Spatial patterns of human gene frequencies in Europe

The aims of this study of spatial patterns of human gene frequencies in Europe are twofold. One is to present new methodology developed for the analysis of such data. The other is to report on the diversity of spatial patterns observed in Europe and their interpretation as evidence of population processes. Spatial variation in 59 allele and haplotype frequencies (26 genetic systems) for polymorphisms in blood antigens, enzymes, and proteins is analyzed for an aggregate of 3,384 localities, using homogeneity tests, one-dimensional and directional spatial correlograms, and SYMAP interpolated surfaces. The data matrices are reduced to reveal the principal patterns by clustering techniques. The findings of this study can be summarized as follows: 1) There is significant heterogeneity in allele frequencies among the localities for all but one genetic system. 2) There are significant spatial patterns for most allele frequencies. 3) There is a substantial minority of clinal patterns in these populations. Clinal trends are found more frequently in HLA alleles than for other variables. North-south and northwest-southwest gradients predominate. 4) There is a strong decline in overall genetic similarity with geographic distance for most variables. 5) There are few, if any, appreciable correlations in pairs of allele frequencies over the continent, and there is little interesting correlation structure in the resulting correlation matrix. 6) Few spatial correlograms are markedly similar to each other, yet they form well-defined clusters. Spatial variation patterns, therefore, differ among allele frequencies. Patterns of human gene frequencies in modern Europe are diverse and complex. No single model suffices for interpretation of the observed genetic structure. Some clinal patterns reported here support the Neolithic demic-expansion hypothesis, others suggest latitudinal selection. Most of the clinal patterns are in HLA alleles, but there is also evidence from ABO for east-west migration diffusion. The majority of patterns are patchy, consistent with hypotheses of isolation by distance or of settlement of genetically differing, subsequently expanding ethnic groups. While undoubtedly there has been an ongoing stochastic process of differentiation consistent with the isolation-by-distance model, this has not obscured the directional patterns caused by migration (demic diffusion), and has perhaps only reinforced the contribution from settlement of ethnic units to patterns of genetic variation. However, the impact of the latter is most difficult to discern and requires further methodological developments.     

Lactate dehydrogenase: a polymorphism of Anoplarchus purpurescens: geographic variation in central California

Previous studies on the muscle lactate dehydrogenase polymorphism of the stichaeid fish Anoplarchus purpurescens in Puget Sound have demonstrated the existence of a clinal pattern of allele frequency. The LDH-A' allele was observed to increase toward the south, with several environmental factors showing correlation with this change in allele frequency. Populations from California were sampled in the present study to determine whether or not gene frequencies along an independent transect near the southern end of the species distribution are consistent with the interpretation that the geographic patterns reflect the influence of environmental factors. In California, the LDH-A' allele decreases in frequency to the south. This observation necessitates the reevaluation of possible environmental influences on the LDH polymorphism. Only one of several proposed hypotheses is completely consistent with the geographic patterns observed along both the Washington and California transects. However, the genetic differentiation along the California coast cannot be unequivically ascribed to the influence of environmental factors; current morphological data indicate the possibility of historical influences on the population genetic structure of California A. purpurescens.     

Genetic variability in white-tailed deer (Odocoileus virginianus) and its relationship to environmental parameters and herd origin (Cervidae)

Allozyme variation was examined in 1571 white-tailed deer (Odocoileus virginianus) from 29 localities in Tennessee by starch gel electrophoresis. For 11 polymorphic loci, sex-related, age-related and temporal differences were minimal. However, significant spatial hererogeneity was evident in genotypes (contingency table results), allele frequencies (F _ST=0.057) and heterozygosity. Heterozygosity ranged from 16.9% to 26.8% with a mean of 22.9%. The spatial pattern of allele frequencies determined from Rogers' coefficients of genetic similarity indicated associations based on geographic proximity and stocking history. In hierarchial analyses, physiographic regions accounted for more of the total gene diversity than herd origin groups (populations of similar origin) but less than individual populations. For five loci, physiographic regions accounted for more of the gene diversity than populations, suggesting a selection role in the observed genetic variability. Bivariate and canonical correlation analyses revealed significant associations between environmental and genetic variables. Temperature variables and allele frequencies for three loci (alcohol dehydrogenase, alpha-glycerophosphate dehydrogenase, sorbitol dehydrogenase) had the prominent roles in the multivariate association between environmental and genetic variables. Herd origin, gene flow and selection appear to be involved in the gene diversity in deer from Tennesee.     

