The Effect of Pleistocene Climate Fluctuations on Distribution of European Abalone (<Emphasis Type="Italic">Haliotis tuberculata</Emphasis>), Revealed by Combined Mitochondrial and Nuclear Marker Analyses

The genetic differentiation among the populations of the European abalone Haliotis tuberculata was investigated using different markers to better understand the evolutionary history and exchanges between populations. Three markers were used: mitochondrial cytochrome oxidase I (COI), the sperm lysin nuclear gene, and eight nuclear microsatellites. These markers present different characteristics concerning mutation rate and inheritance, which provided complementary information about abalone history and gene diversity. Genetic diversity and relationships among subspecies were calculated from a sample of approximately 500 individuals, collected from 17 different locations in the north-eastern Atlantic Ocean, Macaronesia, and Mediterranean Sea. COI marker was used to explore the phylogeny of the species with a network analysis and two phylogenetic methods. The analysis revealed 18 major haplotypes grouped into two distinct clades with a pairwise sequence divergence up to 3.5 %. These clades do not correspond to subspecies but revealed many contacts along Atlantic coast during the Pleistocene interglaciations. The sperm lysin gene analysis separated two different subtaxa: one associated to Macaronesian islands, and the other to all other populations. Moreover, a small population of the northern subtaxon was isolated in the Adriatic Sea—probably before the separation of the two lineages—and evolved independently. Microsatellites were analyzed by different genetics methods, including the Bayesian clustering method and migration patterns analysis. It revealed genetically distinct microsatellite patterns among populations from Mediterranean Sea, Brittany and Normandy, Morocco, and Canary and Balearic islands. Gene flow is asymmetric among the regions; the Azores and the Canary Islands are particularly isolated and have low effective population sizes. Our results support the hypothesis that climate changes since the Pleistocene glaciations have played a major role in the geographic distribution of the European abalone. Traces of these events related to maternal inheritance were shown on COI marker.     

Historical population dynamics and demography of the Eastern Atlantic pomacentrid Chromis limbata (Valenciennes, 1833)

Recent studies have focused on the relationship between the marine fauna of the Eastern Atlantic and the Mediterranean Sea, but within the Atlantic, little is known about genetic relationships between populations of the Macaronesian islands. In this study, we tested whether the paleo-climatology and paleo-oceanography of the region could predict the genetic relationships among three Eastern Atlantic populations (Azores, Madeira, and Canaries) of a damselfish, Chromis limbata, and compared our results with its Mediterranean and adjacent Atlantic sister species, Chromis chromis. We combined phylogeographic and coalescent approaches using the fast evolving mitochondrial control region gene. No population structure was found for the three archipelagos. The coalescence time estimated for C. limbata (0.857-1.17 Mya) was much greater than that estimated for C. chromis. We propose that this difference reflects differences in glaciating extents in the Northeastern Atlantic and the Mediterranean. Diversity indexes (Hd and genetic distances) together with historical demographic parameters of C. limbata (Theta and g) revealed a more stable population history when compared to C. chromis. Our results suggest that the Macaronesian populations of C. limbata have probably been less affected by the last glaciation than the Mediterranean populations of C. chromis. Migration across the three archipelagos was estimated and a prevailing northwest trend was detected. This result supports the idea of a colonization of the Azores by warm water fish from Madeira or the westernmost Canary islands which acted as major glacial refugia for the tropical and subtropical marine fauna during the glaciations.     

Strong population genetic structure and contrasting demographic histories for the small-spotted catshark (Scyliorhinus canicula) in the Mediterranean Sea

