Fishery genetics have greatly changed our understanding of population dynamics and structuring in marine fish. In this study, we show that the Atlantic Bluefin tuna (ABFT, Thunnus thynnus), an oceanic predatory species exhibiting highly migratory behavior, large population size, and high potential for dispersal during early life stages, displays significant genetic differences over space and time, both at the fine and large scales of variation. We compared microsatellite variation of contemporary (n = 256) and historical (n = 99) biological samples of ABFTs of the central-western Mediterranean Sea, the latter dating back to the early 20th century. Measures of genetic differentiation and a general heterozygote deficit suggest that differences exist among population samples, both now and 96-80 years ago. Thus, ABFTs do not represent a single panmictic population in the Mediterranean Sea. Statistics designed to infer changes in population size, both from current and past genetic variation, suggest that some Mediterranean ABFT populations, although still not severely reduced in their genetic potential, might have suffered from demographic declines. The short-term estimates of effective population size are straddled on the minimum threshold (effective population size = 500) indicated to maintain genetic diversity and evolutionary potential across several generations in natural populations.ancient DNA | effective population size | genetic structure | large pelagic fishes | Thunnus thynnus

BackgroundAtlantic Bluefin Tuna (ABFT) shows complex demography and ecological variation in the Mediterranean Sea. Genetic surveys have detected significant, although weak, signals of population structuring; catch series analyses and tagging programs identified complex ABFT spatial dynamics and migration patterns. Here, we tested the hypothesis that the genetic structure of the ABFT in the Mediterranean is correlated with mean surface temperature and salinity.MethodologyWe used six samples collected from Western and Central Mediterranean integrated with a new sample collected from the recently identified easternmost reproductive area of Levantine Sea. To assess population structure in the Mediterranean we used a multidisciplinary framework combining classical population genetics, spatial and Bayesian clustering methods and a multivariate approach based on factor analysis.ConclusionsFST analysis and Bayesian clustering methods detected several subpopulations in the Mediterranean, a result also supported by multivariate analyses. In addition, we identified significant correlations of genetic diversity with mean salinity and surface temperature values revealing that ABFT is genetically structured along two environmental gradients. These results suggest that a preference for some spawning habitat conditions could contribute to shape ABFT genetic structuring in the Mediterranean. However, further studies should be performed to assess to what extent ABFT spawning behaviour in the Mediterranean Sea can be affected by environmental variation.

Running head: Allopatric cryptic speciation and population structuring in skates-2-ABSTRACT Aim Geographical (allopatric) speciation is a dynamic process whose footprints in the living world are a continuum of stages of increasing divergence. Geographical speciation can also contribute to the evolution of marine taxa. This study looked for two of these evolutionary stages (i.e. structured populations and sibling species) in the diversification patterns of two Atlantic skates (Raja, suborder Rajoidea) which exhibited high morphological and ecological conservativism. Location E Atlantic, Mediterranean, W Indian Methods Phylogeographical and population genetic analyses were performed by surveying DNA variation of 10 population samples assigned to the European Raja clavata and to the S African R. straeleni. Polymorphisms were detected by sequencing a mtDNA control region (CR) fragment and genotyping amplified fragment length polymorphism (AFLP) loci. Several statistical tests were used to explore genetic differentiation and population demography. Results CR haplotypes clustered in two clades consistent with taxon zoogeography. Mean sequence divergence between allopatric taxa amounted to 2% and Bayesian estimate of the time of the most recent common ancestor dated their separation between 0.155 and 1.3 Myr. Isolation-by-distance between European and S African demes was inferred from a significant correlation between coastal and genetic distances at AFLP loci. Null or low gene flow estimates suggested reproductive isolation between allopatric taxa. After separation, taxa have expanded moderately since 30-45 Kyr. Geographical subgrouping of CR haplotypes and significant genetic heterogeneity of samples at both markers featured the Atlantic and Mediterranean thornback skates, revealing pronounced levels of population structuring in this widely distributed taxon. Main conclusions In spite of the pronounced morpho-anatomical conservativism, R. clavata and R. straeleni are allopatric sibling species which diverged in the Pleistocene. A recent southward dispersal of European R. clavata-like elements along with the W African shelf with the budding of S African R. straeleni is ostensible. The tumultuous Quaternary palaeoclimatic history of equatorial and tropical Africa with the succession of glacial and interglacial palaeoenvironments could have promoted the repeated geographical isolation of local demes in relatively restricted refugial areas. Within the evolutionary trajectories experienced by Rajoidea, structured populations and allopatric sibling species could frequently represent intermediate frames of the microevolutionary animation proposed by Ernst Mayr to model allopatric speciation.

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