Extensive population subdivision of the cuttlefish Sepia officinalis (Mollusca: Cephalopoda) around the Iberian Peninsula indicated by microsatellite DNA variation

The Atlantic Ocean-Mediterranean Sea junction has been proposed as an important phylogeographical area on the basis of concordance in genetic patterns observed at allozyme, mtDNA and microsatellite DNA markers in several marine species. This study presents microsatellite DNA data for a mobile invertebrate species in this area, the cuttlefish Sepia officinalis, allowing comparison of this relatively new class of DNA marker with previous allozyme results, and examination of the relative effects on gene flow of the Strait of Gibraltar and the Almería-Oran oceanographic front. Genetic variation at seven microsatellite loci screened in six samples from NE Atlantic and Mediterranean coasts of the Iberian Peninsula was high (mean Na = 9.6, mean H(e) = 0.725). Microsatellites detected highly significant subpopulation structuring (F(ST)= 0.061; R(ST) = 0.104), consistent with an isolation-by-distance model of low levels of gene flow. Distinct and significant clinal changes in allele frequencies between Atlantic and Mediterranean samples found at five out of seven loci, however indicate these results might be also consistent with an alternative model of secondary contact and introgression between previously isolated and divergent populations, as previously proposed for other marine species from the Atlantic-Mediterranean area. A pronounced 'step' change between SW Mediterranean samples associated with the Almería-Oran front suggests this oceanographic feature may represent a contemporary barrier to gene flow.     

Phylogeography of the marbled crab Pachygrapsus marmoratus (Decapoda,Grapsidae) along part of the African Mediterranean coast reveals genetic homogeneity across the Siculo-Tunisian Strait versus heterogeneity across the Gibraltar Strait

We investigate the influence of previously postulated biogeographic barriers in the Mediterranean Sea on the population genetic structure of a highly dispersive and continuously distributed coastal species. In particular, we examine nuclear and mitochondrial genetic variation in the marbled crab, Pachygrapsus marmoratus, across part of the African Mediterranean coast in order to assess the influence of the Siculo-Tunisian Strait on its population genetic structure. Four polymorphic microsatellite loci were genotyped for 110 individuals, collected from eight locations covering parts of the Algerian, Tunisian and Libyan coasts. In addition, mtDNA corresponding to the Cox1 gene was sequenced for 80 samples. The corresponding results show contrasting patterns of genetic differentiation. While mtDNA results revealed a homogeneous haplotype composition in our study area, microsatellite data depicted genetic differentiation among populations, but not associated with any geographic barrier. This pattern, already recorded for this species from different geographic regions, may hint at the involvement of a complex series of abiotic and biotic factors in determining genetic structure. Demographic history reconstruction, inferred from mtDNA data, supports demographic and spatial expansion for the North African metapopulation dating back to the Mid-Pleistocene and following an historical bottleneck. Comparison of these African mitochondrial sequences with new sequences from a Turkish population and previously published sequences revealed a weak but significant separation of Atlantic and Mediterranean populations across the Gibraltar Strait, which was not recorded in previous studies of this grapsid species.     

Female philopatry in coastal basins and male dispersion across the North Atlantic in a highly mobile marine species, the sperm whale (Physeter macrocephalus)

The mechanisms that determine population structure in highly mobile marine species are poorly understood, but useful towards understanding the evolution of diversity, and essential for effective conservation and management. In this study, we compare putative sperm whale populations located in the Gulf of Mexico, western North Atlantic, Mediterranean Sea and North Sea using mtDNA control region sequence data and 16 polymorphic microsatellite loci. The Gulf of Mexico, western North Atlantic and North Sea populations each possessed similar low levels of haplotype and nucleotide diversity at the mtDNA locus, while the Mediterranean Sea population showed no detectable mtDNA diversity. Mitochondrial DNA results showed significant differentiation between all populations, while microsatellites showed significant differentiation only for comparisons with the Mediterranean Sea, and at a much lower level than seen for mtDNA. Samples from either side of the North Atlantic in coastal waters showed no differentiation for mtDNA, while North Atlantic samples from just outside the Gulf of Mexico (the western North Atlantic sample) were highly differentiated from samples within the Gulf at this locus. Our analyses indicate a previously unknown fidelity of females to coastal basins either side of the North Atlantic, and suggest the movement of males among these populations for breeding.     

