Exact moment calculations for genetic models with migration,mutation, and drift

Using properties of moment stationarity we develop exact expressions for the mean and covariance of allele frequencies at a single locus for a set of populations subject to drift, mutation, and migration. Some general results can be obtained even for arbitrary mutation and migration matrices, for example: (1) Under quite general conditions, the mean vector depends only on mutation rates, not on migration rates or the number of populations. (2) Allele frequencies covary among all pairs of populations connected by migration. As a result, the drift, mutation, migration process is not ergodic when any finite number of populations is exchanging genes. In addition, we provide closed-form expressions for the mean and covariance of allele frequencies in Wright's finite-island model of migration under several simple models of mutation, and we show that the correlation in allele frequencies among populations can be very large for realistic rates of mutation unless an enormous number of populations are exchanging genes. As a result, the traditional diffusion approximation provides a poor approximation of the stationary distribution of allele frequencies among populations. Finally, we discuss some implications of our results for measures of population structure based on Wright's F-statistics.     

Patterns of differentiation and hybridization in North American wolflike canids, revealed by analysis of microsatellite loci

Genetic divergence and gene flow among closely related populations are difficult to measure because mutation rates of most nuclear loci are so low that new mutations have not had sufficient time to appear and become fixed. Microsatellite loci are repeat arrays of simple sequences that have high mutation rates and are abundant in the eukaryotic genome. Large population samples can be screened for variation by using the polymerase chain reaction and polyacrylamide gel electrophoresis to separate alleles. We analyzed 10 microsatellite loci to quantify genetic differentiation and hybridization in three species of North American wolflike canids. We expected to find a pattern of genetic differentiation by distance to exist among wolflike canid populations, because of the finite dispersal distances of individuals. Moreover, we predicted that, because wolflike canids are highly mobile, hybrid zones may be more extensive and show substantial changes in allele frequency, relative to nonhybridizing populations. We demonstrate that wolves and coyotes do not show a pattern of genetic differentiation by distance. Genetic subdivision in coyotes, as measured by theta and Gst, is not significantly different from zero, reflecting persistent gene flow among newly established populations. However, gray wolves show significant subdivision that may be either due to drift in past Ice Age refugia populations or a result of other causes. Finally, in areas where gray wolves and coyotes hybridize, allele frequencies of gray wolves are affected, but those of coyotes are not. Past hybridization between the two species in the south-central United States may account for the origin of the red wolf.      

Unraveling the Effects of Selection and Demography on Immune Gene Variation in Free-Ranging Plains Zebra (Equus quagga) Populations

Demography, migration and natural selection are predominant processes affecting the distribution of genetic variation among natural populations. Many studies use neutral genetic markers to make inferences about population history. However, the investigation of functional coding loci, which directly reflect fitness, is critical to our understanding of species'' ecology and evolution. Immune genes, such as those of the Major Histocompatibility Complex (MHC), play an important role in pathogen recognition and provide a potent model system for studying selection. We contrasted diversity patterns of neutral data with MHC loci, ELA-DRA and -DQA, in two southern African plains zebra (Equus quagga) populations: Etosha National Park, Namibia, and Kruger National Park, South Africa. Results from neutrality tests, along with observations of elevated diversity and low differentiation across populations, supported previous genus-level evidence for balancing selection at these loci. Despite being low, MHC divergence across populations was significant and may be attributed to drift effects typical of geographically separated populations experiencing little to no gene flow, or alternatively to shifting allele frequency distributions driven by spatially variable and fluctuating pathogen communities. At the DRA, zebra exhibited geographic differentiation concordant with microsatellites and reduced levels of diversity in Etosha due to highly skewed allele frequencies that could not be explained by demography, suggestive of spatially heterogeneous selection and local adaptation. This study highlights the complexity in which selection affects immune gene diversity and warrants the need for further research on the ecological mechanisms shaping patterns of adaptive variation among natural populations.     

