Ecotypes of an ecologically dominant prairie grass (Andropogon gerardii) exhibit genetic divergence across the U.S. Midwest grasslands' environmental gradient

Big bluestem (Andropogon gerardii) is an ecologically dominant grass with wide distribution across the environmental gradient of U.S. Midwest grasslands. This system offers an ideal natural laboratory to study population divergence and adaptation in spatially varying climates. Objectives were to: (i) characterize neutral genetic diversity and structure within and among three regional ecotypes derived from 11 prairies across the U.S. Midwest environmental gradient, (ii) distinguish between the relative roles of isolation by distance (IBD) vs. isolation by environment (IBE) on ecotype divergence, (iii) identify outlier loci under selection and (iv) assess the association between outlier loci and climate. Using two primer sets, we genotyped 378 plants at 384 polymorphic AFLP loci across regional ecotypes from central and eastern Kansas and Illinois. Neighbour‐joining tree and PCoA revealed strong genetic differentiation between Kansas and Illinois ecotypes, which was better explained by IBE than IBD. We found high genetic variability within prairies (80%) and even fragmented Illinois prairies, surprisingly, contained high within‐prairie genetic diversity (92%). Using Bayenv 2, 14 top‐ranked outlier loci among ecotypes were associated with temperature and precipitation variables. Six of seven BayeScan F_ST outliers were in common with Bayenv 2 outliers. High genetic diversity may enable big bluestem populations to better withstand changing climates; however, population divergence supports the use of local ecotypes in grassland restoration. Knowledge of genetic variation in this ecological dominant and other grassland species will be critical to understanding grassland response and restoration challenges in the face of a changing climate.     

Drivers of population genetic differentiation in the wild: isolation by dispersal limitation,isolation by adaptation and isolation by colonization

Empirical population genetic studies have been dominated by a neutralist view, according to which gene flow and drift are the main forces driving population genetic structure in nature. The neutralist view in essence describes a process of isolation by dispersal limitation (IBDL) that generally leads to a pattern of isolation by distance (IBD). Recently, however, conceptual frameworks have been put forward that view local genetic adaptation as an important driver of population genetic structure. Isolation by adaptation (IBA) and monopolization (M) posit that gene flow among natural populations is reduced as a consequence of local genetic adaptation. IBA stresses that effective gene flow is reduced among habitats that show dissimilar ecological characteristics, leading to a pattern of isolation by environment. In monopolization, local genetic adaptation of initial colonizing genotypes results in a reduction in gene flow that fosters the persistence of founder effects. Here, we relate these different processes driving landscape genetic structure to patterns of IBD and isolation by environment (IBE). We propose a method to detect whether IBDL, IBA and M shape genetic differentiation in natural landscapes by studying patterns of variation at neutral and non‐neutral markers as well as at ecologically relevant traits. Finally, we reinterpret a representative number of studies from the recent literature by associating patterns to processes and identify patterns associated with local genetic adaptation to be as common as IBDL in structuring regional genetic variation of populations in the wild. Our results point to the importance of quantifying environmental gradients and incorporating ecology in the analysis of population genetics.     

Genomic footprints of adaptation in a cooperatively breeding tropical bird across a vegetation gradient

Identifying the genetic basis of phenotypic variation and its relationship with the environment is key to understanding how local adaptations evolve. Such patterns are especially interesting among populations distributed across habitat gradients, where genetic structure can be driven by isolation by distance (IBD) and/or isolation by environment (IBE). Here, we used variation in ~1,600 high‐quality SNPs derived from paired‐end sequencing of double‐digest restriction site‐associated DNA (ddRAD‐Seq) to test hypotheses related to IBD and IBE in the Yucatan jay (Cyanocorax yucatanicus), a tropical bird endemic to the Yucatán Peninsula. This peninsula is characterized by a precipitation and vegetation gradient—from dry to evergreen tropical forests—that is associated with morphological variation in this species. We found a moderate level of nucleotide diversity (π = .008) and little evidence for genetic differentiation among vegetation types. Analyses of neutral and putatively adaptive SNPs (identified by complementary genome‐scan approaches) indicate that IBD is the most reliable explanation to account for frequency distribution of the former, while IBE has to be invoked to explain those of the later. These results suggest that selective factors acting along a vegetation gradient can promote local adaptation in the presence of gene flow in a vagile, nonmigratory and geographically restricted species. The putative candidate SNPs identified here are located within or linked to a variety of genes that represent ideal targets for future genomic surveys.     

