Genetically distinct populations of northern shrimp,Pandalus borealis,in the North Atlantic: adaptation to different temperatures as an isolation factor

The large‐scale population genetic structure of northern shrimp, Pandalus borealis, was investigated over the species’ range in the North Atlantic, identifying multiple genetically distinct groups. Genetic divergence among sample localities varied among 10 microsatellite loci (range: F_ST = ?0.0002 to 0.0475) with a highly significant average (F_ST = 0.0149; P < 0.0001). In contrast, little or no genetic differences were observed among temporal replicates from the same localities (F_ST = 0.0004; P = 0.33). Spatial genetic patterns were compared to geographic distances, patterns of larval drift obtained through oceanographic modelling, and temperature differences, within a multiple linear regression framework. The best‐fit model included all three factors and explained approximately 29% of all spatial genetic divergence. However, geographic distance and larval drift alone had only minor effects (2.5–4.7%) on large‐scale genetic differentiation patterns, whereas bottom temperature differences explained most (26%). Larval drift was found to promote genetic homogeneity in parts of the study area with strong currents, but appeared ineffective across large temperature gradients. These findings highlight the breakdown of gene flow in a species with a long pelagic larval phase (up to 3 months) and indicate a role for local adaptation to temperature conditions in promoting evolutionary diversification and speciation in the marine environment.     

Landscape genetic structure of Scirpus mariqueter reveals a putatively adaptive differentiation under strong gene flow in estuaries

Estuarine organisms grow in highly heterogeneous habitats, and their genetic differentiation is driven by selective and neutral processes as well as population colonization history. However, the relative importance of the processes that underlie genetic structure is still puzzling. Scirpus mariqueter is a perennial grass almost limited in the Changjiang River estuary and its adjacent Qiantang River estuary. Here, using amplified fragment length polymorphism (AFLP), a moderate‐high level of genetic differentiation among populations (range F_ST: 0.0310–0.3325) was showed despite large ongoing dispersal. FLOCK assigned all individuals to 13 clusters and revealed a complex genetic structure. Some genetic clusters were limited in peripheries compared with very mixing constitution in center populations, suggesting local adaptation was more likely to occur in peripheral populations. 21 candidate outliers under positive selection were detected, and further, the differentiation patterns correlated with geographic distance, salinity difference, and colonization history were analyzed with or without the outliers. Combined results of AMOVA and IBD based on different dataset, it was found that the effects of geographic distance and population colonization history on isolation seemed to be promoted by divergent selection. However, none‐liner IBE pattern indicates the effects of salinity were overwhelmed by spatial distance or other ecological processes in certain areas and also suggests that salinity was not the only selective factor driving population differentiation. These results together indicate that geographic distance, salinity difference, and colonization history co‐contributed in shaping the genetic structure of S. mariqueter and that their relative importance was correlated with spatial scale and environment gradient.     

Population structure of the dusky pipefish (Syngnathus floridae) from the Atlantic and Gulf of Mexico,as revealed by mitochondrial DNA and microsatellite analyses

