Geographic Patterns Of Genetic Variation Research Articles

Using dense locality sampling resolves the subtle genetic population structure of the dispersive fish species Plecoglossus altivelis.

In dispersive species with continuous distributions, genetic differentiation between local populations is often absent or subtle and thus difficult to detect. To incorporate such subtle differentiation into management plans, it may be essential to analyse many samples from many localities using adequate numbers of high-resolution genetic markers. Here, we evaluated the usefulness of dense locality sampling in resolving genetic population structure in the ayu (Plecoglossus altivelis), a dispersive fish important in Japanese inland fisheries. Genetic variability in, and differentiation between, ayu populations around the Japan-Ryukyu Archipelago were investigated in 4746 individuals collected from 120 localities by genotyping 12 microsatellite markers. These individuals represented the two subspecies of ayu, namely the Ryukyuan subspecies (Plecoglossus altivelis ryukyuensis) and both amphidromous and landlocked forms of the nominotypical subspecies (P.a.altivelis) along the archipelago. We successfully detected an absence of genetic differentiation within the landlocked form and subtle but significant differentiation and clear geographic patterns of genetic variation among populations of the amphidromous form, which had been considered genetically homogeneous. This suggests that dense locality sampling effectively resolves subtle differences in genetic population structure, reducing stochastic deviation in the detection of genetic differentiation and geographic patterns in local populations of this dispersive species. Resampling analyses based on empirical data sets clearly demonstrate the effectiveness of increasing the number of locality samples for stable and reliable estimations of genetic fixation indices. The genetic population structure observed within the amphidromous form provides useful information for identifying management or conservation units in ayu.

Role of geographical provenance in the response of silver fir seedlings to experimental warming and drought.

Changes in climate can alter the distribution and population dynamics of tree species by altering their recruitment patterns, especially at range edges. However, geographical patterns of genetic diversity could buffer the negative consequences of changing climate at rear range edges where populations might also harbour individuals with drought-adapted genotypes. Silver fir (Abies alba Mill.) reaches its south-western distribution limit in the Spanish Pyrenees, where recent climatic dieback events have disproportionately affected westernmost populations. We hypothesized that silver fir populations from the eastern Pyrenees are less vulnerable to the expected changing climate due to the inclusion of drought-resistant genotypes. We performed an experiment under strictly controlled conditions simulating projected warming and drought compared with current conditions and analysed physiology, growth and survival of silver fir seedlings collected from eastern and western Pyrenean populations. Genetic analyses separated eastern and western provenances in two different lineages. Climate treatments affected seedling morphology and survival of both lineages in an overall similar way: elevated drought diminished survival and induced a higher biomass allocation to roots. Increased temperature and drought provoked more negative stem water potentials and increased δ13C ratios in leaves. Warming reduced nitrogen concentration and increased soluble sugar content in leaves, whereas drought increased nitrogen concentration. Lineage affected these physiological parameters, with western seedlings being more sensitive to warming and drought increase in terms of δ13C, nitrogen and content of soluble sugars. Our results demonstrate that, in A. alba, differences in the physiological response of this species to drought are also associated with differences in biogeographical history.

Genetic evidence for central‐marginal hypothesis in a Cenozoic relict tree species across its distribution in China

