Phylogeography and genetic connectivity of the marine macro‐alga Sargassum ilicifolium (Phaeophyceae,Ochrophyta) in the northwestern Pacific1

The evolutionary influences of historical and contemporary factors on the population connectivity and phylogeographic structure of a brown seaweed, Sargassum ilicifolium, were elucidated using the nuclear ITS2 and mitochondrial COI markers for the collections newly sampled within its distribution range in the northwestern Pacific (NWP). Significant genetic structure at variable levels was identified between populations (pairwise F_ST) and among populations grouped by geographical proximity (Φ_CT among regions). The adjacent groups of populations with moderate structure revealed from AMOVA appeared to have high genetic connectivity. However, a lack of genealogical concordance with the geographic distribution was uncovered for S. ilicifolium from the NWP. Such genetic homogeneity is interpreted as a result of the interaction between postglacial recolonization and dynamic oceanic current regimes in the region. Two separated glacial refugia, the South China Sea and the Okinawa Trough, in the marginal seas of east China were recognized based on the presence of endemic haplotypes and high haplotype diversity in the populations at southern China and northeast of Taiwan. Populations persisting in these refugia may have served as the source for recolonization in the NWP with the rise of sea level during the warmer interglacial periods. The role of oceanic currents in maintaining genetic connectivity of S. ilicifolium in the region was further corroborated by the coherence between the direction of oceanic currents and that of gene flow, especially along the eastern coast of Taiwan. This study underlines the interaction between historical postglacial recolonization and contemporary coastal hydrodynamics in contributing to population connectivity and distribution for this tropical seaweed in the NWP.     

祁连山区特有物种黑虎耳草的居群遗传多样性研究

利用叶绿体基因(rbcL和trnS-G)及核糖体DNA内转录间隔区(ITS),对祁连山区狭域分布的特有物种黑虎耳草8个居群(115个个体)进行遗传多样性研究,旨在揭示黑虎耳草的居群遗传结构及其历史进化过程。结果表明:(1)所有取样个体共检测到4个cpDNA单倍型和9个ITS单倍型,其中祁连山东南部的居群固定较多的单倍型和特有单倍型,而西北部居群只固定少数几个广泛分布的单倍型,且遗传多样性普遍较低。(2)基于cpDNA数据和ITS数据的分子变异分析(AMOVA)显示,遗传变异主要来源于居群内。(3)基于cpDNA数据的中性检验表明,Tajima’s D(-1.012 30,P 0.05)和FuLi’s D*(-2.066 77,P 0.05)均为负值,均不显著;歧点分布分析结果显示,黑虎耳草居群经历过近期的扩张事件。根据物种现有遗传分布格局推测,黑虎耳草在第四纪冰期时退缩到祁连山东南部的边缘避难所,间冰期或冰期后回迁到祁连山西北部地区,在回迁过程中由于奠基者效应导致祁连山西北部的居群仅固定少数广泛分布的单倍型,并呈现出较低的遗传多样性;由于居群较小且相互隔离,该物种经历了严重的瓶颈效应和遗传漂变,导致该物种总遗传多样性(H_T)和居群平均遗传多样性(H_S)远低于虎耳草属其他青藏高原-喜马拉雅广域分布的物种。     

Postglacial recolonization in a cold climate specialist in western Europe: patterns of genetic diversity in the adder (Vipera berus) support the central–marginal hypothesis

Understanding the impact of postglacial recolonization on genetic diversity is essential in explaining current patterns of genetic variation. The central–marginal hypothesis (CMH) predicts a reduction in genetic diversity from the core of the distribution to peripheral populations, as well as reduced connectivity between peripheral populations. While the CMH has received considerable empirical support, its broad applicability is still debated and alternative hypotheses predict different spatial patterns of genetic diversity. Using microsatellite markers, we analysed the genetic diversity of the adder (Vipera berus) in western Europe to reconstruct postglacial recolonization. Approximate Bayesian Computation (ABC) analyses suggested a postglacial recolonization from two routes: a western route from the Atlantic Coast up to Belgium and a central route from the Massif Central to the Alps. This cold‐adapted species likely used two isolated glacial refugia in southern France, in permafrost‐free areas during the last glacial maximum. Adder populations further from putative glacial refugia had lower genetic diversity and reduced connectivity; therefore, our results support the predictions of the CMH. Our study also illustrates the utility of highly variable nuclear markers, such as microsatellites, and ABC to test competing recolonization hypotheses.     