Aim To elucidate the historical phylogeography of the dusky pipefish (Syngnathus floridae) in the North American Atlantic and Gulf of Mexico ocean basins. Location Southern Atlantic Ocean and northern Gulf of Mexico within the continental United States. Methods A 394‐bp fragment of the mitochondrial cytochrome b gene and a 235‐bp fragment of the mitochondrial control region were analysed from individuals from 10 locations. Phylogenetic reconstruction, haplotype network, mismatch distributions and analysis of molecular variance were used to infer population structure between ocean basins and time from population expansion within ocean basins. Six microsatellite loci were also analysed to estimate population structure and gene flow among five populations using genetic distance methods (F_ST, Nei’s genetic distance), isolation by distance (Mantel’s test), coalescent‐based estimates of genetic diversity and migration patterns, Bayesian cluster analysis and bottleneck simulations. Results Mitochondrial analyses revealed significant structuring between ocean basins in both cytochrome b (Φ_ST = 0.361, P < 0.0001; Φ_CT = 0.312, P < 0.02) and control region (Φ_ST = 0.166, P < 0.0001; Φ_CT = 0.128, P < 0.03) sequences. However, phylogenetic reconstructions failed to show reciprocal monophyly in populations between ocean basins. Microsatellite analyses revealed significant population substructuring between all locations sampled except for the two locations that were in closest proximity to each other (global F_ST value = 0.026). Bayesian analysis of microsatellite data also revealed significant population structuring between ocean basins. Coalescent‐based analyses of microsatellite data revealed low migration rates among all sites. Mismatch distribution analysis of mitochondrial loci supports a sudden population expansion in both ocean basins in the late Pleistocene, with the expansion of Atlantic populations occurring more recently. Main conclusions Present‐day populations of S. floridae do not bear the mitochondrial DNA signature of the strong phylogenetic discontinuity between the Atlantic and Gulf coasts of North America commonly observed in other species. Rather, our results suggest that Atlantic and Gulf of Mexico populations of S. floridae are closely related but nevertheless exhibit local and regional population structure. We conclude that the present‐day phylogeographic pattern is the result of a recent population expansion into the Atlantic in the late Pleistocene, and that life‐history traits and ecology may play a pivotal role in shaping the realized geographical distribution pattern of this species.     

Microsatellite DNA markers for the study of Atlantic salmon (Salmo salar) kinship,population structure,and mixed‐fishery analyses

Eleven microsatellite DNA loci were identified and characterized for Atlantic salmon (Salmo salar) collected from the Penobscot River, Maine, USA and the River Nith, Scotland, UK. The markers revealed high levels of genetic diversity (seven to 48 alleles per locus), heterozygosity (to 100%), and allelic heterogeneity (all comparisons). Considerable differentiation was observed as the genetic distance (chord) between the two collections was 0.680 and the pairwise F_ST, 0.12, was highly significant. These findings are consistent with patterns of continental‐level differentiation observed previously using an alternate suite of microsatellite loci. Locus‐by‐locus analyses of molecular variance suggested that most markers were suitable for delineating kinships and population genetic structure.     

Local selection and population structure in a deep‐sea fish,the roundnose grenadier (Coryphaenoides rupestris)

Local populations within a species can become isolated by stochastic or adaptive processes, though it is most commonly the former that we quantify. Using presumably neutral markers we can assess the time‐dependent process of genetic drift, and thereby quantify patterns of differentiation in support of the effective management of diversity. However, adaptive differences can be overlooked in these studies, and these are the very characteristics that we hope to conserve by managing neutral diversity. In this study, we used 16 hypothetically neutral microsatellite markers to investigate the genetic structure of the roundnose grenadier in the North Atlantic. We found that one locus was a clear outlier under directional selection, with F_ST values much greater than at the remaining loci. Differentiation between populations at this locus was related to depth, suggesting directional selection, presumably acting on a linked locus. Considering only the loci identified as neutral, there remained significant population structure over the region of the North Atlantic studied. In addition to a weak pattern of isolation by distance, we identified a putative barrier to gene flow between sample sites either side of the Charlie‐Gibbs Fracture Zone, which marks the location where the sub‐polar front crosses the Mid‐Atlantic Ridge. This may reflect a boundary across which larvae are differentially distributed in separate current systems to some extent, promoting differentiation by drift. Structure due to both drift and apparent selection should be considered in management policy.     

Genetic discontinuity among regional populations of <Emphasis Type="Italic">Lophelia pertusa</Emphasis> in the North Atlantic Ocean

Knowledge of the degree to which populations are connected through larval dispersal is imperative to effective management, yet little is known about larval dispersal ability or population connectivity in Lophelia pertusa, the dominant framework-forming coral on the continental slope in the North Atlantic Ocean. Using nine microsatellite DNA markers, we assessed the spatial scale and pattern of genetic connectivity across a large portion of the range of L. pertusa in the North Atlantic Ocean. A Bayesian modeling approach found four distinct genetic groupings corresponding to ocean regions: Gulf of Mexico, coastal southeastern U.S., New England Seamounts, and eastern North Atlantic Ocean. An isolation-by-distance pattern was supported across the study area. Estimates of pairwise population differentiation were greatest with the deepest populations, the New England Seamounts (average F _ST = 0.156). Differentiation was intermediate with the eastern North Atlantic populations (F _ST = 0.085), and smallest between southeastern U.S. and Gulf of Mexico populations (F _ST = 0.019), with evidence of admixture off the southeastern Florida peninsula. Connectivity across larger geographic distances within regions suggests that some larvae are broadly dispersed. Heterozygote deficiencies were detected within the majority of localities suggesting deviation from random mating. Gene flow between ocean regions appears restricted, thus, the most effective management scheme for L. pertusa involves regional reserve networks.     