AbstractAimThis study tests predictions of the central‐marginal (C‐M) hypothesis using geographical patterns of genetic variation in a Cenozoic relict tree species Euptelea pleiospermum. Additionally, we explore the extent to which post‐glacial recolonization and landscape barriers created by topographical heterogeneity shape spatial genetic variation.LocationSouth‐west and central subtropical China.MethodsUsing microsatellite data of 678 individuals from 21 populations, we documented geographical patterns of genetic diversity and population genetic structure, supplemented with current and past (Last Glacial Maximum, LGM) distributions based on species distribution models (SDMs). Genetic structure was determined by non‐spatial and spatially sensitive Bayesian clustering, analysis of molecular variance, barrier analysis and a multivariate population graphing approach. We also examined both historical and contemporary gene flow.ResultsGenetic diversity significantly declined with distance from centre and showed unimodal patterns along both latitude and longitude. The C‐M pattern of genetic diversity along latitudinal gradient is high‐latitude‐skewed, with the peak at higher portion of the species' latitudinal extent. The Sichuan Basin divided individuals into south and north clusters, whereas the Qinba Mountains did not. The general shape of the predicted distribution during the LGM is strongly similar with that of current distribution, except the Sichuan Basin.Main conclusionsOur study provides genetic evidence for the C‐M hypothesis in a Cenozoic relict tree species across its distribution in China. The Sichuan Basin, rather than the Qinba Mountains, acts as dispersal barrier for a mountain tree species. Our results suggest that in situ refugia were maintained across southwest and central China during the LGM. The slight post‐glacial northward expansion and asymmetrical south–north historical‐gene flow did not result in a low‐latitude‐skewed C‐M pattern of genetic diversity. Instead, complex topography in combination with the C‐M dispersal dynamics shaped the latitudinal pattern of genetic diversity.

Patterns of neutral and adaptive genetic diversity across the natural range of sugar pine (Pinus lambertiana Dougl.)

Demographic and environmental forces shape geographical patterns of genetic diversity. Knowledge thereof is not only important for evolutionary ecologists but, in light of future climate change, will be of interest to conservation biologists as well. Sugar pine (Pinus lambertiana Dougl.) is an ecologically important species found in mixed conifer forests across western North America. We applied a candidate-gene-based environmental study to infer spatial patterns in neutral genetic variation and to identify genetic variants associated with local adaptation to drought. Using a panel of 186 candidate gene single nucleotide polymorphisms (SNP), we genotyped 313 individual trees sampled across the entire state of California, USA. We found evidence for a large-scale subdivision into two genetic clusters along the latitudinal axis and increased genetic similarity among sugar pines within a 200–300-km boundary. Associating allelic to environmental variation indicated nine putative SNPs related to local adaptation to drought. These results provide insights into neutral population structure across the natural range of sugar pine and further substantiated a key role of the mitochondrial import inner membrane machinery in enhanced tolerance to drought and constitute important steps into unravelling the eco-evolutionary dynamics in sugar pine.

Variation of craniodental traits in russet rats Euryoryzomys russatus (Wagner, 1848) (Rodentia: Cricetidae: Sigmodontinae) from Eastern Atlantic Forest

The analyses of geographic variation and the detection of discontinuities among populations of a given taxa is a fundamental step on evolutionary studies. Some recent studies have demonstrated that along the Atlantic Forest of eastern Brazil there are some phylogenetic and phylogeographic discontinuities recovered with molecular markers for several groups of organisms, granting the proposition of biogeographic hypothesis for species diversification in this biome. For instance, a phylogeographic study using cytochrome b sequences demonstrated geographic pattern of genetic variation in the oryzomyine rodent Euryoryzomys russatus. Considering the widespread occurrence of E. russatus, its susceptibility to fragmentation, and the existence of geographic structure in the genetic variation mentioned above, E. russatus stands as an interesting species to describe the geographic pattern of craniodental variation. Therefore, we aim to evaluate the morphometric variation patterns coupled with the actual knowledge regarding the evolution of the Atlantic Forest biota, in order to test the hypothesis that the phenotype of E. russatus exhibits a structured pattern of variation along the Atlantic Forest similar to that described for the cytochrome b gene on continental and coastal islands samples. Our results showed that there is congruence between the gaps here described on morphometric data and the genetic data described in literature. We also detected important variation in size between some insular populations and the continent. Geographic patterns of morphometric variation observed for E. russatus were compared to other patterns of diversity for the Atlantic biome, and discussed under historical biogeographic context. We concluded that study of morphometric variation might offer important support to phylogeographic and biogeographic hypothesis based on molecular markers and provide a better scenario on the expression of the phenotypic variation.

