Drastic post‐LGM expansion and lack of historical genetic structure of a subtropical fig‐pollinating wasp (Ceratosolen sp. 1) of Ficus septica in Taiwan

The climatic oscillations of the last glacial period have had profound influences on the demography and levels of genetic diversity of extant species. Molecular evidence of glacial effects on temperate species has been well documented, whereas little is known regarding that on subtropical species. Here we present analyses based on partial sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene (1052 bp) and genotypes at 15 microsatellite loci to investigate the historical demography, population structure and ongoing gene flow of an undescribed fig‐pollinating wasp (Ceratosolen sp. 1) of Ficus septica in subtropical Taiwan. Reconstructed historical demography based on the coalescent tree of COI sequences suggests that C. sp. 1 has undergone a drastic population expansion which was tightly coupled with climatic changes since the last glacial maximum (LGM). The magnitude of the population size change was approximately 500‐fold, indicating that the population of this wasp and its host was likely highly compressed during the last glacial period. The lack of significant population differentiation (F_ST < 0.02, for all pairwise F_ST values) may be due to rapid postglacial expansion facilitated by long‐distance dispersal, although a low frequency of first‐generation migrants was detected. Our results clearly demonstrate how recent climatic changes since the LGM and dispersal ability have jointly shaped the genetic composition of a subtropical fig‐pollinating wasp.     

Using genetic variation to infer associations with climate in the common frog,Rana temporaria

Recent and historical species' associations with climate can be inferred using molecular markers. This knowledge of population and species‐level responses to climatic variables can then be used to predict the potential consequences of ongoing climate change. The aim of this study was to predict responses of Rana temporaria to environmental change in Scotland by inferring historical and contemporary patterns of gene flow in relation to current variation in local thermal conditions. We first inferred colonization patterns within Europe following the last glacial maximum by combining new and previously published mitochondrial DNA sequences. We found that sequences from our Scottish samples were identical to (92%), or clustered with, the common haplotype previously identified from Western Europe. This clade showed very low mitochondrial variation, which did not allow inference of historical colonization routes but did allow interpretation of patterns of current fine‐scale population structure without consideration of confounding historical variation. Second, we assessed fine‐scale microsatellite‐based patterns of genetic variation in relation to current altitudinal temperature gradients. No population structure was found within altitudinal gradients (average F_ST = 0.02), despite a mean annual temperature difference of 4.5 °C between low‐ and high‐altitude sites. Levels of genetic diversity were considerable and did not vary between sites. The panmictic population structure observed, even along temperature gradients, is a potentially positive sign for R. temporaria persistence in Scotland in the face of a changing climate. This study demonstrates that within taxonomic groups, thought to be at high risk from environmental change, levels of vulnerability can vary, even within species.     

Genetic connectivity among swarming sites in the wide ranging and recently declining little brown bat (Myotis lucifugus)

Characterizing movement dynamics and spatial aspects of gene flow within a species permits inference on population structuring. As patterns of structuring are products of historical and current demographics and gene flow, assessment of structure through time can yield an understanding of evolutionary dynamics acting on populations that are necessary to inform management. Recent dramatic population declines in hibernating bats in eastern North America from white‐nose syndrome have prompted the need for information on movement dynamics for multiple bat species. We characterized population genetic structure of the little brown bat, Myotis lucifugus, at swarming sites in southeastern Canada using 9 nuclear microsatellites and a 292‐bp region of the mitochondrial genome. Analyses of F_ST, Φ_ST, and Bayesian clustering (STRUCTURE) found weak levels of genetic structure among swarming sites for the nuclear and mitochondrial genome (Global F_ST = 0.001, P < 0.05, Global Φ_ST = 0.045, P < 0.01, STRUCTURE K = 1) suggesting high contemporary gene flow. Hierarchical AMOVA also suggests little structuring at a regional (provincial) level. Metrics of nuclear genetic structure were not found to differ between males and females suggesting weak asymmetries in gene flow between the sexes. However, a greater degree of mitochondrial structuring does support male‐biased dispersal long term. Demographic analyses were consistent with past population growth and suggest a population expansion occurred from approximately 1250 to 12,500 BP, following Pleistocene deglaciation in the region. Our study suggests high gene flow and thus a high degree of connectivity among bats that visit swarming sites whereby mainland areas of the region may be best considered as one large gene pool for management and conservation.     