Coastal and demersal chondrichthyans, such as the small-spotted catshark, are expected to exhibit genetic differentiation in areas of complex geomorphology like the Mediterranean Basin because of their limited dispersal ability. To test this hypothesis, we used a fragment of the mitochondrial cytochrome c oxidase subunit I gene and 12 nuclear microsatellite loci in order to investigate the genetic structure and historical demography of this species, and to identify potential barriers to gene flow. Samples were collected from the Balearic Islands, the Algerian Basin, the Ionian Sea, the Corinthian Gulf and various locations across the Aegean Sea. Additional sequences from the Atlantic and the Levantine Basin retrieved from GenBank were included in the mitochondrial DNA analysis. Both mitochondrial and nuclear microsatellite DNA data revealed a strong genetic subdivision, mainly between the western and eastern Mediterranean, whereas the Levantine Basin shared haplotypes with both areas. The geographic isolation of the Mediterranean basins seems to enforce the population genetic differentiation of the species, with the deep sea acting as a strong barrier to its dispersal. Contrasting historical demographic patterns were also observed in different parts of the species'' distribution, most notably a population growth trend in the western Mediterranean/Atlantic area and a slight decreasing one in the Aegean Sea. The different effects of the Pleistocene glacial periods on the habitat availability may explain the contrasting demographic patterns observed. The current findings suggest that the small-spotted catshark exhibits several genetic stocks in the Mediterranean, although further study is needed.     

Distributional and demographic consequences of Pleistocene climate fluctuations for a marine demersal fish in the north-eastern Atlantic

Aim The Pleistocene glaciations were the most significant historical event during the evolutionary life span of most extant species. However, little is known about the consequences of these climate changes for the distribution and demography of marine animals of the north‐eastern Atlantic. The present study focuses on the phylogeographic and demographic patterns of the sand goby, Pomatoschistus minutus (Teleostei: Gobiidae), a small marine demersal fish. Location North‐eastern Atlantic, Mediterranean, Irish, North and Baltic seas. Methods Analysis was carried out by sequencing the mtDNA cytochrome b gene of sand gobies from 12 localities throughout the species’ range, and using this information in combination with published data of allozyme markers and mtDNA control region sequences. Several phylogenetic methods and a network analysis were used to explore the phylogeographic pattern. The historical demography of P. minutus was studied through a mismatch analysis and a Bayesian skyline plot. Results Reciprocal monophyly was found between a Mediterranean Sea (MS) clade and an Atlantic Ocean (AO) clade, both with a Middle Pleistocene origin. The AO Clade contains two evolutionary significant units (ESUs): the Iberian Peninsula (IB) Group and the North Atlantic (NA) Group. These two groups diverged during Middle Pleistocene glacial cycles. For the NA Group there is evidence for geographic sorting of the ancestral haplotypes with recent radiations in the Baltic Sea, Irish Sea, North Sea and Bay of Biscay. The demographic histories of the Mediterranean Clade and the two Atlantic ESUs were influenced mainly by expansions dated as occurring during the Middle Pleistocene glaciations and post‐Eem, respectively. Main conclusions The pre‐LGM (Last Glacial Maximum) subdivision signals were not erased for P. minutus during the LGM. Middle Pleistocene glaciations yielded isolated and differently evolving sets of populations. In contrast to the case for most other taxa, only the northern Atlantic group contributed to the post‐glacial recolonization. The historical demography of Mediterranean sand gobies was influenced mainly by Middle Pleistocene glaciations, in contrast to that of the Atlantic populations, which was shaped by Late Pleistocene expansions.     

Phylogeography of the common shrimp, Crangon crangon (L.) across its distribution range

The common or brown shrimp Crangon crangon (L.) is a highly abundant and important taxon, both ecologically and commercially, yet knowledge on its population structure and historical biogeography is limited. We studied population genetic structure across the distribution range of this species by sequencing a 388 bp fragment of the cytochrome-c-oxidase I gene for 140 individuals from 25 locations. Strong population structuring and high levels of genetic diversity were observed. Four main phylogroups were uncovered: northeastern Atlantic, western Mediterranean, Adriatic Sea and Black Sea. Gene flow of these shrimp across known oceanographical barriers (e.g., the Strait of Gibraltar and/or Oran-Almeria front, Sicilian Straits, and Turkish Straits) is severely restricted. The oldest and most variable populations currently inhabit the western Mediterranean. The observed absence of structure across the entire northeastern Atlantic shelf is proposed not to be due to gene flow, but to relatively recent colonization following the glacial cycles of the late Pleistocene. Black Sea shrimp are currently disconnected from Mediterranean populations, and colonization is inferred, on the basis of coalescent analysis, to have happened relatively recently, but possibly earlier than 7000 years ago. We postulate the hypothesis that C. crangon survived the last brackish-water (<7 per thousand) period inside the Black Sea and/or one of the adjacent inland seas. We conclude that (1) common shrimp populations from different basins are strongly differentiated, (2) gene flow across basins is probably very limited, and (3) the biogeographic history of the taxon is largely in accordance with the geographic history of its distribution range. This study provides further evidence that high population connectivity of marine species (e.g., by policy makers) should not be assumed.     