Joint inferences from cytoplasmic DNA and fossil data provide evidence for glacial vicariance and contrasted post‐glacial dynamics in tamarack, a transcontinental conifer

AbstractAimTamarack (Larix laricina) is an early‐successional transcontinental boreal conifer occurring within the spruce‐fir dominated forest. The aim was to infer the species biogeographical history and to assess the putative genetic imprint left by interspecific competition during post‐glacial migration, using cytoplasmic DNA and fossil data.LocationForty‐five locations were sampled across the transcontinental range spanning the North American boreal forest.MethodsA total of 621 trees were scanned for mitochondrial and chloroplast DNA polymorphisms to reveal geographical patterns of genetic diversity, differentiation, and population structure throughout the species range. Published pollen records were analysed to assess the chronology of post‐glacial colonization of Larix sp. relative to more competitive tree taxa, Picea sp. and Abies sp..ResultsGenotyping resulted in two mitotypes (one locus) and 24 chlorotypes (three cpSSR loci). Bayesian assignment test based on cpDNA data detected three groups: eastern North America, western North America and Alaska. CpDNA population differentiation was higher in the western part of the range relative to the eastern part. Post‐glacial colonization chronology derived from fossil data indicated that Larix colonized western North America at least 4000 years after Picea and Abies, but shortly preceded them in eastern North America.Main conclusionsCytoplasmic and fossil data provided support for four distinct glacial lineages. Two lineages would have persisted south of the Laurentide ice sheet, while the two remaining ones likely originate from northern refugia located in Beringia and Labrador. Larix establishment was possibly hindered by earlier establishment of more competitive taxa in western North America, which resulted in high genetic differentiation among western populations. These results provide support for a putative role of interspecific competition in structuring the standing genetic variation at the time of post‐glacial colonization.

A Spatial Framework for Understanding Population Structure and Admixture.

Geographic patterns of genetic variation within modern populations, produced by complex histories of migration, can be difficult to infer and visually summarize. A general consequence of geographically limited dispersal is that samples from nearby locations tend to be more closely related than samples from distant locations, and so genetic covariance often recapitulates geographic proximity. We use genome-wide polymorphism data to build “geogenetic maps,” which, when applied to stationary populations, produces a map of the geographic positions of the populations, but with distances distorted to reflect historical rates of gene flow. In the underlying model, allele frequency covariance is a decreasing function of geogenetic distance, and nonlocal gene flow such as admixture can be identified as anomalously strong covariance over long distances. This admixture is explicitly co-estimated and depicted as arrows, from the source of admixture to the recipient, on the geogenetic map. We demonstrate the utility of this method on a circum-Tibetan sampling of the greenish warbler (Phylloscopus trochiloides), in which we find evidence for gene flow between the adjacent, terminal populations of the ring species. We also analyze a global sampling of human populations, for which we largely recover the geography of the sampling, with support for significant histories of admixture in many samples. This new tool for understanding and visualizing patterns of population structure is implemented in a Bayesian framework in the program SpaceMix.

Phylogeography of a Morphologically Cryptic Golden Mole Assemblage from South-Eastern Africa.

The Greater Maputaland-Pondoland-Albany (GMPA) region of southern Africa was recently designated as a centre of vertebrate endemism. The phylogeography of the vertebrate taxa occupying this region may provide insights into the evolution of faunal endemism in south-eastern Africa. Here we investigate the phylogeographic patterns of an understudied small mammal species assemblage (Amblysomus) endemic to the GMPA, to test for cryptic diversity within the genus, and to better understand diversification across the region. We sampled specimens from 50 sites across the distributional range of Amblysomus, with emphasis on the widespread A. hottentotus, to analyse geographic patterns of genetic diversity using mitochondrial DNA (mtDNA) and nuclear intron data. Molecular dating was used to elucidate the evolutionary and phylogeographic history of Amblysomus. Our phylogenetic reconstructions show that A. hottentotus comprises several distinct lineages, or evolutionarily significant units (ESUs), some with restricted geographic ranges and thus worthy of conservation attention. Divergence of the major lineages dated to the early Pliocene, with later radiations in the GMPA during the late-Pliocene to early-Pleistocene. Evolutionary diversification within Amblysomus may have been driven by uplift of the Great Escarpment c. 5–3 million years ago (Ma), habitat changes associated with intensification of the east-west rainfall gradient across South Africa and the influence of subsequent global climatic cycles. These drivers possibly facilitated geographic spread of ancestral lineages, local adaptation and vicariant isolation. Our study adds to growing empirical evidence identifying East and southern Africa as cradles of vertebrate diversity.

