationships among traits. We examine context-dependent genetic effects at pleiotropic loci associated with normal variation in multiple metabolic syndrome (MetS components (obesity, dyslipidemia, and diabetes-related traits. MetS prevalence is increasing in Western societies and, while environmental in origin, presents substantial variation in individual response. We identify 23 pleiotropic MetS quantitative trait loci (QTL in an F(16 advanced intercross between the LG/J and SM/J inbred mouse strains (Wustl:LG,SM-G16; n = 1002. Half of each family was fed a high-fat diet and half fed a low-fat diet; and additive, dominance, and parent-of-origin imprinting genotypic effects were examined in animals partitioned into sex, diet, and sex-by-diet cohorts. We examine the context-dependency of the underlying additive, dominance, and imprinting genetic effects of the traits associated with these pleiotropic QTL. Further, we examine sequence polymorphisms (SNPs between LG/J and SM/J as well as differential expression of positional candidate genes in these regions. We show that genetic associations are different in different sex, diet, and sex-by-diet settings. We also show that over- or underdominance and ecological cross-over interactions for single phenotypes may not be common, however multidimensional synthetic phenotypes at loci with pleiotropic effects can produce situations that favor the maintenance of genetic variation in populations. Our findings have important implications for evolution and the notion of personalized medicine.

  7. A theoretical analysis of population genetics of plants on restored habitats

    Energy Technology Data Exchange (ETDEWEB)

    Bogoliubov, A.G. [Botanical Institute, Russian Academy of Science, St. Petersburg (Russian Federation); Loehle, C. [Argonne National Lab., IL (United States)

    1995-02-01

    Seed and propagules used for habitat restoration are not likely to be closely adapted to local site conditions. Rapid changes of genotypes frequencies on local microsites and/or microevolution would allow plants to become better adapted to a site. These same factors would help to maintain genetic diversity and ensure the survival of small endangered populations. We used population genetics models to examine the selection of genotypes during establishment on restored sites. Vegetative spread was shown to affect selection and significantly reduce genetic diversity. To study general microevolution, we linked a model of resource usage with a genetics model and analyzed competition between genotypes. A complex suite of feasible ecogenetic states was shown to result. The state actually resulting would depend strongly on initial conditions. This analysis indicated that genetic structure can vary locally and can produce overall genetic variability that is not simply the result of microsite adaptations. For restoration activities, the implication is that small differences in seed source could lead to large differences in local genetic structure after selection.

  8. A theoretical analysis of population genetics of plants on restored habitats

    Energy Technology Data Exchange (ETDEWEB)

    Bogoliubov, A.G. [Russian Academy of Science, St. Petersburg (Russian Federation). Botanical Inst.; Loehle, C. [Argonne National Lab., IL (United States). Environmental Research Div.

    1997-07-01

    Seed and propagules used for habitat restoration are not likely to be closely adapted to local site conditions. Rapid changes of genotypes frequencies on local microsites and/or microevolution would allow plants to become better adapted to a site. These same factors would help to maintain genetic diversity and ensure the survival of small endangered populations. The authors used population genetics models to examine the selection of genotypes during establishment on restored sites. Vegetative spread was shown to affect selection and significantly reduce genetic diversity. To study general microevolution, the authors linked a model of resource usage with a genetics model and analyzed competition between genotypes. A complex suite of feasible ecogenetic states was shown to result. The state actually resulting would depend strongly on initial conditions. This analysis indicated that genetic structure can vary locally and can produce overall genetic variability that is not simply the result of microsite adaptations. For restoration activities, the implication is that small differences in seed source could lead to large differences in local genetic structure after selection.

  9. Shallow Population Genetic Structures of Thread-sail Filefish (Stephanolepis cirrhifer) Populations from Korean Coastal Waters.

    Science.gov (United States)

    Yoon, M; Park, W; Nam, Y K; Kim, D S

    2012-02-01

    Genetic diversities, population genetic structures and demographic histories of the thread-sail filefish Stephanolepis cirrhifer were investigated by nucleotide sequencing of 336 base pairs of the mitochondrial DNA (mtDNA) control region in 111 individuals collected from six populations in Korean coastal waters. A total of 70 haplotypes were defined by 58 variable nucleotide sites. The neighbor-joining tree of the 70 haplotypes was shallow and did not provide evidence of geographical associations. Expansion of S. cirrhifer populations began approximate 51,000 to 102,000 years before present, correlating with the period of sea level rise since the late Pleistocene glacial maximum. High levels of haplotype diversities (0.974±0.029 to 1.000±0.076) and nucleotide diversities (0.014 to 0.019), and low levels of genetic differentiation among populations inferred from pairwise population F ST values (-0.007 to 0.107), support an expansion of the S. cirrhifer population. Hierarchical analysis of molecular variance (AMOVA) revealed weak but significant genetic structures among three groups (F CT = 0.028, p<0.05), and no genetic variation within groups (0.53%; F SC = 0.005, p = 0.23). These results may help establish appropriate fishery management strategies for stocks of S. cirrhifer and related species.

  10. Shallow Population Genetic Structures of Thread-sail Filefish ( Populations from Korean Coastal Waters

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    M. Yoon

    2012-02-01

    Full Text Available Genetic diversities, population genetic structures and demographic histories of the thread-sail filefish Stephanolepis cirrhifer were investigated by nucleotide sequencing of 336 base pairs of the mitochondrial DNA (mtDNA control region in 111 individuals collected from six populations in Korean coastal waters. A total of 70 haplotypes were defined by 58 variable nucleotide sites. The neighbor-joining tree of the 70 haplotypes was shallow and did not provide evidence of geographical associations. Expansion of S. cirrhifer populations began approximate 51,000 to 102,000 years before present, correlating with the period of sea level rise since the late Pleistocene glacial maximum. High levels of haplotype diversities (0.974±0.029 to 1.000±0.076 and nucleotide diversities (0.014 to 0.019, and low levels of genetic differentiation among populations inferred from pairwise population FST values (−0.007 to 0.107, support an expansion of the S. cirrhifer population. Hierarchical analysis of molecular variance (AMOVA revealed weak but significant genetic structures among three groups (FCT = 0.028, p<0.05, and no genetic variation within groups (0.53%; FSC = 0.005, p = 0.23. These results may help establish appropriate fishery management strategies for stocks of S. cirrhifer and related species.

  11. Genetic characterization of natural populations of pineapple guava (Acca sellowiana, with heterologous microsatellites markers

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    Karine Louise dos Santos

    2011-12-01

    Full Text Available Pineapple guava (Acca sellowiana is a native species from south Brazil and northeast Uruguay, and due to the unique flavor of its fruits, it is an income-generating alternative to small farmers. Knowledge on genetic diversity is an important tool for genetic improvement and conservation. Aiming to increase the knowledge with regarde to the species genetic diversity, fi ve natural populations of A. sellowiana were analyzed through microsatellites markers developed from Eucalyptus grandis W. Hill ex Maiden x E. urophylla S.T. Blake complex. Using 10 pairs of selected markers, 122 plants were characterized. The mean values for expected and observed heterozigosity were 0.42 and 0.47, respectively. The fˆ estimates did not differ from zero to four out of the five populations evaluated, suggesting a small inbreeding effect. In addition, private alleles and high genetic divergence was observed. the average genetic divergence among the populations was st Fˆ = 0,13 e st Rˆ = 0,14, mostly due to the incidenceof rare or exclusive alleles among some populations.

  12. Population genetic analysis of Enterocytozoon bieneusi in humans.

    Science.gov (United States)

    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. Published by Elsevier Ltd.

  13. Chronic irradiation as an ecological factor affecting genetic population structure

    International Nuclear Information System (INIS)

    Kal'chenko, V.A.; Kalabushkin, B.A.; Rubanovich, A.V.

    1991-01-01

    Genetic structure of two Centaurea scabiosa L. populations was studied by frequency distribution of leucine aminopeptidase (LAP) locus genotypes. The experimental population has been growing under conditions of chronic irradiation, with the dose per generation amounting to 1.2 to 25.5 Gy. In it, mutational variants are observed with a frequency of 5.4.10(-3)-4.5.10(-2) per generation (as compared to control population frequency at 5.4.10(-4)). Indexes for heterozygosity, mean number of genotypes, and effective number of alleles were higher in the experimental population. Segregation analysis revealed no differences in viability in the control population, and all genotypic combinations were found to be nearly neutral. In the experimental population, however, significant differences in relative viability of the genotypes were disclosed. The relative viability of heterozygotes for mutant allele C' was nearly maximum, while heterozygotes for other mutant alleles showed minimum viability. We reach the conclusion that the differences in genetic structure of the populations under investigation can be explained by the chronic irradiation factor that brought out differences in adaptability of both normal and mutant genotypes. The suggestion is that intra-locus interactions of the C' allele with normal alleles determine plant resistance to a wide range of unfavorable environmental conditions

  14. Non-invasive genetic censusing and monitoring of primate populations.

    Science.gov (United States)

    Arandjelovic, Mimi; Vigilant, Linda

    2018-03-01

    Knowing the density or abundance of primate populations is essential for their conservation management and contextualizing socio-demographic and behavioral observations. When direct counts of animals are not possible, genetic analysis of non-invasive samples collected from wildlife populations allows estimates of population size with higher accuracy and precision than is possible using indirect signs. Furthermore, in contrast to traditional indirect survey methods, prolonged or periodic genetic sampling across months or years enables inference of group membership, movement, dynamics, and some kin relationships. Data may also be used to estimate sex ratios, sex differences in dispersal distances, and detect gene flow among locations. Recent advances in capture-recapture models have further improved the precision of population estimates derived from non-invasive samples. Simulations using these methods have shown that the confidence interval of point estimates includes the true population size when assumptions of the models are met, and therefore this range of population size minima and maxima should be emphasized in population monitoring studies. Innovations such as the use of sniffer dogs or anti-poaching patrols for sample collection are important to ensure adequate sampling, and the expected development of efficient and cost-effective genotyping by sequencing methods for DNAs derived from non-invasive samples will automate and speed analyses. © 2018 Wiley Periodicals, Inc.

  15. Genetic variation of cowslip (Primula veris L. populations (West Poland

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    Maria Morozowska

    2011-01-01

    Full Text Available Genetic variation of twelve Polish populations of Primula veris L. from western Poland was investigated in respect of six enzyme systems: 6-phosphogluconate dehydrogenase (6PGD, diaphorase (DIA, menadione reductase (MNR, formate dehydrogenase (FDH, isocitrate dehydrogenase (IDH and glutamate oxaloacetate transaminase (GOT. Only two of them (6PGD and DIA were polymorphic and all populations were compared according to four loci and eight alleles. For 6PGD only one out of the two detected loci (locus 6PGD-2 was polymorphic and consisted of three alleles a, b and c. For DIA each of two detected loci had two alleles. For 6PGD-2 one population was monomorphic and four populations were monomorphic for DIA-1 and DIA-2. The rest of the populations were polymorphic with low frequency of heterozygotes. The low heterozygosity level, found in the examined populations, was confirmed by high values of the fixation index (F. The level of genetic differentiation among GST populations specified for each polymorphic loci, was equal to 0.045 for 6PGD-2 and had the value of 0.078 for DIA-2 and 0.186 for DIA-1. Nm value for polymorphic loci was 1.10 for DIA-1 and 2.94 for DIA-2, and for 6PGD-2 was 5.33, what indicates some gene flow between the examined populations. The dendrogram constructed on the basis of genotype frequencies showed that the populations were divided into two groups, however the most southern population No. 2 was clearly similar to the northern population No. 8.

  16. Genetic structure of a unique admixed population: implications for medical research.

    Science.gov (United States)

    Patterson, Nick; Petersen, Desiree C; van der Ross, Richard E; Sudoyo, Herawati; Glashoff, Richard H; Marzuki, Sangkot; Reich, David; Hayes, Vanessa M

    2010-02-01

    STATEMENT: In naming population groups, we think a chief aim is to use terms that the group members use themselves, or find familiar and comfortable. The terms used in this manuscript to describe populations are as historically correct as possible and are chosen so as not to offend any population group. Two of the authors (DCP and REvdR) belong to the Coloured population, with one of the authors (REvdR) having contributed extensively to current literature on the history of the Coloured people of South Africa and served as Vice-President of the South African Institute of Race Relations. According to the 2001 South African census (http://www.statssa.gov.za/census01/HTML/CInBrief/CIB2001.pdf), "Statistics South Africa continues to classify people by population group, in order to monitor progress in moving away from the apartheid-based discrimination of the past. However, membership of a population group is now based on self-perception and self-classification, not on a legal definition. Five options were provided on the questionnaire, Black African, Coloured, Indian or Asian, White and Other. Responses in the category 'Other' were very few and were therefore imputed". We have elected to use the term Bushmen rather than San to refer to the hunter-gatherer people of Southern Africa. Although they have no collective name for themselves, this decision was based on the term Bushmen (or Bossiesman) being the more familiar to the communities themselves, while the term San is the more accepted academic classification. Understanding human genetic structure has fundamental implications for understanding the evolution and impact of human diseases. In this study, we describe the complex genetic substructure of a unique and recently admixed population arising approximately 350 years ago as a direct result of European settlement in South Africa. Analysis was performed using over 900 000 genome-wide single nucleotide polymorphisms in 20 unrelated ancestry-informative marker selected

  17. Local Genetic Correlation Gives Insights into the Shared Genetic Architecture of Complex Traits.

    Science.gov (United States)

    Shi, Huwenbo; Mancuso, Nicholas; Spendlove, Sarah; Pasaniuc, Bogdan

    2017-11-02

    Although genetic correlations between complex traits provide valuable insights into epidemiological and etiological studies, a precise quantification of which genomic regions disproportionately contribute to the genome-wide correlation is currently lacking. Here, we introduce ρ-HESS, a technique to quantify the correlation between pairs of traits due to genetic variation at a small region in the genome. Our approach requires GWAS summary data only and makes no distributional assumption on the causal variant effect sizes while accounting for linkage disequilibrium (LD) and overlapping GWAS samples. We analyzed large-scale GWAS summary data across 36 quantitative traits, and identified 25 genomic regions that contribute significantly to the genetic correlation among these traits. Notably, we find 6 genomic regions that contribute to the genetic correlation of 10 pairs of traits that show negligible genome-wide correlation, further showcasing the power of local genetic correlation analyses. Finally, we report the distribution of local genetic correlations across the genome for 55 pairs of traits that show putative causal relationships. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  18. Genetic and phenotypic characterization of complex hereditary spastic paraplegia

    Science.gov (United States)

    Kara, Eleanna; Tucci, Arianna; Manzoni, Claudia; Lynch, David S.; Elpidorou, Marilena; Bettencourt, Conceicao; Chelban, Viorica; Manole, Andreea; Hamed, Sherifa A.; Haridy, Nourelhoda A.; Federoff, Monica; Preza, Elisavet; Hughes, Deborah; Pittman, Alan; Jaunmuktane, Zane; Brandner, Sebastian; Xiromerisiou, Georgia; Wiethoff, Sarah; Schottlaender, Lucia; Proukakis, Christos; Morris, Huw; Warner, Tom; Bhatia, Kailash P.; Korlipara, L.V. Prasad; Singleton, Andrew B.; Hardy, John; Wood, Nicholas W.; Lewis, Patrick A.

    2016-01-01

    Abstract The hereditary spastic paraplegias are a heterogeneous group of degenerative disorders that are clinically classified as either pure with predominant lower limb spasticity, or complex where spastic paraplegia is complicated with additional neurological features, and are inherited in autosomal dominant, autosomal recessive or X-linked patterns. Genetic defects have been identified in over 40 different genes, with more than 70 loci in total. Complex recessive spastic paraplegias have in the past been frequently associated with mutations in SPG11 (spatacsin), ZFYVE26/SPG15 , SPG7 (paraplegin) and a handful of other rare genes, but many cases remain genetically undefined. The overlap with other neurodegenerative disorders has been implied in a small number of reports, but not in larger disease series. This deficiency has been largely due to the lack of suitable high throughput techniques to investigate the genetic basis of disease, but the recent availability of next generation sequencing can facilitate the identification of disease-causing mutations even in extremely heterogeneous disorders. We investigated a series of 97 index cases with complex spastic paraplegia referred to a tertiary referral neurology centre in London for diagnosis or management. The mean age of onset was 16 years (range 3 to 39). The SPG11 gene was first analysed, revealing homozygous or compound heterozygous mutations in 30/97 (30.9%) of probands, the largest SPG11 series reported to date, and by far the most common cause of complex spastic paraplegia in the UK, with severe and progressive clinical features and other neurological manifestations, linked with magnetic resonance imaging defects. Given the high frequency of SPG11 mutations, we studied the autophagic response to starvation in eight affected SPG11 cases and control fibroblast cell lines, but in our restricted study we did not observe correlations between disease status and autophagic or lysosomal markers. In the remaining

  19. Change in genetic size of small-closed populations: lessons from a domestic mammal population

    Directory of Open Access Journals (Sweden)

    Farhad Ghafouri-Kesbi

    2010-01-01

    Full Text Available The aim of this study was to monitor changes in genetic size of a small-closed population of Iranian Zandi sheep, by using pedigree information from animals born between 1991 and 2005. The genetic size was assessed by using measures based on the probability of identity-by-descend of genes (coancestry, f, and effective population size, Ne, as well as measures based on probability of gene origin (effective number of founders, f e, effective number of founder genomes, f g, and effective number of non-founder genomes, f ne. Average coancestry, or the degree of genetic similarity of individuals, increased from 0.81% to 1.44% during the period 1993 to 2005, at the same time that Ne decreased from 263 to 93. The observed trend for f e was irregular throughout the experiment in a way that f e was 68, 87, 77, 92, and 80 in 1993, 1996, 1999, 2002, and 2005, respectively. Simultaneously, f g, the most informative effective number, decreased from 61 to 35. The index of genetic diversity (GD which was obtained from estimates of f g,decreased about 2% throughout the period studied. In addition, a noticeable reduction was observed in the estimates of f ne from 595 in 1993 to 61 in 2005. The higher than 1 ratio of f e to f g indicated the presence of bottlenecks and genetic drift in the development of this population of Zandi sheep. From 1993 to 1999, f ne was much higher than f e, thereby indicating that with respect to loss of genetic diversity, the unequal contribution of founders was more important than the random genetic drift in non-founder generations. Subsequently, random genetic drift in non-founder generations was the major reason for f e> f ne. The minimization of average coancestry in new reproductive individuals was recommended as a means of preserving the population against a further loss in genetic diversity.

  20. Impact of the mitochondrial genetic background in complex III deficiency.

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    Mari Carmen Gil Borlado

    Full Text Available BACKGROUND: In recent years clinical evidence has emphasized the importance of the mtDNA genetic background that hosts a primary pathogenic mutation in the clinical expression of mitochondrial disorders, but little experimental confirmation has been provided. We have analyzed the pathogenic role of a novel homoplasmic mutation (m.15533 A>G in the cytochrome b (MT-CYB gene in a patient presenting with lactic acidosis, seizures, mild mental delay, and behaviour abnormalities. METHODOLOGY: Spectrophotometric analyses of the respiratory chain enzyme activities were performed in different tissues, the whole muscle mitochondrial DNA of the patient was sequenced, and the novel mutation was confirmed by PCR-RFLP. Transmitochondrial cybrids were constructed to confirm the pathogenicity of the mutation, and assembly/stability studies were carried out in fibroblasts and cybrids by means of mitochondrial translation inhibition in combination with blue native gel electrophoresis. PRINCIPAL FINDINGS: Biochemical analyses revealed a decrease in respiratory chain complex III activity in patient's skeletal muscle, and a combined enzyme defect of complexes III and IV in fibroblasts. Mutant transmitochondrial cybrids restored normal enzyme activities and steady-state protein levels, the mutation was mildly conserved along evolution, and the proband's mother and maternal aunt, both clinically unaffected, also harboured the homoplasmic mutation. These data suggested a nuclear genetic origin of the disease. However, by forcing the de novo functioning of the OXPHOS system, a severe delay in the biogenesis of the respiratory chain complexes was observed in the mutants, which demonstrated a direct functional effect of the mitochondrial genetic background. CONCLUSIONS: Our results point to possible pitfalls in the detection of pathogenic mitochondrial mutations, and highlight the role of the genetic mtDNA background in the development of mitochondrial disorders.

  1. Complex chloroplast RNA metabolism: just debugging the genetic programme?

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    Schmitz-Linneweber Christian

    2008-08-01

    Full Text Available Abstract Background The gene expression system of chloroplasts is far more complex than that of their cyanobacterial progenitor. This gain in complexity affects in particular RNA metabolism, specifically the transcription and maturation of RNA. Mature chloroplast RNA is generated by a plethora of nuclear-encoded proteins acquired or recruited during plant evolution, comprising additional RNA polymerases and sigma factors, and sequence-specific RNA maturation factors promoting RNA splicing, editing, end formation and translatability. Despite years of intensive research, we still lack a comprehensive explanation for this complexity. Results We inspected the available literature and genome databases for information on components of RNA metabolism in land plant chloroplasts. In particular, new inventions of chloroplast-specific mechanisms and the expansion of some gene/protein families detected in land plants lead us to suggest that the primary function of the additional nuclear-encoded components found in chloroplasts is the transgenomic suppression of point mutations, fixation of which occurred due to an enhanced genetic drift exhibited by chloroplast genomes. We further speculate that a fast evolution of transgenomic suppressors occurred after the water-to-land transition of plants. Conclusion Our inspections indicate that several chloroplast-specific mechanisms evolved in land plants to remedy point mutations that occurred after the water-to-land transition. Thus, the complexity of chloroplast gene expression evolved to guarantee the functionality of chloroplast genetic information and may not, with some exceptions, be involved in regulatory functions.

  2. Genetic structure and gene flows within horses: a genealogical study at the french population scale.

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    Pauline Pirault

    Full Text Available Since horse breeds constitute populations submitted to variable and multiple outcrossing events, we analyzed the genetic structure and gene flows considering horses raised in France. We used genealogical data, with a reference population of 547,620 horses born in France between 2002 and 2011, grouped according to 55 breed origins. On average, individuals had 6.3 equivalent generations known. Considering different population levels, fixation index decreased from an overall species FIT of 1.37%, to an average [Formula: see text] of -0.07% when considering the 55 origins, showing that most horse breeds constitute populations without genetic structure. We illustrate the complexity of gene flows existing among horse breeds, a few populations being closed to foreign influence, most, however, being submitted to various levels of introgression. In particular, Thoroughbred and Arab breeds are largely used as introgression sources, since those two populations explain together 26% of founder origins within the overall horse population. When compared with molecular data, breeds with a small level of coancestry also showed low genetic distance; the gene pool of the breeds was probably impacted by their reproducer exchanges.

  3. Genetic structure and gene flows within horses: a genealogical study at the french population scale.

    Science.gov (United States)

    Pirault, Pauline; Danvy, Sophy; Verrier, Etienne; Leroy, Grégoire

    2013-01-01

    Since horse breeds constitute populations submitted to variable and multiple outcrossing events, we analyzed the genetic structure and gene flows considering horses raised in France. We used genealogical data, with a reference population of 547,620 horses born in France between 2002 and 2011, grouped according to 55 breed origins. On average, individuals had 6.3 equivalent generations known. Considering different population levels, fixation index decreased from an overall species FIT of 1.37%, to an average [Formula: see text] of -0.07% when considering the 55 origins, showing that most horse breeds constitute populations without genetic structure. We illustrate the complexity of gene flows existing among horse breeds, a few populations being closed to foreign influence, most, however, being submitted to various levels of introgression. In particular, Thoroughbred and Arab breeds are largely used as introgression sources, since those two populations explain together 26% of founder origins within the overall horse population. When compared with molecular data, breeds with a small level of coancestry also showed low genetic distance; the gene pool of the breeds was probably impacted by their reproducer exchanges.

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

    Science.gov (United States)

    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.

  5. Phylogenetic relationships and genetic diversity of the Polypedates leucomystax complex in Thailand

    Directory of Open Access Journals (Sweden)

    Kittisak Buddhachat

    2018-01-01

    Full Text Available Taxonomic uncertainty of the Asian tree frog Polypedates leucomystax complex presents the challenging task of inferring its biogeographical history. Here, we describe its dispersion and the genetic relationships among different populations in Thailand, where we connect the population of the P. leucomystax complex of the Sunda Islands to the Indochina (mainland population based on analyses of 266 sequences of the mitochondrial cytochrome c oxidase subunit I (COI gene. Our maternal genealogy implies that there are four well-supported lineages in Thailand, consisting of Northern A (clade A: Polypedates sp., Nan (clade B: P. cf. impresus, Southern (clade C: P. cf. leucomystax and Northern D (clade D: P. cf. megacephalus, with Bayesian posterior probability >0.9. Phylogeny and haplotype networks indicate that clades A, B and D are sympatric. In contrast, clade C (P. cf. leucomystax and clade D (P. cf. megacephalus are genetically divergent due to the geographical barrier of the Isthmus of Kra, resulting in an allopatric distribution. Climatic conditions, in particular differences in rainfall on each side of the Isthmus of Kra, may play an important role in limiting the immigration of both clades. For the within-populations of either clades C or D, there was no significant correlation between geographic and genetic distance by the isolation-by-distance test, indicating intraspecific-dispersal of each clade. Population expansion occurred in clade C, whereas clade D showed a constant population. Taken together, the P. leucomystax complex in South East Asia may have diversified under climatic pressure, leading to allopatric and/or sympatric speciation.

  6. A population on the edge: genetic diversity and population structure of the world's northernmost harbour seals (Phoca vitulina)

    DEFF Research Database (Denmark)

    Andersen, Liselotte Wesley; Lydersen, Christian; Frie, Anne Kirstine

    2011-01-01

    insight into consequences of population declines in a broader conservation context. The harbour seal population at Svalbard is the world's northernmost harbour seal population. Nothing is known about the genetic diversity, distinctiveness or origin of this small, marginalized mammalian population. Thus......  It is crucial to examine the genetic diversity and structure of small, isolated populations, especially those at the edge of their distribution range, because they are vulnerable to stochastic processes if genetic diversity is low and isolation level high, and because such populations provide...... microsatellites and variation in the D-loop. Each of the four locations was a genetically distinct population. The Svalbard population was highly genetically distinct, had reduced genetic diversity, received limited gene flow, had a rather low effective population size and showed an indication of having...

  7. Distribution and population genetics of walleye and sauger

    Science.gov (United States)

    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”.

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

    Science.gov (United States)

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

    2014-12-01

    The distribution, abundance, and diversity of life on Earth have been greatly shaped by human activities. This includes the geographic expansion of parasites; however, measuring the extent to which humans have influenced the dissemination and population structure of parasites has been challenging. In-depth comparisons among parasite populations extending to landscape-level processes affecting disease emergence have remained elusive. New research methods have enhanced our capacity to discern human impact, where the tools of population genetics and molecular epidemiology have begun to shed light on our historical and ongoing influence. Only since the 1990s have parasitologists coupled morphological diagnosis, long considered the basis of surveillance and biodiversity studies, with state-of-the-art tools enabling variation to be examined among, and within, parasite populations. Prior to this time, populations were characterized only by phenotypic attributes such as virulence, infectivity, host range, and geographical location. The advent of genetic/molecular methodologies (multilocus allozyme electrophoresis, polymerase chain reaction-DNA [PCR-DNA] fragments analysis, DNA sequencing, DNA microsatellites, single nucleotide polymorphisms, etc.) have transformed our abilities to reveal variation among, and within, populations at local, regional, landscape, and global scales, and thereby enhanced our understanding of the biosphere. Numerous factors can affect population structure among parasites, e.g., evolutionary and ecological history, mode of reproduction and transmission, host dispersal, and life-cycle complexity. Although such influences can vary considerably among parasite taxa, anthropogenic factors are demonstrably perturbing parasite fauna. Minimal genetic structure among many geographically distinct (isolated) populations is a hallmark of human activity, hastened by geographic introductions, environmental perturbation, and global warming. Accelerating

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

    Science.gov (United States)

    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. © 2010 Blackwell Publishing Ltd.

  10. The Individual and Population Genetics of Antibody Immunity.

    Science.gov (United States)

    Watson, Corey T; Glanville, Jacob; Marasco, Wayne A

    2017-07-01

    Antibodies (Abs) produced by immunoglobulin (IG) genes are the most diverse proteins expressed in humans. While part of this diversity is generated by recombination during B-cell development and mutations during affinity maturation, the germ-line IG loci are also diverse across human populations and ethnicities. Recently, proof-of-concept studies have demonstrated genotype-phenotype correlations between specific IG germ-line variants and the quality of Ab responses during vaccination and disease. However, the functional consequences of IG genetic variation in Ab function and immunological outcomes remain underexplored. In this opinion article, we outline interconnections between IG genomic diversity and Ab-expressed repertoires and structure. We further propose a strategy for integrating IG genotyping with functional Ab profiling data as a means to better predict and optimize humoral responses in genetically diverse human populations, with immediate implications for personalized medicine. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Quantifying population genetic differentiation from next-generation sequencing data

    DEFF Research Database (Denmark)

    Fumagalli, Matteo; Garrett Vieira, Filipe Jorge; Korneliussen, Thorfinn Sand

    2013-01-01

    method for quantifying population genetic differentiation from next-generation sequencing data. In addition, we present a strategy to investigate population structure via Principal Components Analysis. Through extensive simulations, we compare the new method herein proposed to approaches based...... on genotype calling and demonstrate a marked improvement in estimation accuracy for a wide range of conditions. We apply the method to a large-scale genomic data set of domesticated and wild silkworms sequenced at low coverage. We find that we can infer the fine-scale genetic structure of the sampled......Over the last few years, new high-throughput DNA sequencing technologies have dramatically increased speed and reduced sequencing costs. However, the use of these sequencing technologies is often challenged by errors and biases associated with the bioinformatical methods used for analyzing the data...

  12. Genetic polymorphism and population structure of Echinococcus ortleppi.

    Science.gov (United States)

    Addy, F; Wassermann, M; Banda, F; Mbaya, H; Aschenborn, J; Aschenborn, O; Koskei, P; Umhang, G; DE LA Rue, M; Elmahdi, I E; Mackenstedt, U; Kern, P; Romig, T

    2017-04-01

    The zoonotic cestode Echinococcus ortleppi (Lopez-Neyra and Soler Planas, 1943) is mainly transmitted between dogs and cattle. It occurs worldwide but is only found sporadically in most regions, with the notable exception of parts of southern Africa and South America. Its epidemiology is little understood and the extent of intraspecific variability is unknown. We have analysed in the present study the genetic diversity among 178 E. ortleppi isolates from sub-Saharan Africa, Europe and South America using the complete mitochondrial cox1 (1608 bp) and nad1 (894 bp) DNA sequences. Genetic polymorphism within the loci revealed 15 cox1 and six nad1 haplotypes, respectively, and 20 haplotypes of the concatenated genes. Presence of most haplotypes was correlated to geographical regions, and only one haplotype had a wider spread in both eastern and southern Africa. Intraspecific microvariance was low in comparison with Echinococcus granulosus sensu stricto, despite the wide geographic range of examined isolates. In addition, the various sub-populations showed only subtle deviation from neutrality and were mostly genetically differentiated. This is the first insight into the population genetics of the enigmatic cattle adapted Echinococcus ortleppi. It, therefore, provides baseline data for biogeographical comparison among E. ortleppi endemic regions and for tracing its translocation paths.