Gene Flow and Selection in a Cline

A model of the effect of gene flow and natural selection in a continuously distributed, infinite population is developed. Different patterns of spatial variation in selective pressures are considered, including a step change in the environment, a "pocket" in the environment and a periodically varying environment. Also, the problem of the effect of a geographic barrier to dispersal is analyzed. The results are: (1) there is a characteristic length scale of variation of gene frequencies, (see PDF). The population cannot respond to changes in environmental conditions which occur over a distance less than the characteristic length. The result does not depend either on the pattern of variation in selective pressures or on the exact shape of the dispersal function. (2) The reduction in the fitness of the heterozygote causes a cline in gene frequencies to become steeper. (3) A geographic barrier to dispersal causes a drastic change in the gene frequencies at the barrier only when almost all of the individuals trying to cross the barrier are stopped.     

Adaptive chromosomal divergence driven by mixed geographic mode of evolution

Chromosomal inversions are ubiquitous in nature and of great significance for understanding adaptation and speciation. Inversions were the first markers used to investigate the genetic structure of natural populations, leading to the concept of coadapted gene complexes and theories concerning founder effects and genetic drift in small populations. However, we still lack elements of a general theory accounting for the origins and distribution of inversions in nature. Here, we use computer simulations to show that a "mixed geographic mode" of evolution involving allopatric separation of populations followed by secondary contact and gene flow generates chromosomal divergence by natural selection under wider conditions than previous hypotheses. This occurs because inversions arising in allopatry contain a full complement of locally adapted genes. Once gene flow ensues, reduced recombination within inversions keeps these favorable genotypic combinations intact, resulting in inverted genomic regions being favored over collinear regions. This process allows inversions to establish to high frequencies. Our model can account for several classic patterns in the geographic distribution of inversions and highlights how selection on standing genetic variation allows rapid chromosomal evolution without the waiting time for new mutations. As inversion differences often separate closely related taxa, mixed modes of divergence could be common.     

Impact of Selection and Demography on the Diffusion of Lactase Persistence

Background

The lactase enzyme allows lactose digestion in fresh milk. Its activity strongly decreases after the weaning phase in most humans, but persists at a high frequency in Europe and some nomadic populations. Two hypotheses are usually proposed to explain the particular distribution of the lactase persistence phenotype. The gene-culture coevolution hypothesis supposes a nutritional advantage of lactose digestion in pastoral populations. The calcium assimilation hypothesis suggests that carriers of the lactase persistence allele(s) (LCT*P) are favoured in high-latitude regions, where sunshine is insufficient to allow accurate vitamin-D synthesis. In this work, we test the validity of these two hypotheses on a large worldwide dataset of lactase persistence frequencies by using several complementary approaches.

Methodology

We first analyse the distribution of lactase persistence in various continents in relation to geographic variation, pastoralism levels, and the genetic patterns observed for other independent polymorphisms. Then we use computer simulations and a large database of archaeological dates for the introduction of domestication to explore the evolution of these frequencies in Europe according to different demographic scenarios and selection intensities.

Conclusions

Our results show that gene-culture coevolution is a likely hypothesis in Africa as high LCT*P frequencies are preferentially found in pastoral populations. In Europe, we show that population history played an important role in the diffusion of lactase persistence over the continent. Moreover, selection pressure on lactase persistence has been very high in the North-western part of the continent, by contrast to the South-eastern part where genetic drift alone can explain the observed frequencies. This selection pressure increasing with latitude is highly compatible with the calcium assimilation hypothesis while the gene-culture coevolution hypothesis cannot be ruled out if a positively selected lactase gene was carried at the front of the expansion wave during the Neolithic transition in Europe.     