中国东亚飞蝗四个地理种群遗传结构的比较研究

利用水平切片淀粉凝胶电泳技术,分析了不同蝗区东亚飞蝗四个地理种群的遗传结构。在检测的20个酶基因座位中,四个种群均表现出一定的遗传多态性, 多态位点的百分率普遍偏高 (P=70%～80%),但由于杂合子数目较少而使每个位点的平均杂合度观察值偏低(H_o=0.023～0.032)。对每个基因座位的各基因型进行χ²检验, 除 Adk-1、Gdh-1、G3pd-1和Pgm-1在部分种群符合Hardy-Weinberg平衡外,其余绝大多数基因座位的基因型频率显著偏离Hardy-Weinberg平衡。从F统计量看,四个种群之间的遗传分化较低(F_st=0.0606 )。它表明： 东亚飞蝗较强的长距离迁飞行为增加了种群之间的基因交流, 降低了种群之间的遗传分化。根据Nei的遗传一致度（I）和Roger的遗传距离（D）进行分析, 在山西临猗与山西永济(I=0.964, D=0.175)、河南中牟与江苏沛县种群(I=0.957, D=0.160)之间,呈现出较高的遗传一致度和较小的遗传距离。结果表明： 迁飞性蝗虫东亚飞蝗种群之间的遗传分化与地理距离呈正相关。     

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

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

Selective pressures on MHC class II genes in the guppy (Poecilia reticulata) as inferred by hierarchical analysis of population structure

Genes of the major histocompatibility complex, which are the most polymorphic of all vertebrate genes, are a pre‐eminent system for the study of selective pressures that arise from host–pathogen interactions. Balancing selection capable of maintaining high polymorphism should lead to the homogenization of MHC allele frequencies among populations, but there is some evidence to suggest that diversifying selection also operates on the MHC. However, the pattern of population structure observed at MHC loci is likely to depend on the spatial and/or temporal scale examined. Here, we investigated selection acting on MHC genes at different geographic scales using Venezuelan guppy populations inhabiting four regions. We found a significant correlation between MHC and microsatellite allelic richness across populations, which suggests the role of genetic drift in shaping MHC diversity. However, compared to microsatellites, more MHC variation was explained by differences between populations within larger geographic regions and less by the differences between the regions. Furthermore, among proximate populations, variation in MHC allele frequencies was significantly higher compared to microsatellites, indicating that selection acting on MHC may increase population structure at small spatial scales. However, in populations that have significantly diverged at neutral markers, the population‐genetic signature of diversifying selection may be eradicated in the long term by that of balancing selection, which acts to preserve rare alleles and thus maintain a common pool of MHC alleles.     

Microgeographic genetic variation in the apple maggot rhagoletis pomonella

We examined electrophoretic variability at five enzyme loci in the apple maggot fly, Rhagoletis pomonella, on a microgeographic scale. Treating flies from individual hawthorn trees as separate populations, we estimated F(ST) values from allele frequencies. The results indicate that there is significant allele frequency heterogeneity among fly populations over a small spatial scale at some loci but not at others. This variation among loci in degree of differentiation is itself statistically significant, casting doubt on the role of genetic drift in maintaining the heterogeneity. There is also heterogeneity between years in flies from a given tree. These data provide a baseline with which future work on genetic differentiation among apple maggot populations associated with different species of host plants may be compared.     