Marked mitochondrial DNA differences between Mediterranean and Atlantic populations of the swordfish, Xiphias gladius

Restriction analysis of mitochondrial DNA (mtDNA) from 204 individuals of swordfish (Xiphias gladius) revealed no differentiation among samples from three sites in the Mediterranean Sea (Greece, Italy, Spain), but a high degree of differentiation between Mediterranean samples and a sample from the Gulf of Guinea. A fifth sample from the Atlantic side of the Straits of Gibraltar (Tarifa) consisted mostly of mitotypes that are common in the Mediterranean, but contained several of mtDNA types of the Guinea sample not found in the Mediterranean. We conclude that, in spite of free migration of swordfish across the Straits of Gibraltar, little genetic exchange occurs between the populations inhabiting the Mediterranean Sea and the tropical Atlantic ocean. This is the first evidence of genetic differentiation among geographic populations of this highly mobile species that supports a world-wide fishery.     

The Atlantic-Mediterranean transition: discordant genetic patterns in two seabream species, Diplodus puntazzo (Cetti) and Diplodus sargus (L.)

Sparids are a group of demersal perciform fish of high commercial value, which have experienced an extensive radiation, particularly in the Mediterranean, where they occupy a variety of different niches. The present study focuses on two species: Diplodus sargus and D. puntazzo, presenting a wide distribution from the Mediterranean to the eastern Atlantic coasts. They display similar ecological behaviour and are evolutionary closely related. Both are highly appreciated in fisheries and D. puntazzo is currently under domestication process. However, little is know on their population structure and it is an open question whether any genetic differentiation exists at the geographic level. To address this issue we examined sequence variation of a portion of the mitochondrial DNA (mtDNA) control region in population samples of each of the two species collected over a wide geographic range. In addition to the mtDNA, analysis of nuclear loci (allozymes) was included in the study to compare patterns revealed by nuclear and mitochondrial markers. The studied samples covered an area from the eastern Mediterranean to the Portuguese coasts immediately outside the Gibraltar Strait. The two species revealed a level of sequence polymorphism remarkably different for the control region with the D. puntazzo and D. sargus showing 111 and 28 haplotypes, respectively. Such a difference was not detected with allozyme markers. The two species also showed large differences in their population structure. While D. puntazzo presented a marked genetic divergence between the Atlantic and Mediterranean samples, D. sargus showed little intraspecific differentiation. These results were supported using both mtDNA and allozyme markers, and were interpreted as the consequence of differences in the history of the two species such as fluctuations in the effective population size due to bottlenecks and expansions, possibly combined with present-day differences in levels of gene flow.     

Barriers to Gene Flow in the Marine Environment: Insights from Two Common Intertidal Limpet Species of the Atlantic and Mediterranean

Knowledge of the scale of dispersal and the mechanisms governing gene flow in marine environments remains fragmentary despite being essential for understanding evolution of marine biota and to design management plans. We use the limpets Patella ulyssiponensis and Patella rustica as models for identifying factors affecting gene flow in marine organisms across the North-East Atlantic and the Mediterranean Sea. A set of allozyme loci and a fragment of the mitochondrial gene cytochrome C oxidase subunit I were screened for genetic variation through starch gel electrophoresis and DNA sequencing, respectively. An approach combining clustering algorithms with clinal analyses was used to test for the existence of barriers to gene flow and estimate their geographic location and abruptness. Sharp breaks in the genetic composition of individuals were observed in the transitions between the Atlantic and the Mediterranean and across southern Italian shores. An additional break within the Atlantic cluster separates samples from the Alboran Sea and Atlantic African shores from those of the Iberian Atlantic shores. The geographic congruence of the genetic breaks detected in these two limpet species strongly supports the existence of transpecific barriers to gene flow in the Mediterranean Sea and Northeastern Atlantic. This leads to testable hypotheses regarding factors restricting gene flow across the study area.     

