Population genetic structure of the cyclic snowshoe hare (Lepus americanus) in southwestern Yukon,Canada

Spatial population structure has important ecological and evolutionary consequences. Little is known about the population structure of snowshoe hares (Lepus americanus), despite their ecological importance in North American boreal forests. We used seven variable microsatellite DNA loci to determine the spatial genetic structure of snowshoe hares near Kluane Lake, Yukon during a cyclic population peak. We sampled 317 hares at 12 sites separated by distances ranging from 3 to 140 km, and used 46 additional samples from Alaska and Montana. The level of genetic variation was high (13.4 alleles/locus, 0.67 expected heterozygosity) and the distribution of alleles and genotypes was not homogeneous across the sites. The degree of differentiation was low among Yukon sites (FST = 0.015) and between Yukon and Alaska (FST = 0.012), but the Montana site was highly differentiated (FST = 0.20). A weak pattern of isolation by distance was found over the Yukon study area, with an indication that local genetic drift may be important in shaping the regional genetic structure. Landscape barriers expected to influence gene flow did not consistently affect genetic structure, although there was evidence for a partial barrier effect of Kluane Lake. The high level of inferred gene flow confirms that snowshoe hare dispersal is widespread, successful and equal between the sexes. A stepping-stone model of gene flow, potentially influenced by the synchronous density cycle, appears to best explain the observed genetic structure. Our results suggest that despite their dramatic fluctuations in density, snowshoe hares in the northern boreal forest have a large evolutionary effective population size and are not strongly subdivided by either physical or social barriers to gene flow.     

Contrasting patterns of mitochondrial and microsatellite population structure in fragmented populations of greater prairie-chickens

Greater prairie-chickens (Tympanuchus cupido pinnatus) were once found throughout the tallgrass prairie of midwestern North America but over the last century these prairies have been lost or fragmented by human land use. As a consequence, many current populations of prairie-chickens have become isolated and small. This fragmentation of populations is expected to lead to reductions in genetic variation as a result of random genetic drift and a decrease in gene flow. As expected, we found that genetic variation at both microsatellite DNA and mitochondrial DNA (mtDNA) markers was reduced in smaller populations, particularly in Wisconsin. There was relatively little range-wide geographical structure (FST) when we examined mtDNA haplotypes but there was a significant positive relationship between genetic (FST) and geographical distance (isolation by distance). In contrast, microsatellite DNA loci revealed significant geographical structure (FST) and a weak effect of isolation by distance throughout the range. These patterns were much stronger when populations with reduced levels of genetic variability (Wisconsin) were removed from the analyses. This suggests that the effects of genetic drift were stronger than gene flow at microsatellite loci, whereas these forces were in range-wide equilibrium at mtDNA markers. These differences between the two molecular markers may be explained by a larger effective population size (Ne) for mtDNA, which is expected in species such as prairie-chickens that have female-biased dispersal and high levels of polygyny. Our results suggest that historic populations of prairie-chickens were once interconnected by gene flow but current populations are now isolated. Thus, maintaining gene flow may be important for the long-term persistence of prairie-chicken populations.     

Habitat‐linked genetic structure for white‐crowned sparrow (Zonotrichia leucophrys): Local factors shape population genetic structure

Ecological, environmental, and geographic factors all influence genetic structure. Species with broad distributions are ideal systems because they cover a range of ecological and environmental conditions allowing us to test which components predict genetic structure. This study presents a novel, broad geographic approach using molecular markers, morphology, and habitat modeling to investigate rangewide and local barriers causing contemporary genetic differentiation within the geographical range of three white‐crowned sparrow (Zonotrichia leucophrys) subspecies: Z. l. gambelii, Z. l. oriantha, and Z. l. pugetensis. Three types of genetic markers showed geographic distance between sampling sites, elevation, and ecosystem type are key factors contributing to population genetic structure. Microsatellite markers revealed white‐crowned sparrows do not group by subspecies, but instead indicated four groupings at a rangewide scale and two groupings based on coniferous and deciduous ecosystems at a local scale. Our analyses of morphological variation also revealed habitat differences; sparrows from deciduous ecosystems are larger than individuals from coniferous ecosystems based on principal component analyses. Habitat modeling showed isolation by distance was prevalent in describing genetic structure, but isolation by resistance also had a small but significant influence. Not only do these findings have implications concerning the accuracy of subspecies delineations, they also highlight the critical role of local factors such as habitat in shaping contemporary population genetic structure of species with high dispersal ability.     

