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.     

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.     

Drift happens: Molecular genetic diversity and differentiation among populations of jewelweed (Impatiens capensis Meerb.) reflect fragmentation of floodplain forests

Landscape features often shape patterns of gene flow and genetic differentiation in plant species. Populations that are small and isolated enough also become subject to genetic drift. We examined patterns of gene flow and differentiation among 12 floodplain populations of the selfing annual jewelweed (Impatiens capensis Meerb.) nested within four river systems and two major watersheds in Wisconsin, USA. Floodplain forests and marshes provide a model system for assessing the effects of habitat fragmentation within agricultural/urban landscapes and for testing whether rivers act to genetically connect dispersed populations. We generated a panel of 12,856 single nucleotide polymorphisms and assessed genetic diversity, differentiation, gene flow, and drift. Clustering methods revealed strong population genetic structure with limited admixture and highly differentiated populations (mean multilocus F_ST = 0.32, F_ST’ = 0.33). No signals of isolation by geographic distance or environment emerged, but alleles may flow along rivers given that genetic differentiation increased with river distance. Differentiation also increased in populations with fewer private alleles (R² = 0.51) and higher local inbreeding (R² = 0.22). Populations varied greatly in levels of local inbreeding (F_IS = 0.2–0.9) and F_IS increased in more isolated populations. These results suggest that genetic drift dominates other forces in structuring these Impatiens populations. In rapidly changing environments, species must migrate or genetically adapt. Habitat fragmentation limits both processes, potentially compromising the ability of species to persist in fragmented landscapes.     

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.     

High degree of genetic differentiation in marine three‐spined sticklebacks (Gasterosteus aculeatus)

Populations of widespread marine organisms are typically characterized by a low degree of genetic differentiation in neutral genetic markers, but much less is known about differentiation in genes whose functional roles are associated with specific selection regimes. To uncover possible adaptive population divergence and heterogeneous genomic differentiation in marine three‐spined sticklebacks (Gasterosteus aculeatus), we used a candidate gene‐based genome‐scan approach to analyse variability in 138 microsatellite loci located within/close to (<6 kb) functionally important genes in samples collected from ten geographic locations. The degree of genetic differentiation in markers classified as neutral or under balancing selection—as determined with several outlier detection methods—was low (F_ST = 0.033 or 0.011, respectively), whereas average F_ST for directionally selected markers was significantly higher (F_ST = 0.097). Clustering analyses provided support for genomic and geographic heterogeneity in selection: six genetic clusters were identified based on allele frequency differences in the directionally selected loci, whereas four were identified with the neutral loci. Allelic variation in several loci exhibited significant associations with environmental variables, supporting the conjecture that temperature and salinity, but not optic conditions, are important drivers of adaptive divergence among populations. In general, these results suggest that in spite of the high degree of physical connectivity and gene flow as inferred from neutral marker genes, marine stickleback populations are strongly genetically structured in loci associated with functionally relevant genes.     

Genetic structure of refugial populations of the temperate plant Shortia rotundifolia (Diapensiaceae) on a subtropical island

Continental island systems harbour relict biota and populations that might have migrated during glacial periods due to the formation of landbridges. Here we analysed the genetic structure of relict populations of the temperate plant Shortia rotundifolia on the subtropical island of Iriomotejima, Japan. This plant, which inhabits riparian environments, is designated “near threatened”. Only five extant populations have been found on the island. Our analyses of 10 nuclear microsatellite loci detected genetic diversity of H _E = 0.488 and H _O = 0.358 for all populations of S. rotundifolia on the island. A high inbreeding coefficient for all populations together (F _IS = 0.316) and each population separately (F _IS = 0.258–0.497) might be attributable to crossing among closely related descendants within a population, an idea that is supported by the relatedness coefficient. These results and an examination of the populations’ demographic histories suggest that the extant populations on Iriomotejima have not experienced a recent population bottleneck. The five extant populations were genetically differentiated (F _ST = 0.283; P < 0.001), suggesting low seed dispersal by gravity and/or low pollen flow via pollinators in the riparian environment. In addition, population differentiation was not related to genetic distance, implying that at one time, ancestral populations might have been distributed over a wider area of the island. However, population fragmentation and range contraction might have occurred at random during the postglacial period.     