Phylogeography of the Atlanto-Mediterranean sea cucumber Holothuria (Holothuria) mammata: the combined effects of historical processes and current oceanographical pattern

We assessed the genetic structure of populations of the widely distributed sea cucumber Holothuria (Holothuria) mammata Grube, 1840, and investigated the effects of marine barriers to gene flow and historical processes. Several potential genetic breaks were considered, which would separate the Atlantic and Mediterranean basins, the isolated Macaronesian Islands from the other locations analysed, and the Western Mediterranean and Aegean Sea (Eastern Mediterranean). We analysed mitochondrial 16S and COI gene sequences from 177 individuals from four Atlantic locations and four Mediterranean locations. Haplotype diversity was high (H=0.9307 for 16S and 0.9203 for COI), and the haplotypes were closely related (π=0.0058 for 16S and 0.0071 for COI). The lowest genetic diversities were found in the Aegean Sea population. Our results showed that the COI gene was more variable and more useful for the detection of population structure than the 16S gene. The distribution of mtDNA haplotypes, the pairwise F(ST) values and the results of exact tests and amova revealed: (i) a significant genetic break between the population in the Aegean Sea and those in the other locations, as supported by both mitochondrial genes, and (ii) weak differentiation of the Canary and Azores Islands from the other populations; however, the populations from the Macaronesian Islands, Algarve and West Mediterranean could be considered to be a panmictic metapopulation. Isolation by distance was not identified in H. (H.) mammata. Historical events behind the observed findings, together with the current oceanographic patterns, were proposed and discussed as the main factors that determine the population structure and genetic signature of H. (H.) mammata.     

Maintenance of genetic differentiation across a transition zone in the sea: discordance between nuclear and cytoplasmic markers

To investigate the origin and maintenance of the genetic discontinuity between Atlantic and Mediterranean populations of the common sea bass (Dicentrarchus labrax) we analysed the genetic variation at a fragment of mitochondrial cytochrome b sequence for 18 population samples. The result were also compared with new or previously published microsatellite data. Seven mitochondrial haplotypes and an average nucleotidic divergence of 0.02 between Atlantic and Mediterranean populations that matches a Pleistocene allopatric isolation were found. The frequency variation at the cytochrome b locus was many times greater between Atlantic and Mediterranean populations (theta(C) = 0.67) than at microsatellite loci (theta(N)= 0.02). The examination of the different evolutionary forces at play suggests that a sex-biased hybrid breakdown is a likely explanation for part of the observed discrepancy between mitochondrial and nuclear loci. In addition, an analysis is made of the correlation between microsatellite loci points towards the possible existence of a hybrid zone in samples from the Alboran Sea.     

Phylogeography of the marine isopod Stenosoma nadejda (Rezig, 1989) in North African Atlantic and western Mediterranean coasts reveals complex differentiation patterns and a new species

The transition zone between the Mediterranean and Atlantic basins has been extensively addressed in phylogeographical studies of marine species. However, biases exist towards the analysis of highly dispersive species, and there is a higher sampling effort in European coasts compared to North Africa. This may be hindering a detailed understanding of the historical and contemporary processes that shaped patterns of population genetic structure in the region. In the present study, we investigated the phylogeographical and phylogenetic patterns of mitochondrial cytochrome c oxidase subunit I sequences from a species with direct development and low dispersal abilities, Stenosoma nadejda (Rezig, 1989). The study area included 13 localities along the Atlantic and Mediterranean North African coasts, as well as the Alboran Sea. A new Stenosoma species, from the coasts of Algeria and Alboran Island, was discovered. For S. nadejda, phylogeographical analyses revealed three distinct clades: one in the Iberian Atlantic plus the Alboran Sea, one in the western Mediterranean, and another in the Atlantic coast of Africa. Haplotypes from the Alboran Island were more related to those from the western Mediterranean coast (east of the Almeria–Oran Front). Given the strong differentiation, it is probable that this species survived in multiple glacial refugia during the Pleistocenic glaciations. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 419–431.     

