From global to local genetic structuring in the red gorgonian Paramuricea clavata: the interplay between oceanographic conditions and limited larval dispersal

Defining the scale of connectivity among marine populations and identifying the barriers to gene flow are tasks of fundamental importance for understanding the genetic structure of populations and for the design of marine reserves. Here, we investigated the population genetic structure at three spatial scales of the red gorgonian Paramuricea clavata (Cnidaria, Octocorallia), a key species dwelling in the coralligenous assemblages of the Mediterranean Sea. Colonies of P. clavata were collected from 39 locations across the Mediterranean Sea from Morocco to Turkey and analysed using microsatellite loci. Within three regions (Medes, Marseille and North Corsica), sampling was obtained from multiple locations and at different depths. Three different approaches (measures of genetic differentiation, Bayesian clustering and spatially explicit maximum‐difference algorithm) were used to determine the pattern of genetic structure. We identified genetic breaks in the spatial distribution of genetic diversity, which were concordant with oceanographic conditions in the Mediterranean Sea. We revealed a high level of genetic differentiation among populations and a pattern of isolation by distance across the studied area and within the three regions, underlining short effective larval dispersal in this species. We observed genetic differentiation among populations in the same locality dwelling at different depths, which may be explained by local oceanographic conditions and which may allow a process of local adaptation of the populations to their environment. We discuss the implications of our results for the conservation of the species, which is exposed to various threats.     

Analysis of microsatellite loci variations in herring (Clupea pallasii marisalbi) from the White Sea

The genetic diversity among spawning groups of herring from different parts of the White Sea was assessed using ten microsatellite loci. All loci were polymorphic with the expected heterozygosity estimates varying in the range of 12.7–94.1% (mean was 59.5%). The degree of genetic differentiation displayed by White Sea herring was statistically significant (θ = 2.03%). The level of pairwise genetic differentiation F _ST was 0–0.085, and it was statistically significant in most of the comparison pairs between the herring samples. A hierarchical analysis of molecular variance (AMOVA) revealed the statistically significant differentiation of White Sea herring. 96.59% genetic variation was found within the samples and 3.41% variation was found among the populations. The main component of interpopulation diversity (1.85%) falls at the differences between two ecological forms of herring, spring- and summer-spawning. Within the spring-spawning form, the presence of local stocks in Kandalaksha Bay, Onega Bay, and Dvina Bay was demonstrated.     

Population structure and variability of Pacific herring (<Emphasis Type="Italic">Clupea pallasii</Emphasis>) in the White Sea,Barents and Kara Seas revealed by microsatellite DNA analyses

Pacific herring, Clupea pallasii, have recently colonised the northeast Atlantic and Arctic Oceans in the early Holocene. In a relatively short evolutionary time, the herring formed a community with a complex population structure. Previous genetic studies based on morphological, allozyme and mitochondrial DNA data have supported the existence of two herring subspecies from the White Sea and eastern Barents and Kara Seas (C. p. marisalbi and C. p. suworowi, respectively). However, the population structure of the White Sea herring has long been debated and remains controversial. The analyses of morphological and allozyme data have previously identified local spawning groups of herring in the White Sea, whereas mtDNA markers have not revealed any differentiation. We conducted one of the first studies of microsatellite variation for the purpose of investigating the genetic structure and relationship of Pacific herring among ten localities in the White Sea, the Barents Sea and the Kara Sea. Using classical genetic variance-based methods (hierarchical AMOVA, overall and pairwise F _ST comparisons), as well as the Bayesian clustering, we infer considerable genetic diversity and population structure in herring at ten microsatellite loci. Genetic differentiation was the most pronounced between the White Sea (C. p. marisalbi) versus the Barents and Kara seas (Chesha–Pechora herring, C. p. suworowi). While microsatellite variation in all C. pallasii was considerable, genetic diversity was significantly lower in C. p. suworowi, than in C. p. marisalbi. Also, tests of genetic differentiation were indicating significant differentiation within the White Sea herring between sympatric summer- and spring-spawning groups, in comparison with genetic homogeneity of the Chesha–Pechora herring.     