  13. A complex scenario of tuberculosis transmission is revealed through genetic and epidemiological surveys in Porto.

    Science.gov (United States)

    Rito, Teresa; Matos, Carlos; Carvalho, Carlos; Machado, Henrique; Rodrigues, Gabriela; Oliveira, Olena; Ferreira, Eduarda; Gonçalves, Jorge; Maio, Lurdes; Morais, Clara; Ramos, Helena; Guimarães, João Tiago; Santos, Catarina L; Duarte, Raquel; Correia-Neves, Margarida

    2018-01-25

    Tuberculosis (TB) incidence is decreasing worldwide and eradication is becoming plausible. In low-incidence countries, intervention on migrant populations is considered one of the most important strategies for elimination. However, such measures are inappropriate in European areas where TB is largely endemic, such as Porto in Portugal. We aim to understand transmission chains in Porto through a genetic characterization of Mycobacterium tuberculosis strains and through a detailed epidemiological evaluation of cases. We genotyped the M. tuberculosis strains using the MIRU-VNTR system. We performed an evolutionary reconstruction of the genotypes with median networks, used in this context for the first time. TB cases from a period of two years were evaluated combining genetic, epidemiological and georeferencing information. The data reveal a unique complex scenario in Porto where the autochthonous population acts as a genetic reservoir of M. tuberculosis diversity with discreet episodes of transmission, mostly undetected using classical epidemiology alone. Although control policies have been successful in decreasing incidence in Porto, the discerned complexity suggests that, for elimination to be a realistic goal, strategies need to be adjusted and coupled with a continuous genetic characterization of strains and detailed epidemiological evaluation, in order to successfully identify and interrupt transmission chains.

  14. Quantitative genetics of migration syndromes: a study of two barn swallow populations.

    Science.gov (United States)

    Teplitsky, C; Mouawad, N G; Balbontin, J; De Lope, F; Møller, A P

    2011-09-01

    Migration is a complex trait although little is known about genetic correlations between traits involved in such migration syndromes. To assess the migratory responses to climate change, we need information on genetic constraints on evolutionary potential of arrival dates in migratory birds. Using two long-term data sets on barn swallows Hirundo rustica (from Spain and Denmark), we show for the first time in wild populations that spring arrival dates are phenotypically and genetically correlated with morphological and life history traits. In the Danish population, length of outermost tail feathers and wing length were negatively genetically correlated with arrival date. In the Spanish population, we found a negative genetic correlation between arrival date and time elapsed between arrival date and laying date, constraining response to selection that favours both early arrival and shorter delays. This results in a decreased rate of adaptation, not because of constraints on arrival date, but constraints on delay before breeding, that is, a trait that can be equally important in the context of climate change. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

  15. Genetic Evidence for Recent Population Mixture in India

    OpenAIRE

    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 ...

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

    Science.gov (United States)

    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. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  17. Plasmodium falciparum: genetic diversity and complexity of infections in an isolated village in western Thailand.

    Science.gov (United States)

    Tanabe, Kazuyuki; Zollner, Gabriela; Vaughan, Jefferson A; Sattabongkot, Jetsumon; Khuntirat, Benjawan; Honma, Hajime; Mita, Toshihiro; Tsuboi, Takafumi; Coleman, Russell

    2015-06-01

    Genetic diversity of Plasmodium falciparum is intimately associated with morbidity, mortality and malaria control strategies. It is therefore imperative to study genetic makeup and population structure of this parasite in endemic areas. In Kong Mong Tha, an isolated village in western Thailand, the majority of P. falciparum infections are asymptomatic. In this study we investigated complexity of infections and single nucleotide polymorphisms (SNPs) in the P. falciparum population of Kong Mong Tha, and compared results with those previously obtained from Mae Sod, in northwestern Thailand, where the majority of infections were symptomatic. Using PCR-based determination of the 5' merozoite surface protein 1 gene (msp1) recombinant types, we found that 39% of 59 P. falciparum isolates from Kong Mong Tha had multiple 5' recombinant types with a mean number of 1.54. These values were much lower than those obtained from Mae Sod: 96% for multiple infections and with a mean number of 3.61. Analysis of full-length sequences of two housekeeping genes, the P-type Ca(2+)-transporting ATPase gene (n=33) plus adenylosuccinate lyase gene (n=33), and three vaccine candidate antigen genes, msp1 (n=26), the circumsporozoite protein gene, csp (n=30) and the apical membrane antigen 1 gene, ama 1 (n=32), revealed that in all of these genes within-population SNP diversity was at similar levels between Kong Mong Tha and Mae Sod, suggesting that the extent of MOI and clinical manifestations of malaria are not strongly associated with genetic diversity. Additionally, we did not detect significant genetic differentiation between the two parasite populations, as estimated by the Wright's fixation index of inter-population variance in allele frequencies, suggesting that gene flow prevented the formation of population structuring. Thus, this study highlights unique features of P. falciparum populations in Thailand. The implications of these finding are discussed. © 2013.

  18. Genome complexity, robustness and genetic interactions in digital organisms

    Science.gov (United States)

    Lenski, Richard E.; Ofria, Charles; Collier, Travis C.; Adami, Christoph

    1999-08-01

    Digital organisms are computer programs that self-replicate, mutate and adapt by natural selection. They offer an opportunity to test generalizations about living systems that may extend beyond the organic life that biologists usually study. Here we have generated two classes of digital organism: simple programs selected solely for rapid replication, and complex programs selected to perform mathematical operations that accelerate replication through a set of defined `metabolic' rewards. To examine the differences in their genetic architecture, we introduced millions of single and multiple mutations into each organism and measured the effects on the organism's fitness. The complex organisms are more robust than the simple ones with respect to the average effects of single mutations. Interactions among mutations are common and usually yield higher fitness than predicted from the component mutations assuming multiplicative effects; such interactions are especially important in the complex organisms. Frequent interactions among mutations have also been seen in bacteria, fungi and fruitflies. Our findings support the view that interactions are a general feature of genetic systems.

  19. Genetic characteristics of inflammatory bowel disease in a Japanese population.

    Science.gov (United States)

    Fuyuno, Yuta; Yamazaki, Keiko; Takahashi, Atsushi; Esaki, Motohiro; Kawaguchi, Takaaki; Takazoe, Masakazu; Matsumoto, Takayuki; Matsui, Toshiyuki; Tanaka, Hiroki; Motoya, Satoshi; Suzuki, Yasuo; Kiyohara, Yutaka; Kitazono, Takanari; Kubo, Michiaki

    2016-07-01

    Crohn's disease (CD) and ulcerative colitis (UC) are two major forms of inflammatory bowel disease (IBD). Meta-analyses of genome-wide association studies (GWAS) have identified 163 susceptibility loci for IBD among European populations; however, there is limited information for IBD susceptibility in a Japanese population. We performed a GWAS using imputed genotypes of 743 IBD patients (372 with CD and 371 with UC) and 3321 controls. Using 100 tag single-nucleotide polymorphisms (SNPs) (P Japanese and European populations. In the IBD GWAS, two East Asia-specific IBD susceptibility loci were identified in the Japanese population: ATG16L2-FCHSD2 and SLC25A15-ELF1-WBP4. Among 163 reported SNPs in European IBD patients, significant associations were confirmed in 18 (8 CD-specific, 4 UC-specific, and 6 IBD-shared). In Japanese CD patients, genes in the Th17-IL23 pathway showed stronger genetic effects, whereas the association of genes in the autophagy pathway was limited. The association of genes in the epithelial barrier and the Th17-IL23R pathways were similar in the Japanese and European UC populations. We confirmed two IBD susceptibility loci as common for CD and UC, and East Asian-specific. The genetic architecture in UC appeared to be similar between Europeans and East Asians, but may have some differences in CD.

  20. Molecular population genetics of inversion breakpoint regions in Drosophila pseudoobscura.

    Science.gov (United States)

    Wallace, Andre G; Detweiler, Don; Schaeffer, Stephen W

    2013-07-08

    Paracentric inversions in populations can have a profound effect on the pattern and organization of nucleotide variability along a chromosome. Regions near inversion breakpoints are expected to have greater levels of differentiation because of reduced genetic exchange between different gene arrangements whereas central regions in the inverted segments are predicted to have lower levels of nucleotide differentiation due to greater levels of genetic flux among different karyotypes. We used the inversion polymorphism on the third chromosome of Drosophila pseudoobscura to test these predictions with an analysis of nucleotide diversity of 18 genetic markers near and away from inversion breakpoints. We tested hypotheses about how the presence of different chromosomal arrangements affects the pattern and organization of nucleotide variation. Overall, markers in the distal segment of the chromosome had greater levels of nucleotide heterozygosity than markers within the proximal segment of the chromosome. In addition, our results rejected the hypothesis that the breakpoints of derived inversions will have lower levels of nucleotide variability than breakpoints of ancestral inversions, even when strains with gene conversion events were removed. High levels of linkage disequilibrium were observed within all 11 breakpoint regions as well as between the ends of most proximal and distal breakpoints. The central region of the chromosome had the greatest levels of linkage disequilibrium compared with the proximal and distal regions because this is the region that experiences the highest level of recombination suppression. These data do not fully support the idea that genetic exchange is the sole force that influences genetic variation on inverted chromosomes.

  1. Population genetics and comparative genetics of CLDN1, a gene involved in hepatitis C virus entry

    NARCIS (Netherlands)

    Bekker, Vincent; O'Brien, Thomas R.; Chanock, Stephen

    2009-01-01

    The claudin-1 gene (CLDN1) is a member of a family of genes that encodes proteins found in tight junctions and it has recently been implicated as one of several receptors for late stage binding of hepatitis C virus (HCV). Exploration of the population genetics of this gene could be informative,

  2. Invasion success in Cogongrass (Imperata cylindrica): A population genetic approach exploring genetic diversity and historical introductions

    Science.gov (United States)

    Rima D. Lucardi; Lisa E. Wallace; Gary N. Ervin

    2014-01-01

    Propagule pressure significantly contributes to and limits the potential success of a biological invasion, especially during transport, introduction, and establishment. Events such as multiple introductions of foreign parent material and gene flow among them can increase genetic diversity in founding populations, often leading to greater invasion success. We applied...

  3. Population genetic history of Aristeus antennatus (Crustacea: Decapoda in the Western and Central Mediterranean Sea.

    Directory of Open Access Journals (Sweden)

    Annamaria Marra

    Full Text Available 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

  4. Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex.

    Directory of Open Access Journals (Sweden)

    Daniel Garrido-Sanz

    Full Text Available The Pseudomonas fluorescens complex includes Pseudomonas strains that have been taxonomically assigned to more than fifty different species, many of which have been described as plant growth-promoting rhizobacteria (PGPR with potential applications in biocontrol and biofertilization. So far the phylogeny of this complex has been analyzed according to phenotypic traits, 16S rDNA, MLSA and inferred by whole-genome analysis. However, since most of the type strains have not been fully sequenced and new species are frequently described, correlation between taxonomy and phylogenomic analysis is missing. In recent years, the genomes of a large number of strains have been sequenced, showing important genomic heterogeneity and providing information suitable for genomic studies that are important to understand the genomic and genetic diversity shown by strains of this complex. Based on MLSA and several whole-genome sequence-based analyses of 93 sequenced strains, we have divided the P. fluorescens complex into eight phylogenomic groups that agree with previous works based on type strains. Digital DDH (dDDH identified 69 species and 75 subspecies within the 93 genomes. The eight groups corresponded to clustering with a threshold of 31.8% dDDH, in full agreement with our MLSA. The Average Nucleotide Identity (ANI approach showed inconsistencies regarding the assignment to species and to the eight groups. The small core genome of 1,334 CDSs and the large pan-genome of 30,848 CDSs, show the large diversity and genetic heterogeneity of the P. fluorescens complex. However, a low number of strains were enough to explain most of the CDSs diversity at core and strain-specific genomic fractions. Finally, the identification and analysis of group-specific genome and the screening for distinctive characters revealed a phylogenomic distribution of traits among the groups that provided insights into biocontrol and bioremediation applications as well as their role as

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

    Science.gov (United States)

    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.

  6. Population genetic data of the NGM SElect STR loci in Chinese Han population from Zhejiang region, China.

    Science.gov (United States)

    Zhou, Anju; Wu, Weiwei; Liu, Qiuling; Wu, Yeda; Lu, Dejian

    2013-03-01

    Genetic variations of the 17 NGM SElect STR loci in Chinese Han samples from the Zhejiang region were analyzed. The results show that the NGM SElect is a highly genetic informative system in Zhejiang Han, and this population shows quite different genetic data from other major populations in the world with the exception of the Fujian Han.

  7. Perceptions regarding genetic testing in populations at risk for nephropathy.

    Science.gov (United States)

    Freedman, Barry I; Fletcher, Alison J; Sanghani, Vivek R; Spainhour, Mitzie; Graham, Angelina W; Russell, Gregory B; Cooke Bailey, Jessica N; Iltis, Ana S; King, Nancy M P

    2013-01-01

    Population ancestry-based differences exist in genetic risk for many kidney diseases. Substantial debate remains regarding returning genetic test results to participants. African-Americans (AAs) and European-Americans (EAs) at risk for end-stage kidney disease were queried for views on the value and use of genetic testing in research. A standardized survey regarding attitudes toward genetic testing was administered to 130 individuals (64 AA, 66 EA) with first-degree relatives on dialysis. Fisher's exact test was used to assess differences in participant attitudes between population groups. Mean (SD) age of surveyed AAs and EAs was 45.5 (12.8) and 50.5 (14.4) years, respectively (p = 0.04), with similar familial relationships (p = 0.22). AAs and EAs wished to know their test results if risk could be: (1) reduced by diet or exercise (100 and 98%, p = 0.99); (2) reduced by medical treatment (100 and 98%, p = 0.99), or (3) if no treatments were available (90 and 82%, p = 0.21). If informed they lacked a disease susceptibility variant, 87% of AAs and 88% of EAs would be extremely or pretty likely to inform family members (p = 0.84). If informed they had a disease susceptibility variant, 92% of AAs and 89% of EAs would be extremely or pretty likely to inform their family (p = 0.43). Attitudes toward obtaining and using genetic test results for disease in research contexts were similar in AAs and EAs at risk for end-stage kidney disease. A substantial majority would want information regardless of available treatments and would share the information with the family. These results have important implications for patient care, study design and the informed consent process. © 2013 S. Karger AG, Basel.

  8. Study of human genetic diversity : inferences on population origin and history

    OpenAIRE

    Haber, Marc, 1980-

    2013-01-01

    Patterns of human genetic diversity suggest that all modern humans originated from a small population in Africa that expanded rapidly 50,000 years ago to occupy the whole world. While moving into new environments, genetic drift and natural selection affected populations differently, creating genetic structure. By understanding the genetic structure of human populations, we can reconstruct human history and understand the genetic basis of diseases. The work presented here contributes to the on...

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

    Science.gov (United States)

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

    2013-03-01

    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.

  10. Integrating common and rare genetic variation in diverse human populations.

    Science.gov (United States)

    Altshuler, David M; Gibbs, Richard A; Peltonen, Leena; Altshuler, David M; Gibbs, Richard A; Peltonen, Leena; Dermitzakis, Emmanouil; Schaffner, Stephen F; Yu, Fuli; Peltonen, Leena; Dermitzakis, Emmanouil; Bonnen, Penelope E; Altshuler, David M; Gibbs, Richard A; de Bakker, Paul I W; Deloukas, Panos; Gabriel, Stacey B; Gwilliam, Rhian; Hunt, Sarah; Inouye, Michael; Jia, Xiaoming; Palotie, Aarno; Parkin, Melissa; Whittaker, Pamela; Yu, Fuli; Chang, Kyle; Hawes, Alicia; Lewis, Lora R; Ren, Yanru; Wheeler, David; Gibbs, Richard A; Muzny, Donna Marie; Barnes, Chris; Darvishi, Katayoon; Hurles, Matthew; Korn, Joshua M; Kristiansson, Kati; Lee, Charles; McCarrol, Steven A; Nemesh, James; Dermitzakis, Emmanouil; Keinan, Alon; Montgomery, Stephen B; Pollack, Samuela; Price, Alkes L; Soranzo, Nicole; Bonnen, Penelope E; Gibbs, Richard A; Gonzaga-Jauregui, Claudia; Keinan, Alon; Price, Alkes L; Yu, Fuli; Anttila, Verneri; Brodeur, Wendy; Daly, Mark J; Leslie, Stephen; McVean, Gil; Moutsianas, Loukas; Nguyen, Huy; Schaffner, Stephen F; Zhang, Qingrun; Ghori, Mohammed J R; McGinnis, Ralph; McLaren, William; Pollack, Samuela; Price, Alkes L; Schaffner, Stephen F; Takeuchi, Fumihiko; Grossman, Sharon R; Shlyakhter, Ilya; Hostetter, Elizabeth B; Sabeti, Pardis C; Adebamowo, Clement A; Foster, Morris W; Gordon, Deborah R; Licinio, Julio; Manca, Maria Cristina; Marshall, Patricia A; Matsuda, Ichiro; Ngare, Duncan; Wang, Vivian Ota; Reddy, Deepa; Rotimi, Charles N; Royal, Charmaine D; Sharp, Richard R; Zeng, Changqing; Brooks, Lisa D; McEwen, Jean E

    2010-09-02

    Despite great progress in identifying genetic variants that influence human disease, most inherited risk remains unexplained. A more complete understanding requires genome-wide studies that fully examine less common alleles in populations with a wide range of ancestry. To inform the design and interpretation of such studies, we genotyped 1.6 million common single nucleotide polymorphisms (SNPs) in 1,184 reference individuals from 11 global populations, and sequenced ten 100-kilobase regions in 692 of these individuals. This integrated data set of common and rare alleles, called 'HapMap 3', includes both SNPs and copy number polymorphisms (CNPs). We characterized population-specific differences among low-frequency variants, measured the improvement in imputation accuracy afforded by the larger reference panel, especially in imputing SNPs with a minor allele frequency of populations supports deeper interrogation of genomic variation and its role in human disease, and serves as a step towards a high-resolution map of the landscape of human genetic variation.

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

    Science.gov (United States)

    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

  12. Genetic Divergence of the Rhesus Macaque Major Histocompatibility Complex

    Science.gov (United States)

    Daza-Vamenta, Riza; Glusman, Gustavo; Rowen, Lee; Guthrie, Brandon; Geraghty, Daniel E.

    2004-01-01

    The major histocompatibility complex (MHC) is comprised of the class I, class II, and class III regions, including the MHC class I and class II genes that play a primary role in the immune response and serve as an important model in studies of primate evolution. Although nonhuman primates contribute significantly to comparative human studies, relatively little is known about the genetic diversity and genomics underlying nonhuman primate immunity. To address this issue, we sequenced a complete rhesus macaque MHC spanning over 5.3 Mb, and obtained an additional 2.3 Mb from a second haplotype, including class II and portions of class I and class III. A major expansion of from six class I genes in humans to as many as 22 active MHC class I genes in rhesus and levels of sequence divergence some 10-fold higher than a similar human comparison were found, averaging from 2% to 6% throughout extended portions of class I and class II. These data pose new interpretations of the evolutionary constraints operating between MHC diversity and T-cell selection by contrasting with models predicting an optimal number of antigen presenting genes. For the clinical model, these data and derivative genetic tools can be implemented in ongoing genetic and disease studies that involve the rhesus macaque. PMID:15289473

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

    International Nuclear Information System (INIS)

    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.

    2016-01-01

    Full text: 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. (author)

  14. Unexpected high genetic diversity in small populations suggests maintenance by associative overdominance

    DEFF Research Database (Denmark)

    Schou, Mads F.; Loeschcke, Volker; Bechsgaard, Jesper

    2017-01-01

    fragmented populations. More genetic diversity was retained in areas of low recombination, suggesting that associative overdominance, driven by disfavoured homozygosity of recessive deleterious alleles, is responsible for the maintenance of genetic diversity in smaller populations. Consistent...

  15. Analysis of genetic diversity in a close population of Zandi sheep ...

    Indian Academy of Sciences (India)

    of the effective population size (Ne) for extending popula- tion genetics theory developed ..... animal genetic resources management plans: management of small populations at risk. Food and Agriculture Organization,. Rome, Italy. Fisher R. A. ...

  16. The Effect of Multiple Paternity on Genetic Diversity of Small Populations during and after Colonisation

    KAUST Repository

    Rafajlović, Marina; Eriksson, Anders; Rimark, Anna; Hintz-Saltin, Sara; Charrier, Gré gory; Panova, Marina; André , Carl; Johannesson, Kerstin; Mehlig, Bernhard

    2013-01-01

    Genetic variation within and among populations is influenced by the genetic content of the founders and the migrants following establishment. This is particularly true if populations are small, migration rate low and habitats arranged in a stepping

  17. [Prospect and application of microsatellite population genetics in study of geoherbs].

    Science.gov (United States)

    Zhang, Wen-Jing; Zhang, Yong-Qing; Yuan, Qing-Jun; Huang, Lu-Qi; Jiang, Dan; Jing, Li

    2013-12-01

    The author introduces the basic concepts of microsatellite and population genetics and its characteristics, expounds the application of these theories for population genetic structure and genetic diversity, gene flow and evolutionary significant unit ESU division research. This paper discuss its applicationin study of genetic causes, origin of cultivation, different regional origins of geoherbs, aiming at providing a new theory and method for geoherbs.

  18. The Driving Forces of Cultural Complexity : Neanderthals, Modern Humans, and the Question of Population Size.

    Science.gov (United States)

    Fogarty, Laurel; Wakano, Joe Yuichiro; Feldman, Marcus W; Aoki, Kenichi

    2017-03-01

    The forces driving cultural accumulation in human populations, both modern and ancient, are hotly debated. Did genetic, demographic, or cognitive features of behaviorally modern humans (as opposed to, say, early modern humans or Neanderthals) allow culture to accumulate to its current, unprecedented levels of complexity? Theoretical explanations for patterns of accumulation often invoke demographic factors such as population size or density, whereas statistical analyses of variation in cultural complexity often point to the importance of environmental factors such as food stability, in determining cultural complexity. Here we use both an analytical model and an agent-based simulation model to show that a full understanding of the emergence of behavioral modernity, and the cultural evolution that has followed, depends on understanding and untangling the complex relationships among culture, genetically determined cognitive ability, and demographic history. For example, we show that a small but growing population could have a different number of cultural traits from a shrinking population with the same absolute number of individuals in some circumstances.

  19. Estimation of the Genetic Diversity in Tetraploid Alfalfa Populations Based on RAPD Markers for Breeding Purposes

    Directory of Open Access Journals (Sweden)

    Slobodan Katic

    2011-08-01

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

  20. skeleSim: an extensible, general framework for population genetic simulation in R

    Science.gov (United States)

    Parobek, Christian M.; Archer, Frederick I.; DePrenger-Levin, Michelle E.; Hoban, Sean M.; Liggins, Libby; Strand, Allan E.

    2016-01-01

    Simulations are a key tool in molecular ecology for inference and forecasting, as well as for evaluating new methods. Due to growing computational power and a diversity of software with different capabilities, simulations are becoming increasingly powerful and useful. However, the widespread use of simulations by geneticists and ecologists is hindered by difficulties in understanding these softwares’ complex capabilities, composing code and input files, a daunting bioinformatics barrier, and a steep conceptual learning curve. skeleSim (an R package) guides users in choosing appropriate simulations, setting parameters, calculating genetic summary statistics, and organizing data output, in a reproducible pipeline within the R environment. skeleSim is designed to be an extensible framework that can ‘wrap’ around any simulation software (inside or outside the R environment) and be extended to calculate and graph any genetic summary statistics. Currently, skeleSim implements coalescent and forward-time models available in the fastsimcoal2 and rmetasim simulation engines to produce null distributions for multiple population genetic statistics and marker types, under a variety of demographic conditions. skeleSim is intended to make simulations easier while still allowing full model complexity to ensure that simulations play a fundamental role in molecular ecology investigations. skeleSim can also serve as a teaching tool: demonstrating the outcomes of stochastic population genetic processes; teaching general concepts of simulations; and providing an introduction to the R environment with a user-friendly graphical user interface (using shiny). PMID:27736016

  1. Three Molecular Markers Show No Evidence of Population Genetic Structure in the Gouldian Finch (Erythrura gouldiae.

    Directory of Open Access Journals (Sweden)

    Peri E Bolton

    Full Text Available Assessment of genetic diversity and connectivity between regions can inform conservation managers about risk of inbreeding, potential for adaptation and where population boundaries lie. The Gouldian finch (Erythrura gouldiae is a threatened species in northern Australia, occupying the savannah woodlands of the biogeographically complex monsoon tropics. We present the most comprehensive population genetic analysis of diversity and structure the Gouldian finch using 16 microsatellite markers, mitochondrial control region and 3,389 SNPs from genotyping-by-sequencing. Mitochondrial diversity is compared across three related, co-distributed finches with different conservation threat-statuses. There was no evidence of genetic differentiation across the western part of the range in any of the molecular markers, and haplotype diversity but not richness was lower than a common co-distributed species. Individuals within the panmictic population in the west may be highly dispersive within this wide area, and we urge caution when interpreting anecdotal observations of changes to the distribution and/or flock sizes of Gouldian finch populations as evidence of overall changes to the population size of this species.

  2. Possible implication of the genetic composition of the Lutzomyia longipalpis (Diptera: Psychodidae) populations in the epidemiology of the visceral leishmaniasis.

    Science.gov (United States)

    Rocha, Leonardo de Souza; Falqueto, Aloisio; Dos Santos, Claudiney Biral; Grimaldi, Gabriel Júnior; Cupolillo, Elisa

    2011-09-01

    Lutzomyia longipalpis (Diptera: Psychodidae) is the principal vector of American visceral leishmaniasis. Several studies have indicated that the Lu. longipalpis population structure is complex. It has been suggested that genetic divergence caused by genetic drift, selection, or both may affect the vectorial capacity of Lu. longipalpis. However, it remains unclear whether genetic differences among Lu. longipalpis populations are directly implicated in the transmission features of visceral leishmaniasis. We evaluated the genetic composition and the patterns of genetic differentiation among Lu. longipalpis populations collected from regions with different patterns of transmission of visceral leishmaniasis by analyzing the sequence variation in the mitochondrial cytochrome b gene. Furthermore, we investigated the temporal distribution of haplotypes and compared our results with those obtained in a previous study. Our data indicate that there are differences in the haplotype composition and that there has been significant differentiation between the analyzed populations. Our results reveal that measures used to control visceral leishmaniasis might have influenced the genetic composition of the vector population. This finding raises important questions concerning the epidemiology of visceral leishmaniasis, because these differences in the genetic structures among populations of Lu. longipalpis may have implications with respect to their efficiency as vectors for visceral leishmaniasis.

  3. Contribution of Large Region Joint Associations to Complex Traits Genetics

    Science.gov (United States)

    Paré, Guillaume; Asma, Senay; Deng, Wei Q.

    2015-01-01

    A polygenic model of inheritance, whereby hundreds or thousands of weakly associated variants contribute to a trait’s heritability, has been proposed to underlie the genetic architecture of complex traits. However, relatively few genetic variants have been positively identified so far and they collectively explain only a small fraction of the predicted heritability. We hypothesized that joint association of multiple weakly associated variants over large chromosomal regions contributes to complex traits variance. Confirmation of such regional associations can help identify new loci and lead to a better understanding of known ones. To test this hypothesis, we first characterized the ability of commonly used genetic association models to identify large region joint associations. Through theoretical derivation and simulation, we showed that multivariate linear models where multiple SNPs are included as independent predictors have the most favorable association profile. Based on these results, we tested for large region association with height in 3,740 European participants from the Health and Retirement Study (HRS) study. Adjusting for SNPs with known association with height, we demonstrated clustering of weak associations (p = 2x10-4) in regions extending up to 433.0 Kb from known height loci. The contribution of regional associations to phenotypic variance was estimated at 0.172 (95% CI 0.063-0.279; p < 0.001), which compared favorably to 0.129 explained by known height variants. Conversely, we showed that suggestively associated regions are enriched for known height loci. To extend our findings to other traits, we also tested BMI, HDLc and CRP for large region associations, with consistent results for CRP. Our results demonstrate the presence of large region joint associations and suggest these can be used to pinpoint weakly associated SNPs. PMID:25856144

  4. Genetic population structure of marine viral haemorrhagic septicaemia virus (VHSV)

    DEFF Research Database (Denmark)

    Snow, M.; Bain, N.; Black, J.

    2004-01-01

    The nucleotide sequences of a specific region of the nucleoprotein gene were compared in order to investigate the genetic population structure of marine viral haemorrhagic septicaemia virus (VHSV). Analysis of the sequence from 128 isolates of diverse geographic and host origin renders this the m......The nucleotide sequences of a specific region of the nucleoprotein gene were compared in order to investigate the genetic population structure of marine viral haemorrhagic septicaemia virus (VHSV). Analysis of the sequence from 128 isolates of diverse geographic and host origin renders...... this the most comprehensive molecular epidemiological study of marine VHSV conducted to date. Phylogenetic analysis of nucleoprotein gene sequences confirmed the existence of the 4 major genotypes previously identified based on N- and subsequent G-gene based analyses. The range of Genotype I included subgroups...... of isolates associated with rainbow trout aquaculture (Genotype la) and those from the Baltic marine environment (Genotype Ib) to emphasise the relatively close genetic relationship between these isolates. The existence of an additional genotype circulating within the Baltic Sea (Genotype II) was also...

  5. Genetic Diversity in Natural Populations of New World Leishmania

    Directory of Open Access Journals (Sweden)

    Cupolillo Elisa

    1998-01-01

    Full Text Available Our results have shown the wide diversity of parasites within New World Leishmania. Biochemical and molecular characterization of species within the genus has revealed that much of the population heterogeneity has a genetic basis. The source of genetic diversity among Leishmania appears to arise from predominantly asexual, clonal reproduction, although occasional bouts of sexual reproduction can not be ruled out. Genetic variation is extensive with some clones widely distributed and others seemingly unique and localized to a particular endemic focus. Epidemiological studies of leishmaniasis has been directed to the ecology and dynamics of transmission of Leishmania species/variants, particularly in localized areas. Future research using molecular techniques should aim to identify and follow Leishmania types in nature and correlate genetic typing with important clinical characteristics such as virulence, pathogenicity, drug resistance and antigenic variation. The epidemiological significance of such variation not only has important implications for the control of the leishmaniases, but would also help to elucidate the evolutionary biology of the causative agents.

