Emergent patterns of population genetic structure for a coral reef community

What shapes variation in genetic structure within a community of codistributed species is a central but difficult question for the field of population genetics. With a focus on the isolated coral reef ecosystem of the Hawaiian Archipelago, we assessed how life history traits influence population genetic structure for 35 reef animals. Despite the archipelago's stepping stone configuration, isolation by distance was the least common type of genetic structure, detected in four species. Regional structuring (i.e. division of sites into genetically and spatially distinct regions) was most common, detected in 20 species and nearly in all endemics and habitat specialists. Seven species displayed chaotic (spatially unordered) structuring, and all were nonendemic generalist species. Chaotic structure also associated with relatively high global F_ST. Pelagic larval duration (PLD) was not a strong predictor of variation in population structure (R² = 0.22), but accounting for higher F_ST values of chaotic and invertebrate species, compared to regionally structured and fish species, doubled the power of PLD to explain variation in global F_ST (adjusted R² = 0.50). Multivariate correlation of eight species traits to six genetic traits highlighted dispersal ability, taxonomy (i.e. fish vs. invertebrate) and habitat specialization as strongest influences on genetics, but otherwise left much variation in genetic traits unexplained. Considering that the study design controlled for many sampling and geographical factors, the extreme interspecific variation in spatial genetic patterns observed for Hawaìi marine species may be generated by demographic variability due to species‐specific abundance and migration patterns and/or seascape and historical factors.     

Environmental and topographic variables shape genetic structure and effective population sizes in the endangered Yosemite toad

Aim Describing the landscape variables that accurately reflect how environmental and topographic variations affect population connectivity and demography is a major goal of landscape genetics and conservation biology. However, few landscape genetics studies have quantified the relationships between landscape variables and effective population size (N_e), although N_e is a key conservation and population genetics parameter. In this study, I estimated genetic structure and effective population sizes in the Yosemite toad (Bufo canorus) and tested for associations with environmental and geographic variables. Location Yosemite National Park, California, USA. Methods I estimated F_ST, D_ps and N_e using 10 microsatellite loci amplified from 781 individuals from 24 populations. I used three landscape variables (environmental variation, topography and slope) to generate geographic distance models and a series of regression analyses to identify the variables that contributed to genetic structure in this species. I also tested for correlations between N_e and a suite of variables, including geographic and genetic isolation, habitat suitability, elevation, temperature and precipitation. Results I found substantial variation in genetic distances between populations (F_ST = 0.004–0.396, D_ps = 0.045–0.839) and in effective population sizes (N_e = 9–52). Environmental variation and slope played important roles in explaining variation in genetic distances, and precipitation variables were significantly correlated with N_e. Main conclusions These results show that environmental and topographic variables are both important for understanding population connectivity in B. canorus and provide some of the first evidence, in any species, for a link between environmental variables and effective population size.     

Combining multiple analytical approaches for the identification of population structure and genetic delineation of two subspecies of the endemic Arabian burnet moth Reissita simonyi (Zygaenidae; Lepidoptera)

Habitat fragmentation and landscape topology may influence the genetic structure and connectivity between natural populations. Six microsatellite loci were used to infer the population structure of 35 populations (N = 788) of the alpine Arabian burnet moth Reissita simonyi (Lepidoptera, Zygaenidae) in Yemen and Oman. Due to the patchy distribution of larval food plants, R. simonyi is not continuously distributed throughout the studied area and the two recognized subspecies of this endemic species (Reissita s. simonyi/R. s. yemenicola) are apparently discretely distributed. All microsatellites showed prevalence of null alleles and therefore a thorough investigation of the impact of null alleles on different population genetic parameters (F _ST, inbreeding coefficients, and Population Graph topologies) is given. In general, null alleles reduced genetic covariance and independence of allele frequencies resulting in a more connected genetic topology in Population Graphs and an overestimation of pairwise F _ST values and inbreeding coefficients. Despite the presence of null alleles, Population Graphs also showed a much higher genetic connectivity within subspecies (and lower genetic differentiation (via F _ST)) than between; supporting existing taxonomic distinction. Partial Mantel tests showed that both geographical distance and altitude were highly correlated with the observed distribution of genetic structure within R. simonyi. In conclusion, we identified geographical and altitudinal distances in R. simonyi as well as an intervening desert area to be the main factors for spatial genetic structure in this species and show that the taxonomic division into two subspecies is confirmed by genetic analysis.     

