Infer Population Genetic Structure Research Articles

Genetic analysis of harvest samples reveals population structure in a highly mobile generalist carnivore.

Delineating wildlife population boundaries is important for effective population monitoring and management. The bobcat (Lynx rufus) is a highly mobile generalist carnivore that is ecologically and economically important. We sampled 1225 bobcats harvested in South Dakota, USA (2014-2019), of which 878 were retained to assess genetic diversity and infer population genetic structure using 17 microsatellite loci. We assigned individuals to genetic clusters (K) using spatial and nonspatial Bayesian clustering algorithms and quantified differentiation (F ST and ) among clusters. We found support for population genetic structure at K = 2 and K = 4, with pairwise F ST and values indicating weak to moderate differentiation, respectively, among clusters. For K = 2, eastern and western clusters aligned closely with historical bobcat management units and were consistent with a longitudinal suture zone for bobcats previously identified in the Great Plains. We did not observe patterns of population genetic structure aligning with major rivers or highways. Genetic divergence observed at K = 4 aligned roughly with ecoregion breaks and may be associated with environmental gradients, but additional sampling with more precise locational data may be necessary to validate these patterns. Our findings reveal that cryptic population structure may occur in highly mobile and broadly distributed generalist carnivores, highlighting the importance of considering population structure when establishing population monitoring programs or harvest regulations. Our study further demonstrates that for elusive furbearers, harvest can provide an efficient, broad-scale sampling approach for genetic population assessments.

Balancing selection shapes population differentiation of major histocompatibility complex genes in wild golden snub-nosed monkeys

Abstract Small and isolated populations face several intrinsic risks, such as genetic drift, inbreeding depression, and reduced gene flow. Thus, patterns of genetic diversity and differentiation have become an important focus of conservation genetics research. The golden snub-nosed monkey Rhinopithecus roxellana, an endangered species endemic to China, has experienced rapid reduction in population size and severe population fragmentation over the past few decades. We measured the patterns of genetic diversity and population differentiation using both neutral microsatellites and adaptive major histocompatibility complex (MHC) genes in 2 R. roxellana populations (DPY and GNG) distributed on the northern and southern slopes of the Qinling Mountains, respectively. Eight MHC-linked haplotypes formed by 5 DQA1 alleles, 5 DQB1 alleles, 5 DRB1 alleles, and 4 DRB2 alleles were detected in the 2 populations. The larger GNG population showed higher genetic variation for both MHC and microsatellites than the smaller DPY population, suggesting an effect of genetic drift on genetic variation. Genetic differentiation index (FST) outlier analyses, principal coordinate analysis (PCoA), and inferred population genetic structure showed lower genetic differentiation in the MHC variations than microsatellites, suggesting that pathogen-mediated balancing selection, rather than local adaptation, homogenized the MHC genes of both populations. This study indicates that both balancing selection and genetic drift may shape genetic variation and differentiation in small and fragmented populations.

The role of oceanic currents in the dispersal and connectivity of the mangrove Rhizophora mangle on the Southwest Atlantic region.

Dispersal is a crucial mechanism to living beings, allowing them to reach new resources such that populations and species can occupy new environments. However, directly observing the dispersal mechanisms of widespread species can be costly or even impractical, which is the case for mangrove trees. The influence of ocean currents on mangrove dispersal is increasingly evident; however, few studies mechanistically relate the patterns of population distribution with the dispersal by oceanic currents under an integrated framework. Here, we evaluate the role of oceanic currents on connectivity of Rhizophora mangle along the Southwest Atlantic. We inferred population genetic structure and migration rates, simulated the displacement of propagules and tested our hypotheses with Mantel tests and redundancy analysis. We observed populations structured in two major groups, north and south, which is corroborated by other studies with Rhizophora and other coastal plants. Inferred recent migration rates do not indicate ongoing gene flow between sites. Conversely, long-term migration rates were low across groups and contrasting dispersal patterns within each one, which is consistent with long-distance dispersal events. Our hypothesis tests suggest that both isolation by distance and isolation by oceanography (derived from the oceanic currents) can explain the neutral genetic variation of R. mangle in the region. Our findings expand current knowledge of mangrove connectivity and highlight how the association of molecular methods with oceanographic simulations improve the interpretation of the dispersal process. This integrative approach is a cost- and time-efficient strategy to include dispersal and connectivity data into marine protected areas planning and management.