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

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

DNA barcoding of the northern Northeast Atlantic skates (Chondrichthyes,Rajiformes), with remarks on the widely distributed starry ray

The skate fauna in the northern Northeast (NE) Atlantic is poorly investigated, and misidentifications are common. Here, ‘DNA barcoding’ was used to analyse 105 specimens of 15 species previously reported from the area to investigate the occurrence of species. Of these 15 species, three were new to the region and confirmed with voucher specimens. Three previously reported taxa were not obtained from the study area, providing a total number of 12 skate species for the northern NE Atlantic. Only one specimen of the critically endangered Dipturus batis complex was found. It occurs frequently in the literature and commercial fisheries catch records, and we argue that the vast majority of these are misidentifications. Due to striking differences in Amblyraja radiata life history parameters across the North Atlantic, cryptic species diversity has previously been suspected. A total of 80 A. radiata cytochrome c oxidase subunit I sequences from across the North Atlantic were sampled, and the highest fixation index (F_ST) was found when maximising geographical distance (F_ST = 0.133). A lower index was found when grouped according to life history (F_ST = 0.067). These results are not strongly supportive for the occurrence of cryptic species.     

A meta-analysis of the effects of plant traits and geographical scale on the magnitude of adaptive differentiation as measured by the difference between QST and FST

The impact of directional selection on specific trait types in plant species, and how a species’ life history mediates this response to selection remains understudied. Discovering such interactions is however crucial for understanding the interplay between ecological and genetic processes underlying local adaptation in plants, and to evaluate a species’ evolutionary potential with respect to changing environments. Furthermore, it remains unclear whether the degree of adaptive differentiation generally increases with the geographical distance between plant populations. Here, we present a weighted mixed model based meta-analysis aimed at unraveling the potential interactions between plant trait types, life history characteristics and Q_ST–F_ST comparisons, and assessing the effect of geographical scale on population differentiation. Based on 51 studies we found that Q_ST values exceeded their corresponding F_ST values in 71.74 % out of 401 cases. Furthermore, different trait types were found to be differently susceptible to natural selection and the magnitude of Q_ST–F_ST comparisons was mediated by a plant species’ life span. These findings may be closely related to the genetic architectures of trait types and life histories, with the proportion of large-effect genes likely shaping the response to natural selection. Q_ST–F_ST values also increased with increasing distance between populations, pinpointing the combined effects of environmental differentiation and isolation by distance on the magnitude of population divergence. Finally, our model showed an inverse relationship between F_ST and Q_ST–F_ST values, presumably resulting from isolation by distance, the exchange of advantageous alleles, or genetic correlations among traits.     

Spatial structure of genetic variation and primary succession in the pioneer tree species Antirhea borbonica on La Réunion

In habitats where colonization and extinction are recurrent, the distribution of gene frequencies among patches of suitable habitat may reflect the age structure of different populations. In this study, we quantify population genetic structure for a pioneer tree species, Antirhea borbonica, in a chrono-sequence of primary succession on the lava flows of the Piton de La Fournaise volcano (La Réunion). Using microsatellite loci and amplified fragment length polymorphism (AFLP) markers, we quantified genetic variation within and among populations for early- and late-succession populations in a landscape where extinction and recolonization are recurrent (the ‘Grand Brûlé’) and for late-succession populations in a more stable landscape. This study produced three main results. First, we detected no evidence that founder events increase genetic differentiation among colonizing populations; F_ST values among early- and among late-succession populations were similar. Second, we found no evidence for isolation by distance; genetic distance was not correlated with spatial distance within and among populations. Third, F_IS values are consistently high in all populations, despite the fact that A. borbonica populations are functionally close to dioecy and thus expected to have an outcrossing mating system. Multiple colonization events from different sources may limit differentiation among young populations and spatial isolation may enhance differentiation among late-succession populations. Ecological processes acting during colonization may create the conditions for spatial aggregation within pioneer populations, and thus contribute to the high F_IS values.     