Genetic structure and gene flow in an endangered perennial grass, <Emphasis Type="Italic">Arctophila fulva</Emphasis> var. <Emphasis Type="Italic">pendulina</Emphasis>

Arctophila fulva var. pendulina is a rare endemic perennial grass confined to seashore and riverbank meadows around the Bothnian Bay, the northernmost part of the Baltic Sea. The number of A. fulva populations has decreased during the last few decades in Finland and Sweden, and nowadays there are only eight populations left in the drainage area of the Bothnian Bay. We investigated the distribution of genetic variation within and between six subpopulations in the largest remaining population at Liminka Bay, Finland, using amplified fragment length polymorphism (AFLP) markers. Relatively high amounts of variation were found in the subpopulations, the mean Nei’s expected heterozygosity being typical (0.267) for an outcrossing species. Despite the fact that no seedlings or viable seeds of A. fulva have been found in the previous field studies, the observed high genotypic diversity suggested that sexual reproduction has played an important role at some time during the history of the studied A. fulva population. Analysis of population structure revealed a low level of genotypic differentiation (Φ_ST=0.046) between subpopulations, and also significant sub-structuring within subpopulations. Isolation-by-distance between subpopulations was present on scales larger than 1 km. The overall pattern of genetic variation within and between subpopulations suggest that the population has characters of both stepping-stone and metapopulation models. Because our results suggested that subpopulations are more or less ephemeral, the conservation and management effort in this species should be targeted to conservation of the required habitat of the species instead of extant subpopulations.     

How river structure and biological traits influence gene flow: a population genetic study of two stream invertebrates with differing dispersal abilities

1. Determined by landscape structure as well as dispersal‐related traits of species, connectivity influences various key aspects of population biology, ranging from population persistence to genetic structure and diversity. Here, we investigated differences in small‐scale connectivity in terms of gene flow between populations of two ecologically important invertebrates with contrasting dispersal‐related traits: an amphipod (Gammarus fossarum) with a purely aquatic life cycle and a mayfly (Baetis rhodani) with a terrestrial adult stage. 2. We used highly polymorphic markers to estimate genetic differentiation between populations of both species within a Swiss pre‐alpine catchment and compared these results to the broader‐scale genetic structure within the Rhine drainage. Landscape genetic approaches were used to test for correlations of genetic and geographical structures and in‐stream barrier effects. 3. We found overall very weak genetic structure in populations of B. rhodani. In contrast, G. fossarum showed strong genetic differentiation, even at spatial scales of a few kilometres, and a clear pattern of isolation by distance. Genetic diversity decreased from downstream towards upstream populations of G. fossarum, suggesting asymmetric gene flow. Correlation of genetic structure with landscape topography was more pronounced in the amphipod. Our study also indicates that G. fossarum might be capable of dispersing overland in headwater regions and of crossing small in‐stream barriers. 4. We speculate that differences in dispersal capacity but also habitat specialisation and potentially the extent of local adaptation could be responsible for the differences in genetic differentiation found between the two species. These results highlight the importance of taking into account dispersal‐related traits when planning management and conservation strategies.     

Comparative analysis of genetic variability of white sea cod (Gadus morhua marisalbi) at allozyme and microsatellite markers

Variability of cod spawning and feeding schools from Kandalaksha Bay of the White Sea, was examined at six allozyme and eight microsatellite loci. The degree of genetic differentiation at allozyme loci constituted θ = 0.36% [95% bootstrap interval 0.0458; 0.6743]. The differentiation estimates obtained using microsatellite markers were higher, θ = 1.33% [0.057; 3.11]. It was demonstrated that the level of genetic diversity in the White Sea cod was lower than that established for the Atlantic cod from Barents Sea using the same set of allozyme and microsatellite markers. The genetic data obtained support the opinion that the White Sea cod is a reproductively independent group formed as a result of the Holocene dispersal of Atlantic cod.     

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.     

Quantifying Spatial Genetic Structuring in Mesophotic Populations of the Precious Coral Corallium rubrum

While shallow water red coral populations have been overharvested in the past, nowadays, commercial harvesting shifted its pressure on mesophotic organisms. An understanding of red coral population structure, particularly larval dispersal patterns and connectivity among harvested populations is paramount to the viability of the species. In order to determine patterns of genetic spatial structuring of deep water Corallium rubrum populations, for the first time, colonies found between 58–118 m depth within the Tyrrhenian Sea were collected and analyzed. Ten microsatellite loci and two regions of mitochondrial DNA (mtMSH and mtC) were used to quantify patterns of genetic diversity within populations and to define population structuring at spatial scales from tens of metres to hundreds of kilometres. Microsatellites showed heterozygote deficiencies in all populations. Significant levels of genetic differentiation were observed at all investigated spatial scales, suggesting that populations are likely to be isolated. This differentiation may by the results of biological interactions, occurring within a small spatial scale and/or abiotic factors acting at a larger scale. Mitochondrial markers revealed significant genetic structuring at spatial scales greater then 100 km showing the occurrence of a barrier to gene flow between northern and southern Tyrrhenian populations. These findings provide support for the establishment of marine protected areas in the deep sea and off-shore reefs, in order to effectively maintain genetic diversity of mesophotic red coral populations.     