The genetic population structure of Thunnus thynnus (Linnaeus, 1758) in the Mediterranean Sea,a controversial issue

The Atlantic bluefin tuna (ABFT), Thunnus thynnus (Linnaeus, 1758), is an important commercial species managed as two different stocks, western and eastern Atlantic, with their spawning grounds in the Gulf of Mexico and in the Mediterranean Sea, respectively. The eastern Atlantic stock has been overexploited in the last decades, leading to the application of specific management measures introduced by the International Commission for the Atlantic Tuna (ICCAT). A clear understanding of the genetic structure of ABFT Mediterranean population should be pursued in order to support management decisions. To date the genetic studies on the Mediterranean ABFT, carried out with different molecular markers and sampling procedures, have produced unclear results. Here, we analysed ABFT samples from central and western Mediterranean Sea with mitochondrial sequences and 11 microsatellite loci to investigate, among the others, the area of the Strait of Messina, where environmental conditions seem to support a resident population of ABFT. Furthermore, genetic analyses of mitochondrial sequences were carried out including nucleotide sequences of Adriatic ABFT wild larvae retrieved from GenBank. Among the investigated areas a genetic differentiation was detected between the Strait of Messina and the Tyrrhenian Sea with microsatellite loci according to the exact G test, but not to the Bayesian analyses carried out with STRUCTURE. The analyses with mitochondrial sequences do not reveal any differentiation among sampled areas, however, a highly significant genetic divergence was observed between the Adriatic mitochondrial sequences retrieved from GenBank and the central‐western Mediterranean sequences obtained in the present work. Our results provide some evidence of population structure of Mediterranean ABFT adding pieces to a still unclear picture.     

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.     

Facts and uncertainties about the genetic population structure of Atlantic bluefin tuna (<Emphasis Type="Italic">Thunnus thynnus</Emphasis>) in the Mediterranean. Implications for fishery management

The Atlantic bluefin tuna (Thunnus thynnus) is an extraordinary fish that has amazed humanity since ancient times. However, the continuous overexploitation of this fishery, particularly in the Mediterranean Sea, could result in a total collapse of this resource. Currently, this species is managed as two stocks: Western Atlantic and Mediterranean-Eastern Atlantic, with a recognized genetic differentiation between them. On the other hand, the population structure within the Mediterranean Sea is still unclear. The biological data supports the idea of two separate populations in the eastern and western Mediterranean basins. However, nuclear microsatellite and mitochondrial DNA (mtDNA) analyses of two samples representative of these two basins result in a lack of heterogeneity. A comparison of these results with previously published studies reveals some discrepancies. We have compared 59 genetic differentiation tests that include samples within the Mediterranean. Of these, about 60% gave significant differentiation while the remaining 40% were non-significant. But, when only nuclear-based loci were considered, genetic differentiation was detected in up to 73% of the cases with an average significant F _ST of only 0.018, whereas the average significant F _ST of the mtDNA-based studies was significantly higher (0.029). However, in some cases, it is difficult to reconcile the biology of the species with the results suggesting genetic differentiation. In conclusion, although it is not yet possible to reach a definitive conclusion about the population structure, but considering all biological and genetic data, we suggest an independent management approach for each basin to avoid the impact of a type II error that could lead to the possible loss of the regional subpopulations.     

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.     