Genetic differentiation between the ant Myrmica rubra and its microgynous social parasite

Hymenopteran inquiline species have been proposed to originate by sympatric speciation through intraspecific social parasitism. One such parasite, Myrmica microrubra, was recently synonymized with its Myrmica rubra host, because comparisons across Europe indicated insufficient genetic differentiation. Here, we use microsatellite markers to study genetic differentiation more precisely in a sample of Finnish M. rubra and its inquilines collected at two localities, supplemented with mitochondrial DNA sequences. The parasite had much lower genetic variation than the host at three of the four loci studied. Genetic differentiation between the host populations was moderate (F _ST = 0.089), whereas the parasite populations were more strongly subdivided (F _ST = 0.440). The host and parasite were highly genetically differentiated both across populations (F _ST = 0.346) and in strict sympatry (0.327, 0.364), a result that remained robust both in a haplotype network and in PCA ordination. Individual assignments of genotypes indicated that gene flow between sympatric host and inquiline populations is reduced by about an order of magnitude relative to the gene flow within the morphs. Our results suggest that the parasitic morph of M. rubra may be an incipient species, but it remains unclear to what extent the observed genetic differentiation between host and inquiline is due to possible assortative mating and selection against hybrids or to recurrent bottlenecking and genetic drift. We conclude that an explicitly functional species concept would be unambiguous in treating this inquiline as a full species, as it begets its own kind and maintains its integrity in spite of occasional interbreeding with the host.     

Genetic variation amongst viviparid snails in the genus Mekongia (Prosobranchia: Viviparidae) in Thailand

Allozyme variation in viviparid snails from the genus Mekongia in Thailand were examined across the different species, subspecies and geographical locations (river drainage systems). Using horizontal starch gel electrophoresis, 11 presumed allozyme loci (eight polymorphic) from eight enzyme systems were screened. Heterozygosity was moderately low (Hexp = 0.000–0.109, mean = 0.037). One population of Mekongia pongensis (Nong Khai) was monomorphic at all 11 examined loci in contrast to the other two populations, suggesting bottleneck within this population. Populations were more differentiated in the Mekongia sphaericula complex (F_ST = 0.587) than in either the Mekongia swainsoni complex (F_ST = 0.161) or M. pongensis species (F_ST = 0.073). Mekongia sphaericula sphaericula and Mekongia sphaericula extensa exhibited fixed allele differences at two loci, a high genetic distance (D = 0.265–0.300) and a potential polyphyletic relationship, suggesting two distinct lineages (species).     

Adaptive genetic variation distinguishes Chilean blue mussels (Mytilus chilensis) from different marine environments

Chilean mussel populations have been thought to be panmictic with limited genetic structure. Genotyping‐by‐sequencing approaches have enabled investigation of genomewide variation that may better distinguish populations that have evolved in different environments. We investigated neutral and adaptive genetic variation in Mytilus from six locations in southern Chile with 1240 SNPs obtained with RAD‐seq. Differentiation among locations with 891 neutral SNPs was low (F_ST = 0.005). Higher differentiation was obtained with a panel of 58 putative outlier SNPs (F_ST = 0.114) indicating the potential for local adaptation. This panel identified clusters of genetically related individuals and demonstrated that much of the differentiation (~92%) could be attributed to the three major regions and environments: extreme conditions in Patagonia, inner bay influenced by aquaculture (Reloncaví), and outer bay (Chiloé Island). Patagonia samples were most distinct, but additional analysis carried out excluding this collection also revealed adaptive divergence between inner and outer bay samples. The four locations within Reloncaví area were most similar with all panels of markers, likely due to similar environments, high gene flow by aquaculture practices, and low geographical distance. Our results and the SNP markers developed will be a powerful tool supporting management and programs of this harvested species.     