Isolation by environment in White‐breasted Nuthatches (Sitta carolinensis) of the Madrean Archipelago sky islands: a landscape genomics approach

Understanding landscape processes driving patterns of population genetic differentiation and diversity has been a long‐standing focus of ecology and evolutionary biology. Gene flow may be reduced by historical, ecological or geographic factors, resulting in patterns of isolation by distance (IBD) or isolation by environment (IBE). Although IBE has been found in many natural systems, most studies investigating patterns of IBD and IBE in nature have used anonymous neutral genetic markers, precluding inference of selection mechanisms or identification of genes potentially under selection. Using landscape genomics, the simultaneous study of genomic and ecological landscapes, we investigated the processes driving population genetic patterns of White‐breasted Nuthatches (Sitta carolinensis) in sky islands (montane forest habitat islands) of the Madrean Archipelago. Using more than 4000 single nucleotide polymorphisms and multiple tests to investigate the relationship between genetic differentiation and geographic or ecological distance, we identified IBE, and a lack of IBD, among sky island populations of S. carolinensis. Using three tests to identify selection, we found 79 loci putatively under selection; of these, seven matched CDS regions in the Zebra Finch. The loci under selection were highly associated with climate extremes (maximum temperature of warmest month and minimum precipitation of driest month). These results provide evidence for IBE – disentangled from IBD – in sky island vertebrates and identify potential adaptive genetic variation.     

Partitioning the effects of isolation by distance,environment, and physical barriers on genomic divergence between parapatric threespine stickleback

Genetic divergence between populations is shaped by a combination of drift, migration, and selection, yielding patterns of isolation‐by‐distance (IBD) and isolation‐by‐environment (IBE). Unfortunately, IBD and IBE may be confounded when comparing divergence across habitat boundaries. For instance, parapatric lake and stream threespine stickleback (Gasterosteus aculeatus) may have diverged due to selection against migrants (IBE), or mere spatial separation (IBD). To quantitatively partition the strength of IBE and IBD, we used recently developed population genetic software (BEDASSLE) to analyze partial genomic data from three lake‐stream clines on Vancouver Island. We find support for IBD within each of three outlet streams (unlike prior studies of lake‐stream stickleback). In addition, we find evidence for IBE (controlling for geographic distance): the genetic effect of habitat is equivalent to geographic separation of ～1.9 km of IBD. Remarkably, of our three lake‐stream pairs, IBE is strongest where migration between habitats is easiest. Such microgeographic genetic divergence would require exceptionally strong divergent selection, which multiple experiments have failed to detect. Instead, we propose that nonrandom dispersal (e.g., habitat choice) contributes to IBE. Supporting this conclusion, we show that the few migrants between habitats are a nonrandom subset of the phenotype distribution of the source population.     

Genomics of the divergence continuum in an African plant biodiversity hotspot,I: drivers of population divergence in Restio capensis (Restionaceae)

Understanding the drivers of population divergence, speciation and species persistence is of great interest to molecular ecology, especially for species‐rich radiations inhabiting the world's biodiversity hotspots. The toolbox of population genomics holds great promise for addressing these key issues, especially if genomic data are analysed within a spatially and ecologically explicit context. We have studied the earliest stages of the divergence continuum in the Restionaceae, a species‐rich and ecologically important plant family of the Cape Floristic Region (CFR) of South Africa, using the widespread CFR endemic Restio capensis (L.) H.P. Linder & C.R. Hardy as an example. We studied diverging populations of this morphotaxon for plastid DNA sequences and >14 400 nuclear DNA polymorphisms from Restriction site Associated DNA (RAD) sequencing and analysed the results jointly with spatial, climatic and phytogeographic data, using a Bayesian generalized linear mixed modelling (GLMM) approach. The results indicate that population divergence across the extreme environmental mosaic of the CFR is mostly driven by isolation by environment (IBE) rather than isolation by distance (IBD) for both neutral and non‐neutral markers, consistent with genome hitchhiking or coupling effects during early stages of divergence. Mixed modelling of plastid DNA and single divergent outlier loci from a Bayesian genome scan confirmed the predominant role of climate and pointed to additional drivers of divergence, such as drift and ecological agents of selection captured by phytogeographic zones. Our study demonstrates the usefulness of population genomics for disentangling the effects of IBD and IBE along the divergence continuum often found in species radiations across heterogeneous ecological landscapes.     