Fine scale genetic structure in the wild ancestor of maize (Zea mays ssp. parviglumis)

Analysis of fine scale genetic structure in continuous populations of outcrossing plant species has traditionally been limited by the availability of sufficient markers. We used a set of 468 SNPs to characterize fine‐scale genetic structure within and between two dense stands of the wild ancestor of maize, teosinte (Zea mays ssp. parviglumis). Our analyses confirmed that teosinte is highly outcrossing and showed little population structure over short distances. We found that the two populations were clearly genetically differentiated, although the actual level of differentiation was low. Spatial autocorrelation of relatedness was observed within both sites but was somewhat stronger in one of the populations. Using principal component analysis, we found evidence for significant local differentiation in the population with stronger spatial autocorrelation. This differentiation was associated with pronounced shifts in the first two principal components along the field. These shifts corresponded to changes in allele frequencies, potentially due to local topographical features. There was little evidence for selection at individual loci as a contributing factor to differentiation. Our results demonstrate that significant local differentiation may, but need not, co‐occur with spatial autocorrelation of relatedness. The present study represents one of the most detailed analyses of local genetic structure to date and provides a benchmark for future studies dealing with fine scale patterns of genetic diversity in natural plant populations.     

Highly differentiated population structure of a Mangrove species, Bruguiera gymnorhiza (Rhizophoraceae) revealed by one nuclear GapCp and one chloroplast intergenic spacer trnF–trnL

To evaluate the genetic diversity of a mangrove species and clarify the genetic structure of its populations, we studied nucleotide polymorphism in two DNA regions of Bruguiera gymnorhiza collected from the southern islands of Japan, Thailand, Malaysia, Indonesia, Micronesia, and India. The two DNA sequences were the chloroplast (cp) intergenic spacer between trnL and trnF genes (ca. 300 bp), and a part (ca. 550 bp) of the nuclear gene coding for glyceraldehyde-3-phosphate dehydrogenase (GapCp). Little polymorphism was found within each of the three geographical regions, Pacific Ocean, Bay of Bengal and Arabian Sea. Throughout the vast regions east of the Malay peninsula including Indonesia, Thailand, Micronesia and the southern islands of Japan (Pacific Ocean), essentially only one haplotype (apart from variation in number of a T repeat) was present. A second haplotype was present on the western coast of Malay Peninsula and the eastern coast of India (Bay of Bengal). On the southwest of Malay Peninsula both of these haplotypes were present. Finally a third haplotype was found only on the western coast of India (Arabian Sea). When taken over all geographic populations, total nucleotide variation within the species was large (μ = 0.006, average of the two genes). Our results are consistent with the hypothesis that this low genetic diversity within any local population and differentiation between the different oceans or regions are caused by very low gene flow between each of the different oceans coupled with frequent fluctuation of population sizes due to the change in sea level. The significance of these results is discussed from evolutionary point of the mangrove forests.     

Primula farinosa in Denmark; genetic diversity and population management

During the past centuries Danish populations of Primula farinosa have seriously declined in number. We investigated the genetic structure and genetic diversity of plants of seven populations from two different regions, Zealand and Bornholm in Denmark, using three AFLP markers. Two populations from nearby Scania, Sweden were included as reference. We found 54 unambiguously polymorphic loci. The genetic structure analysis suggested division of the 268 plants into three distinct groups, to a large extent matching the geographical distribution of the populations. Analysis of molecular variance (AMOVA) indicated significant genetic differentiation of 67% within populations and 33% among the populations. Our results suggest that genetic differentiation among regions and unique local genetic diversity should carefully be considered in future conservation attempts if we are to maintain as much genetic variation as possible. We present a historical overview of the decline in Danish populations and discuss conservation management and restoration strategies.     