Mitochondrial DNA variation in a species with two mitochondrial genomes: the case of Mytilus galloprovincialis from the Atlantic, the Mediterranean and the Black Sea

We have examined mitochondrial DNA (mtDNA) variation in samples of the mussel Mytilus galloprovincialis from the Black Sea, the Mediterranean and the Spanish Atlantic coast by scoring for presence or absence of cleavage at 20 restriction sites of a fragment of the COIII gene and at four restriction sites of the 16S RNA gene. This species contains two types of mtDNA genomes, one that is transmitted maternally (the F type) and one that is transmitted paternally (the M type). The M genome evolves at a higher rate than the F genome. Normally, females are homoplasmic for an F type and males are heteroplasmic for an F and an M type. Occasionally molecules from the F lineage invade the paternal transmission route, resulting in males that carry two F-type mtDNA genomes. These features of the mussel mtDNA system give rise to a new set of questions when using mtDNA variation in population studies and phylogeny. We show here that the two mtDNA types provide different information with regard to amounts of variation and genetic distances among populations. The F genome exhibits higher degrees of diversity within populations, while the M genome produces higher degrees of differentiation among populations. There is a strong differentiation between the Atlantic and the Black Sea. The Mediterranean samples have intermediate haplotype frequencies, yet are much closer to the Black Sea than to the Atlantic. We conclude that in this species gene flow among the three Seas is restricted and not enough to erase the combined effect of mutation and random drift. In one sample, that from the Black Sea, the majority of males did not contain an M mtDNA type. This suggests that a molecule of the maternal lineage has recently invaded the paternal route and has increased its frequency in the population to the point that the present pool of paternally transmitted mtDNA molecules is highly heterogeneous and cannot be used to read the population's history. This liability of the paternal route means that in species with doubly uniparental inheritance, the maternal lineage provides more reliable information for population and phylogenetic studies.     

Cryptic speciation and genetic structure of widely distributed brittle stars (Ophiuroidea) in Europe

Pérez‐Portela, R., Almada, V. & Turon, X. (2012). Cryptic speciation and genetic structure of widely distributed brittle stars (Ophiuroidea) in Europe. —Zoologica Scripta, 00, 000–000. The development of molecular techniques has led to the detection of numerous cases of cryptic speciation within widely distributed marine invertebrate species and important taxonomic revisions in all the major marine taxa. In this study, we analysed a controversial marine species complex in the genus Ophiothrix, a widespread taxon in European waters traditionally assigned to two nominal species, Ophiothrix fragilis and O. quinquemaculata. These species are important components of the rocky shores and deep marine benthos along the North Atlantic and Mediterranean littoral. Their status (including variants of both species) has remained contentious due to overlapping variability in morphological characters. In this study, we analysed the genetic and morphological differences of Ophiothrix lineages along the Atlantic and Mediterranean coasts. We also assessed population genetic structure in the Atlantic and Mediterranean basins by sequencing two mitochondrial genes, the 16S rRNA gene and COI gene, of 221 specimens from 13 locations. Phylogenetic analyses demonstrated the existence of two genetically distinct lineages, attributable to two different species although unrelated to previous taxonomic distinctions. Morphological differences could also be detected between these lineages. Samples from the Northeast Atlantic and one from the deep Mediterranean grouped within Lineage I, whereas Lineage II pooled together the southern Atlantic and rocky shallow Mediterranean samples. In the northern region of the Iberian Peninsula and at a deep locality in the Mediterranean, both lineages overlap. Speciation processes likely happened during the Mio–Pliocene transition (about 4.8–7.5 million years ago), when marine‐level oscillations led to the blockage of major marine corridors in Europe and promoted genetic isolation by vicariance. Secondary contact between lineages following sea‐level increases and recolonization during the refilling of the Mediterranean after the Miocene salinity crisis could explain the present‐day distribution of genetic variability. No barriers to gene flow along the Atlanto‐Mediterranean area were detected for Lineage II, and the lack of genetic structure could be caused by a mixture of several factors, such as wide dispersal potential, recent demographic expansion and large population size.     