Evidence for multiple Pleistocene refugia in the postglacial expansion of the eastern tiger salamander,Ambystoma tigrinum tigrinum

Abstract Pleistocene glaciations were important determinants of historical migration and, hence, current levels of genetic diversity within and among populations. In many cases, these historical migrations led to the existence of disjunct populations of plants and animals. However, the origin and timing of arrival of these disjunct populations is often debated. In the current study, we identify potential refugia and estimate the timing of vicariance events of the eastern tiger salamander, Ambystoma tigrinum tigrinum , using mitochondrial sequence data. The results suggest a vicariant event 0.75–2 million years ago, separating the tiger salamanders to the east and west of the Apalachicola River Basin. East of the Appalachians, there appear to be multiple independent refugia with little migration among the remaining populations. In particular, populations along the Atlantic Coastal Plain were likely isolated in a coastal plain refugium in the Carolinas. Migrants from this refugium were the likely source of colonists for populations occupying previously glaciated areas along the northeastern Atlantic Coast. A second potential refugium occurs in the Blue Ridge Mountains of western Virginia. This refugium contains a disjunct population of the eastern tiger salamander, as well as a community of nearly 70 other disjunct plant and animal species. The tiger salamanders here have been isolated from other populations for 200,000–500,000 years. These results suggest that disjunct mountain populations of Coastal Plain species may have existed in situ throughout the Pleistocene in Appalachian refugia. Therefore, these disjunct populations are not of recent origin, but rather exist as relicts of a warmer, more widespread fauna and flora that is now restricted to the Coastal Plain.     

PHYLOGEOGRAPHIC PATTERNS INDICATE TRANSATLANTIC MIGRATION FROM EUROPE TO NORTH AMERICA IN THE RED SEAWEED CHONDRUS CRISPUS (GIGARTINALES,RHODOPHYTA)1

Inferring how the Pleistocene climate oscillations have repopulated the extant population structure of Chondrus crispus Stackh. in the North Atlantic Ocean is important both for our understanding of the glacial episode promoting diversification and for the conservation and development of marine organisms. C. crispus is an ecologically and commercially important red seaweed with broad distributions in the North Atlantic. Here, we employed both partial mtDNA Cox1 and nrDNA internal transcribed spacer region 2 (ITS2) sequences to explore the genetic structure of 17 C. crispus populations from this area. Twenty‐eight and 30 haplotypes were inferred from these two markers, respectively. Analysis of molecular variance (AMOVA) and of the population statistic Φ_ST not only revealed significant genetic structure within C. crispus populations but also detected significant levels of genetic subdivision among and within populations in the North Atlantic. On the basis of high haplotype diversity and the presence of endemic haplotypes, we postulate that C. crispus had survived in Pleistocene glacial refugia in the northeast Atlantic, such as the English Channel and the northwestern Iberian Peninsula. We also hypothesize that C. crispus from the English Channel refugium repopulated most of northeastern Europe and recolonized northeastern North America in the Late Pleistocene. The observed phylogeographic pattern of C. crispus populations is in agreement with a scenario in which severe Quaternary glaciations influenced the genetic structure of North Atlantic marine organisms with contiguous population expansion and locally restricted gene flow coupled with a transatlantic dispersal in the Late Pleistocene.     