Quantifying past and present connectivity illuminates a rapidly changing landscape for the African elephant

There is widespread concern about impacts of land‐use change on connectivity among animal and plant populations, but those impacts are difficult to quantify. Moreover, lack of knowledge regarding ecosystems before fragmentation may obscure appropriate conservation targets. We use occurrence and population genetic data to contrast connectivity for a long‐lived mega‐herbivore over historical and contemporary time frames. We test whether (i) historical gene flow is predicted by persistent landscape features rather than human settlement, (ii) contemporary connectivity is most affected by human settlement and (iii) recent gene flow estimates show the effects of both factors. We used 16 microsatellite loci to estimate historical and recent gene flow among African elephant (Loxodonta africana) populations in seven protected areas in Tanzania, East Africa. We used historical gene flow (F_ST and G'_ST) to test and optimize models of historical landscape resistance to movement. We inferred contemporary landscape resistance from elephant resource selection, assessed via walking surveys across ~15 400 km² of protected and unprotected lands. We used assignment‐based recent gene flow estimates to optimize and test the contemporary resistance model, and to test a combined historical and contemporary model. We detected striking changes in connectivity. Historical connectivity among elephant populations was strongly influenced by slope but not human settlement, whereas contemporary connectivity was influenced most by human settlement. Recent gene flow was strongly influenced by slope but was also correlated with contemporary resistance. Inferences across multiple timescales can better inform conservation efforts on large and complex landscapes, while mitigating the fundamental problem of shifting baselines in conservation.     

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.     

Multilocus phylogeography and population structure of common eiders breeding in North America and Scandinavia

Aim Glacial refugia during the Pleistocene had major impacts on the levels and spatial apportionment of genetic diversity of species in northern latitude ecosystems. We characterized patterns of population subdivision, and tested hypotheses associated with locations of potential Pleistocene refugia and the relative contribution of these refugia to the post‐glacial colonization of North America and Scandinavia by common eiders (Somateria mollissima). Specifically, we evaluated localities hypothesized as ice‐free areas or glacial refugia for other Arctic vertebrates, including Beringia, the High Arctic Canadian Archipelago, Newfoundland Bank, Spitsbergen Bank and north‐west Norway. Location Alaska, Canada, Norway and Sweden. Methods Molecular data from 12 microsatellite loci, the mitochondrial DNA (mtDNA) control region, and two nuclear introns were collected and analysed for 15 populations of common eiders (n = 716) breeding throughout North America and Scandinavia. Population genetic structure, historical population fluctuations and gene flow were inferred using F‐statistics, analyses of molecular variance, and multilocus coalescent analyses. Results Significant inter‐population variation in allelic and haplotypic frequencies were observed (nuclear DNA F_ST = 0.004–0.290; mtDNA Φ_ST = 0.051–0.927). Whereas spatial differentiation in nuclear genes was concordant with subspecific designations, geographic proximity was more predictive of inter‐population variance in mitochondrial DNA haplotype frequency. Inferences of historical population demography were consistent with restriction of common eiders to four geographic areas during the Last Glacial Maximum: Belcher Islands, Newfoundland Bank, northern Alaska and Svalbard. Three of these areas coincide with previously identified glacial refugia: Newfoundland Bank, Beringia and Spitsbergen Bank. Gene‐flow and clustering analyses indicated that the Beringian refugium contributed little to common eider post‐glacial colonization of North America, whereas Canadian, Scandinavian and southern Alaskan post‐glacial colonization is likely to have occurred in a stepwise fashion from the same glacial refugium. Main conclusions Concordance of proposed glacial refugia used by common eiders and other Arctic species indicates that Arctic and subarctic refugia were important reservoirs of genetic diversity during the Pleistocene. Furthermore, suture zones identified at MacKenzie River, western Alaska/Aleutians and Scandinavia coincide with those identified for other Arctic vertebrates, suggesting that these regions were strong geographic barriers limiting dispersal from Pleistocene refugia.     