Low but significant genetic differentiation underlies biologically meaningful phenotypic divergence in a large Atlantic salmon population

Despite decades of research assessing the genetic structure of natural populations, the biological meaning of low yet significant genetic divergence often remains unclear due to a lack of associated phenotypic and ecological information. At the same time, structured populations with low genetic divergence and overlapping boundaries can potentially provide excellent models to study adaptation and reproductive isolation in cases where high‐resolution genetic markers and relevant phenotypic and life history information are available. Here, we combined single nucleotide polymorphism (SNP)‐based population inference with extensive phenotypic and life history data to identify potential biological mechanisms driving fine‐scale subpopulation differentiation in Atlantic salmon (Salmo salar) from the Teno River, a major salmon river in Europe. Two sympatrically occurring subpopulations had low but significant genetic differentiation (F_ST = 0.018) and displayed marked differences in the distribution of life history strategies, including variation in juvenile growth rate, age at maturity and size within age classes. Large, late‐maturing individuals were virtually absent from one of the two subpopulations, and there were significant differences in juvenile growth rates and size at age after oceanic migration between individuals in the respective subpopulations. Our findings suggest that different evolutionary processes affect each subpopulation and that hybridization and subsequent selection may maintain low genetic differentiation without hindering adaptive divergence.     

Geographic clines in wing morphology relate to colonization history in New World but not Old World populations of yellow dung flies

Geographic clines offer insights about putative targets and agents of natural selection as well as tempo and mode of adaptation. However, demographic processes can lead to clines that are indistinguishable from adaptive divergence. Using the widespread yellow dung fly Scathophaga stercoraria (Diptera: Scathophagidae), we examine quantitative genetic differentiation (Q_ST) of wing shape across North America, Europe, and Japan, and compare this differentiation with that of ten microsatellites (F_ST). Morphometric analyses of 28 populations reared at three temperatures revealed significant thermal plasticity, sexual dimorphism, and geographic differentiation in wing shape. In North America morphological differentiation followed the decline in microsatellite variability along the presumed route of recent colonization from the southeast to the northwest. Across Europe, where S. stercoraria presumably existed for much longer time and where no molecular pattern of isolation by distance was evident, clinal variation was less pronounced despite significant morphological differentiation (Q_ST>F_ST). Shape vector comparisons further indicate that thermal plasticity (hot‐to‐cold) does not mirror patterns of latitudinal divergence (south‐to‐north), as might have been expected under a scenario with temperature as the major agent of selection. Our findings illustrate the importance of detailed phylogeographic information when interpreting geographic clines of dispersal traits in an adaptive evolutionary framework.     

Single nucleotide polymorphism discovery in albacore and Atlantic bluefin tuna provides insights into worldwide population structure

The optimal management of the commercially important, but mostly over‐exploited, pelagic tunas, albacore (Thunnus alalunga Bonn., 1788) and Atlantic bluefin tuna (BFT; Thunnus thynnus L., 1758), requires a better understanding of population structure than has been provided by previous molecular methods. Despite numerous studies of both species, their population structures remain controversial. This study reports the development of single nucleotide polymorphisms (SNPs) in albacore and BFT and the application of these SNPs to survey genetic variability across the geographic ranges of these tunas. A total of 616 SNPs were discovered in 35 albacore tuna by comparing sequences of 54 nuclear DNA fragments. A panel of 53 SNPs yielded F_ST values ranging from 0.0 to 0.050 between samples after genotyping 460 albacore collected throughout the distribution of this species. No significant heterogeneity was detected within oceans, but between‐ocean comparisons (Atlantic, Pacific and Indian oceans along with Mediterranean Sea) were significant. Additionally, a 17‐SNP panel was developed in Atlantic BFT by cross‐species amplification in 107 fish. This limited number of SNPs discriminated between samples from the two major spawning areas of Atlantic BFT (F_ST = 0.116). The SNP markers developed in this study can be used to genotype large numbers of fish without the need for standardizing alleles among laboratories.     