Landscape structure and the genetic effects of a population collapse

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

Marine landscapes and population genetic structure of herring (Clupea harengus L.) in the Baltic Sea

Numerically small but statistically significant genetic differentiation has been found in many marine fish species despite very large census population sizes and absence of obvious barriers to migrating individuals. Analyses of morphological traits have previously identified local spawning groups of herring (Clupea harengus L.) in the environmentally heterogeneous Baltic Sea, whereas allozyme markers have not revealed differentiation. We analysed variation at nine microsatellite loci in 24 samples of spring-spawning herring collected at 11 spawning locations throughout the Baltic Sea. Significant temporal differentiation was observed at two locations, which we ascribe to sympatrically spawning but genetically divergent 'spawning waves'. Significant differentiation was also present on a geographical scale, though pairwise F(ST) values were generally low, not exceeding 0.027. Partial Mantel tests showed no isolation by geographical distance, but significant associations were observed between genetic differentiation and environmental parameters (salinity and surface temperature) (0.001 < P < or = 0.099), though these outcomes were driven mainly by populations in the southwestern Baltic Sea, which also exhibits the steepest environmental gradients. Application of a novel method for detecting barriers to gene flow by combining geographical coordinates and genetic differentiation allowed us to identify two zones of lowered gene flow. These zones were concordant with the separation of the Baltic Sea into major basins, with environmental gradients and with differences in migration behaviour. We suggest that similar use of landscape genetics approaches may increase the understanding of the biological significance of genetic differentiation in other marine fishes.     

Hierarchical population structure and genetic diversity of lake trout (Salvelinus namaycush) in a dendritic system in Northern Labrador

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Population genetic structure, gene flow and sex-biased dispersal in frillneck lizards (Chlamydosaurus kingii)

By using both mitochondrial and nuclear multiloci markers, we explored population genetic structure, gene flow and sex-specific dispersal of frillneck lizards ( Chlamydosaurus kingii ) sampled at three locations, separated by 10 to 50 km, in a homogenous savannah woodland in tropical Australia. Apart from a recombinant lizard, the mitochondrial analyses revealed two nonoverlapping haplotypes/populations, while the nuclear markers showed that the frillneck lizards represented three separate clusters/populations. Due to the small population size of the mtDNA, fixation may occur via founder effects and/or drift. We therefore suggest that either of these two processes, or a combination of the two, are the most likely causes of the discordant results obtained from the mitochondrial and the nuclear markers. In contrast to the nonoverlapping mitochondrial haplotypes, in 12 out of 74 lizards, mixed nuclear genotypes were observed, hence revealing a limited nuclear gene flow. Although gene flow should ultimately result in a blending of the populations, we propose that the distinct nuclear population structure is maintained by frequent fires resulting in local bottlenecks, and concomitant spatial separation of the frillneck lizard populations. Limited mark–recapture data and the difference in distribution of the mitochondrial and nuclear markers suggest that the mixed nuclear genotypes were caused by juvenile male-biased dispersal.     

