Matrilineal genetic structure and female-mediated gene flow in red grouse (Lagopus lagopus scoticus): an analysis using mitochondrial DNA

Abstract.— DNA sequence variation at the hypervariable 5'end of the mitochondrial control region was examined in 247 individuals to detect genetic divergence among 14 populations of red grouse ( Lagopus lagopus scoticus ) in northeastern Scotland. Ten haplotypes were resolved, several of which were shared among populations. Analysis of molecular variance, Nei's yST, and a cladistic estimate of the amount of gene flow indicated a lack of overall population differentiation. Patterns of overall panmixia are in stark contrast to previous reports of localized subdivision among the same set of populations detected using hypervariable microsatellite markers. Because grouse cocks are territorial and show extreme natal philopatry and females are the dispersing sex, such discordance could be explained by sexbiased dispersal, with extensive female-mediated gene flow preventing mitochondrial DNA divergence. However, it is difficult to reconcile how effective dispersal of females would not homogenize both mitochondrial and nuclear structure simultaneously. We use a model that examines the spatial and temporal dynamics of diparentally and uniparentally inherited genes to show that, under realistic ecological scenarios and with specific differences in the dispersal of males and females, the local effective size of the nuclear genome can be less than that of the mitochondrial and the patterns of structuring we observe are meaningful.     

Weak large‐scale population genetic structure in a philopatric seabird,the European Shag Phalacrocorax aristotelis

Quantifying population genetic structure is fundamental to testing hypotheses regarding gene flow, population divergence and dynamics across large spatial scales. In species with highly mobile life‐history stages, where it is unclear whether such movements translate into effective dispersal among discrete philopatric breeding populations, this approach can be particularly effective. We used seven nuclear microsatellite loci and mitochondrial DNA (ND2) markers to quantify population genetic structure and variation across 20 populations (447 individuals) of one such species, the European Shag, spanning a large geographical range. Despite high breeding philopatry, rare cross‐sea movements and recognized subspecies, population genetic structure was weak across both microsatellites and mitochondrial markers. Furthermore, although isolation‐by‐distance was detected, microsatellite variation provided no evidence that open sea formed a complete barrier to effective dispersal. These data suggest that occasional long‐distance, cross‐sea movements translate into gene flow across a large spatial scale. Historical factors may also have shaped contemporary genetic structure: cluster analyses of microsatellite data identified three groups, comprising colonies at southern, mid‐ and northern latitudes, and similar structure was observed at mitochondrial loci. Only one private mitochondrial haplotype was found among subspecies, suggesting that this current taxonomic subdivision may not be mirrored by genetic isolation.     

Phylogeography of the pine processionary moth Thaumetopoea wilkinsoni in the Near East

Phylogeographic structure of the eastern pine processionary moth Thaumetopoea wilkinsoni was explored in this study by means of nested clade phylogeographic analyses of COI and COII sequences of mitochondrial DNA and Bayesian estimates of divergence times. Intraspecific relationships were inferred and hypotheses tested to understand historical spread patterns and spatial distribution of genetic variation. Analyses revealed that all T. wilkinsoni sequences were structured in three clades, which were associated with two major biogeographic events, the colonization of the island of Cyprus and the separation of southwestern and southeastern Anatolia during the Pleistocene. Genetic variation in populations of T. wilkinsoni was also investigated using amplified fragment length polymorphisms and four microsatellite loci. Contrasting nuclear with mitochondrial data revealed recurrent gene flow between Cyprus and the mainland, related to the long-distance male dispersal. In addition, a reduction in genetic variability was observed at both mitochondrial and nuclear markers at the expanding boundary of the range, consistent with a recent origin of these populations, founded by few individuals expanding from nearby localities. In contrast, several populations fixed for one single mitochondrial haplotype showed no reduction in nuclear variability, a pattern that can be explained by recurrent male gene flow or selective sweeps at the mitochondrial level. The use of both mitochondrial and nuclear markers was essential in understanding the spread patterns and the population genetic structure of T. wilkinsoni, and is recommended to study colonizing species characterized by sex-biased dispersal.     