  6. Development and pilot evaluation of novel genetic educational materials designed for an underserved patient population.

    Science.gov (United States)

    Lubitz, Rebecca Jean; Komaromy, Miriam; Crawford, Beth; Beattie, Mary; Lee, Robin; Luce, Judith; Ziegler, John

    2007-01-01

    Genetic counseling for BRCA1 and BRCA2 mutations involves teaching about hereditary cancer, genetics and risk, subjects that are difficult to grasp and are routinely misunderstood. Supported by a grant from the Avon Foundation, the UCSF Cancer Risk Program started the first genetic testing and counseling service for a population of traditionally underserved women of varied ethnic and social backgrounds at the San Francisco General Hospital (SFGH). Informed by educational theory and clinical experience, we devised and piloted two simplified explanations of heredity and genetic risk, with the aim of uncovering how to best communicate genetics and risk to this underserved population. A "conventional" version comprised pictures of genes, pedigrees, and quantitative representations of risk. A "colloquial" pictorial version used an analogy of the "information book" of genes, family stories and vignettes, and visual representations of risk, without using scientific words such as genes or chromosomes. A verbal narrative accompanied each picture. We presented these modules to four focus groups of five to eight women recruited from the SFGH Family Practice Clinic. Overall, women preferred a picture-based approach and commented that additional text would have been distracting. The majority of women preferred the colloquial version because it was easier to understand and better conveyed a sense of comfort and hope. We conclude that simplicity, analogies, and familiarity support comprehension while vignettes, family stories, and photos of real people provide comfort and hope. These elements may promote understanding of complex scientific topics in healthcare, particularly when communicating with patients who come from disadvantaged backgrounds.

  7. Molecular markers for genetic diversity, gene flow and genetic population structure of freshwater mussel species

    Directory of Open Access Journals (Sweden)

    AB Choupina

    Full Text Available Freshwater mussel species are in global decline. Anthropogenic changes of river channels and the decrease of autochthonous fish population, the natural hosts of mussels larval stages (glochidia, are the main causes. Therefore, the conservation of mussel species depends not only on habitat conservation, but also on the availability of the fish host. In Portugal, information concerning most of the mussel species is remarkably scarce. One of the most known species, Unio pictorum is also in decline however, in the basins of the rivers Tua and Sabor (Northeast of Portugal, there is some indication of relatively large populations. The aforementioned rivers can be extremely important for this species conservation not only in Portugal, but also in the remaining Iberian Peninsula. Thus, it is important to obtain data concerning Unio pictorum bioecology (distribution, habitat requirements, population structure, genetic variability, reproductive cycle and recruitment rates, as well as the genetic variability and structure of the population. Concomitantly, information concerning fish population structure, the importance of the different fish species as “glochidia” hosts and their appropriate density to allow effective mussel recruitment, will also be assessed. The achieved data is crucial to obtain information to develop effective management measures in order to promote the conservation of this bivalve species, the conservation of autochthonous fish populations, and consequently the integrity of the river habitats.

  8. Change in genetic size of small-closed populations: Lessons from a domestic mammal population.

    Science.gov (United States)

    Ghafouri-Kesbi, Farhad

    2010-10-01

    The aim of this study was to monitor changes in genetic size of a small-closed population of Iranian Zandi sheep, by using pedigree information from animals born between 1991 and 2005. The genetic size was assessed by using measures based on the probability of identity-by-descend of genes (coancestry, f, and effective population size, N(e) ), as well as measures based on probability of gene origin (effective number of founders, f(e) , effective number of founder genomes, f(g) , and effective number of non-founder genomes, f(ne) ). Average coancestry, or the degree of genetic similarity of individuals, increased from 0.81% to 1.44% during the period 1993 to 2005, at the same time that N(e) decreased from 263 to 93. The observed trend for f(e) was irregular throughout the experiment in a way that f(e) was 68, 87, 77, 92, and 80 in 1993, 1996, 1999, 2002, and 2005, respectively. Simultaneously, f(g) , the most informative effective number, decreased from 61 to 35. The index of genetic diversity (GD) which was obtained from estimates of f(g) , decreased about 2% throughout the period studied. In addition, a noticeable reduction was observed in the estimates of f(ne) from 595 in 1993 to 61 in 2005. The higher than 1 ratio of f(e) to f(g) indicated the presence of bottlenecks and genetic drift in the development of this population of Zandi sheep. From 1993 to 1999, f(ne) was much higher than f(e) , thereby indicating that with respect to loss of genetic diversity, the unequal contribution of founders was more important than the random genetic drift in non-founder generations. Subsequently, random genetic drift in non-founder generations was the major reason for f(e) > f(ne) . The minimization of average coancestry in new reproductive individuals was recommended as a means of preserving the population against a further loss in genetic diversity.

  9. Genetic diversity and differentiation of Mongolian indigenous cattle populations

    Energy Technology Data Exchange (ETDEWEB)

    Lkhagva, B [International Livestock Research Institute - ILRI, P.O. Box 30709, Nairobi (Kenya) and Mongolian State Agricultural University, Zaisan, Ulaanbaatar 210153 (Mongolia); Ochieng, J W; Hanotte, O; Jianlin, H [International Livestock Research Institute - ILRI, P.O. Box 30709, Nairobi (Kenya); Yoon, D H [National Livestock Research Institute, RDA, 441-350, Suwon (Korea)

    2003-07-01

    Livestock production plays an important role in Mongolian economy. Over the last decade it has contributed to around 80-90% of the gross domestic agricultural products and to 30% of the revenues generated from exportations. Cattle is one of the five traditional and most important livestock species of Mongolia together with horse, sheep, goat and camel. Out of a total of 1.57 millions Mongolian cattle, 1.55 millions supposedly belong to three indigenous Bos taurus cattle breeds, namely Mongol, Selenge and Khalkhun Golun, all herded under extensive pastoral systems. Indigenous Mongolian cattle are generally small but look sturdy and strong. They have a well-off coat of hair, solid forward looking shoulders and short stubby snouts, and they are used for meat, milk and transport. Beef production contributes to 30% of the total meat supply in Mongolia. The Mongol breed is by the far the commonest with 1.53 million animals and it is found almost throughout the country. The Selenge breed, found in Selenge province and numbering 9000 heads, was developed in middle of the 20th century by crossing the Kazakh Whiteheaded with the local Mongol cattle. The Khalkhun Golun breed was developed from local Mongol cattle and it is distributed in Eastern and Suhbaatar provinces with about 10,000 heads. Until now, to the best of our knowledge, only a single population of Mongolian cattle has been studied with microsatellite DNA markers and no information is available on the genetic relationship between the Mongolian indigenous cattle breeds. In this study, we collected samples from two populations of the Mongol cattle (sampled at Ikhtamir soum in North Hangay province and Tsogt soum in Govi Altay province) and one population of the Khalkhun Golun cattle (sampled at Tumentsogt soum in Suhbaatar province). Samples were characterised with nine microsatellite markers MGTG4B, ILSTS005, ILSTS006, ILSTS008, ILSTS023, ILSTS028, ILSTS036, ILSTS050 and ILSTS103. To assess the genetic diversity

  10. Population genetics of foxtail millet and its wild ancestor

    Directory of Open Access Journals (Sweden)

    Wang Yongfang

    2010-10-01

    Full Text Available Abstract Background Foxtail millet (Setaria italica (L. P. Beauv., one of the most ancient domesticated crops, is becoming a model system for studying biofuel crops and comparative genomics in the grasses. However, knowledge on the level of genetic diversity and linkage disequilibrium (LD is very limited in this crop and its wild ancestor, green foxtail (Setaria viridis (L. P. Beauv.. Such information would help us to understand the domestication process of cultivated species and will allow further research in these species, including association mapping and identification of agricultural significant genes involved in domestication. Results In this study, we surveyed DNA sequence for nine loci across 50 accessions of cultivated foxtail millet and 34 of its wild progenitor. We found a low level of genetic diversity in wild green foxtail (θ = 0.0059, θ means Watterson's estimator of θ. Despite of a 55% loss of its wild diversity, foxtail millet still harbored a considerable level of diversity (θ = 0.0027 when compared to rice and sorghum (θ = 0.0024 and 0.0034, respectively. The level of LD in the domesticated foxtail millet extends to 1 kb, while it decayed rapidly to a negligible level within 150 bp in wild green foxtail. Using coalescent simulation, we estimated the bottleneck severity at k = 0.6095 when ρ/θ = 1. These results indicated that the domestication bottleneck of foxtail millet was more severe than that of maize but slightly less pronounced than that of rice. Conclusions The results in this study establish a general framework for the domestication history of foxtail millet. The low level of genetic diversity and the increased level of LD in foxtail millet are mainly caused by a population bottleneck, although gene flow from foxtail millet to green foxtail is another factor that may have shaped the pattern of genetic diversity of these two related gene pools. The knowledge provided in this study will benefit future population

  11. Genetic parameters on Bali cattle progeny test population

    Science.gov (United States)

    Hariansyah, A. R.; Raharjo, A.; Zainuri, A.; Parwoto, Y.; Prasetiyo, D.; Prastowo, S.; Widyas, N.

    2018-03-01

    Bali cattle (Bos javanicus) is Indonesian indigenous cattle with having superior genetics potential on fitness traits in tropical environment and low feed quality. Bali Cattle Breeding Center Pulukan Indonesia conducted progeny test per annum in order to select bulls using offspring’s phenotype. This paper aimed to estimate the genetic parameters of yearling weight in Bali cattle progeny test populations and to observe the variation between periods in the above breeding center. Data were collected from the year of 2013 to 2014. There were four bulls (3 tests, 1 AI control) in 2013 and five bulls (4 tests, 1 AI) in 2014. Thirty breeding females were allocated per paddock per bull and allowed to mate naturally. In total 80 and 104 offspring’s records were obtained from 2013 and 2014 data, respectively. We built half-sib family model to estimate the additive genetic variance due to the sire and later estimate the breeding value (EBV) of each sire. Results showed that in 2013 the heritability (h2) for yearling weight was 0.19 while in 2014 was 0.79. In both years, tested bulls had higher EBV compared to the control bulls. The remarkable difference of heritability between years was due to the variations among bull candidates which might differ every year with regards to their origins. The fact that the EBV of tested bulls were higher than the control bulls gave us insight that despite the conservation policy and the continuous departure of Bali cattle bulls outside the Island, the population could still maintain its genetic quality.

  12. The Hidden Complexity of Mendelian Traits across Natural Yeast Populations

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    Jing Hou

    2016-07-01

    Full Text Available Mendelian traits are considered to be at the lower end of the complexity spectrum of heritable phenotypes. However, more than a century after the rediscovery of Mendel’s law, the global landscape of monogenic variants, as well as their effects and inheritance patterns within natural populations, is still not well understood. Using the yeast Saccharomyces cerevisiae, we performed a species-wide survey of Mendelian traits across a large population of isolates. We generated offspring from 41 unique parental pairs and analyzed 1,105 cross/trait combinations. We found that 8.9% of the cases were Mendelian. Further tracing of causal variants revealed background-specific expressivity and modified inheritances, gradually transitioning from Mendelian to complex traits in 30% of the cases. In fact, when taking into account the natural population diversity, the hidden complexity of traits could be substantial, confounding phenotypic predictability even for simple Mendelian traits.

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

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    Rico, Y; Wagner, H H

    2016-11-01

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

  14. Genetic health and population monitoring of two small black bear (Ursus americanus populations in Alabama, with a regional perspective of genetic diversity and exchange.

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    John P Draper

    Full Text Available One of the major concerns in conservation today is the loss of genetic diversity which is a frequent consequence of population isolation and small population sizes. Fragmentation of populations and persecution of carnivores has posed a substantial threat to the persistence of free ranging carnivores in North America since the arrival of European settlers. Black bears have seen significant reductions in range size from their historic extent, which is most pronounced in the southeastern United States and even more starkly in Alabama where until recently bears were reduced to a single geographically isolated population in the Mobile River Basin. Recently a second population has naturally re-established itself in northeastern Alabama. We sought to determine size, genetic diversity and genetic connectivity for these two populations in relation to other regional populations. Both populations of black bears in Alabama had small population sizes and had moderate to low genetic diversity, but showed different levels of connectivity to surrounding populations of bears. The Mobile River Basin population had a small population size at only 86 individuals (76-124, 95% C.I., the lowest genetic diversity of compared populations (richness = 2.33, Ho and He = 0.33, and showed near complete genetic isolation from surrounding populations across multiple tests. The newly recolonizing population in northeastern Alabama had a small but growing population doubling in 3 years (34 individuals 26-43, 95% C.I., relatively moderate genetic diversity compared to surrounding populations (richness = 3.32, Ho = 0.53, He = 0.65, and showed a high level of genetic connectivity with surrounding populations.

  15. Genetic health and population monitoring of two small black bear (Ursus americanus) populations in Alabama, with a regional perspective of genetic diversity and exchange.

    Science.gov (United States)

    Draper, John P; Waits, Lisette P; Adams, Jennifer R; Seals, Christopher L; Steury, Todd D

    2017-01-01

    One of the major concerns in conservation today is the loss of genetic diversity which is a frequent consequence of population isolation and small population sizes. Fragmentation of populations and persecution of carnivores has posed a substantial threat to the persistence of free ranging carnivores in North America since the arrival of European settlers. Black bears have seen significant reductions in range size from their historic extent, which is most pronounced in the southeastern United States and even more starkly in Alabama where until recently bears were reduced to a single geographically isolated population in the Mobile River Basin. Recently a second population has naturally re-established itself in northeastern Alabama. We sought to determine size, genetic diversity and genetic connectivity for these two populations in relation to other regional populations. Both populations of black bears in Alabama had small population sizes and had moderate to low genetic diversity, but showed different levels of connectivity to surrounding populations of bears. The Mobile River Basin population had a small population size at only 86 individuals (76-124, 95% C.I.), the lowest genetic diversity of compared populations (richness = 2.33, Ho and He = 0.33), and showed near complete genetic isolation from surrounding populations across multiple tests. The newly recolonizing population in northeastern Alabama had a small but growing population doubling in 3 years (34 individuals 26-43, 95% C.I.), relatively moderate genetic diversity compared to surrounding populations (richness = 3.32, Ho = 0.53, He = 0.65), and showed a high level of genetic connectivity with surrounding populations.

  16. HLA-C molecular characterization of a Lebanese population and genetic structure of 39 populations from Europe to India-Pakistan.

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    Buhler, S; Megarbane, A; Lefranc, G; Tiercy, J-M; Sanchez-Mazas, A

    2006-07-01

    Lebanon is located at a continental crossroad between Europe, Africa, and Asia. This region has been the center of wide-scale movements of populations as well as the theater of genetic and cultural trade off among neighboring populations. In this study, HLA-C alleles were characterized by a PCR-SSOP (sequence-specific oligonucleotide probes) hybridization protocol in a sample of 97 Lebanese. A total of 23 alleles were identified with four predominant, Cw*0401, Cw*0602, Cw*0701/06, and Cw*1203, accounting for almost 60% of HLA-C allele frequencies. We included the Lebanese data into a broad analysis of the HLA-C genetic structure of a large set of populations located in Europe, the Middle East, and the Indian subcontinent. Our results indicate that Lebanese exhibit an intermediate genetic profile among the populations from the Middle East, which constitute a rather homogeneous genetic group. In Europe, a high correlation coefficient is found between genetic and geographic distances. In this continent, we also identified a significant genetic frontier following a north-east to south-west axis. This frontier cuts through the Alps and the Pyrenees, thus separating the north-western European populations from those located in the eastern and Mediterranean areas. Finally, the populations from India - Pakistan are very heterogeneous, particularly the Dravidians. Their differentiation has probably been caused by rapid genetic drift under complex influences of cultural, linguistic, and/or religious barriers. Overall, the results show that the HLA-C genetic patterns of these three geographic regions, i.e., the Middle East, Europe, and India-Pakistan, have been shaped by very different genetic histories.

  17. [Population genetic study of Russian cosmonauts and test subjects: genetic demographic parameters and immunogenetic markers].

    Science.gov (United States)

    Kurbatova, O L; Pobedonostseva, E Iu; Prokhorovskaia, V D; Kholod, O N; Evsiukov, A N; Bogomolov, V V; Voronkov, Iu I; Filatova, L M; Larina, O N; Sidorenko, L A; Morgun, V V; Kasparanskiĭ, R R; Altukhov, Iu P

    2006-10-01

    Genetic demographic characteristics and immunogenetic markers (blood groups ABO, Rhesus, MNSs, P, Duffy, Kidd, and Kell) have been studied in a group of 132 Russian cosmonauts and test subjects (CTSG). Analysis of pedigrees has shown a high exogamy in the preceding generations: almost half of the subjects have mixed ethnic background. According to the results of genetic demographic analysis, a sample from the Moscow population was used as control group (CG). Comparison between the CTSG and CG has demonstrated significant differences in genotype frequencies for several blood group systems. The CTSG is characterized by a decreased proportion of rare interlocus genotypic combinations and an increased man heterozygosity. Analysis of the distributions of individual heterozygosity for loci with codominant expression of alleles has shown that highly heterozygous loci are more frequent in the CTSG. Taking into account that the CTSG has been thoroughly selected from the general population, it is concluded that heterozygosity is related to successful adaptation to a space flight.

  18. In the heartland of Eurasia: the multilocus genetic landscape of Central Asian populations

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    Martínez-Cruz, Begoña; Vitalis, Renaud; Ségurel, Laure; Austerlitz, Frédéric; Georges, Myriam; Théry, Sylvain; Quintana-Murci, Lluis; Hegay, Tatyana; Aldashev, Almaz; Nasyrova, Firuza; Heyer, Evelyne

    2011-01-01

    Located in the Eurasian heartland, Central Asia has played a major role in both the early spread of modern humans out of Africa and the more recent settlements of differentiated populations across Eurasia. A detailed knowledge of the peopling in this vast region would therefore greatly improve our understanding of range expansions, colonizations and recurrent migrations, including the impact of the historical expansion of eastern nomadic groups that occurred in Central Asia. However, despite its presumable importance, little is known about the level and the distribution of genetic variation in this region. We genotyped 26 Indo-Iranian- and Turkic-speaking populations, belonging to six different ethnic groups, at 27 autosomal microsatellite loci. The analysis of genetic variation reveals that Central Asian diversity is mainly shaped by linguistic affiliation, with Turkic-speaking populations forming a cluster more closely related to East-Asian populations and Indo-Iranian speakers forming a cluster closer to Western Eurasians. The scattered position of Uzbeks across Turkic- and Indo-Iranian-speaking populations may reflect their origins from the union of different tribes. We propose that the complex genetic landscape of Central Asian populations results from the movements of eastern, Turkic-speaking groups during historical times, into a long-lasting group of settled populations, which may be represented nowadays by Tajiks and Turkmen. Contrary to what is generally thought, our results suggest that the recurrent expansions of eastern nomadic groups did not result in the complete replacement of local populations, but rather into partial admixture. PMID:20823912

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

    Science.gov (United States)

    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

  20. The impact of translocations on neutral and functional genetic diversity within and among populations of the Seychelles warbler.

    Science.gov (United States)

    Wright, David J; Spurgin, Lewis G; Collar, Nigel J; Komdeur, Jan; Burke, Terry; Richardson, David S

    2014-05-01

    Translocations are an increasingly common tool in conservation. The maintenance of genetic diversity through translocation is critical for both the short- and long-term persistence of populations and species. However, the relative spatio-temporal impacts of translocations on neutral and functional genetic diversity, and how this affects genetic structure among the conserved populations overall, have received little investigation. We compared the impact of translocating different numbers of founders on both microsatellite and major histocompatibility complex (MHC) class I diversity over a 23-year period in the Seychelles warbler (Acrocephalus sechellensis). We found low and stable microsatellite and MHC diversity in the source population and evidence for only a limited loss of either type of diversity in the four new populations. However, we found evidence of significant, but low to moderate, genetic differentiation between populations, with those populations established with fewer founders clustering separately. Stochastic genetic capture (as opposed to subsequent drift) was the main determinant of translocated population diversity. Furthermore, a strong correlation between microsatellite and MHC differentiation suggested that neutral processes outweighed selection in shaping MHC diversity in the new populations. These data provide important insights into how to optimize the use of translocation as a conservation tool. © 2014 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

  1. Resolving the Complex Genetic Basis of Phenotypic Variation and Variability of Cellular Growth.

    Science.gov (United States)

    Ziv, Naomi; Shuster, Bentley M; Siegal, Mark L; Gresham, David

    2017-07-01

    In all organisms, the majority of traits vary continuously between individuals. Explaining the genetic basis of quantitative trait variation requires comprehensively accounting for genetic and nongenetic factors as well as their interactions. The growth of microbial cells can be characterized by a lag duration, an exponential growth phase, and a stationary phase. Parameters that characterize these growth phases can vary among genotypes (phenotypic variation), environmental conditions (phenotypic plasticity), and among isogenic cells in a given environment (phenotypic variability). We used a high-throughput microscopy assay to map genetic loci determining variation in lag duration and exponential growth rate in growth rate-limiting and nonlimiting glucose concentrations, using segregants from a cross of two natural isolates of the budding yeast, Saccharomyces cerevisiae We find that some quantitative trait loci (QTL) are common between traits and environments whereas some are unique, exhibiting gene-by-environment interactions. Furthermore, whereas variation in the central tendency of growth rate or lag duration is explained by many additive loci, differences in phenotypic variability are primarily the result of genetic interactions. We used bulk segregant mapping to increase QTL resolution by performing whole-genome sequencing of complex mixtures of an advanced intercross mapping population grown in selective conditions using glucose-limited chemostats. We find that sequence variation in the high-affinity glucose transporter HXT7 contributes to variation in growth rate and lag duration. Allele replacements of the entire locus, as well as of a single polymorphic amino acid, reveal that the effect of variation in HXT7 depends on genetic, and allelic, background. Amplifications of HXT7 are frequently selected in experimental evolution in glucose-limited environments, but we find that HXT7 amplifications result in antagonistic pleiotropy that is absent in naturally

  2. Genet-specific DNA methylation probabilities detected in a spatial epigenetic analysis of a clonal plant population.

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    Kiwako S Araki

    Full Text Available In sessile organisms such as plants, spatial genetic structures of populations show long-lasting patterns. These structures have been analyzed across diverse taxa to understand the processes that determine the genetic makeup of organismal populations. For many sessile organisms that mainly propagate via clonal spread, epigenetic status can vary between clonal individuals in the absence of genetic changes. However, fewer previous studies have explored the epigenetic properties in comparison to the genetic properties of natural plant populations. Here, we report the simultaneous evaluation of the spatial structure of genetic and epigenetic variation in a natural population of the clonal plant Cardamine leucantha. We applied a hierarchical Bayesian model to evaluate the effects of membership of a genet (a group of individuals clonally derived from a single seed and vegetation cover on the epigenetic variation between ramets (clonal plants that are physiologically independent individuals. We sampled 332 ramets in a 20 m × 20 m study plot that contained 137 genets (identified using eight SSR markers. We detected epigenetic variation in DNA methylation at 24 methylation-sensitive amplified fragment length polymorphism (MS-AFLP loci. There were significant genet effects at all 24 MS-AFLP loci in the distribution of subepiloci. Vegetation cover had no statistically significant effect on variation in the majority of MS-AFLP loci. The spatial aggregation of epigenetic variation is therefore largely explained by the aggregation of ramets that belong to the same genets. By applying hierarchical Bayesian analyses, we successfully identified a number of genet-specific changes in epigenetic status within a natural plant population in a complex context, where genotypes and environmental factors are unevenly distributed. This finding suggests that it requires further studies on the spatial epigenetic structure of natural populations of diverse organisms

  3. Genet-specific DNA methylation probabilities detected in a spatial epigenetic analysis of a clonal plant population.

    Science.gov (United States)

    Araki, Kiwako S; Kubo, Takuya; Kudoh, Hiroshi

    2017-01-01

    In sessile organisms such as plants, spatial genetic structures of populations show long-lasting patterns. These structures have been analyzed across diverse taxa to understand the processes that determine the genetic makeup of organismal populations. For many sessile organisms that mainly propagate via clonal spread, epigenetic status can vary between clonal individuals in the absence of genetic changes. However, fewer previous studies have explored the epigenetic properties in comparison to the genetic properties of natural plant populations. Here, we report the simultaneous evaluation of the spatial structure of genetic and epigenetic variation in a natural population of the clonal plant Cardamine leucantha. We applied a hierarchical Bayesian model to evaluate the effects of membership of a genet (a group of individuals clonally derived from a single seed) and vegetation cover on the epigenetic variation between ramets (clonal plants that are physiologically independent individuals). We sampled 332 ramets in a 20 m × 20 m study plot that contained 137 genets (identified using eight SSR markers). We detected epigenetic variation in DNA methylation at 24 methylation-sensitive amplified fragment length polymorphism (MS-AFLP) loci. There were significant genet effects at all 24 MS-AFLP loci in the distribution of subepiloci. Vegetation cover had no statistically significant effect on variation in the majority of MS-AFLP loci. The spatial aggregation of epigenetic variation is therefore largely explained by the aggregation of ramets that belong to the same genets. By applying hierarchical Bayesian analyses, we successfully identified a number of genet-specific changes in epigenetic status within a natural plant population in a complex context, where genotypes and environmental factors are unevenly distributed. This finding suggests that it requires further studies on the spatial epigenetic structure of natural populations of diverse organisms, particularly for

  4. Transferrin variation and genetic structure of reindeer populations in Scandinavia

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    Knut H. Røed

    1987-06-01

    Full Text Available Polyacrylamide gel electrophoresis was used to analyse transferrin variation in herds of semi-domestic reindeer from Scandinavia. The results are compared with previously reported values for other populations of both semi-domestic and wild reindeer using the same techniques as in the present study. In all populations the number of alleles was high, ranging from seven to eleven, and the heterozygosity was correspondingly high, with a mean of 0.749. This high genetic variation in all populations suggests that inbreeding is not widespread among Scandinavian reindeer. The pattern of allele frequency distribution indicates a high degree of genetic heterogeneity in the transferrin locus, both between the different semi-domestic herds and between the different wild populations. The mean value of genetic distance was 0.069 between semi-domestic herds and 0.091 between wild populations. Between semi-domestic and wild populations the genetic distance was particularly high, with a mean of 0.188. This high value was mainly due to a different pattern in the distribution of the two most common transferrin alleles: Tfu was most common among semi-domestic herds, while TfEI was most common among wild populations. These differences in transferrin allele distribution are discussed in relation to possible different origins of semi-domestic and wild reindeer in Scandinavia, or alternatively, to different selection forces acting on transferrin genotypes in semi-domestic and wild populations.Transferrin-variasjon og genetisk struktur hos rein i Skandinavia.Abstact in Norwegian / Sammendrag: Transferrin-variasjon i tamreinflokker ble analysert ved hjelp av polyacrylamid gel elektroforese. Resultatene er sammenlignet med verdier som tidligere er beskrevet for både tamrein og villrein hvor det ble benyttet samme metode som i denne undersøkelsen. I alle populasjonene ble det registrert et høyt antall alleler (7-11 og heterozygositeten var tilsvarende høy med en

  5. Population genetic structure, linkage disequilibrium and effective population size of conserved and extensively raised village chicken populations of Southern Africa

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    Khulekhani Sedwell Khanyile

    2015-02-01

    Full Text Available Extensively raised village chickens are considered a valuable source of biodiversity, with genetic variability developed over thousands of years that ought to be characterised and utilized. Surveys that can reveal a population’s genetic structure and provide an insight into its demographic history will give valuable information 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 0.29-0.36, was observed between SNP markers that were less than 10kb 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 500kb. 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 population

  6. Turtle soup, Prohibition, and the population genetic structure of Diamondback Terrapins (Malaclemys terrapin).

    Science.gov (United States)

    Converse, Paul E; Kuchta, Shawn R; Hauswaldt, J Susanne; Roosenburg, Willem M

    2017-01-01

    Diamondback terrapins (Malaclemys terrapin) were a popular food item in early twentieth century America, and were consumed in soup with sherry. Intense market demand for terrapin meat resulted in population declines, notably along the Atlantic seaboard. Efforts to supply terrapins to markets resulted in translocation events, as individuals were moved about to stock terrapin farms. However, in 1920 the market for turtle soup buckled with the enactment of the eighteenth amendment to the United States' Constitution-which initiated the prohibition of alcoholic drinks-and many terrapin fisheries dumped their stocks into local waters. We used microsatellite data to show that patterns of genetic diversity along the terrapin's coastal range are consistent with historical accounts of translocation and cultivation activities. We identified possible instances of human-mediated dispersal by estimating gene flow over historical and contemporary timescales, Bayesian model testing, and bottleneck tests. We recovered six genotypic clusters along the Gulf and Atlantic coasts with varying degrees of admixture, including increased contemporary gene flow from Texas to South Carolina, from North Carolina to Maryland, and from North Carolina to New York. In addition, Bayesian models incorporating translocation events outperformed stepping-stone models. Finally, we were unable to detect population bottlenecks, possibly due to translocation reintroducing genetic diversity into bottlenecked populations. Our data suggest that current patterns of genetic diversity in the terrapin were altered by the demand for turtle soup followed by the enactment of alcohol prohibition. In addition, our study shows that population genetic tools can elucidate metapopulation dynamics in taxa with complex genetic histories impacted by anthropogenic activities.

  7. Genetic admixture and population substructure in Guanacaste Costa Rica.

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    Zhaoming Wang

    2010-10-01

    Full Text Available The population of Costa Rica (CR represents an admixture of major continental populations. An investigation of the CR population structure would provide an important foundation for mapping genetic variants underlying common diseases and traits. We conducted an analysis of 1,301 women from the Guanacaste region of CR using 27,904 single nucleotide polymorphisms (SNPs genotyped on a custom Illumina InfiniumII iSelect chip. The program STRUCTURE was used to compare the CR Guanacaste sample with four continental reference samples, including HapMap Europeans (CEU, East Asians (JPT+CHB, West African Yoruba (YRI, as well as Native Americans (NA from the Illumina iControl database. Our results show that the CR Guanacaste sample comprises a three-way admixture estimated to be 43% European, 38% Native American and 15% West African. An estimated 4% residual Asian ancestry may be within the error range. Results from principal components analysis reveal a correlation between genetic and geographic distance. The magnitude of linkage disequilibrium (LD measured by the number of tagging SNPs required to cover the same region in the genome in the CR Guanacaste sample appeared to be weaker than that observed in CEU, JPT+CHB and NA reference samples but stronger than that of the HapMap YRI sample. Based on the clustering pattern observed in both STRUCTURE and principal components analysis, two subpopulations were identified that differ by approximately 20% in LD block size averaged over all LD blocks identified by Haploview. We also show in a simulated association study conducted within the two subpopulations, that the failure to account for population stratification (PS could lead to a noticeable inflation in the false positive rate. However, we further demonstrate that existing PS adjustment approaches can reduce the inflation to an acceptable level for gene discovery.

