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1.
Mitochondrial DNA polymorphisms were analyzed in of 1,610 randomly chosen adult men from 11 different regions from southeastern Europe (Croatians, Bosnians and Herzegovinians, Serbians, Macedonians and Macedonian Romani). MtDNA HVS-I region together with RFLP sites diagnostic for main Euroasian and African mtDNA haplogroups were typed to determine haplogroup frequency distribution. The most frequent haplogroup in studied populations was H with the exception of Macedonian Romani among whom the most frequent were South Asian (Indian) specific variants of haplogroup M. The multidimensional scaling plot showed two clusters of populations and two outliers (Macedonian Romani and the most distant from mainland Croatian island of Korcula). The first cluster was formed by populations from three Croatian islands (Hvar, Krk and Brac) and the second cluster was formed by Macedonians, Serbians, Croatians from mainland and coast, Herzegovinians, Bosnians, Slovenians, Poles and Russians. The present analysis does not address a precise evaluation of phylogenetic relations of studied populations although some conclusions about historical migrations could be noticed. More extended conclusions will be possible after deeper phylogenetic and statistical analyses.  相似文献   

2.
Research to understand human genomic variation and its implications in health has great potential to contribute in the reduction of health disparities. Biological anthropology can play important roles in genomics and health disparities research using a biocultural approach. This paper argues that racial/ethnic categories should not be used as a surrogate for sociocultural factors or global genomic clusters in biomedical research or clinical settings, because of the high genetic heterogeneity that exists within traditional racial/ethnic groups. Genetic ancestry is used to show variation in ancestral genomic contributions to recently admixed populations in the United States, such as African Americans and Hispanic/Latino Americans. Genetic ancestry estimates are also used to examine the relationship between ancestry-related biological and sociocultural factors affecting health disparities. To localize areas of genomes that contribute to health disparities, admixture mapping and genome-wide association studies (GWAS) are often used. Recent GWAS have identified many genetic variants that are highly differentiated among human populations that are associated with disease risk. Some of these are population-specific variants. Many of these variants may impact disease risk and help explain a portion of the difference in disease burden among racial/ethnic groups. Genetic ancestry is also of particular interest in precision medicine and disparities in drug efficacy and outcomes. By using genetic ancestry, we can learn about potential biological differences that may contribute to the heterogeneity observed across self-reported racial groups.  相似文献   

3.
Contemporary genetic variation among Latin Americans human groups reflects population migrations shaped by complex historical, social and economic factors. Consequently, admixture patterns may vary by geographic regions ranging from countries to neighborhoods. We examined the geographic variation of admixture across the island of Puerto Rico and the degree to which it could be explained by historic and social events. We analyzed a census-based sample of 642 Puerto Rican individuals that were genotyped for 93 ancestry informative markers (AIMs) to estimate African, European and Native American ancestry. Socioeconomic status (SES) data and geographic location were obtained for each individual. There was significant geographic variation of ancestry across the island. In particular, African ancestry demonstrated a decreasing East to West gradient that was partially explained by historical factors linked to the colonial sugar plantation system. SES also demonstrated a parallel decreasing cline from East to West. However, at a local level, SES and African ancestry were negatively correlated. European ancestry was strongly negatively correlated with African ancestry and therefore showed patterns complementary to African ancestry. By contrast, Native American ancestry showed little variation across the island and across individuals and appears to have played little social role historically. The observed geographic distributions of SES and genetic variation relate to historical social events and mating patterns, and have substantial implications for the design of studies in the recently admixed Puerto Rican population. More generally, our results demonstrate the importance of incorporating social and geographic data with genetics when studying contemporary admixed populations.  相似文献   