Resurrecting an extinct salmon evolutionarily significant unit: archived scales, historical DNA and implications for restoration

Archival scales from 603 sockeye salmon (Oncorhynchus nerka), sampled from May to July 1924 in the lower Columbia River, were analysed for genetic variability at 12 microsatellite loci and compared to 17 present‐day O. nerka populations—exhibiting either anadromous (sockeye salmon) or nonanadromous (kokanee) life histories—from throughout the Columbia River Basin, including areas upstream of impassable dams built subsequent to 1924. Statistical analyses identified four major genetic assemblages of sockeye salmon in the 1924 samples. Two of these putative historical groupings were found to be genetically similar to extant evolutionarily significant units (ESUs) in the Okanogan and Wenatchee Rivers (pairwise F_ST = 0.004 and 0.002, respectively), and assignment tests were able to allocate 77% of the fish in these two historical groupings to the contemporary Okanogan River and Lake Wenatchee ESUs. A third historical genetic grouping was most closely aligned with contemporary sockeye salmon in Redfish Lake, Idaho, although the association was less robust (pairwise F_ST = 0.060). However, a fourth genetic grouping did not appear to be related to any contemporary sockeye salmon or kokanee population, assigned poorly to the O. nerka baseline, and had distinctive early return migration timing, suggesting that this group represents a historical ESU originating in headwater lakes in British Columbia that was probably extirpated sometime after 1924. The lack of a contemporary O. nerka population possessing the genetic legacy of this extinct ESU indicates that efforts to reestablish early‐migrating sockeye salmon to the headwater lakes region of the Columbia River will be difficult.     

Differential effects of historical migration,glaciations and human impact on the genetic structure and diversity of the mountain pasture weed Veratrum album L.

Aim Today’s genetic population structure and diversity of species can be understood as the result of range expansion from the area of origin, past climatic oscillations and contemporary processes. We examined the relative importance of these factors in Veratrum album L., a toxic weed of mountain grasslands. Location Continental Europe. Methods Forty populations from the Asian border (Urals and Caucasus) to Portugal were studied using amplified fragment length polymorphisms (AFLPs) combined with selected plant and population measures. The data were analysed with phylogenetic, population genetic and regression methods inferring both genetic structure and diversity from geographic and ecological factors. Results Fragment frequency clines together with genetic distance clustering and principal coordinates analysis indicated an east–west direction in the genetic structure of V. album, suggesting ancient migration into Europe from a proposed Asian origin. However, the strong geographic pattern in the genetic structure, pronounced isolation by distance (R² = 0.74) and moderate overall population differentiation (F_ST = 0.13) suggests high historical gene flow, possibly during glacials, and vicariance into mountainous regions during interglacials. Occurrence of V. album during the last glaciation in several areas along the periphery of the Alps and recolonization of this mountain range from both eastern and central–western areas was indicated. Genetic diversity was highest in central Europe, a pattern that did not agree with the expectations from east–west migration into Europe. Furthermore, managed habitats showed higher levels of genetic diversity compared to unmanaged habitats. Stepwise linear regression determined shoot density and soil phosphorus as the main predictors of within‐population genetic diversity (R² = 0.40). Main conclusions Our results showed that V. album retained genetic imprints of historical range expansion into Europe, although this was alleviated by the influence of climatic oscillations and contemporary processes. For example, genetic population structure was strongly affected by post‐glacial vicariance while patterns of genetic diversity seemed mainly to be influenced by human land use. Our findings highlight the importance of applying a synthetic approach, testing the influence of both historical and contemporary processes on genetic structure and diversity in order to understand complex phylogeographic patterns. This may especially apply to widespread species, such as weeds. Implications of our findings for biological control are briefly discussed.     