Spatial and temporal genetic structure of the planktonic Sagitta setosa (Chaetognatha) in European seas as revealed by mitochondrial and nuclear DNA markers

Little is known about the spatial and temporal scales at which planktonic organisms are genetically structured. A previous study of mitochondrial DNA (mtDNA) in the holoplanktonic chaetognath Sagitta setosa revealed strong phylogeographic structuring suggesting that Northeast (NE) Atlantic, Mediterranean and Black Sea populations are genetically disjunct. The present study used a higher sampling intensity and a combination of mitochondrial and four microsatellite markers to reveal population structuring between and within basins. Between basins, both marker sets indicated significant differentiation confirming earlier results that gene flow is probably absent between the respective S. setosa populations. At the within-basin scale, we found no evidence of spatial or temporal structuring within the NE Atlantic. In the Mediterranean basin, both marker sets indicated significant structuring, but only the mtDNA data indicated a sharp genetic division between Adriatic and all other Mediterranean populations. Data were inconclusive about population structuring in the Black Sea. The levels of differentiation indicated by the two marker sets differed substantially, with far less pronounced structure detected by microsatellite than mtDNA data. This study also uncovered the presence of highly divergent mitochondrial lineages that were discordant with morphology, geography and nuclear DNA. We thus propose the hypothesis that highly divergent mitochondrial lineages may be present within interbreeding S. setosa populations.     

High genetic differentiation of red gorgonian populations from the Atlantic Ocean and the Mediterranean Sea

Patterns of genetic variation within a species may be used to infer past events in the evolutionary history of marine species. In the present study we aimed to compare the genetic diversity of the red gorgonian Paramuricea clavata in the Atlantic Ocean and the Mediterranean Sea. For genetic markers we used microsatellites and a mitochondrial gene fragment. Our results revealed a distinct genetic composition and diversity between the Mediterranean and the Atlantic. The Mediterranean samples had higher microsatellite heterozygosity, allelic richness and private allelic richness. The hypotheses that can explain these patterns are the isolation of Atlantic populations and/or a founder effect. Additionally, a clear difference was obtained from the mitochondrial locus, since sequences from Atlantic and Mediterranean samples diverged by 1%, which is high for soft corals.     

Genetic structuring of Patagonian toothfish populations in the Southwest Atlantic Ocean: the effect of the Antarctic Polar Front and deep-water troughs as barriers to genetic exchange

The environmental and/or life history factors affecting genetic exchange in marine species with potential for high dispersal are of great interest, not only from an evolutionary standpoint but also with regard to effective management. Previous genetic studies have demonstrated substantial differentiation among populations of the Patagonian toothfish around the Southern Ocean, indicating breakdown of gene flow across large distances between inhabited shelf areas. The present study examined genetic structuring through analysis of microsatellite loci and restriction fragment length polymorphism (RFLP) of the mitochondrial ND2 gene and control region of the toothfish population in the SW Atlantic, allowing examination of the relative effects of the Antarctic Polar Front (APF), deep-water troughs and distance between sites. Mitochondrial DNA (mtDNA) data indicated a sharp genetic division between the Patagonian Shelf/North Scotia Ridge and the Shag Rocks/South Georgia samples, whereas microsatellite data showed much less distinct structuring and an intermediate position of the North Scotia Ridge samples. We suggest these data indicate that the APF, as a barrier to larval dispersal, is the major inhibitor of genetic exchange between toothfish populations, with deep-water troughs and distance between sites contributing to genetic differentiation by inhibiting migration of relatively sedentary adults. We also suggest that differences between mtDNA and nuclear DNA population patterns may reflect either genome population size effects or (putative) male-biased dispersal.     