Holocene re‐colonisation,central–marginal distribution and habitat specialisation shape population genetic patterns within an Atlantic European grass species

Corynephorus canescens (L.) P.Beauv. is an outbreeding, short‐lived and wind‐dispersed grass species, highly specialised on scattered and disturbance‐dependent habitats of open sandy sites. Its distribution ranges from the Iberian Peninsula over Atlantic regions of Western and Central Europe, but excludes the two other classical European glacial refuge regions on the Apennine and Balkan Peninsulas. To investigate genetic patterns of this uncommon combination of ecological and biogeographic species characteristics, we analysed AFLP variation among 49 populations throughout the European distribution range, expecting (i) patterns of SW European glacial refugia and post‐glacial expansion to the NE; (ii) decreasing genetic diversity from central to marginal populations; and (iii) interacting effects of high gene flow and disturbance‐driven genetic drift. Decreasing genetic diversity from SW to NE and distinct gene pool clustering imply refugia on the Iberian Peninsula and in western France, from where range expansion originated towards the NE. High genetic diversity within and moderate genetic differentiation among populations, and a significant pattern of isolation‐by‐distance indicate a gene flow drift equilibrium within C. canescens, probably due to its restriction to scattered and dynamic habitats and limited dispersal distances. These features, as well as the re‐colonisation history, were found to affect genetic diversity gradients from central to marginal populations. Our study emphasises the need for including the specific ecology into analyses of species (re–)colonisation histories and range centre–margin analyses. To account for discontinuous distributions, new indices of marginality were tested for their suitability in studies of centre–periphery gradients.     

基于叶绿体DNA非编码序列的蒙古扁桃谱系地理学研究

该研究选取中国西北干旱区第三纪孑遗植物蒙古扁桃（Amygdalus mongolica）,基于叶绿体DNA非编码trnH psbA序列对蒙古扁桃17个居群324个个体进行了谱系地理学研究。结果表明：（1）蒙古扁桃trnH psbA序列长度350 bp,变异位点63个,共有9种单倍型,居群间总遗传多样性为（H_t）为0.758,居群内平均遗传多样性为（H_s）为0.203,贺兰山东麓及阴山南麓边缘的居群具有较高的单倍型多样性及核苷酸多样性并固定较多特有单倍型,推测这2个地区是蒙古扁桃在第四纪冰期时的重要避难所。（2）AMOVA分析表明,居群间的遗传变异为83.84%,居群内的遗传变异为16.16%,居群间遗传分化系数N_st>G_st（N_st=0.733, G_st=0.655, P>0.05）,表明蒙古扁桃不存在明显的谱系地理结构;根据单倍型地理分布及网络关系图,把蒙古扁桃自然地理居群分为东、西两大地理组群,而且东、西地理组群没有共享单倍型;居群遗传结构分析表明,两大地理组群遗传分化较大。（3）蒙古扁桃居群在间冰期或冰期后经历了近期的居群扩张,由于奠基者效应使得多数居群只固定了单一的单倍型。     

Population genetic structure of the point-head flounder, <Emphasis Type="Italic">Cleisthenes herzensteini</Emphasis>, in the Northwestern Pacific