The genetic variability of the red king crab, <Emphasis Type="Italic">Paralithodes camtschatica</Emphasis> (Tilesius, 1815) (Anomura,Lithodidae) introduced into the Barents Sea compared with samples from the Bering Sea and Kamchatka region using eleven microsatellite loci

The intentional introduction of red king crab, Paralithodes camtschatica (Tilesius, 1815) in the Barents Sea represent one of a few successful cases and one that now supports a commercial fishery. Introductions of alien species into new environments are often associated with genetic bottlenecks, which cause a reduction in the genetic variation, and this could be important for the spreading potential of the species in the Atlantic Ocean. Red king crab samples collected in the Varangerfjord located on the Barents Sea (northern Norway) were compared with reference crab samples collected from the Bering Sea and Kamchatka regions in the Pacific Ocean. All samples were screened for eleven microsatellite loci, based on the development of species-specific primers. The observed number of alleles per locus was similar, and no reduction in genetic variation, including gene diversity and allelic richness, was detected between the Varangerfjord sample and the reference sample from Okhotsk Sea near Kamchatka, indicating no genetic bottlenecking at least for the microsatellite loci investigated. The same results were found in comparison with the sample from Bering Sea. The level of genetic differentiation among the samples, measured as overall F _ST across all loci, was relatively low (0.0238) with a range of 0.0035–0.1000 for the various loci investigated. The largest pairwise F _ST values were found between the Bering Sea and Varangerfjord/Barents Sea samples, with a value of 0.0194 across all loci tested. The lowest value (0.0101) was found between the Varangerfjord and Kamchatka samples. Genetic differentiation based on exact tests on allele frequencies revealed highly significant differences between all pairwise comparisons. The high level of genetic variation found in the Varangerfjord/Barents Sea sample could be of significance with respect to further spreading of the species to other regions in the North Atlantic Ocean.     

Morphological and genetic variation of Fucus in the eastern Gulf of Bothnia,northern Baltic Sea

Fucus vesiculosus and F. radicans (Phaeophyceae) are important habitat-formers on rocky shores in the Bothnian Sea. While both species occur sympatrically along the entire western Bothnian Sea coast, F. radicans has been found only in the northern part of the eastern coast. According to previous studies, the two species can be distinguished based on morphology, F. radicans having narrower thalli and a bushier appearance. However, marine mapping in the eastern Bothnian Sea has revealed that high morphological variation in Fucus, partly caused by gradients in salinity and exposure, makes differentiation between the two species difficult. We studied morphological and genetic variation to find out whether the two Fucus species can be differentiated in the south-eastern Bothnian Sea, and if F. radicans occurs in the area. The study was carried out in six subareas including 350 km of coast, with a salinity gradient of 3.5–6.5 PSU, and varying wave exposure. We found a gradual change towards smaller and narrower thalli and a higher number of holdfasts in Fucus populations when moving northwards to lower salinities. Distinct Fucus morphs were often found within the study sites but the morphs were genetically differentiated only at one study site in the Skaftung subarea, suggesting the occurrence of both species. However, in the Vasa subarea the sample size for analysing genetic differentiation was low due to high clonality. In the Luvia subarea south of Skaftung, Fucus morphology corresponded to that of F. radicans in earlier studies but the population was genetically more similar to F. vesiculosus in the southern subareas. We conclude that by using only morphological characteristics it is not possible to differentiate between the two species in central and northern parts of the eastern Bothnian Sea. Based on genetic analyses, the southernmost known occurrence of F. radicans in the eastern Bothnian Sea is in Skaftung.     

Landscape-level spatial genetic structure in Quercus acutissima (Fagaceae)

Quercus acutissima (Fagaceae), a deciduous broad-leaved tree, is an important forest element in hillsides of South Korea. We used allozyme loci, Wright's F statistics, and multilocus spatial autocorrelation statistics to examine the distribution of genetic diversity within and among three local populations and the spatial genetic structure at a landscape scale (15 ha, 250 × 600 m) on Oenaro Island, South Korea. Levels of genetic diversity in Q. acutissima populations were comparable to mean values for other oak species. A moderate but significant deficit of heterozygotes (mean F(IS) = 0.069) was detected within local populations and low but significant differentiation was observed among populations (F(ST) = 0.010). Spatial autocorrelation analyses revealed little evidence of significant genetic structure at spatial scales of 100-120 m. The failure to detect genetic structure within populations may be due to intraspecific competition or random mortality among saplings, resulting in extensive thinning within maternal half-sib groups. Alternatively, low genetic differentiation at the landscape scale indicates substantial gene flow among local populations. Although wind-borne pollen may be the primary source of gene flow in Q. acutissima, these results suggest that acorn movement by animals may be more extensive than previously anticipated. Comparison of these genetic data for Oenaro Island with a disturbed isolated inland population suggests that population-to-population differences in internal genetic structure may be influenced by local variation in regeneration environment (e.g., disturbance).     