GENETIC ISOLATION BY ENVIRONMENT OR DISTANCE: WHICH PATTERN OF GENE FLOW IS MOST COMMON?

Gene flow among populations can enhance local adaptation if it introduces new genetic variants available for selection, but strong gene flow can also stall adaptation by swamping locally beneficial genes. These outcomes can depend on population size, genetic variation, and the environmental context. Gene flow patterns may align with geographic distance (IBD—isolation by distance), whereby immigration rates are inversely proportional to the distance between populations. Alternatively gene flow may follow patterns of isolation by environment (IBE), whereby gene flow rates are higher among similar environments. Finally, gene flow may be highest among dissimilar environments (counter‐gradient gene flow), the classic “gene‐swamping” scenario. Here we survey relevant studies to determine the prevalence of each pattern across environmental gradients. Of 70 studies, we found evidence of IBD in 20.0%, IBE in 37.1%, and both patterns in 37.1%. In addition, 10.0% of studies exhibited counter‐gradient gene flow. In total, 74.3% showed significant IBE patterns. This predominant IBE pattern of gene flow may have arisen directly through natural selection or reflect other adaptive and nonadaptive processes leading to nonrandom gene flow. It also precludes gene swamping as a widespread phenomenon. Implications for evolutionary processes and management under rapidly changing environments (e.g., climate change) are discussed.     

The influence of landscape configuration and environment on population genetic structure in a sedentary passerine: insights from loci located in different genomic regions

The study of the factors structuring genetic variation can help to infer the neutral and adaptive processes shaping the demographic and evolutionary trajectories of natural populations. Here, we analyse the role of isolation by distance (IBD), isolation by resistance (IBR, defined by landscape composition) and isolation by environment (IBE, estimated as habitat and elevation dissimilarity) in structuring genetic variation in 25 blue tit (Cyanistes caeruleus) populations. We typed 1385 individuals at 26 microsatellite loci classified into two groups by considering whether they are located into genomic regions that are actively (TL; 12 loci) or not (NTL; 14 loci) transcribed to RNA. Population genetic differentiation was mostly detected using the panel of NTL. Landscape genetic analyses showed a pattern of IBD for all loci and the panel of NTL, but genetic differentiation estimated at TL was only explained by IBR models considering high resistance for natural vegetation and low resistance for agricultural lands. Finally, the absence for IBE suggests a lack of divergent selection pressures associated with differences in habitat and elevation. Overall, our study shows that markers located in different genomic regions can yield contrasting inferences on landscape‐level patterns of realized gene flow in natural populations.     

The role of geography and ecology in shaping repeated patterns of morphological and genetic differentiation between European minnows (Phoxinus phoxinus) from the Pyrenees and the Alps

Neutral and selective processes can drive repeated patterns of evolution in different groups of populations experiencing similar ecological gradients. In this paper, we used a combination of nuclear and mitochondrial DNA markers, as well as geometric morphometrics, to investigate repeated patterns of morphological and genetic divergence of European minnows in two mountain ranges: the Pyrenees and the Alps. European minnows (Phoxinus phoxinus) are cyprinid fish inhabiting most freshwater bodies in Europe, including those in different mountain ranges that could act as major geographical barriers to gene flow. We explored patterns of P. phoxinus phenotypic and genetic diversification along a gradient of altitude common to the two mountain ranges, and tested for isolation by distance (IBD), isolation by environment (IBE) and isolation by adaptation (IBA). The results indicated that populations from the Pyrenees and the Alps belong to two well differentiated, reciprocally monophyletic mtDNA lineages. Substantial genetic differentiation due to geographical isolation within and between populations from the Pyrenees and the Alps was also found using rapidly evolving AFLPs markers (isolation by distance or IBD), as well as morphological differences between mountain ranges. Also, morphology varied strongly with elevation and so did genetic differentiation to a lower extent. Despite moderate evidence for IBE and IBA, and therefore of repeated evolution, substantial population heterogeneity was found at the genetic level, suggesting that selection and population specific genetic drift act in concert to affect genetic divergence.     