Differential introgression from a sister species explains high FST outlier loci within a mussel species

Scanning genomes for loci with high levels of population differentiation has become a standard of population genetics. F_ST outlier loci are most often interpreted as signatures of local selection, but outliers might arise for many other reasons too often left unexplored. Here, we tried to identify further the history and genetic basis underlying strong differentiation at F_ST outlier loci in a marine mussel. A genome scan of genetic differentiation has been conducted between Atlantic and Mediterranean populations of Mytilus galloprovincialis. The differentiation was low overall (F_ST = 0.03), but seven loci (2%) were strong F_ST outliers. We then analysed DNA sequence polymorphism at two outlier loci. The genetic structure proved to be the consequence of differential introgression of alleles from the sister‐hybridizing species Mytilus edulis. Surprisingly, the Mediterranean population was the most introgressed at these two loci, although the contact zone between the two species is nowadays localized along the Atlantic coasts of France and the British Isles. A historical contact between M. edulis and Mediterranean M. galloprovincialis should have happened during glacial periods. It proved difficult to disentangle two hypotheses: (i) introgression was adaptive, implying edulis alleles have been favoured in Mediterranean populations, or (ii) the genetic architecture of the barrier to edulis gene flow is different between the two M. galloprovincialis backgrounds. Five of the seven outliers between M. galloprovincialis populations were also outliers between M. edulis and Atlantic M. galloprovincialis, which would support the latter hypothesis. Differential introgression across semi‐permeable barriers to gene flow is a neglected scenario to interpret outlying loci that may prove more widespread than anticipated.     

Development of genetic diversity,differentiation and structure over 500 years in four ponderosa pine populations

Population history plays an important role in shaping contemporary levels of genetic variation and geographic structure. This is especially true in small, isolated range‐margin populations, where effects of inbreeding, genetic drift and gene flow may be more pronounced than in large continuous populations. Effects of landscape fragmentation and isolation distance may have implications for persistence of range‐margin populations if they are demographic sinks. We studied four small, disjunct populations of ponderosa pine over a 500‐year period. We coupled demographic data obtained through dendroecological methods with microsatellite data to discern how and when contemporary levels of allelic diversity, among and within‐population levels of differentiation, and geographic structure, arose. Alleles accumulated rapidly following initial colonization, demonstrating proportionally high levels of gene flow into the populations. At population sizes of approximately 100 individuals, allele accumulation saturated. Levels of genetic differentiation among populations (F_ST and Jost's D_est) and diversity within populations (F_IS) remained stable through time. There was no evidence of geographic genetic structure at any time in the populations' history. Proportionally, high gene flow in the early stages of population growth resulted in rapid accumulation of alleles and quickly created relatively homogenous genetic patterns among populations. Our study demonstrates that contemporary levels of genetic diversity were formed quickly and early in population development. How contemporary genetic diversity accumulates over time is a key facet of understanding population growth and development. This is especially relevant given the extent and speed at which species ranges are predicted to shift in the coming century.     

Historical vicariance and male-mediated gene flow in the toad-headed lizards Phrynocephalus przewalskii