  8. Tetralogy of Fallot and Hypoplastic Left Heart Syndrome – Complex Clinical Phenotypes Meet Complex Genetic Networks

    Science.gov (United States)

    Lahm, Harald; Schön, Patric; Doppler, Stefanie; Dreßen, Martina; Cleuziou, Julie; Deutsch, Marcus-André; Ewert, Peter; Lange, Rüdiger; Krane, Markus

    2015-01-01

    In many cases congenital heart disease (CHD) is represented by a complex phenotype and an array of several functional and morphological cardiac disorders. These malformations will be briefly summarized in the first part focusing on two severe CHD phenotypes, hypoplastic left heart syndrome (HLHS) and tetralogy of Fallot (TOF). In most cases of CHD the genetic origin remains largely unknown, though the complexity of the clinical picture strongly argues against a dysregulation which can be attributed to a single candidate gene but rather suggests a multifaceted polygenetic origin with elaborate interactions. Consistent with this idea, genome-wide approaches using whole exome sequencing, comparative sequence analysis of multiplex families to identify de novo mutations and global technologies to identify single nucleotide polymorphisms, copy number variants, dysregulation of the transcriptome and epigenetic variations have been conducted to obtain information about genetic alterations and potential predispositions possibly linked to the occurrence of a CHD phenotype. In the second part of this review we will summarize and discuss the available literature on identified genetic alterations linked to TOF and HLHS. PMID:26069455

  9. Bat population genetics and Lyssavirus presence in Great Britain.

    Science.gov (United States)

    Smith, G C; Aegerter, J N; Allnutt, T R; MacNicoll, A D; Learmount, J; Hutson, A M; Atterby, H

    2011-10-01

    Most lyssaviruses appear to have bat species as reservoir hosts. In Europe, of around 800 reported cases in bats, most were of European bat lyssavirus type 1 (EBLV-1) in Eptesicus serotinus (where the bat species was identified). About 20 cases of EBLV-2 were recorded, and these were in Myotis daubentonii and M. dasycneme. Through a passive surveillance scheme, Britain reports about one case a year of EBLV-2, but no cases of the more prevalent EBLV-1. An analysis of E. serotinus and M. daubentonii bat genetics in Britain reveals more structure in the former population than in the latter. Here we briefly review these differences, ask if this correlates with dispersal and movement patterns and use the results to suggest an hypothesis that EBLV-2 is more common than EBLV-1 in the UK, as genetic data suggest greater movement and regular immigration from Europe of M. daubentonii. We further suggest that this genetic approach is useful to anticipate the spread of exotic diseases in bats in any region of the world.

  10. Demography, genetic diversity, and population relationships among Argentinean Mapuche Indians

    Directory of Open Access Journals (Sweden)

    Alicia S. Goicoechea

    2000-09-01

    Full Text Available Fertility, mortality and migration data from four Mapuche Indian communities located along a 215-km NE-SW linear area in the Province of Río Negro, Argentina, were collated with genetic information furnished by nine blood group systems and by mtDNA haplogroups. The demographic and genetic data indicated a clear dichotomy, which split the four populations into two groups of two. Differing degrees of non-Indian exchanges was probably the main determining factor for this separation. Total genetic variability was very similar in all groups, and the interpopulational variability accounted for only 10% of the total variability. A low prevalence of the Diego(a antigen among the Mapuche was confirmed. The fact that significant genetic heterogeneity and population clusters were found in such a small territorial region attests to the sensitivity of demographic and genetic approaches in unraveling human history.Dados relativos a fertilidade, mortalidade e migração de quatro comunidades de índios Mapuche localizadas em uma área linear na direção nordeste-sudoeste com 215 km de extensão na Província de Rio Negro, Argentina, foram associados com a informação genética fornecida por nove sistemas de grupos sangüíneos e os haplogrupos do DNA mitocondrial. Ambos os tipos de informação apontam claramente para uma dicotomia, as quatro populações sendo divididas em grupos de duas. O principal fator responsável por esta separação é provavelmente graus diferentes de mistura com não-índios. A variabilidade genética total foi muito similar em todos os grupos, aquela entre populações sendo de apenas 10% deste valor. Foi confirmada a baixa prevalência do antígeno Diego(a entre os Mapuche. O fato de que heterogeneidade genética significativa e conjuntos populacionais diversos foram observados em uma região territorial tão pequena demonstra a sensibilidade dos enfoques demográfico e genético no esclarecimento da história humana.

  11. Population genetics of the Chilean frog Batrachyla Leptopus (Leptodactylidae

    Directory of Open Access Journals (Sweden)

    J.R. Formas

    2000-03-01

    Full Text Available Electrophoretic variation of proteins encoded by 14 loci was analyzed in eight (five continental and three insular populations of the Chilean leptodactylid frog Batrachyla leptopus. The overall proportion of polymorphic loci was estimated to be 18.7% and the average number of alleles per locus, 1.2, while observed and expected heterozygosities were 1.7 and 5.1%, respectively. The estimated coefficient of genetic identity was 0.940; the corresponding figure for genetic distance was 0.063. F-statistics analysis showed a total inbreeding coefficient (Fit of 0.855 and high levels of genetic subdivision (Fst = 0.596 as well as of inbreeding within populations (Fis = 0.640. However, there was only a moderate level of genetic differentiation (Fst = 0.181 between the insular group of populations and the continental group.A variação eletroforética de proteínas codificadas por 14 loci foi analisada em oito populações (5 continentais e 3 insulares da rã leptodactilídea chilena Batrachyla leptopus. A proporção geral de loci polimórficos foi estimada como sendo de 18,7% e o número médio de alelos por loco, 1,2, enquanto que as heterozigosidades observada e esperada foram 1,7 e 5,1%, respectivamente. O coeficiente esperado de identidade genética foi 0,940; o número correspondente para a distância genética foi 0,063. A análise estatística F mostrou um coeficiente de endogamia total (Fit de 0,855 e altos níveis de subdivisão genética (Fst = 0,596, assim como de endogamia dentro das populações (Fis = 0,640. Contudo, houve apenas um nível moderado de diferenciação genética (Fst = 0,181 entre o grupo insular de populações e o grupo continental.

  12. Genetic diversity of macauba from natural populations of Brazil.

    Science.gov (United States)

    da Conceição, Léo Duc Haa Carson Schwartzhaupt; Antoniassi, Rosemar; Junqueira, Nilton Tadeu Vilela; Braga, Marcelo Fideles; de Faria-Machado, Adelia Ferreira; Rogério, Joice Barbosa; Duarte, Iara Duprat; Bizzo, Humberto Ribeiro

    2015-09-04

    The macauba has been identified as the most promising native species for the production of vegetable oil and biomass. Several studies confirm its potential for numerous purposes (liquid and solid biofuels, food, cosmetics and pharmaceuticals), but this Brazilian biodiversity resource has been little explored, and work aimed at their domestication and genetic improvement are relatively recent. This study consisted of a multivariate approach to levels of trans fatty acids, oil yield and physical characteristics found in fruits of macauba of natural populations. The objective was to quantify the genetic variability among 35 genotypes of natural populations of macauba from 16 locations in different regions of Brazil. Euclidean Distance measurements were estimated and the cluster analysis obtained by the UPGMA method considering separately the fatty acid profile, and traits related to physical part and the fruits oil content. It was observed the formation of seven groups for the profile of fatty acids and five groups for physical characteristics and oil yield. Large variations were observed for different types of mesocarp (pulp) fatty acids and kernel. Oleic acid (18: 1) in mesocarp was the largest contribution to the total divergence. The results indicate variations to the physical characteristics and oil yield, especially the oil percentage in mesocarp and weight of the whole fruit which contributed 64.58% of the divergence between genotypes. The study identified genotypes potential to generate variability and obtaining selection gains, directing plant breeding programs according with demands of oils market.

  13. Estimates of genetic variability in mutated population of triticum aestivum

    International Nuclear Information System (INIS)

    Larik, A.S.; Siddiqui, K.A.; Soomoro, A.H.

    1980-01-01

    M 2 populations of four cultivars of Mexican origin (Mexipak-65, Nayab, Pak-70 and 6134 x C-271) and two locally bred cultivars (H-68 and C-591) of bread wheat, triticum aestivum (2n = 6x = AA BB DD) derived from six irradiation treatments (gamma rays 60sub(Co); 10, 15 and 20 kR and fast neutrons; 300, 600 and 900 RADS) were critically examined for spike length, spikelets per spike, grains per spike and grain yield. Genotypes varied significantly (p>=0.01) for all the characters. Irradiation treatment were instrumental in creating significant variability for all the characters, indicating that varieties did not perform uniformly across different gamma rays as well as fast neutron treatments. In the M 2 generation there was a considerable increase in variance for all the four metrical traits. Comparisons were made between controls and treated populations. Mutagenic treatments shifted the mean values mostly towards the negative direction, but the shift was not unidirectional nor equally effective for all the characters. The differences in mean values and the nature of variability observed in M 2 indicated a possible preference of selection M 3 generation. In general, estimates of genetic variability and heritability (b.s) increased with increasing doses of gamma rays and fast neutrons. Genetic advance also exhibited similar trend. The observed variability can be utilized in the evolution of new varieties. (authors)

  14. Integration of population genetic structure and plant response to climate change: sustaining genetic resources through evaluation of projected threats

    Science.gov (United States)

    Bryce A. Richardson; Marcus V. Warwell; Mee-Sook Kim; Ned B. Klopfenstein; Geral I. McDonald

    2010-01-01

    To assess threats or predict responses to disturbances, or both, it is essential to recognize and characterize the population structures of forest species in relation to changing environments. Appropriate management of these genetic resources in the future will require (1) understanding the existing genetic diversity/variation and population structure of forest trees...

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

    Science.gov (United States)

    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

  16. Genetic structure of natural populations: Final technical report

    International Nuclear Information System (INIS)

    Ayala, F.J.

    1987-01-01

    We determined the LD 50 for individuals with any one of four genetic constitutions. The LD 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

  17. Patterns of ancestry and genetic diversity in reintroduced populations of the slimy sculpin: Implications for conservation

    Science.gov (United States)

    Huff, David D.; Miller, Loren M.; Vondracek, Bruce C.

    2010-01-01

    Reintroductions are a common approach for preserving intraspecific biodiversity in fragmented landscapes. However, they may exacerbate the reduction in genetic diversity initially caused by population fragmentation because the effective population size of reintroduced populations is often smaller and reintroduced populations also tend to be more geographically isolated than native populations. Mixing genetically divergent sources for reintroduction purposes is a practice intended to increase genetic diversity. We documented the outcome of reintroductions from three mixed sources on the ancestral composition and genetic variation of a North American fish, the slimy sculpin (Cottus cognatus). We used microsatellite markers to evaluate allelic richness and heterozygosity in the reintroduced populations relative to computer simulated expectations. Sculpins in reintroduced populations exhibited higher levels of heterozygosity and allelic richness than any single source, but only slightly higher than the single most genetically diverse source population. Simulations intended to mimic an ideal scenario for maximizing genetic variation in the reintroduced populations also predicted increases, but they were only moderately greater than the most variable source population. We found that a single source contributed more than the other two sources at most reintroduction sites. We urge caution when choosing whether to mix source populations in reintroduction programs. Genetic characteristics of candidate source populations should be evaluated prior to reintroduction if feasible. When combined with knowledge of the degree of genetic distinction among sources, simulations may allow the genetic diversity benefits of mixing populations to be weighed against the risks of outbreeding depression in reintroduced and nearby populations.

  18. Amodified probabilistic genetic algorithm for the solution of complex constrained optimization problems

    OpenAIRE

    Vorozheikin, A.; Gonchar, T.; Panfilov, I.; Sopov, E.; Sopov, S.

    2009-01-01

    A new algorithm for the solution of complex constrained optimization problems based on the probabilistic genetic algorithm with optimal solution prediction is proposed. The efficiency investigation results in comparison with standard genetic algorithm are presented.

  19. DNA variation of the mammalian major histocompatibility complex reflects genomic diversity and population history

    International Nuclear Information System (INIS)

    Yuhki, Naoya; O'Brien, S.J.

    1990-01-01

    The major histocompatibility complex (MHC) is a multigene complex of tightly linked homologous genes that encode cell surface antigens that play a key role in immune regulation and response to foreign antigens. In most species, MHC gene products display extreme antigenic polymorphism, and their variability has been interpreted to reflect an adaptive strategy for accommodating rapidly evolving infectious agents that periodically afflict natural populations. Determination of the extent of MHC variation has been limited to populations in which skin grafting is feasible or for which serological reagents have been developed. The authors present here a quantitative analysis of restriction fragment length polymorphism of MHC class I genes in several mammalian species (cats, rodents, humans) known to have very different levels of genetic diversity based on functional MHC assays and on allozyme surveys. When homologous class I probes were employed, a notable concordance was observed between the extent of MHC restriction fragment variation and functional MHC variation detected by skin grafts or genome-wide diversity estimated by allozyme screens. These results confirm the genetically depauperate character of the African cheetah, Acinonyx jubatus, and the Asiatic lion, Panthera leo persica; further, they support the use of class I MHC molecular reagents in estimating the extent and character of genetic diversity in natural populations

  20. DNA variation of the mammalian major histocompatibility complex reflects genomic diversity and population history

    Energy Technology Data Exchange (ETDEWEB)

    Yuhki, Naoya; O' Brien, S.J. (National Cancer Institute, Frederick, MD (USA))

    1990-01-01

    The major histocompatibility complex (MHC) is a multigene complex of tightly linked homologous genes that encode cell surface antigens that play a key role in immune regulation and response to foreign antigens. In most species, MHC gene products display extreme antigenic polymorphism, and their variability has been interpreted to reflect an adaptive strategy for accommodating rapidly evolving infectious agents that periodically afflict natural populations. Determination of the extent of MHC variation has been limited to populations in which skin grafting is feasible or for which serological reagents have been developed. The authors present here a quantitative analysis of restriction fragment length polymorphism of MHC class I genes in several mammalian species (cats, rodents, humans) known to have very different levels of genetic diversity based on functional MHC assays and on allozyme surveys. When homologous class I probes were employed, a notable concordance was observed between the extent of MHC restriction fragment variation and functional MHC variation detected by skin grafts or genome-wide diversity estimated by allozyme screens. These results confirm the genetically depauperate character of the African cheetah, Acinonyx jubatus, and the Asiatic lion, Panthera leo persica; further, they support the use of class I MHC molecular reagents in estimating the extent and character of genetic diversity in natural populations.

  1. Continuous Influx of Genetic Material from Host to Virus Populations.

    Directory of Open Access Journals (Sweden)

    Clément Gilbert

    2016-02-01

    Full Text Available 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.

  2. Genetic management strategies for controlling infectious diseases in livestock populations

    Directory of Open Access Journals (Sweden)

    Bishop Stephen C

    2003-06-01

    Full Text Available Abstract This paper considers the use of disease resistance genes to control the transmission of infection through an animal population. Transmission is summarised by R0, the basic reproductive ratio of a pathogen. If R0 > 1.0 a major epidemic can occur, thus a disease control strategy should aim to reduce R0 below 1.0, e.g. by mixing resistant with susceptible wild-type animals. Suppose there is a resistance allele, such that transmission of infection through a population homozygous for this allele will be R02 01, where R01 describes transmission in the wildtype population. For an otherwise homogeneous population comprising animals of these two groups, R0 is the weighted average of the two sub-populations: R0 = R01ρ + R02 (1 - ρ, where ρ is the proportion of wildtype animals. If R01 > 1 and R02 0 ≤ 1, i.e. ρ ≤ (R0 - R02/(R01 - R02. If R02 = 0, the proportion of resistant animals must be at least 1 - 1/R01. For an n genotype model the requirement is still to have R0 ≤ 1.0. Probabilities of epidemics in genetically mixed populations conditional upon the presence of a single infected animal were derived. The probability of no epidemic is always 1/(R0 + 1. When R0 ≤ 1 the probability of a minor epidemic, which dies out without intervention, is R0/(R0 + 1. When R0 > 1 the probability of a minor and major epidemics are 1/(R0 + 1 and (R0 - 1/(R0 + 1. Wherever possible a combination of genotypes should be used to minimise the invasion possibilities of pathogens that have mutated to overcome the effects of specific resistance alleles.

  3. Linguistic, geographic and genetic isolation: a collaborative study of Italian populations.

    Science.gov (United States)

    Capocasa, Marco; Anagnostou, Paolo; Bachis, Valeria; Battaggia, Cinzia; Bertoncini, Stefania; Biondi, Gianfranco; Boattini, Alessio; Boschi, Ilaria; Brisighelli, Francesca; Caló, Carla Maria; Carta, Marilisa; Coia, Valentina; Corrias, Laura; Crivellaro, Federica; De Fanti, Sara; Dominici, Valentina; Ferri, Gianmarco; Francalacci, Paolo; Franceschi, Zelda Alice; Luiselli, Donata; Morelli, Laura; Paoli, Giorgio; Rickards, Olga; Robledo, Renato; Sanna, Daria; Sanna, Emanuele; Sarno, Stefania; Sineo, Luca; Taglioli, Luca; Tagarelli, Giuseppe; Tofanelli, Sergio; Vona, Giuseppe; Pettener, Davide; Destro Bisol, Giovanni

    2014-01-01

    The animal and plant biodiversity of the Italian territory is known to be one of the richest in the Mediterranean basin and Europe as a whole, but does the genetic diversity of extant human populations show a comparable pattern? According to a number of studies, the genetic structure of Italian populations retains the signatures of complex peopling processes which took place from the Paleolithic to modern era. Although the observed patterns highlight a remarkable degree of genetic heterogeneity, they do not, however, take into account an important source of variation. In fact, Italy is home to numerous ethnolinguistic minorities which have yet to be studied systematically. Due to their difference in geographical origin and demographic history, such groups not only signal the cultural and social diversity of our country, but they are also potential contributors to its bio-anthropological heterogeneity. To fill this gap, research groups from four Italian Universities (Bologna, Cagliari, Pisa and Roma Sapienza) started a collaborative study in 2007, which was funded by the Italian Ministry of Education, University and Research and received partial support by the Istituto Italiano di Antropologia. In this paper, we present an account of the results obtained in the course of this initiative. Four case-studies relative to linguistic minorities from the Eastern Alps, Sardinia, Apennines and Southern Italy are first described and discussed, focusing on their micro-evolutionary and anthropological implications. Thereafter, we present the results of a systematic analysis of the relations between linguistic, geographic and genetic isolation. Integrating the data obtained in the course of the long-term study with literature and unpublished results on Italian populations, we show that a combination of linguistic and geographic factors is probably responsible for the presence of the most robust signatures of genetic isolation. Finally, we evaluate the magnitude of the diversity

  4. Closure of population biobanks and direct-to-consumer genetic testing companies.

    Science.gov (United States)

    Zawati, Ma'n H; Borry, Pascal; Howard, Heidi Carmen

    2011-09-01

    Genetic research gained new momentum with the completion of the Human Genome Project in 2003. Formerly centered on the investigation of single-gene disorders, genetic research is increasingly targeting common complex diseases and in doing so is studying the whole genome, the environment and its impact on genomic variation. Consequently, biobanking initiatives have emerged around the world as a tool to sustain such progress. Whether they are small scale or longitudinal, public or private, commercial or non-commercial, biobanks should consider the possibility of closure. Interestingly, while raising important ethical issues, this topic has hardly been explored in the literature. Indeed, ethical issues associated with sale, insolvency, end of funding, or transfer of materials to other entities (which are all issues either related to or possible consequences of closure) are seldom the subject of discussion. In an attempt to fill this gap, this paper will discuss-using population and direct-to-consumer (DTC) genetic testing companies' biobanks as case studies-(1) international and national normative documents addressing the issue of closure and (2) the internal policies of population biobanks and DTC genetic testing companies. The analysis will inform the debate on biobank closure and elucidate the underlying ethical issues, which include, but are not limited to informed consent, storage and privacy.

  5. Tools for Genetic Studies in Experimental Populations of Polyploids

    Directory of Open Access Journals (Sweden)

    Peter M. Bourke

    2018-04-01

    Full Text Available Polyploid organisms carry more than two copies of each chromosome, a condition rarely tolerated in animals but which occurs relatively frequently in the plant kingdom. One of the principal challenges faced by polyploid organisms is to evolve stable meiotic mechanisms to faithfully transmit genetic information to the next generation upon which the study of inheritance is based. In this review we look at the tools available to the research community to better understand polyploid inheritance, many of which have only recently been developed. Most of these tools are intended for experimental populations (rather than natural populations, facilitating genomics-assisted crop improvement and plant breeding. This is hardly surprising given that a large proportion of domesticated plant species are polyploid. We focus on three main areas: (1 polyploid genotyping; (2 genetic and physical mapping; and (3 quantitative trait analysis and genomic selection. We also briefly review some miscellaneous topics such as the mode of inheritance and the availability of polyploid simulation software. The current polyploid analytic toolbox includes software for assigning marker genotypes (and in particular, estimating the dosage of marker alleles in the heterozygous condition, establishing chromosome-scale linkage phase among marker alleles, constructing (short-range haplotypes, generating linkage maps, performing genome-wide association studies (GWAS and quantitative trait locus (QTL analyses, and simulating polyploid populations. These tools can also help elucidate the mode of inheritance (disomic, polysomic or a mixture of both as in segmental allopolyploids or reveal whether double reduction and multivalent chromosomal pairing occur. An increasing number of polyploids (or associated diploids are being sequenced, leading to publicly available reference genome assemblies. Much work remains in order to keep pace with developments in genomic technologies. However, such

  6. Tools for Genetic Studies in Experimental Populations of Polyploids.

    Science.gov (United States)

    Bourke, Peter M; Voorrips, Roeland E; Visser, Richard G F; Maliepaard, Chris

    2018-01-01

    Polyploid organisms carry more than two copies of each chromosome, a condition rarely tolerated in animals but which occurs relatively frequently in the plant kingdom. One of the principal challenges faced by polyploid organisms is to evolve stable meiotic mechanisms to faithfully transmit genetic information to the next generation upon which the study of inheritance is based. In this review we look at the tools available to the research community to better understand polyploid inheritance, many of which have only recently been developed. Most of these tools are intended for experimental populations (rather than natural populations), facilitating genomics-assisted crop improvement and plant breeding. This is hardly surprising given that a large proportion of domesticated plant species are polyploid. We focus on three main areas: (1) polyploid genotyping; (2) genetic and physical mapping; and (3) quantitative trait analysis and genomic selection. We also briefly review some miscellaneous topics such as the mode of inheritance and the availability of polyploid simulation software. The current polyploid analytic toolbox includes software for assigning marker genotypes (and in particular, estimating the dosage of marker alleles in the heterozygous condition), establishing chromosome-scale linkage phase among marker alleles, constructing (short-range) haplotypes, generating linkage maps, performing genome-wide association studies (GWAS) and quantitative trait locus (QTL) analyses, and simulating polyploid populations. These tools can also help elucidate the mode of inheritance (disomic, polysomic or a mixture of both as in segmental allopolyploids) or reveal whether double reduction and multivalent chromosomal pairing occur. An increasing number of polyploids (or associated diploids) are being sequenced, leading to publicly available reference genome assemblies. Much work remains in order to keep pace with developments in genomic technologies. However, such technologies

  7. Population genetic structure and conservation genetics of threatened Okaloosa darters (Etheostoma okaloosae).

    Science.gov (United States)

    Austin, James D.; Jelks, Howard L.; Tate, Bill; Johnson, Aria R.; Jordan, Frank

    2011-01-01

    Imperiled Okaloosa darters (Etheostoma okaloosae) are small, benthic fish limited to six streams that flow into three bayous of Choctawhatchee Bay in northwest Florida, USA. We analyzed the complete mitochondrial cytochrome b gene and 10 nuclear microsatellite loci for 255 and 273 Okaloosa darters, respectively. Bayesian clustering analyses and AMOVA reflect congruent population genetic structure in both mitochondrial and microsatellite DNA. This structure reveals historical isolation of Okaloosa darter streams nested within bayous. Most of the six streams appear to have exchanged migrants though they remain genetically distinct. The U.S. Fish and Wildlife Service recently reclassified Okaloosa darters from endangered to threatened status. Our genetic data support the reclassification of Okaloosa darter Evolutionary Significant Units (ESUs) in the larger Tom's, Turkey, and Rocky creeks from endangered to threatened status. However, the three smaller drainages (Mill, Swift, and Turkey Bolton creeks) remain at risk due to their small population sizes and anthropogenic pressures on remaining habitat. Natural resource managers now have the evolutionary information to guide recovery actions within and among drainages throughout the range of the Okaloosa darter.

  8. Population genetic structure of Diaphorina citri Kuwayama (Hemiptera: Liviidae): host-driven genetic differentiation in China.

    Science.gov (United States)

    Meng, Lixue; Wang, Yongmo; Wei, Wen-Hua; Zhang, Hongyu

    2018-01-24

    The Asian citrus psyllid Diaphorina citri Kuwayama is a major pest in citrus production, transmitting Candidatus Liberibacter asiaticus. It has spread widely across eastern and southern China. Unfortunately, little is known about the genetic diversity and population structure of D. citri, making pest control difficult. In this study, nine specifically developed SSR markers and three known mitochondrial DNA were used for population genetics study of D. citri using 225 samples collected from all 7 distribution regions in China. Based on the SSR data, D. citri was found highly diverse with a mean observed heterozygosity of 0.50, and three subgroups were structured by host plant: (i) Shatangju, NF mandarin and Ponkan; (ii) Murraya paniculata and Lemon; (iii) Citrus unshiu, Bingtangcheng, Summer orange and Navel. No significant genetic differences were found with mtDNA data. We suggested the host-associated divergence is likely to have occurred very recently. A unimodal distribution of paired differences, the negative and significant Tajima's D and Fu's F S parameters among mtDNA suggested a recent demographic expansion. The extensive citrus cultivation and increased suitable living habitat was recommended as a key for this expansion event.

  9. Genetic algorithms applied to nonlinear and complex domains; TOPICAL

    International Nuclear Information System (INIS)

    Barash, D; Woodin, A E

    1999-01-01

    The dissertation, titled ''Genetic Algorithms Applied to Nonlinear and Complex Domains'', describes and then applies a new class of powerful search algorithms (GAS) to certain domains. GAS are capable of solving complex and nonlinear problems where many parameters interact to produce a ''final'' result such as the optimization of the laser pulse in the interaction of an atom with an intense laser field. GAS can very efficiently locate the global maximum by searching parameter space in problems which are unsuitable for a search using traditional methods. In particular, the dissertation contains new scientific findings in two areas. First, the dissertation examines the interaction of an ultra-intense short laser pulse with atoms. GAS are used to find the optimal frequency for stabilizing atoms in the ionization process. This leads to a new theoretical formulation, to explain what is happening during the ionization process and how the electron is responding to finite (real-life) laser pulse shapes. It is shown that the dynamics of the process can be very sensitive to the ramp of the pulse at high frequencies. The new theory which is formulated, also uses a novel concept (known as the (t,t') method) to numerically solve the time-dependent Schrodinger equation Second, the dissertation also examines the use of GAS in modeling decision making problems. It compares GAS with traditional techniques to solve a class of problems known as Markov Decision Processes. The conclusion of the dissertation should give a clear idea of where GAS are applicable, especially in the physical sciences, in problems which are nonlinear and complex, i.e. difficult to analyze by other means

  10. Genetic algorithms applied to nonlinear and complex domains

    International Nuclear Information System (INIS)

    Barash, D; Woodin, A E

    1999-01-01

    The dissertation, titled ''Genetic Algorithms Applied to Nonlinear and Complex Domains'', describes and then applies a new class of powerful search algorithms (GAS) to certain domains. GAS are capable of solving complex and nonlinear problems where many parameters interact to produce a ''final'' result such as the optimization of the laser pulse in the interaction of an atom with an intense laser field. GAS can very efficiently locate the global maximum by searching parameter space in problems which are unsuitable for a search using traditional methods. In particular, the dissertation contains new scientific findings in two areas. First, the dissertation examines the interaction of an ultra-intense short laser pulse with atoms. GAS are used to find the optimal frequency for stabilizing atoms in the ionization process. This leads to a new theoretical formulation, to explain what is happening during the ionization process and how the electron is responding to finite (real-life) laser pulse shapes. It is shown that the dynamics of the process can be very sensitive to the ramp of the pulse at high frequencies. The new theory which is formulated, also uses a novel concept (known as the (t,t') method) to numerically solve the time-dependent Schrodinger equation Second, the dissertation also examines the use of GAS in modeling decision making problems. It compares GAS with traditional techniques to solve a class of problems known as Markov Decision Processes. The conclusion of the dissertation should give a clear idea of where GAS are applicable, especially in the physical sciences, in problems which are nonlinear and complex, i.e. difficult to analyze by other means

  11. Green turtle (Chelonia mydas genetic diversity at Paranaguá Estuarine Complex feeding grounds in Brazil

    Directory of Open Access Journals (Sweden)

    Juliana Costa Jordão

    2015-09-01

    Full Text Available Sea turtles are marine reptiles that undertake long migrations through their life, with limited information regarding juvenile stages. Feeding grounds (FGs, where they spend most of their lives, are composed by individuals from different natal origins, known as mixed stock populations. The aim of this study was to assess genetic composition, natal origins and demographic history of juvenile green turtles (Chelonia mydas at the Paranaguá Estuarine Complex (PEC, Brazil, considered a Natural World Heritage site. Tissue samples of stranded animals were collected (n = 60, and 700 bp mitochondrial DNA sequences were generated and compared to shorter sequences from previously published studies. Global exact tests of differentiation revealed significant differences among PEC and the other FGs, except those at the South Atlantic Ocean. Green turtles at PEC present genetic signatures similar to those of nesting females from Ascension Island, Guinea Bissau and Aves Island/Surinam. Population expansion was evidenced to have occurred 20–25 kYA, reinforcing the hypothesis of recovery from Southern Atlantic refugia after the last Glacial Maximum. These results contribute to a better understanding of the dynamics of green turtle populations at a protected area by providing knowledge on the dispersion patterns and reinforcing the importance of the interconnectivity between nesting and foraging populations.