High levels of variation despite genetic fragmentation in populations of the endangered mountain pygmy-possum, Burramys parvus, in alpine Australia

In endangered mammals, levels of genetic variation are often low and this is accompanied by genetic divergence among populations. The mountain pygmy-possum (Burramys parvus) is an endangered marsupial restricted to the alpine region of Victoria and New South Wales, Australia. By scoring variation at eight microsatellite loci, we found that B. parvus populations exhibit high levels of genetic divergence and fall into three distinct groups from the northern, central and southern areas of the distribution of this species, consistent with previous assessments of mitochondrial DNA variation. F(ST) values between populations from these regions ranged from 0.19 to 0.54. Within the central area, there was further genetic fragmentation, and a linear association between genetic and geographical distance. This pattern is likely to reflect limited dispersal across barriers despite the fact that individual B. parvus can move several kilometres. Levels of genetic variation within populations were high with the exception of a southern population where there was evidence of inbreeding. From a conservation perspective, all three areas where B. parvus are found should be considered as separate gene pools; management of populations within these areas needs to take into account the low gene flow between populations, as well as threats posed by roads, resorts and other developments in the alpine region. The low genetic variability and inbreeding in the southern population is of particular concern given the high levels of variability in other B. parvus populations.     

Is Gene Flow Promoting the Reversal of Pleistocene Divergence in the Mountain Chickadee (Poecile gambeli)?

The Pleistocene glacial cycles left a genetic legacy on taxa throughout the world; however, the persistence of genetic lineages that diverged during these cycles is dependent upon levels of gene flow and introgression. The consequences of secondary contact among taxa may reveal new insights into the history of the Pleistocene’s genetic legacy. Here, we use phylogeographic methods, using 20 nuclear loci from regional populations, to infer the consequences of secondary contact following divergence in the Mountain Chickadee (Poecile gambeli). Analysis of nuclear data identified two geographically-structured genetic groups, largely concordant with results from a previous mitochondrial DNA (mtDNA) study. Additionally, the estimated multilocus divergence times indicate a Pleistocene divergence, and are highly concordant with mtDNA. The previous mtDNA study showed a paucity of sympatry between clades, while nuclear patterns of gene flow show highly varied patterns between populations. The observed pattern of gene flow, from coalescent-based analyses, indicates southern populations in both clades exhibit little gene flow within or between clades, while northern populations are experiencing higher gene flow within and between clades. If this pattern were to persist, it is possible the historical legacy of Pleistocene divergence may be preserved in the southern populations only, and the northern populations would become a genetically diverse hybrid species.     

Mitochondrial DNA and microsatellite variation in the eider duck (Somateria mollissima) indicate stepwise postglacial colonization of Europe and limited current long-distance dispersal

To unravel the postglacial colonization history and the current intercolony dispersal in the common eider, Somateria mollissima, we analysed genetic variation at a part of the mitochondrial control region and five unlinked autosomal microsatellite loci in 175 eiders from 11 breeding colonies, covering the entire European distribution range of this species. As a result of extreme female philopatry, mitochondrial DNA differentiation is substantial both among local colonies and among distant geographical regions. Our study further corroborates the previous hypothesis of a single Pleistocene refugium for European eiders. A nested clade analysis on mitochondrial haplotypes suggests that (i) the Baltic Sea eider population is genetically closest to a presumably ancestral population and that (ii) the postglacial recolonization progressed in a stepwise fashion via the North Sea region and the Faroe Islands to Iceland. Current long-distance dispersal is limited. Differentiation among colonies is much less pronounced at microsatellite loci. The geographical pattern of this nuclear genetic variation is to a large extent explained by isolation by distance. As female dispersal is very limited, the geographical pattern of nuclear variation is probably explained by male-mediated gene flow among breeding colonies. Our study provides genetic evidence for the assumed prominent postglacial colonization route shaping the present terrestrial fauna of the North Atlantic islands Iceland and the Faroes. It suggests that this colonization had been a stepwise process originating in continental Europe. It is the first molecular study on eider duck populations covering their entire European distribution range.     

The microevolution of the Galápagos marine iguana Amblyrhynchus cristatus assessed by nuclear and mitochondrial genetic analyses

Marine iguanas may have inhabited the Galápagos archipelago and its former, now sunken islands for more than 10 million years (Myr). It is therefore surprising that morphological and immunological data indicate little evolutionary divergence within the genus. We utilized mitochondrial DNA (mtDNA) sequence analyses and nuclear DNA fingerprinting to re-evaluate the level and pattern of genetic differentiation among 22 marine iguana populations from throughout the archipelago. Both genetic marker systems detect a low level of within-genus divergence, but they show contrasting levels of geographical subdivision among the populations. The mitochondrial gene pools of populations from different regions of the archipelago are isolated, and the mtDNA pattern appears to follow the sequence in which the islands were colonized by marine iguanas. Conversely, the nuclear DNA study indicates substantial interpopulational gene exchange, and the geographical distribution of the nuclear markers seems to be determined by isolation by distance among the populations. The natural history of marine iguanas suggests that the contrasting nuclear and mitochondrial DNA patterns result from an asymmetric migration behaviour of the two sexes, with higher (active and passive) interisland dispersal for males than females. Separate genetic analyses for the sexes appear to support this hypophesis. Based on these findings, a scenario is proposed that explains the marine iguanas' low genetic divergence, notwithstanding their long evolutionary history in the Galápagos archipelago.     