Intraspecific phylogenies can provide useful insights into how populations have been shaped by historical and contemporary processes. To determine the population genetic structure and the demographic and colonization history of Cleisthenes herzensteini in the Northwestern Pacific, one hundred and twenty-one individuals were sampled from six localities along the coastal regions of Japan and the Yellow Sea of China. Mitochondrial DNA variation was analyzed using DNA sequence data from the 5′ end of control region. High levels of haplotype diversity (>0.96) were found for all populations, indicating a high level of genetic diversity. No pattern of isolation by distance was detected among the population differentiation throughout the examined range. Analyses of molecular variance (AMOVA) and the conventional population statistic Fst revealed no significant population genetic structure among populations. According to the exact test of differentiation among populations, the null hypothesis that C. herzensteini within the examined range constituted a non-differential mtDNA gene pool was accepted. The demographic history of C. herzensteini was examined using neutrality test and mismatch distribution analyses and results indicated Pleistocene population expansion (about 94–376 kya) in the species, which was consistent with the inference result of nested clade phylogeographical analysis (NCPA) showing contiguous range expansion for C. herzensteini. The lack of phylogeographical structure for the species may reflect a recent range expansion after the glacial maximum and insufficient time to attain migration-drift equilibrium.     

Extinction and recolonization of maritime Antarctica in the limpet Nacella concinna (Strebel, 1908) during the last glacial cycle: toward a model of Quaternary biogeography in shallow Antarctic invertebrates

Quaternary glaciations in Antarctica drastically modified geographical ranges and population sizes of marine benthic invertebrates and thus affected the amount and distribution of intraspecific genetic variation. Here, we present new genetic information in the Antarctic limpet Nacella concinna, a dominant Antarctic benthic species along shallow ice‐free rocky ecosystems. We examined the patterns of genetic diversity and structure in this broadcast spawner along maritime Antarctica and from the peri‐Antarctic island of South Georgia. Genetic analyses showed that N. concinna represents a single panmictic unit in maritime Antarctic. Low levels of genetic diversity characterized this population; its median‐joining haplotype network revealed a typical star‐like topology with a short genealogy and a dominant haplotype broadly distributed. As previously reported with nuclear markers, we detected significant genetic differentiation between South Georgia Island and maritime Antarctica populations. Higher levels of genetic diversity, a more expanded genealogy and the presence of more private haplotypes support the hypothesis of glacial persistence in this peri‐Antarctic island. Bayesian Skyline plot and mismatch distribution analyses recognized an older demographic history in South Georgia. Approximate Bayesian computations did not support the persistence of N. concinna along maritime Antarctica during the last glacial period, but indicated the resilience of the species in peri‐Antarctic refugia (South Georgia Island). We proposed a model of Quaternary Biogeography for Antarctic marine benthic invertebrates with shallow and narrow bathymetric ranges including (i) extinction of maritime Antarctic populations during glacial periods; (ii) persistence of populations in peri‐Antarctic refugia; and (iii) recolonization of maritime Antarctica following the deglaciation process.     

Demographic history of the trace metal hyperaccumulator Noccaea caerulescens (J. Presl and C. Presl) F. K. Mey. in Western Europe

Noccaea caerulescens (Brassicaceae) is a major pseudometallophyte model for the investigation of the genetics and evolution of metal hyperaccumulation in plants. We studied the population genetics and demographic history of this species to advance the understanding of among‐population differences in metal hyperaccumulation and tolerance abilities. Sampling of seven to 30 plants was carried out in 62 sites in Western Europe. Genotyping was carried out using a combination of new chloroplast and nuclear neutral markers. A strong genetic structure was detected, allowing the definition of three genetic subunits. Subunits showed a good geographic coherence. Accordingly, distant metallicolous populations generally belonged to distinct subunits. Approximate Bayesian computation analysis of demographic scenarios among subunits further supported a primary isolation of populations from the southern Massif Central prior to last glacial maximum, whereas northern populations may have derived during postglacial recolonization events. Estimated divergence times among subunits were rather recent in comparison with the species history, but certainly before the establishment of anthropogenic metalliferous sites. Our results suggest that the large‐scale genetic structure of N. caerulescens populations pre‐existed to the local adaptation to metalliferous sites. The population structure of quantitative variation for metal‐related adaptive traits must have established independently in isolated gene pools. However, features of the most divergent genetic unit (e.g. extreme levels of Cd accumulation observed in previous studies) question the putative relationships between adaptive evolution of metal‐related traits and subunits isolation. Finally, admixture signals among distant metallicolous populations suggest a putative role of human activities in facilitating long‐distance genetic exchanges.     