Mating system divergence affects the distribution of sequence diversity within and among populations of recently diverged subspecies of Clarkia xantiana (Onagraceae).

The population biology of outcrossing and self-fertilizing taxa is thought to differ because of the advantage that selfers have in colonizing unoccupied sites where mates and pollinators may be limiting (Baker's Law). This reduced tendency for outcrossers to colonize new sites, along with their greater dependence on pollinators to disperse pollen, has the potential to differently influence the genetic diversity and structure of outcrossing and selfing populations. We conducted a comparative population genetic study of two sister outcrossing and selfing subspecies of Clarkia xantiana that have very recently diverged. We used DNA sequence variation (>40 kb from eight nuclear loci) from large samples of individuals from 14 populations to assess geographic patterns of genetic diversity and make inferences about the demographic and colonization histories of each subspecies. We show that sequence variation is strongly reduced across all selfing populations. The demographic history of selfing populations exhibits recent colonization bottlenecks, whereas such bottlenecks are rarely observed for the outcrosser. The greater effect of genetic drift in the selfer has resulted in strong population genetic structure, but with no pattern of isolation by distance. By contrast, the stronger effect of gene flow in the outcrosser has resulted in considerably less structure, but a significant pattern of isolation by distance. Taken together, our results suggest that selfing populations are not at migration-drift equilibrium, are affected by strong episodes of genetic drift during colonization, and experience little or no subsequent gene flow from other populations after those founder events.

Geographic patterns of genetic diversity in two species complexes of Canadian marine bivalves

Larval development has strong impacts on dispersal potential and gene flow among populations of marine invertebrates. However, Pleistocene glaciations have also played an important role in shaping population structure in benthic taxa in the Northern Hemisphere, even those with planktotrophic larvae. Each glacial advance tended to fragment species distributions, often separating populations for long periods and setting the stage for their differentiation. This study examines patterns of sequence divergence of the mitochondrial cytochrome c oxidase subunit I gene in North American populations of two bivalve species complexes, Hiatella arctica s. l. and Macoma balthica s. l., with complementary data from the nuclear internal transcribed spacer-2 (ITS2) gene for the latter. Our results confirm the presence of two known species from the M. balthica complex in Canada, but also provide evidence for a third clade in Atlantic Canada. Our study confirms that the H. arctica complex in Canada contains at least four species, with support for a novel clade (Hiatella N) in the northeastern Pacific. Our results extend the range of a previously identified Hiatella clade (K) to include the northwestern Atlantic. Both M. balthica s. l. and H. arctica s. l. have broad Holarctic distributions and planktotrophic larvae, but this work reveals differences in phylogeographic structure and genetic diversity.

Conservation genetics and geographic patterns of genetic variation of endangered shrub Ammopiptanthus (Fabaceae) in northwestern China

Phylogeographic patterns of Ammopiptanthus in northwestern China were examined with internal transcribed spacer (ITS) and three chloroplast intergenic spacers (trnH–psbA, trnL–trnF, and trnS–trnG). Two ITS genotypes (a–b) and 8 chloroplast haplotypes (A–H) were detected. Both ITS genotypes and chloroplast lineages were split in two geographic regions: western Xinjiang and the Alxa Desert. This lineage split was also supported by AMOVA analysis and the Mantel test. AMOVA showed that 89.81 % of variance in Ammopiptanthus occurred between the two geographic regions, and correlation between genetic distances and geographical distances was significant (r = 0.757, p < 0.0001). All populations in western Xinjiang shared haplotype A with high frequency, and range expansion was strongly supported by negative Fu’s FS value, and mismatch distribution analysis, whereas populations in the Alxa Desert had higher genetic diversity and structure. We speculate that the cold and dry climate during the early Quaternary fragmented habitats of the species, limiting gene flow between regions, and interglacial periods most likely led to the range expansion in western Xinjiang. The low genetic diversity of Ammopiptanthus indicate a significant extinction risk, and protective measures should be taken immediately.