Phylogeography and Pleistocene refugia of the Little Owl Athene noctua inferred from mtDNA sequence data

Pleistocene glaciations greatly affected the distribution of genetic diversity in animal populations. The Little Owl is widely distributed in temperate regions and could have survived the last glaciations in southern refugia. To describe the phylogeographical structure of European populations, we sequenced the mitochondrial cytochrome c oxidase I (COI) and control region (CR1) in 326 individuals sampled from 22 locations. Phylogenetic analyses of COI identified two deeply divergent clades: a western haplogroup distributed in western and northwestern Europe, and an eastern haplogroup distributed in southeastern Europe. Faster evolving CR1 sequences supported the divergence between these two main clades, and identified three subgroups within the eastern clade: Balkan, southern Italian and Sardinian. Divergence times estimated from COI with fossil calibrations indicate that the western and eastern haplogroups split 2.01–1.71 Mya. Slightly different times for splits were found using the standard 2% rate and 7.3% mtDNA neutral substitution rate. CR1 sequences dated the origin of endemic Sardinian haplotypes at 1.04–0.26 Mya and the split between southern Italian and Balkan haplogroups at 0.72–0.21 Mya, coincident with the onset of two Pleistocene glaciations. Admixture of mtDNA haplotypes was detected in northern Italy and in central Europe. These findings support a model of southern Mediterranean and Balkan refugia, with postglacial expansion and secondary contacts for Little Owl populations. Central and northern Europe was predominantly recolonized by Little Owls from Iberia, whereas expansion out of the Balkans was more limited. Northward expansion of the Italian haplogroup was probably prevented by the Alps, and the Sardinian haplotypes remained confined to the island. Results showed a clear genetic pattern differentiating putative subspecies. Genetic distances between haplogroups were comparable with those recorded between different avian species.     

Phylogeography and palaeodistribution modelling of Nassauvia subgenus Strongyloma (Asteraceae): exploring phylogeographical scenarios in the Patagonian steppe

The Patagonian steppe is an immense, cold, arid region, yet phylogeographically understudied. Nassauvia subgen. Strongyloma is a characteristic element of the steppe, exhibiting a continuum of morphological variation. This taxon provides a relevant phylogeographical model not only to understand how past environmental changes shaped the genetic structure of its populations, but also to explore phylogeographical scenarios at the large geographical scale of the Patagonian steppe. Here, we (1) assess demographic processes and historical events that shaped current geographic patterns of haplotypic diversity; (2) analyze hypotheses of isolation in refugia, fragmentation of populations, and/or colonization of available areas during Pleistocene glaciations; and (3) model extant and palaeoclimatic distributions to support inferred phylogeographical patterns. Chloroplast intergenic spacers, rpl32–trnL and trnQ–5′rps16, were sequenced for 372 individuals from 63 populations. Nested clade analysis, analyses of molecular variance, and neutrality tests were performed to assess genetic structure and range expansion. The present potential distribution was modelled and projected onto a last glacial maximum (LGM) model. Of 41 haplotypes observed, ten were shared among populations associated with different morphological variants. Populations with highest haplotype diversity and private haplotypes were found in central‐western and south‐eastern Patagonia, consistent with long‐term persistence in refugia during Pleistocene. Palaeomodelling suggested a shift toward the palaeoseashore during LGM; new available areas over the exposed Atlantic submarine platform were colonized during glaciations with postglacial retraction of populations. A scenario of fragmentation and posterior range expansion may explain the observed patterns in the center of the steppe, which is supported by palaeomodelling. Northern Patagonian populations were isolated from southern populations by the Chubut and the Deseado river basins during glaciations. Pleistocene glaciations indirectly impacted the distribution, demography, and diversification of subgen. Strongyloma through decreased winter temperatures and water availability in different areas of its range.     

Evolutionary history of Lissotriton helveticus: multilocus assessment of ancestral vs. recent colonization of the Iberian Peninsula