Using mitochondrial and microsatellite DNA data and a population genetic approach, we tested male‐mediated gene flow in the toad‐headed lizards Phrynocephalus przewalskii. The mitochondrial DNA (ND2 gene), on the one hand, revealed two major lineages and a strong population genetic structure (F_ST = 0.692; F_ST′ = 0.995). The pairwise differences between the two lineages ranged from 2.1% to 6.4% and the geographical division of the two lineages coincided with a mountain chain consisting of the Helan and Yin Mountains, suggesting a historical vicariant pattern. On the other hand, the nuclear microsatellite DNA revealed a significant but small population genetic structure (F_ST = 0.017; F_ST′ = 0.372). The pairwise F_ST among the nine populations examined with seven microsatellite DNA loci ranged from 0.0062 to 0.0266; the assignment test failed to detect any naturally occurring population clusters. Furthermore, the populations demonstrated a weak isolation by distance and a northeast to southwest clinal variation, rather than a vicariant pattern. A historical vicariant event followed by male‐mediated gene flow appears to be the best explanation for the data. Approximately 2–5 Ma, climatic change may have created an uninhabitable zone along the Helan‐Yin mountain chain and initiated the divergence between the two mitochondrial lineages. With further climatic changes, males were able to disperse across the mountain chain, causing sufficient gene flow that eventually erased the vicariant pattern and drastically reduced the population genetic structure, while females remained philopatric and maintained the mitochondrial DNA (mtDNA) divergence. Although polygyny mating system and female philopatry may partially contribute to the reduced movement of females, other hypotheses, such as female intrasexual aggression, should also be explored.     

Spatial Patterns of Haplotype Variation in the Epiphytic Bromeliad Catopsis nutans

Identifying factors governing the origin, distribution, and maintenance of Neotropical plant diversity is an enduring challenge. To explore the complex and dynamic historical processes that shaped contemporary genetic patterns for a Central American plant species, we investigated the spatial distribution of chloroplast haplotypes of a geographically and environmentally widespread epiphytic bromeliad with wind‐dispersed seeds, Catopsis nutans, in Costa Rica. We hypothesized that genetic discontinuities occur between northwestern and southwestern Pacific slope populations, resembling patterns reported for other plant taxa in the region. Using non‐coding chloroplast DNA from 469 individuals and 23 populations, we assessed the influences of geographic and environmental distance as well as historical climatic variation on the genetic structure of populations spanning >1200 m in elevation. Catopsis nutans revealed seven haplotypes with low within‐population diversity (mean haplotype richness = 1.2) and moderate genetic structure (F_ST = 0.699). Pairwise F_ST was significantly correlated with both geographic and environmental distance. The frequency of dominant haplotypes was significantly correlated with elevation. A cluster of nine Pacific lowland populations exhibited a distinct haplotype profile and contained five of the seven haplotypes, suggesting historical isolation and limited seed‐mediated gene flow with other populations. Paleodistribution models indicated lowland and upland habitats in this region were contiguous through past climatic oscillations. Based on our paleodistribution analysis and comparable prior phylogeographic studies, the genetic signature of recent climatic oscillations are likely superimposed upon the distribution of anciently divergent lineages. Our study highlights the unique phylogeographic history of a Neotropical plant species spanning an elevation gradient.     

Genetic variability,local selection and demographic history: genomic evidence of evolving towards allopatric speciation in Asian seabass

Genomewide analysis of genetic divergence is critically important in understanding the genetic processes of allopatric speciation. We sequenced RAD tags of 131 Asian seabass individuals of six populations from South‐East Asia and Australia/Papua New Guinea. Using 32 433 SNPs, we examined the genetic diversity and patterns of population differentiation across all the populations. We found significant evidence of genetic heterogeneity between South‐East Asian and Australian/Papua New Guinean populations. The Australian/Papua New Guinean populations showed a rather lower level of genetic diversity. F_ST and principal components analysis revealed striking divergence between South‐East Asian and Australian/Papua New Guinean populations. Interestingly, no evidence of contemporary gene flow was observed. The demographic history was further tested based on the folded joint site frequency spectrum. The scenario of ancient migration with historical population size changes was suggested to be the best fit model to explain the genetic divergence of Asian seabass between South‐East Asia and Australia/Papua New Guinea. This scenario also revealed that Australian/Papua New Guinean populations were founded by ancestors from South‐East Asia during mid‐Pleistocene and were completely isolated from the ancestral population after the last glacial retreat. We also detected footprints of local selection, which might be related to differential ecological adaptation. The ancient gene flow was examined and deemed likely insufficient to counteract the genetic differentiation caused by genetic drift. The observed genomic pattern of divergence conflicted with the ‘genomic islands’ scenario. Altogether, Asian seabass have likely been evolving towards allopatric speciation since the split from the ancestral population during mid‐Pleistocene.     

