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Atlantic Bluefin Tuna show a complex demography in the Mediterranean Sea despite it is a little basin in comparison to the long transatlantic migrations they perform. The weak population genetic structure detected through common summary statistics is difficult to infer using more sophisticated tools. An improved version of the Bayesian clustering program STRUCTURE, was used to analyse ABFT samples from the Mediterranean sea. To corroborate clustering results multivariate methods were applied to extract information from genetic markers without the use of the strong assumptions made by classical Bayesian clustering methods. Genetic and multivariate analyses detected the presence of a south to north genetic structuring through the Mediterranean Sea. Moreover correlation analyses suggested that environmental factors could have a role in shaping the identified genetic differentiation. This study confirms and defines ABFT structure in the Mediterranean Sea and highlight the influence of the environmental features on the genetic diversity of populations.

We assessed spatio-temporal genetic patterns in Mediterranean samples of bluefin tuna (BFT) to look for signs of population structuring and genetic erosion, which might be related to stock overexploitation and depletion. We analyzed microsatellite variation at seven neutral loci on seven contemporary bluefin tuna samples collected from the Alboran Sea to the Levant Sea (N=316) and in two historical samples (N=99) collected from 1911 to 1926 in the southern Tyrrhenian and Adriatic Seas. We found signs of widespread and deep spatial genetic structuring in both contemporary (mean FST =0.014, P < 0.0001) and historical bluefin tunas (FST=0.020, P < 0.0001). These findings coherently confirm previous data obtained on a limited number of samples and reinforce the possibility that the Mediterranean is inhabited by reproductively isolated sub-populations. Temporal genetic analyses did not find evidence of genetic bottlenecks in Mediterranean bluefin tuna samples. However, since samples displayed heterogeneity of population demographic parameters, Mediterranean bluefin tuna subpopulations might have partially independent dynamics. Our results illustrate that in Mediterranean, structured bluefin tuna populations retain a high level of genetic diversity across space and time, despite possible demographic declines and population changes., Nous avons évalué les schémas génétiques spatio-temporels dans des échantillons méditerranéens de thon rouge (BFT) en vue de rechercher des indices de structuration de la population et d’érosion génétique, lesquels pourraient être liés à la surexploitation et à la raréfaction du stock. Nous avons analysé la variation micro-satellitaire chez sept locus neutres de sept échantillons contemporains de thon rouge prélevés de la mer d’Alboran à la mer Levantine (N=316) et dans deux échantillons historiques (N=99) prélevés de 1911 à 1926 dans la mer Tyrrhénienne méridionale et la mer Adriatique. Nous avons trouvé des indices de structuration génétique spatiale très marquée et étendue dans les deux échantillons de thon rouge, contemporains (moyenne FST =0,014, P < 0,0001) et historiques (FST=0,020, P < 0,0001). Ces découvertes confirment de façon cohérente les données antérieures obtenues sur un nombre limité d’échantillons et renforcent la possibilité selon laquelle la Méditerranée est habitée par des sous-populations isolées sur le plan de la reproduction. Les analyses génétiques temporelles n’ont trouvé aucune preuve de goulets d’étranglement génétiques dans les échantillons de thon rouge de la Méditerranée. Toutefois, comme les échantillons ont fait apparaître une hétérogénéité dans les paramètres démographiques de la population, les souspopulations de thon rouge de la Méditerranée pourraient avoir des dynamiques partiellement indépendantes. Nos résultats illustrent le fait qu'en Méditerranée, les populations structurées de thon rouge font apparaître un niveau élevé de diversité génétique dans le temps et dans l’espace, malgré d’éventuelles chutes démographiques et de possibles changements de population., Se han evaluado los patrones genéticos espaciotemporales en las muestras mediterráneas de atún rojo (BFT) para hallar indicios de estructuración de la población y de erosión genética, que podrían estar relacionados con la sobreexplotación y agotamiento del stock. Se analizó la variación microsatélite en siete loci neutrales de siete muestras de atún rojo contemporáneas recogidas desde el mar de Alborán hasta el mar de Levante (N=316) y en dos muestras históricas (N=99), recopiladas desde 1911 hasta 1926 en el mar Adriático y Tirreno meridional. Se hallaron signos de estructuración genética espacial muy marcada y extendida en ambas muestras de atún rojo, contemporáneas (media FST =0,014; P < 0,0001) e histórica (FST=0,020; P < 0,0001). Estos hallazgos confirman con coherencia los datos anteriores obtenidos para un número limitado de muestras y refuerzan la posibilidad de que el Mediterráneo esté habitado por subpoblaciones aisladas desde el punto de vista reproductivo. Los análisis genéticos temporales no evidenciaron embudos genéticos en las muestras de atún rojo del Mediterráneo. Sin embargo, dado que las muestras presentaban cierta heterogeneidad en los parámetros demográficos de población, las subpoblaciones de atún rojo del Mediterráneo podrían tener dinámicas parcialmente independientes. Nuestros resultados ilustran el hecho de que, en el Mediterráneo, las poblaciones estructuradas de atún rojo muestran un algo grado de diversidad genética en el tiempo y en el espacio, a pesar de los posibles descensos demográficos y cambios en la población.