4.
Aim Understanding the importance of ecological factors in the origin and maintenance of patterns of phenotypic variation among populations, in an explicit geographical context, is one of the main goals of human biology, ecology and evolutionary biology. Here we study the ecological factors responsible for craniofacial variation among human populations from South America. Location South America. Methods We studied a dataset of 718 males from 40 South American populations, coming from groups that inhabited different geographical and ecological regions. Cranial size and shape variation were studied using 30 cranial measurements. We first used spatial correlograms and interpolated maps to address spatial patterns. We then regressed the shape (principal component scores) and size variables against ecology (mean annual temperature and diet) using multiple and multivariate spatial regression. Finally, the expected magnitudes of shape and size divergence under the influence of genetic drift and mutations alone were evaluated using neutral expectation for the divergence rate. Results The spatial correlograms showed a cline affecting the entire South American distribution. Interpolated maps showed that size and allometric shape vary from south‐east to north‐west. Multiple and multivariate regression analyses suggested that diet has the largest and most significant effect on this pattern of size and allometric shape variation. Finally, the results of the divergence rate test suggested that random processes alone cannot account for the morphological divergence exhibited by cranial size and allometric shape scores among southernmost populations. Main conclusions Correlograms, spatial regression and divergence rate analyses showed that although local factors (neutral processes or local environmental conditions) are important to explain spatial interpopulation differentiation in cranial characteristics among these populations, there is significant correlation of cranial size and allometric shape variation with diet. Gene flow among human populations, or local environmental conditions, could explain spatial variation mainly at smaller spatial scales, whereas the large‐scale pattern of the South American dataset is mainly related to the high proportion of carbohydrates and low proportion of proteins consumed.  相似文献   

5.
Asthma originates from genetic and environmental factors with about half the risk of disease attributable to heritable causes. Genome-wide association studies, mostly in populations of European ancestry, have identified numerous asthma-associated single nucleotide polymorphisms (SNPs). Studies in populations with diverse ancestries allow both for identification of robust associations that replicate across ethnic groups and for improved resolution of associated loci due to different patterns of linkage disequilibrium between ethnic groups. Here we report on an analysis of 745 African-American subjects with asthma and 3,238 African-American control subjects from the Candidate Gene Association Resource (CARe) Consortium, including analysis of SNPs imputed using 1,000 Genomes reference panels and adjustment for local ancestry. We show strong evidence that variation near RAD50/IL13, implicated in studies of European ancestry individuals, replicates in individuals largely of African ancestry. Fine mapping in African ancestry populations also refined the variants of interest for this association. We also provide strong or nominal evidence of replication at loci near ORMDL3/GSDMB, IL1RL1/IL18R1, and 10p14, all previously associated with asthma in European or Japanese populations, but not at the PYHIN1 locus previously reported in studies of African-American samples. These results improve the understanding of asthma genetics and further demonstrate the utility of genetic studies in populations other than those of largely European ancestry.  相似文献   

6.
Assessing the immediate and long‐term evolutionary consequences of human‐mediated hybridization is of major concern for conservation biology. Several studies have documented how selection in interaction with recombination modulates introgression at a genome‐wide scale, but few have considered the dynamics of this process within and among chromosomes. Here, we used an exploited freshwater fish, the brook charr (Salvelinus fontinalis), for which decades of stocking practices have resulted in admixture between wild populations and an introduced domestic strain, to assess both the temporal dynamics and local chromosomal variation in domestic ancestry. We provide a detailed picture of the domestic ancestry patterns across the genome using about 33,000 mapped single nucleotide polymorphisms genotyped in 611 individuals from 24 supplemented populations. For each lake, we distinguished early‐ and late‐generation hybrids using information regarding admixture tracts. To assess the selective outcomes following admixture we then evaluated the relationship between recombination and admixture proportions at three different scales: the whole genome, chromosomes and within 2‐Mb windows. This allowed us to detect a wide range of evolutionary mechanisms varying along the genome, as reflected by the finding of favoured or disfavoured introgression of domestic haplotypes. Among these, the main factor modulating local ancestry was probably the presence of deleterious recessive mutations in the wild populations, which can be efficiently hidden to selection in the presence of long admixture tracts. Overall, our results emphasize the relevance of taking into consideration local ancestry information to assess both the temporal and the chromosomal variation in local admixture ancestry toward better understanding post‐hybridization evolutionary outcomes.  相似文献   

7.
Local adaptation of interacting species to one another indicates geographically variable reciprocal selection. This process of adaptation is central in the organization and maintenance of genetic variation across populations. Given that the strength of selection and responses to it often vary in time and space, the strength of local adaptation should in theory vary between generations and among populations. However, such spatiotemporal variation has rarely been explicitly demonstrated in nature and local adaptation is commonly considered to be relatively static. We report persistent local adaptation of the short‐lived herbivore Abrostola asclepiadis to its long‐lived host plant Vincetoxicum hirundinaria over three successive generations in two studied populations and considerable temporal variation in local adaptation in six populations supporting the geographic mosaic theory. The observed variation in local adaptation among populations was best explained by geographic distance and population isolation, suggesting that gene flow reduces local adaptation. Changes in herbivore population size did not conclusively explain temporal variation in local adaptation. Our results also imply that short‐term studies are likely to capture only a part of the existing variation in local adaptation.  相似文献   