  12. Population Genetic Structure of the Tropical Two-Wing Flyingfish (Exocoetus volitans.

    Directory of Open Access Journals (Sweden)

    Eric A Lewallen

    Full Text Available Delineating populations of pantropical marine fish is a difficult process, due to widespread geographic ranges and complex life history traits in most species. Exocoetus volitans, a species of two-winged flyingfish, is a good model for understanding large-scale patterns of epipelagic fish population structure because it has a circumtropical geographic range and completes its entire life cycle in the epipelagic zone. Buoyant pelagic eggs should dictate high local dispersal capacity in this species, although a brief larval phase, small body size, and short lifespan may limit the dispersal of individuals over large spatial scales. Based on these biological features, we hypothesized that E. volitans would exhibit statistically and biologically significant population structure defined by recognized oceanographic barriers. We tested this hypothesis by analyzing cytochrome b mtDNA sequence data (1106 bps from specimens collected in the Pacific, Atlantic and Indian oceans (n = 266. AMOVA, Bayesian, and coalescent analytical approaches were used to assess and interpret population-level genetic variability. A parsimony-based haplotype network did not reveal population subdivision among ocean basins, but AMOVA revealed limited, statistically significant population structure between the Pacific and Atlantic Oceans (ΦST = 0.035, p<0.001. A spatially-unbiased Bayesian approach identified two circumtropical population clusters north and south of the Equator (ΦST = 0.026, p<0.001, a previously unknown dispersal barrier for an epipelagic fish. Bayesian demographic modeling suggested the effective population size of this species increased by at least an order of magnitude ~150,000 years ago, to more than 1 billion individuals currently. Thus, high levels of genetic similarity observed in E. volitans can be explained by high rates of gene flow, a dramatic and recent population expansion, as well as extensive and consistent dispersal throughout the geographic

  13. Population Genetic Structure of the Tropical Two-Wing Flyingfish (Exocoetus volitans)

    Science.gov (United States)

    Lewallen, Eric A.; Bohonak, Andrew J.; Bonin, Carolina A.; van Wijnen, Andre J.; Pitman, Robert L.; Lovejoy, Nathan R.

    2016-01-01

    Delineating populations of pantropical marine fish is a difficult process, due to widespread geographic ranges and complex life history traits in most species. Exocoetus volitans, a species of two-winged flyingfish, is a good model for understanding large-scale patterns of epipelagic fish population structure because it has a circumtropical geographic range and completes its entire life cycle in the epipelagic zone. Buoyant pelagic eggs should dictate high local dispersal capacity in this species, although a brief larval phase, small body size, and short lifespan may limit the dispersal of individuals over large spatial scales. Based on these biological features, we hypothesized that E. volitans would exhibit statistically and biologically significant population structure defined by recognized oceanographic barriers. We tested this hypothesis by analyzing cytochrome b mtDNA sequence data (1106 bps) from specimens collected in the Pacific, Atlantic and Indian oceans (n = 266). AMOVA, Bayesian, and coalescent analytical approaches were used to assess and interpret population-level genetic variability. A parsimony-based haplotype network did not reveal population subdivision among ocean basins, but AMOVA revealed limited, statistically significant population structure between the Pacific and Atlantic Oceans (ΦST = 0.035, p<0.001). A spatially-unbiased Bayesian approach identified two circumtropical population clusters north and south of the Equator (ΦST = 0.026, p<0.001), a previously unknown dispersal barrier for an epipelagic fish. Bayesian demographic modeling suggested the effective population size of this species increased by at least an order of magnitude ~150,000 years ago, to more than 1 billion individuals currently. Thus, high levels of genetic similarity observed in E. volitans can be explained by high rates of gene flow, a dramatic and recent population expansion, as well as extensive and consistent dispersal throughout the geographic range of the

  14. Origin, evolution, and population genetics of the selfish Segregation Distorter gene duplication in European and African populations of Drosophila melanogaster.

    Science.gov (United States)

    Brand, Cara L; Larracuente, Amanda M; Presgraves, Daven C

    2015-05-01

    Meiotic drive elements are a special class of evolutionarily "selfish genes" that subvert Mendelian segregation to gain preferential transmission at the expense of homologous loci. Many drive elements appear to be maintained in populations as stable polymorphisms, their equilibrium frequencies determined by the balance between drive (increasing frequency) and selection (decreasing frequency). Here we show that a classic, seemingly balanced, drive system is instead characterized by frequent evolutionary turnover giving rise to dynamic, rather than stable, equilibrium frequencies. The autosomal Segregation Distorter (SD) system of the fruit fly Drosophila melanogaster is a selfish coadapted meiotic drive gene complex in which the major driver corresponds to a partial duplication of the gene Ran-GTPase activating protein (RanGAP). SD chromosomes segregate at similar, low frequencies of 1-5% in natural populations worldwide, consistent with a balanced polymorphism. Surprisingly, our population genetic analyses reveal evidence for parallel, independent selective sweeps of different SD chromosomes in populations on different continents. These findings suggest that, rather than persisting at a single stable equilibrium, SD chromosomes turn over frequently within populations. © 2015 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

  15. Nutritional habits, lifestyle, and genetic predisposition in cardiovascular and metabolic traits in Turkish population.

    Science.gov (United States)

    Karaca, Sefayet; Erge, Sema; Cesuroglu, Tomris; Polimanti, Renato

    2016-06-01

    Cardiovascular and metabolic traits (CMT) are influenced by complex interactive processes including diet, lifestyle, and genetic predisposition. The present study investigated the interactions of these risk factors in relation to CMTs in the Turkish population. We applied bootstrap agglomerative hierarchical clustering and Bayesian network learning algorithms to identify the causative relationships among genes involved in different biological mechanisms (i.e., lipid metabolism, hormone metabolism, cellular detoxification, aging, and energy metabolism), lifestyle (i.e., physical activity, smoking behavior, and metropolitan residency), anthropometric traits (i.e., body mass index, body fat ratio, and waist-to-hip ratio), and dietary habits (i.e., daily intakes of macro- and micronutrients) in relation to CMTs (i.e., health conditions and blood parameters). We identified significant correlations between dietary habits (soybean and vitamin B12 intakes) and different cardiometabolic diseases that were confirmed by the Bayesian network-learning algorithm. Genetic factors contributed to these disease risks also through the pleiotropy of some genetic variants (i.e., F5 rs6025 and MTR rs180508). However, we also observed that certain genetic associations are indirect since they are due to the causative relationships among the CMTs (e.g., APOC3 rs5128 is associated with low-density lipoproteins cholesterol and, by extension, total cholesterol). Our study applied a novel approach to integrate various sources of information and dissect the complex interactive processes related to CMTs. Our data indicated that complex causative networks are present: causative relationships exist among CMTs and are affected by genetic factors (with pleiotropic and non-pleiotropic effects) and dietary habits. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. The population genetics of X-autosome synthetic lethals and steriles.

    Science.gov (United States)

    Lachance, Joseph; Johnson, Norman A; True, John R

    2011-11-01

    Epistatic interactions are widespread, and many of these interactions involve combinations of alleles at different loci that are deleterious when present in the same individual. The average genetic environment of sex-linked genes differs from that of autosomal genes, suggesting that the population genetics of interacting X-linked and autosomal alleles may be complex. Using both analytical theory and computer simulations, we analyzed the evolutionary trajectories and mutation-selection balance conditions for X-autosome synthetic lethals and steriles. Allele frequencies follow a set of fundamental trajectories, and incompatible alleles are able to segregate at much higher frequencies than single-locus expectations. Equilibria exist, and they can involve fixation of either autosomal or X-linked alleles. The exact equilibrium depends on whether synthetic alleles are dominant or recessive and whether fitness effects are seen in males, females, or both sexes. When single-locus fitness effects and synthetic incompatibilities are both present, population dynamics depend on the dominance of alleles and historical contingency (i.e., whether X-linked or autosomal mutations occur first). Recessive synthetic lethality can result in high-frequency X-linked alleles, and dominant synthetic lethality can result in high-frequency autosomal alleles. Many X-autosome incompatibilities in natural populations may be cryptic, appearing to be single-locus effects because one locus is fixed. We also discuss the implications of these findings with respect to standing genetic variation and the origins of Haldane's rule.

  17. Properties of global- and local-ancestry adjustments in genetic association tests in admixed populations.

    Science.gov (United States)

    Martin, Eden R; Tunc, Ilker; Liu, Zhi; Slifer, Susan H; Beecham, Ashley H; Beecham, Gary W

    2018-03-01

    Population substructure can lead to confounding in tests for genetic association, and failure to adjust properly can result in spurious findings. Here we address this issue of confounding by considering the impact of global ancestry (average ancestry across the genome) and local ancestry (ancestry at a specific chromosomal location) on regression parameters and relative power in ancestry-adjusted and -unadjusted models. We examine theoretical expectations under different scenarios for population substructure; applying different regression models, verifying and generalizing using simulations, and exploring the findings in real-world admixed populations. We show that admixture does not lead to confounding when the trait locus is tested directly in a single admixed population. However, if there is more complex population structure or a marker locus in linkage disequilibrium (LD) with the trait locus is tested, both global and local ancestry can be confounders. Additionally, we show the genotype parameters of adjusted and unadjusted models all provide tests for LD between the marker and trait locus, but in different contexts. The local ancestry adjusted model tests for LD in the ancestral populations, while tests using the unadjusted and the global ancestry adjusted models depend on LD in the admixed population(s), which may be enriched due to different ancestral allele frequencies. Practically, this implies that global-ancestry adjustment should be used for screening, but local-ancestry adjustment may better inform fine mapping and provide better effect estimates at trait loci. © 2017 WILEY PERIODICALS, INC.

  18. Analysis of the genetic structure of allopatric populations of Lutzomyia umbratilis using the period clock gene.

    Science.gov (United States)

    de Souza Freitas, Moises Thiago; Ríos-Velasquez, Claudia Maria; da Silva, Lidiane Gomes; Costa, César Raimundo Lima; Marcelino, Abigail; Leal-Balbino, Tereza Cristina; Balbino, Valdir de Queiroz; Pessoa, Felipe Arley Costa

    2016-02-01

    In South America, Lutzomyia umbratilis is the main vector of Leishmania guyanensis, one of the species involved in the transmission of American tegumentary leishmaniasis. In Brazil, L. umbratilis has been recorded in the Amazon region, and an isolated population has been identified in the state of Pernambuco, Northeastern region. This study assessed the phylogeographic structure of three allopatric Brazilian populations of L. umbratilis. Samples of L. umbratilis were collected from Rio Preto da Eva (north of the Amazon River, Amazonas), from Manacapuru (south of the Amazon River), and from the isolated population in Recife, Pernambuco state. These samples were processed to obtain sequences of the period gene. Phylogenetic analysis revealed the presence of two distinct monophyletic clades: one clade comprised of the Recife and Rio Preto da Eva samples, and one clade comprised of the Manacapuru samples. Comparing the Manacapuru population with the Recife and Rio Preto da Eva populations revealed high indices of interpopulational divergence. Phylogenetic analysis indicated that geographical distance and environmental differences have not modified the ancestral relationship shared by the Recife and Rio Preto da Eva populations. Genetic similarities suggest that, in evolutionary terms, these populations are more closely related to each other than to the Manacapuru population. These results confirm the existence of an L. umbratilis species complex composed of at least two incipient species. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

  19. Multilayered Genetic and Omics Dissection of Mitochondrial Activity in a Mouse Reference Population

    Science.gov (United States)

    Wu, Yibo; Williams, Evan G.; Dubuis, Sébastien; Mottis, Adrienne; Jovaisaite, Virginija; Houten, Sander M.; Argmann, Carmen A.; Faridi, Pouya; Wolski, Witold; Kutalik, Zoltán; Zamboni, Nicola; Auwerx, Johan; Aebersold, Ruedi

    2014-01-01

    SUMMARY The manner by which genotype and environment affect complex phenotypes is one of the fundamental questions in biology. In this study, we quantified the transcriptome—a subset of the metabolome—and, using targeted proteomics, quantified a subset of the liver proteome from 40 strains of the BXD mouse genetic reference population on two diverse diets. We discovered dozens of transcript, protein, and metabolite QTLs, several of which linked to metabolic phenotypes. Most prominently, Dhtkd1 was identified as a primary regulator of 2-aminoadipate, explaining variance in fasted glucose and diabetes status in both mice and humans. These integrated molecular profiles also allowed further characterization of complex pathways, particularly the mitochondrial unfolded protein response (UPRmt). UPRmt shows strikingly variant responses at the transcript and protein level that are remarkably conserved among C. elegans, mice, and humans. Overall, these examples demonstrate the value of an integrated multilayered omics approach to characterize complex metabolic phenotypes. PMID:25215496

  20. Temporal changes in genetic variation of boll weevil (Coleoptera: Curculionidae) populations, and implications for population assignment in eradication zones

    Science.gov (United States)

    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...

  1. Population specific genetic heterogeneity of familial hypercholesterolemia in South Africa.

    Science.gov (United States)

    Smyth, Natalie; Ramsay, Michèle; Raal, Frederick J

    2018-04-01

    To describe the prevalence and population-specific genetic heterogeneity of familial hypercholesterolemia in South Africa. This review highlights the paucity of data on familial hypercholesterolemia in South Africa, and the urgent need to uncover the mutation profiles in lipid-associated genes, causing an increase in LDL-cholesterol in the different ethnic groups. Case reports and small studies have shown that familial hypercholesterolemia, although apparently uncommon, is present in black Africans. Local founder effects have led to an increased prevalence of familial hypercholesterolemia in several South African populations: Afrikaner founder mutations (c.681 C>G, c.1285 G>A, c.523 G>A), Ashkenazi founder mutation (c.654_656del) and possible Indian founder mutation (c.2054 C>T). Preliminary data in black Africans with elevated LDL-cholesterol identified a possible common mutation, c.137_142del. The South African multiethnic society and well described founder effects emphasize the need for differential approaches to diagnosis and management of familial hypercholesterolemia. Studies involving larger cohorts and inclusive of different ethnicities are paramount to establishing an accurate prevalence of familial hypercholesterolemia in black Africans, not only in South Africa but in the Sub-Saharan African region. It is clear that the estimated world prevalence of one in 250 cannot be generally applied across African populations.

  2. Spatial genetic analyses reveal cryptic population structure and migration patterns in a continuously harvested grey wolf (Canis lupus population in north-eastern Europe.

    Directory of Open Access Journals (Sweden)

    Maris Hindrikson

    Full Text Available Spatial genetics is a relatively new field in wildlife and conservation biology that is becoming an essential tool for unravelling the complexities of animal population processes, and for designing effective strategies for conservation and management. Conceptual and methodological developments in this field are therefore critical. Here we present two novel methodological approaches that further the analytical possibilities of STRUCTURE and DResD. Using these approaches we analyse structure and migrations in a grey wolf (Canislupus population in north-eastern Europe. We genotyped 16 microsatellite loci in 166 individuals sampled from the wolf population in Estonia and Latvia that has been under strong and continuous hunting pressure for decades. Our analysis demonstrated that this relatively small wolf population is represented by four genetic groups. We also used a novel methodological approach that uses linear interpolation to statistically test the spatial separation of genetic groups. The new method, which is capable of using program STRUCTURE output, can be applied widely in population genetics to reveal both core areas and areas of low significance for genetic groups. We also used a recently developed spatially explicit individual-based method DResD, and applied it for the first time to microsatellite data, revealing a migration corridor and barriers, and several contact zones.

  3. [Genetic differentiation of Isaria farinosa populations in Anhui Province of East China].

    Science.gov (United States)

    Sun, Zhao-Hong; Luan, Feng-Gang; Zhang, Da-Min; Chen, Ming-Jun; Wang, Bin; Li, Zeng-Zhi

    2011-11-01

    Isaria farinosa is an important entomopathogenic fungus. By using ISSR, this paper studied the genetic heterogeneity of six I. farinosa populations at different localities of Anhui Province, East China. A total of 98.5% polymorphic loci were amplified with ten polymorphic primers, but the polymorphism at population level varied greatly, within the range of 59.6%-93.2%. The genetic differentiation index (G(st)) between the populations based on Nei's genetic heterogenesis analysis was 0.3365, and the gene flow (N(m)) was 0.4931. The genetic differentiation between the populations was lower than that within the populations, suggesting that the genetic variation of I. farinosa mainly come from the interior of the populations. The UPGMA clustering based on the genetic similarities between the isolates revealed that the Xishan population was monophylectic, while the other five populations were polyphylectic, with the Yaoluoping population being the most heterogenic and the Langyashan population being the least heterogenic. No correlations were observed between the geographic distance and the genetic distance of the populations. According to the UPGMA clustering based on the genetic distance between the populations, the six populations were classified into three groups, and this classification was accorded with the clustering based on geographic environment, suggesting the effects of environmental heterogeneity on the population heterogeneity.

  4. Can small wildlife conservancies maintain genetically stable populations of large mammals? Evidence for increased genetic drift in geographically restricted populations of Cape buffalo in East Africa

    DEFF Research Database (Denmark)

    Heller, R; Okello, J B A; Siegismund, H

    2010-01-01

    populations, the level of genetic differentiation found here is comparable to that among pan-African populations. Overall, correlations between conservancy area and indices of genetic diversity suggest buffalo populations inhabiting small parks are showing signs of genetic erosion, stressing the need for more......The Cape buffalo (Syncerus caffer caffer) is one of the dominant and most widespread herbivores in sub-Saharan Africa. High levels of genetic diversity and exceptionally low levels of population differentiation have been found in the Cape buffalo compared to other African savannah ungulates...... active management of such populations. Our findings raise concerns about the future of other African savannah ungulates with lower population sizes and inferior dispersal capabilities compared with the buffalo....

  5. Ethical and legal issues arising from complex genetic disorders. DOE final report

    Energy Technology Data Exchange (ETDEWEB)

    Andrews, Lori

    2002-10-09

    The project analyzed the challenges raised by complex genetic disorders in genetic counselling, for clinical practice, for public health, for quality assurance, and for protection against discrimination. The research found that, in some settings, solutions created in the context of single gene disorders are more difficult to apply to complex disorders. In other settings, the single gene solutions actually backfired and created additional problems when applied to complex genetic disorders. The literature of five common, complex genetic disorders--Alzheimer's, asthma, coronary heart disease, diabetes, and psychiatric illnesses--was evaluated in depth.

  6. Genetic Background and Population Genetics of Hungarian Brown Trout Populations Using PCR-RFLP and Microsatellite Markers

    Directory of Open Access Journals (Sweden)

    Ágnes Ősz

    2015-12-01

    4 University of West Hungary, Mosonmagyaróvár Vár 2., 9200 Mosonmagyaróvár, Hungary Based on the analyses of the mitochondrial DNA of several European brown trout populations, five evolutionary lineages of brown trout were indentified (Atlantic, Danubian, Mediterranean, Adriatic, Marble. The species is bred primarily for stock enhancement of natural waters, however the most hatchery-maintained broodstocks originate from the Atlantic lineage. Due to the hydrogeography of Hungary our stocks should theoretically belong to the Danubian lineage; however, this has not been investigated earlier by genetic studies. For our genetic analysis, 702 fin clips were collected from two brown trout broodstocks (Lillafüred and Szilvásvárad as well as populations of natural streams (Bán, Jósva, Kemence, Apátkút, Bittva and Kölöntés in Hungary. Sequencing of the control region in mitochondrial DNA, three PCR-RFLP (mitochondrial DNA control region, lactate dehydrogenase and somatolactin genes and five microsatellite markers were used to distinguish between Danubian and Atlantic lineages of brown trout. The proportion of the mitochondrial haplotype of the Danubian lineage was low, with the exception of the Apátkúti, Kölöntés streams and Szilvásvárad broodstock. Analyses of nuclear PCR-RFLP and microsatellites markers showed various distributions of alleles characteristic of the Atlantic or Danubian lineages, although the Atlantic genotype has dominated in all population. In case of the analyses of microsatellites the polymorphism varied greatly at all locations. In addition we found several alleles that were not described earlier in other populations. Those alleles probably would be typical of Hungarian brown trout populations. Overall the populations were effectively in Hardy-Weinberg equilibrium for both PCR-RFLP and microsatellite markers. The remarkably high proportion of allochthonous Atlantic alleles in the analyzed sites is a clear indicator of the import

  7. Pioneer study of population genetics of Rhodnius ecuadoriensis (Hemiptera: Reduviidae) from the central coastand southern Andean regions of Ecuador.

    Science.gov (United States)

    Villacís, Anita G; Marcet, Paula L; Yumiseva, César A; Dotson, Ellen M; Tibayrenc, Michel; Brenière, Simone Frédérique; Grijalva, Mario J

    2017-09-01

    Effective control of Chagas disease vector populations requires a good understanding of the epidemiological components, including a reliable analysis of the genetic structure of vector populations. Rhodnius ecuadoriensis is the most widespread vector of Chagas disease in Ecuador, occupying domestic, peridomestic and sylvatic habitats. It is widely distributed in the central coast and southern highlands regions of Ecuador, two very different regions in terms of bio-geographical characteristics. To evaluate the genetic relationship among R. ecuadoriensis populations in these two regions, we analyzed genetic variability at two microsatellite loci for 326 specimens (n=122 in Manabí and n=204 in Loja) and the mitochondrial cytochrome b gene (Cyt b) sequences for 174 individuals collected in the two provinces (n=73 and=101 in Manabí and Loja respectively). The individual samples were grouped in populations according to their community of origin. A few populations presented positive F IS, possible due to Wahlund effect. Significant pairwise differentiation was detected between populations within each province for both genetic markers, and the isolation by distance model was significant for these populations. Microsatellite markers showed significant genetic differentiation between the populations of the two provinces. The partial sequences of the Cyt b gene (578bp) identified a total of 34 haplotypes among 174 specimens sequenced, which translated into high haplotype diversity (Hd=0.929). The haplotype distribution differed among provinces (significant Fisher's exact test). Overall, the genetic differentiation of R. ecuadoriensis between provinces detected in this study is consistent with the biological and phenotypic differences previously observed between Manabí and Loja populations. The current phylogenetic analysis evidenced the monophyly of the populations of R. ecuadoriensis within the R. pallescens species complex; R. pallescens and R. colombiensis were more

  8. Genetic linkage mapping in an F2 perennial ryegrass population using DArT markers

    DEFF Research Database (Denmark)

    Tomaszewski, Céline; Byrne, Stephen; Foito, Alexandra

    2012-01-01

    Perennial ryegrass is the principal forage grass species used in temperate agriculture. In recent years, significant efforts have been made to develop molecular marker strategies to allow cost-effective characterization of a large number of loci simultaneously. One such strategy involves using DAr......T markers, and a DArT array has recently been developed for the Lolium-Festuca complex. In this study, we report the first use of the DArTFest array to generate a genetic linkage map based on 326 markers in a Lolium perenne F2 population, consisting of 325 genotypes. For proof of concept, the map was used...

  9. Genetic diversity in different populations of sloths assessed by DNA fingerprinting

    Directory of Open Access Journals (Sweden)

    MORAES N.

    2002-01-01

    Full Text Available In this study we analyzed a population of Bradypus torquatus with individuals originally distributed in different localities of Bahia, and two populations of B. variegatus with individuals from Bahia and São Paulo States. Using the DNA fingerprinting method, we assessed the genetic variability within and between populations. Analysis of the DNA profiles revealed genetic similarity indices ranging from 0.34 ± 0.07 to 0.87 ± 0.04. Similar low levels of genetic variability were found only in isolated mammalian populations or among related individuals. This study presents the first analyses of genetic diversity in sloth populations.

  10. Molecular mechanisms of drug resistance in natural Leishmania populations vary with genetic background.

    Directory of Open Access Journals (Sweden)

    Saskia Decuypere

    Full Text Available The evolution of drug-resistance in pathogens is a major global health threat. Elucidating the molecular basis of pathogen drug-resistance has been the focus of many studies but rarely is it known whether a drug-resistance mechanism identified is universal for the studied pathogen; it has seldom been clarified whether drug-resistance mechanisms vary with the pathogen's genotype. Nevertheless this is of critical importance in gaining an understanding of the complexity of this global threat and in underpinning epidemiological surveillance of pathogen drug resistance in the field. This study aimed to assess the molecular and phenotypic heterogeneity that emerges in natural parasite populations under drug treatment pressure. We studied lines of the protozoan parasite Leishmania (L. donovani with differential susceptibility to antimonial drugs; the lines being derived from clinical isolates belonging to two distinct genetic populations that circulate in the leishmaniasis endemic region of Nepal. Parasite pathways known to be affected by antimonial drugs were characterised on five experimental levels in the lines of the two populations. Characterisation of DNA sequence, gene expression, protein expression and thiol levels revealed a number of molecular features that mark antimonial-resistant parasites in only one of the two populations studied. A final series of in vitro stress phenotyping experiments confirmed this heterogeneity amongst drug-resistant parasites from the two populations. These data provide evidence that the molecular changes associated with antimonial-resistance in natural Leishmania populations depend on the genetic background of the Leishmania population, which has resulted in a divergent set of resistance markers in the Leishmania populations. This heterogeneity of parasite adaptations provides severe challenges for the control of drug resistance in the field and the design of molecular surveillance tools for widespread

  11. Temporal dynamics of genetic variability in a mountain goat (Oreamnos americanus) population.

    Science.gov (United States)

    Ortego, Joaquín; Yannic, Glenn; Shafer, Aaron B A; Mainguy, Julien; Festa-Bianchet, Marco; Coltman, David W; Côté, Steeve D

    2011-04-01

    The association between population dynamics and genetic variability is of fundamental importance for both evolutionary and conservation biology. We combined long-term population monitoring and molecular genetic data from 123 offspring and their parents at 28 microsatellite loci to investigate changes in genetic diversity over 14 cohorts in a small and relatively isolated population of mountain goats (Oreamnos americanus) during a period of demographic increase. Offspring heterozygosity decreased while parental genetic similarity and inbreeding coefficients (F(IS) ) increased over the study period (1995-2008). Immigrants introduced three novel alleles into the population and matings between residents and immigrants produced more heterozygous offspring than local crosses, suggesting that immigration can increase population genetic variability. The population experienced genetic drift over the study period, reflected by a reduced allelic richness over time and an 'isolation-by-time' pattern of genetic structure. The temporal decline of individual genetic diversity despite increasing population size probably resulted from a combination of genetic drift due to small effective population size, inbreeding and insufficient counterbalancing by immigration. This study highlights the importance of long-term genetic monitoring to understand how demographic processes influence temporal changes of genetic diversity in long-lived organisms. © 2011 Blackwell Publishing Ltd.

  12. Population size does not explain past changes in cultural complexity.

    Science.gov (United States)

    Vaesen, Krist; Collard, Mark; Cosgrove, Richard; Roebroeks, Wil

    2016-04-19

    Demography is increasingly being invoked to account for features of the archaeological record, such as the technological conservatism of the Lower and Middle Pleistocene, the Middle to Upper Paleolithic transition, and cultural loss in Holocene Tasmania. Such explanations are commonly justified in relation to population dynamic models developed by Henrich [Henrich J (2004)Am Antiq69:197-214] and Powell et al. [Powell A, et al. (2009)Science324(5932):1298-1301], which appear to demonstrate that population size is the crucial determinant of cultural complexity. Here, we show that these models fail in two important respects. First, they only support a relationship between demography and culture in implausible conditions. Second, their predictions conflict with the available archaeological and ethnographic evidence. We conclude that new theoretical and empirical research is required to identify the factors that drove the changes in cultural complexity that are documented by the archaeological record.

  13. New Algorithm of Automatic Complex Password Generator Employing Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Sura Jasim Mohammed

    2018-01-01

    Full Text Available Due to the occurred increasing in information sharing, internet popularization, E-commerce transactions, and data transferring, security and authenticity become an important and necessary subject. In this paper an automated schema was proposed to generate a strong and complex password which is based on entering initial data such as text (meaningful and simple information or not, with the concept of encoding it, then employing the Genetic Algorithm by using its operations crossover and mutation to generated different data from the entered one. The generated password is non-guessable and can be used in many and different applications and internet services like social networks, secured system, distributed systems, and online services. The proposed password generator achieved diffusion, randomness, and confusions, which are very necessary, required and targeted in the resulted password, in addition to the notice that the length of the generated password differs from the length of initial data, and any simple changing and modification in the initial data produces more and clear modification in the generated password. The proposed work was done using visual basic programing language.

  14. Heritability and demographic analyses in the large isolated population of Val Borbera suggest advantages in mapping complex traits genes.

    Directory of Open Access Journals (Sweden)

    Michela Traglia

    2009-10-01

    Full Text Available Isolated populations are a useful resource for mapping complex traits due to shared stable environment, reduced genetic complexity and extended Linkage Disequilibrium (LD compared to the general population. Here we describe a large genetic isolate from the North West Apennines, the mountain range that runs through Italy from the North West Alps to the South.The study involved 1,803 people living in 7 villages of the upper Borbera Valley. For this large population cohort, data from genealogy reconstruction, medical questionnaires, blood, anthropometric and bone status QUS parameters were evaluated. Demographic and epidemiological analyses indicated a substantial genetic component contributing to each trait variation as well as overlapping genetic determinants and family clustering for some traits.The data provide evidence for significant heritability of medical relevant traits that will be important in mapping quantitative traits. We suggest that this population isolate is suitable to identify rare variants associated with complex phenotypes that may be difficult to study in larger but more heterogeneous populations.

  15. High genetic connectivity among estuarine populations of the riverbream Acanthopagrus vagus along the southern African coast

    Science.gov (United States)

    Oosthuizen, Carel J.; Cowley, Paul D.; Kyle, Scotty R.; Bloomer, Paulette

    2016-12-01

    Physical and/or physiological constraints are assumed to isolate fish populations confined to or dependent on estuarine habitats. Strong isolation by distance is thus expected to affect connectivity. Such structuring has important implications for sustainable utilisation and replenishment of estuarine stocks that are heavily exploited. Here we present a preliminary investigation of the phylogenetic relationships of the riverbream (Acanthopagrus species) along the southern African coast and the geographic genetic structure of what appears to be a locally endemic species or lineage. Mitochondrial DNA (mtDNA) cytochrome b sequences support the notion that the species occurring along the southern African coast is A. vagus and not A. berda as previously thought. Yet, the taxonomy of this widespread Indo-West Pacific species or species-complex requires more in-depth investigation. No genetic differentiation was detected among estuarine populations of A. vagus based on the analyses of mtDNA ND2 gene sequences and 10 polymorphic nuclear microsatellite markers. The star-like genealogy and statistical analyses are consistent with a recent population expansion event. Spatial analyses of microsatellite genotypes fail to reject the null hypothesis of panmixia, indicative of a recent population expansion or ongoing gene flow between different estuaries. The northern localities were identified as containing most of the observed variation. This study not only provides insight into the phylogenetic relationship of A. vagus relative to other Acanthopagrus species but also sheds light on the demographic history and contemporary gene flow of the species.

  16. The Druze: a population genetic refugium of the Near East.

    Directory of Open Access Journals (Sweden)

    Liran I Shlush

    Full Text Available 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.

  17. Genealogical data in population medical genetics: field guidelines

    Directory of Open Access Journals (Sweden)

    Fernando A. Poletta

    2014-01-01

    Full Text Available 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.