Spatial differences in genetic diversity and northward migration suggest genetic erosion along the boreal caribou southern range limit and continued range retraction

With increasing human activities and associated landscape changes, distributions of terrestrial mammals become fragmented. These changes in distribution are often associated with reduced population sizes and loss of genetic connectivity and diversity (i.e., genetic erosion) which may further diminish a species' ability to respond to changing environmental conditions and lead to local population extinctions. We studied threatened boreal caribou (Rangifer tarandus caribou) populations across their distribution in Ontario/Manitoba (Canada) to assess changes in genetic diversity and connectivity in areas of high and low anthropogenic activity. Using data from >1,000 caribou and nine microsatellite loci, we assessed population genetic structure, genetic diversity, and recent migration rates using a combination of network and population genetic analyses. We used Bayesian clustering analyses to identify population genetic structure and explored spatial and temporal variation in those patterns by assembling networks based on R_ST and F_ST as historical and contemporary genetic edge distances, respectively. The Bayesian clustering analyses identified broad‐scale patterns of genetic structure and closely aligned with the R_ST network. The F_ST network revealed substantial contemporary genetic differentiation, particularly in areas presenting contemporary anthropogenic disturbances and habitat fragmentation. In general, relatively lower genetic diversity and greater genetic differentiation were detected along the southern range limit, differing from areas in the northern parts of the distribution. Moreover, estimation of migration rates suggested a northward movement of animals away from the southern range limit. The patterns of genetic erosion revealed in our study suggest ongoing range retraction of boreal caribou in central Canada.     

Seascape continuity plays an important role in determining patterns of spatial genetic structure in a coral reef fish

Detecting patterns of spatial genetic structure (SGS) can help identify intrinsic and extrinsic barriers to gene flow within metapopulations. For marine organisms such as coral reef fishes, identifying these barriers is critical to predicting evolutionary dynamics and demarcating evolutionarily significant units for conservation. In this study, we adopted an alternative hypothesis‐testing framework to identify the patterns and predictors of SGS in the Caribbean reef fish Elacatinus lori. First, genetic structure was estimated using nuclear microsatellites and mitochondrial cytochrome b sequences. Next, clustering and network analyses were applied to visualize patterns of SGS. Finally, logistic regressions and linear mixed models were used to identify the predictors of SGS. Both sets of markers revealed low global structure: mitochondrial Φ_ST = 0.12, microsatellite F_ST = 0.0056. However, there was high variability among pairwise estimates, ranging from no differentiation between sites on contiguous reef (Φ_ST = 0) to strong differentiation between sites separated by ocean expanses ≥ 20 km (maximum Φ_ST = 0.65). Genetic clustering and statistical analyses provided additional support for the hypothesis that seascape discontinuity, represented by oceanic breaks between patches of reef habitat, is a key predictor of SGS in E. lori. Notably, the estimated patterns and predictors of SGS were consistent between both sets of markers. Combined with previous studies of dispersal in E. lori, these results suggest that the interaction between seascape continuity and the dispersal kernel plays an important role in determining genetic connectivity within metapopulations.     

Evidence for interannual variation in genetic structure of Dungeness crab (Cancer magister) along the California Current System