Genetic and morphological analyses of tub gurnard Chelidonichthys lucerna populations in Turkish marine waters

Genetic and morphological structure of tub gurnard Chelidonichthys lucerna populations in Turkish marine waters were investigated with mtDNA sequencing of 16S rRNA and morphological characters. C. lucerna samples were collected from the Black Sea, Marmara, Aegean and northeastern Mediterranean coasts of Turkey. The lowest genetic diversity was found in the northeastern Mediterranean (Iskenderun Bay) population, while the highest was in the Marmara population with overall average value of genetic diversity within populations. A total of 14 haplotypes was found, and the highest haplotype diversity was in the Black Sea whereas the lowest was in the northeastern Mediterranean population (Iskenderun Bay). The Black Sea and Iskenderun Bay populations showed the least genetic divergence (0.001081), while the highest was between the Marmara Sea and northeastern Mediterranean (Antalya Bay) populations (0.002067). Pairwise comparisons of genetic distance revealed statistically significant differences (P < 0.05) between the Marmara and both the Aegean and northeastern Mediterranean (Antalya Bay) samples. Neighbour joining tree analyses clustered the northeastern Mediterranean populations (Antalya Bay and Iskenderun Bay) as genetically more interrelated populations, whereas the Aegean Sea population was clustered as most isolated one. Discriminant function analysis of morphological characters showed that only the Black Sea population is differentiated from the other populations.     

Landscape genetics of a specialized grasshopper inhabiting highly fragmented habitats: a role for spatial scale

Aim The study of geographical discontinuities in the distribution of genetic variability in natural populations is a central topic in both evolutionary and conservation research. In this study, we aimed to analyse (1) the factors associated with genetic diversity at the landscape spatial scale in the highly specialized grasshopper Mioscirtus wagneri and (2) to identify the relative contribution of alternative factors to the observed patterns of genetic structure in this species. Location La Mancha region, Central Spain. Methods We sampled 28 populations of the grasshopper M. wagneri and genotyped 648 individuals at seven microsatellite loci. We employed a causal modelling approach to identify the most influential variables associated with genetic differentiation within a multiple hypothesis‐testing framework. Results We found that genetic diversity differs among populations located in different river basins and decreases with population isolation. Causal modelling analyses showed variability in the relative influence of the studied landscape features across different spatial scales. When a highly isolated population is considered, the analyses suggested that geographical distance is the only factor explaining the genetic differentiation between populations. When that population is excluded, the causal modelling analysis revealed that elevation and river basins are also relevant factors contributing to explaining genetic differentiation between the studied populations. Main conclusions These results indicate that the spatial scale considered and the inclusion of outlier populations may have important consequences on the inferred contribution of alternative landscape factors on the patterns of genetic differentiation even when all populations are expected to similarly respond to landscape structure. Thus, a multiscale perspective should also be incorporated into the landscape genetics framework to avoid biased conclusions derived from the spatial scale analysed and/or the geographical distribution of the studied populations.     

Migration and recovery of the genetic diversity during the increasing density phase in cyclic vole populations

In cyclic populations, high genetic diversity is currently reported despite the periodic low numbers experienced by the populations during the low phases. Here, we report spatio-temporal monitoring at a very fine scale of cyclic populations of the fossorial water vole (Arvicola terrestris) during the increasing density phase. This phase marks the transition from a patchy structure (demes) during low density to a continuous population in high density. We found that the genetic diversity was effectively high but also that it displayed a local increase within demes over the increasing phase. The genetic diversity remained relatively constant when considering all demes together. The increase in vole abundance was also correlated with a decrease of genetic differentiation among demes. Such results suggest that at the end of the low phase, demes are affected by genetic drift as the result of being small and geographically isolated. This leads to a loss of local genetic diversity and a spatial differentiation among demes. This situation is counterbalanced during the increasing phase by the spatial expansion of demes and the increase of the effective migration among differentiated demes. We provide evidences that in cyclic populations of the fossorial water voles, the relative influence of drift operating during low density populations and migration occurring principally while population size increases interacts closely to maintain high genetic diversity.     