In the presence of population structure: From genomics to candidate genes underlying local adaptation

Understanding the genomic signatures, genes, and traits underlying local adaptation of organisms to heterogeneous environments is of central importance to the field evolutionary biology. To identify loci underlying local adaptation, models that combine allelic and environmental variation while controlling for the effects of population structure have emerged as the method of choice. Despite being evaluated in simulation studies, there has not been a thorough investigation of empirical evidence supporting local adaptation across these alleles. To evaluate these methods, we use 875 Arabidopsis thaliana Eurasian accessions and two mixed models (GEMMA and LFMM) to identify candidate SNPs underlying local adaptation to climate. Subsequently, to assess evidence of local adaptation and function among significant SNPs, we examine allele frequency differentiation and recent selection across Eurasian populations, in addition to their distribution along quantitative trait loci (QTL) explaining fitness variation between Italy and Sweden populations and cis‐regulatory/nonsynonymous sites showing significant selective constraint. Our results indicate that significant LFMM/GEMMA SNPs show low allele frequency differentiation and linkage disequilibrium across locally adapted Italy and Sweden populations, in addition to a poor association with fitness QTL peaks (highest logarithm of odds score). Furthermore, when examining derived allele frequencies across the Eurasian range, we find that these SNPs are enriched in low‐frequency variants that show very large climatic differentiation but low levels of linkage disequilibrium. These results suggest that their enrichment along putative functional sites most likely represents deleterious variation that is independent of local adaptation. Among all the genomic signatures examined, only SNPs showing high absolute allele frequency differentiation (AFD) and linkage disequilibrium (LD) between Italy and Sweden populations showed a strong association with fitness QTL peaks and were enriched along selectively constrained cis‐regulatory/nonsynonymous sites. Using these SNPs, we find strong evidence linking flowering time, freezing tolerance, and the abscisic‐acid pathway to local adaptation.     

Different processes shape the patterns of divergence in the nuclear and chloroplast genomes of a relict tree species in East Asia

Isolation by spatial distance (IBD), environment (IBE), and historical climatic instability (IBI) are three common processes assessed in phylogeographic and/or landscape genetic studies. However, the relative contributions of these three processes with respect to spatial genetic patterns have seldom been compared. Moreover, whether the relative contribution differs in different regions or when assessed using different genetic markers has rarely been reported. Lindera obtusiloba has been found to have two sister genetic clades of chloroplast (cpDNA) and nuclear microsatellite (nSSR), both of which show discontinuous distribution in northern and southern East Asia. In this study, we used the Mantel test and multiple matrix regression with randomization (MMRR) to determine the relative contributions of IBD, IBE, and IBI with respect to L. obtusiloba populations. Independent Mantel tests and MMRR calculations were conducted for two genetic data sets (cpDNA and nSSR) and for different regions (the overall species range, and northern and southern subregions of the range). We found a significant IBI pattern in nSSR divergence for all assessed regions, whereas no clear IBI pattern was detected with respect to cpDNA. In contrast, significant (or marginal) divergent IBD patterns were detected for cpDNA in all regions, whereas although a significant IBE was apparent with respect to the overall range, the effect was not detected in the two subregions. The differences identified in nSSR and cpDNA population divergence may be related to differences in the heredity and ploidy of the markers. Compared with the southern region, the northern region showed less significant correlation patterns, which may be related to the shorter population history and restricted population range. The findings of this study serve to illustrate that comparing between markers or regions can contribute to gaining a better understanding the population histories of different genomes or within different regions of a species' range.     