The population genetics of a solitary oligolectic sweat bee, Lasioglossum (Sphecodogastra) oenotherae (Hymenoptera: Halictidae)

Strong evidence exists for global declines in pollinator populations. Data on the population genetics of solitary bees, especially diet specialists, are generally lacking. We studied the population genetics of the oligolectic bee Lasioglossum oenotherae, a specialist on the pollen of evening primrose (Onagraceae), by genotyping 455 females from 15 populations across the bee's North American range at six hyper-variable microsatellite loci. We found significant levels of genetic differentiation between populations, even at small geographic scales, as well as significant patterns of isolation by distance. However, using multilocus genotype assignment tests, we detected 11 first-generation migrants indicating that L. oenotherae's sub-populations are experiencing ongoing gene flow. Southern populations of L. oenotherae were significantly more likely to deviate from Hardy-Weinberg equilibrium and from genotypic equilibrium, suggesting regional differences in gene flow and/or drift and inbreeding. Short-term N(e) estimated using temporal changes in allele frequencies in several populations ranged from approximately 223 to 960. We discuss our findings in terms of the conservation genetics of specialist pollinators, a group of considerable ecological importance.     

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

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

Offspring sex ratio under inbreeding and outbreeding in a gynodioecious plant

Silene vulgaris is a gynodioecious plant native to Eurasia and now found throughout much of North America. Using hermaphrodite plants from three geographic regions (Stamford, NY; Broadway,VA; and Giles Co., VA) and four local populations within each region, we employed a hierarchical crossing design to explore the geographic structure of sex determining genes. Sex determination in this species is cytonuclear involving multiple cytoplasmic male sterility and nuclear restorer loci. Due to dominance effects within nuclear restorer loci, self-fertilization of hermaphrodites heterozygous at restorer loci should produce some homozygous recessive female offspring. Female offspring may also result from outcrossing among related individuals. At greater geographic and genetic distances, mismatches between cytoplasmic and nuclear sex determining genes should also produce high frequencies of female offspring if coevolution between cytoplasmic and nuclear sex determining alleles occurs independently among widely separated populations. We found evidence of dominance effects among nuclear restorer loci but no evidence of nuclear-cytoplasmic mismatches at the regional level. Of 63 maternal lines, 55 produced at least one female offspring when self-fertilized. Outcrossing within populations produced significantly fewer female offspring than self-fertilization. Outcrossing among regions produced the lowest proportion of female offspring, significantly fewer than outcrossing among populations within regions. Regions responded differently to among-region outcrossing with pollen donors from the two Virginia regions producing far fewer female offspring with New York dams than crosses among New York populations. These results indicate that nuclear restoration is complex, involving multiple loci with epistatic interactions and that most hermaphrodites in nature are heterozygous at one or more restorer locus. Further, regional differences in restorer frequencies indicate significant genetic structure for sex determining genes at large geographic scales, perhaps reflecting invasion history.     

Divergent evolution of molecular markers during laboratory adaptation in Drosophila subobscura

The impact of genetic drift in population divergence can be elucidated using replicated laboratory experiments. In the present study we used microsatellite loci to study the genetic variability and differentiation of laboratory populations of Drosophila subobscura derived from a common ancestral natural population after 49 generations in the laboratory. We found substantial genetic variability in all our populations. The high levels of genetic variability, similar across replicated populations, suggest that careful maintenance procedures can efficiently reduce the loss of genetic variability in captive populations undergoing adaptation, even without applying active management procedures with conservation purposes, in organisms that generate a high number of offspring such as Drosophila. Nevertheless, there was a significant genetic differentiation between replicated populations. This shows the importance of genetic drift, acting through changes in allele frequencies among populations, even when major changes in the degree of genetic diversity in each population are not involved.     

An exploratory analysis of geographic genetic variation in southern African nyala (Tragelaphus angasii)

We report patterns of genetic variation based on microsatellite, allozyme and mitochondrial control region markers in nyala from geographic locations sampled in South Africa, Mozambique, Malawi and Zimbabwe. Highly significant differences were observed among allele frequencies at three microsatellite loci between populations from KwaZulu-Natal, Limpopo and Malawi, with the Malawi and KwaZulu-Natal groupings showing the highest differentiation (R_ST=0.377). Allozyme frequencies showed minor, non-statistically significant regional differences among the South African populations, with maximum F_ST values of 0.048–0.067. Mitochondrial DNA analyses indicated a unique haplotype in each location sampled. Since none of these indices of population differentiation showed significant correlation to absolute geographic distance, we conclude that geographic variation in this species is probably a function of a distribution pattern stemming from habitat specificity. It is suggested that translocations among geographically distant regional populations be discouraged at present, pending a more elaborate investigation. Transfer of native individuals among local populations may, however, be required for minimizing the likelihood of inbreeding depression developing in small captive populations.     