Extensive sampling of polar bears (Ursus maritimus) in the Northwest Passage (Canadian Arctic Archipelago) reveals population differentiation across multiple spatial and temporal scales

As global warming accelerates the melting of Arctic sea ice, polar bears (Ursus maritimus) must adapt to a rapidly changing landscape. This process will necessarily alter the species distribution together with population dynamics and structure. Detailed knowledge of these changes is crucial to delineating conservation priorities. Here, we sampled 361 polar bears from across the center of the Canadian Arctic Archipelago spanning the Gulf of Boothia (GB) and M'Clintock Channel (MC). We use DNA microsatellites and mitochondrial control region sequences to quantify genetic differentiation, estimate gene flow, and infer population history. Two populations, roughly coincident with GB and MC, are significantly differentiated at both nuclear (F_ST = 0.01) and mitochondrial (Φ_ST = 0.47; F_ST = 0.29) loci, allowing Bayesian clustering analyses to assign individuals to either group. Our data imply that the causes of the mitochondrial and nuclear genetic patterns differ. Analysis of mtDNA reveals the matrilineal structure dates at least to the Holocene, and is common to individuals throughout the species’ range. These mtDNA differences probably reflect both genetic drift and historical colonization dynamics. In contrast, the differentiation inferred from microsatellites is only on the scale of hundreds of years, possibly reflecting contemporary impediments to gene flow. Taken together, our data suggest that gene flow is insufficient to homogenize the GB and MC populations and support the designation of GB and MC as separate polar bear conservation units. Our study also provide a striking example of how nuclear DNA and mtDNA capture different aspects of a species demographic history.     

Contrasted patterns of mitochondrial and nuclear structure among nursery colonies of the bat Myotis myotis

Thirteen nursery colonies of Myotis myotis were sampled in central Europe to investigate the dispersal behaviour of this bat species. Mitochondrial DNA sequences of 260 bats reveal the occurrence of three evolutionary lineages that have probably originated in distinct glacial refugia and meet in a contact zone near the Alps. Moreover, the strong haplotypic segregation (Φ_ST=0.540) suggests that breeding females are philopatric. Contrastingly, the low population structure at 15 microsatellite loci (F_ST=0.022), suggests the homogenizing effect of nuclear gene flow. The different perspectives given by these two markers are consistent with strong male‐biased dispersal. As a result of female philopatry, the local haplotypic variability seems to be largely influenced by historical processes of colonization. Conversely, the homogeneity of nuclear variability within roosts that are located north of the Alps seems to mainly reflect contemporary gene flow. Finally, despite the fact that females are faithful to their natal colony, movements of both males and females occur outside the breeding period. Mitochondrial survey of individuals sampled exclusively in nurseries may thus poorly reflect the metapopulation dynamics of this species.     

Global population genetic dynamics of a highly migratory,apex predator shark

Knowledge of genetic connectivity dynamics in the world's large‐bodied, highly migratory, apex predator sharks across their global ranges is limited. One such species, the tiger shark (Galeocerdo cuvier), occurs worldwide in warm temperate and tropical waters, uses remarkably diverse habitats (nearshore to pelagic) and possesses a generalist diet that can structure marine ecosystems through top‐down processes. We investigated the phylogeography and the global population structure of this exploited, phylogenetically enigmatic shark by using 10 nuclear microsatellites (n = 380) and sequences from the mitochondrial control region (CR, n = 340) and cytochrome oxidase I gene (n = 100). All three marker classes showed the genetic differentiation between tiger sharks from the western Atlantic and Indo‐Pacific ocean basins (microsatellite F_ST > 0.129; CR Φ_ST > 0.497), the presence of North vs. southwestern Atlantic differentiation and the isolation of tiger sharks sampled from Hawaii from other surveyed locations. Furthermore, mitochondrial DNA revealed high levels of intraocean basin matrilineal population structure, suggesting female philopatry and sex‐biased gene flow. Coalescent‐ and genetic distance‐based estimates of divergence from CR sequences were largely congruent (d_corr = 0.0015–0.0050), indicating a separation of Indo‐Pacific and western Atlantic tiger sharks <1 million years ago. Mitochondrial haplotype relationships suggested that the western South Atlantic Ocean was likely a historical connection for interocean basin linkages via the dispersal around South Africa. Together, the results reveal unexpectedly high levels of population structure in a highly migratory, behaviourally generalist, cosmopolitan ocean predator, calling for management and conservation on smaller‐than‐anticipated spatial scales.     