THE EFFECTS OF THE RELATIVE GEOGRAPHIC SCALES OF GENE FLOW AND SELECTION ON MORPH FREQUENCIES IN THE WALKING-STICK TIMEMA CRISTINAE

Gene frequencies in large populations are determined by a balance between selection and gene flow between neighborhoods of different selection regimes. This balance is affected by the area of the patches of a given selection regime relative to the gene-flow distance. If patches are small relative to gene-flow distance, similarity in the total area occupied by different patch types is a crucial condition for the stability of polymorphisms. However, if patches are larger than the gene-flow distance, then the relative area of different patch types is less important because of reduced gene flow resulting from isolation by distance. Two morphs (striped and unstriped) of the walking-stick Timema cristinae were each strongly associated with patches of distinct species of food plants on which they are most cryptic. The frequency of a morph was high on the plant on which it is most cryptic when either: (1) the area occupied by the food plant (patch) was very large; (2) the patch was completely isolated from other patches; or (3) the patch was larger than adjacent patches. Results (1) and (2) are consistent with isolation-by-distance models, and result (3) is consistent with Levene's multiple-niche polymorphism model.     

HIERARCHICAL GENETIC STRUCTURE AND GENE FLOW IN MACROGEOGRAPHIC POPULATIONS OF THE EASTERN TENT CATERPILLAR (MALACOSOMA AMERICANUM)

Genetic structure and inferred rates of gene flow in macrogeographic populations of the eastern tent caterpillar Malacosoma americanum were analyzed at two hierarchical scales: local demes and regional subpopulations. Wright's F-statistics were used to estimate population genetic structure using multilocus genotypic data generated electrophoretically. Estimated values of F_ST and the distribution of private alleles were then used to obtain indirect estimates of gene flow. We found modest, though significant, genetic structure at both spatial scales, a pattern consistent with high rates of gene flow over the large distances involved. Modest values obtained for Nei's genetic distance also suggested high levels of gene flow across the range of this species, although some gene-flow restriction resulting from isolation by distance was suggested by a positive regression of genetic distance on geographic distance. The observed homogeneity at enzyme loci across the range of M. americanum parallels the reported uniformity in morphology, suggesting a general absence of local genetic differentiation in this widely distributed species. The genetic homogeneity observed in this wide-ranging insect is discussed in terms of organism-specific environmental experience at different spatial scales. Some organisms occupying apparently heterogeneous environments may ameliorate unsuitable local conditions through microhabitat selection or behavioral modification of their microenvironment. This may be accomplished in M. americanum through group shelter construction and behavioral thermoregulation, closely tying thermoregulation to social biology in this species. If in this way the tent helps produce an effectively homogeneous environment for this species across its extensive range, this system may provide a unique example of how social behavior can influence the distribution of genetic variation in a population.     

Affinities among Melanesians,Micronesians, and Polynesians: a neutral biparental genetic perspective

The human colonization of Remote Oceania, the vast Pacific region including Micronesia, Polynesia, and Melanesia beyond the northern Solomon Islands, ranks as one of the greatest achievements of prehistory. Many aspects of human diversity have been examined in an effort to reconstruct this late Holocene expansion. Archaeolinguistic analyses describe a rapid expansion of Austronesian-speaking "Lapita people" from Taiwan out into the Pacific. Analyses of biological markers, however, indicate genetic contributions from Pleistocene-settled Near Oceania into Micronesia and Polynesia, and genetic continuity across Melanesia. Thus, conflicts between archaeolinguistic and biological patterns suggest either linguistic diffusion or gene flow across linguistic barriers throughout Melanesia. To evaluate these hypotheses and the general utility of linguistic patterns for conceptualizing Pacific prehistory, we analyzed 14 neutral, biparental genetic (short tandem repeat) loci from 965 individuals representing 27 island Southeast Asian, Melanesian, Micronesian, and Polynesian populations. Population bottlenecks during the colonization of Remote Oceania are indicated by a statistically significant regression of loss of heterozygosity on migration distance from island Southeast Asia (r = 0.78, p < 0.001). Genetic and geographic distances were consistently correlated (r > 0.35, p < 0.006), indicating extensive gene flow primarily focused among neighboring populations. Significant correlations between linguistic and geographic patterns and between genetic and linguistic patterns depended upon the inclusion of Papuan speakers in the analyses. These results are consistent with an expansion of Austronesian-speaking populations out of island Southeast Asia and into Remote Oceania, followed by substantial gene flow from Near Oceanic populations. Although linguistic and genetic distinctions correspond at times, particularly between Western and Central-Eastern Micronesia, gene flow has reduced the utility of linguistic data within Melanesia. Overall, geographic proximity is a better predictor of biparental genetic relationships than linguistic affinities.     