Genetic diversity of Lavandula multifida L. (Lamiaceae) in Tunisia: implication for conservation

The genetic variation within and among eight Tunisian natural populations of Lavandula multifida L., from different bioclimatic zones was assessed using random amplified polymorphic DNA (RAPDs). Of a total of 97 generated bands from seven selected primers, 84 bands were polymorphic. The genetic diversity within a population was high and varied according to the populations (0.308 < H’ < 0.459) without relationships to altitudes or pluviothermic indices of sites. The genetic differentiation among populations was high (G_ST = 0.395 and Φ_ST = 0.318). All population pairs were significantly differentiated. Among populations, within ecological groups genetic structure was high (0.219); whilst among them it was low (Φ_CT = 0.049; P < 0.05). The correlation between Φ_ST and geographic distance matrices among pairs of populations was not significant, suggesting that genetic connectivity between populations has a stochastic component at all spatial scales. The neighbour‐joining cluster analysis showed that individuals from each population clustered together. UPGMA cluster analysis showed that population groupings are not strictly in accordance with bioclimates or geographic location. The genetic differentiation in L. multifida could have occurred at local scales because of genetic drift. Efforts should be made to protect all populations. The maintenance of substantial population size should be initiated via fencing and controlling collection to restore the regeneration of populations.     

Microgeographic structure of Anopheles gambiae in western Kenya based on mtDNA and microsatellite loci

The population genetic structure of the Anopheles gambiae in western Kenya was studied using length variation at five microsatellite loci and sequence variation in a 648-nt mtDNA fragment. Mosquitoes were collected from houses in villages spanning up to 50 km distance, The following questions were answered, (i) Are mosquitoes in a house more related genetically to each other than mosquitoes between houses? (ii) What degree of genetic differentiation occurs on these geographical scales? (iii) How consistent are the results obtained with both types of genetic markers? At the house level, no differentiation was detected by F_ST and R_ST, and the band sharing index test revealed no significant associations of alleles across loci. Likewise, indices of kinship based on mtDNA haplotypes in houses were even lower than in the pooled sample. Therefore, the hypothesis that mosquitoes in a house are more related genetically was rejected. At increasing geographical scales, microsatellite allele distributions were similar among all population samples and no subdivision of the gene pool was detected by F_ST or R_ST. Likewise, estimates of haplotype divergence of mtDNA between populations were not higher than the within population estimates, and mtDNA-based F_ST values were not significantly different from zero. That sequence variation in mtDNA provided matching results with microsatellite loci (while high genetic variation was observed in all loci), suggested that this pattern represents the whole genome. The minimum area associated with a deme of A. gambiae in western Kenya is therefore larger than 50 km in diameter.     

Landscape genetic structure of <Emphasis Type="Italic">Betula maximowicziana</Emphasis> in the Chichibu mountain range,central Japan

We evaluated the genetic structure of 16 Betula maximowicziana populations in the Chichibu mountain range, central Japan, located within a 25-km radius; all but two populations were at altitudes of 1,100–1,400 m. The results indicate the effects of geographic topology on the landscape genetic structure of the populations and should facilitate the development of local-scale strategies to conserve and manage them. Analyses involving 11 nuclear simple sequence repeat loci showed that most populations had similar intrapopulation genetic diversity parameters. Population differentiation (F _ST = 0.021, G′_ST = 0.033) parameters for the populations examined were low but were relatively high compared to those obtained in a previous study covering populations in a much larger area with a radius of approximately 1,000 km (F _ST = 0.062, G′_ST = 0.102). Three populations (Iriyama, Kanayamasawa, and Nishizawa) were differentiated from the other populations by Monmonier’s and spatial analysis of molecular variance algorithms or by STRUCTURE analysis. Since a high mountain ridge (nearly 2,000 m) separates the Kanayamasawa and Nishizawa populations from the other 14 populations and the Kanayamasawa and Nishizawa populations are themselves separated by another mountain ridge, the genetic structure appears to be partly due to mountain ridges acting as genetic barriers and restricting gene flow. However, the Iriyama population is genetically different but not separated by any clear geographic barrier. These results show that the landscape genetic structure is complex in the mountain range and we need to pay attention, within landscape genetic studies and conservation programs, to geographic barriers and local population differentiation.     