Landscape genetic structure of Scirpus mariqueter reveals a putatively adaptive differentiation under strong gene flow in estuaries

Estuarine organisms grow in highly heterogeneous habitats, and their genetic differentiation is driven by selective and neutral processes as well as population colonization history. However, the relative importance of the processes that underlie genetic structure is still puzzling. Scirpus mariqueter is a perennial grass almost limited in the Changjiang River estuary and its adjacent Qiantang River estuary. Here, using amplified fragment length polymorphism (AFLP), a moderate‐high level of genetic differentiation among populations (range F_ST: 0.0310–0.3325) was showed despite large ongoing dispersal. FLOCK assigned all individuals to 13 clusters and revealed a complex genetic structure. Some genetic clusters were limited in peripheries compared with very mixing constitution in center populations, suggesting local adaptation was more likely to occur in peripheral populations. 21 candidate outliers under positive selection were detected, and further, the differentiation patterns correlated with geographic distance, salinity difference, and colonization history were analyzed with or without the outliers. Combined results of AMOVA and IBD based on different dataset, it was found that the effects of geographic distance and population colonization history on isolation seemed to be promoted by divergent selection. However, none‐liner IBE pattern indicates the effects of salinity were overwhelmed by spatial distance or other ecological processes in certain areas and also suggests that salinity was not the only selective factor driving population differentiation. These results together indicate that geographic distance, salinity difference, and colonization history co‐contributed in shaping the genetic structure of S. mariqueter and that their relative importance was correlated with spatial scale and environment gradient.     

Widespread evidence for incipient ecological speciation: a meta‐analysis of isolation‐by‐ecology

Ecologically mediated selection has increasingly become recognised as an important driver of speciation. The correlation between neutral genetic differentiation and environmental or phenotypic divergence among populations, to which we collectively refer to as isolation‐by‐ecology (IBE), is an indicator of ecological speciation. In a meta‐analysis framework, we determined the strength and commonality of IBE in nature. On the basis of 106 studies, we calculated a mean effect size of IBE with and without controlling for spatial autocorrelation among populations. Effect sizes were 0.34 (95% CI 0.24–0.42) and 0.26 (95% CI 0.13–0.37), respectively, indicating that an average of 5% of the neutral genetic differentiation among populations was explained purely by ecological contrast. Importantly, spatial autocorrelation reduced IBE correlations for environmental variables, but not for phenotypes. Through simulation, we showed how the influence of isolation‐by‐distance and spatial autocorrelation of ecological variables can result in false positives or underestimated correlations if not accounted for in the IBE model. Collectively, this meta‐analysis showed that ecologically induced genetic divergence is pervasive across time‐scales and taxa, and largely independent of the choice of molecular marker. We discuss the importance of these results in the context of adaptation and ecological speciation and suggest future research avenues.     

Are habitat fragmentation,local adaptation and isolation‐by‐distance driving population divergence in wild rice Oryza rufipogon?

Habitat fragmentation weakens the connection between populations and is accompanied with isolation by distance (IBD) and local adaptation (isolation by adaptation, IBA), both leading to genetic divergence between populations. To understand the evolutionary potential of a population and to formulate proper conservation strategies, information on the roles of IBD and IBA in driving population divergence is critical. The putative ancestor of Asian cultivated rice (Oryza sativa) is endangered in China due to habitat loss and fragmentation. We investigated the genetic variation in 11 Chinese Oryza rufipogon populations using 79 microsatellite loci to infer the effects of habitat fragmentation, IBD and IBA on genetic structure. Historical and current gene flows were found to be rare (m_h = 0.0002–0.0013, m_c = 0.007–0.029), indicating IBD and resulting in a high level of population divergence (F_ST = 0.343). High within‐population genetic variation (H_E = 0.377–0.515), relatively large effective population sizes (N_e = 96–158), absence of bottlenecks and limited gene flow were found, demonstrating little impact of recent habitat fragmentation on these populations. Eleven gene‐linked microsatellite loci were identified as outliers, indicating local adaptation. Hierarchical AMOVA and partial Mantel tests indicated that population divergence of Chinese O. rufipogon was significantly correlated with environmental factors, especially habitat temperature. Common garden trials detected a significant adaptive population divergence associated with latitude. Collectively, these findings imply that IBD due to historical rather than recent fragmentation, followed by local adaptation, has driven population divergence in O. rufipogon.     

Genetic and morphological differentiation in Populus nigra L.: isolation by colonization or isolation by adaptation?

