The geological history of the Mediterranean Sea, its hydrography and connection with the Atlantic Ocean have been well documented Despite a wealth of historical and oceanographic data, the Atlantic–Mediterranean transition remains controversial at the biological level as there are discordant results regarding the biogeographical separation between the Atlantic and Mediterranean biota The opening of the Strait of Gibraltar at the end of the Messinian Salinity Crisis (some 533 million years ago), removed the land barrier that impeded the marine biota allowing it to disperse freely into the Mediterranean Sea However, present day genetic patterns suggest a limitation to gene flow for some marine species, preventing population admixture In the last few years, a large number of studies have challenged the hypothesis of the Strait of Gibraltar representing a phylogeographical break A review of more than 70 papers reveals no obvious relationship between either dispersal ability or life history, and observed patterns of partial or complete genetic isolation between Atlantic and Mediterranean populations We re-analysed a selection of this large body of data (20 studies in total) in order to provide a homogeneous and coherent view on the generality of the phylogeographical patterns and the presence of a phylogeographical barrier This offered the opportunity to summarize the state of the art on this matter and reach some general conclusions on the evolutionary history across the Atlantic–Mediterranean range Geographically, some species in the transition zone showed step changes of allele frequencies associated with the Almeria-Oran Front rather than with the Strait of Gibraltar itself A major part of the data describe evolutionary events well within the time frame of the Quaternary age as very few taxa pre-date closure of the Tethys Sea Results point to a combined signature of vicariance, palaeoclimate fluctuation and life-history traits on the Atlantic–Mediterranean phylogeographical patterns Principal component analysis failed to show any particular association between biological traits and genetic variables It would argue that organismal determinism may play a far less significant role than marine biogeographers have generally believed

Pillars of Hercules: is the Atlantic–Mediterranean transition a phylogeographical break?

The phylogenetic relationships of 106 European cyprinid taxa were determined based on the complete nucleotide sequence (1140 bp) of the mitochondrial cytochrome b gene. The molecular phylogeny was used (1) to revise the current systematics of European cyprinids, (2) to establish the phylogenetic utility of traditional morphological characters that are widely used in Cyprinidae systematics, and (3) to discuss alternative hypotheses on the biogeography of the family in Europe. The age of the major lineages within European cyprinids was tentatively estimated with a molecular clock and showed full agreement with the fossil record of the group. Moreover, the results provided unambiguous evidence for a close phylogenetic affinity of some Caucasian and Greek endemic cyprinid taxa (e.g., B. capito and B. brachycephalus and Leuciscus keadicus, Barbus graecus, and B. albanicus, respectively) to Iberian and North African, but not Central European, cyprinids. The existence of such unexpected phylogenetic relationships refutes the classical hypothesis on the biogeography of European cyprinids, which assumes a dispersal of the cyprinid fauna from central Europe to southern Europe and northern Africa during the Miocene (and, hence, predicts a close phylogenetic relationship of all Caucasian, Greek, Iberian, and North African cyprinids to central European taxa). Instead, the existence of a Mediterranean realm independent of the central European route seems plausible based on the molecular evidence. It is likely that the new biogeographical scenario proposed here might apply to other primary freshwater European animals with low dispersal abilities, including fish, amphibians, and invertebrates.

Molecular evidence on the evolutionary and biogeographical patterns of European cyprinids.

Background
Leuciscinae is a subfamily belonging to the Cyprinidae fish family that is widely distributed in Circum-Mediterranean region. Many efforts have been carried out to deciphering the evolutionary history of this group. Thus, different biogeographical scenarios have tried to explain the colonization of Europe and Mediterranean area by cyprinids, such as the "north dispersal" or the "Lago Mare dispersal" models. Most recently, Pleistocene glaciations influenced the distribution of leuciscins, especially in North and Central Europe. Weighing up these biogeographical scenarios, this paper constitutes not only the first attempt at deciphering the mitochondrial and nuclear relationships of Mediterranean leuciscins but also a test of biogeographical hypotheses that could have determined the current distribution of Circum-Mediterranean leuciscins.

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Phylogenetic relationships and biogeographical patterns in Circum-Mediterranean Subfamily Leuciscinae (Teleostei, Cyprinidae) inferred from both mitochondrial and nuclear data