The genomic and epigenetic footprint of local adaptation to variable climates in kiwifruit.

A full understanding of adaptive genetic variation at the genomic level will help address questions of how organisms adapt to diverse climates. Actinidia eriantha is a shade-tolerant species, widely distributed in the southern tropical region of China, occurring in spatially heterogeneous environments. In the present study we combined population genomic, epigenomic, and environmental association analyses to infer population genetic structure and positive selection across a climatic gradient, and to assess genomic offset to climatic change for A. eriantha. The population structure is strongly shaped by geography and influenced by restricted gene flow resulting from isolation by distance due to habitat fragmentation. In total, we identified 102 outlier loci and annotated 455 candidate genes associated with the genomic basis of climate adaptation, which were enriched in functional categories related to development processes and stress response; both temperature and precipitation are important factors driving adaptive variation. In addition to single-nucleotide polymorphisms (SNPs), a total of 27 single-methylation variants (SMVs) had significant correlation with at least one of four climatic variables and 16 SMVs were located in or adjacent to genes, several of which were predicted to be involved in plant response to abiotic or biotic stress. Gradient forest analysis indicated that the central/east populations were predicted to be at higher risk of future population maladaptation under climate change. Our results demonstrate that local climate factors impose strong selection pressures and lead to local adaptation. Such information adds to our understanding of adaptive mechanisms to variable climates revealed by both population genome and epigenome analysis.

Comparative phylogeography of a restricted and a widespread heather: genetic evidence of multiple independent introductions ofErica mackayanainto Ireland from northern Spain

AbstractSpecies of flora and fauna occurring in the west of Ireland and south-west Europe, known as Lusitanian elements, constitute a puzzling case of isolated populations of uncertain origin. Here we studied the population genetic structure of the heather Erica mackayana in Ireland and northern Spain and compared it with its widespread close relative Erica tetralix using single nucleotide polymorphisms (SNPs). We reconstructed phylogenetic relationships using maximum likelihood (ML), inferred population genetic structure using cluster assignment and principal component analysis, and estimated population genetic diversity. The cluster analysis and ML phylogenetic tree showed a geographical pattern for E. tetralix supporting a post-glacial migration from Iberia to Ireland. In contrast, Irish populations of E. mackayana were supported in independent clades in the phylogenetic tree and shared clusters with Iberian populations in the structure analysis, and FST values were lower among Irish and Spanish populations than among Irish ones. This suggests that Irish populations of E. mackayana are the result of recent multiple independent introductions from its native area in northern Spain, probably assisted by humans. However, the origin of the largest Irish population at Roundstone Bog is unclear and should be further investigated. Post-glacial, long-distance dispersal is the most plausible explanation for Lusitanian species distribution in Ireland.

Population genomic structure in Goodman's mouse lemur reveals long-standing separation of Madagascar's Central Highlands and eastern rainforests.

Madagascar's Central Highlands are largely composed of grasslands, interspersed with patches of forest. The historical perspective was that Madagascar's grasslands had anthropogenic origins, but emerging evidence suggests that grasslands were a component of the pre-human Central Highlands vegetation. Consequently, there is now vigorous debate regarding the extent to which these grasslands have expanded due to anthropogenic pressures. Here, we shed light on the temporal dynamics of Madagascar's vegetative composition by conducting a population genomic investigation of Goodman's mouse lemur (Microcebus lehilahytsara; Cheirogaleidae). These small-bodied primates occur both in Madagascar's eastern rainforests and in the Central Highlands, making them a valuable indicator species. Population divergences among forest-dwelling mammals will reflect changes to their habitat, including fragmentation, whereas patterns of post-divergence gene flow can reveal formerly wooded migration corridors. To explore these patterns, we used RADseq data to infer population genetic structure, demographic models of post-divergence gene flow, and population size change through time. The results offer evidence that open habitats are an ancient component of the Central Highlands, and that widespread forest fragmentation occurred naturally during a period of decreased precipitation near the last glacial maximum. Models of gene flow suggest that migration across the Central Highlands has been possible from the Pleistocene through the recent Holocene via riparian corridors. Though our findings support the hypothesis that Central Highland grasslands predate human arrival, we also find evidence for human-mediated population declines. This highlights the extent to which species imminently threatened by human-mediated deforestation may already be vulnerable from paleoclimatic conditions.