8.
Admixture and recombination create populations and genomes with genetic ancestry from multiple source populations. Analyses of genetic ancestry in admixed populations are relevant for trait and disease mapping, studies of speciation, and conservation efforts. Consequently, many methods have been developed to infer genome-average ancestry and to deconvolute ancestry into continuous local ancestry blocks or tracts within individuals. Current methods for local ancestry inference perform well when admixture occurred recently or hybridization is ongoing, or when admixture occurred in the distant past such that local ancestry blocks have fixed in the admixed population. However, methods to infer local ancestry frequencies in isolated admixed populations still segregating for ancestry do not exist. In the current paper, I develop and test a continuous correlated beta process model to fill this analytical gap. The method explicitly models autocorrelations in ancestry frequencies at the population-level and uses discriminant analysis of SNP windows to take advantage of ancestry blocks within individuals. Analyses of simulated data sets show that the method is generally accurate such that ancestry frequency estimates exhibited low root-mean-square error and were highly correlated with the true values, particularly when large (±10 or ±20) SNP windows were used. Along these lines, the proposed method outperformed post hoc inference of ancestry frequencies from a traditional hidden Markov model (i.e., the linkage model in structure), particularly when admixture occurred more distantly in the past with little on-going gene flow or was followed by natural selection. The reliability and utility of the method was further assessed by analyzing genetic ancestry in an admixed human population (Uyghur) and three populations from a hybrid zone between Mus domesticus and M. musculus. Considerable variation in ancestry frequencies was detected within and among chromosomes in the Uyghur, with a large region of excess French ancestry harboring a gene with a known disease association. Similar variation was detected in the mouse hybrid zone, with notable constancy in regions of excess ancestry among admixed populations. By filling what has been an analytical gap, the proposed method should be a useful tool for many biologists. A computer program (popanc), written in C++, has been developed based on the proposed method and is available on-line at http://sourceforge.net/projects/popanc/.  相似文献   

9.
The identification of geographic population structure and genetic ancestry on the basis of a minimal set of genetic markers is desirable for a wide range of applications in medical and forensic sciences. However, the absence of sharp discontinuities in the neutral genetic diversity among human populations implies that, in practice, a large number of neutral markers will be required to identify the genetic ancestry of one individual. We showed that it is possible to reduce the amount of markers required for detecting continental population structure to only 10 single-nucleotide polymorphisms (SNPs), by applying a newly developed ascertainment algorithm to Affymetrix GeneChip Mapping 10K SNP array data that we obtained from samples of globally dispersed human individuals (the Y Chromosome Consortium panel). Furthermore, this set of SNPs was able to recover the genetic ancestry of individuals from all four continents represented in the original data set when applied to an independent, much larger, worldwide population data set (Centre d'Etude du Polymorphisme Humain-Human Genome Diversity Project Cell Line Panel). Finally, we provide evidence that the unusual patterns of genetic variation we observed at the respective genomic regions surrounding the five most informative SNPs is in agreement with local positive selection being the explanation for the striking SNP allele-frequency differences we found between continental groups of human populations.  相似文献   