To test vicariant speciation hypotheses derived from geological evidence of the closing of the Tethys Sea, we reconstruct phylogenetic relationships of the predominantly fresh-water killifish genus Aphanius using 3263 aligned base pairs of mitochondrial DNA from samples representing 49 populations of 13 species. We use additional 11 cyprinodontid species as outgroup taxa. Genes analysed include those encoding the partial 12S and 16S ribosomal RNAs; transfer RNAs for valine, leucine, isoleucine, glutamine, methionine, tryptophan, alanine, asparagine, cysteine and tyrosine; and complete nicotinamide adenine dinucleotide dehydrogenase subunit I and II. Molecular substitution rate for this DNA region is estimated at of 8.6 +/- 0.1 x 10(-9) substitutions base pair(-1) year(-1), and is derived from a well dated transgression of the Red Sea into the Wadi Sirhan of Jordan 13 million years ago; an alternate substitution rate of 1.1 +/- 0.2 x 10(-8) substitutions base pair(-1) year(-1) is estimated from fossil evidence. Aphanius forms two major clades which correspond to the former eastern and western Tethys Sea. Within the eastern clade Oligocene divergence into a fresh-water clade inhabiting the Arabian Peninsula and an euhaline clade inhabiting coastal area from Pakistan to Somalia is observed. Within the western Tethys Sea clade we observe a middle Oligocene divergence into Iberian Peninsula and Atlas Mountains, and Turkey and Iran sections. Within Turkey we observe a large amount of genetic differentiation correlated with late Miocene orogenic events. Based on concordance of patterns of phylogenetic relationships and area relationships derived from geological and fossil data, as well as temporal congruence of these patterns, we support a predominantly vicariant-based speciation hypothesis for the genus Aphanius. An exception to this pattern forms the main clade of A. fasciatus, an euhaline circum-Mediterranean species, which shows little genetic differentiation or population structuring, thus providing no support for the hypothesis of vicariant differentiation associated with the Messinian Salinity Crisis. The two phylogenetically deepest events were also likely driven by ecological changes associated with the closing of the Tethys Sea.

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Closing of the Tethys Sea and the phylogeny of Eurasian killifishes (Cyprinodontiformes: Cyprinodontidae).

We studied the genetic structure at six microsatellite loci of the Mediterranean sea bass ( Dicentrarchus labrax ) on 19 samples collected from different localities in the western and eastern Mediterranean basins. Significant divergence was found between the two basins. The distance tree showed two separate clusters of populations which matched well with geography, with the noticeable exception of one Egyptian sample which grouped within the western clade, a fact attributable to the introduction of aquaculture broodstock. No heterogeneity was observed within the western basin ( θ = 0.0014 and n.s.). However, a significant level of differentiation was found among samples of the eastern Mediterranean ( θ = 0.026 and p 0.001). These results match with water currents but probably not with the dispersal abilities of this fish species. We thus hypothesize that selective forces are at play which limit long–range dispersal, a fact to be taken into account in the debate about speciation processes in the marine environment.

Fragmentation of sea bass populations in the western and eastern Mediterranean as revealed by microsatellite polymorphism.

The present paper reports on a molecular study based on 12S rRNA and 16S rRNA mitochondrial genes partly sequenced in 13 species of western Mediterranean gobies, three of which are strictly freshwater-dwelling. A total of 867 bp were aligned and used for the phylogenetic reconstruction. Two major lineages were identified, one clustering the sand gobies in a monophyletic clade. Relationships among taxa based on sequence analysis only partly match those based on morphological criteria, suggesting that the latter are somehow insufficient to correctly establish phylogenetic relationships within this family. The results provide evidence for a multiple independent evolution of the freshwater lifestyle in Knipowitschia and Padogobius lineages. On the basis of the present results, it is uncertain whether the freshwater preference within the genus Padogobius originated twice independently in P. nigricans and P. martensii or only once in their common ancestor. Estimation of the ages of the two major lineages of this group of fish with a molecular clock (in combination with the construction of a linearized tree) suggests that they are much older (at least 40 Myr) than previously thought. Thus, there should be no correlation between their diversification and the Miocene-Pliocene geological events, including the so-called Messinian salinity crisis, which occurred about 10 MYA and is believed to have played a role in their evolution. Alternatively, these gobies would have an evolutionary rate at least fourfold faster than those of other vertebrates.

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Messinian salinity crisis and the origin of freshwater lifestyle in western Mediterranean gobies.

PCR and direct sequencing of 300 to 377-bp fragments of the cytochrome b mitochondrial gene were carried out in 40 specimens of European sea bass, Dicentrarchus labrax L., collected at different sites in the Mediterranean basin and representing wild and farmed populations. Sequence analysis revealed 6 transitional changes, which generated 5 different haplotypes (A-E). Only one mutation was nonsynonymous because it occurred in the first position of a codon leading to the replacement of valine by isoleucine. The genotypic distribution revealed that haplotype B was not present in the farm samples, whereas its frequency in the wild samples exceeded 30%. In contrast, haplotypes D and E were found in farmed populations but not in the wild populations. The comparison among wild populations showed a nonhomogeneous distribution of the two most frequent haplotypes, A and B.

Mitochondrial DNA sequence variation in the European sea bass, Dicentrarchus labrax L. (Serranidae): evidence of differential haplotype distribution in natural and farmed populations.

Colombo L

Papers

Messinian salinity crisis and the origin of freshwater lifestyle in western Mediterranean gobies.

Mitochondrial DNA sequence variation in the European sea bass, Dicentrarchus labrax L. (Serranidae): evidence of differential haplotype distribution in natural and farmed populations.