BIOCHEMICAL GENETICS OF MOSQUITOFISH. IV. CHANGES OF ALLELE FREQUENCIES THROUGH TIME AND SPACE

Gene frequency data from samples of Gambusia affinis populations at 76 localities across the Savannah River drainage were used to investigate temporal and spatial patterns in population genetic structure. Localities in the Par Pond system on the Savannah River Plant were sampled in 1971, 1977, and 1979. Allelic frequencies in these populations were generally stable through time, although significant temporal changes were observed among samples from Pond C, an impoundment receiving thermal effluent. Significant spatial heterogeneity in allele frequencies was observed on both microgeographic and regional scales. Populations within the Par Pond system were spatially subdivided at four of the five loci surveyed (mean F_ST = 0.051). Subdivision was even more pronounced when samples from across the Savannah River drainage were compared (mean F_ST = 0.196). A hierarchial analysis of gene diversity (G_ST) demonstrated that most of the genic diversity across the drainage exists as within-subdivision diversity. Even when populations from such contrasting habitats as rivers, creeks, ponds, and reservoirs are compared, an average of only 13% of the total gene diversity was attributed to between-group diversity. Greatest between-group gene diversity was observed when reservoirs were compared with one another. This general pattern of low between-habitat diversity suggests that differential selection pressures are not playing a major role in producing the observed levels of subdivision. In the Par Pond system, neither single locus nor multilocus genetic distances were significantly associated with geographic distance or with its reciprocal. For samples from over the Savannah River drainage, significant correlations between genetic and geographic distance were observed only for the Gpi-2 and Pgm-2 loci. Thus, there was a general lack of concordance between genetic and geographic distances. Spatial autocorrelation demonstrated patterns consistent with Wright's isolation by distance model. Significant positive correlations in allelic frequencies among neighboring populations were observed for five of six alleles; allelic frequencies in more distantly separated populations were typically not correlated.     

Coevolutionary clines across selection mosaics

Abstract. Much of the dynamics of coevolution may be driven by the interplay between geographic variation in reciprocal selection (selection mosaics) and the homogenizing action of gene flow. We develop a genetic model of geographically structured coevolution in which gene flow links coevolving communities that may differ in both the direction and magnitude of reciprocal selection. The results show that geographically structured coevolution may lead to allele-frequency clines within both interacting species when fitnesses are spatially uniform or spatially heterogeneous. Furthermore, the results show that the behavior and shape of clines differ dramatically among different types of coevolutionary interaction. Antagonistic interactions produce dynamic clines that change shape rapidly through time, producing shifting patterns of local adaptation and maladaptation. Unlike antagonistic interactions, mutualisms generate stable equilibrium patterns that lead to fixed spatial patterns of adaptation. Interactions that vary between mutualism and antagonism produce both equilibrium and dynamic clines. Furthermore, the results demonstrate that these interactions may allow mutualisms to persist throughout the geographic range of an interaction, despite pockets of locally antagonistic selection. In all cases, the coevolved spatial patterns of allele frequencies are sensitive to the relative contributions of gene flow, selection, and overall habitat size, indicating that the appropriate scale for studies of geographically structured coevolution depends on the relative contributions of each of these factors.     