Genetic and ecological data provide incongruent interpretations of population structure and dispersal in naturally subdivided populations of white-tailed ptarmigan (Lagopus leucura)

The dispersal of individuals among populations affects the demographic and adaptive trajectories of animal populations and is fundamental to understanding population dynamics. White-tailed ptarmigan (Lagopus leucura) are a high elevation grouse species that live year-round in patchily distributed alpine areas in western North America. We investigated the patterns of dispersal and identified barriers to gene flow for a threatened subspecies (L. l. saxatilis) endemic to Vancouver Island, Canada. Connectivity among seven sites was examined using nine microsatellite loci (n = 133 individuals, H(O) = 0.62, mean number of alleles = 10) and direct movement observations using radio-telemetry (n = 118 individuals). Average movement distances of individuals measured by radio-telemetry were 0.63-3.23 km and considerably less than the shortest distance between sampling sites (18 km). Furthermore, despite extensive radio-telemetry data, movement was never observed between any of the seven sampling sites. In contrast, genetic results (STRUCTURE, TESS) showed connectivity among most of the seven sampling sites and suggested that genetic variation is best explained by two clusters of individuals which separated the South sampling site from all other areas of Vancouver Island. Analysis of molecular data also showed a generally consistent pattern of isolation by distance (Mantel test r = 0.11, P < 0.01) with large areas of unsuitable low elevation habitat possibly acting as barriers to gene flow. Despite the naturally subdivided distribution of populations, white-tailed ptarmigan do not fit well into any common definition of a metapopulation. We conclude the incongruities between the genetic and radio-telemetry data are best explained by episodic dispersal patterns. In this study, we demonstrated the importance of combining genetic and ecological data in understanding patterns of dispersal and population structure.     

Genetic diversity and genetic structure of populations of Ranunculus japonicus Thunb. (Ranunculaceae)

Abstract In order to clarify the genetic diversity and population structure of Ranunculus japonicus , allozymic analysis was conducted on 60 populations in southwestern Japan. Considerable genetic variati ons were detected among the populations of R. japonicus . The genetic diversities within species ( H _es = 0.215) and within populations ( H _ep = 0.172) were slightly higher than those of other perennial herbs with widespread distribution and outcrossing plants. Significantly higher values of fixation index were detected in some populations, which might have arisen from restricted mating partners. The majority of genetic variation (approx. 80%) resided within a population and a moderate level of genetic differentiation ( G _ST = 0.203) was observed among populations. The F _ST value (0.203) suggests the existence of a substantial population structure in this species. The highly significant correlation between geographic distance and F _ST values indicates that isolation by distance has played an important role in the construction of the genetic structure of this species.     

Different landscape effects on the genetic structure of two broadly distributed woody legumes,Acacia salicina and A. stenophylla (Fabaceae)

Restoring degraded landscapes has primarily focused on re‐establishing native plant communities. However, little is known with respect to the diversity and distribution of most key revegetation species or the environmental and anthropogenic factors that may affect their demography and genetic structure. In this study, we investigated the genetic structure of two widespread Australian legume species (Acacia salicina and Acacia stenophylla) in the Murray–Darling Basin (MDB), a large agriculturally utilized region in Australia, and assessed the impact of landscape structure on genetic differentiation. We used AFLP genetic data and sampled a total of 28 A. salicina and 30 A. stenophylla sampling locations across southeastern Australia. We specifically evaluated the importance of four landscape features: forest cover, land cover, water stream cover, and elevation. We found that both species had high genetic diversity (mean percentage of polymorphic loci, 55.1% for A. salicina versus. 64.3% for A. stenophylla) and differentiation among local sampling locations (A. salicina: Φ_PT = 0.301, 30%; A. stenophylla: Φ_PT = 0.235, 23%). Population structure analysis showed that both species had high levels of structure (6 clusters each) and admixture in some sampling locations, particularly A. stenophylla. Although both species have a similar geographic range, the drivers of genetic connectivity for each species were very different. Genetic variation in A. salicina seems to be mainly driven by geographic distance, while for A. stenophylla, land cover appears to be the most important factor. This suggests that for the latter species, gene flow among populations is affected by habitat fragmentation. We conclude that these largely co‐occurring species require different management actions to maintain population connectivity. We recommend active management of A. stenophylla in the MDB to improve gene flow in the adversity of increasing disturbances (e.g., droughts) driven by climate change and anthropogenic factors.     