The coalescent process in models with selection, recombination and geographic subdivision

A population genetic model with a single locus at which balancing selection acts and many linked loci at which neutral mutations can occur is analysed using the coalescent approach. The model incorporates geographic subdivision with migration, as well as mutation, recombination, and genetic drift of neutral variation. It is found that geographic subdivision can affect genetic variation even with high rates of migration, providing that selection is strong enough to maintain different allele frequencies at the selected locus. Published sequence data from the alcohol dehydrogenase locus of Drosophila melanogaster are found to fit the proposed model slightly better than a similar model without subdivision.     

Genetic variation at nine short tandem repeat loci among islanders of the eastern Adriatic coast of Croatia

We have analyzed the extent of genetic variation at nine autosomal short tandem repeat loci (D3S1358, VWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317, D7S820) among six populations from Croatia: five distributed in the islands of the eastern Adriatic coast and one from the mainland. The purpose is to investigate the usefulness of these loci in detecting regional genetic differentiation in the studied populations. Significant heterogeneity among the island and mainland populations is revealed in the distributions of allele frequencies; however, the absolute magnitude of the coefficient of gene differentiation is small but significant. The summary measures of genetic variation, namely, heterozygosity, number of alleles, and allele size variance, do not indicate reduced genetic variation in the island populations compared to the mainland population. In contrast to the two measures of genetic variation, allele size variance and within-locus heterozygosity, the imbalance index (beta) indicates evidence of recent expansion of population sizes in all islands and in the mainland. High mutation rates of the studied loci together with local drift effects are likely explanations for interisland genetic variation and the observed lack of reduced genetic diversity among the island populations.     

Molecular evidence for selection on female color polymorphism in the damselfly Ischnura graellsii

The significance of female color polymorphism in Odonata remains controversial despite many field studies. The importance of random factors (founder effects, genetic drift and migration) versus selective forces for the maintenance of this polymorphism is still discussed. In this study, we specifically test whether the female color polymorphism of Ischnura graellsii (Odonata, Coenagrionidae) is under selection in the wild. We compared the degree of genetic differentiation based on RAPD markers (assumed to be neutral) with the degree of differentiation based on color alleles. Weir and Cockerham's theta values showed a significant degree of population differentiation for both sets of loci (RAPD and color alleles) but the estimated degree of population differentiation (theta) was significantly greater for the set of RAPD loci. This result shows that some sort of selection contributes to the maintenance of similar color morph frequencies across the studied populations. Our results combined with those of previous field studies suggest that at least in some I. graellsii populations, density-dependent mechanisms might help to prevent the loss of this polymorphism but cannot explain the similarity in morph frequencies among populations.     

The effect of natural selection on estimates of genetic divergence among populations of the Atlantic salmon

The effect of natural selection on the _mMEP-2 * locus on measures of genetic divergence among Atlantic salmon populations was investigated by examining the pattern of change in the level of genetic differentiation (F_ST) averaged over loci when data on the _mMEP-2 * locus were either included or excluded. The level of F_ST among populations at various geographic scales was estimated from allele frequencies at up to four loci (_s AAT-4 *, IDDH-1 *, IDHP-3 *, and _mMEP-2 *). At smaller geographic scales (within river systems or limited geographic regions) levels of variance in _mMEP-2 * allele frequencies were reduced relative to mean levels. At larger geographic scales (across continents or the species range) variation in _mMEP-2 * allele frequencies was greater than mean levels. These results suggest an a priori hypothesis for the effect of selection on the _mMEP-2 * locus which may be applied in future studies on variation in protein coding or other (e.g. mini- and microsatellite) loci in the Atlantic salmon. It is recommended that estimates of gene flow among populations of the Atlantic salmon based on mean F _ST estimates which include data on the _mMEP-2 * locus should be viewed with caution.     