Population Structure and Diversity in European Honey Bees (Apismellifera L.)-An Empirical Comparison of Pool and Individual Whole-Genome Sequencing.

Background: Whole-genome sequencing has become routine for population genetic studies. Sequencing of individuals provides maximal data but is rather expensive and fewer samples can be studied. In contrast, sequencing a pool of samples (pool-seq) can provide sufficient data, while presenting less of an economic challenge. Few studies have compared the two approaches to infer population genetic structure and diversity in real datasets. Here, we apply individual sequencing (ind-seq) and pool-seq to the study of Western honey bees (Apis mellifera). Methods: We collected honey bee workers that belonged to 14 populations, including 13 subspecies, totaling 1347 colonies, who were individually (139 individuals) and pool-sequenced (14 pools). We compared allele frequencies, genetic diversity estimates, and population structure as inferred by the two approaches. Results: Pool-seq and ind-seq revealed near identical population structure and genetic diversities, albeit at different costs. While pool-seq provides genome-wide polymorphism data at considerably lower costs, ind-seq can provide additional information, including the identification of population substructures, hybridization, or individual outliers. Conclusions: If costs are not the limiting factor, we recommend using ind-seq, as population genetic structure can be inferred similarly well, with the advantage gained from individual genetic information. Not least, it also significantly reduces the effort required for the collection of numerous samples and their further processing in the laboratory.

Habitat association constrains population history in two sympatric ovenbirds along Amazonian floodplains

AbstractAimAmazonian floodplains include distinct types of seasonally flooded habitats, determined by the flooding regime and sedimentation dynamics. Some bird species prefer specific habitat types within the floodplains. To investigate whether distinct habitats are differentially affected by geologic and climatic history, we compare population history in a sympatric and closely related pair of ovenbird species with different habitat associations.LocationAmazonian floodplains.TaxaSynallaxis albigularis and Mazaria propinqua (Aves; Furnariidae).MethodsOccurrence records were obtained from museums and public databases. Genomic data included nuclear loci (UCE) and the mitogenome for 49 samples. SNPs from UCE data were used to infer population genetic structure and effective migration. Mitogenomes were used to build phylogenetic trees and chronograms. Both datasets were used to infer historical demographic changes and test demographic scenarios.ResultsS. albigularis includes geographically structured mtDNA clades with a crown age of 250 ka, whereas M. propinqua includes a single clade with a crown age of 38 ka. Effective migration is lower at the base of the Andes for S. albigularis and at the lower Negro River for M. propinqua. Population expansion is detected for both species during the Quaternary, but was steeper and more recent in M. propinqua.Main conclusionsThe differences in population histories relate to distinct habitat associations along Amazonian floodplains. Preference of M. propinqua for more ephemeral island habitats may favour local extinctions, leading to demographic change, low genetic variability, no population structure and smaller effective population size. In contrast, more resilient habitats along the floodplains inhabited by S. albigularis may sustain local populations, generating and maintaining local diversity. Our results suggest that climatic variations of the late Pleistocene and Holocene caused changes in distribution and connectivity of the different types of habitats along the Amazonian floodplains, affecting gene flow and population sizes of associated bird populations.

Major inconsistencies of inferred population genetic structure estimated in a large set of domestic horse breeds using microsatellites.

STRUCTURE remains the most applied software aimed at recovering the true, but unknown, population structure from microsatellite or other genetic markers. About 30% of structure‐based studies could not be reproduced (Molecular Ecology, 21, 2012, 4925). Here we use a large set of data from 2,323 horses from 93 domestic breeds plus the Przewalski horse, typed at 15 microsatellites, to evaluate how program settings impact the estimation of the optimal number of population clusters K opt that best describe the observed data. Domestic horses are suited as a test case as there is extensive background knowledge on the history of many breeds and extensive phylogenetic analyses. Different methods based on different genetic assumptions and statistical procedures (dapc, flock, PCoA, and structure with different run scenarios) all revealed general, broad‐scale breed relationships that largely reflect known breed histories but diverged how they characterized small‐scale patterns. structure failed to consistently identify K opt using the most widespread approach, the ΔK method, despite very large numbers of MCMC iterations (3,000,000) and replicates (100). The interpretation of breed structure over increasing numbers of K, without assuming a K opt, was consistent with known breed histories. The over‐reliance on K opt should be replaced by a qualitative description of clustering over increasing K, which is scientifically more honest and has the advantage of being much faster and less computer intensive as lower numbers of MCMC iterations and repetitions suffice for stable results. Very large data sets are highly challenging for cluster analyses, especially when populations with complex genetic histories are investigated.