The influence of spatial scale on the genetic structure of a widespread tropical wetland tree, Pterocarpus officinalis (Fabaceae)

Identifying factors that cause genetic differentiation in plant populations and the spatial scale at which genetic structuring can be detected will help to understand plant population dynamics and identify conservation units. In this study, we determined the genetic structure and diversity of Pterocarpus officinalis, a widespread tropical wetland tree, at three spatial scales: (1) drainage basin “watershed” (<10 km), (2) within Puerto Rico (<100 km), and (3) Caribbean-wide (>1000 km) using AFLP. At all three spatial scales, most of the genetic variation occurred within populations, but as the spatial scale increased from the watershed to the Caribbean region, there was an increase in the among population variation (Φ_ST=0.19 to Φ_ST=0.53). At the watershed scale, there was no significant differentiation (P=0.77) among populations in the different watersheds, although there was some evidence that montane and coastal populations differed (P<0.01). At the island scale, there was significant differentiation (P<0.001) among four populations in Puerto Rico. At the regional scale (>1000 km), we found significant differentiation (P<0.001) between island and continental populations in the Caribbean region, which we attributed to factors associated with the colonization history of P. officinalis in the Neotropics. Given that genetic structure can occur from local to regional spatial scales, it is critical that conservation recommendations be based on genetic information collected at the appropriate spatial scale.     

Local genetic structure in the critically endangered,cave‐associated perennial herb Primulina tabacum (Gesneriaceae)

The local spatial genetic structures of cave‐associated plants are seldom studied. Given that these plants are mainly confined to small areas in and around the entrances of caves, we hypothesized that they might lack genetic structures at local scales. To test this hypothesis, we sampled two large populations (named D and T) of a critically endangered perennial herb, Primulina tabacum, which is endemic to karst caves in southern China. We analysed nine microsatellite loci and sequenced four chloroplast DNA (cpDNA) intergenic spacer regions to study the genetic diversity and structure within and between both populations. Both populations have distinct genetic characteristics. Samples from two subpopulations in population D showed considerable genetic divergence. This is not consistent with the hypothesis that P. tabacum has a weak genetic structure at a local scale. However, 94% of the individuals in population T shared the same multilocus genotype, which indicates little genetic structure within this population. The contributions of seed flow, pollen flow and (sub)population history to the genetic diversity and structure in each and both populations are discussed. Our study is the first to investigate local genetic diversity and structure in a cave‐associated plant, and provides valuable information for the sustainable conservation of such species. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 747–756.     

Outlier SNP markers reveal fine‐scale genetic structuring across European hake populations (Merluccius merluccius)

Shallow population structure is generally reported for most marine fish and explained as a consequence of high dispersal, connectivity and large population size. Targeted gene analyses and more recently genome‐wide studies have challenged such view, suggesting that adaptive divergence might occur even when neutral markers provide genetic homogeneity across populations. Here, 381 SNPs located in transcribed regions were used to assess large‐ and fine‐scale population structure in the European hake (Merluccius merluccius), a widely distributed demersal species of high priority for the European fishery. Analysis of 850 individuals from 19 locations across the entire distribution range showed evidence for several outlier loci, with significantly higher resolving power. While 299 putatively neutral SNPs confirmed the genetic break between basins (F_CT = 0.016) and weak differentiation within basins, outlier loci revealed a dramatic divergence between Atlantic and Mediterranean populations (F_CT range 0.275–0.705) and fine‐scale significant population structure. Outlier loci separated North Sea and Northern Portugal populations from all other Atlantic samples and revealed a strong differentiation among Western, Central and Eastern Mediterranean geographical samples. Significant correlation of allele frequencies at outlier loci with seawater surface temperature and salinity supported the hypothesis that populations might be adapted to local conditions. Such evidence highlights the importance of integrating information from neutral and adaptive evolutionary patterns towards a better assessment of genetic diversity. Accordingly, the generated outlier SNP data could be used for tackling illegal practices in hake fishing and commercialization as well as to develop explicit spatial models for defining management units and stock boundaries.