Recent physical connections may explain weak genetic structure in western Alaskan chum salmon (Oncorhynchus keta) populations

Low genetic divergence at neutral loci among populations is often the result of high levels of contemporary gene flow. Western Alaskan summer‐run chum salmon (Oncorhynchus keta) populations demonstrate weak genetic structure, but invoking contemporary gene flow as the basis for the low divergence is problematic because salmon home to their natal streams and some of the populations are thousands of kilometers apart. We used genotypes from microsatellite and single nucleotide polymorphism loci to investigate alternative explanations for the current genetic structure of chum salmon populations from western Alaska. We also estimated current levels of gene flow among Kuskokwim River populations. Our results suggest that weak genetic structure is best explained by physical connections that occurred after the Holocene Thermal Maximum among the Yukon, Kuskokwim, and Nushagak drainages that allowed gene flow to occur among now distant populations.     

景观遗传学原理及其在生境片断化遗传效应研究中的应用

景观遗传学是近年来在景观生态学和种群遗传学之间形成的一个交叉领域,强调景观的组成、空间构型和环境梯度对基因流、种群遗传空间结构和局域种群适应的影响。景观遗传学尚未成为一门独立的学科,其理论基础主要来自分子遗传学、种群生物学和景观生态学。现代分子遗传标记技术、遥感和GIS支持下的景观分析和空间统计方法的综合运用是景观遗传学主要研究途径。系统介绍了景观遗传学的基础概念,关键科学问题,基本理论框架,及其与相邻研究领域的关系,综述了景观遗传学最为关注的现实课题——景观碎裂化的种群遗传效应的研究进展,主要涉及生境片断化的遗传效应、不同属性的物种响应、以及生境片断化过程的选择作用等方面。通过采取一种跨尺度的视角,景观遗传学研究显著深化了关于景观碎裂化对生物多样性影响的理解。     

Landscape effects on extremely fragmented populations of a rare solitary bee, Colletes floralis

Globally, there is concern over the decline of bees, an ecologically important group of pollinating insects. Genetic studies provide insights into population structure that are crucial for conservation management but that would be impossible to obtain by conventional ecological methods. Yet conservation genetic studies of bees have primarily focussed on social species rather than the more species‐rich solitary bees. Here, we investigate the population structure of Colletes floralis, a rare and threatened solitary mining bee, in Ireland and Scotland using nine microsatellite loci. Genetic diversity was surprisingly as high in Scottish (Hebridean island) populations at the extreme northwestern edge of the species range as in mainland Irish populations further south. Extremely high genetic differentiation among populations was detected; multilocus F_ST was up to 0.53, and and D_est were even higher (maximum: 0.85 and 1.00, respectively). A pattern of isolation by distance was evident for sites separated by land. Water appears to act as a substantial barrier to gene flow yet sites separated by sea did not exhibit isolation by distance. C. floralis populations are extremely isolated and probably not in regional migration‐drift equilibrium. GIS‐based landscape genetic analysis reveals urban areas as a potential and substantial barrier to gene flow. Our results highlight the need for urgent site‐specific management action to halt the decline of this and potentially other rare solitary bees.     

Nonequilibrium conditions following landscape rearrangement: the relative contribution of past and current hydrological landscapes on the genetic structure of a stream-dwelling fish