Fine-scale analysis reveals cryptic landscape genetic structure in desert tortoises

Characterizing the effects of landscape features on genetic variation is essential for understanding how landscapes shape patterns of gene flow and spatial genetic structure of populations. Most landscape genetics studies have focused on patterns of gene flow at a regional scale. However, the genetic structure of populations at a local scale may be influenced by a unique suite of landscape variables that have little bearing on connectivity patterns observed at broader spatial scales. We investigated fine-scale spatial patterns of genetic variation and gene flow in relation to features of the landscape in desert tortoise (Gopherus agassizii), using 859 tortoises genotyped at 16 microsatellite loci with associated data on geographic location, sex, elevation, slope, and soil type, and spatial relationship to putative barriers (power lines, roads). We used spatially explicit and non-explicit Bayesian clustering algorithms to partition the sample into discrete clusters, and characterize the relationships between genetic distance and ecological variables to identify factors with the greatest influence on gene flow at a local scale. Desert tortoises exhibit weak genetic structure at a local scale, and we identified two subpopulations across the study area. Although genetic differentiation between the subpopulations was low, our landscape genetic analysis identified both natural (slope) and anthropogenic (roads) landscape variables that have significantly influenced gene flow within this local population. We show that desert tortoise movements at a local scale are influenced by features of the landscape, and that these features are different than those that influence gene flow at larger scales. Our findings are important for desert tortoise conservation and management, particularly in light of recent translocation efforts in the region. More generally, our results indicate that recent landscape changes can affect gene flow at a local scale and that their effects can be detected almost immediately.     

Evolutionary diversification through hybridization in a wild host-pathogen interaction

Coevolutionary outcomes between interacting species are predicted to vary across landscapes, as environmental conditions, gene flow, and the strength of selection vary among populations. Using a combination of molecular, experimental, and field approaches, we describe how broad-scale patterns of environmental heterogeneity, genetic divergence, and regional adaptation have the potential to influence coevolutionary processes in the Linum marginale-Melampsora lini plant-pathogen interaction. We show that two genetically and geographically divergent pathogen lineages dominate interactions with the host across Australia, and demonstrate a hybrid origin for one of the lineages. We further demonstrate that the geographic divergence of the two lineages of M. lini in Australia is related to variation among lineages in virulence, life-history characteristics, and response to environmental conditions. When correlated with data describing regional patterns of variation in host resistance diversity and mating system these observations highlight the potential for gene flow and geographic selection mosaics to generate and maintain coevolutionary diversification in long-standing host-pathogen interactions.     

Genomic differentiation between temperate and tropical Australian populations of Drosophila melanogaster

Determining the genetic basis of environmental adaptation is a central problem of evolutionary biology. This issue has been fruitfully addressed by examining genetic differentiation between populations that are recently separated and/or experience high rates of gene flow. A good example of this approach is the decades-long investigation of selection acting along latitudinal clines in Drosophila melanogaster. Here we use next-generation genome sequencing to reexamine the well-studied Australian D. melanogaster cline. We find evidence for extensive differentiation between temperate and tropical populations, with regulatory regions and unannotated regions showing particularly high levels of differentiation. Although the physical genomic scale of geographic differentiation is small--on the order of gene sized--we observed several larger highly differentiated regions. The region spanned by the cosmopolitan inversion polymorphism In(3R)P shows higher levels of differentiation, consistent with the major difference in allele frequencies of Standard and In(3R)P karyotypes in temperate vs. tropical Australian populations. Our analysis reveals evidence for spatially varying selection on a number of key biological processes, suggesting fundamental biological differences between flies from these two geographic regions.     

Genetic differentiation in South Amerindians is related to environmental and cultural diversity: evidence from the Y chromosome