High genetic diversity with low connectivity among Mauritia flexuosa (Arecaceae) stands from Ecuadorean Amazonia

Mauritia flexuosa dominated palm swamps are an important forest resource covering over 30,000 km² across the Amazon basin. In Ecuadorean Amazonia, Mauritia flexuosa, a dioecious and arborescent palm species, forms small and isolated populations or large and dense stands on poorly drained soils. How these populations are genetically interconnected and how genetic diversity varies between cohorts of different ages remains little studied although they are important for conservation of these ecosystems. The genetic structure of Mauritia flexuosa was studied in five natural stands using eight microsatellite loci and two cohorts (seedling and adults). In addition, age structure and sex ratio within the stands were assessed using transects. The age structure of the studied Mauritia flexuosa stands is represented by a high number of seedlings (mean = 1,153.6/ha) and adults (mean = 563.2/ha), with a sex ratio favoring female individuals (1.42:1). These stands are also characterized by a fine‐scale genetic structure, high observed heterozygosity (mean: H_{O seedlings}=0.52; H_{O adults}=0.52), high inbreeding (mean: F_{IS seedlings} = 0.26; F_{IS adults} = 0.26), low number of migrants (N_m=0.29), strong genetic differentiation (mean: pairwise R_ST/ D‐values _seedlings = 0.08/ 0.74; mean R_ST/D‐values _adults = 0.17/ 0.76), and an average effective population size (N_e) of 191.42 individuals. No intergenerational genetic variation was detected between seedlings and adults. We suggest that the high genetic diversity and inbreeding as well as the strong differentiation among stands of these populations could be explained, at least partially, by a low genetic connectivity among populations. Destructive harvesting of its fruits and defaunation will be major threats to Mauritia flexuosa populations in the future. Abstract in Spanish is available with online material     

GENETIC STRUCTURE IN POPULATIONS OF FUCUS VESICULOSUS (PHAEOPHYCEAE) OVER SPATIAL SCALES FROM 10 M TO 800 KM1

Recent studies showing consequences of species’ genetic diversity on ecosystem performance raise the concern of how key ecosystem species are genetically structured. The bladder wrack Fucus vesiculosus L. is a dominant species of macroalga in the northern Atlantic, and it is particularly important as a habitat‐forming species in the Baltic Sea. We examined the genetic structure of populations of F. vesiculosus with a hierarchical approach from a within‐shore scale (10 m) to a between‐seas scale (Baltic Sea–Skagerrak, 800 km). Analysis of five microsatellite loci showed that population differentiation was generally strong (average F_ST = 12%), being significant at all spatial scales investigated (10¹, 10³, 10^4–5, 10⁶ m). Genetic differentiation between seas (Baltic Sea and Skagerrak) was substantial. Nevertheless, the effects of isolation by distance were stronger within seas than between seas. Notably, Baltic summer‐reproducing populations showed a strong within‐sea, between‐area (70 km) genetic structure, while Baltic autumn‐reproducing populations and Skagerrak summer‐reproducing populations revealed most genetic diversity between samples within areas (<1 km). Despite such differences in overall structure, Baltic populations of summer‐ and autumn‐reproducing morphs did not separate in a cluster analysis, indicating minor, if any, barriers to gene flow between them. Our results have important implications for management and conservation of F. vesiculosus, and we raise a number of concerns about how genetic variability should be preserved within this species.     

Environmental correlates of phenotypic variation: do variable tidal regimes influence morphology in intertidal seaweeds?

Seaweed morphology is often shaped by the hydrodynamic environment. However, exposure to air at low tide represents an additional factor potentially affecting the morphology of intertidal species. Here, we examined the relationships between the morphology of Hormosira banksii, an important intertidal habitat‐forming seaweed in southern Australia, and environmental factors across multiple spatial scales around the island of Tasmania, Australia. Tasmania is surrounded by a diverse coastline with differences in wave exposure, tidal parameters, and temperature. We sampled Hormosira from four regions (100s km apart), three sites (10s km apart) within each region, and two zones (meters apart; eulittoral and sublittoral) at each site, and measured multiple morphological variables to test for differences in morphology at those different spatial scales. Thirteen environmental variables reflecting wave exposure, tidal conditions, and temperature for each site were generated to assess the relationship between Hormosira morphology and environmental variation. Morphology varied at all spatial scales examined. Most notably, north coast individuals had a distinct morphology, generally having smaller vesicles and shorter fronds, compared to other regions. Tidal conditions were the main environmental factors separating north coast sites from other sites and tidal regime was identified as the best predictor of morphological differences between regions. In contrast to other studies, we found little evidence that wave exposure was associated with morphological variation. Overall, our study emphasizes the role of tidal conditions, associated with emersion stress during low tide, in affecting the morphology of intertidal seaweeds.     