Identifying processes underlying the genetic and morphological differences among populations is a central question of evolutionary biology. Forest trees typically contain high levels of neutral genetic variation, and genetic differences are often correlated with geographic distance between populations [isolation by distance (IBD)] or are due to historic vicariance events [isolation by colonization (IBC)]. In contrast, morphological differences are largely due to local adaptation. Here, we examined genetic (microsatellite) and morphological (from a common garden experiment) variation in Populus nigra L., European black poplar, collected from 13 sites across western Europe and grown in a common garden in Belgium. Significant genetic differentiation was observed, with populations from France displaying greater admixture than the distinct Spanish and central European gene pools, consistent with previously described glacial refugia (IBC). Many quantitative traits displayed a bimodal distribution, approximately corresponding to small‐leaf and large‐leaf ecotypes. Examination of nine climatic variables revealed the sampling locations to have diverse climates, and although the correlation between morphological and climatic differences was significant, the pattern was not consistent with strict local adaptation. Partial Mantel tests based on multivariate summary statistics identified significant residual correlation in comparisons of small‐leaf to large‐leaf ecotypes, and within the small‐leaf samples, but not within large‐leaf ecotypes, indicating that variation within the small‐leaf morphotype in particular may be adaptive. Some small‐leaf populations experience climates very similar to those in large‐leaf sites. We conclude that adaptive differentiation and persistent IBC acted in combination to produce the genetic and morphological patterns observed in P. nigra.     

Evaluation of demographic history and neutral parameterization on the performance of FST outlier tests

F_ST outlier tests are a potentially powerful way to detect genetic loci under spatially divergent selection. Unfortunately, the extent to which these tests are robust to nonequilibrium demographic histories has been understudied. We developed a landscape genetics simulator to test the effects of isolation by distance (IBD) and range expansion on F_ST outlier methods. We evaluated the two most commonly used methods for the identification of F_ST outliers (FDIST2 and BayeScan, which assume samples are evolutionarily independent) and two recent methods (FLK and Bayenv2, which estimate and account for evolutionary nonindependence). Parameterization with a set of neutral loci (‘neutral parameterization’) always improved the performance of FLK and Bayenv2, while neutral parameterization caused FDIST2 to actually perform worse in the cases of IBD or range expansion. BayeScan was improved when the prior odds on neutrality was increased, regardless of the true odds in the data. On their best performance, however, the widely used methods had high false‐positive rates for IBD and range expansion and were outperformed by methods that accounted for evolutionary nonindependence. In addition, default settings in FDIST2 and BayeScan resulted in many false positives suggesting balancing selection. However, all methods did very well if a large set of neutral loci is available to create empirical P‐values. We conclude that in species that exhibit IBD or have undergone range expansion, many of the published F_ST outliers based on FDIST2 and BayeScan are probably false positives, but FLK and Bayenv2 show great promise for accurately identifying loci under spatially divergent selection.     

Climatic drivers of leaf traits and genetic divergence in the tree Annona crassiflora: a broad spatial survey in the Brazilian savannas

The Cerrado is the largest South American savanna and encompasses substantial species diversity and environmental variation. Nevertheless, little is known regarding the influence of the environment on population divergence of Cerrado species. Here, we searched for climatic drivers of genetic (nuclear microsatellites) and leaf trait divergence in Annona crassiflora, a widespread tree in the Cerrado. The sampling encompassed all phytogeographic provinces of the continuous area of the Cerrado and included 397 individuals belonging to 21 populations. Populations showed substantial genetic and leaf trait divergence across the species' range. Our data revealed three spatially defined genetic groups (eastern, western and southern) and two morphologically distinct groups (eastern and western only). The east‐west split in both the morphological and genetic data closely mirrors previously described phylogeographic patterns of Cerrado species. Generalized linear mixed effects models and multiple regression analyses revealed several climatic factors associated with both genetic and leaf trait divergence among populations of A. crassiflora. Isolation by environment (IBE) was mainly due to temperature seasonality and precipitation of the warmest quarter. Populations that experienced lower precipitation summers and hotter winters had heavier leaves and lower specific leaf area. The southwestern area of the Cerrado had the highest genetic diversity of A. crassiflora, suggesting that this region may have been climatically stable. Overall, we demonstrate that a combination of current climate and past climatic changes have shaped the population divergence and spatial structure of A. crassiflora. However, the genetic structure of A. crassiflora reflects the biogeographic history of the species more strongly than leaf traits, which are more related to current climate.     