Phylogeographic structure and postglacial evolutionary history of water voles (Arvicola terrestris) in the United Kingdom

The phylogeographic pattern of mitochondrial DNA variation in water voles (Arvicola terrestris) from 57 localities across the United Kingdom and representative samples from Spain, France, Switzerland and Finland was determined from sequence variation in the central portion of the control region. Twenty-seven different haplotypes were resolved which formed two distinct phylogenetic clades. This major division separated haplotypes found in Scotland from those found in England and Wales. Nested clade analysis of haplotypes indicated that such a division was a consequence of allopatric fragmentation. The haplotypes found in Switzerland, France and Spain clustered with Scottish haplotypes, whereas the haplotype from Finland clustered with the English/Welsh haplotypes. These patterns indicate that contemporary Scottish populations are derived from an Iberian glacial refugium, whereas English and Welsh populations are derived from an eastern European refugium. As such, the postglacial recolonization of the United Kingdom must have involved two colonization events, either in different localities with no subsequent contact, or as two waves separated over time, with the second wave of colonizers displacing the first. An analysis of molecular variance (AMOVA) identified significant population genetic divergence within both the major clades, indicative of restricted gene flow and regional population isolation. The implications of both phylogeographical and population genetic structure are discussed in context with the conservation of water voles in Britain.     

Genetic evidence supports song learning in the three-wattled bellbird Procnias tricarunculata (Cotingidae)

Vocal learning is thought to have evolved in three clades of birds (parrots, hummingbirds, and oscine passerines), and three clades of mammals (whales, bats, and primates). Behavioural data indicate that, unlike other suboscine passerines, the three-wattled bellbird Procnias tricarunculata (Cotingidae) is capable of vocal learning. Procnias tricarunculata shows conspicuous vocal ontogeny, striking geographical variation in song, and rapid temporal change in song within a population. Deprivation studies of vocal development in P. tricarunculata are impractical. Here, we report evidence from mitochondrial DNA sequences and nuclear microsatellite loci that genetic variation within and among the four allopatric breeding populations of P. tricarunculata is not congruent with variation in vocal behaviour. Sequences of the mitochondrial DNA control region document extensive haplotype sharing among localities and song types, and no phylogenetic resolution of geographical populations or behavioural groups. The vocally differentiated, allopatric breeding populations of P. tricarunculata are only weakly genetically differentiated populations, and are not distinct taxa. Mitochondrial DNA and microsatellite variation show small (2.9% and 13.5%, respectively) but significant correlation with geographical distance, but no significant residual variation by song type. Estimates of the strength of selection that would be needed to maintain the observed geographical pattern in vocal differentiation if songs were genetically based are unreasonably high, further discrediting the hypothesis of a genetic origin of vocal variation. These data support a fourth, phylogenetically independent origin of avian vocal learning in Procnias. Geographical variations in P. tricarunculata vocal behaviour are likely culturally evolved dialects.     

Fine‐scale patterns of genetic divergence within and between morphologically variable subspecies of the sea urchin Heliocidaris erythrogramma (Echinometridae)