Rapid and strong population genetic differentiation and genomic signatures of climatic adaptation in an invasive mealybug

AbstractAimA growing number of studies suggest that adaptation of invasive species plays key roles in their successful establishment in novel environments. However, adaptation of invasive species to climatic conditions remains poorly characterized. This study aimed to understand the population genetic structure produced by the cotton mealybug Phenacoccus solenopsis invasion and to identify preliminary signals of selection during its range expansion.LocationChina.MethodsWe examined genetic structure of 11 populations across China using SNPs, microsatellites and a segment of mitochondrial cox1 gene. ADMIXTURE, STRUCTURE and DAPC were used to infer population genetic structure; the dispersal routes were reconstructed by the DIYABC; SNPs potentially related to climate adaptation were identified by using four populations differentiation methods and three environmental association methods.ResultsStrong genetic differentiation was found among populations with FST values ranging from 0.097 to 0.640 based on SNPs. Populations located at the northern expansion edge exhibited the highest genetic differentiation and the lowest genetic diversity. Demographic analyses indicated that all populations were introduced from a single source population with small effective size and low recent gene flow. RDA analysis showed that climatic variables explained a higher proportion of genetic variance (43%) compared to population structure variables (15%). The top climatic variables associated with genetic differentiation were precipitation of the mean temperature of warmest quarter, mean temperature of driest quarter and isothermality. Genes related to climate candidate SNPs were mainly enriched to pathways of development, energy and xenobiotic metabolisms.Main conclusionsWe found that extremely rapid and strong population genetic differentiation among populations appears to have developed after introduction in the cotton mealybug. Our study points to rapid neutral evolution and suggests possible climatic adaptation despite low genetic diversity in this invasive species.

Cryptic genetic diversity, population structure, and gene flow in the Mojave rattlesnake (Crotalus scutulatus)

The Mojave rattlesnake (Crotalus scutulatus) inhabits deserts and arid grasslands of the western United States and Mexico. Despite considerable interest in its highly toxic venom and the recognition of two subspecies, no molecular studies have characterized range-wide genetic diversity and population structure or tested species limits within C. scutulatus. We used mitochondrial DNA and thousands of nuclear loci from double-digest restriction site associated DNA sequencing to infer population genetic structure throughout the range of C. scutulatus, and to evaluate divergence times and gene flow between populations. We find strong support for several divergent mitochondrial and nuclear clades of C. scutulatus, including splits coincident with two major phylogeographic barriers: the Continental Divide and the elevational increase associated with the Central Mexican Plateau. We apply Bayesian clustering, phylogenetic inference, and coalescent-based species delimitation to our nuclear genetic data to test hypotheses of population structure. We also performed demographic analyses to test hypotheses relating to population divergence and gene flow. Collectively, our results support the existence of four distinct lineages within C. scutulatus, and genetically defined populations do not correspond with currently recognized subspecies ranges. Finally, we use approximate Bayesian computation to test hypotheses of divergence among multiple rattlesnake species groups distributed across the Continental Divide, and find evidence for co-divergence at this boundary during the mid-Pleistocene.

StructureSelector: A web-based software to select and visualize the optimal number of clusters using multiple methods.

Inferences of population genetic structure are of great importance to the fields of ecology and evolutionary biology. The program structure has been widely used to infer population genetic structure. However, previous studies demonstrated that uneven sampling often leads to wrong inferences on hierarchical structure. The most widely used ΔK method tends to identify the uppermost hierarchy of population structure. Recently, four alternative statistics (medmedk, medmeak, maxmedk and maxmeak) were proposed, which appear to be more accurate than the previously used methods for both even and uneven sampling data. However, the lack of easy-to-use software limits the use of these appealing new estimators. Here, we developed a web-based user-friendly software structureselector to calculate the four appealing alternative statistics together with the commonly used Ln Pr(X|K) and ΔK statistics. structureselector accepts the result files of structure, admixture or faststructure as input files. It reports the "best" K for each estimator, and the results are available as HTML or tab separated tables. The program can also generate graphical representations for specific K, which can be easily downloaded from the server. The software is freely available at http://lmme.qdio.ac.cn/StructureSelector/.