Using a combination of population‐ and individual‐based analytical approaches, we provide a comprehensive examination of genetic connectivity of Dungeness crab (Cancer magister) along ~1,200 km of the California Current System (CCS). We sampled individuals at 33 sites in 2012 to establish a baseline of genetic diversity and hierarchal population genetic structure and then assessed interannual variability in our estimates by sampling again in 2014. Genetic diversity showed little variation among sites or across years. In 2012, we observed weak genetic differentiation among sites (F_ST range = ?0.005–0.014) following a pattern of isolation by distance (IBD) and significantly high relatedness among individuals within nine sampling sites. In 2014, pairwise F_ST estimates were lower (F_ST range = ?0.014–0.007), there was no spatial autocorrelation, and fewer sites had significant evidence of relatedness. Based on these findings, we propose that interannual variation in the physical oceanographic conditions of the CCS influences larval recruitment and thus gene flow, contributing to interannual variation in population genetic structure. Estimates of effective population size (N_e) were large in both 2012 and 2014. Together, our results suggest that Dungeness crab in the CCS may constitute a single evolutionary population, although geographically limited dispersal results in an ephemeral signal of IBD. Furthermore, our findings demonstrate that populations of marine organisms may be susceptible to temporal changes in population genetic structure over short time periods; thus, interannual variability in population genetic measures should be considered.     

Is life history a barrier to dispersal? Contrasting patterns of genetic differentiation along an oceanographically complex coast

Extreme variation in early life‐history strategies is considered a moderately good predictor of genetic subdivision and hence dispersal for a range of marine species. In reality, however, a good deal of population differentiation must reflect historical effects, more subtle variation in life histories, and, particularly, the interaction of larvae with oceanographic processes. Using a combination of allozyme and microsatellite markers, we show that the large‐scale genetic structure of populations of three species (direct and planktonically developing cushion stars and a planktonic developing sea anemone that is also asexually viviparous) varies consistently, in line with the predicted capacity for dispersal within three geographic regions. We detected high levels of genetic subdivision for the direct developing cushion star (F_ST = 0.6), low levels for the planktonically developing cushion star (F_ST = 0.009), and intermediate levels for the sexual/asexual sea anmone (F_ST = 0.19). These patterns are exhibited despite the highly variable patterns of current movement and the presence of biogeographic barriers. Our results suggest that, although there is large scale genetic differentiation for two species, patterns of population connectivity are remarkably consistent within major regions and do not reflect variation in major oceanographic processes or genetic discontinuity coincident with biogeographic boundaries. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 106–116.     

Population structure and genetic diversity of black redhorse (Moxostoma duquesnei) in a highly fragmented watershed

Dams have the potential to affect population size and connectivity, reduce genetic diversity, and increase genetic differences among isolated riverine fish populations. Previous research has reported adverse effects on the distribution and demographics of black redhorse (Moxostoma duquesnei), a threatened fish species in Canada. However, effects on genetic diversity and population structure are unknown. We used microsatellite DNA markers to assess the number of genetic populations in the Grand River (Ontario) and to test whether dams have resulted in a loss of genetic diversity and increased genetic differentiation among populations. Three hundred and seventy-seven individuals from eight Grand River sites were genotyped at eight microsatellite loci. Measures of genetic diversity were moderately high and not significantly different among populations; strong evidence of recent population bottlenecks was not detected. Pairwise F_ST and exact tests identified weak (global F_ST = 0.011) but statistically significant population structure, although little population structuring was detected using either genetic distances or an individual-based clustering method. Neither geographic distance nor the number of intervening dams were correlated with pairwise differences among populations. Tests for regional equilibrium indicate that Grand River populations were either in equilibrium between gene flow and genetic drift or that gene flow is more influential than drift. While studies on other species have identified strong dam-related effects on genetic diversity and population structure, this study suggests that barrier permeability, river fragment length and the ecological characteristics of affected species can counterbalance dam-related effects.     

Macaronesia: a source of hidden genetic diversity for post‐glacial recolonization of western Europe in the leafy liverwort Radula lindenbergiana