Serial founder effects and genetic differentiation during worldwide range expansion of monarch butterflies

Range expansions can result in founder effects, increasing genetic differentiation between expanding populations and reducing genetic diversity along the expansion front. However, few studies have addressed these effects in long-distance migratory species, for which high dispersal ability might counter the effects of genetic drift. Monarchs (Danaus plexippus) are best known for undertaking a long-distance annual migration in North America, but have also dispersed around the world to form populations that do not migrate or travel only short distances. Here, we used microsatellite markers to assess genetic differentiation among 18 monarch populations and to determine worldwide colonization routes. Our results indicate that North American monarch populations connected by land show limited differentiation, probably because of the monarch''s ability to migrate long distances. Conversely, we found high genetic differentiation between populations separated by large bodies of water. Moreover, we show evidence for serial founder effects across the Pacific, suggesting stepwise dispersal from a North American origin. These findings demonstrate that genetic drift played a major role in shaping allele frequencies and created genetic differentiation among newly formed populations. Thus, range expansion can give rise to genetic differentiation and declines in genetic diversity, even in highly mobile species.     

Species status and population genetic structure of the flightless chafer beetles Prodontria modesta and P. bicolorata (Coleoptera; Scarabaeidae) from South Island, New Zealand

This study uses isozyme electrophoresis to investigate the systematic status of two rare flightless chafer beetle species, Prodontria modesta and P. bicolorata , currently distinguished solely on the basis of colour. Seven polymorphic loci were analysed for the species in sympatry and allopatry. In sympatry, gene frequencies imply no genetic barrier between the two colour forms. Wright's hierarchical F-statistics were calculated to determine how the genetic variation is partitioned across the geographic range of the two species. Strong geographic structuring occurs at the population level but there is little genetic differentiation attributable to species. Comparisons of morphological measurements are in support of the electrophoretic results. The systematic significance of the two distinct colour forms is thus questionable. Under the biological, recognition or phylogenetic species concepts, the genetic data suggest that there is only one species, polytypic for a colour pattern. Most of the genetic diversity of this group of beetles lies within and among populations, which differ quite markedly over their geographic range, rather than between the two named species.     

A microsatellite analysis of natterjack toad, Bufo calamita, metapopulations

Although it is widely recognised that spatial subdivision of populations is common in nature, there is no consensus as to how metapopulation dynamics affect genetic diversity. We investigated the genetic differentiation of natterjack toads, Bufo calamita , in three regions of Britain where habitat continuity indicated the likely occurrence of extensive metapopulations. Our intention was to determine whether genetic analysis supported the existence of metapopulation structures, if so of what type, and to identify barriers to migration between subpopulations. Allele frequencies were determined across eight polymorphic microsatellite loci for a total of 24 toad subpopulations at three separate sites. Genetic differentiation was assessed using five measures of genetic distance, notably F _ST , R _ST , Nei's standard distance D _s , Δμ² and the Cavalli-Sforza chord distance D _c . B. calamita exhibited small but significant levels of genetic differentiation between subpopulations in all three study areas, and genetic and geographic distance correlations indicated isolation-by-distance effects in all three cases. The effects on correlation strengths of compensation for positive (sea, rivers, urban development) and negative (pond clusters) barriers to toad migration between the subpopulations in each area were also determined. D _c , a measure which assumes that differentiation is caused by drift with negligible mutation effect, yielded the most plausible interpretation of metapopulation structures. Overall the patterns of genetic variation suggested the existence of a mixed metapopulation model for this species, with high levels of gene flow compatible with one version of the classical model but often supported by particularly stable subpopulations as in the mainland-island model.