10.
Biogeographic studies in Amazonia typically describe biodiversity across interfluvia, rarely within them, where geographic variability in morphological traits might be observed. We tested for intraspecific phenotypic variation in three bird species within the Purus–Madeira interfluvium (Central Amazon) and whether phenotypes were correlated with environmental heterogeneity or geographic distance among sites. We compared coloration indexes derived from reflectance spectra and morphometrics of up to five adult individuals of each sex among 11 sites within the interfluvium and contrasted them with proxies for geographic distance and environmental variation (tree basal area and bird community). Environmental heterogeneity was minimally spatially autocorrelated, and there were no obvious geographical barriers to dispersal in the study region. The null hypothesis was that we would see either no phenotypic variation or random variation that was not explained by the tested variables. Half of the cases analyzed showed intraspecific morphological variation. Coloration varied more frequently than morphometrics, and color was better explained by environmental heterogeneity, particularly in males, whereas brightness also varied with geographic distance. Geographic distance explained the only case of variation in morphometrics. Our results indicate that coloration, particularly plumage brightness, is more labile than morphometric traits and that plumage color might be under stronger effects of local adaptation than brightness, which also seems to be under effects of neutral drift and gene flow among populations. Higher frequencies of association between male coloration and the environment suggest a role of non-arbitrary mechanisms of sexual selection on the expression of male phenotypes, whereas arbitrary intersexual selection might explain the randomly distributed variation that is not explained by environmental heterogeneity or geographic distance. We revealed intraspecific phenotypic variation in a spatial extent usually not considered in biogeographic studies in the Amazon and demonstrate that both local adaptation and neutral drift are important to explain intraspecific trait diversification at this geographical scale.  相似文献   

11.
The abundance and diversity of parasites vary among different populations of host species. In some host-parasite associations, much of the variation seems to depend on the identity of the host species, whereas in other cases it is better explained by local environmental conditions. The few parasite taxa investigated to date make it difficult to discern any general pattern governing large-scale variation in abundance or diversity. Here, we test whether the abundance and diversity of gamasid mites parasitic on small mammals across different regions of the Palaearctic are determined mainly by host identity or by parameters of the abiotic environment. Using data from 42 host species from 26 distinct regions, we found that mite abundances on different populations of the same host species were more similar to each other than expected by chance, and varied significantly among host species, with half of the variance among samples explained by differences between host species. A similar but less pronounced pattern was observed for mite diversity, measured both as species richness and as the taxonomic distinctness of mite species within an assemblage. Strong environmental effects were also observed, with local temperature and precipitation correlating with mite abundance and species richness, respectively, across populations of the same host species, for many of the host species examined. These results are compared to those obtained for other groups of parasites, notably fleas, and discussed in light of attempts to find general rules governing the geographical variation in the abundance and diversity of parasite assemblages.  相似文献   

12.
The global dispersal of anatomically modern humans over the past 100,000 years has produced patterns of phenotypic variation that have exerted—and continue to exert—powerful influences on the lives of individuals and the experiences of groups. The recency of our common ancestry and continued gene flow among populations have resulted in less genetic differentiation among geographically distributed human populations than is observed in many other mammalian species. Nevertheless, differences in appearance have contributed to the development of ideas about “race” and “ethnicity” that often include the belief that significant inherited differences distinguish humans. The use of racial, ethnic, and ancestral categories in genetics research can imply that group differences arise directly through differing allele frequencies, with little influence from socially mediated mechanisms. At the same time, careful investigations of the biological, environmental, social, and psychological attributes associated with these categories will be an essential component of cross-disciplinary research into the origins, prevention, and treatment of common diseases, including those diseases that differ in prevalence among groups.  相似文献   

13.
Adaptive ecological differentiation among sympatric populations is promoted by environmental heterogeneity, strong local selection and restricted gene flow. High gene flow, on the other hand, is expected to homogenize genetic variation among populations and therefore prevent local adaptation. Understanding how local adaptation can persist at the spatial scale at which gene flow occurs has remained an elusive goal, especially for wild vertebrate populations. Here, we explore the roles of natural selection and nonrandom gene flow (isolation by breeding time and habitat choice) in restricting effective migration among local populations and promoting generalized genetic barriers to neutral gene flow. We examined these processes in a network of 17 breeding ponds of the moor frog Rana arvalis, by combining environmental field data, a common garden experiment and data on variation in neutral microsatellite loci and in a thyroid hormone receptor (TRβ) gene putatively under selection. We illustrate the connection between genotype, phenotype and habitat variation and demonstrate that the strong differences in larval life history traits observed in the common garden experiment can result from adaptation to local pond characteristics. Remarkably, we found that haplotype variation in the TRβ gene contributes to variation in larval development time and growth rate, indicating that polymorphism in the TRβ gene is linked with the phenotypic variation among the environments. Genetic distance in neutral markers was correlated with differences in breeding time and environmental differences among the ponds, but not with geographical distance. These results demonstrate that while our study area did not exceed the scale of gene flow, ecological barriers constrained gene flow among contrasting habitats. Our results highlight the roles of strong selection and nonrandom gene flow created by phenological variation and, possibly, habitat preferences, which together maintain genetic and phenotypic divergence at a fine‐grained spatial scale.  相似文献   