Exome resequencing reveals signatures of demographic and adaptive processes across the genome and range of black cottonwood (Populus trichocarpa)

Extant variation in temperate and boreal plant species has been influenced by both demographic histories associated with Pleistocene glacial cycles and adaptation to local climate. We used sequence capture to investigate the role of these neutral and adaptive processes in shaping diversity in black cottonwood (Populus trichocarpa). Nucleotide diversity and Tajima's D were lowest at replacement sites and highest at intergenic sites, while LD showed the opposite pattern. With samples grouped into three populations arrayed latitudinally, effective population size was highest in the north, followed by south and centre, and LD was highest in the south followed by the north and centre, suggesting a possible northern glacial refuge. F_ST outlier analysis revealed that promoter, 5′‐UTR and intronic sites were enriched for outliers compared with coding regions, while no outliers were found among intergenic sites. Codon usage bias was evident, and genes with synonymous outliers had 30% higher average expression compared with genes containing replacement outliers. These results suggest divergent selection related to regulation of gene expression is important to local adaptation in P. trichocarpa. Finally, within‐population selective sweeps were much more pronounced in the central population than in putative northern and southern refugia, which may reflect the different demographic histories of the populations and concomitant effects on signatures of genetic hitchhiking from standing variation.     

Contrasting phylogeographical patterns of two closely related species, Machilus thunbergii and Machilus kusanoi (Lauraceae), in Taiwan

Aim The purpose of this paper was to study the patterns of genetic variation, demographic history, haplotype relationships and potential location of diversity centres of two closely related species, Machilus thunbergii and Machilus kusanoi. Location The phylogeography of M. thunbergii and M. kusanoi was examined by sampling 110 and 106 individuals from 25 and 16 sampling sites, respectively, across their distributional range in Taiwan. Machilus thunbergii is distributed on the Asian mainland, South Korea, southern Japan, the Ryukyus, Taiwan and the Philippines, whereas M. kusanoi is endemic to Taiwan. These two species are closely related, and both are widely distributed in Taiwan but occupy different altitudinal zones and habitats. Methods The range‐wide variation of M. thunbergii and M. kusanoi in Taiwan was studied using chloroplast DNA (cpDNA) variations. A haplotype network was constructed with the computer program tcs . Nested clade analysis was conducted with the computer program ceodis , and various parameters of genetic diversity were calculated and neutrality tested by the computer program Dna SP. Population differentiation was estimated using the programs arlequin and hapstep . The contribution of the populations to gene diversity and to allelic richness was calculated using the software contrib . The level of divergence for each population from the remaining populations was calculated as the mean value of pairwise F_ST for each population against the rest of the populations. Results Extremely low levels of genetic differentiation were found for both species. This result suggested that these two species probably survived in multiple relict refugia with different population sizes throughout the island during low‐temperature periods of the Pleistocene. In addition, nested clade analysis (NCA) of cpDNA haplotypes indicated that restricted gene flow with isolation‐by‐distance characterized the recolonization after the Pleistocene by Tashueshan and Shiouhluan populations of M. thunbergii in the north‐central area west of the Central Mountain Range (CMR). In contrast, NCA analysis indicated that a major diversity centre on the southern tip of the island (Kending population) and contiguous range expansion characterized the recolonization by M. kusanoi of northern areas along the east side of the CMR. The major diversity centres found for the two species examined were further supported by the results of the mean F_ST for individual populations in comparison with other populations, and of the contribution of the divergence component to the total diversity. Main conclusions This research supports the multiple relict refugia hypothesis for both species investigated. Populations of M. thunbergii at Shiouhluan and Tashueshan in the north‐central area west of the CMR represent a diversity centre currently expanding its size. A diversity centre at the southern‐edge population of M. kusanoi, and a contiguous range expansion from Kending, were found. These results indicate that the M. thunbergii populations at Tashueshan and Shiouhluan and the M. kusanoi population at Kending, and even Soukar, are evolutionarily significant units for conservation programmes.     