Aim Bryophytes exhibit apparently low rates of endemism in Macaronesia and differ from angiosperms in their diversity patterns by the widespread occurrence of endemics within and among archipelagos. This paper investigates the phylogeography of the leafy liverwort Radula lindenbergiana to determine: (1) whether or not morphologically cryptic diversification has occurred in Macaronesia, and (2) the relationships between Macaronesian and continental populations. Location Macaronesia, Europe, Africa. Methods Eighty‐four samples were collected across the species’ distribution range and sequenced at four chloroplast DNA (cpDNA) loci (atpB–rbcL, trnG, trnL and rps4). Phylogenetic reconstructions and Bayesian ancestral area reconstructions were used in combination with population genetics statistics (H, N_ST, F_ST) to describe the pattern of present genetic diversity in R. lindenbergiana and infer its biogeographic history. Results Patterns of genetic diversity in R. lindenbergiana exhibit a striking westwards gradient, wherein haplotype (0.90) and nucleotide (0.0038 ± 0.0019) diversity peak in Macaronesia, with a substantial endemic component. We found 20.9% of the genetic variance between biogeographic regions, and most pairwise F_ST comparisons between regions are significantly different from zero. The global N_ST (0.78) is significantly higher than the global F_ST (0.20), providing evidence for the presence of phylogeographic signal in the data. Ancestral area reconstructions suggest that the haplotypes currently found in western Europe share a Macaronesian common ancestor. Main conclusions The haplotype diversification exhibited by R. lindenbergiana in Macaronesia is comparable to that reported for many angiosperm groups at the species level. The apparent lack of radiation among Macaronesian bryophytes may thus reflect the reduced morphology of bryophytes in comparison with angiosperms. The high diversity found among Macaronesian haplotypes, especially in Madeira and the Canary Islands, and the significant N_ST/F_ST ratio between Macaronesia and all the other biogeographic regions (an indication that mutation rate exceeds dispersal rates) suggest that Macaronesian archipelagos could have served as a refugium during the Quaternary glaciations. Many haplotypes currently found in Europe share a Macaronesian common ancestor, and this further suggests that Macaronesia might have played a key role in the back‐colonization of the continent.     

Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis)

The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction‐site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small N_e (range = 2.1–89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome‐wide divergence. Nonetheless, outlier tests identified 3.6–6.6% of loci as high F_ST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high F_ST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small N_e in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential.     

Preferred habitat and effective population size drive landscape genetic patterns in an endangered species

Landscape genetics provides a framework for pinpointing environmental features that determine the important exchange of migrants among populations. These studies usually test the significance of environmental variables on gene flow, yet ignore one fundamental driver of genetic variation in small populations, effective population size, N_e. We combined both approaches in evaluating genetic connectivity of a threatened ungulate, woodland caribou. We used least-cost paths to calculate matrices of resistance distance for landscape variables (preferred habitat, anthropogenic features and predation risk) and population-pairwise harmonic means of N_e, and correlated them with genetic distances, F_ST and D_c. Results showed that spatial configuration of preferred habitat and N_e were the two best predictors of genetic relationships. Additionally, controlling for the effect of N_e increased the strength of correlations of environmental variables with genetic distance, highlighting the significant underlying effect of N_e in modulating genetic drift and perceived spatial connectivity. We therefore have provided empirical support to emphasize preventing increased habitat loss and promoting population growth to ensure metapopulation viability.     

Fine scale patterns of migration and gene flow in the endangered mound spring snail, <Emphasis Type="Italic">Fonscochlea accepta</Emphasis> (Mollusca:Hydrobiidae) in arid Australia

Naturally patchy ecosystems are models for other systems currently undergoing anthropogenic habitat fragmentation. Understanding patterns of gene flow in these model systems can help us manage species and ecosystems threatened by human impacts. The mound springs of central Australia represent such a natural model ecosystem, supporting a unique aquatic fauna distributed within an inhospitable arid landscape. Moreover, these springs are being impacted by over extraction of groundwater, providing a unique opportunity to look at dispersal in a patchy habitat that is changing. The present study represents the first fine scale analysis of gene flow under different scenarios of habitat connectivity for the endangered mound spring snail, Fonscochlea accepta. Within a single spring group pairwise estimates of F _ST between springs were very low (ave 0.015) with no association found between genetic distance and a series of geographical distance matrices based on the degree of habitat connectivity among the springs: results implying unstructured dispersal and limited population isolation. However, results from Bayesian assignment tests showed that on average approximately 97% of snails were assigned to their spring of origin. In a preliminary analysis at broader geographic scales (among spring groups) the results from F _ST estimates, Mantel correlation analyses and assignment tests all suggest much stronger and geographically correlated population structuring. While varying results from F-statistics and Bayesian analyses stem from the different information they utilise, together they provide data on contemporary and historical estimates of gene flow and the influence of landscape dynamics on the spatial genetic patterning of the springs.     