Interpreting patterns of population structure in nature is often challenging, especially in dynamic landscapes where population genetic connectivity evolves over time. In this study, we document the absence of migration-drift equilibrium in a stream-dwelling euryhaline fish resulting from past fine-scale drainage rearrangements and evaluate the relative contribution of past and current hydrological landscapes on observed population structure. Based on allelic variation at nine microsatellite loci, genetic relationships among 12 populations of brook charr, Salvelinus fontinalis, from Gros Morne National Park of Canada (GMNP, Newfoundland, Canada) did not reflect current stream hierarchical structure. In addition, we observed no correlation between population differentiation and contemporary landscape features (waterway distance and sums of altitudinal differences). Instead, population relationships were consistent with historical hydrological structure predicted a priori based on geomorphological and biogeographical evidences. Also, population differentiation was strongly correlated with inferred historical landscape features. Contemporary barriers have apparently preserved the signature of past genetic connectivity by constraining gene flow. Based on the relationships between population differentiation and current and past landscape features at various spatial scales, we suggest that brook charr genetic diversity in GMNP is mostly the result of small distance migrations at the time of colonization and subsequent differentiation through drift. This study highlights the potential of approaching landscapes from a combination of contemporary and historical perspectives when interpreting nonequilibrium population structures resulting from landscape rearrangement.     

Genetic structure of the cyclic fossorial water vole (Arvicola terrestris): landscape and demographic influences

Genetic structure can be strongly affected by landscape features and variation through time and space of demographic parameters such as population size and migration rate. The fossorial water vole (Arvicola terrestris) is a cyclic species characterized by large demographic fluctuations over short periods of time. The outbreaks do not occur everywhere at the same time but spread as a wave at a regional scale. This leads to a pattern of large areas (i.e. some hundreds of km2), each with different vole abundances, at any given time. Here, we describe the abundance and genetic structures in populations of the fossorial water vole. We use the data to try to understand how landscape and demographic features act to shape the genetic structure. The spatial variability of vole abundance was assessed from surface indices, collected in spring 2002 (April) in eastern central France. Genetic variability was analysed using eight microsatellite loci at 23 localities sampled between October 2001 and April 2002. We found some congruence between abundance and genetic structures. At a regional scale, the genetic disruptions were associated with both sharp relief and transition between an area of low abundance and another of high abundance. At a local scale, we observed a variation of the isolation-by-distance pattern according to the abundance level of vole populations. From these results we suggest that the dispersal pattern in cyclic rodent populations varies throughout the demographic cycle.     

Landscape models for nuclear genetic diversity and genetic structure in white-footed mice (Peromyscus leucopus)

Dramatic changes in the North American landscape over the last 12 000 years have shaped the genomes of the small mammals, such as the white-footed mouse (Peromyscus leucopus), which currently inhabit the region. However, very recent interactions of populations with each other and the environment are expected to leave the most pronounced signature on rapidly evolving nuclear microsatellite loci. We analyzed landscape characteristics and microsatellite markers of P. leucopus populations along a transect from southern Ohio to northern Michigan, in order to evaluate hypotheses about the spatial distribution of genetic heterogeneity. Genetic diversity increased to the north and was best approximated by a single-variable model based on habitat availability within a 0.5-km radius of trapping sites. Interpopulation differentiation measured by clustering analysis was highly variable and not significantly related to latitude or habitat availability. Interpopulation differentiation measured as F_ST values and chord distance was correlated with the proportion of habitat intervening, but was best explained by agricultural distance and by latitude. The observed gradients in diversity and interpopulation differentiation were consistent with recent habitat availability being the major constraint on effective population size in this system, and contradicted the predictions of both the postglacial expansion and core-periphery hypotheses.     

Dispersal and genetic structure in the American marten, Martes americana

Natal dispersal in a vagile carnivore, the American marten (Martes americana), was studied by comparing radio-tracking data and microsatellite genetic structure in two populations occupying contrasting habitats. The genetic differentiation determined among groups of individuals using F(ST) indices appeared to be weak in both landscapes, and showed no increase with geographical distance. Genetic structure investigated using pairwise genetic distances between individuals conversely showed a pattern of isolation by distance (IBD), but only in the population occurring in a homogeneous high-quality habitat, therefore showing the advantage of individual-based analyses in detecting within-population processes and local landscape effects. The telemetry study of juveniles revealed a leptokurtic distribution of dispersal distances in both populations, and estimates of the mean squared parent-offspring axial distance (sigma2) inferred both from the genetic pattern of IBD and from the radio-tracking survey showed that most juveniles make little contribution to gene flow.     