  18. Population genetics of the HRAS1 minisatellite locus

    Energy Technology Data Exchange (ETDEWEB)

    Devlin, B.; Risch, N. (Yale Univ., New Haven, CT (United States)); Krontiris, T. (Tufts Univ., Boston, MA (United States) New England Medical Center Hospital, Boston, MA (United States))

    1993-12-01

    Several years ago it was reported that rare HRAS1 VNTR alleles occurred more frequently in US Caucasian cancer patients than in unaffected controls. Such an association, in theory, could be caused by undetected population heterogeneity. Also, in a study clearly relevant to this issue, it was recently reported that significant deviations from Hardy-Weinberg equilibrium exist at this locus in a sample of US Caucasians. These considerations motivate population genetic analysis of the HRAS1 locus. From published studies of the HRAS1 VNTR locus, which classified alleles into types, the authors found only small differences in the allele frequency distributions of samples from various European nations, although there were larger differences among ethnic groups (African American, Caucasian, and Oriental). In an analysis of variation of rare-allele frequencies among samples from four European nations, most of the variance was attributable to molecular methodology, and very little of the variance was accounted for by nationality. In addition, the authors showed that mixture of European subpopulations should result in only minor deviations from expected genotype proportions in a Caucasian database and demonstrated that there was no significant deviation from Hardy-Weinberg equilibrium in the HRAS1 data. 35 refs., 4 tabs.

  19. Genetic evidence on the origins of Indian caste populations.

    Science.gov (United States)

    Bamshad, M; Kivisild, T; Watkins, W S; Dixon, M E; Ricker, C E; Rao, B B; Naidu, J M; Prasad, B V; Reddy, P G; Rasanayagam, A; Papiha, S S; Villems, R; Redd, A J; Hammer, M F; Nguyen, S V; Carroll, M L; Batzer, M A; Jorde, L B

    2001-06-01

    The origins and affinities of the approximately 1 billion people living on the subcontinent of India have long been contested. This is owing, in part, to the many different waves of immigrants that have influenced the genetic structure of India. In the most recent of these waves, Indo-European-speaking people from West Eurasia entered India from the Northwest and diffused throughout the subcontinent. They purportedly admixed with or displaced indigenous Dravidic-speaking populations. Subsequently they may have established the Hindu caste system and placed themselves primarily in castes of higher rank. To explore the impact of West Eurasians on contemporary Indian caste populations, we compared mtDNA (400 bp of hypervariable region 1 and 14 restriction site polymorphisms) and Y-chromosome (20 biallelic polymorphisms and 5 short tandem repeats) variation in approximately 265 males from eight castes of different rank to approximately 750 Africans, Asians, Europeans, and other Indians. For maternally inherited mtDNA, each caste is most similar to Asians. However, 20%-30% of Indian mtDNA haplotypes belong to West Eurasian haplogroups, and the frequency of these haplotypes is proportional to caste rank, the highest frequency of West Eurasian haplotypes being found in the upper castes. In contrast, for paternally inherited Y-chromosome variation each caste is more similar to Europeans than to Asians. Moreover, the affinity to Europeans is proportionate to caste rank, the upper castes being most similar to Europeans, particularly East Europeans. These findings are consistent with greater West Eurasian male admixture with castes of higher rank. Nevertheless, the mitochondrial genome and the Y chromosome each represents only a single haploid locus and is more susceptible to large stochastic variation, bottlenecks, and selective sweeps. Thus, to increase the power of our analysis, we assayed 40 independent, biparentally inherited autosomal loci (1 LINE-1 and 39 Alu elements

  20. The Genetic Diversity and Structure of Linkage Disequilibrium of the MTHFR Gene in Populations of Northern Eurasia.

    Science.gov (United States)

    Trifonova, E A; Eremina, E R; Urnov, F D; Stepanov, V A

    2012-01-01

    The structure of the haplotypes and linkage disequilibrium (LD) of the methylenetetrahydrofolate reductase gene (MTHFR) in 9 population groups from Northern Eurasia and populations of the international HapMap project was investigated in the present study. The data suggest that the architecture of LD in the human genome is largely determined by the evolutionary history of populations; however, the results of phylogenetic and haplotype analyses seems to suggest that in fact there may be a common "old" mechanism for the formation of certain patterns of LD. Variability in the structure of LD and the level of diversity of MTHFRhaplotypes cause a certain set of tagSNPs with an established prognostic significance for each population. In our opinion, the results obtained in the present study are of considerable interest for understanding multiple genetic phenomena: namely, the association of interpopulation differences in the patterns of LD with structures possessing a genetic susceptibility to complex diseases, and the functional significance of the pleiotropicMTHFR gene effect. Summarizing the results of this study, a conclusion can be made that the genetic variability analysis with emphasis on the structure of LD in human populations is a powerful tool that can make a significant contribution to such areas of biomedical science as human evolutionary biology, functional genomics, genetics of complex diseases, and pharmacogenomics.

  1. Genetic diversity of Pinus halepensis Mill. populations detected by RAPD loci

    OpenAIRE

    Gómez , Aránzazu; Alía , Ricardo; Bueno , María

    2001-01-01

    International audience; Genetic diversity of Pinus halepensis Mill. was analysed in nine populations (six Spanish populations and one each from Tunisia, France and Greece). Twenty four RAPD loci were amplified with 60 megagametophyte DNA samples from each population. Populations' contribution to Nei gene diversity and to allelic richness were calculated. Results showed higher within population genetic variation but also a $G_{{\\rm ST}} = 13.6\\%$ higher than those detected in previous studies ...

  2. Integrating genetic data and population viability analyses for the identification of harbour seal (Phoca vitulina) populations and management units

    DEFF Research Database (Denmark)

    Olsen, Morten Tange; Andersen, Liselotte Wesley; Dietz, Rune

    2014-01-01

    present a novel approach, integrating genetic, life-history and demographic data to identify populations and management units in southern Scandinavian harbour seals. First, 15 microsatellite markers and model- and distance-based genetic clustering methods were used to determine the population genetic...... structure in harbour seals. Second, we used harbour seal demographic and life-history data to conduct population viability analyses (PVAs) in the VORTEX simulation model in order to determine whether the inferred genetic units could be classified as management units according to Lowe and Allendorf's (2010......, and that the combined use of genetic data and PVAs constitute a promising approach for delineating populations and management units. This article is protected by copyright. All rights reserved....

  3. Genetic background and climatic droplet keratopathy incidence in a Mapuche population from Argentina.

    Science.gov (United States)

    Schurr, Theodore G; Dulik, Matthew C; Cafaro, Thamara A; Suarez, María F; Urrets-Zavalia, Julio A; Serra, Horacio M

    2013-01-01

    To determine whether the incidence of and susceptibility to climatic droplet keratopathy (CDK), an acquired, often bilateral degenerative corneal disease, is influenced by the genetic background of the individuals who exhibit the disorder. To determine whether the disease expression was influenced by the genetic ancestry of CDK cases in native Mapuche of the northwest area of Patagonia in Argentina, we examined mitochondrial DNA and Y-chromosome variation in 53 unrelated individuals. Twenty-nine of them were part of the CDK (patient) population, while 24 were part of the control group. The analysis revealed the maternal and paternal lineages that were present in the two study groups. This analysis demonstrated that nearly all persons had a Native American mtDNA background, whereas 50% of the CDK group and 37% of the control group had Native American paternal ancestry, respectively. There was no significant difference in the frequencies of mtDNA haplogroups between the CDK patient and control groups. Although the Y-chromosome data revealed differences in specific haplogroup frequencies between these two groups, there was no statistically significant relationship between individual paternal genetic backgrounds and the incidence or stage of disease. These results indicate a lack of correlation between genetic ancestry as represented by haploid genetic systems and the incidence of CDK in Mapuche populations. In addition, the mtDNA appears to play less of a role in CDK expression than for other complex diseases linked to bioenergetic processes. However, further analysis of the mtDNA genome sequence and other genes involved in corneal function may reveal the more precise role that mitochondria play in the expression of CDK.

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

    Science.gov (United States)

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

    2009-01-01

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

  5. Genetic Diversity, Population Structure and Ancestral Origin of Australian Wheat

    Directory of Open Access Journals (Sweden)

    Reem Joukhadar

    2017-12-01

    Full Text Available Since the introduction of wheat into Australia by the First Fleet settlers, germplasm from different geographical origins has been used to adapt wheat to the Australian climate through selection and breeding. In this paper, we used 482 cultivars, representing the breeding history of bread wheat in Australia since 1840, to characterize their diversity and population structure and to define the geographical ancestral background of Australian wheat germplasm. This was achieved by comparing them to a global wheat collection using in-silico chromosome painting based on SNP genotyping. The global collection involved 2,335 wheat accessions which was divided into 23 different geographical subpopulations. However, the whole set was reduced to 1,544 accessions to increase the differentiation and decrease the admixture among different global subpopulations to increase the power of the painting analysis. Our analysis revealed that the structure of Australian wheat germplasm and its geographic ancestors have changed significantly through time, especially after the Green Revolution. Before 1920, breeders used cultivars from around the world, but mainly Europe and Africa, to select potential cultivars that could tolerate Australian growing conditions. Between 1921 and 1970, a dependence on African wheat germplasm became more prevalent. Since 1970, a heavy reliance on International Maize and Wheat Improvement Center (CIMMYT germplasm has persisted. Combining the results from linkage disequilibrium, population structure and in-silico painting revealed that the dependence on CIMMYT materials has varied among different Australian States, has shrunken the germplasm effective population size and produced larger linkage disequilibrium blocks. This study documents the evolutionary history of wheat breeding in Australia and provides an understanding for how the wheat genome has been adapted to local growing conditions. This information provides a guide for industry to

  6. Genetic Diversity, Population Structure and Ancestral Origin of Australian Wheat.

    Science.gov (United States)

    Joukhadar, Reem; Daetwyler, Hans D; Bansal, Urmil K; Gendall, Anthony R; Hayden, Matthew J

    2017-01-01

    Since the introduction of wheat into Australia by the First Fleet settlers, germplasm from different geographical origins has been used to adapt wheat to the Australian climate through selection and breeding. In this paper, we used 482 cultivars, representing the breeding history of bread wheat in Australia since 1840, to characterize their diversity and population structure and to define the geographical ancestral background of Australian wheat germplasm. This was achieved by comparing them to a global wheat collection using in-silico chromosome painting based on SNP genotyping. The global collection involved 2,335 wheat accessions which was divided into 23 different geographical subpopulations. However, the whole set was reduced to 1,544 accessions to increase the differentiation and decrease the admixture among different global subpopulations to increase the power of the painting analysis. Our analysis revealed that the structure of Australian wheat germplasm and its geographic ancestors have changed significantly through time, especially after the Green Revolution. Before 1920, breeders used cultivars from around the world, but mainly Europe and Africa, to select potential cultivars that could tolerate Australian growing conditions. Between 1921 and 1970, a dependence on African wheat germplasm became more prevalent. Since 1970, a heavy reliance on International Maize and Wheat Improvement Center (CIMMYT) germplasm has persisted. Combining the results from linkage disequilibrium, population structure and in-silico painting revealed that the dependence on CIMMYT materials has varied among different Australian States, has shrunken the germplasm effective population size and produced larger linkage disequilibrium blocks. This study documents the evolutionary history of wheat breeding in Australia and provides an understanding for how the wheat genome has been adapted to local growing conditions. This information provides a guide for industry to assist with

  7. Alu repeats as markers for human population genetics

    Energy Technology Data Exchange (ETDEWEB)

    Batzer, M.A.; Alegria-Hartman, M. [Lawrence Livermore National Lab., CA (United States); Bazan, H. [Louisiana State Univ., New Orleans, LA (United States). Medical Center] [and others

    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.

  8. Complexity and simplification in understanding recruitment in benthic populations

    KAUST Repository

    Pineda, Jesús

    2008-11-13

    Research of complex systems and problems, entities with many dependencies, is often reductionist. The reductionist approach splits systems or problems into different components, and then addresses these components one by one. This approach has been used in the study of recruitment and population dynamics of marine benthic (bottom-dwelling) species. Another approach examines benthic population dynamics by looking at a small set of processes. This approach is statistical or model-oriented. Simplified approaches identify "macroecological" patterns or attempt to identify and model the essential, "first-order" elements of the system. The complexity of the recruitment and population dynamics problems stems from the number of processes that can potentially influence benthic populations, including (1) larval pool dynamics, (2) larval transport, (3) settlement, and (4) post-settlement biotic and abiotic processes, and larval production. Moreover, these processes are non-linear, some interact, and they may operate on disparate scales. This contribution discusses reductionist and simplified approaches to study benthic recruitment and population dynamics of bottom-dwelling marine invertebrates. We first address complexity in two processes known to influence recruitment, larval transport, and post-settlement survival to reproduction, and discuss the difficulty in understanding recruitment by looking at relevant processes individually and in isolation. We then address the simplified approach, which reduces the number of processes and makes the problem manageable. We discuss how simplifications and "broad-brush first-order approaches" may muddle our understanding of recruitment. Lack of empirical determination of the fundamental processes often results in mistaken inferences, and processes and parameters used in some models can bias our view of processes influencing recruitment. We conclude with a discussion on how to reconcile complex and simplified approaches. Although it

  9. Seasonal genetic variation associated with population dynamics of a poecilogonous polychaete worm

    DEFF Research Database (Denmark)

    Thonig, Anne; Banta, Gary Thomas; Hansen, Benni Winding

    2017-01-01

    Poecilogonous species show variation in developmental mode, with larvae that differ both morphologically and ecologically. The spionid polychaete Pygospio elegans shows variation in developmental mode not only between populations, but also seasonally within populations. We investigated...... differentiation at two of the sites. The seasonal genetic shift correlated with the appearance of new size cohorts in the populations. Additionally, we found that the genetic composition of reproductive individuals did not always reflect the genetic composition of the entire sample, indicating that variance...

  10. Relationships among walleye population characteristics and genetic diversity in northern Wisconsin Lakes

    Science.gov (United States)

    Waterhouse, Matthew D.; Sloss, Brian L.; Isermann, Daniel A.

    2014-01-01

    The maintenance of genetic integrity is an important goal of fisheries management, yet little is known regarding the effects of management actions (e.g., stocking, harvest regulations) on the genetic diversity of many important fish species. Furthermore, relationships between population characteristics and genetic diversity remain poorly understood. We examined relationships among population demographics (abundance, recruitment, sex ratio, and mean age of the breeding population), stocking intensity, and genetic characteristics (heterozygosity, effective number of alleles, allelic richness, Wright's inbreeding coefficient, effective population size [Ne], mean d2 [a measure of inbreeding], mean relatedness, and pairwise population ΦST estimates) for 15 populations of Walleye Sander vitreus in northern Wisconsin. We also tested for potential demographic and genetic influences on Walleye body condition and early growth. Combinations of demographic variables explained 47.1–79.8% of the variation in genetic diversity. Skewed sex ratios contributed to a reduction in Ne and subsequent increases in genetic drift and relatedness among individuals within populations; these factors were correlated to reductions in allelic richness and early growth rate. Levels of inbreeding were negatively related to both age-0 abundance and mean age, suggesting Ne was influenced by recruitment and generational overlap. A negative relationship between the effective number of alleles and body condition suggests stocking affected underlying genetic diversity of recipient populations and the overall productivity of the population. These relationships may result from poor performance of stocked fish, outbreeding depression, or density-dependent factors. An isolation-by-distance pattern of genetic diversity was apparent in nonstocked populations, but was disrupted in stocked populations, suggesting that stocking affected genetic structure. Overall, demographic factors were related to genetic

  11. Genetic genealogy comes of age: perspectives on the use of deep-rooted pedigrees in human population genetics.

    Science.gov (United States)

    Larmuseau, M H D; Van Geystelen, A; van Oven, M; Decorte, R

    2013-04-01

    In this article, we promote the implementation of extensive genealogical data in population genetic studies. Genealogical records can provide valuable information on the origin of DNA donors in a population genetic study, going beyond the commonly collected data such as residence, birthplace, language, and self-reported ethnicity. Recent studies demonstrated that extended genealogical data added to surname analysis can be crucial to detect signals of (past) population stratification and to interpret the population structure in a more objective manner. Moreover, when in-depth pedigree data are combined with haploid markers, it is even possible to disentangle signals of temporal differentiation within a population genetic structure during the last centuries. Obtaining genealogical data for all DNA donors in a population genetic study is a labor-intensive task but the vastly growing (genetic) genealogical databases, due to the broad interest of the public, are making this job more time-efficient if there is a guarantee for sufficient data quality. At the end, we discuss the advantages and pitfalls of using genealogy within sampling campaigns and we provide guidelines for future population genetic studies. Copyright © 2013 Wiley Periodicals, Inc.

  12. Sampling genetic diversity in the sympatrically and allopatrically speciating Midas cichlid species complex over a 16 year time series

    Directory of Open Access Journals (Sweden)

    Bunje Paul ME

    2007-02-01

    Full Text Available Abstract Background Speciation often occurs in complex or uncertain temporal and spatial contexts. Processes such as reinforcement, allopatric divergence, and assortative mating can proceed at different rates and with different strengths as populations diverge. The Central American Midas cichlid fish species complex is an important case study for understanding the processes of speciation. Previous analyses have demonstrated that allopatric processes led to species formation among the lakes of Nicaragua as well as sympatric speciation that is occurring within at least one crater lake. However, since speciation is an ongoing process and sampling genetic diversity of such lineages can be biased by collection scheme or random factors, it is important to evaluate the robustness of conclusions drawn on individual time samples. Results In order to assess the validity and reliability of inferences based on different genetic samples, we have analyzed fish from several lakes in Nicaragua sampled at three different times over 16 years. In addition, this time series allows us to analyze the population genetic changes that have occurred between lakes, where allopatric speciation has operated, as well as between different species within lakes, some of which have originated by sympatric speciation. Focusing on commonly used genetic markers, we have analyzed both DNA sequences from the complete mitochondrial control region as well as nuclear DNA variation at ten microsatellite loci from these populations, sampled thrice in a 16 year time period, to develop a robust estimate of the population genetic history of these diversifying lineages. Conclusion The conclusions from previous work are well supported by our comprehensive analysis. In particular, we find that the genetic diversity of derived crater lake populations is lower than that of the source population regardless of when and how each population was sampled. Furthermore, changes in various estimates of

  13. polymapR - linkage analysis and genetic map construction from F1 populations of outcrossing polyploids.

    Science.gov (United States)

    Bourke, Peter M; van Geest, Geert; Voorrips, Roeland E; Jansen, Johannes; Kranenburg, Twan; Shahin, Arwa; Visser, Richard G F; Arens, Paul; Smulders, Marinus J M; Maliepaard, Chris

    2018-05-02

    Polyploid species carry more than two copies of each chromosome, a condition found in many of the world's most important crops. Genetic mapping in polyploids is more complex than in diploid species, resulting in a lack of available software tools. These are needed if we are to realise all the opportunities offered by modern genotyping platforms for genetic research and breeding in polyploid crops. polymapR is an R package for genetic linkage analysis and integrated genetic map construction from bi-parental populations of outcrossing autopolyploids. It can currently analyse triploid, tetraploid and hexaploid marker datasets and is applicable to various crops including potato, leek, alfalfa, blueberry, chrysanthemum, sweet potato or kiwifruit. It can detect, estimate and correct for preferential chromosome pairing, and has been tested on high-density marker datasets from potato, rose and chrysanthemum, generating high-density integrated linkage maps in all of these crops. polymapR is freely available under the general public license from the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/package=polymapR. Chris Maliepaard chris.maliepaard@wur.nl or Roeland E. Voorrips roeland.voorrips@wur.nl. Supplementary data are available at Bioinformatics online.

  14. The Genetic Structure of Wild Orobanche cumana Wallr. (Orobanchaceae Populations in Eastern Bulgaria Reflects Introgressions from Weedy Populations

    Directory of Open Access Journals (Sweden)

    Rocío Pineda-Martos

    2014-01-01

    Full Text Available 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.

  15. The Genetic Structure of Wild Orobanche cumana Wallr. (Orobanchaceae) Populations in Eastern Bulgaria Reflects Introgressions from Weedy Populations

    Science.gov (United States)

    Pineda-Martos, Rocío; Pujadas-Salvà, Antonio J.; Fernández-Martínez, José M.; Stoyanov, Kiril; 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

  16. Population structure, genetic variation and linkage disequilibrium in perennial ryegrass populations divergently selected for freezing tolerance

    Directory of Open Access Journals (Sweden)

    Mallikarjuna Rao eKovi

    2015-11-01

    Full Text Available Low temperature is one of the abiotic stresses seriously affecting the growth of perennial ryegrass (Lolium perenne L. Understanding the genetic control of freezing tolerance would aid in the development of cultivars of perennial ryegrass with improved adaptation to frost. 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 control population were genotyped using 278 genome-wide SNPs derived from Lolium perenne L. transcriptome sequence. Our studies showed 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 detected six loci under directional selection. These outlier loci are most probably linked to genes involved in freezing tolerance, cold adaptation and abiotic stress and might be the potential marker resources for breeding perennial ryegrass cultivars with improved freezing tolerance.

  17. Urban habitat fragmentation and genetic population structure of bobcats in coastal southern California

    Science.gov (United States)

    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.

  18. Genetic variation facilitates seedling establishment but not population growth rate of a perennial invader.

    Science.gov (United States)

    Li, Shou-Li; Vasemägi, Anti; Ramula, Satu

    2016-01-01

    Assessing the demographic consequences of genetic variation is fundamental to invasion biology. However, genetic and demographic approaches are rarely combined to explore the effects of genetic variation on invasive populations in natural environments. This study combined population genetics, demographic data and a greenhouse experiment to investigate the consequences of genetic variation for the population fitness of the perennial, invasive herb Lupinus polyphyllus. Genetic and demographic data were collected from 37 L. polyphyllus populations representing different latitudes in Finland, and genetic variation was characterized based on 13 microsatellite loci. Associations between genetic variation and population size, population density, latitude and habitat were investigated. Genetic variation was then explored in relation to four fitness components (establishment, survival, growth, fecundity) measured at the population level, and the long-term population growth rate (λ). For a subset of populations genetic variation was also examined in relation to the temporal variability of λ. A further assessment was made of the role of natural selection in the observed variation of certain fitness components among populations under greenhouse conditions. It was found that genetic variation correlated positively with population size, particularly at higher latitudes, and differed among habitat types. Average seedling establishment per population increased with genetic variation in the field, but not under greenhouse conditions. Quantitative genetic divergence (Q(ST)) based on seedling establishment in the greenhouse was smaller than allelic genetic divergence (F'(ST)), indicating that unifying selection has a prominent role in this fitness component. Genetic variation was not associated with average survival, growth or fecundity measured at the population level, λ or its variability. The study suggests that although genetic variation may facilitate plant invasions by

  19. Considerations for subgroups and phenocopies in complex disease genetics.

    Directory of Open Access Journals (Sweden)

    Ryan Ramanujam

    Full Text Available The number of identified genetic variants associated to complex disease cannot fully explain heritability. This may be partially due to more complicated patterns of predisposition than previously suspected. Diseases such as multiple sclerosis (MS may consist of multiple disease causing mechanisms, each comprised of several elements. We describe how the effect of subgroups can be calculated using the standard association measurement odds ratio, which is then manipulated to provide a formula for the true underlying association present within the subgroup. This is sensitive to the initial minor allele frequencies present in both cases and the subgroup of patients. The methodology is then extended to the χ(2 statistic, for two related scenarios. First, to determine the true χ(2 when phenocopies or disease subtypes reduce association and are reclassified as controls when calculating statistics. Here, the χ(2 is given by (1 + σ * (a + b/(c + d/(1 - σ, or (1 + σ/(1 - σ for equal numbers of cases and controls. Second, when subgroups corresponding to heterogeneity mask the true effect size, but no reclassification is made. Here, the proportion increase in total sample size required to attain the same χ(2 statistic as the subgroup is given as γ = (1 - σ/2/((1 - σ(1 - σc/(a + c(1 - σd/(b + d, and a python script to calculate and plot this value is provided at kirc.se. Practical examples show how in a study of modest size (1000 cases and 1000 controls, a non-significant SNP may exceed genome-wide significance when corresponding to a subgroup of 20% of cases, and may occur in heterozygous form in all cases. This methodology may explain the modest association found in diseases such as MS wherein heterogeneity confounds straightforward measurement of association.

  20. Clinical and genetic characteristics of Pseudohypoparathyroidism in the Chinese population.

    Science.gov (United States)

    Chu, Xueying; Zhu, Yan; Wang, Ou; Nie, Min; Quan, Tingting; Xue, Yu; Wang, Wenbo; Jiang, Yan; Li, Mei; Xia, Weibo; Xing, Xiaoping

    2018-02-01

    Pseudohypoparathyroidism (PHP) is caused by mutations and epimutations in the GNAS locus, and characterized by the possibility of resistance to multiple hormones and Albright's hereditary osteodystrophy. PHP can be classified into the forms 1A/C, sporadic 1B and familial 1B. To obtain an overall view of the clinical and genetic characteristics of the Chinese PHP patient population. From 2000 to 2016, 120 patients were recruited and studied using Sanger sequencing, methylation-specific multiple ligation-dependent probe amplification (MS-MLPA) and combined bisulfite restriction analysis (COBRA). Of these patients, 104 had positive molecular alterations indicative of certain forms of PHP and were included in data analysis. Clinical and laboratory features were compared between PHP1A/C and PHP1B patients. Ten PHP1A/C, 21 familial PHP1B and 73 sporadic PHP1B patients were identified. Four novel GNAS mutations were discovered in these patients, including c.1038+1G>T, c.530+2T>C, c.880_883delCAAG and c.311_312delAAG, insT. The most common symptoms in this series were recurrent tetany (89.4%) and epilepsy (47.1%). The prevalence of weight excess increased with age for PHP1B (10%-35%) and PHP1A/C (50%-75%). Intracranial calcification had a prevalence of 94.6% and correlated with seizures (r = .227, P = .029). Cataracts occurred in 56.2% PHP patients, and there was a trend towards longer disease duration in patients with cataracts (P = .051). Statistically significant differences (P PHP1B and PHP1A/C patients, including age of onset (10 vs 7 year), short stature (21.3% vs 70%), rounded face (60.6% vs 100%), brachydactyly (25.5% vs 100%), ectopic ossification (1.1% vs 40%) and TSH resistance (44.6% vs 90%), respectively. This study is the largest single-centre series of PHP patients and summarizes the clinical and genetic features of the Chinese PHP population. While there was substantial clinical overlap between PHP1A/C and PHP1B, differences in disease progression

  1. Genetic diversity and landscape genetic structure of otter (Lutra lutra) populations in Europe

    DEFF Research Database (Denmark)

    Mucci, Nadia; Arrendal, Johanna; Ansorge, Hermann

    2010-01-01

    Eurasian otter populations strongly declined and partially disappeared due to global and local causes (habitat destruction, water pollution, human persecution) in parts of their continental range. Conservation strategies, based on reintroduction projects or restoration of dispersal corridors...... and landscape genetic analyses however indicate that local populations are genetically differentiated, perhaps as consequence of post-glacial demographic fluctuations and recent isolation. These results delineate a framework that should be used for implementing conservation programs in Europe, particularly...

  2. Trapped in the extinction vortex? Strong genetic effects in a declining vertebrate population

    Directory of Open Access Journals (Sweden)

    Larsson Mikael

    2010-02-01

    Full Text Available Abstract Background Inbreeding and loss of genetic diversity are expected to increase the extinction risk of small populations, but detailed tests in natural populations are scarce. We combine long-term population and fitness data with those from two types of molecular markers to examine the role of genetic effects in a declining metapopulation of southern dunlins Calidris alpina schinzii, an endangered shorebird. Results The decline is associated with increased pairings between related individuals, including close inbreeding (as revealed by both field observations of parentage and molecular markers. Furthermore, reduced genetic diversity seems to affect individual fitness at several life stages. Higher genetic similarity between mates correlates negatively with the pair's hatching success. Moreover, offspring produced by related parents are more homozygous and suffer from increased mortality during embryonic development and possibly also after hatching. Conclusions Our results demonstrate strong genetic effects in a rapidly declining population, emphasizing the importance of genetic factors for the persistence of small populations.

  3. GENETIC VARIABILITY OF POLYMESODA EROSA POPULATION IN THE SEGARA ANAKAN CILACAP

    Directory of Open Access Journals (Sweden)

    AGUS NURYANTO

    2010-01-01

    Full Text Available Mud clams, Polymesoda erosa, in the Segara Anakan Cilacap are highly exploited by the local communities for daily consumption. This is presumed causing population decline and potentially causing loss of genetic diversity. Genetic diversity level within population can be obtained by population genetic study using molecular marker such as randomly amplified polymorphic DNA (RAPD. Here we amplified RAPD marker using ten arbitrary primers to assess genetic diversity of P. erosa population in the Segara Anakan Cilacap to provide genetic data for its sustainable use. The results proved that the use of RAPD marker has high polymorphisms. The mud clam population also showed a high level of heterozygosity and genetic diversity. This has important implication for the management plan towards sustainable use of P. erosa in the Segara Anakan Cilacap.

  4. Genetic diversity and population structure of Sitodiplosis mosellana in Northern China.

    Directory of Open Access Journals (Sweden)

    Yun Duan

    Full Text Available 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 (F ST = 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 (F ST = 0.116, Nm = 1.89 than those in the eastern group (F ST = 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.

  5. Neutral Theory: From Complex Population History to Natural Selection and Sociocultural Phenomena in Human Populations.

    Science.gov (United States)

    Austerlitz, Frédéric; Heyer, Evelyne

    2018-06-01

    Here, we present a synthetic view on how Kimura's Neutral theory has helped us gaining insight on the different evolutionary forces that shape human evolution. We put this perspective in the frame of recent emerging challenges: the use of whole genome data for reconstructing population histories, natural selection on complex polygenic traits, and integrating cultural processes in human evolution.

  6. European rational approach for the genetics of diabetic complications--EURAGEDIC: patient populations and strategy

    DEFF Research Database (Denmark)

    Tarnow, L.; Groop, P.H.; Hadjadj, S.

    2008-01-01

    in 541 independent parent-offspring trios with or without diabetic nephropathy was applied for validation of consistency. Candidate genes were selected based on previous linkage studies, knowledge of metabolic pathways, and animal models. A comprehensive SNP discovery in more than 100 candidate genes......BACKGROUND: Diabetic nephropathy is likely to be a complex genetic trait. To date, most diabetic nephropathy candidate gene studies have tested a limited number of genes and variants in small sized populations, or in populations that were poorly matched or phenotyped. The main objective...... of the EURAGEDIC study was to address these problems. METHODS: Single nucleotide polymorphisms (SNPs) in candidate genes were tested for association with overt diabetic nephropathy (persistent albuminuria >300 mg/24 h) in a large (n=2499) Type 1 diabetes case/control study. Testing for transmission disequilibrium...