CONE: Community Oriented Network Estimation Is a Versatile Framework for Inferring Population Structure in Large-Scale Sequencing Data.

Estimation of genetic population structure based on molecular markers is a common task in population genetics and ecology. We apply a generalized linear model with LASSO regularization to infer relationships between individuals and populations from molecular marker data. Specifically, we apply a neighborhood selection algorithm to infer population genetic structure and gene flow between populations. The resulting relationships are used to construct an individual-level population graph. Different network substructures known as communities are then dissociated from each other using a community detection algorithm. Inference of population structure using networks combines the good properties of: (i) network theory (broad collection of tools, including aesthetically pleasing visualization), (ii) principal component analysis (dimension reduction together with simple visual inspection), and (iii) model-based methods (e.g., ancestry coefficient estimates). We have named our process CONE (for community oriented network estimation). CONE has fewer restrictions than conventional assignment methods in that properties such as the number of subpopulations need not be fixed before the analysis and the sample may include close relatives or involve uneven sampling. Applying CONE on simulated data sets resulted in more accurate estimates of the true number of subpopulations than model-based methods, and provided comparable ancestry coefficient estimates. Inference of empirical data sets of teosinte single nucleotide polymorphism, bacterial disease outbreak, and the human genome diversity panel illustrate that population structures estimated with CONE are consistent with the earlier findings

Population Genetic Structure and Potential Incursion Pathways of the Bluetongue Virus Vector Culicoides brevitarsis (Diptera: Ceratopogonidae) in Australia.

Culicoides brevitarsis is a vector of the bluetongue virus (BTV), which infects sheep and cattle. It is an invasive species in Australia with an assumed Asian/South East Asian origin. Using one mitochondrial marker (i.e., part of the cytochrome oxidase subunit I gene) and six nuclear markers, we inferred population genetic structure and possible incursion pathways for Australian C. brevitarsis. Nine mitochondrial haplotypes, with low nucleotide sequence diversity (0.0–0.7%) among these, were identified in a sample of 70 individuals from seven sites. Both sets of markers revealed a homogeneous population structure, albeit with evidence of isolation by distance and two genetically distinct clusters distributed along a north-to-south cline. No evidence of a cryptic species complex was found. The geographical distribution of the mitochondrial haplotypes is consistent with at least two incursion pathways into Australia since the arrival of suitable livestock hosts. By contrast, 15 mitochondrial haplotypes, with up to four times greater nucleotide sequence diversity (0.0–2.9%) among these, were identified in a sample of 16 individuals of the endemic C. marksi (sampled from a site in South Australia and another in New South Wales). A phylogenetic tree inferred using the mitochondrial marker revealed that the Australian and Japanese samples of C. brevitarsis are as evolutionarily different from one another as some of the other Australian species (e.g., C. marksi, C. henryi, C. pallidothorax) are. The phylogenetic tree placed four of the species endemic to Australia (C. pallidothorax, C. bundyensis, C. marksi, C. henryi) in a clade, with a fifth such species (C. bunrooensis) sharing a common ancestor with that clade and a clade comprising two Japanese species (C. verbosus, C. kibunensis).

Analysis of Genetic Diversity and Population Structure for the Native Tree Viburnum rufidulum Occurring in Kentucky and Tennessee