Detection of environmental and morphological adaptation despite high landscape genetic connectivity in a pest grasshopper (Phaulacridium vittatum)

Widespread species that exhibit both high gene flow and the capacity to occupy heterogeneous environments make excellent models for examining local selection processes along environmental gradients. Here we evaluate the influence of temperature and landscape variables on genetic connectivity and signatures of local adaptation in Phaulacridium vittatum, a widespread agricultural pest grasshopper, endemic to Australia. With sampling across a 900‐km latitudinal gradient, we genotyped 185 P. vittatum from 19 sites at 11,408 single nucleotide polymorphisms (SNPs) using ddRAD sequencing. Despite high gene flow across sites (pairwise F_ST = 0.0003–0.08), landscape genetic resistance modelling identified a positive nonlinear effect of mean annual temperature on genetic connectivity. Urban areas and water bodies had a greater influence on genetic distance among sites than pasture, agricultural areas and forest. Together, F_ST outlier tests and environmental association analysis (EAA) detected 242 unique SNPs under putative selection, with the highest numbers associated with latitude, mean annual temperature and body size. A combination of landscape genetic connectivity analysis together with EAA identified mean annual temperature as a key driver of both neutral gene flow and environmental selection processes. Gene annotation of putatively adaptive SNPs matched with gene functions for olfaction, metabolic detoxification and ultraviolet light shielding. Our results imply that this widespread agricultural pest has the potential to spread and adapt under shifting temperature regimes and land cover change.     

GENETIC STRUCTURE OF GIANT CLAM (TRIDACNA MAXIMA) POPULATIONS IN THE WEST PACIFIC IS NOT CONSISTENT WITH DISPERSAL BY PRESENT-DAY OCEAN CURRENTS

The Pacific marine biota, particularly species with long planktonic larval stages, are thought to disperse widely throughout the Pacific via ocean currents. The little genetic data available to date has supported this view in that little or no significant regional differentiation of populations has been found over large geographical distances. However, recent data from giant clams has demonstrated not only significant regional differentiation of populations, but routes of gene flow that run perpendicular to the main present-day ocean currents. Extensive surveys of genetic variation at eight polymorphic loci in 19 populations of the giant clam Tridacna maxima, sampled throughout the West and Central Pacific, confirmed that the patterns of variation seen so far in T. gigas were not unique to that species, and may reflect a fundamental genetic structuring of shallow-water marine taxa. Populations of T. maxima within highly connected reef systems like the Great Barrier Reef were panmictic (average F_ST < 0.003), but highly significant genetic differences between reef groups on different archipelagos (average F_ST = 0.084) and between West and Central Pacific regions (average F_ST = 0.156) were found. Inferred gene flow was high (N_em usually > 5) between the Philippines and the Great Barrier Reef, between the Philippines and Melanesia (the Solomon Islands and Fiji), and between the Philippines and the Central Pacific island groups (Marshall Islands, Kiribati, Tuvalu and Cook Islands). Gene flow was low between these three sets of island chains (N_em < 2). These routes of gene flow are perpendicular to present-day ocean currents. It is suggested that the spatial patterns of gene frequencies reflect past episodes of dispersal at times of lower sea levels which have not been erased by subsequent dispersal by present-day circulation. The patterns are consistent with extensive dispersal of marine species in the Pacific, and with traditional views of dispersal from the Indo-Malay region. However, they demonstrate that dispersal along present-day ocean surface currents cannot be assumed, that other mechanisms may operate today or that major dispersal events are intermittent (perhaps separated by several thousands of years), and that the nature and timing of dispersal of Pacific marine species is more complex than has been thought.     