The spatial scale over which genetic divergences occur between populations and the extent that they are paralleled by morphological differences can vary greatly among marine species. In the present study, we use a hierarchical spatial design to investigate genetic structure in Heliocidaris erythrogramma occurring on near shore limestone reefs in Western Australia. These reefs are inhabited by two distinct subspecies: the thick‐spined Heliocidaris erythrogramma armigera and the thin‐spined Heliocidaris erythrogramma erythrogramma, each of which also have distinct colour patterns. In addition to pronounced morphological variation, H. erythrogramma exhibits a relatively short (3–4 days) planktonic phase before settlement and metamorphosis, which limits their capacity for dispersal. We used microsatellite markers to determine whether patterns of genetic structure were influenced more by morphological or life history limitations to dispersal. Both individual and population‐level analyses found significant genetic differentiation between subspecies, which was independent of geographical distance. Genetic diversity was considerably lower within H. e. erythrogramma than within H. e. armigera and genetic divergence was four‐fold greater between subspecies than among populations within subspecies. This pattern was consistent even at fine spatial scales (< 5 km). We did detect some evidence of gene flow between the subspecies; however, it appears to be highly restricted. Within subspecies, genetic structure was more clearly driven by dispersal capacity, although weak patterns of isolation‐by‐distance suggest that there may be other factors limiting gene exchange between populations. Our results show that spatial patterns of genetic structure in Western Australian H. erythrogramma is influenced by a range of factors but is primarily correlated with the distribution of morphologically distinct subspecies. This suggests the presence of reproductive barriers to gene exchange between them and demonstrates that morphological variation can be a good predictor of genetic divergence. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 103 , 578–592.     

Genetic insights into the evolution of Scots pine,Pinus sylvestris L., in Scotland

Summary

Present day populations of native Scots pine contain a wealth of genetic variation. The arrangement of this variation within and among populations has been influenced by a number of processes in the past. These include patterns of recolonization of Scotland after glaciation, gene flow among populations, and natural selection acting at both a regional and local scale. By analyzing present day patterns of genetic variation, insights into past evolution can be obtained. Suitable analysis of genetic variation for monoterpenes, enzymes, mitochondrial DNA and quantitative characters such as growth rate and phenology in native pine indicate two origins for Scottish populations, substantial adaptive divergence from continental populations, and the presence of local adaptation within Scotland. The implications for conservation and future research are addressed.     

Patterns of population subdivision, gene flow and genetic variability in the African wild dog (Lycaon pictus)

African wild dogs are large, highly mobile carnivores that are known to disperse over considerable distances and are rare throughout much of their geographical range. Consequently, genetic variation within and differentiation between geographically separated populations is predicted to be minimal. We determined the genetic diversity of mitochondrial DNA (mtDNA) control region sequences and microsatellite loci in seven populations of African wild dogs. Analysis of mtDNA nucleotide diversity suggests that, historically, wild dog populations have been small relative to other large carnivores. However, population declines due to recent habitat loss have not caused a dramatic reduction in genetic diversity. We found one historical and eight recent mtDNA genotypes in 280 individuals that defined two highly divergent clades. In contrast to a previous, more limited, mtDNA analysis, sequences from these clades are not geographically restricted to eastern or southern African populations. Rather, we found a large admixture zone spanning populations from Botswana, Zimbabwe and south-eastern Tanzania. Mitochondrial and microsatellite differentiation between populations was significant and unique mtDNA genotypes and alleles characterized the populations. However, gene flow estimates (Nm) based on microsatellite data were generally greater than one migrant per generation. In contrast, gene flow estimates based on the mtDNA control region were lower than expected given differences in the mode of inheritance of mitochondrial and nuclear markers which suggests a male bias in long-distance dispersal.     

Postglacial intra-lacustrine divergence of Icelandic threespine stickleback morphs in three neovolcanic lakes

The geographical context of divergence and local adaptation of lacustrine fish is controversial. Despite recent theoretical support for sympatric and parapatric divergence, empirical studies providing unequivocal support for this remain scant. An important component of such a case would be where multiple lakes have different morphs and a range of markers, both mitochondrial and nuclear, show monophyly within lakes. Here we describe such a situation for threespine sticklebacks in three lakes in Iceland. By analysing the variation at nuclear and mitochondrial markers in several freshwater and marine populations as well as three pairs of intra-lacustrine morphs we infer their phylogenetic relationships and colonization pattern. There were high levels of microsatellite variation in all populations and no evidence was found for either repeated colonization of marine fish or colonization from distinct glacial refugia. Intra-lacustrine threespine stickleback morphs in all three lakes show significant genetic divergence probably indicating restricted gene flow.     