Molecular phylogeography of Dryas integrifolia: glacial refugia and postglacial recolonization

Chloroplast DNA variation in the Arctic plant species Dryas integrifolia (Rosaceae) was analysed in relation to both the present-day geographical distribution of populations and to Pleistocene fossil records of this species. The phylogeographical structure was weak but the analysis of haplotype diversity revealed several groups of haplotypes having present-day geographical ranges that overlap locations postulated from geographical and fossil evidence to have been glacial refugia. Based on this information we infer that two important refugial sources of Arctic recolonization by this species were Beringia and the High Arctic. Two other putative refugia, located southeast of the ice sheet and along coastal regions of the eastern Arctic may have served as sources for recolonization of smaller portions of the Arctic. The genetic substructure in the species is mostly due to variation among populations regardless of the ecogeographical region in which they are found. Spatial autocorrelation at the regional scale was also detected. High levels of diversity both within populations and ecogeographical regions are probably indicative of population establishment from several sources possibly combined with recent gene flow.     

PHENOTYPIC DIFFERENTIATION AT SOUTHERN LIMIT BORDERS: THE CASE STUDY OF TWO FUCOID MACROALGAL SPECIES WITH DIFFERENT LIFE‐HISTORY TRAITS1

Marginal populations are often geographically isolated, smaller, and more fragmented than central populations and may frequently have to face suboptimal local environmental conditions. Persistence of these populations frequently involves the development of adaptive traits at phenotypic and genetic levels. We compared population structure and demographic variables in two fucoid macroalgal species contrasting in patterns of genetic diversity and phenotypic plasticity at their southern distribution limit with a more central location. Models were Ascophyllum nodosum (L.) Le Jol. (whose extreme longevity and generation overlap may buffer genetic loss by drift) and Fucus serratus L. (with low genetic diversity at southern margins). At edge locations, both species exhibited trends in life‐history traits compatible with population persistence but by using different mechanisms. Marginal populations of A. nodosum had higher reproductive output in spite of similar mortality rates at all life stages, making edge populations denser and with smaller individuals. In F. serratus, rather than demographic changes, marginal populations differed in habitat, occurring restricted to a narrower vertical habitat range. We conclude that persistence of both A. nodosum and F. serratus at the southern‐edge locations depends on different strategies. Marginal population persistence in A. nodosum relies on a differentiation in life‐history traits, whereas F. serratus, putatively poorer in evolvability potential, is restricted to a narrower vertical range at border locations. These results contribute to the general understanding of mechanisms that lead to population persistence at distributional limits and to predict population resilience under a scenario of environmental change.     

Patterns of seed dispersal and pollen flow in Quercus garryana (Fagaceae) following post-glacial climatic changes