Viburnum rufidulum is a deciduous tree native to North America that has four-season appeal, which provides commercial horticultural value. In addition, the plant has unique and attractive red pubescence on leaf buds and petioles, common to no other Viburnum species. As habitat undergoes development and subsequent fragmentation of native plant populations, it is important to have baseline genetic information for this species. Little is known about the genetic diversity within populations of V. rufidulum. In this study, seven microsatellite loci were used to measure genetic diversity, population structure, and gene flow of 235 V. rufidulum trees collected from 17 locations in Kentucky and Tennessee. The genotype data were used to infer population genetic structure using the program InStruct and to construct an unweighted pair group method with arithmetic mean dendrogram. A single population was indicated by the program InStruct and the dendrogram clustered the locations into two groups; however, little bootstrap support was evident. Observed and expected heterozygosity were 0.49 and 0.78, respectively. Low-to-moderate genetic differentiation (FST = 0.06) with evidence of gene flow (Nm = 4.82) was observed among 17 populations of V. rufidulum. A significant level of genetic diversity was evident among V. rufidulum populations with most of the genetic variations among individual trees (86.37%) rather than among populations (13.63%), and a Mantel test revealed significant correlation between genetic and geographical distance (r = 0.091, P = 0.001). The microsatellites developed herein provide an initial assessment or a baseline of genetic diversity for V. rufidulum in a limited area of the southeastern region of the United States. The markers are a genetic resource and can be of assistance in breeding programs, germplasm assessment, and future studies of V. rufidulum populations, as this is the first study to provide genetic diversity data for this native species.

Population Genetic Structure of the Cotton Bollworm Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) in India as Inferred from EPIC-PCR DNA Markers

Helicoverpa armigera is an important pest of cotton and other agricultural crops in the Old World. Its wide host range, high mobility and fecundity, and the ability to adapt and develop resistance against all common groups of insecticides used for its management have exacerbated its pest status. An understanding of the population genetic structure in H. armigera under Indian agricultural conditions will help ascertain gene flow patterns across different agricultural zones. This study inferred the population genetic structure of Indian H. armigera using five Exon-Primed Intron-Crossing (EPIC)-PCR markers. Nested alternative EPIC markers detected moderate null allele frequencies (4.3% to 9.4%) in loci used to infer population genetic structure but the apparently genome-wide heterozygote deficit suggests in-breeding or a Wahlund effect rather than a null allele effect. Population genetic analysis of the 26 populations suggested significant genetic differentiation within India but especially in cotton-feeding populations in the 2006–07 cropping season. In contrast, overall pair-wise F ST estimates from populations feeding on food crops indicated no significant population substructure irrespective of cropping seasons. A Baysian cluster analysis was used to assign the genetic make-up of individuals to likely membership of population clusters. Some evidence was found for four major clusters with individuals in two populations from cotton in one year (from two populations in northern India) showing especially high homogeneity. Taken as a whole, this study found evidence of population substructure at host crop, temporal and spatial levels in Indian H. armigera, without, however, a clear biological rationale for these structures being evident.

Phylogeography of a species complex of lowland Neotropical rain forest trees (Carapa, Meliaceae)

AbstractAim Many tropical tree species have poorly delimited taxonomic boundaries and contain undescribed or cryptic species. We examined the genetic structure of a species complex in the tree genus Carapa in the Neotropics in order to evaluate age, geographic patterns of diversity and evolutionary relationships, and to quantify levels of introgression among currently recognized species.Location Lowland moist forests in the Guiana Shield, the Central and Western Amazon Basin, Chocó and Central America.Methods Genetic structure was analysed using seven nuclear simple sequence repeats (nuSSR), five chloroplast SSRs (cpSSR), and two chloroplast DNA (cpDNA) intergenic sequences (trnH–psbA and trnC–ycf6). Bayesian clustering analysis of the SSR data was used to infer population genetic structure and to assign 324 samples to their most likely genetic cluster. Bayesian coalescence analyses were performed on the two cpDNA markers to estimate evolutionary relationships and divergence times.Results Two genetic clusters (nu_guianensis and nu_surinamensis) were detected, which correspond to the Neotropical species C. guianensis (sensu latu) and C. surinamensis. Fourteen cpDNA haplotypes clustered into six haplogroups distributed between the two nuclear genetic clusters. Divergence between the haplogroups was initiated in the Miocene, with some haplotype structure evolving as recently as the Pleistocene. The absence of complete lineage sorting between the nuclear and chloroplast genomes and the presence of hybrid individuals suggest that interspecific reproductive barriers are incomplete. NuSSR diversity was highest in C. guianensis and, within C. guianensis, cpDNA diversity was highest in the Central and Western Amazon Basin. Regional genetic differentiation was strong but did not conform to an isolation‐by‐distance process or exhibit a phylogeographical signal.Main conclusions The biogeographical history of Neotropical Carapa appears to have been influenced by events that took place during the Neogene. Our results point to an Amazonian centre of origin and diversification of Neotropical Carapa, with subsequent migration to the Pacific coast of South America and Central America. Gene flow apparently occurs among species, and introgression events are supported by inconsistencies between chloroplast and nuclear lineage sorting. The absence of phylogeographical structure may be a result of the ineffectiveness of geographical barriers among populations and of reproductive isolation mechanisms among incipient and cryptic species in this species complex.