The geographic structure of Y-chromosome variability has been analyzed in native populations of South America, through use of the high-frequency Native American haplogroup defined by the DYS199-T allele and six Y-chromosome-linked microsatellites (DYS19, DYS389A, DYS389B, DYS390, DYS391, and DYS393), analyzed in 236 individuals. The following pattern of within- and among-population variability emerges from the analysis of microsatellite data: (1) the Andean populations exhibit significantly higher levels of within-population variability than do the eastern populations of South America; (2) the spatial-autocorrelation analysis suggests a significant geographic structure of Y-chromosome genetic variability in South America, although a typical evolutionary pattern could not be categorically identified; and (3) genetic-distance analyses and the analysis of molecular variance suggest greater homogeneity between Andean populations than between non-Andean ones. On the basis of these results, we propose a model for the evolution of the male lineages of South Amerindians that involves differential patterns of genetic drift and gene flow. In the western part of the continent, which is associated with the Andean area, populations have relatively large effective sizes and gene-flow levels among them, which has created a trend toward homogenization of the gene pool. On the other hand, eastern populations-settled in the Amazonian region, the central Brazilian plateau, and the Chaco region-have exhibited higher rates of genetic drift and lower levels of gene flow, with a resulting trend toward genetic differentiation. This model is consistent with the linguistic and cultural diversity of South Amerindians, the environmental heterogeneity of the continent, and the available paleoecological data.     

Integrating patterns of thermal tolerance and phenotypic plasticity with population genetics to improve understanding of vulnerability to warming in a widespread copepod

Differences in population vulnerability to warming are defined by spatial patterns in thermal adaptation. These patterns may be driven by natural selection over spatial environmental gradients, but can also be shaped by gene flow, especially in marine taxa with high dispersal potential. Understanding and predicting organismal responses to warming requires disentangling the opposing effects of selection and gene flow. We begin by documenting genetic divergence of thermal tolerance and developmental phenotypic plasticity. Ten populations of the widespread copepod Acartia tonsa were collected from sites across a large thermal gradient, ranging from the Florida Keys to Northern New Brunswick, Canada (spanning over 20° latitude). Thermal performance curves (TPCs) from common garden experiments revealed local adaptation at the sampling range extremes, with thermal tolerance increasing at low latitudes and decreasing at high latitudes. The opposite pattern was observed in phenotypic plasticity, which was strongest at high latitudes. No relationship was observed between phenotypic plasticity and environmental variables. Instead, the results are consistent with the hypothesis of a trade‐off between thermal tolerance and the strength of phenotypic plasticity. Over a large portion of the sampled range, however, we observed a remarkable lack of differentiation of TPCs. To examine whether this lack of divergence is the result of selection for a generalist performance curve or constraint by gene flow, we analyzed cytochrome oxidase I mtDNA sequences, which revealed four distinct genetic clades, abundant genetic diversity, and widely distributed haplotypes. Strong divergence in thermal performance within genetic clades, however, suggests that the pace of thermal adaptation can be relatively rapid. The combined insight from the laboratory physiological experiments and genetic data indicate that gene flow constrains differentiation of TPCs. This balance between gene flow and selection has implications for patterns of vulnerability to warming. Taking both genetic differentiation and phenotypic plasticity into account, our results suggest that local adaptation does not increase vulnerability to warming, and that low‐latitude populations in general may be more vulnerable to predicted temperature change over the next century.     

Factors Affecting Geographic Variation in Echolocation Calls of the Endemic Myotis davidii in China

The sensory drive hypothesis of speciation predicts that divergence in communication systems will occur when environments differ and that this sensory divergence can ultimately promote speciation. The factors affecting geographic evolution in acoustic signals remain poorly understood, especially in the contexts of high gene flow. This study investigated variation patterns in peak frequency emitted by the Chinese endemic Myotis davidii on a broad geographic scale by evaluating the relative importance of morphological, environmental, geographic, and genetic variables. Significant variation in peak frequency was observed among regions, but peak frequencies among populations within region had some percentage of similarity. Differences in peak frequency were not associated with morphological difference, genetic structure, and geographic distance among regions, which suggested that peak frequency divergences in M. davidii were not the primary driver of regions' isolation in a context of weak gene flow. Within the Middle East Plain (MEP), one of the regions delineated in this study, peak frequency differences of M. davidii were not significantly correlated with genetic distance and geographic distance among populations, suggesting that peak frequency was not be subject to cultural drift within MEP. Our results provide evidence that geographic variation in echolocation call design may evolve as a consequence of local adaptation to climate conditions.     