Population genetics of Atlantic bluefin tuna,Thunnus thynnus (Linnaeus, 1758), in the Mediterranean: implications for its conservation management

The movement of Atlantic bluefin tuna (ABFT) across international boundaries necessitates traceability strategies that would provide more accurate information needed for stock assessment. The Mediterranean Sea is one of the main contributors to ABFT reproduction and global population genetic diversity. In the present study this genetic variability was investigated using 193 samples of adult bluefin tuna from Spain, Turkey and Malta – a longitudinal distance of 3400 km. Analysed were 13 microsatellite loci (eight of which were newly‐tested) as genetic markers for the population study. Allele richness measured per locus and sampling location varied from 1.89 to 8.88, taking into account rarefaction. ABFT private alleles were detected in each of the three sampling sites. No significant spatial genetic divergence was found between pairs at the studied locations (F_ST values <0.0001; P‐values >0.05). Bayesian clustering analysis corroborated a single and panmictic ABFT population in the Mediterranean Sea. Statistical power analyses indicated a high probability of detecting genetic differentiation and population structure with the sample size and microsatellites used, even at an F_ST value of 0.005. From the results it may be postulated that migrating ABFT during the spawning season are allowing gene flow within the Mediterranean Sea. The complex interplay of movements, including plasticity in the selection of spawning sites with increasing age and environmental conditions, require multiple and new fisheries monitoring and management techniques in order to target the ABFT long‐term conservation effectively.     

Genetic variation and population structure in black-grass (Alopecurus myosuroides Huds.), a successful, herbicide-resistant, annual grass weed of winter cereal fields

Black‐grass (Alopecurus myosuroides) is an allogamous grass weed common in cereal fields of northern Europe, which developed resistance to a widely used family of herbicides, the ACCase‐inhibiting herbicides. Resistance is caused by mutations at the ACCase gene and other, metabolism‐based, mechanisms. We investigated the genetic structure of 36 populations of black‐grass collected in one region of France (Côte d’Or), using 116 amplified fragment length polymorphism (AFLP) loci and sequence data at the ACCase gene. The samples were characterized for their level of herbicide resistance and genotyped for seven known ACCase mutations conferring resistance. All samples contained herbicide‐resistant plants, and 19 contained ACCase mutations. The genetic diversity at AFLP loci was high (H_T = 0.246), while differentiation among samples was low (F_ST = 0.023) and no isolation by distance was detected. Genetic diversity within samples did not vary with the frequency of herbicide resistance. A Bayesian algorithm was used to infer population structure. The two genetic clusters inferred were not associated with any geographical structure or with herbicide resistance. A high haplotype diversity (H_d = 0.873) and low differentiation (G_ST = 0.056) were observed at ACCase. However, haplotype diversity within samples decreased with the frequency of ACCase‐based resistance. We suggest that the genetic structure of black‐grass is affected by its recent expansion as a weed. Our data demonstrate that the strong selection imposed by herbicides did not modify the genome‐wide genetic structure of an allogamous weed that probably has large effective population sizes. Our study gives keys to a better understanding of the evolution of successful, noxious weeds in modern agriculture.     

Contemporary habitat loss reduces genetic diversity in an ecologically specialized butterfly