The Pleistocene was characterized by climatic changes that greatly altered the distribution of organisms. Population extinctions, bottlenecks, isolation, range expansions and contractions were often associated with glaciations, leaving signatures in the spatial patterns of genetic diversity across species. Lissotriton helveticus belongs to a Pan-European lineage of newts that were strongly affected by glaciations and represent an excellent model to analyse the effect of generalized climatic changes in phylogeographic patterns. We studied the genetic diversity of the species using data from two mitochondrial and three nuclear genes analyzed in a Bayesian phylogenetic framework to investigate the historical processes shaping spatial patterns of genetic diversity. Mitochondrial haplotypes cluster in four different groups present in the Iberian Peninsula and of Pleistocene origin, probably by allopatric fragmentation. Nuclear genes present no obvious geographic structure patterns, suggesting gene flow and generalized incomplete lineage sorting. Populations north of the Pyrenees are closely related to those from northeastern Iberia, suggesting recent range expansion from this region. Historical demographic analyses indicate a demographic expansion starting about 100,000years ago and more recent population declines. Compared to other Lissotriton species, L. helveticus includes only relatively young genetic lineages, suggesting a Central European pre-Pleistocene distribution followed by complete extirpation of the species during glaciations in that area. Historical demographic trends in the Iberian Peninsula are reversed with respect to the more Mediterranean species Lissotriton boscai, indicating different responses of both species to climate changes. Diversity patterns among Lissotriton species seem to be defined by four main factors: ancestral distributions, colonization capabilities, interactions with other species and effective population sizes. Differences in these factors define two types of species, referred to as "R" (refugia) and "S" (sanctuaries) that explain part of the diversity in patterns of genetic diversity created by glaciations in Western Europe.     

Intraspecific genetic structure,divergence and high rates of clonality in an amphi‐Atlantic starfish

Intraspecific genetic diversity and divergence have a large influence on the adaption and evolutionary potential of species. The widely distributed starfish, Coscinasterias tenuispina, combines sexual reproduction with asexual reproduction via fission. Here we analyse the phylogeography of this starfish to reveal historical and contemporary processes driving its intraspecific genetic divergence. We further consider whether asexual reproduction is the most important method of propagation throughout the distribution range of this species. Our study included 326 individuals from 16 populations, covering most of the species’ distribution range. A total of 12 nuclear microsatellite loci and sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene were analysed. COI and microsatellites were clustered in two isolated lineages: one found along the southwestern Atlantic and the other along the northeastern Atlantic and Mediterranean Sea. This suggests the existence of two different evolutionary units. Marine barriers along the European coast would be responsible for population clustering: the Almeria–Oran Front that limits the entrance of migrants from the Atlantic to the Mediterranean, and the Siculo‐Tunisian strait that divides the two Mediterranean basins. The presence of identical genotypes was detected in all populations, although two monoclonal populations were found in two sites where annual mean temperatures and minimum values were the lowest. Our results based on microsatellite loci showed that intrapopulation genetic diversity was significantly affected by clonality whereas it had lower effect for the global phylogeography of the species, although still some impact on populations’ genetic divergence could be observed between some populations.     

Chromosome polymorphisms track trans‐Atlantic divergence and secondary contact in Atlantic salmon

Pleistocene glaciations drove repeated range contractions and expansions shaping contemporary intraspecific diversity. Atlantic salmon (Salmo salar) in the western and eastern Atlantic diverged >600,000 years before present, with the two lineages isolated in different southern refugia during glacial maxima, driving trans‐Atlantic genomic and karyotypic divergence. Here, we investigate the genomic consequences of glacial isolation and trans‐Atlantic secondary contact using 108,870 single nucleotide polymorphisms genotyped in 80 North American and European populations. Throughout North America, we identified extensive interindividual variation and discrete linkage blocks within and between chromosomes with known trans‐Atlantic differences in rearrangements: Ssa01/Ssa23 translocation and Ssa08/Ssa29 fusion. Spatial genetic analyses suggest independence of rearrangements, with Ssa01/Ssa23 showing high European introgression (>50%) in northern populations indicative of post‐glacial trans‐Atlantic secondary contact, contrasting with low European ancestry genome‐wide (3%). Ssa08/Ssa29 showed greater intrapopulation diversity, suggesting a derived chromosome fusion polymorphism that evolved within North America. Evidence of potential selection on both genomic regions suggests that the adaptive role of rearrangements warrants further investigation in Atlantic salmon. Our study highlights how Pleistocene glaciations can influence large‐scale intraspecific variation in genomic architecture of northern species.     