Pattern‐oriented modelling of population genetic structure

Although several statistical approaches can be used to describe patterns of genetic variation and infer stochastic differentiation, selective responses, or interruptions of gene flow due to physical or environmental barriers, it is worthwhile to note that similar processes, controlled by several parameters in theoretical models, frequently give rise to similar patterns. Here, we develop a Pattern‐Oriented Modelling (POM) approach that allows us to determine how a complex set of parameters potentially driving empirical genetic differentiation among populations generate alternative scenarios that can be fitted to observed data. We generated 10 000 random combinations of parameters related to population size, gene flow and response to gradients (both driven by dispersal and selection) in a spatially explicit model, and analysed simulated patterns with F_ST statistics and mean correlograms using Moran's I spatial autocorrelation coefficients. These statistics were compared with observed patterns for a tree species endemic to the Brazilian Cerrado. For a best match with observed F_ST (equal to 0.182), the important parameters driving simulated scenario are mainly related to population structure, including low population size with closed populations (low N_m), strong distance decay of gene flow, in addition to a strong effect of the initial variance of allele frequencies. These scenarios present a low autocorrelation of allele frequencies. Best matching of correlograms, on the other hand, appears in simulations with a large population size, high N_m and low population differentiation and F_ST (as well as more gene flow). Thus, targeting the two statistics (correlograms and F_ST) shows that best matches with empirical data with two distinct sets of parameters in the simulations, because observed patterns involve both a relatively high F_ST and significant autocorrelation. This conflict can be resolved by assuming that initial variance in allele frequencies can be interpreted as reflecting deep‐time historical variation and evolutionary dynamics of allele frequencies, creating a relatively high level of population differentiation, whereas current patterns in gene flow creates spatial autocorrelation. This make sense in terms of the previous knowledge on population differentiation in D. alata, especially if patterns are explained by a combination of isolation‐by‐distance and allelic surfing due to range expansion after the last glacial maximum. This reveals the potential for more complex applications of POM in population genetics. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 1152–1161.     

Genetic diversity and historical population structure of Schizopygopsis pylzovi (Teleostei: Cyprinidae) in the Qinghai–Tibetan Plateau