A comparison of four methods for detecting weak genetic structure from marker data

Genetic structure is ubiquitous in wild populations and is the result of the processes of natural selection, genetic drift, mutation, and gene flow. Genetic drift and divergent selection promotes the generation of genetic structure, while gene flow homogenizes the subpopulations. The ability to detect genetic structure from marker data diminishes rapidly with a decreasing level of differentiation among subpopulations. Weak genetic structure may be unimportant over evolutionary time scales but could have important implications in ecology and conservation biology. In this paper we examine methods for detecting and quantifying weak genetic structures using simulated data. We simulated populations consisting of two putative subpopulations evolving for up to 50 generations with varying degrees of gene flow (migration), and varying amounts of information (allelic diversity). There are a number of techniques available to detect and quantify genetic structure but here we concentrate on four methods: F(ST), population assignment, relatedness, and sibship assignment. Under the simple mating system simulated here, the four methods produce qualitatively similar results. However, the assignment method performed relatively poorly when genetic structure was weak and we therefore caution against using this method when the analytical aim is to detect fine-scale patterns. Further work should examine situations with different mating systems, for example where a few individuals dominate reproductive output of the population. This study will help workers to design their experiments (e.g., sample sizes of markers and individuals), and to decide which methods are likely to be most appropriate for their particular data.     

Microgeographic genetic structure and gene flow in Hibiscus moscheutos (Malvaceae) populations

Microgeographic genetic variation in populations of a wetland macrophyte, Hibiscus moscheutos L. (Malvaceae), was investigated using allozyme polymorphism. The species is a self-compatible insect-pollinated perennial, and seeds are water dispersed (hydrochory). Six hundred plants were analyzed from eight brackish and two freshwater populations within the Rhode River watershed/estuarine system. The genetic structure of the populations was assessed by fixation indices and spatial autocorrelation analyses. The degree of genetic differentiation among sites and gene flow between all paired combinations of sites (M ) was analyzed using three hypothetical gene flow models. Fixation indices indicated almost complete panmixia within populations, and spatial autocorrelations showed that genotypes were randomly distributed within sites, most likely the result of water dispersal of seeds. Allele frequencies were significantly different among sites, and estimated FST indicated moderate genetic differentiation (_ = 0.062). Genetic differences between populations were mostly explained by a gene flow model that accounted for the location of populations relative to the tidal stream. The importance of hydrochory in affecting spatial genetic structure was thus suggested both within and among H. moscheutos populations.     

Landscape genetics and hierarchical genetic structure in Atlantic salmon: the interaction of gene flow and local adaptation

Disentangling evolutionary forces that may interact to determine the patterns of genetic differentiation within and among wild populations is a major challenge in evolutionary biology. The objective of this study was to assess the genetic structure and the potential influence of several ecological variables on the extent of genetic differentiation at multiple spatial scales in a widely distributed species, the Atlantic salmon, Salmo salar . A total of 2775 anadromous fish were sampled from 51 rivers along the North American Atlantic coast and were genotyped using 13 microsatellites. A Bayesian analysis clustered these populations into seven genetically and geographically distinct groups, characterized by different environmental and ecological factors, mainly temperature. These groups were also characterized by different extent of genetic differentiation among populations. Dispersal was relatively high and of the same magnitude within compared to among regional groups, which contrasted with the maintenance of a regional genetic structure. However, genetic differentiation was lower among populations exchanging similar rates of local as opposed to inter-regional migrants, over the same geographical scale. This raised the hypothesis that gene flow could be constrained by local adaptation at the regional scale. Both coastal distance and temperature regime were found to influence the observed genetic structure according to landscape genetic analyses. The influence of other factors such as latitude, river length and altitude, migration tactic, and stocking was not significant at any spatial scale. Overall, these results suggested that the interaction between gene flow and thermal regime adaptation mainly explained the hierarchical genetic structure observed among Atlantic salmon populations.