Aim We examined the genetic structure of Quercus garryana to infer post‐glacial patterns of seed dispersal and pollen flow to test the hypotheses that (1) peripheral populations are genetically distinct from core populations and from one another; (2) genetic diversity declines towards the poleward edge of the species’ range; and (3) genetic diversity in the chloroplast genome, a direct measure of seed dispersal patterns, declines more sharply with increasing latitude than diversity in the nuclear genome. We address our findings in the context of known historical oak distribution from pollen core data derived from previously published research. Location Oak–savanna ecosystems from southern Oregon, USA (core populations/non‐glaciated range) northward to Vancouver Island, British Columbia, Canada (peripheral populations/glaciated range). Methods We genotyped 378 trees from 22 sites with five chloroplast and seven nuclear microsatellite loci. For both sets of markers, we estimated genetic diversity and differentiation using an analysis of molecular variance and generated Mantel correlograms to detect genetic and geographical distance correlations. For the nuclear markers, we also used a Bayesian approach to infer population substructure. Results There was a large degree of population differentiation revealed by six chloroplast haplotypes, with little (≤ 3) or no haplotype diversity within sites. Peripheral island locations shared the same, maternally inherited chloroplast haplotype, whereas locations in mainland Washington had greater haplotype diversity. In contrast, genetic diversity of the nuclear markers was high at all locations sampled. Populations clustered into two groups and were significantly positively correlated over large spatial scales (≤ 200 km), although allele richness decreased significantly with latitude. Population substructure was observed between core and peripheral populations because rare alleles were absent in peripheral localities and common allele frequencies differed. Main conclusions The observed pattern of chloroplast haplotype loss at the northern periphery suggests restricted seed dispersal events from mainland sites to peripheral islands. This pattern was unexpected, however, as refugial oak populations remained near the current post‐glacial range even during the Last Glacial Maximum. Using nuclear markers, we found high within‐population diversity and population differentiation only over large spatial scales, suggesting that pollen flow is relatively high among populations.     

The effect of past climatic oscillations on spatial genetic structure of Atraphaxis manshurica (Polygonoideae) in the Horqin sandlands,northern China

To investigate the effect of past climate oscillations on the genetic diversity and demographic history of organisms in the Horqin sandlands, at the margin of the monsoonal zone in northern China. We selected Atraphaxis manshurica as a model and examined the spatial genetic structure in populations of this species across most of its covered range. Five haplotypes were identified on the basis of two chloroplast DNA sequences (psbK-psbI and psbB-psbH) in 127 individuals from 11 natural populations. The total genetic diversity (H_T = 0.437) of A. manshurica is low compared with species to the west in arid northwestern China, outside of monsoonal influence. Analysis of molecular variance (AMOVA) indicates that genetic differentiation primarily occurred among two geographical groups distinguished by spatial analysis of molecular variance (SAMOVA). The BEAST molecular clock approach revealed that genetic divergence of the species mostly occurred in middle-late Pleistocene, in accordance with the periodic glacial periods and accompanying monsoonal changes. From species distribution modeling (SDM), we found that the species experienced range contraction and southward retreat during the Last Glacial Maximum (LGM). The current genetic pattern and demographic history may have thus been shaped by glacial–interglacial cycles and changes of habitat since the middle Pleistocene.     

A range-wide genetic bottleneck overwhelms contemporary landscape factors and local abundance in shaping genetic patterns of an alpine butterfly (Lepidoptera: Pieridae: Colias behrii)

Spatial and environmental heterogeneity are major factors in structuring species distributions in alpine landscapes. These landscapes have also been affected by glacial advances and retreats, causing alpine taxa to undergo range shifts and demographic changes. These nonequilibrium population dynamics have the potential to obscure the effects of environmental factors on the distribution of genetic variation. Here, we investigate how demographic change and environmental factors influence genetic variation in the alpine butterfly Colias behrii. Data from 14 microsatellite loci provide evidence of bottlenecks in all population samples. We test several alternative models of demography using approximate Bayesian computation (ABC), with the results favouring a model in which a recent bottleneck precedes rapid population growth. Applying independent calibrations to microsatellite loci and a nuclear gene, we estimate that this bottleneck affected both northern and southern populations 531–281 years ago, coinciding with a period of global cooling. Using regression approaches, we attempt to separate the effects of population structure, geographical distance and landscape on patterns of population genetic differentiation. Only 40% of the variation in F_ST is explained by these models, with geographical distance and least‐cost distance among meadow patches selected as the best predictors. Various measures of genetic diversity within populations are also decoupled from estimates of local abundance and habitat patch characteristics. Our results demonstrate that demographic change can have a disproportionate influence on genetic diversity in alpine species, contrasting with other studies that suggest landscape features control contemporary demographic processes in high‐elevation environments.     