14.
Ecologists have examined the synchronization of population dynamics across space as a means to understand how populations respond to climate variation. However, response diversity may reflect important variation among local population dynamics driven by population‐specific responses to regional environmental change. We used long‐term data on sockeye salmon Oncorhynchus nerka from pristine watersheds of southwestern Alaska to show that populations spawning in close proximity (<40 km) to one another have a limited degree of synchrony in their dynamics, even after accounting for density‐dependent processes. In fact, the dynamics of local populations of stream‐spawning sockeye salmon were no more coherent than those of stocks at a much coarser resolution across this region of Alaska. We examined four hypotheses to explain the observed patterns of asynchrony among stream‐spawning populations, and found that populations spawning in dissimilar habitats, and using different nursery lakes were less synchronized in their productivity. Similarity in the age structure of spawning adults was less correlated with synchrony in productivity. These results emphasize the importance of maintaining diverse spawning and rearing habitat for the conservation of Pacific salmon, and should guide conservation planning for Pacific salmon populations in regions where natural dynamics have been altered by habitat loss, hatchery practices, and over‐fishing.  相似文献   

15.
The relative contributions of ancestry, chance, and past and ongoing election to variation in one adaptive (larval feeding rate) and one seemingly nonadaptive (pupation height) trait were determined in populations ofDrosophila melanogaster adapting to either low or high larval densities in the laboratory. Larval feeding rates increased rapidly in response to high density, and the effects of ancestry, past selection and chance were ameliorated by ongoing selection within 15–20 generations. Similarly, in populations previously kept at high larval density, and then switched to low larval density, the decline of larval feeding rate to ancestral levels was rapid (15-20 generations) and complete, providing support for a previously stated hypothesis regarding the costs of faster feeding inDrosophila larvae. Variation among individuals was the major contributor to variation in pupation height, a trait that would superficially appear to be nonadaptive in the environmental context of the populations used in this study because it did not diverge between sets of populations kept at low versus high larval density for many generations. However, the degree of divergence among populations (FST) for pupation height was significantly less than expected for a selectively neutral trait, and we integrate results from previous studies to suggest that the variation for pupation height among populations is constrained by stabilizing selection, with a flat, plateau-like fitness function that, consequently, allows for substantial phenotypic variation within populations. Our results support the view that the genetic imprints of history (ancestry and past selection) in outbreeding sexual populations are typically likely to be transient in the face of ongoing selection and recombination. The results also illustrate the heuristic point that different forms of selection-for example directional versus stabilizing selection—acting on a trait in different populations may often not be due to differently shaped fitness functions, but rather due to differences in how the fitness function maps onto the actual distribution of phenotypes in a given population. We discuss these results in the light of previous work on reverse evolution, and the role of ancestry, chance, and past and ongoing selection in adaptive evolution.  相似文献   

16.
Variation in gene expression is a fundamental aspect of human phenotypic variation. Several recent studies have analyzed gene expression levels in populations of different continental ancestry and reported population differences at a large number of genes. However, these differences could largely be due to non-genetic (e.g., environmental) effects. Here, we analyze gene expression levels in African American cell lines, which differ from previously analyzed cell lines in that individuals from this population inherit variable proportions of two continental ancestries. We first relate gene expression levels in individual African Americans to their genome-wide proportion of European ancestry. The results provide strong evidence of a genetic contribution to expression differences between European and African populations, validating previous findings. Second, we infer local ancestry (0, 1, or 2 European chromosomes) at each location in the genome and investigate the effects of ancestry proximal to the expressed gene (cis) versus ancestry elsewhere in the genome (trans). Both effects are highly significant, and we estimate that 12±3% of all heritable variation in human gene expression is due to cis variants.  相似文献   