Evaluation of the geographical pattern of genetic diversity of Glycine soja and Glycine max based on four single copy nuclear gene loci: For conservation of soybean germplasm

Genetic diversity and its geographical patterns play a very important role in species conservation and exploitation. Here, nucleotide polymorphism patterns of four single copy nuclear gene loci in wild (Glycine soja) and cultivated soybean (Glycine max) populations from different geographical regions as well as their demographic history were analyzed. The results showed that: (1) Southern subpopulation has the highest, while central subpopulation revealed the lowest genetic diversity among three Chinese G. soja subpopulations. (2) Northern Chinese G. max subpopulation depicted higher genetic diversity than other two Chinese, Korean, Japanese and American G. max subpopulations. (3) Significant genetic differentiation (P < 0.001) was observed among Chinese G. soja subpopulations from three ecological zones. There was also a significant genetic differentiation（P < 0.01）between three Chinese and Japanese subpopulations of G. max. (4) The demographic dynamics revealed that effective population size of G. soja is expanding, while it was constant in G. max. G. soja is a useful germplasm resource to widen the genetic diversity of G. max. This study suggests that native populations of G. soja from different geo-ecological regions should be protected to conserve the genetic diversity.

Geographic patterns of genetic variation in three genomes of North American diploid strawberries with special reference toFragaria vescasubsp.bracteata

Geographic patterns of genetic variation in wild species reflect the interplay of ecological and evolutionary processes. We assessed genetic variation in three genomes across four North American diploid strawberry taxa, with special emphasis on the gynodioecious Fragaria vesca subsp. bracteata (A.Heller) Staudt. Specifically, we sequenced one chloroplast (rpoC2) and two mitochondrial (atp8 and atp8-orf225) genes along with several nuclear microsatellite markers. In addition, we assessed indicators of breeding system (pollen viability and female frequency) for all taxa. The geographic perspective on the distribution of cytoplasmic and nuclear variation revealed the genetic affiliation of the restricted taxa (Fragaria vesca subsp. californica (Cham. &amp; Schltdl.) Staudt and Fragaria mexicana Schltdl.) with the widespread F. vesca subsp. bracteata and identified a hotspot of hybridization within gynodioecious F. vesca subsp. bracteata. Higher pollen viability of hermaphrodites was found in the three hermaphroditic taxa relative to the gynodioecious one. Although theoretically predicted to be associated, the proportion of females within F. vesca subsp. bracteata populations was not correlated with population-level genetic variation, suggesting that the history of hybridization or population size variation is more influential on the distribution of genetic variation than sex ratio in this gynodioecious species. The documented patterns of genetic variation in this complex serve as an important point of reference for future ecological and evolutionary research in diploid Fragaria.

Genetic diversity of Italian goat breeds assessed with a medium-density SNP chip.

BackgroundAmong the European countries, Italy counts the largest number of local goat breeds. Thanks to the recent availability of a medium-density SNP (single nucleotide polymorphism) chip for goat, the genetic diversity of Italian goat populations was characterized by genotyping samples from 14 Italian goat breeds that originate from different geographical areas with more than 50 000 SNPs evenly distributed on the genome.ResultsAnalysis of the genotyping data revealed high levels of genetic polymorphism and an underlying North–south geographic pattern of genetic diversity that was highlighted by both the first dimension of the multi-dimensional scaling plot and the Neighbour network reconstruction. We observed a moderate and weak population structure in Northern and Central-Southern breeds, respectively, with pairwise FST values between breeds ranging from 0.013 to 0.164 and 7.49 % of the total variance assigned to the between-breed level. Only 2.11 % of the variance explained the clustering of breeds into geographical groups (Northern, Central and Southern Italy and Islands).ConclusionsOur results indicate that the present-day genetic diversity of Italian goat populations was shaped by the combined effects of drift, presence or lack of gene flow and, to some extent, by the consequences of traditional management systems and recent demographic history. Our findings may constitute the starting point for the development of marker-assisted approaches, to better address future breeding and management policies in a species that is particularly relevant for the medium- and long-term sustainability of marginal regions.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-015-0140-6) contains supplementary material, which is available to authorized users.