Reconciling patterns of genetic variation with stream structure, earth history and biology in the Australian freshwater fish Craterocephalus stercusmuscarum (Atherinidae)

We examined the consequences of barriers, stream architecture and putative dispersal capability on levels of genetic differentiation among populations of the freshwater fish Craterocephalus stercusmuscarum. Seven polymorphic allozyme loci and sequences of a 498-bp fragment of the ATPase 6 mitochondrial DNA (mtDNA) gene were used to assess patterns of genetic variation among 16 populations from upland and lowland streams of five drainages in northern Queensland, Australia. Concordant patterns at both genetic markers revealed that there were significant levels of genetic subdivision among all populations, while an analysis of molecular variation showed that the distribution of genetic diversity was not consistent with contemporary drainage structure. There were reciprocally monophyletic mtDNA clades and fixed or large frequency differences at allozyme loci either side of instream barriers such as waterfalls. This implied barriers were effective in restricting gene flow between upland and lowland populations separated by waterfalls. However, there were two genetically distinct groups in upland areas, even within the same subcatchment, as well as high levels of genetic subdivision among lowland populations, suggesting barriers alone do not explain the patterns of genetic diversity. The data revealed a complex phylogeographic pattern, which we interpreted to be the result of one or more invasion events of independent lineages to different sections of each drainage, possibly mediated by well documented geomorphological changes. Our results highlight the importance of earth structure and history in shaping population genetic structure in stream organisms where dispersal capability may be limited, and reveal that the contemporary structure of drainages is not necessarily a good indicator of genetic relationships among populations.     

Microsatellite data resolve phylogeographic patterns in European grayling, Thymallus thymallus, Salmonidae

The phylogeography of an endangered salmonid, European grayling (Thymallus thymallus), was studied based on analysis of 17 nuclear microsatellite DNA loci. In agreement with earlier mitochondrial DNA (mtDNA) studies, phylogenetic relationships of the populations suggested that northern Europe was colonized from two distinct Pleistocene refugia. Furthermore, microsatellites revealed highly supported grouping of mainland Swedish, Norwegian, Danish, German and Slovenian populations, suggesting that grayling from the northwestern and central Europe have descended from their southern conspecifics. The level of divergence between populations was substantial, even across short geographical distances. Although this was in part due to postglacial colonization patterns and contemporary barriers for gene flow, the high divergence estimates between hydrologically connected sampling locations implied efficient interpopulation reproductive isolation. Microsatellites revealed that the populations exhibited, on average, only 3.5 (+/-2.2) alleles per locus, indicating that T. thymallus has strikingly low levels of intrapopulation genetic diversity as compared with other freshwater fish species. Accordingly, as indicated by analysis of molecular variance (AMOVA), only 49.1-58.0% of the total grayling microsatellite diversity resided within populations. A latitudinal genetic diversity gradient, potentially resulting from glaciation-mediated founder events, was not evident. Alternatively, it is possible that grayling display limited dispersal behaviour/capability, leading to low long-term effective population sizes and, consequently, depauperate intrapopulation polymorphism. These findings have implications for conservation of T. thymallus. Importantly, they exemplify that microsatellites can be highly informative for intraspecific phylogeography studies dealing with substantial divergence scales.     

Phylogeography of the Chinese endemic freshwater crab Sinopotamon acutum (Brachyura,Potamidae)

Phylogeographical inferences based on multiple molecular markers from different modes of inheritance (i.e. mtDNA and nucDNA) can help to explore drivers of current species divergence over different timescales and allow a deeper understanding of evolutionary processes. River systems and mountains, owing to their drainage networks and complex topography, are often a high priority when inferring external causes of phylogeographical patterns. Here, we selected the Chinese endemic freshwater crab Sinopotamon acutum inhabiting drainage networks across the Qinling–Daba Mountains, a watershed that divides northern from southern fauna in China, as a model species (1) to investigate whether river networks and mountain systems act as barriers in shaping the phylogeography of freshwater crabs and (2) to test the impact of historic environments and ecological habitats on crab distribution. Phylogenetic tree and network analyses based on mtDNA revealed divergence between eastern and western populations, but microsatellite DNA did not recover this. Frequent and male‐biased gene flow is evident. The adjacent tributaries, such as Weihe River 1 and Hanjiang River 1, although isolated by Qinling Mts, have low genetic variation in mtDNA. In addition, microsatellite DNA showed low variation between all rivers. Frequent gene flow, genetic variation and mitochondrial genetic structure in S. acutum indicated that the Qinling–Daba Mountains have had no effect on divergence in this species; instead, hydrological networks across these mountains serve as a continuous migration corridor for these crabs. Glacial refugia are probably responsible for the initial isolation of the eastern and western clades, and local adaptations after dispersal have further driven divergence. Cytonuclear discordance in phylogeographical patterns may be attributable to ongoing male‐biased gene flow.     