  7. Genetic variability for tuber yield, quality, and virus disease complex ...

    African Journals Online (AJOL)

    Some cultivars e.g. Munyeera, New Kawogo, Silk and Sowola which showed high flowering ability failed to fertilise and set seed when crossed to specific cultivars. Preliminary genetic analysis for yield and quality following crossing elite 7 female and 6 male cultivars in a North Carolina 2 mating design showed wide genetic ...

  8. Population genetic analysis reveals barriers and corridors for gene flow within and among riparian populations of a rare plant.

    Science.gov (United States)

    Hevroy, Tanya H; Moody, Michael L; Krauss, Siegfried L

    2018-02-01

    Landscape features and life-history traits affect gene flow, migration and drift to impact on spatial genetic structure of species. Understanding this is important for managing genetic diversity of threatened species. This study assessed the spatial genetic structure of the rare riparian Grevillea sp. Cooljarloo (Proteaceae), which is restricted to a 20 km 2 region impacted by mining in the northern sandplains of the Southwest Australian Floristic Region, an international biodiversity hotspot. Within creek lines and floodplains, the distribution is largely continuous. Models of dispersal within riparian systems were assessed by spatial genetic analyses including population level partitioning of genetic variation and individual Bayesian clustering. High levels of genetic variation and weak isolation by distance within creek line and floodplain populations suggest large effective population sizes and strong connectivity, with little evidence for unidirectional gene flow as might be expected from hydrochory. Regional clustering of creek line populations and strong divergence among creek line populations suggest substantially lower levels of gene flow among creek lines than within creek lines. There was however a surprising amount of genetic admixture in floodplain populations, which could be explained by irregular flooding and/or movements by highly mobile nectar-feeding bird pollinators. Our results highlight that for conservation of rare riparian species, avoiding an impact to hydrodynamic processes, such as water tables and flooding dynamics, may be just as critical as avoiding direct impacts on the number of plants.

  9. Genetic origin of goat populations in Oman revealed by mitochondrial DNA analysis

    Science.gov (United States)

    Gaafar, Osman Mahgoub; Costa, Vânia; Neira, Agusto Luzuriaga; Al-Atiyat, Raed Mahmoud; Beja-Pereira, Albano

    2017-01-01

    The Sultanate of Oman has a complex mosaic of livestock species and production systems, but the genetic diversity, demographic history or origins of these Omani animals has not been expensively studied. Goats might constitute one of the most abundant and important domestic livestock species since the Neolithic transition. Here, we examined the genetic diversity, origin, population structure and demographic history of Omani goats. Specifically, we analyzed a 525-bp fragment of the first hypervariable region of the mitochondrial DNA (mtDNA) control region from 69 Omani individuals and compared this fragment with 17 mtDNA sequences from Somalia and Yemen as well as 18 wild goat species and 1,198 previously published goat sequences from neighboring countries. The studied goat breeds show substantial diversity. The haplotype and nucleotide diversities of Omani goats were found equal to 0.983 ± 0.006 and 0.0284 ± 0.014, respectively. The phylogenetic analyses allowed us to classify Omani goats into three mtDNA haplogroups (A, B and G): haplogroup A was found to be predominant and widely distributed and accounted for 80% of all samples, and haplogroups B and G exhibited low frequencies. Phylogenetic comparisons with wild goats revealed that five of the native Omani goat populations originate from Capra aegagrus. Furthermore, most comparisons of pairwise population FST values within and between these five Omani goat breeds as well as between Omani goats and nine populations from nearby countries were not significant. These results suggest strong gene flow among goat populations caused by the extensive transport of goats and the frequent movements of human populations in ancient Arabia. The findings improve our understanding of the migration routes of modern goats from their region of domestication into southeastern Arabia and thereby shed light on human migratory and commercial networks during historical times. PMID:29281717

  10. Genetic origin of goat populations in Oman revealed by mitochondrial DNA analysis.

    Science.gov (United States)

    Al-Araimi, Nasser Ali; Gaafar, Osman Mahgoub; Costa, Vânia; Neira, Agusto Luzuriaga; Al-Atiyat, Raed Mahmoud; Beja-Pereira, Albano

    2017-01-01

    The Sultanate of Oman has a complex mosaic of livestock species and production systems, but the genetic diversity, demographic history or origins of these Omani animals has not been expensively studied. Goats might constitute one of the most abundant and important domestic livestock species since the Neolithic transition. Here, we examined the genetic diversity, origin, population structure and demographic history of Omani goats. Specifically, we analyzed a 525-bp fragment of the first hypervariable region of the mitochondrial DNA (mtDNA) control region from 69 Omani individuals and compared this fragment with 17 mtDNA sequences from Somalia and Yemen as well as 18 wild goat species and 1,198 previously published goat sequences from neighboring countries. The studied goat breeds show substantial diversity. The haplotype and nucleotide diversities of Omani goats were found equal to 0.983 ± 0.006 and 0.0284 ± 0.014, respectively. The phylogenetic analyses allowed us to classify Omani goats into three mtDNA haplogroups (A, B and G): haplogroup A was found to be predominant and widely distributed and accounted for 80% of all samples, and haplogroups B and G exhibited low frequencies. Phylogenetic comparisons with wild goats revealed that five of the native Omani goat populations originate from Capra aegagrus. Furthermore, most comparisons of pairwise population FST values within and between these five Omani goat breeds as well as between Omani goats and nine populations from nearby countries were not significant. These results suggest strong gene flow among goat populations caused by the extensive transport of goats and the frequent movements of human populations in ancient Arabia. The findings improve our understanding of the migration routes of modern goats from their region of domestication into southeastern Arabia and thereby shed light on human migratory and commercial networks during historical times.

  11. A longitudinal genetic survey identifies temporal shifts in the population structure of Dutch house sparrows

    Science.gov (United States)

    Cousseau, L; Husemann, M; Foppen, R; Vangestel, C; Lens, L

    2016-01-01

    Dutch house sparrow (Passer domesticus) densities dropped by nearly 50% since the early 1980s, and similar collapses in population sizes have been reported across Europe. Whether, and to what extent, such relatively recent demographic changes are accompanied by concomitant shifts in the genetic population structure of this species needs further investigation. Therefore, we here explore temporal shifts in genetic diversity, genetic structure and effective sizes of seven Dutch house sparrow populations. To allow the most powerful statistical inference, historical populations were resampled at identical locations and each individual bird was genotyped using nine polymorphic microsatellites. Although the demographic history was not reflected by a reduction in genetic diversity, levels of genetic differentiation increased over time, and the original, panmictic population (inferred from the museum samples) diverged into two distinct genetic clusters. Reductions in census size were supported by a substantial reduction in effective population size, although to a smaller extent. As most studies of contemporary house sparrow populations have been unable to identify genetic signatures of recent population declines, results of this study underpin the importance of longitudinal genetic surveys to unravel cryptic genetic patterns. PMID:27273323

  12. Genetic diversity based on 28S rDNA sequences among populations of Culex quinquefasciatus collected at different locations in Tamil Nadu, India.

    Science.gov (United States)

    Sakthivelkumar, S; Ramaraj, P; Veeramani, V; Janarthanan, S

    2015-09-01

    The basis of the present study was to distinguish the existence of any genetic variability among populations of Culex quinquefasciatus which would be a valuable tool in the management of mosquito control programmes. In the present study, population of Cx. quinquefasciatus collected at different locations in Tamil Nadu were analyzed for their genetic variation based on 28S rDNA D2 region nucleotide sequences. A high degree of genetic polymorphism was detected in the sequences of D2 region of 28S rDNA on the predicted secondary structures in spite of high nucleotide sequence similarity. The findings based on secondary structure using rDNA sequences suggested the existence of a complex genotypic diversity of Cx. quinquefasciatus population collected at different locations of Tamil Nadu, India. This complexity in genetic diversity in a single mosquito population collected at different locations is considered an important issue towards their influence and nature of vector potential of these mosquitoes.

  13. Diversity and population-genetic properties of copy number variations and multicopy genes in cattle

    Science.gov (United States)

    Bickhart, Derek M.; Xu, Lingyang; Hutchison, Jana L.; Cole, John B.; Null, Daniel J.; Schroeder, Steven G.; Song, Jiuzhou; Garcia, Jose Fernando; Sonstegard, Tad S.; Van Tassell, Curtis P.; Schnabel, Robert D.; Taylor, Jeremy F.; Lewin, Harris A.; Liu, George E.

    2016-01-01

    The diversity and population genetics of copy number variation (CNV) in domesticated animals are not well understood. In this study, we analysed 75 genomes of major taurine and indicine cattle breeds (including Angus, Brahman, Gir, Holstein, Jersey, Limousin, Nelore, and Romagnola), sequenced to 11-fold coverage to identify 1,853 non-redundant CNV regions. Supported by high validation rates in array comparative genomic hybridization (CGH) and qPCR experiments, these CNV regions accounted for 3.1% (87.5 Mb) of the cattle reference genome, representing a significant increase over previous estimates of the area of the genome that is copy number variable (∼2%). Further population genetics and evolutionary genomics analyses based on these CNVs revealed the population structures of the cattle taurine and indicine breeds and uncovered potential diversely selected CNVs near important functional genes, including AOX1, ASZ1, GAT, GLYAT, and KRTAP9-1. Additionally, 121 CNV gene regions were found to be either breed specific or differentially variable across breeds, such as RICTOR in dairy breeds and PNPLA3 in beef breeds. In contrast, clusters of the PRP and PAG genes were found to be duplicated in all sequenced animals, suggesting that subfunctionalization, neofunctionalization, or overdominance play roles in diversifying those fertility-related genes. These CNV results provide a new glimpse into the diverse selection histories of cattle breeds and a basis for correlating structural variation with complex traits in the future. PMID:27085184

  14. STAT4 is a genetic risk factor for systemic sclerosis in a Chinese population.

    Science.gov (United States)

    Yi, L; Wang, J C; Guo, X J; Gu, Y H; Tu, W Z; Guo, G; Yang, L; Xiao, R; Yu, L; Mayes, M D; Assassi, S; Jin, L; Zou, H J; Zhou, X D

    2013-01-01

    Systemic sclerosis (SSc) is an immune-mediated and complex genetic disease. An association of single-nucleotide polymorphisms (SNPs) in the STAT4 gene with SSc has been reported in European Caucasians, North Americans and Japanese. We undertook the current study to examine whether the STAT4 SNPs are also associated with susceptibility to SSc and SSc subsets in a Han Chinese population. A total of 453 Han Chinese patients with SSc and 534 healthy controls were examined in the study. The SNPs rs7574865, rs10168266 and rs3821236 of the STAT4 gene were examined with SNP TaqMan assays. The T-allele carriers of rs7574865 and rs10168266 were strongly associated with the presence of anti-topoisomerase I (ATA) and pulmonary fibrosis in SSc patients, as well as with diffuse cutaneous SSc (dcSSc). The presence of anti-centromere (ACA) and limited cutaneous SSc (lcSSc) did not show significant association with any of the examined SNPs. The results were consistent with previous reports in other ethnic populations in supporting the notion that polymorphisms of STAT4 may play an important role in susceptibility to SSc. It also revealed different genetic aspects of SSc subsets in a Han Chinese population.

  15. Genetic diversity and population structure in Polygonum cespitosum: insights to an ongoing plant invasion.

    Directory of Open Access Journals (Sweden)

    Silvia Matesanz

    Full Text Available Molecular markers can help elucidate how neutral evolutionary forces and introduction history contribute to genetic variation in invaders. We examined genetic diversity, population structure and colonization patterns in the invasive Polygonum cespitosum, a highly selfing, tetraploid Asian annual introduced to North America. We used nine diploidized polymorphic microsatellite markers to study 16 populations in the introduced range (northeastern North America, via the analyses of 516 individuals, and asked the following questions: 1 Do populations have differing levels of within-population genetic diversity? 2 Do populations form distinct genetic clusters? 3 Does population structure reflect either geographic distances or habitat similarities? We found low heterozygosity in all populations, consistent with the selfing mating system of P. cespitosum. Despite the high selfing levels, we found substantial genetic variation within and among P. cespitosum populations, based on the percentage of polymorphic loci, allelic richness, and expected heterozygosity. Inferences from individual assignment tests (Bayesian clustering and pairwise FST values indicated high among-population differentiation, which indicates that the effects of gene flow are limited relative to those of genetic drift, probably due to the high selfing rates and the limited seed dispersal ability of P. cespitosum. Population structure did not reflect a pattern of isolation by distance nor was it related to habitat similarities. Rather, population structure appears to be the result of the random movement of propagules across the introduced range, possibly associated with human dispersal. Furthermore, the high population differentiation, genetic diversity, and fine-scale genetic structure (populations founded by individuals from different genetic sources in the introduced range suggest that multiple introductions to this region may have occurred. High genetic diversity may further

  16. The Genetic Structure of Australian Populations of Mycosphaerella musicola Suggests Restricted Gene Flow at the Continental Scale.

    Science.gov (United States)

    Hayden, H L; Carlier, J; Aitken, E A B

    2005-05-01

    ABSTRACT Mycosphaerella musicola causes Sigatoka disease of banana and is endemic to Australia. The population genetic structure of M. musicola in Australia was examined by applying single-copy restriction fragment length polymorphism probes to hierarchically sampled populations collected along the Australian east coast. The 363 isolates studied were from 16 plantations at 12 sites in four different regions, and comprised 11 populations. These populations displayed moderate levels of gene diversity (H = 0.142 to 0.369) and similar levels of genotypic richness and evenness. Populations were dominated by unique genotypes, but isolates sharing the same genotype (putative clones) were detected. Genotype distribution was highly localized within each population, and the majority of putative clones were detected for isolates sampled from different sporodochia in the same lesion or different lesions on a plant. Multilocus gametic disequilibrium tests provided further evidence of a degree of clonality within the populations at the plant scale. A complex pattern of population differentiation was detected for M. musicola in Australia. Populations sampled from plantations outside the two major production areas were genetically very different to all other populations. Differentiation was much lower between populations of the two major production areas, despite their geographic separation of over 1,000 km. These results suggest low gene flow at the continental scale due to limited spore dispersal and the movement of infected plant material.

  17. Quantifying selection in evolving populations using time-resolved genetic data

    Science.gov (United States)

    Illingworth, Christopher J. R.; Mustonen, Ville

    2013-01-01

    Methods which uncover the molecular basis of the adaptive evolution of a population address some important biological questions. For example, the problem of identifying genetic variants which underlie drug resistance, a question of importance for the treatment of pathogens, and of cancer, can be understood as a matter of inferring selection. One difficulty in the inference of variants under positive selection is the potential complexity of the underlying evolutionary dynamics, which may involve an interplay between several contributing processes, including mutation, recombination and genetic drift. A source of progress may be found in modern sequencing technologies, which confer an increasing ability to gather information about evolving populations, granting a window into these complex processes. One particularly interesting development is the ability to follow evolution as it happens, by whole-genome sequencing of an evolving population at multiple time points. We here discuss how to use time-resolved sequence data to draw inferences about the evolutionary dynamics of a population under study. We begin by reviewing our earlier analysis of a yeast selection experiment, in which we used a deterministic evolutionary framework to identify alleles under selection for heat tolerance, and to quantify the selection acting upon them. Considering further the use of advanced intercross lines to measure selection, we here extend this framework to cover scenarios of simultaneous recombination and selection, and of two driver alleles with multiple linked neutral, or passenger, alleles, where the driver pair evolves under an epistatic fitness landscape. We conclude by discussing the limitations of the approach presented and outlining future challenges for such methodologies.

  18. DEVELOPMENT OF AQUATIC MODELS FOR TESTING THE RELATIONSHIP BETWEEN GENETIC DIVERSITY AND POPULATION EXTINCTION RISK

    Science.gov (United States)

    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 ...

  19. Microgeographic and temporal genetic variation in populations of the bluetongue virus vector Culicoides variipennis (Diptera: Ceratopogonidae).

    Science.gov (United States)

    Tabachnick, W J

    1992-05-01

    Seven Colorado populations of the bluetongue virus vector Culicoides varipennis (Coquillett) were analyzed for genetic variation at 19-21 isozyme loci. Permanent populations, which overwinter as larvae, showed little temporal genetic change at 19 loci. PGD and MDH showed seasonal changes in gene frequencies, attributable to selection at two permanent populations. Two temporary populations showed low heterozygosity compared with permanent populations. Independent estimates of gene flow, calculated using FST and the private allele method, were Nm* = 2.15 and 6.95, respectively. Colorado C. variipennis permanent populations showed high levels of gene flow which prevented significant genetic differentiation due to genetic drift. Temporary populations showed significant gene frequency differences from nearby permanent populations due to the "founder effect" associated with chance colonization.

  20. Complex spatial dynamics maintain northern leopard frog (Lithobates pipiens) genetic diversity in a temporally varying landscape

    Science.gov (United States)

    Mushet, David M.; Euliss, Ned H.; Chen, Yongjiu; Stockwell, Craig A.

    2013-01-01

    In contrast to most local amphibian populations, northeastern populations of the Northern Leopard Frog (Lithobates pipiens) have displayed uncharacteristically high levels of genetic diversity that have been attributed to large, stable populations. However, this widely distributed species also occurs in areas known for great climatic fluctuations that should be reflected in corresponding fluctuations in population sizes and reduced genetic diversity. To test our hypothesis that Northern Leopard Frog genetic diversity would be reduced in areas subjected to significant climate variability, we examined the genetic diversity of L. pipiens collected from 12 sites within the Prairie Pothole Region of North Dakota. Despite the region's fluctuating climate that includes periods of recurring drought and deluge, we found unexpectedly high levels of genetic diversity approaching that of northeastern populations. Further, genetic structure at a landscape scale was strikingly homogeneous; genetic differentiation estimates (Dest) averaged 0.10 (SD = 0.036) across the six microsatellite loci we studied, and two Bayesian assignment tests (STRUCTURE and BAPS) failed to reveal the development of significant population structure across the 68 km breadth of our study area. These results suggest that L. pipiens in the Prairie Pothole Region consists of a large, panmictic population capable of maintaining high genetic diversity in the face of marked climate variability.

  1. Population genetic data of Investigator HDplex markers in Han population from Southern China.

    Science.gov (United States)

    Liu, Qiuling; Nan, Hailun; He, Xin; Wu, Weiwei; Lu, Dejian

    2018-02-17

    Allele frequencies and forensic statistical parameters for 12 STRs contained in the Investigator HDplex Kit (D2S1360, D3S1744, D4S2366, D5S2500, SE33, D6S474, D7S1517, D8S1132, D10S2325, D12S391, D18S51, and D21S2055) were estimated from a sample of 503 unrelated individuals from the Guangdong Han population of South China. No significant departure from the Hardy-Weinberg equilibrium or genetic linkage disequilibrium was observed (after Bonferroni correction). The expected heterozygosity ranged from 0.6411 to 0.9414. The allele frequencies in Guangdong Han significantly differed from that in Shanghai Han, Korea, Northern Italian, Swedish, Dutch, Somalia, and Argentinean populations at 2 to 12 loci. The markers included in the kit have highly polymorphic information that could be used for forensic DNA analysis as potential tools for differentiating Han population from other populations in the world.

  2. Approximate maximum likelihood estimation for population genetic inference.

    Science.gov (United States)

    Bertl, Johanna; Ewing, Gregory; Kosiol, Carolin; Futschik, Andreas

    2017-11-27

    In many population genetic problems, parameter estimation is obstructed by an intractable likelihood function. Therefore, approximate estimation methods have been developed, and with growing computational power, sampling-based methods became popular. However, these methods such as Approximate Bayesian Computation (ABC) can be inefficient in high-dimensional problems. This led to the development of more sophisticated iterative estimation methods like particle filters. Here, we propose an alternative approach that is based on stochastic approximation. By moving along a simulated gradient or ascent direction, the algorithm produces a sequence of estimates that eventually converges to the maximum likelihood estimate, given a set of observed summary statistics. This strategy does not sample much from low-likelihood regions of the parameter space, and is fast, even when many summary statistics are involved. We put considerable efforts into providing tuning guidelines that improve the robustness and lead to good performance on problems with high-dimensional summary statistics and a low signal-to-noise ratio. We then investigate the performance of our resulting approach and study its properties in simulations. Finally, we re-estimate parameters describing the demographic history of Bornean and Sumatran orang-utans.

  3. Population genetic structure of urban malaria vector Anopheles stephensi in India.

    Science.gov (United States)

    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. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. eQTL Networks Reveal Complex Genetic Architecture in the Immature Soybean Seed

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    Yung-Tsi Bolon

    2014-03-01

    Full Text Available The complex network of regulatory factors and interactions involved in transcriptional regulation within the seed is not well understood. To evaluate gene expression regulation in the immature seed, we utilized a genetical genomics approach on a soybean [ (L. Merr.] recombinant inbred line (RIL population and produced a genome-wide expression quantitative trait loci (eQTL dataset. The validity of the dataset was confirmed by mapping the eQTL hotspot for flavonoid biosynthesis-related genes to a region containing repeats of chalcone synthase (CHS genes known to correspond to the soybean inhibitor locus that regulates seed color. We then identified eQTL for genes with seed-specific expression and discovered striking eQTL hotspots at distinct genomic intervals on chromosomes (Chr 20, 7, and 13. The main eQTL hotspot for transcriptional regulation of fatty acid biosynthesis genes also coincided with regulation of oleosin genes. Transcriptional upregulation of genesets from eQTL with opposite allelic effects were also found. Gene–eQTL networks were constructed and candidate regulatory genes were identified from these three key loci specific to seed expression and enriched in genes involved in seed oil accumulation. Our data provides new insight into the complex nature of gene networks in the immature soybean seed and the genetic architecture that contributes to seed development.

  5. Environmental heterogeneity explains the genetic structure of Continental and Mediterranean populations of Fraxinus angustifolia Vahl.

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    Martina Temunović

    Full Text Available 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.

  6. The population genetics of cultivation: domestication of a traditional Chinese medicine, Scrophularia ningpoensis Hemsl. (Scrophulariaceae.

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    Chuan Chen

    Full Text Available 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

  7. The population genetics of cultivation: domestication of a traditional Chinese medicine, Scrophularia ningpoensis Hemsl. (Scrophulariaceae).

    Science.gov (United States)

    Chen, Chuan; Li, Pan; Wang, Rui-Hong; Schaal, Barbara A; Fu, Cheng-Xin

    2014-01-01

    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. 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. These results suggest that cultivated S. ningpoensis has experienced dramatic loss of genetic diversity under anthropogenic influence. We postulate that strong artificial selection for medicinal quality has

  8. Genetic polymorphism of blood proteins in a population of shetland ponies

    NARCIS (Netherlands)

    Buis, R.C.

    1976-01-01

    Genetic variation of proteins (protein polymorphism) is widespread among many animal species. The biological significance of protein polymorphism has been the subject of many studies. This variation has a supporting function for population genetic studies as a source of genetic markers. In

  9. World without borders-genetic population structure of a highly migratory marine predator, the blue shark (Prionace glauca).

    Science.gov (United States)

    Veríssimo, Ana; Sampaio, Íris; McDowell, Jan R; Alexandrino, Paulo; Mucientes, Gonzalo; Queiroz, Nuno; da Silva, Charlene; Jones, Catherine S; Noble, Leslie R

    2017-07-01

    Highly migratory, cosmopolitan oceanic sharks often exhibit complex movement patterns influenced by ontogeny, reproduction, and feeding. These elusive species are particularly challenging to population genetic studies, as representative samples suitable for inferring genetic structure are difficult to obtain. Our study provides insights into the genetic population structure one of the most abundant and wide-ranging oceanic shark species, the blue shark Prionace glauca, by sampling the least mobile component of the populations, i.e., young-of-year and small juveniles (<2 year; N  = 348 individuals), at three reported nursery areas, namely, western Iberia, Azores, and South Africa. Samples were collected in two different time periods (2002-2008 and 2012-2015) and were screened at 12 nuclear microsatellites and at a 899-bp fragment of the mitochondrial control region. Our results show temporally stable genetic homogeneity among the three Atlantic nurseries at both nuclear and mitochondrial markers, suggesting basin-wide panmixia. In addition, comparison of mtDNA CR sequences from Atlantic and Indo-Pacific locations also indicated genetic homogeneity and unrestricted female-mediated gene flow between ocean basins. These results are discussed in light of the species' life history and ecology, but suggest that blue shark populations may be connected by gene flow at the global scale. The implications of the present findings to the management of this important fisheries resource are also discussed.

  10. Genetic structure of Rajaka caste and affinities with other caste populations of Andhra Pradesh, India.

    Science.gov (United States)

    Parvatheesam, C; Babu, B V; Babu, M C

    1997-01-01

    The present study gives an account of the genetic structure in terms of distribution of a few genetic markers, viz., A1A2B0, Rh(D), G6PD deficiency and haemoglobin among the Rajaka caste population of Andhra Pradesh, India. The genetic relationships of the Rajaka caste with other Andhra caste populations were investigated in terms of genetic distance, i.e., Sq B (mn) of Balakrishnan and Sanghvi. Relatively lesser distance was established between the Rajaka and two Panchama castes. Also, the pattern of genetic distance corroborates the hierarchical order of the Hindu varna system.

  11. Genetic diversity of populations of the dioecious Myrsine coriacea (Primulaceae in the Atlantic Forest

    Directory of Open Access Journals (Sweden)

    Roberta Pena da Paschoa

    2018-04-01

    Full Text Available ABSTRACT Although a species’ sexual system may influence the genetic diversity of its populations in their natural environment, there have been few such studies involving indigenous species of the Atlantic Forest. Here we study Myrsine coriacea, a dioecious tree widely used in reforestation programs despite a lack of information about its natural interpopulation genetic variation. To address this knowledge gap, intra- and interpopulation genetic diversity were measured for male and female individuals of ten natural populations using ISSR markers. Greater intrapopulation genetic diversity indicated interpopulation gene flow, regardless of isolation and distance between populations. Multivariate analyses detected significant differences in genetic diversity between populations, but not between males and females, which indicates that genetic diversity did not differ between the two sex morphs. Distance between populations was unrelated to genetic diversity. Myrsine coriacea has not experienced a loss of genetic variability despite the characteristic segregated spatial distribution of its populations. These results suggest that obligatory cross-pollination and dispersal by birds may be important mechanisms for the maintenance of genetic diversity in natural populations of M. coriacea.

  12. Genetic Diversity and Population Structure of F3:6 Nebraska Winter Wheat Genotypes Using Genotyping-By-Sequencing.

    Science.gov (United States)

    Eltaher, Shamseldeen; Sallam, Ahmed; Belamkar, Vikas; Emara, Hamdy A; Nower, Ahmed A; Salem, Khaled F M; Poland, Jesse; Baenziger, Peter S

    2018-01-01

    The availability of information on the genetic diversity and population structure in wheat ( Triticum aestivum L.) breeding lines will help wheat breeders to better use their genetic resources and manage genetic variation in their breeding program. The recent advances in sequencing technology provide the opportunity to identify tens or hundreds of thousands of single nucleotide polymorphism (SNPs) in large genome species (e.g., wheat). These SNPs can be utilized for understanding genetic diversity and performing genome wide association studies (GWAS) for complex traits. In this study, the genetic diversity and population structure were investigated in a set of 230 genotypes (F 3:6 ) derived from various crosses as a prerequisite for GWAS and genomic selection. Genotyping-by-sequencing provided 25,566 high-quality SNPs. The polymorphism information content (PIC) across chromosomes ranged from 0.09 to 0.37 with an average of 0.23. The distribution of SNPs markers on the 21 chromosomes ranged from 319 on chromosome 3D to 2,370 on chromosome 3B. The analysis of population structure revealed three subpopulations (G1, G2, and G3). Analysis of molecular variance identified 8% variance among and 92% within subpopulations. Of the three subpopulations, G2 had the highest level of genetic diversity based on three genetic diversity indices: Shannon's information index ( I ) = 0.494, diversity index ( h ) = 0.328 and unbiased diversity index (uh) = 0.331, while G3 had lowest level of genetic diversity ( I = 0.348, h = 0.226 and uh = 0.236). This high genetic diversity identified among the subpopulations can be used to develop new wheat cultivars.

  13. Patterns and processes in the genetic differentiation of the Brachionus calyciflorus complex, a passively dispersing freshwater zooplankton.

    Science.gov (United States)

    Xiang, Xian-ling; Xi, Yi-long; Wen, Xin-li; Zhang, Gen; Wang, Jin-xia; Hu, Ke

    2011-05-01

    Elucidating the evolutionary patterns and processes of extant species is an important objective of any research program that seeks to understand population divergence and, ultimately, speciation. The island-like nature and temporal fluctuation of limnetic habitats create opportunities for genetic differentiation in rotifers through space and time. To gain further understanding of spatio-temporal patterns of genetic differentiation in rotifers other than the well-studied Brachionus plicatilis complex in brackish water, a total of 318 nrDNA ITS sequences from the B. calyciflorus complex in freshwater were analysed using phylogenetic and phylogeographic methods. DNA taxonomy conducted by both the sequence divergence and the GMYC model suggested the occurrence of six potential cryptic species, supported also by reproductive isolation among the tested lineages. The significant genetic differentiation and non-significant correlation between geographic and genetic distances existed in the most abundant cryptic species, BcI-W and Bc-SW. The large proportion of genetic variability for cryptic species Bc-SW was due to differences between sampling localities within seasons, rather than between different seasons. Nested Clade Analysis suggested allopatric or past fragmentation, contiguous range expansion and long-distance colonization possibly coupled with subsequent fragmentation as the probable main forces shaping the present-day phylogeographic structure of the B. calyciflorus species complex. Copyright © 2011 Elsevier Inc. All rights reserved.

  14. Genomic hotspots for adaptation: the population genetics of Müllerian mimicry in Heliconius erato.

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    Brian A Counterman

    2010-02-01

    Full Text Available Wing pattern evolution in Heliconius butterflies provides some of the most striking examples of adaptation by natural selection. The genes controlling pattern variation are classic examples of Mendelian loci of large effect, where allelic variation causes large and discrete phenotypic changes and is responsible for both convergent and highly divergent wing pattern evolution across the genus. We characterize nucleotide variation, genotype-by-phenotype associations, linkage disequilibrium (LD, and candidate gene expression patterns across two unlinked genomic intervals that control yellow and red wing pattern variation among mimetic forms of Heliconius erato. Despite very strong natural selection on color pattern, we see neither a strong reduction in genetic diversity nor evidence for extended LD across either patterning interval. This observation highlights the extent that recombination can erase the signature of selection in natural populations and is consistent with the hypothesis that either the adaptive radiation or the alleles controlling it are quite old. However, across both patterning intervals we identified SNPs clustered in several coding regions that were strongly associated with color pattern phenotype. Interestingly, coding regions with associated SNPs were widely separated, suggesting that color pattern alleles may be composed of multiple functional sites, conforming to previous descriptions of these loci as "supergenes." Examination of gene expression levels of genes flanking these regions in both H. erato and its co-mimic, H. melpomene, implicate a gene with high sequence similarity to a kinesin as playing a key role in modulating pattern and provides convincing evidence for parallel changes in gene regulation across co-mimetic lineages. The complex genetic architecture at these color pattern loci stands in marked contrast to the single casual mutations often identified in genetic studies of adaptation, but may be more indicative

  15. Genetic structure of lake whitefish, Coregonus clupeaformis, populations in the northern main basin of Lake Huron

    Science.gov (United States)

    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.