Genes Left Behind: Climate Change Threatens Cryptic Genetic Diversity in the Canopy-Forming Seaweed Bifurcaria bifurcata.

The global redistribution of biodiversity will intensify in the coming decades of climate change, making projections of species range shifts and of associated genetic losses important components of conservation planning. Highly-structured marine species, notably brown seaweeds, often harbor unique genetic variation at warmer low-latitude rear edges and thus are of particular concern. Here, a combination of Ecological Niche Models (ENMs) and molecular data is used to forecast the potential near-future impacts of climate change for a warm-temperate, canopy forming seaweed, Bifurcaria bifurcata. ENMs for B. bifurcata were developed using marine and terrestrial climatic variables, and its range projected for 2040-50 and 2090-2100 under two greenhouse emission scenarios. Geographical patterns of genetic diversity were assessed by screening 18 populations spawning the entire distribution for two organelle genes and 6 microsatellite markers. The southern limit of B. bifurcata was predicted to shift northwards to central Morocco by the mid-century. By 2090-2100, depending on the emission scenario, it could either retreat further north to western Iberia or be relocated back to Western Sahara. At the opposing margin, B. bifurcata was predicted to expand its range to Scotland or even Norway. Microsatellite diversity and endemism were highest in Morocco, where a unique and very restricted lineage was also identified. Our results imply that B. bifurcata will maintain a relatively broad latitudinal distribution. Although its persistence is not threatened, the predicted extirpation of a unique southern lineage or even the entire Moroccan diversity hotspot will erase a rich evolutionary legacy and shrink global diversity to current (low) European levels. NW Africa and similarly understudied southern regions should receive added attention if expected range changes and diversity loss of warm-temperate species is not to occur unnoticed.

Gene flow and geographic variation in natural populations of &lt;i&gt;Alnus acuminata&lt;/i&gt; ssp. arguta (Fagales: Betulaceae) in Costa Rica and Panama

Diecisiete poblaciones naturales de esta especie forestal en Costa Rica y Panamá , fueron investigadas en relación con sus patrones de flujo genético y de variación geográfica. El análisis de flujo genético fue basado en los métodos de los alelo s raros y de FST (Indice de similaridad genética M). Los análisis fueron a su vez basados en los únicos cuatro loci genéticos de un total de 22 investigados que mostraron polimorfismo (POI-B, POM-A, MNR-A and IDH-A). Los análisis de variación geográfica fueron basados en el desarrollo de correlaciones de Pearson entre 4 variables geográficas y 1 4 variables genéticas. Alguna evidencia d e aislamiento por distancia así como un débil flujo genético entre regiones geográficas fue encontrado. Fueron también observados patrones de variación elinal en relación con la altitud (r = -0.62 para la diversidad genética) y latitud (r = -0.77 en POI-B3), que apoyan la hipotesis de aislamiento por distancia para esta especie. No se encontraron a1elos privados en ninguna de las poblaciones investigadas.

Conservation genetics and geographic patterns of genetic variation of the vulnerable officinal herb Fritillaria walujewii (Liliaceae)

The Chinese herb Fritillaria walujewii Regel is an important officinal species that is vulnerable because of over-harvesting. Here, we examined the geographic pattern of genetic variation across the species entire range, to study its evolution process and give implication needed for the conservation. Nine haplotypes were detected on the basis of three chloroplast spacers. The most common haplotype was central in the haplotype network and was distributed widely from the Yili Valley to the eastern Tianshan Mountains. Genetic variation primarily occurred among populations and SAMOVA groups and the analysis of genetic structure showed a significant correlation between genetic and geographical distance. The fragmented distribution of F. walujewii in deep valleys may cause gene-flow barriers among distant populations and, along with genetic drift, has caused high genetic structure in the species. We identified Xinyuan County as the centre of diversification of F. walujewii, and speculated that populations in the eastern Tianshan Mountains were colonised from the Yili Valley. In relation to conservation management, we identified Xinyuan and Zhaosu County as having a high degree of genetic diversity and these should be the areas of the greatest focus for conservation.