Spatial structure of lemming populations (Dicrostonyx groenlandicus) fluctuating in density

The pattern and scale of the genetic structure of populations provides valuable information for the understanding of the spatial ecology of populations, including the spatial aspects of density fluctuations. In the present paper, the genetic structure of periodically fluctuating lemmings (Dicrostonyx groenlandicus) in the Canadian Arctic was analysed using mitochondrial DNA (mtDNA) control region sequences and four nuclear microsatellite loci. Low genetic variability was found in mtDNA, while microsatellite loci were highly variable in all localities, including localities on isolated small islands. For both genetic markers the genetic differentiation was clear among geographical regions but weaker among localities within regions. Such a pattern implies gene flow within regions. Based on theoretical calculations and population census data from a snap-trapping survey, we argue that the observed genetic variability on small islands and the low level of differentiation among these islands cannot be explained without invoking long distance dispersal of lemmings over the sea ice. Such dispersal is unlikely to occur only during population density peaks.     

Limited differentiation in microsatellite DNA variation among northern populations of the yellow warbler: evidence for male‐biased gene flow?

Comparisons of the patterns of differentiation among genetic markers with different modes of inheritance can provide insights into patterns of sex-biased dispersal and gene flow. Here, we compare the patterns of differentiation in six microsatellite loci among eight northern breeding populations of the yellow warbler (Dendroica petechia) with results obtained with mitochondrial DNA. Significant but low levels of differentiation (overall FST = 0.014; overall RST = 0.015) were present across all populations. The level of differentiation is substantially less than that observed in the same samples based on mitochondrial DNA control region variation. The presence of low population imbalance index values and significant isolation-by-distance relationships for both FST and RST suggests that these populations are at evolutionary equilibrium and that the high degree of similarity between populations may be due to high levels of male-biased gene flow. This suggests that there may be significant but previously unappreciated differences in the long-distance and/or episodic dispersal behaviour of males and females in these birds.     

Colonization and dispersal in a social species, the Bechstein's bat (Myotis bechsteinii)

Metapopulation genetic models consider that colonization and dispersal are distinct behaviours. However, whether colonization and dispersal indeed reflect different biological processes in nature is unclear. One possibility to test this assumption is to assess patterns of autosomal and mitochondrial genetic structure in species with strict female philopatry, such as the communally breeding Bechstein's bat. In this species, mitochondrial DNA can spread only when females establish new colonies, and autosomal DNA is transmitted among colonies only when females mate with solitary males born in foreign colonies. Investigating the genetic structure among 37 colonies, we found that autosomal genes followed an island model on a regional scale and a model of isolation by distance on a larger geographical scale. In contrast, mitochondrial genetic structure revealed no pattern of isolation by distance at a large scale but exhibited an effect of ecological barriers on a regional scale. Our results provide strong empirical evidence that colonization and dispersal do not follow the same behavioural rules in this bat, supporting the assumption of metapopulation genetic models.     

Divergence and molecular variation in common whelk Buccinum undatum (Gastropoda: Buccinidae) in Iceland: a trans‐Atlantic comparison

The dispersal and history of species affects their genetic population structure at both small and large geographical scales. The common whelk, Buccinum undatum, is a widespread subtidal gastropod in the North Atlantic that has no planktonic larvae and has thus limited dispersal capacity. The snail, which has been harvested by humans for centuries, is highly variable in morphology. To evaluate the population structure in the rich fishing grounds in western Iceland and its divergence from samples across the Atlantic, genetic patterns based on sequence variation in two mitochondrial (mt)DNA genes (COI and 16S) and five microsatellites were studied and compared with variation in populations from both sides of the Atlantic. Significant differences in allele and haplotype frequencies were found among samples separated by short distances along the coast of Iceland. Partition of the variation showed larger variance among samples obtained from distant regions than from neighbouring sites and genetic distances were correlated with geographical distance among populations in Europe. Phylogeographic patterns in mtDNA reveal different monophyletic lineages on both sides of the Atlantic, which predate the onset of the Ice Age and which may constitute cryptic species. Similar micro‐ and macrogeographical patterns were observed for the mtDNA and microsatellite markers, despite high frequencies of null alleles. Bayesian skyline reconstructions of the demographic history and mismatch distributions suggest that, although sizes of some populations were unaffected by Ice Age glaciations, others show signs of expansion after the Last Glacial Maximum. These phylogeographical patterns are consistent with patterns expected for low dispersal species that have survived in allopatric glacial refugial populations on both sides of the Atlantic and in deep‐sea refugia within each continent. The observed genetic structure has implications for conservation and sustainable management of the harvested populations. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 145–159.