Phylogenetic relationships and introgression patterns between incipient parapatric species of Italian brown trout (Salmo trutta L. complex)

Genetic variation at 47 protein loci was investigated in 16 wild brown trout populations from the Pô basin and three major domesticated stocks used for stocking this area. Twenty-four loci were polymorphic and large frequency differences were found at 15 of them. The most significant allozyme variations were congruent with the mtDNA sequence polymorphism previously observed in the same samples. We confirmed the occurrence of two parapatric incipient species, Salmo marmoratus and S. trutta fario , previously identified by morphological traits. These two species were fixed or nearly fixed for alternate alleles at eight loci (Nei's standard genetic distance = 0.16–0.18), but introgression was detected between adjacent samples of the two forms. Divergence levels at both mtDNA and nuclear loci suggested that the differentiation between S. marmoratus and S. trutta fario started between 3 and 1 million years before present. Variation at protein loci and mtDNA supported the hypothesis that the third species found in this area, S. carpio (an endemic population of the lake Garda) was issued from a recent hybridization of the two first species. Finally, we showed that three of the major Italian fish-farm strains originated from the Atlantic side and displayed substantial genetic differences with the natural populations of the Pô basin. Most of these populations were contaminated by stocking with introgression rate ranging from 0 to 70% and measures of protection and restoration of the rich genetic diversity present in this area should be urgently applied.     

Hierarchical analyses of genetic variation of samples from breeding and feeding grounds confirm the genetic partitioning of northwest Atlantic and South Atlantic populations of swordfish (Xiphias gladius L.)

In species with high migratory potential, the genetic signal revealing population differentiation is often obscured by population admixture. To our knowledge, the explicit comparison of genetic samples from known spawning and feeding areas has not been conducted for any highly migratory pelagic fish species. This study examines the geographic heterogeneity of swordfish mitochondrial DNA (mtDNA) lineages within the Atlantic Ocean using 330 base pairs of sequence of the control region from 480 individuals. Hierarchical analyses of sequence variation were conducted to test whether samples from areas identified as the corresponding spawning and feeding grounds for the northwest (NW) Atlantic (Caribbean and Georges Banks-US northeast) and the South Atlantic (Brazil-Uruguay and Gulf of Guinea), were more closely related to each other than to samples from any other region, including the Mediterranean Sea, the Indian Ocean, and the Pacific Ocean. Phylogeographic analyses reveal that swordfish mtDNA phylogeny is characterized by incomplete lineage sorting and secondary contact of two highly divergent clades. However, despite this complex phylogenetic signature, results from an analysis of nucleotide diversity and from an analysis of molecular variance (AMOVA) were for the most part concordant and indicate that NW Atlantic and South Atlantic swordfish belong to separate populations. The mtDNA distinctiveness of NW Atlantic and South Atlantic swordfish populations is indicative of philopatric behavior in swordfish towards breeding and feeding areas.     

Conservation genetics of the short-beaked common dolphin (<Emphasis Type="Italic">Delphinus delphis</Emphasis>) in the Mediterranean Sea and in the eastern North Atlantic Ocean

Mediterranean Sea common dolphins have recently been listed as ‘endangered’ in the IUCN Red list, due to their reported decline since the middle of the 20th century. However, little is know about the number or distribution of populations in this region. We analysed 118 samples from the Black Sea, Mediterranean Sea and eastern North Atlantic at nine microsatellite nuclear loci and for 428 bps of the mtDNA control region. We found small but significant population differentiation across the basin between the eastern and the western Mediterranean populations at both nuclear and mtDNA markers (microsatellite F _ST = 0.052, mtDNA F _ST = 0.107, P values ≤ 0.001). This matched the differential distribution and habitat use patterns exhibited by this species in the eastern and the western parts of the Mediterranean Sea. The assignment test of a small number of samples from the central Mediterranean could not exclude further population structure in the central area of the basin. No significant genetic differentiation at either marker was observed among the eastern north Atlantic populations, though the Alboran population (inhabiting the Mediterranean waters immediately adjacent the Atlantic ocean) showed significant mtDNA genetic differentiation compared to the Atlantic populations. Directional estimates of gene flow suggested movement of females out of the Mediterranean, which may be relevant to the population decline. Phylogenetic analysis suggested that the observed population structure evolved recently.     