Landscape genomics of Populus trichocarpa: the role of hybridization, limited gene flow, and natural selection in shaping patterns of population structure.

Populus trichocarpa is an ecologically important tree across western North America. We used a large population sample of 498 accessions over a wide geographical area genotyped with a 34K Populus SNP array to quantify geographical patterns of genetic variation in this species (landscape genomics). We present evidence that three processes contribute to the observed patterns: (1) introgression from the sister species P. balsamifera, (2) isolation by distance (IBD), and (3) natural selection. Introgression was detected only at the margins of the species' distribution. IBD was significant across the sampled area as a whole, but no evidence of restricted gene flow was detected in a core of drainages from southern British Columbia (BC). We identified a large number of FST outliers. Gene Ontology analyses revealed that FST outliers are overrepresented in genes involved in circadian rhythm and response to red/far-red light when the entire dataset is considered, whereas in southern BC heat response genes are overrepresented. We also identified strong correlations between geoclimate variables and allele frequencies at FST outlier loci that provide clues regarding the selective pressures acting at these loci.

Phylogeographical study of the alpine plantCassiope lycopodioides(Ericaceae) suggests a range connection between the Japanese archipelago and Beringia during the Pleistocene

Given that East Asia is located south-west of Beringia and was less glaciated during the Pleistocene, species at higher latitudes were able to expand their range in this region during climate cooling. Although southward migration is an inevitable colonization process, the biogeographical history of the disjunct ranges of higher-latitude species in East Asia has been investigated less extensively. Here, we assess whether their disjunct distributions in the Japanese archipelago connected sufficiently with Beringia or persisted in isolation following their establishment. Sequences of nine nuclear loci were determined for Cassiope lycopodioides (Ericaceae) from the Japanese archipelago as well as its surrounding areas, Kamchatka and Alaska. According to the geographical pattern of genetic diversity, the northern populations from Kamchatka to the northern part of the Japanese archipelago were similar genetically and were differentiated from populations in central Japan. Our study suggested that the distribution of C. lycopodioides was connected between the northern part of the Japanese archipelago and south-western Beringia due to Pleistocene climate cooling. Conversely, central Japan harboured a disjunct range after its establishment. These inferences suggest that widespread range expansion in northern East Asia was plausible for species distributed in Beringia. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113, 497–509.

Population genomic variation reveals roles of history, adaptation and ploidy in switchgrass.

Geographic patterns of genetic variation are shaped by multiple evolutionary processes, including genetic drift, migration and natural selection. Switchgrass (Panicum virgatum L.) has strong genetic and adaptive differentiation despite life history characteristics that promote high levels of gene flow and can homogenize intraspecific differences, such as wind-pollination and self-incompatibility. To better understand how historical and contemporary factors shape variation in switchgrass, we use genotyping-by-sequencing to characterize switchgrass from across its range at 98 042 SNPs. Population structuring reflects biogeographic and ploidy differences within and between switchgrass ecotypes and indicates that biogeographic history, ploidy incompatibilities and differential adaptation each have important roles in shaping ecotypic differentiation in switchgrass. At one extreme, we determine that two Panicum taxa are not separate species but are actually conspecific, ecologically divergent types of switchgrass adapted to the extreme conditions of coastal sand dune habitats. Conversely, we identify natural hybrids among lowland and upland ecotypes and visualize their genome-wide patterns of admixture. Furthermore, we determine that genetic differentiation between primarily tetraploid and octoploid lineages is not caused solely by ploidy differences. Rather, genetic diversity in primarily octoploid lineages is consistent with a history of admixture. This suggests that polyploidy in switchgrass is promoted by admixture of diverged lineages, which may be important for maintaining genetic differentiation between switchgrass ecotypes where they are sympatric. These results provide new insights into the mechanisms shaping variation in widespread species and provide a foundation for dissecting the genetic basis of adaptation in switchgrass.