Within the framework of the Italian research project TUNING dealing with the characterization of the spatial and temporal patterns of genetic variation in the Mediterranean tunas and coordinated by the University of Bologna, we tried to reconstruct the demographic history and short-term temporal changes of genetic diversity in the Atlantic bluefin tuna (Thunnus thynnus) of the Mediterranean Sea. Bluefin tuna is experiencing a period of strong overfishing reflected by the lowering of mean age and size of catches, and FAO and ICCAT are adopting measures to recover this species. The comparative study of genetic diversity and genetic differentiation in historical (1900-1930) and contemporary (1999-2007) samples of Atlantic bluefin tuna sampled in the last 100 years in the Western and Central Mediterranean offered the opportunity to assess the impact of industrial fishery on the genetic variation of the stock. Genetic composition of tuna samples at 9 microsatellite loci was dissected by using several programs (Microsatellite, GENETIX 4.05, Arlequin3.01, FSTAT 2.9.3, MNE2, tm3, M_P_VAL, Bottleneck) to detect spatial and temporal changes in the population genetic parameters (gene diversity, genetic differentiation among population samples, effective population size) and to estimate the role of environmental (natural and anthropogenic) factors affecting genetic variation. Significant, if limited spatial heterogeneity was detected across all modern samples (Fst= 0.03, P< 0,0001) as well as significant genetic differentiation between north and south Thyrrenian Sea, and between Adriatic and Thyrrenian Sea. No decrease of genetic variation was observed in modern samples with respect to the ancient one. Both temporal and onesample methods agree that the effective population size is low with respect to comparable Theleost species (Ne= 1000-2000). The two methods we used to detect a bottleneck event had discordant results, with only one (M_P_VAL) clearly detecting a bottleneck. Because only dramatic reductions of population size in a short period result in a detectable signal for the software of Cornuet et al. these results do not rule out the possibility of a demographic decline. Rather they show that, if there was a decline, it was not drastic enough to erase a substancial fraction of DNA diversity, which did not apparently change in the last century.