Aim This study investigated the influence of contemporary habitat loss on the genetic diversity and structure of animal species using a common, but ecologically specialized, butterfly, Theclinesthes albocincta (Lepidoptera: Lycaenidae), as a model. Location South Australia. Methods We used amplified fragment length polymorphism (AFLP) and allozyme datasets to investigate the genetic structure and genetic diversity among populations of T. albocincta in a fragmented landscape and compared this diversity and structure with that of populations in two nearby landscapes that have more continuous distributions of butterflies and their habitat. Butterflies were sampled from 15 sites and genotyped, first using 363 informative AFLP bands and then using 17 polymorphic allozyme loci (n = 248 and 254, respectively). We complemented these analyses with phylogeographic information based on mitochondrial DNA (mtDNA) haplotype information derived from a previous study in the same landscapes. Results Both datasets indicated a relatively high level of genetic structuring across the sampling range (AFLP, F_ST = 0.34; allozyme, F_ST = 0.13): structure was greatest among populations in the fragmented landscape (AFLP, F_ST = 0.15; allozyme, F_ST = 0.13). Populations in the fragmented landscape also had significantly lower genetic diversity than populations in the other two landscapes: there were no detectable differences in genetic diversity between the two continuous landscapes. There was also evidence (r² = 0.33) of an isolation by distance effect across the sampled range of the species. Main conclusions The multiple lines of evidence, presented within a phylogeographic context, support the hypothesis that contemporary habitat fragmentation has been a major driver of genetic erosion and differentiation in this species. Theclinesthes albocincta populations in the fragmented landscape are thus likely to be at greater risk of extinction because of reduced genetic diversity, their isolation from conspecific subpopulations in other landscapes, and other extrinsic forces acting on their small population sizes. Our study provides compelling evidence that habitat loss and fragmentation have significant rapid impacts on the genetic diversity and structure of butterfly populations, especially specialist species with particular habitat preferences and poor dispersal abilities.     

The Pillars of Hercules as a bathymetric barrier to gene flow promoting isolation in a global deep‐sea shark (Centroscymnus coelolepis)

Knowledge of the mechanisms limiting connectivity and gene flow in deep‐sea ecosystems is scarce, especially for deep‐sea sharks. The Portuguese dogfish (Centroscymnus coelolepis) is a globally distributed and near threatened deep‐sea shark. C. coelolepis population structure was studied using 11 nuclear microsatellite markers and a 497‐bp fragment from the mtDNA control region. High levels of genetic homogeneity across the Atlantic (Φ_ST = ?0.0091, F_ST = 0.0024, P > 0.05) were found suggesting one large population unit at this basin. The low levels of genetic divergence between Atlantic and Australia (Φ_ST = 0.0744, P < 0.01; F_ST = 0.0015, P > 0.05) further suggested that this species may be able to maintain some degree of genetic connectivity even across ocean basins. In contrast, sharks from the Mediterranean Sea exhibited marked genetic differentiation from all other localities studied (Φ_ST = 0.3808, F_ST = 0.1149, P < 0.001). This finding suggests that the shallow depth of the Strait of Gibraltar acts as a barrier to dispersal and that isolation and genetic drift may have had an important role shaping the Mediterranean shark population over time. Analyses of life history traits allowed the direct comparison among regions providing a complete characterization of this shark's populations. Sharks from the Mediterranean had markedly smaller adult body size and size at maturity compared to Atlantic and Pacific individuals. Together, these results suggest the existence of an isolated and unique population of C. coelolepis inhabiting the Mediterranean that most likely became separated from the Atlantic in the late Pleistocene.     

Demographic history has shaped the strongly differentiated corkwing wrasse populations in Northern Europe

Understanding the biological processes involved in genetic differentiation and divergence between populations within species is a pivotal aim in evolutionary biology. One particular phenomenon that requires clarification is the maintenance of genetic barriers despite the high potential for gene flow in the marine environment. Such patterns have been attributed to limited dispersal or local adaptation, and to a lesser extent to the demographic history of the species. The corkwing wrasse (Symphodus melops) is an example of a marine fish species where regions of particular strong divergence are observed. One such genetic break occurred at a surprisingly small spatial scale (F_ST ~0.1), over a short coastline (<60 km) in the North Sea‐Skagerrak transition area in southwestern Norway. Here, we investigate the observed divergence and purported reproductive isolation using genome resequencing. Our results suggest that historical events during the post‐glacial recolonization route can explain the present population structure of the corkwing wrasse in the northeast Atlantic. While the divergence across the break is strong, we detected ongoing gene flow between populations over the break suggesting recent contact or negative selection against hybrids. Moreover, we found few outlier loci and no clear genomic regions potentially being under selection. We concluded that neutral processes and random genetic drift e.g., due to founder events during colonization have shaped the population structure in this species in Northern Europe. Our findings underline the need to take into account the demographic process in studies of divergence processes.     

Pattern‐oriented modelling of population genetic structure

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