SPATIAL SCALE OF GENETIC STRUCTURE AND AN INDIRECT ESTIMATE OF GENE FLOW IN EELGRASS,ZOSTERA MARINA

In this study, the first investigation of population structure in an aquatic angiosperm, I show that populations of a marine angiosperm (eelgrass, Zostera marina) are genetically differentiated at a number of spatial scales. I find also that there is no correspondence between geographic and genetic distances separating subpopulations, an increasingly common result in spatially stratified studies of genetic structure in marine invertebrates. F-statistics, calculated for two years from electrophoretic variation at five polymorphic allozyme loci, indicate significant genetic differentiation among sampling quadrats within each of two bays (θ = 0.064-0.208), between tide zones within a bay (θ = 0.025-0.157) and between bays (θ = 0.079). Spatial autocorrelation analysis was used to explore genetic differentiation at smaller spatial scales; estimated patch sizes (within which genetic individuals are randomly associated) indicated no appeciable genetic structure at scales less than 20 m × 20 m. Calculated values of F-statistics were a function of the spatial scale from which samples were drawn: increasing the size of the “subpopulation” included in calculation of fixation indices for the same “total” sample resulted in an increase in the magnitude of f (e.g., from 0.092 to 0.181) and a decrease in θ (e.g., from 0.186 to 0.025). On the basis of the best estimate of the spatial scale of subpopulations, the effective number of migrants per generation (N_em) ranges from 1.1 to 2.8. Genetic consequences of the disturbance regime in the eelgrass habitat sampled were extreme variation between years in the allele richness and proportion of heterozygotes in a sample and a positive relationship between the extinction probability of patches and the genetic variance among them. The changes in F-statistics as a function of sampling scale and the observation that θ among sampled quadrats was positively associated with the probability of extinction among quadrats indicated that indirect estimates of gene flow (N_em) calculated from θ should be cautiously interpreted in populations that may not yet be in drift-migration equilibrium.     

Genetic diversity in fragmented populations of the critically endangered spider orchid Caladenia huegelii: implications for conservation

The Orchidaceae is characterised by a diverse range of life histories, reproductive strategies and geographic distribution, reflected in a variety of patterns in the population genetic structure of different species. In this study, the genetic diversity and structure was assessed within and among remnant populations of the critically endangered sexually deceptive orchid, Caladenia huegelii. This species has experienced severe recent habitat loss in a landscape marked by ancient patterns of population fragmentation within the Southwest Australian Floristic Region, a global biodiversity hotspot. Using seven polymorphic microsatellite loci, high levels of within-population diversity (mean alleles/locus = 6.73; mean H _E = 0.690), weak genetic structuring among 13 remnant populations (F _ST = 0.047) and a consistent deficit of heterozygotes from Hardy–Weinberg expectation were found across all populations (mean F _IS = 0.22). Positive inbreeding coefficients are most likely due to Wahlund effects and/or inbreeding effects from highly correlated paternity and typically low fruit set. Indirect estimates of gene flow (Nm = 5.09 using F _ST; Nm = 3.12 using the private alleles method) among populations reflects a historical capacity for gene flow through long distance pollen dispersal by sexually deceived wasp pollinators and/or long range dispersal of dust-like orchid seed. However, current levels of gene flow may be impacted by habitat destruction, fragmentation and reduced population size. A genetically divergent population was identified, which should be a high priority for conservation managers. Very weak genetic differentiation indicates that the movement and mixing of seeds from different populations for reintroduction programs should result in minimal negative genetic effects.     