Correcting principal component maps for effects of spatial autocorrelation in population genetic data.

In many species, spatial genetic variation displays patterns of “isolation-by-distance.” Characterized by locally correlated allele frequencies, these patterns are known to create periodic shapes in geographic maps of principal components which confound signatures of specific migration events and influence interpretations of principal component analyses (PCA). In this study, we introduced models combining probabilistic PCA and kriging models to infer population genetic structure from genetic data while correcting for effects generated by spatial autocorrelation. The corresponding algorithms are based on singular value decomposition and low rank approximation of the genotypic data. As their complexity is close to that of PCA, these algorithms scale with the dimensions of the data. To illustrate the utility of these new models, we simulated isolation-by-distance patterns and broad-scale geographic variation using spatial coalescent models. Our methods remove the horseshoe patterns usually observed in PC maps and simplify interpretations of spatial genetic variation. We demonstrate our approach by analyzing single nucleotide polymorphism data from the Human Genome Diversity Panel, and provide comparisons with other recently introduced methods.

Exploring Demographic, Physical, and Historical Explanations for the Genetic Structure of Two Lineages of Greater Antillean Bats

Observed patterns of genetic structure result from the interactions of demographic, physical, and historical influences on gene flow. The particular strength of various factors in governing gene flow, however, may differ between species in biologically relevant ways. We investigated the role of demographic factors (population size and sex-biased dispersal) and physical features (geographic distance, island size and climatological winds) on patterns of genetic structure and gene flow for two lineages of Greater Antillean bats. We used microsatellite genetic data to estimate demographic characteristics, infer population genetic structure, and estimate gene flow among island populations of Erophylla sezekorni/E. bombifrons and Macrotus waterhousii (Chiroptera: Phyllostomidae). Using a landscape genetics approach, we asked if geographic distance, island size, or climatological winds mediate historical gene flow in this system. Samples from 13 islands spanning Erophylla's range clustered into five genetically distinct populations. Samples of M. waterhousii from eight islands represented eight genetically distinct populations. While we found evidence that a majority of historical gene flow between genetic populations was asymmetric for both lineages, we were not able to entirely rule out incomplete lineage sorting in generating this pattern. We found no evidence of contemporary gene flow except between two genetic populations of Erophylla. Both lineages exhibited significant isolation by geographic distance. Patterns of genetic structure and gene flow, however, were not explained by differences in relative effective population sizes, island area, sex-biased dispersal (tested only for Erophylla), or surface-level climatological winds. Gene flow among islands appears to be highly restricted, particularly for M. waterhousii, and we suggest that this species deserves increased taxonomic attention and conservation concern.

A comparison of AFLPs and microsatellites to identify the population structure of brown trout (Salmo trutta L.) populations from Hardangervidda, Norway

A total of 495 fish from 11 Hardangervidda lakes were genotyped in order to compare amplified fragment length polymorphisms (AFLP) and microsatellites in terms of their capacity to infer population genetic structure. The 11 microsatellites used in this study gave a greater polymorphism information content and greater gene diversity, with an average of 14.8 alleles per locus, than the six AFLP primer combinations used. However, the AFLPs resulted in 178 polymorphic loci and a 3.1 times larger marker index (effective multiplex ratio multiplied with the gene diversity). Comparable population structuring, for example in terms of distinguishing fish from the different river systems, was obtained with both marker systems. An AFLP and microsatellite multilocus Bayesian assignment test with the structure program divided the fish into six groups largely concurrent with main branches on a population neighbour-joining tree. Yet, the admixture status of individuals is mostly contradictory in the AFLP and the microsatellite analyses. The results are discussed concerning migration between lake populations.