17.
Older Puerto Ricans living in the continental U.S. suffer from higher rates of diabetes, obesity, cardiovascular disease and depression compared to non-Hispanic White populations. Complex diseases, such as these, are likely due to multiple, potentially interacting, genetic, environmental and social risk factors. Presumably, many of these environmental and genetic risk factors are contextual. We reasoned that racial background may modify some of these risk factors and be associated with health disparities among Puerto Ricans. The contemporary Puerto Rican population is genetically heterogeneous and originated from three ancestral populations: European settlers, native Taíno Indians, and West Africans. This rich-mixed ancestry of Puerto Ricans provides the intrinsic variability needed to untangle complex gene–environment interactions in disease susceptibility and severity. Herein, we determined whether a specific ancestral background was associated with either of four major disease outcomes (diabetes, obesity, cardiovascular disease, and depression). We estimated the genetic ancestry of 1,129 subjects from the Boston Puerto Rican Health Study based on genotypes of 100 ancestry informative markers (AIMs). We examined the effects of ancestry on tests of association between single AIMs and disease traits. The ancestral composition of this population was 57.2% European, 27.4% African, and 15.4% Native American. African ancestry was negatively associated with type 2 diabetes and cardiovascular disease, and positively correlated with hypertension. It is likely that the high prevalence rate of diabetes in Africans, Hispanics, and Native Americans is not due to genetic variation alone, but to the combined effects of genetic variation interacting with environmental and social factors. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.  相似文献   

18.
Ecological parameters vary in space, and the resulting heterogeneity of selective forces can drive adaptive population divergence. Clinal variation represents a classical model to study the interplay of gene flow and selection in the dynamics of this local adaptation process. Although geographic variation in phenotypic traits in discrete populations could be remainders of past adaptation, maintenance of adaptive clinal variation requires recurrent selection. Clinal variation in genetically determined traits is generally attributed to adaptation of different genotypes to local conditions along an environmental gradient, although it can as well arise from neutral processes. Here, we investigated whether selection accounts for the strong clinal variation observed in a highly heritable pheomelanin‐based color trait in the European barn owl by comparing spatial differentiation of color and of neutral genes among populations. Barn owl's coloration varies continuously from white in southwestern Europe to reddish‐brown in northeastern Europe. A very low differentiation at neutral genetic markers suggests that substantial gene flow occurs among populations. The persistence of pronounced color differentiation despite this strong gene flow is consistent with the hypothesis that selection is the primary force maintaining color variation among European populations. Therefore, the color cline is most likely the result of local adaptation.  相似文献   

19.
The historical focus on offspring size has been to explain variation among populations, but there have been few attempts to determine whether variation is greatest at population scale. Offspring size variation is typically viewed as an adaptive response to changes in the relationship between offspring size and performance, yet direct tests remain elusive. We partitioned natural variation in offspring size for a marine invertebrate, Watersipora subtorquata, at a range of spatial and temporal scales across southeastern Australia, and we estimated the relationship between offspring size and performance at each population and time. There was significant variation in offspring size among populations, but regional differences explained only approximately 25% of the observed variation, suggesting that there should be a greater focus on small-scale variation in offspring size. We used our data to parameterize an optimality model to generate predictions of offspring size among different populations and times. Differences in the relationship between offspring size and postmetamorphic performance (and therefore changes in size of offspring that were predicted to maximize maternal fitness) among populations and times were associated with differences in offspring sizes among those populations and times. We suggest that interpopulation variation in offspring size can be an adaptive response to local conditions, but the optimal offspring size is surprisingly dynamic.  相似文献   

20.
Contemporary inhabitants of the Balkan Peninsula belong to several ethnic groups of diverse cultural background. In this study, three ethnic groups from Bosnia and Herzegovina - Bosniacs, Bosnian Croats and Bosnian Serbs - as well as the populations of Serbians, Croatians, Macedonians from the former Yugoslav Republic of Macedonia, Montenegrins and Kosovars have been characterized for the genetic variation of 660 000 genome-wide autosomal single nucleotide polymorphisms and for haploid markers. New autosomal data of the 70 individuals together with previously published data of 20 individuals from the populations of the Western Balkan region in a context of 695 samples of global range have been analysed. Comparison of the variation data of autosomal and haploid lineages of the studied Western Balkan populations reveals a concordance of the data in both sets and the genetic uniformity of the studied populations, especially of Western South-Slavic speakers. The genetic variation of Western Balkan populations reveals the continuity between the Middle East and Europe via the Balkan region and supports the scenario that one of the major routes of ancient gene flows and admixture went through the Balkan Peninsula.  相似文献   

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