Fragmentation and comparative genetic structure of four mediterranean woody species: complex interactions between life history traits and the landscape context

Aim The effect of habitat fragmentation on population genetic structure results from the interaction between species’ life history traits and the particular landscape context, and both components are inherently difficult to tease apart. Here, we compare the genetic (allozyme) structure of four co‐occurring woody species with contrasting life histories to explore how well their response to the same fragmentation process can be predicted from their functional traits. Location A highly fragmented forest landscape located in the lower Guadalquivir catchment, south‐western Spain. Methods We sampled four species (Cistus salviifolius, Myrtus communis, Pistacia lentiscus and Quercus coccifera) from the same 23 forest fragments known to form a representative array of habitat characteristics in the region. We assessed genetic diversity (A, H_e and N_g) and differentiation (F_IS and F_ST) for each species and explored their potential drivers using a model‐selection approach with four fragment features (size, historical and current connectivity, and stability) as predictor variables. Results Regional‐scale genetic diversity increased from the shortest‐lived to the longest‐lived species, while population differentiation of the self‐compatible species was roughly double that of the three self‐incompatible species. Fragment size was the only feature that did not consistently affect the genetic diversity of local populations across all species. Three species showed signs of being affected by fragmentation, yet each responded differently to the set of fragment features considered. We observed several trends that were at odds with simple life history‐based predictions but could arise from patterns of gene flow and/or local‐scale demographic processes. Main conclusions Our comparative study of various landscape features and species underscores that the same fragmentation process can have very different, and complex, consequences for the population genetic structure of plants. This idiosyncrasy renders generalizations across natural systems very difficult and highlights the need of context‐oriented guidelines for an efficient conservation management of species‐rich landscapes.     

Contrasting levels of genetic differentiation among populations of wolverines (<Emphasis Type="Italic">Gulo gulo</Emphasis>) from northern Canada revealed by nuclear and mitochondrial loci

Habitat loss, fragmentation, overharvest, and other anthropogenic factors have resulted in population and distribution declines for North American wolverines (Gulo gulo). Currently, wolverines east of the Hudson Bay are endangered and possibly extinct, whereas the status of wolverines throughout the remaining Holarctic is vulnerable. Three previous studies using nuclear loci have detected little to no significant structuring among wolverines sampled across northern Canada. Based on these results it has been suggested that wolverines in northern Canada represent a single, panmictic population. However, as has been shown in numerous studies, in cases of female site fidelity, it is possible to have demographically autonomous populations even with male-biased gene flow. To better assess the genetic structure of wolverines in northern Canada, we examined nine microsatellite loci and DNA sequence variation from a 200 bp fragment of the mitochondrial (mtDNA) control region for 270 wolverines from nine collecting areas representing three regions of northern Canada. In agreement with previous studies, microsatellite analyses revealed a lack of significant population substructure (F _ST=0.0004). However, analysis of molecular variance, comparisons of pairwise F _ST values and nested-clade analysis of the mtDNA data revealed considerable genetic structuring among samples of wolverines from these three regions of northern Canada. These mitochondrial data provide evidence that wolverines in Canada are genetically structured due to female philopatry. The contrasting patterns of genetic differentiation based on nuclear and mitochondrial data highlight the importance of examining both nuclear and mitochondrial loci when attempting to elucidate patterns of genetic structure.     

Limited gene flow among brown bear populations in far Northern Europe? Genetic analysis of the east–west border population in the Pasvik Valley

Noninvasively collected genetic data can be used to analyse large‐scale connectivity patterns among populations of large predators without disturbing them, which may contribute to unravel the species’ roles in natural ecosystems and their requirements for long‐term survival. The demographic history of brown bears (Ursus arctos) in Northern Europe indicates several extinction and recolonization events, but little is known about present gene flow between populations of the east and west. We used 12 validated microsatellite markers to analyse 1580 hair and faecal samples collected during six consecutive years (2005–2010) in the Pasvik Valley at 70°N on the border of Norway, Finland and Russia. Our results showed an overall high correlation between the annual estimates of population size (N_c), density (D), effective size (N_e) and N_e/N_c ratio. Furthermore, we observed a genetic heterogeneity of ～0.8 and high N_e/N_c ratios of ～0.6, which suggests gene flow from the east. Thus, we expanded the population genetic study to include Karelia (Russia, Finland), Västerbotten (Sweden) and Troms (Norway) (477 individuals in total) and detected four distinct genetic clusters with low migration rates among the regions. More specifically, we found that differentiation was relatively low from the Pasvik Valley towards the south and east, whereas, in contrast, moderately high pairwise F_ST values (0.91–0.12) were detected between the east and the west. Our results indicate ongoing limits to gene flow towards the west, and the existence of barriers to migration between eastern and western brown bear populations in Northern Europe.     