Microsatellite and mtDNA analysis of lake trout,Salvelinus namaycush,from Great Bear Lake,Northwest Territories: impacts of historical and contemporary evolutionary forces on Arctic ecosystems

Resolving the genetic population structure of species inhabiting pristine, high latitude ecosystems can provide novel insights into the post‐glacial, evolutionary processes shaping the distribution of contemporary genetic variation. In this study, we assayed genetic variation in lake trout (Salvelinus namaycush) from Great Bear Lake (GBL), NT and one population outside of this lake (Sandy Lake, NT) at 11 microsatellite loci and the mtDNA control region (d‐loop). Overall, population subdivision was low, but significant (global F_ST θ = 0.025), and pairwise comparisons indicated that significance was heavily influenced by comparisons between GBL localities and Sandy Lake. Our data indicate that there is no obvious genetic structure among the various basins within GBL (global F_ST = 0.002) despite the large geographic distances between sampling areas. We found evidence of low levels of contemporary gene flow among arms within GBL, but not between Sandy Lake and GBL. Coalescent analyses suggested that some historical gene flow occurred among arms within GBL and between GBL and Sandy Lake. It appears, therefore, that contemporary (ongoing dispersal and gene flow) and historical (historical gene flow and large founding and present‐day effective population sizes) factors contribute to the lack of neutral genetic structure in GBL. Overall, our results illustrate the importance of history (e.g., post‐glacial colonization) and contemporary dispersal ecology in shaping genetic population structure of Arctic faunas and provide a better understanding of the evolutionary ecology of long‐lived salmonids in pristine, interconnected habitats.     

Local differentiation amidst extensive allele sharing in Oryza nivara and O. rufipogon

Genetic variation patterns within and between species may change along geographic gradients and at different spatial scales. This was revealed by microsatellite data at 29 loci obtained from 119 accessions of three Oryza series Sativae species in Asia Pacific: Oryza nivara Sharma and Shastry, O. rufipogon Griff., and O. meridionalis Ng. Genetic similarities between O. nivara and O. rufipogon across their distribution are evident in the clustering and ordination results and in the large proportion of shared alleles between these taxa. However, local‐level species separation is recognized by Bayesian clustering and neighbor‐joining analyses. At the regional scale, the two species seem more differentiated in South Asia than in Southeast Asia as revealed by F_ST analysis. The presence of strong gene flow barriers in smaller spatial units is also suggested in the analysis of molecular variance (AMOVA) results where 64% of the genetic variation is contained among populations (as compared to 26% within populations and 10% among species). Oryza nivara (H_E = 0.67) exhibits slightly lower diversity and greater population differentiation than O. rufipogon (H_E = 0.70). Bayesian inference identified four, and at a finer structural level eight, genetically distinct population groups that correspond to geographic populations within the three taxa. Oryza meridionalis and the Nepalese O. nivara seemed diverged from all the population groups of the series, whereas the Australasian O. rufipogon appeared distinct from the rest of the species.     

Generation of a neutral FST baseline for testing local adaptation on gill raker number within and between European whitefish ecotypes in the Baltic Sea basin

Divergent selection at ecologically important traits is thought to be a major factor driving phenotypic differentiation between populations. To elucidate the role of different evolutionary processes shaping the variation in gill raker number of European whitefish (Coregonus lavaretus sensu lato) in the Baltic Sea basin, we assessed the relationships between genetic and phenotypic variation among and within three whitefish ecotypes (sea spawners, river spawners and lake spawners). To generate expected neutral distribution of F_ST and to evaluate whether highly variable microsatellite loci resulted in deflated F_ST estimates compared to less variable markers, we performed population genetic simulations under finite island and hierarchical island models. The genetic divergence observed among (F_CT = 0.010) and within (F_ST = 0.014–0.041) ecotypes was rather low. The divergence in gill raker number, however, was substantially higher between sea and river spawners compared to observed microsatellite data and simulated neutral baseline (P_CT > F_CT). This suggests that the differences in gill raker number between sea and river spawners are likely driven by divergent natural selection. We also found strong support for divergent selection on gill raker number among different populations of sea spawners (P_ST > F_ST), most likely caused by highly variable habitat use and diverse diet. The putative role of divergent selection within lake spawners initially inferred from empirical microsatellite data was not supported by simulated F_ST distributions. This work provides a first formal test of divergent selection on gill raker number in Baltic whitefish, and demonstrates the usefulness of population genetic simulations to generate informative neutral baselines for P_ST–F_ST analyses helping to disentangle the effects of stochastic evolutionary processes from natural selection.