Broad Concordance in the Spatial Distribution of Adaptive and Neutral Genetic Variation across an Elevational Gradient in Deer Mice

When species are continuously distributed across environmental gradients, the relative strength of selection and gene flow shape spatial patterns of genetic variation, potentially leading to variable levels of differentiation across loci. Determining whether adaptive genetic variation tends to be structured differently than neutral variation along environmental gradients is an open and important question in evolutionary genetics. We performed exome-wide population genomic analysis on deer mice sampled along an elevational gradient of nearly 4,000 m of vertical relief. Using a combination of selection scans, genotype−environment associations, and geographic cline analyses, we found that a large proportion of the exome has experienced a history of altitude-related selection. Elevational clines for nearly 30% of these putatively adaptive loci were shifted significantly up- or downslope of clines for loci that did not bear similar signatures of selection. Many of these selection targets can be plausibly linked to known phenotypic differences between highland and lowland deer mice, although the vast majority of these candidates have not been reported in other studies of highland taxa. Together, these results suggest new hypotheses about the genetic basis of physiological adaptation to high altitude, and the spatial distribution of adaptive genetic variation along environmental gradients.     

Mitochondrial and nuclear genetic relationships among Pacific Island and Asian populations.

Mitochondrial and autosomal short tandem-repeat (STR) genetic distances among 28 Pacific Island and Asian populations are significantly correlated (r=.25, P<.01) but describe distinct patterns of relationships. Maternally inherited-mtDNA data suggest that Remote Oceanic Islanders originated in island Southeast Asia. In contrast, biparental STR data reveal substantial genetic affinities between Remote Oceanic Islanders and Near Oceanic populations from highland Papua New Guinea and Australia. The low correlation between maternal and biparental genetic markers from the same individuals may reflect differences in genome-effective population sizes or in sex-biased gene flow. To explore these possibilities, we have examined genetic diversity, gene flow, and correlations among genetic, linguistic, and geographic distances within four sets of populations representing potential geographic and cultural spheres of interaction. GST estimates (a measure of genetic differentiation inversely proportional to gene flow) from mtDNA sequences vary between 0.13 and 0.39 and are typically five times greater than GST estimates from STR loci (0.05-0.08). Significant correlations (r>.5, P<.05) between maternal genetic and linguistic distances are coincident with high mtDNA GST estimates (>0.38). Thus, genetic and linguistic distances may coevolve, and their correspondence may be preserved under conditions of genetic isolation. A significant correlation (r=.65, P<.01) between biparental genetic and geographic distances is coincident with a low STR GST estimate (0.05), indicating that isolation by distance is observed under conditions of high nuclear-gene flow. These results are consistent with an initial settlement of Remote Oceania from island Southeast Asia and with extensive postcolonization male-biased gene flow with Near Oceania.     

Genetic architecture and genomic patterns of gene flow between hybridizing species of Picea

Hybrid zones provide an opportunity to study the effects of selection and gene flow in natural settings. We employed nuclear microsatellites (single sequence repeat (SSR)) and candidate gene single-nucleotide polymorphism markers (SNPs) to characterize the genetic architecture and patterns of interspecific gene flow in the Picea glauca × P. engelmannii hybrid zone across a broad latitudinal (40–60 degrees) and elevational (350–3500 m) range in western North America. Our results revealed a wide and complex hybrid zone with broad ancestry levels and low interspecific heterozygosity, shaped by asymmetric advanced-generation introgression, and low reproductive barriers between parental species. The clinal variation based on geographic variables, lack of concordance in clines among loci and the width of the hybrid zone points towards the maintenance of species integrity through environmental selection. Congruency between geographic and genomic clines suggests that loci with narrow clines are under strong selection, favoring either one parental species (directional selection) or their hybrids (overdominance) as a result of strong associations with climatic variables such as precipitation as snow and mean annual temperature. Cline movement due to past demographic events (evidenced by allelic richness and heterozygosity shifts from the average cline center) may explain the asymmetry in introgression and predominance of P. engelmannii found in this study. These results provide insights into the genetic architecture and fine-scale patterns of admixture, and identify loci that may be involved in reproductive barriers between the species.