Inter and intra‐population phenotypic and genotypic structuring in the European whitefish Coregonus lavaretus,a rare freshwater fish in Scotland

This study revealed between‐lake genetic structuring between Coregonus lavaretus collected from the only two native populations of this species in Scotland, U.K. (Lochs Eck and Lomond) evidenced by the existence of private alleles (12 in Lomond and four in Eck) and significant genetic differentiation (F_ST = 0·056) across 10 microsatellite markers. Juvenile C. lavaretus originating from eggs collected from the two lakes and reared in a common‐garden experiment showed clear phenotypic differences in trophic morphology (i.e. head and body shape) between these populations indicating that these characteristics were, at least partly, inherited. Microsatellite analysis of adults collected from different geographic regions within Loch Lomond revealed detectable and statistically significant but relatively weak genetic structuring (F_ST = 0·001–0·024) and evidence of private alleles related to the basin structure of the lake. Within‐lake genetic divergence patterns suggest three possibilities for this observed pattern: (1) differential selection pressures causing divergence into separate gene pools, (2) a collapse of two formerly divergent gene pools and (3) a stable state maintained by balancing selection forces resulting from spatial variation in selection and lake heterogeneity. Small estimates of effective population sizes for the populations in both lakes suggest that the capacity of both populations to adapt to future environmental change may be limited.     

Demography, and genetic and morphological variability of the endangered Sophronitis sincorana (Orchidaceae) in the Chapada Diamantina, Brazil

We carried out a demographic study and evaluated the genetic and morphological variability in five populations of the endangered Sophronitis sincorana (Orchidaceae) endemic to Northeastern Brazil, based on allozyme and morphometric analyses. Plant density was approximately 0.5 plants/m², and the projected total number of plants was approximately 50,000 individuals. However, fruit set and recruitment of individuals are rare. The genetic variability was very high in all populations (P = 100, A = 3.0−3.5, H _e = 0.33−0.48), and all populations presented similar values of morphological variability. Low genetic and morphological structuring were found in the species (F _ST = 0.053, A_MRPP = 0.018). The elevated coefficient of endogamy encountered in populations of S. sincorana indicates the occurrence of structuring within the populations. The lack of correlation between morphological and genetic variation in this species indicates that none of the markers examined should be used separately for either conservation purposes.     

Positive correlation between vegetation dissimilarity and genetic differentiation of Carex sempervirens

Synthesizing genetic data at population level and vegetation data at community level may give insight into how ecological and evolutionary processes associated with different vegetation influence genetic diversity and differentiation of plant populations. We correlated population genetic patterns of Carex sempervirens with community vegetation patterns in abandoned subalpine grassland in the Swiss Alps. Within-population genetic diversity (percentage of polymorphic bands and Nei's gene diversity) of C. sempervirens was not significantly correlated with plant richness, evenness or Shannon's diversity index (Pearson correlation coefficient |r|<0.32, P>0.10). However, the genetic distance (F_ST) between C. sempervirens populations was significantly positively correlated with the vegetation dissimilarity between communities (Mantel's r=0.23, P<0.01). The correlation between the population genetic differentiation and the vegetation dissimilarity was not due to the parallel effects of geographic isolation or site conditions, because F_ST was not correlated with the geographic distance or the pairwise differences in any of the measured site condition parameters. One likely mechanism is that different plant communities were associated with different selective forces, which, in turn, influenced the genetic differentiation between C. sempervirens populations. Another possibility is that the vegetation heterogeneity (dissimilarity) generated ecological barriers against gene flow and thus enhanced the genetic differentiation between C. sempervirens populations.