Spatial and temporal distribution of mitochondrial lineages in the European wild boar

In many terrestrial species, the geographic distribution of DNA lineages was heavily affected by the climatic fluctuations that occurred during the Quaternary, although the impact of human populations, especially on harvested species, might have confounded the pattern in more recent times. In game species such signals are expected to be overshadowed by the effects of more recent management (local extinctions, introductions, translocations). Past global climate changes had a profound impact on the evolutionary history of many species and left a genetic signature which is often still detectable nowadays. The wild boar is one the most widely distributed terrestrial animals, naturally occurring from Western Europe and Northern Africa to Japan. Previous studies in European animals suggested that Iberia, Balkans and Italy played a major role as refugia during the Last Glacial Maxima (LGM), and these three areas were the main responsible for the recolonization of European continent after the LGM. This PhD dissertation investigated the geography of the genetic diversity of the European wild boar (Sus scrofa). It aims to infer how past climate influenced the current observed pattern of genetic diversity distribution of the mitochondrial DNA. A comprehensive dataset of more than 700 sequences from the hypervariable region of the mitochondrial DNA from 74 populations, covering the whole European continent (from Portugal to Russia) was used. The results confirmed the existence of a ubiquitous mitochondrial clade in Europe (E1), a highly differentiated clade exclusive of Italy (E2) and East Asian haplotypes (A) at very low frequencies, presumably introgressed from commercial pig breeds. No Near Eastern haplotype was detected. A clear south-north decreasing gradient of diversity was observed, with maximum levels hosted in presumed glacial refugia. Seven structured groups were found, with distributions highly correlated to geography. Population size within groups was generally constant through time, with only slight recent changes. Sardinia was the most differentiated population, with 64% private haplotypes. A surprising similarity between western (Iberia) and eastern Europe was observed, while central populations showed a higher affinity to the Italian gene pool. Notably, a monophyletic subclade, was shared at high frequencies by Central European (France and Germany) and Italian wild boars. To predict the distribution of the wild boar during the LGM and its relationship with the current distribution of the genetic diversity a maximum entropy method of niche modeling was used. The climate models predicted that Iberia, Balkans and Italy had great habitat suitability during the LGM, serving as refugia. Most part of Europe north to 45°N was unsuitable to the species. Italy and Iberia showed greater suitability when compared to other regions of Europe, which can indicate that these two areas may have retained large population size even during cold periods. The suitability map and the current distribution of the genetic diversity exhibited similar patterns, with northern areas showing low suitability and lower genetic diversity, while southern regions had higher values of suitability and genetic diversity. The current distribution of genetic diversity was highly influenced by past climate events, especially related to the LGM. Post-LGM colonization of the continent from southern refugia can explain the current phylogeographic patterns in the European wild boar. More recent changes to population size and gene flow could have acted more at a local scale, without a great impact on the global framework