Genetic analysis of Pinus strobus and Pinus monticola populations from Canada using ISSR and RAPD markers: development of genome-specific SCAR markers

Pinus is the largest genus of conifers, containing over 100 species and is also the most widespread genus in the Northern Hemisphere. Pinus monticola and P. strobus are two closely related and economically important species in Canada. Morphological and allometric characteristics have been used to assess genetic variation within these two species but these markers are not reliable due to ecological variations. The purpose of the present study was to determine the level of genetic diversity within and among Canadian populations from the two species using molecular markers and to identify and characterize genome-specific inter-simple sequence repeats (ISSR) and random amplified polymorphic DNA (RAPD) markers. The level of genetic variation among populations was much lower for P. monticola than P. strobus. For both species, the among population variation values were smaller than within population variation. The populations from P. monticola were more closely genetically related than populations from P. strobus based on ISSR and RAPD analyses. Six ISSR and four RAPD markers specific to either P. monticola or P. strobus were cloned and sequenced. Primer pairs flanking these specific sequences were designed and genome specific SCAR markers for P. monticola and P. strobus were developed and characterized.     

Isolation by distance,not incipient ecological speciation,explains genetic differentiation in an Andean songbird (Aves: Furnariidae: Cranioleuca antisiensis,Line‐cheeked Spinetail) despite near threefold body size change across an environmental gradient

During the process of ecological speciation, reproductive isolation results from divergent natural selection and leads to a positive correlation between genetic divergence and adaptive phenotypic divergence, that is, isolation by adaptation (IBA). In natural populations, phenotypic differentiation is often autocorrelated with geographic distance, making IBA difficult to distinguish from the neutral expectation of isolation by distance (IBD). We examined these two alternatives in a dramatic case of clinal phenotypic variation in an Andean songbird, the Line‐cheeked Spinetail (Cranioleuca antisiensis). At its geographic extremes, this species shows a near threefold difference in body mass (11.5 to 31.0 g) with marked plumage differences. We analysed phenotypic, environmental and genetic data (5,154 SNPs) from 172 individuals and 19 populations sampled along its linear distribution in the Andes. We found that body mass was tightly correlated with environmental temperature, consistent with local adaptation as per Bergmann's rule. Using a P_ST–F_ST analysis, we found additional support for natural selection driving body mass differentiation, but these results could also be explained by environment‐mediated phenotypic plasticity. When we assessed the relative support for patterns of IBA and IBD using variance partitioning, we found that IBD was the best explanation for genetic differentiation along the cline. Adaptive phenotypic or environmental divergence can reduce gene flow, a pattern interpreted as evidence of ecological speciation's role in diversification. Our results provide a counterexample to this interpretation. Despite conditions conducive to ecological speciation, our results suggest that dramatic size and environmental differentiation within C. antisiensis are not limiting gene flow.     

Environmental gradients predict the genetic population structure of a coral reef fish in the Red Sea

The relatively recent fields of terrestrial landscape and marine seascape genetics seek to identify the influence of biophysical habitat features on the spatial genetic structure of populations or individuals. Over the last few years, there has been accumulating evidence for the effect of environmental heterogeneity on patterns of gene flow and connectivity in marine systems. Here, we investigate the population genetic patterns of an anemonefish, Amphiprion bicinctus, along the Saudi Arabian coast of the Red Sea. We collected nearly one thousand samples from 19 locations, spanning approximately 1500 km, and genotyped them at 38 microsatellite loci. Patterns of gene flow appeared to follow a stepping‐stone model along the northern and central Red Sea, which was disrupted by a distinct genetic break at a latitude of approximately 19°N. The Red Sea is characterized by pronounced environmental gradients along its axis, roughly separating the northern and central from the southern basin. Using mean chlorophyll‐a concentrations as a proxy for this gradient, we ran tests of isolation by distance (IBD, R² = 0.52) and isolation by environment (IBE, R² = 0.64), as well as combined models using partial Mantel tests and multiple matrix regression with randomization (MMRR). We found that genetic structure across our sampling sites may be best explained by a combined model of IBD and IBE (Mantel: R² = 0.71, MMRR: R² = 0.86). Our results highlight the potential key role of environmental patchiness in shaping patterns of gene flow in species with pelagic larval dispersal. We support growing calls for the integration of biophysical habitat characteristics into future studies of population genetic structure.