1. Complete sequences of 1140 base pair of the cytochrome b gene from 133 specimens were obtained from nine localities including the inflow drainage system, isolated lakes and outflow drainage system in Qinghai–Tibetan Plateau to assess genetic diversity and to infer population histories of the freshwater fish Schizopygopsis pylzovi. 2. Nucleotide diversities (π) were moderate (0.0024–0.0045) in populations from the outflow drainage system and Tuosuo Lake, but low (0.0018–0.0021) in populations from Qiadam Basin. It is probable that the low intra‐population variability is related with the paleoenvironmental fluctuation in Qiadam Basin, suggesting that the populations from Qiadam Basin have experienced severe bottleneck events in history. 3. Phylogenetic tree topologies indicate that the individuals from different populations did not form reciprocal monophyly, but the populations from the adjacent drainages cluster geographically. Most population pairwise F_ST tests were significant, with non‐significant pairwise tests between Tuosu Lake and Tuosuo Lake in the north‐west of the Qinghai–Tibetan Plateau. Analysis of molecular variance (amova ) indicates that the significant genetic variation was explained at the levels of catchments within and among, not among specific boundaries or inflow and outflow drainage systems. 4. The nested clade phylogeographical analysis indicates that historical processes are very important in the observed geographical structuring of S. pylzovi, and the contemporary population structure and differentiation of S. pylzovi may be consistent with the historical tectonic events occurred in the course of uplifts of the Qinghai–Tibetan Plateau. Fluctuations of the ecogeographical environment and major hydrographic formation might have promoted contiguous range expansion of freshwater fish populations, whereas the geological barriers among drainages have resulted in the fragmentation of population and restricted the gene flow among populations. 5. The significantly large negative F_s‐value (−24.91, P < 0.01) of Fu's F_s‐test and the unimodal mismatch distribution indicate that the species S. pylzovi underwent a sudden population expansion after the historical tectonic event of the Gonghe Movement. 6. The results of this study indicate that each population from the Qinghai–Tibetan Plateau should be managed and conserved separately and that efforts should be directed towards preserving the genetic integrity of each group.     

Multilocus genetic analyses and spatial modeling reveal complex population structure and history in a widespread resident North American passerine (Perisoreus canadensis)

An increasing body of studies of widely distributed, high latitude species shows a variety of refugial locations and population genetic patterns. We examined the effects of glaciations and dispersal barriers on the population genetic patterns of a widely distributed, high latitude, resident corvid, the gray jay (Perisoreus canadensis), using the highly variable mitochondrial DNA (mtDNA) control region and microsatellite markers combined with species distribution modeling. We sequenced 914 bp of mtDNA control region for 375 individuals from 37 populations and screened seven loci for 402 individuals from 27 populations across the gray jay range. We used species distribution modeling and a range of phylogeographic analyses (haplotype diversity, Φ_ST, SAMOVA, F_ST, Bayesian clustering analyses) to examine evolutionary history and population genetic structure. MtDNA and microsatellite markers revealed significant genetic differentiation among populations with high concordance between markers. Paleodistribution models supported at least five potential areas of suitable gray jay habitat during the last glacial maximum and revealed distributions similar to the gray jay's contemporary during the last interglacial. Colonization from and prolonged isolation in multiple refugia is evident. Historical climatic fluctuations, the presence of multiple dispersal barriers, and highly restricted gene flow appear to be responsible for strong genetic diversification and differentiation in gray jays.     

Diversity and genetic connectivity among populations of a threatened tree (<Emphasis Type="Italic">Dalbergia nigra</Emphasis>) in a recently fragmented landscape of the Brazilian Atlantic Forest

In this study we evaluated the influence of recent landscape fragmentation on the dynamics of remnant fragments from the Brazilian Atlantic Forest. This biome is one of the richest in the world and has been extensively deforested and fragmented. We sampled five populations of the threatened Dalbergia nigra, a tree endemic to the Brazilian Atlantic Forest, two located in a large reserve of continuous forest and three in fragments of different sizes and levels of disturbance. In order to assess historical changes, considering the longevity of the analyzed species, 119 adults and 116 saplings were genotyped for six microsatellite loci. Lower levels of genetic diversity were found in the most impacted fragments when compared to the most preserved population located inside the reserve, and there was significant genetic structure among the populations studied (pairwise F _ST = 0.031–0.152; pairwise D _EST = 0.039–0.301). However, genetic structure among saplings (F _ST = 0.056; D _EST = 0.231) was significantly lower than among adults (F _ST = 0.088; D _EST = 0.275). Estimates of contemporary gene flow based on assignment tests corroborated this result, suggesting that fragmentation led to an increase in gene flow. This connectivity among remnant fragments could mitigate the loss of genetic diversity through a metapopulation dynamic, but the high rate of habitat loss and the unknown long-term genetic effects add uncertainty. These results, taken together with the presence of private alleles in disturbed populations, highlight the importance of preserving the extant fragments.