  16. Genetic diversity of the Ethiopian Grevy's zebra (Equus grevyi) populations that includes a unique population of the Alledeghi Plain.

    Science.gov (United States)

    Kebede, Fanuel; Rosenbom, Sonia; Khalatbari, Leili; Moehlman, Patricia D; Beja-Pereira, Albano; Bekele, Afework

    2016-01-01

    The endangered Grevy's Zebra (Equus grevyi) is confined to the Horn of Africa, specifically Ethiopia and Kenya. It is threatened by habitat loss and fragmentation due to human encroachment of historic range. Knowledge of population genetics is essential for the development of appropriate conservation actions and management. The focus of this study was to assess the heterogeneity and genetic distinctiveness of the two Grevy's zebra populations in Ethiopia. Non-invasive fecal samples (N = 120) were collected during 2009-2010 from Grevy's zebra populations in the Alledeghi Wildlife Reserve and the Sarite area, Ethiopia. Analyses of a 329 bp of the mtDNA control region of 47 sequences, revealed the existence of two unreported haplotypes in the northern population of Alledeghi, that were not shared with the southern population of Sarite. The Sarite population is contiguous with the Grevy's zebra population in Kenya. The nucleotide diversity levels found in both the populations are extremely low.

  17. Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil)

    DEFF Research Database (Denmark)

    Miller, Webb; Hayes, Vanessa M.; Ratan, Aakrosh

    2011-01-01

    The Tasmanian devil (Sarcophilus harrisii) is threatened with extinction because of a contagious cancer known as Devil Facial Tumor Disease. The inability to mount an immune response and to reject these tumors might be caused by a lack of genetic diversity within a dwindling population. Here we...... that the observed low genetic diversity in today's population preceded the Devil Facial Tumor Disease disease outbreak by at least 100 y. Using a genetically characterized breeding stock based on the genome sequence will enable preservation of the extant genetic diversity in future Tasmanian devil populations....

  18. A longitudinal cline characterizes the genetic structure of human populations in the Tibetan plateau

    Science.gov (United States)

    Peter, Benjamin M.; Basnyat, Buddha; Neupane, Maniraj; Beall, Cynthia M.; Childs, Geoff; Craig, Sienna R.; Novembre, John; Di Rienzo, Anna

    2017-01-01

    Indigenous populations of the Tibetan plateau have attracted much attention for their good performance at extreme high altitude. Most genetic studies of Tibetan adaptations have used genetic variation data at the genome scale, while genetic inferences about their demography and population structure are largely based on uniparental markers. To provide genome-wide information on population structure, we analyzed new and published data of 338 individuals from indigenous populations across the plateau in conjunction with worldwide genetic variation data. We found a clear signal of genetic stratification across the east-west axis within Tibetan samples. Samples from more eastern locations tend to have higher genetic affinity with lowland East Asians, which can be explained by more gene flow from lowland East Asia onto the plateau. Our findings corroborate a previous report of admixture signals in Tibetans, which were based on a subset of the samples analyzed here, but add evidence for isolation by distance in a broader geospatial context. PMID:28448508

  19. Genetic impoverishment of the last black grouse (Tetrao tetrix) population in the Netherlands

    NARCIS (Netherlands)

    Larsson, J.K.; Jansman, H.A.H.; Niewold, F.J.J.; Segelbacher, G.; Höglund, J.; Koelewijn, H.P.

    2005-01-01

    We have studied a small isolated bottlenecked population of Black grouse (Tetrao tetrix) in the Netherlands to examine the impact of isolation and reduction in numbers on the genetic diversity. We compared the genetic diversity in the last present Dutch population with Dutch museum samples and three

  20. Rangewide Genetic Variation in Coast Redwood Populations at a Chloroplast Microsatellite Locus

    Science.gov (United States)

    Chris Brinegar

    2012-01-01

    Old growth and second growth populations of coast redwood (Sequoia sempervirens) were sampled at 10 locations throughout its range and analyzed at a highly variable chloroplast microsatellite locus. Very low FST values indicated that there was no significant genetic differentiation between adjacent old growth and second growth populations at each location. Genetic...

  1. Genetic diversity and conservation status of managed vicuña (Vicugna vicugna) populations in Argentina.

    Science.gov (United States)

    Anello, M; Daverio, M S; Romero, S R; Rigalt, F; Silbestro, M B; Vidal-Rioja, L; Di Rocco, F

    2016-02-01

    The vicuña (Vicugna vicugna) was indiscriminately hunted for more than 400 years and, by the end of 1960s, it was seriously endangered. At that time, a captive breeding program was initiated in Argentina by the National Institute of Agricultural Technology (INTA) with the aim of preserving the species. Nowadays, vicuñas are managed in captivity and in the wild to obtain their valuable fiber. The current genetic status of Argentinean vicuña populations is virtually unknown. Using mitochondrial DNA and microsatellite markers, we assessed levels of genetic diversity of vicuña populations managed in the wild and compared it with a captive population from INTA. Furthermore, we examined levels of genetic structure and evidence for historical bottlenecks. Overall, all populations revealed high genetic variability with no signs of inbreeding. Levels of genetic diversity between captive and wild populations were not significantly different, although the captive population showed the lowest estimates of allelic richness, number of mitochondrial haplotypes, and haplotype diversity. Significant genetic differentiation at microsatellite markers was found between free-living populations from Jujuy and Catamarca provinces. Moreover, microsatellite data also revealed genetic structure within the Catamarca management area. Genetic signatures of past bottlenecks were detected in wild populations by the Garza Williamson test. Results from this study are discussed in relation to the conservation and management of the species.

  2. Bridging the gaps between non-invasive genetic sampling and population parameter estimation

    Science.gov (United States)

    Francesca Marucco; Luigi Boitani; Daniel H. Pletscher; Michael K. Schwartz

    2011-01-01

    Reliable estimates of population parameters are necessary for effective management and conservation actions. The use of genetic data for capture­recapture (CR) analyses has become an important tool to estimate population parameters for elusive species. Strong emphasis has been placed on the genetic analysis of non-invasive samples, or on the CR analysis; however,...

  3. Genetic diversity of Dyera polyphylla (Miq.) Steenis populations used in tropical peatland restoration in Indonesia

    NARCIS (Netherlands)

    Tata, Hesti Lestari; Muchugi, A.; Kariba, R.; Noordwijk, van M.

    2018-01-01

    Dyera polyphylla is a native tree species of peat swamp forests in Southeast Asia. Where it has been used in peatland restoration, the trees are of uncertain genetic origin. We analysed the genetic diversity of seven populations of D. polyphylla (9–20 individual trees per population) from both

  4. Genetic structure of local populations of Lutzomyia longipalpis (Diptera: Psychodidae) in central Colombia.

    Science.gov (United States)

    Munstermann, L E; Morrison, A C; Ferro, C; Pardo, R; Torres, M

    1998-01-01

    Lutzomyia longipalpis (Lutz & Neiva), the sand fly vector of American visceral leishmaniasis in the New World tropics, has a broad but discontinuous geographical distribution from southern Mexico to Argentina. A baseline for population genetic structure and genetic variability for this species was obtained by analyzing 5 local, peridomestic populations at the approximate center of its distribution, the Magdalena River Valley of central Colombia. Three populations of L. longipalpis from El Callejón, a small rural community, were compared with 2 populations from neighboring areas 12 and 25 km distant for genetic variation at 15 isoenzyme loci. The mean heterozygosity ranged from 11 to 16%, with 1.2 to 2.3 alleles detected per locus. Nei's genetic distances among the populations were very low, ranging from 0.001 to 0.007. Gene flow estimates based on FST indicated high levels of gene flow among local L. longipalpis populations, with minimal population substructuring.

  5. Habitat Fragmentation Differentially Affects Genetic Variation, Phenotypic Plasticity and Survival in Populations of a Gypsum Endemic

    Directory of Open Access Journals (Sweden)

    Silvia Matesanz

    2017-05-01

    Full Text Available Habitat fragmentation, i.e., fragment size and isolation, can differentially alter patterns of neutral and quantitative genetic variation, fitness and phenotypic plasticity of plant populations, but their effects have rarely been tested simultaneously. We assessed the combined effects of size and connectivity on these aspects of genetic and phenotypic variation in populations of Centaurea hyssopifolia, a narrow endemic gypsophile that previously showed performance differences associated with fragmentation. We grew 111 maternal families sampled from 10 populations that differed in their fragment size and connectivity in a common garden, and characterized quantitative genetic variation, phenotypic plasticity to drought for key functional traits, and plant survival, as a measure of population fitness. We also assessed neutral genetic variation within and among populations using eight microsatellite markers. Although C. hyssopifolia is a narrow endemic gypsophile, we found substantial neutral genetic variation and quantitative variation for key functional traits. The partition of genetic variance indicated that a higher proportion of variation was found within populations, which is also consistent with low population differentiation in molecular markers, functional traits and their plasticity. This, combined with the generally small effect of habitat fragmentation suggests that gene flow among populations is not restricted, despite large differences in fragment size and isolation. Importantly, population’s similarities in genetic variation and plasticity did not reflect the lower survival observed in isolated populations. Overall, our results indicate that, although the species consists of genetically variable populations able to express functional plasticity, such aspects of adaptive potential may not always reflect populations’ survival. Given the differential effects of habitat connectivity on functional traits, genetic variation and fitness

  6. Genetic Diversity and Population Structure in Native Chicken Populations from Myanmar, Thailand and Laos by Using 102 Indels Markers

    Directory of Open Access Journals (Sweden)

    A. A. Maw

    2015-01-01

    Full Text Available The genetic diversity of native chicken populations from Myanmar, Thailand, and Laos was examined by using 102 insertion and/or deletion (indels markers. Most of the indels loci were polymorphic (71% to 96%, and the genetic variability was similar in all populations. The average observed heterozygosities (HO and expected heterozygosities (HE ranged from 0.205 to 0.263 and 0.239 to 0.381, respectively. The coefficients of genetic differentiation (Gst for all cumulated populations was 0.125, and the Thai native chickens showed higher Gst (0.088 than Myanmar (0.041 and Laotian (0.024 populations. The pairwise Fst distances ranged from 0.144 to 0.308 among populations. A neighbor-joining (NJ tree, using Nei’s genetic distance, revealed that Thai and Laotian native chicken populations were genetically close, while Myanmar native chickens were distant from the others. The native chickens from these three countries were thought to be descended from three different origins (K = 3 from STRUCTURE analysis. Genetic admixture was observed in Thai and Laotian native chickens, while admixture was absent in Myanmar native chickens.

  7. A comparative study on genetic and environmental influences on metabolic phenotypes in Eastern (Chinese) and Western (Danish) populations

    DEFF Research Database (Denmark)

    Li, Shuxia

    2015-01-01

    the risk of clinic diseases e.g. diabetes, atherosclerosis, stroke and cardiovascular disease. Metabolic phenotypes, similar to most complex traits, can be influenced by both genetic and environmental factors as well as their interplay. Many family and twin studies have demonstrated both genetic...... and environmental factors play important role in the variation of metabolic phenotypes and intra-individual change over time. Although both genetic and environmental factors are involved the development of metabolic disorders, the role of environment should be emphasized as the expression or function of gene can...... be regulated to adapt to existing environmental circumstance. In other words, adaptive evolution in populations under distinct environmental and cultural circumstances could have resulted in varying genetic basis of metabolic factors and development of metabolic disorders or diseases. Thus, it can...

  8. Genetic diversity and population structure of Pisum sativum accessions for marker-trait association of lipid content

    Directory of Open Access Journals (Sweden)

    Sajjad Ahmad

    2015-06-01

    Full Text Available Field pea (Pisum sativum L. is an important protein-rich pulse crop produced globally. Increasing the lipid content of Pisum seeds through conventional and contemporary molecular breeding tools may bring added value to the crop. However, knowledge about genetic diversity and lipid content in field pea is limited. An understanding of genetic diversity and population structure in diverse germplasm is important and a prerequisite for genetic dissection of complex characteristics and marker-trait associations. Fifty polymorphic microsatellite markers detecting a total of 207 alleles were used to obtain information on genetic diversity, population structure and marker-trait associations. Cluster analysis was performed using UPGMA to construct a dendrogram from a pairwise similarity matrix. Pea genotypes were divided into five major clusters. A model-based population structure analysis divided the pea accessions into four groups. Percentage lipid content in 35 diverse pea accessions was used to find potential associations with the SSR markers. Markers AD73, D21, and AA5 were significantly associated with lipid content using a mixed linear model (MLM taking population structure (Q and relative kinship (K into account. The results of this preliminary study suggested that the population could be used for marker-trait association mapping studies.

  9. Conceptualising population health: from mechanistic thinking to complexity science

    Directory of Open Access Journals (Sweden)

    Jayasinghe Saroj

    2011-01-01

    Full Text Available Abstract The mechanistic interpretation of reality can be traced to the influential work by René Descartes and Sir Isaac Newton. Their theories were able to accurately predict most physical phenomena relating to motion, optics and gravity. This paradigm had at least three principles and approaches: reductionism, linearity and hierarchy. These ideas appear to have influenced social scientists and the discourse on population health. In contrast, Complexity Science takes a more holistic view of systems. It views natural systems as being 'open', with fuzzy borders, constantly adapting to cope with pressures from the environment. These are called Complex Adaptive Systems (CAS. The sub-systems within it lack stable hierarchies, and the roles of agency keep changing. The interactions with the environment and among sub-systems are non-linear interactions and lead to self-organisation and emergent properties. Theoretical frameworks such as epi+demos+cracy and the ecosocial approach to health have implicitly used some of these concepts of interacting dynamic sub-systems. Using Complexity Science we can view population health outcomes as an emergent property of CAS, which has numerous dynamic non-linear interactions among its interconnected sub-systems or agents. In order to appreciate these sub-systems and determinants, one should acquire a basic knowledge of diverse disciplines and interact with experts from different disciplines. Strategies to improve health should be multi-pronged, and take into account the diversity of actors, determinants and contexts. The dynamic nature of the system requires that the interventions are constantly monitored to provide early feedback to a flexible system that takes quick corrections.

  10. Conceptualising population health: from mechanistic thinking to complexity science.

    Science.gov (United States)

    Jayasinghe, Saroj

    2011-01-20

    The mechanistic interpretation of reality can be traced to the influential work by René Descartes and Sir Isaac Newton. Their theories were able to accurately predict most physical phenomena relating to motion, optics and gravity. This paradigm had at least three principles and approaches: reductionism, linearity and hierarchy. These ideas appear to have influenced social scientists and the discourse on population health. In contrast, Complexity Science takes a more holistic view of systems. It views natural systems as being 'open', with fuzzy borders, constantly adapting to cope with pressures from the environment. These are called Complex Adaptive Systems (CAS). The sub-systems within it lack stable hierarchies, and the roles of agency keep changing. The interactions with the environment and among sub-systems are non-linear interactions and lead to self-organisation and emergent properties. Theoretical frameworks such as epi+demos+cracy and the ecosocial approach to health have implicitly used some of these concepts of interacting dynamic sub-systems. Using Complexity Science we can view population health outcomes as an emergent property of CAS, which has numerous dynamic non-linear interactions among its interconnected sub-systems or agents. In order to appreciate these sub-systems and determinants, one should acquire a basic knowledge of diverse disciplines and interact with experts from different disciplines. Strategies to improve health should be multi-pronged, and take into account the diversity of actors, determinants and contexts. The dynamic nature of the system requires that the interventions are constantly monitored to provide early feedback to a flexible system that takes quick corrections.

  11. Complex genetic architecture of cardiac disease in a wild type inbred strain of Drosophila melanogaster.

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    Zhi Zhang

    Full Text Available Natural populations of the fruit fly, Drosophila melanogaster, segregate genetic variation that leads to cardiac disease phenotypes. One nearly isogenic line from a North Carolina peach orchard, WE70, is shown to harbor two genetically distinct heart phenotypes: elevated incidence of arrhythmias, and a dramatically constricted heart diameter in both diastole and systole, with resemblance to restrictive cardiomyopathy in humans. Assuming the source to be rare variants of large effect, we performed Bulked Segregant Analysis using genomic DNA hybridization to Affymetrix chips to detect single feature polymorphisms, but found that the mutant phenotypes are more likely to have a polygenic basis. Further mapping efforts revealed a complex architecture wherein the constricted cardiomyopathy phenotype was observed in individual whole chromosome substitution lines, implying that variants on both major autosomes are sufficient to produce the phenotype. A panel of 170 Recombinant Inbred Lines (RIL was generated, and a small subset of mutant lines selected, but these each complemented both whole chromosome substitutions, implying a non-additive (epistatic contribution to the "disease" phenotype. Low coverage whole genome sequencing was also used to attempt to map chromosomal regions contributing to both the cardiomyopathy and arrhythmia, but a polygenic architecture had to be again inferred to be most likely. These results show that an apparently simple rare phenotype can have a complex genetic basis that would be refractory to mapping by deep sequencing in pedigrees. We present this as a cautionary tale regarding assumptions related to attempts to map new disease mutations on the assumption that probands carry a single causal mutation.

  12. Microsatellite genetic diversity and differentiation of native and introduced grass carp populations in three continents

    Science.gov (United States)

    Chapman, Duane C.; Chen, Qin; Wang, Chenghui; Zhao, Jinlian; Lu, Guoqing; Zsigmond, Jeney; Li, Si-Fa

    2012-01-01

    Grass carp (Ctenopharyngodon idella), a freshwater species native to China, has been introduced to about 100 countries/regions and poses both biological and environmental challenges to the receiving ecosystems. In this study, we analyzed genetic variation in grass carp from three introduced river systems (Mississippi River Basin in US, Danube River in Hungary, and Tone River in Japan) as well as its native ranges (Yangtze, Pearl, and Amur Rivers) in China using 21 novel microsatellite loci. The allelic richness, observed heterozygosity, and within-population gene diversity were found to be lower in the introduced populations than in the native populations, presumably due to the small founder population size of the former. Significant genetic differentiation was found between all pairwise populations from different rivers. Both principal component analysis and Bayesian clustering analysis revealed obvious genetic distinction between the native and introduced populations. Interestingly, genetic bottlenecks were detected in the Hungarian and Japanese grass carp populations, but not in the North American population, suggesting that the Mississippi River Basin grass carp has experienced rapid population expansion with potential genetic diversification during the half-century since its introduction. Consequently, the combined forces of the founder effect, introduction history, and rapid population expansion help explaining the observed patterns of genetic diversity within and among both native and introduced populations of the grass carp.

  13. Molecular genetic diversity in populations of the stingless bee Plebeia remota: A case study

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    Flávio de Oliveira Francisco

    2013-01-01

    Full Text Available Genetic diversity is a major component of the biological diversity of an ecosystem. The survival of a population may be seriously threatened if its genetic diversity values are low. In this work, we measured the genetic diversity of the stingless bee Plebeia remota based on molecular data obtained by analyzing 15 microsatellite loci and sequencing two mitochondrial genes. Population structure and genetic diversity differed depending on the molecular marker analyzed: microsatellites showed low population structure and moderate to high genetic diversity, while mitochondrial DNA (mtDNA showed high population structure and low diversity in three populations. Queen philopatry and male dispersal behavior are discussed as the main reasons for these findings.

  14. Population and genetic outcomes 20 years after reintroducing bobcats (Lynx rufus) to Cumberland Island, Georgia USA

    Science.gov (United States)

    Diefenbach, Duane R.; Hansen, Leslie A.; Bohling, Justin H.; Miller-Butterworth, Cassandra

    2015-01-01

    In 1988–1989, 32 bobcats Lynx rufus were reintroduced to Cumberland Island (CUIS), Georgia, USA, from which they had previously been extirpated. They were monitored intensively for 3 years immediately post-reintroduction, but no estimation of the size or genetic diversity of the population had been conducted in over 20 years since reintroduction. We returned to CUIS in 2012 to estimate abundance and effective population size of the present-day population, as well as to quantify genetic diversity and inbreeding. We amplified 12 nuclear microsatellite loci from DNA isolated from scats to establish genetic profiles to identify individuals. We used spatially explicit capture–recapture population estimation to estimate abundance. From nine unique genetic profiles, we estimate a population size of 14.4 (SE = 3.052) bobcats, with an effective population size (Ne) of 5–8 breeding individuals. This is consistent with predictions of a population viability analysis conducted at the time of reintroduction, which estimated the population would average 12–13 bobcats after 10 years. We identified several pairs of related bobcats (parent-offspring and full siblings), but ~75% of the pairwise comparisons were typical of unrelated individuals, and only one individual appeared inbred. Despite the small population size and other indications that it has likely experienced a genetic bottleneck, levels of genetic diversity in the CUIS bobcat population remain high compared to other mammalian carnivores. The reintroduction of bobcats to CUIS provides an opportunity to study changes in genetic diversity in an insular population without risk to this common species. Opportunities for natural immigration to the island are limited; therefore, continued monitoring and supplemental bobcat reintroductions could be used to evaluate the effect of different management strategies to maintain genetic diversity and population viability. The successful reintroduction and maintenance of a

  15. Current and historical drivers of landscape genetic structure differ in core and peripheral salamander populations.

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    Rachael Y Dudaniec

    Full Text Available With predicted decreases in genetic diversity and greater genetic differentiation at range peripheries relative to their cores, it can be difficult to distinguish between the roles of current disturbance versus historic processes in shaping contemporary genetic patterns. To address this problem, we test for differences in historic demography and landscape genetic structure of coastal giant salamanders (Dicamptodon tenebrosus in two core regions (Washington State, United States versus the species' northern peripheral region (British Columbia, Canada where the species is listed as threatened. Coalescent-based demographic simulations were consistent with a pattern of post-glacial range expansion, with both ancestral and current estimates of effective population size being much larger within the core region relative to the periphery. However, contrary to predictions of recent human-induced population decline in the less genetically diverse peripheral region, there was no genetic signature of population size change. Effects of current demographic processes on genetic structure were evident using a resistance-based landscape genetics approach. Among core populations, genetic structure was best explained by length of the growing season and isolation by resistance (i.e. a 'flat' landscape, but at the periphery, topography (slope and elevation had the greatest influence on genetic structure. Although reduced genetic variation at the range periphery of D. tenebrosus appears to be largely the result of biogeographical history rather than recent impacts, our analyses suggest that inherent landscape features act to alter dispersal pathways uniquely in different parts of the species' geographic range, with implications for habitat management.

  16. Genetic diversity and structure analysis based on hordein protein polymorphism in barley landrace populations from jordan

    International Nuclear Information System (INIS)

    Baloch, A.W.; Ali, M.; Baloch, A.M.; Mangan, B.U.N.; Song, W

    2014-01-01

    Jordan is unanimously considered to be one of the centers of genetic diversity for barley, where wild and landraces of barley has been grown under different climatic conditions. The genetic diversity and genetic structure based on hordein polymorphism was assessed in 90 different accessions collected from four different sites of Jordan. A-PAGE was used to reveal hordein polymorphism among the genotypes. A total of 29 distinct bands were identified, out of them 9 bands were distinguished for D, 11 for C, and 9 for the B hordein regions. The observed genetic similarity was an exceptionally high between the populations than expected, which is probably due to high gene flow estimated between them. The genetic diversity parameters were not differ largely among the populations, indicating that local selection of a particular site did not play a key role in shaping genetic diversity. Analysis of molecular variance (AMOVA) revealed significant population structure when accessions were structured according to population site. There was 94% of hordein variation resided within the populations and only 8% present among the populations. Both Bayesian and Principale Coordinate Analysis (PCoA) concordantly demonstrated admixture genotypes of the landraces barley populations. Consequently, none of the population found to be clustered separately according to its population site. It is concluded that this approach can be useful to explore the germplasm for genetic diversity but perhaps is not suitable for determining phylogenic relations in barley. (author)

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

    Science.gov (United States)

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

    2016-10-24

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

  18. Genealogy construction in a historically isolated population: application to genetic studies of rheumatoid arthritis in the Pima Indian.

    Science.gov (United States)

    Lin, J P; Hirsch, R; Jacobsson, L T; Scott, W W; Ma, L D; Pillemer, S R; Knowler, W C; Kastner, D L; Bale, S J

    1999-01-01

    Due to the characteristics of complex traits, many traits may not be amenable to traditional epidemiologic methods. We illustrate an approach that defines an isolated population as the "unit" for carrying out studies of complex disease. We provide an example using the Pima Indians, a relatively isolated population, in which the incidence and prevalence of Type 2 diabetes, gallbladder disease, and rheumatoid arthritis (RA) are significantly increased compared with the general U.S. population. A previous study of RA in the Pima utilizing traditional methods failed to detect a genetic effect on the occurrence of the disease. Our approach involved constructing a genealogy for this population and using a genealogic index to investigate familial aggregation. We developed an algorithm to identify biological relationships among 88 RA cases versus 4,000 subsamples of age-matched individuals from the same population. Kinship coefficients were calculated for all possible pairs of RA cases, and similarly for the subsamples. The sum of the kinship coefficient among all combination of RA pairs, 5.92, was significantly higher than the average of the 4,000 subsamples, 1.99 (p genealogy can be anticipated to provide valuable information for the genetic study of diseases other than RA. Defining an isolated population as the "unit" in which to assess familial aggregation may be advantageous, especially if there are a limited number of cases in the study population.

  19. Genetic Diversity and Structure of the Apiosporina morbosa Populations on Prunus spp.

    Science.gov (United States)

    Zhang, Jinxiu; Fernando, W G Dilantha; Remphrey, William R

    2005-08-01

    ABSTRACT Populations of Apiosporina morbosa collected from 15 geographic locations in Canada and the United States and three host species, Prunus virginiana, P. pensylvanica, and P. padus, were evaluated using the sequence-related amplified polymorphism (SRAP) technique to determine their genetic diversity and population differentiation. Extensive diversity was detected in the A. morbosa populations, including 134 isolates from Canada and the United States, regardless of the origin of the population. The number of polymorphic loci varied from 6.9 to 82.8% in the geographic populations, and from 41.4 to 79.3% in the populations from four host genotypes based on 58 polymorphic fragments. In all, 44 to 100% of isolates in the geographic populations and 43.6 to 76.2% in populations from four host genotypes represented unique genotypes. Values of heterozygosity (H) varied from 2.8 to 28.3% in the geographic populations and 10.2 to 26.1% in the populations from four host genotypes. In general, the A. morbosa populations sampled from wild chokecherry showed a higher genetic diversity than those populations collected from other host species, whereas the populations isolated from cultivated chokecherry, P. virginiana 'Shubert Select', showed a reduction of genetic diversity compared with populations from wild P. virginiana. Significant population differentiation was found among both the geographic populations (P virginiana were closely clustered, and no population differentiation was detected except for the populations from Morris, Morden, and Winnipeg, Manitoba, Canada. Furthermore, the populations from P. virginiana in the same geographic locations had higher genetic identity and closer genetic distance to each other compared with those from different locations. Four populations from P. virginiana, P. pensylvanica, and P. padus, were significantly differentiated from each other (P P> = 0.334). Indirect estimation of gene flow showed that significant restricted gene flow

  20. Genetic diversity of populations and clones of Rhopilema esculentum in China based on AFLP analysis

    Science.gov (United States)

    Qiao, Hongjin; Liu, Xiangquan; Zhang, Xijia; Jiang, Haibin; Wang, Jiying; Zhang, Limin

    2013-03-01

    Amplified fragment length polymorphisms (AFLP) markers were developed to assess the genetic variation of populations and clones of Rhopilema esculentum Kishinouye (Scyphozoa, Rhizostomatidae). One hundred and seventy-nine loci from 56 individuals of two hatchery populations and two wild populations were genotyped with five primer combinations. The polymorphic ratio, Shannon's diversity index and average heterozygosity were 70.3%, 0.346 and 0.228 for the white hatchery population, 74.3%, 0.313, and 0.201 for the red hatchery population, 79.3%, 0.349, and 0.224 for the Jiangsu wild population, and 74.9%, 0.328 and 0.210 for the Penglai wild population, respectively. Thus, all populations had a relatively high level of genetic diversity. A specific band was identified that could separate the white from the red hatchery population. There was 84.85% genetic differentiation within populations. Individual cluster analysis using unweighted pair-group method with arithmetic mean (UPGMA) suggested that hatchery populations and wild populations could be divided. For the hatchery populations, the white and red populations clustered separately; however, for the wild populations, Penglai and Jiangsu populations clustered together. The genetic diversity at the clone level was also determined. Our data suggest that there are relatively high genetic diversities within populations but low genetic differentiation between populations, which may be related to the long-term use of germplasm resources from Jiangsu Province for artificial seeding and releasing. These findings will benefit the artificial seeding and conservation of the germplasm resources.

  1. Genetic structure of Lutzomyia longipalpis populations in Mato Grosso Do Sul, Brazil, based on microsatellite markers.

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    Mirella F C Santos

    Full Text Available BACKGROUND: Lutzomyialongipalpis (Diptera: Psychodidae is the major vector of Leishmania (Leishmania infantum and thus plays a crucial role in the epidemiology of American visceral leishmaniasis (AVL. This vector is the best studied species of sand fly in the Neotropical region. Many studies claim that this vector is in fact a species complex; however there is still no consensus regarding the number of species that belong into this complex or the geographical distribution of sibling species. The aim of the present study was to analyze the genetic relationships within Lu. longipalpis populations in the state of Mato Grosso do Sul (MS, Brazil. METHODOLOGY/PRINCIPAL FINDINGS: We collected 30 Lu. longipalpis (15 females and 15 males from five localities (Campo Grande, Três Lagoas, Aquidauana, Miranda and Bonito and 30 Lu. Cruzi from Corumbá, totaling 180 sandflies from MS, and 30 Lu. longipalpis from Estrela de Alagoas, state of Alagoas (AL, Northeast Brazil. We show that eight previously described microsatellite loci were sufficient in distinguishing Lu. longipalpis from Lu. Cruzi, which is a closely related species, and in differentiating between Lu. longipalpis collected in MS versus Estrela de Alagoas. Analyses of the genotypes revealed introgression between sympatric Lu. longipalpis and Lu. Cruzi. CONCLUSIONS/SIGNIFICANCE: Our findings support the hypothesis of cryptic species within the Lu. longipalpis complex. Furthermore, our data revealed introgression between Lu. longipalpis and Lu. cruzi. This phenomenon should be further investigated to determine the level and incidence of hybridization between these two species. We also demonstrated that microsatellite markers are a powerful tool for differentiating sand fly populations and species. The present study has elucidated the population structure of Lu. longipalpis in MS and, by extension, the Neotropical Lu. longipalpis complex itself.

  2. Genetic struc