International audience; Detailed population data were obtained on the distribution of novel biallelic markers that finely dissect the human Y-chromosome haplogroup E-M78. Among 6,501 Y chromosomes sampled in 81 human populations worldwide, we found 517 E-M78 chromosomes and assigned them to 10 subhaplogroups. Eleven microsatellite loci were used to further evaluate subhaplogroup internal diversification. The geographic and quantitative analyses of haplogroup and microsatellite diversity is strongly suggestive of a northeastern African origin of E-M78, with a corridor for bidirectional migrations between northeastern and eastern Africa (at least 2 episodes between 23.9-17.3 ky and 18.0-5.9 ky ago), trans-Mediterranean migrations directly from northern Africa to Europe (mainly in the last 13.0 ky), and flow from northeastern Africa to western Asia between 20.0 and 6.8 ky ago. A single clade within E-M78 (E-V13) highlights a range expansion in the Bronze Age of southeastern Europe, which is also detected by haplogroup J-M12. Phylogeography pattern of molecular radiation and coalescence estimates for both haplogroups are similar and reveal that the genetic landscape of this region is, to a large extent, the consequence of a recent population growth in situ rather than the result of a mere flow of western Asian migrants in the early Neolithic. Our results not only provide a refinement of previous evolutionary hypotheses but also well-defined time frames for past human movements both in northern/eastern Africa and western Eurasia.

In order to attain a finer reconstruction of the peopling of southern and central-eastem Europe from the Levant, we determined the frequencies of eight lineages internal to the Y chromosomal haplogroup J, defined by biallelic markers, in 22 population samples obtained with a fine-grained sampling scheme. Our results partially resolve a major multifurcation of lineages within the haplogroup. Analyses of molecular variance show that the area covered by haplogroup J dispersal is characterized by a significant degree of molecular radiation for unique event polymorphisms within the haplogroup, with a higher incidence of the most derived sub-haplogroups on the northern Mediterranean coast, from Turkey westward; here, J diversity is not simply a subset of that present in the area in which this haplogroup, first originated. Dating estimates, based on simple tandem repeat loci (STR) diversity within each lineage, confirmed the presence of a major population structuring at the time of spread of haplogroup J in Europe and a punctuation in the peopling of this continent in the post-Neolithic, compatible with the expansion of the Greek world. We also present here, for the first time, a novel method for comparative dating of lineages, free of assumptions of STR mutation rates.

Tn this work we focus on a microsatellite-defined Y-chromosomal lineage (network 1.2) identified by us and reported in previous studies, whose geographic distribution and antiquity appear to be compatible with the Neolithic spread of farmers. Here, we set network 1.2 in the Y-chromosomal phylogenetic tree, date it with respect to other lineages associated with the same movements by other authors, examine its diversity by means of tri- and tetranucleotide loci and discuss the implications hi reconstructing the spread of this group of chromosomes in the Mediterranean area. Our results define a tripartite phylogeny wit-bin HG 9 (Rosser et al. 2000) with the deepest branching defined by alleles T (Haplogroup Eu 10) or G (Haplogroup Eu9) at M172 (Semino et al. 2000), and a subsequent branching within Eu9 defined by network 1.2. Population distributions of HG 9 and network 1.2 show that their occurrence in the surveyed area is not due to the spread of people from a single parental population but, rather, to a process punctuated by at least two phases. Our data identify the wide area of the Balkans, Aegean and Anatolia as the possible homeland harbouring the largest variation within network 1.2. The use of recently proposed tests based on the stepwise mutation model suggests that its spread was associated to a population expansion, xvith a high rate of male gene flow in the Turkish Greek area.

Molecular and genetic approaches now provide powerful tools for investigating the origin of human populations and the evolution of genes affecting both complex and monogenic traits. This allows a biologically appropriate classification of individuals and population groups based on genotypes and gene frequencies rather than appearance; this information will facilitate disease risk assessment. Many of the observed differences in gene frequencies between human populations may be accounted for by population movements, and it is difficult to assess how large a role natural selection has played in population differentiation. For several disease genes there is evidence that environmental agents, such as infectious pathogens, dietary factors, and environmental toxins, have been responsible for an increased frequency in some populations. Further examples of such selection may emerge from current efforts to define the genetic basis of many polygenic common diseases. We need more information on molecular genetic differences between human populations; we could obtain that information from the successful completion of the Human Genome Project and the proposed Human Genome Diversity Project.