Population differentiation and evolution in the common guillemot Uria aalge

Common (Uria aalge) and Brünnich's guillemots (U. Iomvia) are colonial seabirds that nest in temperate to arctic oceans throughout the Northern hemisphere. They are very similar in the characteristics of ecology, demography and life history that are thought to determine the extent of differentiation among populations, yet geographic variation in morphology is notably greater in common guillemots. Despite evidence of strong natal philopatry, previous analyses of allozymes and the mitochondrial cytochrome b gene revealed little genetic differentiation among North Atlantic colonies of Brünnich's guillemots. To determine if the more extensive morphological variability in common guillemots reflects greater genetic variability, we sequenced part of the cytochrome b gene for 160 common guillemots from 10 colonies distributed throughout the Northern hemisphere. Genotype frequencies and phylogenetic relationships among genotypes both indicated that Atlantic and Pacific populations are genetically distinct. Genetic divergence among genotypes suggested that differentiation of these populations has resulted from separation by Pleistocene glaciers and the Bering Landbridge, as well as by currently unsuitable breeding habitat in the Arctic Ocean. Cytochrome b genotype frequencies also differed among Atlantic colonies, and appeared to define a cline similar to that described for morphological characters. Analyses of sequence variation suggested that this variation probably results from secondary contact between two refugial populations from the Pleistocene glaciations, rather than from isolation by distance or selection. In contrast, the Atlantic population of Brünnich's guillemots appears to have arisen through recent expansion of a single homogeneous refugial population.     

Signature of an early genetic bottleneck in a population of Moroccan sardines (Sardina pilchardus)

Fishery assessment models meant to determine sustainability of commercial marine fish failed to predict recent stock collapses due to overexploitation. One flaw of assessment models is that they strongly rely on catch and age-composition statistics, but largely ignore the genetic background of the studied populations. We examined population genetic structure of sardine (Sardina pilchardus) in the centraleastern and northeastern Atlantic Ocean and Mediterranean Sea to aid fishery management of this heavily fished small pelagic species. We found that sardine has a striking mitochondrial control region, and sequenced a fragment of 387 bp of its 5'-end in 261 individuals collected off the coasts of Morocco (Dakhla, Tantan, Safi, Larache, and Nador), Portugal (Quarteira), Spain (Pasajes, Barcelona), and Greece (Kavala). High levels of haplotypic diversity rendered a rather unresolved NJ phylogeny. The recovered tree had no phylogeographic structuring except for the clustering of 13 individuals of Safi. In contrast, individuals grouped together according to the presence or absence of a 13-bp insertion in the sequence. Phi(ST) pairwise comparisons and molecular variance analyses supported genetic differentiation between the population of Pasajes (Bay of Biscay), and those of the Mediterranean Sea and Moroccan coast, with a contact zone around the Strait of Gibraltar. This result confirms the existence of two subspecies, S. pilchardus pilchardus and S. pilchardus sardina that were previously identified based on meristics and morphometry. Mismatch distribution analysis showed that sardine populations are expanding since the Pleistocene. Surprisingly, the population of Safi showed strong and statistically significant levels of genetic differentiation that could be related with isolation and genetic drift. Comparative analysis of the Safi population versus the rest including mismatch distributions, and a Bayesian skyline plot suggest that the Safi population likely underwent an early genetic bottleneck. The genetic singularity of the Safi population could have been responsible for the historical collapse of this sardine stock in the 1970s.     

Testing hypotheses of population structuring in the Northeast Atlantic Ocean and Mediterranean Sea using the common cuttlefish Sepia officinalis

Population structuring in species inhabiting marine environments such as the Northeast Atlantic Ocean (NEA) and Mediterranean Sea (MS) has usually been explained based on past and present physical barriers to gene flow and isolation by distance (IBD). Here, we examined the relative importance of these factors on population structuring of the common cuttlefish Sepia officinalis by using methods of phylogenetic inference and hypothesis testing coupled with coalescent and classical population genetic parameter estimation. Individuals from 10 Atlantic and 15 Mediterranean sites were sequenced for 659 bp of the mitochondrial COI gene (259 sequences). IBD seems to be the main factor driving present and past genetic structuring of Sepia populations across the NEA-MS, both at large and small geographical scales. Such an evolutionary process agrees well with some of the biological features characterizing this cuttlefish species (short migrations, nektobenthic habit, benthic eggs hatching directly to benthic juveniles). Despite the many barriers to migration/gene flow suggested in the NEA-MS region, genetic population fragmentation due to past isolation of water masses (Pleistocene; 0.56 million years ago) and/or present-day oceanographic currents was only detected between the Aegean-Ionian and western Mediterranean Seas. Restricted gene flow associated with the Almería-Oran hydrographic front was also suggested between southern and eastern Spanish populations. Distinct population boundaries could not be clearly determined, except for the Aegean-Ionian stock. Two Atlantic and five Mediterranean samples showed evidence of current decline in genetic diversity, which may indicate over-exploitation of Sepia in both marine regions.     