Range edges and the molecular divergence of Greya moth populations

Aim We investigated the geographical pattern of genetic divergence and demographic history in the prodoxid moth Greya obscura throughout its entire geographical range in far western North America and compared it to the geographical patterns found in a previously studied species, Greya politella, which co‐occurs over the same range, in the same habitats, and on the same host plants. Location The study included sites distributed throughout the California Floristic Province. Methods We used analysis of cytochrome c oxidase subunit I (COI) and amplified fragment length polymorphisms to evaluate the pattern and history of genetic continuity among populations. Results Greya obscura populations show a history of spatial expansion with considerable haplotype diversity in the centre of the geographical range. As with G. politella, some range‐edge populations of G. obscura are sufficiently divergent (6.7% in COI) to be considered as potentially cryptic species. Greya obscura and G. politella, however, differ in the specific range‐edge sites showing greatest genetic divergence and cryptic speciation. Main conclusions These results corroborate the view that range edges are important cradles of divergence and speciation. In addition, the results indicate that the geographical pattern of divergence at edges may differ even among closely related species occupying the same habitats and using the same hosts.     

Evidence for a large-scale population structure of Arabidopsis thaliana from genome-wide single nucleotide polymorphism markers

Population-based methods for the genetic mapping of adaptive traits and the analysis of natural selection require that the population structure and demographic history of a species are taken into account. We characterized geographic patterns of genetic variation in the model plant Arabidopsis thaliana by genotyping 115 genome-wide single nucleotide polymorphism (SNP) markers in 351 accessions from the whole species range using a matrix-assisted laser desorption/ionization time-of-flight assay, and by sequencing of nine unlinked short genomic regions in a subset of 64 accessions. The observed frequency distribution of SNPs is not consistent with a constant-size neutral model of sequence polymorphism due to an excess of rare polymorphisms. There is evidence for a significant population structure as indicated by differences in genetic diversity between geographic regions. Accessions from Central Asia have a low level of polymorphism and an increased level of genome-wide linkage disequilibrium (LD) relative to accessions from the Iberian Peninsula and Central Europe. Cluster analysis with the structure program grouped Eurasian accessions into K=6 clusters. Accessions from the Iberian Peninsula and from Central Asia constitute distinct populations, whereas Central and Eastern European accessions represent admixed populations in which genomes were reshuffled by historical recombination events. These patterns likely result from a rapid postglacial recolonization of Eurasia from glacial refugial populations. Our analyses suggest that mapping populations for association or LD mapping should be chosen from regional rather than a species-wide sample or identified genetically as sets of individuals with similar average genetic distances. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Variation in the chloroplast DNA of Swiss stone pine (Pinus cembra L.) reflects contrasting post-glacial history of populations from the Carpathians and the Alps