Phylogeography and phylogeny of the epineritic cosmopolitan bonitos of the genus Sarda (Cuvier): inferred patterns of intra‐ and inter‐oceanic connectivity derived from nuclear and mitochondrial DNA data

Aim To reconstruct the phylogenetic relationships of the four species of the genus Sarda (Sarda sarda, Sarda orientalis, Sarda australis and Sarda chilensis) and their phylogeographic history in the context of historical and ecological biogeography. Also, to reconstruct within‐species phylogenetic relationships to test whether the North Atlantic and Mediterranean populations of Atlantic bonito (S. sarda) warrant subspecies status, and the validity of the allopatric northern and southern populations of eastern Pacific bonito (S. chiliensis), recognized as S. chiliensis lineolata and S. chiliensis chiliensis. Location Representative samples of all four Sarda species collected world‐wide were analysed. Methods Phylogenetic inference was carried out with neighbour‐joining, maximum parsimony and maximum likelihood, employing nucleotide sequences of the mitochondrial DNA (mtDNA) control region I (CR‐I) and of the single‐copy nuclear DNA (nDNA) Tmo‐4c4 gene. Analysis of molecular variance was used on the mtDNA data to estimate the extent of geographic population structuring. Results Gene trees derived from mtDNA and nDNA data yielded concordant phylogenies that support the monophyly of the genus Sarda. The following sibling pairs received strong statistical support: striped bonito (S. orientalis) with Australian bonito (S. australis), and Atlantic bonito (S. sarda) with eastern Pacific bonito (S. chiliensis). Furthermore, the origin of S. sarda mtDNA is paraphyletic with respect to S. chiliensis, and these results are indicative of introgression. The analysis of Tmo‐4c4 sequences corroborates the ancestral hybridization between these allopatric species. Comparisons of north‐west Atlantic and Mediterranean populations of S. sarda using mtDNA CR‐I data revealed substantial genetic differentiation. By contrast, no differences between the putative northern and southern allopatric subspecies of S. chiliensis were detected. Main conclusions The monophyly of the genus Sarda as indicated by morphology is corroborated using both molecular markers. However, molecular phylogenies depicted a paraphyletic relationship between S. sarda and S. chiliensis. This phylogeographical relationship is better explained by an ancestral introgression facilitated by trans‐Arctic contact during the Pleistocene. The pronounced genetic differentiation between S. sarda samples from the north‐west Atlantic and the Mediterranean is consistent with the differentiation of these two regions, but not with the amphi‐Atlantic speciation hypothesis. Finally, the S. chiliensis lineolata and S. chiliensis chiliensis subspecies status is not supported by the molecular data.     

Congruence in genetic markers used to describe Mediterranean and Atlantic populations of European hake (Merluccius merluccius L. 1758)

Eight samples of the hake, Merluccius merluccius L., from the Mediterranean basin (370 fishes total) and one from the Atlantic ocean (50 fishes) were analysed in order to assess genetic variability and describe genetic population structure. Five polymorphic protein coding loci were scored (ADH*, PGI‐1*, PGI‐2*, PGM* and SOD‐1*) in eight samples, together with a haplotype variation of four samples, obtained from polymerase chain reaction/restriction fragment length polymorphism (PCR–RFLP) analysis on the mitochondrial DNA control region. The average value for observed heterozygosity was typically higher than expected (showing an excess of heterozygotes among the samples) whereas the haplotype diversity at mtDNA was very low. Samples originating from inside the Mediterranean basin appeared genetically homogeneous but the sample originating from the Atlantic was heterogeneous compared with the Mediterranean populations. Nuclear and mitochondrial gene analysis showed similar results supporting that the Strait of Gibraltar may be considered as a breakpoint area to gene flow.