High levels of population subdivision in a morphologically conserved Mediterranean toad (Alytes cisternasii) result from recent,multiple refugia: evidence from mtDNA,microsatellites and nuclear genealogies

Pleistocene glaciations often resulted in differentiation of taxa in southern European peninsulas, producing the high levels of endemism characteristic of these regions (e.g. the Iberian Peninsula). Despite their small ranges, endemic species often exhibit high levels of intraspecific differentiation as a result of a complex evolutionary history dominated by successive cycles of fragmentation, expansion and subsequent admixture of populations. Most evidence so far has come from the study of species with an Atlantic distribution in northwestern Iberia, and taxa restricted to Mediterranean‐type habitats remain poorly studied. The Iberian Midwife toad (Alytes cisternasii) is a morphologically conserved species endemic to southwestern and central Iberia and a typical inhabitant of Mediterranean habitats. Applying highly variable genetic markers from both mitochondrial and nuclear genomes to samples collected across the species’ range, we found evidence of high population subdivision within A. cisternasii. Mitochondrial haplotypes and microsatellites show geographically concordant patterns of genetic diversity, suggesting population fragmentation into several refugia during Pleistocene glaciations followed by subsequent events of geographical and demographic expansions with secondary contact. In addition, the absence of variation at the nuclear β‐fibint7 and Ppp3caint4 gene fragments suggests that populations of A. cisternasii have been recurrently affected by episodes of extinction and recolonization, and that documented patterns of population subdivision are the outcome of recent and multiple refugia. We discuss the evolutionary history of the species with particular interest in the increasing relevance of Mediterranean refugia for the survival of genetically differentiated populations during the Pleistocene glaciations as revealed by studies in co‐distributed taxa.     

Genetic differentiation and secondary contact zone in the seagrass Cymodocea nodosa across the Mediterranean–Atlantic transition region

Aim A central question in evolutionary ecology is the nature of environmental barriers that can limit gene flow and induce population genetic divergence, a first step towards speciation. Here we study the geographical barrier constituted by the transition zone between the Atlantic Ocean and the Mediterranean Sea, using as our model Cymodocea nodosa, a seagrass distributed throughout the Mediterranean and in the Atlantic, from central Portugal to Mauritania. We also test predictions about the genetic footprints of Pleistocene glaciations. Location The Atlantic–Mediterranean transition region and adjacent areas in the Atlantic (Mauritania to south‐west Portugal) and the Mediterranean. Methods We used eight microsatellite markers to compare 20 seagrass meadows in the Atlantic and 27 meadows in the Mediterranean, focusing on the transition between these basins. Results Populations from these two regions form coherent groups containing several unique, high‐frequency alleles for the Atlantic and for the Mediterranean, with some admixture west of the Almeria–Oran Front (Portugal, south‐west Spain and Morocco). These are populations where only one or a few genotypes were found, for all but Cadiz, but remarkably still show the footprint of a contact zone. This extremely low genotypic richness at the Atlantic northern edge contrasts with the high values (low clonality) at the Atlantic southern edge and in most of the Mediterranean. The most divergent populations are those at the higher temperature range limits: the southernmost Atlantic populations and the easternmost Mediterranean, both potential footprints of vicariance. Main conclusions A biogeographical transition region occurs close to the Almeria–Oran front. A secondary contact zone in Atlantic Iberia and Morocco results from two distinct dispersal sources: the Mediterranean and southernmost Atlantic populations, possibly during warmer interglacial or post‐glacial periods. The presence of high‐frequency diagnostic alleles in present‐day disjunct populations from the southernmost Atlantic region indicates that their separation from all remaining populations is ancient, and suggests an old, stable rear edge.