Aim To characterize the genetic structure and diversity of Pinus cembra L. populations native to two disjunct geographical areas, the Alps and the Carpathians, and to evaluate the rate of genetic differentiation among populations. Location The Swiss Alps and the Carpathians. Methods We screened 28 populations at three paternally inherited chloroplast simple sequence repeats (cpSSRs) for length variation in their mononucleotide repeats. Statistical analysis assessed haplotypic variation and fixation indices. Hierarchical analysis of molecular variance (AMOVA), Mantel test, spatial analysis of molecular variance (SAMOVA) and barrier analyses were applied to evaluate the geographical partitioning of genetic diversity across the species’ range. Results Haplotypic diversity was generally high throughout the natural range of P. cembra, with the mean value substantially higher in the Carpathians (H = 0.53) than in the Alps (H = 0.35). The isolated Carpathian populations showed the highest haplotype diversity among the populations originating from the High Tatras (Velka Studena Dolina) and South Carpathians (Retezat Mountains). AMOVA revealed that only 3% of the total genetic variation derived from genetic differentiation between the two mountain ranges. Differentiation among Carpathian populations was higher (F_ST = 0.19) than among Alpine populations (F_ST = 0.04). Low, but significant, correlation was found between the geographical and genetic distances among pairs of populations (r = 0.286, P < 0.001). SAMOVA results revealed no evident geographical structure of populations. barrier analysis showed the strongest differentiation in the eastern part of the species’ range, i.e. in the Carpathians. Main conclusions The populations of P. cembra within the two parts of the species’ range still share many cpDNA haplotypes, suggesting a common gene pool conserved from a previously large, continuous distribution range. Carpathian populations have maintained high haplotypic variation, even higher than Alpine populations, despite their small population sizes and spatial isolation. Based on our results, we emphasize the importance of the Carpathian populations of Swiss stone pine for conservation. These populations comprise private haplotypes and they may represent a particular legacy of the species’ evolutionary history.     

Population genetic structure and phylogeographical pattern of rice grasshopper, <Emphasis Type="Italic">Oxya hyla intricata</Emphasis>, across Southeast Asia

The rice grasshopper, Oxya hyla intricata, is a rice pest in Southeast Asia. In this study, population genetic diversity and structure of this Oxya species was examined using both DNA sequences and AFLP technology. The samples of 12 populations were collected from four Southeast Asian countries, among which 175 individuals were analysed using mitochondrial DNA cytochrome c oxidase subunit I (COI) sequences, and 232 individuals were examined using amplified fragment length polymorphisms (AFLP) to test whether the phylogeographical pattern and population genetics of this species are related to past geological events and/or climatic oscillations. No obvious trend of genetic diversity was found along a latitude/longitude gradient among different geographical groups. Phylogenetic analysis indicated three deep monophyletic clades that approximately correspond to three geographical regions separated by high mountains and a deep strait, and TCS analysis also revealed three disconnected networks, suggesting that spatial and temporal separations by vicariance, which were also supported by AMOVA as a source of the molecular variance presented among groups. Gene flow analysis showed that there had been frequent historical gene flow among local populations in different regions, but the networks exhibited no shared haplotype among populations. In conclusion, the past geological events and climatic fluctuations are the most important factor on the phylogeographical structure and genetic patterns of O. hyla intricata in Southeast Asia. Habitat, vegetation, and anthropogenic effect may also contribute to gene flow and introgression of this species. Moreover, temperature, abundant rainfall and a diversity of graminaceous species are beneficial for the migration of O. hyla intricata. High haplotype diversity, deep phylogenetic division, negative Fu’s F _s values and unimodal and multimodal distribution shapes all suggest a complicated demographic expansion pattern of these O. hyla intricata populations, which might have been caused by climatic oscillations during glacial periods in the Quaternary.     

Demographic inference and genetic diversity of <Emphasis Type="Italic">Octopus mimus</Emphasis> (Cephalopoda: Octopodidae) throughout the Humboldt Current System

Climatic and oceanographic events occurring during the last glacial cycle in the Humboldt Current System (HCS) have left genetic footprints in marine invertebrate populations. The objective of this study was to evaluate the effect of the glacial period on Octopus mimus populations found throughout the HCS. This species lays a large number of small eggs which hatch into planktonic paralarvae with the potential to undergo wide dispersal. We sequenced the COIII gene to perform phylogeographic analyses of 197 octopuses sampled from seven localities. The genetic diversity of Octopus mimus was low and decreased towards the southern end of the distribution range, which comprises a single population. The haplotype genealogy and Bayesian Skyride plot suggest that O. mimus underwent a demographic expansion after the last glacial maximum (LGM). This would imply a contraction of the range of this organism toward northern latitudes during the LGM followed by southward expansion and recolonization once the contemporary interglacial period began.