Analyzing the impact of migration on the genetic diversity of cattle and goat breeds

The aim of this thesis is to study the genetic diversity of goat and cattle populations, especially from the Mediterranean basin, to understand the impact of migration on the gene pools of these species. The study 1 aimed to analyze the genetic impact of post-domestication dispersal of modern goats in Europe and Africa. We have retrieved genetic data from over a thousand populations in both continents. In Europe, we found distinct genetic differences among Northern European breeds and British-Irish populations compared to others. In Africa, in contrast, we have identified five main clusters which coincide with the northern, southern, eastern, and western parts of the continent plus the island of Madagascar. The study explored whether genetic diversity correlated with the distance of goat populations from the initial domestication center in Anatolia. In Europe, a negative diversity correlation with distance was observed only when including island populations. In contrast, in Africa, significant negative correlations were found in both datasets (with and without islands). This suggests that maritime diffusion likely played a bigger role in Europe, while overland dispersal was more significant in Africa. Geographic and biological barriers also seemed to limit gene flow among African populations. In studies 2 and 3, we have investigated the genetic consequences of the African introgression of Mediterranean cattle and goat breeds. More specifically, in study 2, we aimed to determine the origins and magnitude of the African introgression of the Murciano-Granadina dairy breed, which is mainly distributed in Southern Spain. To do so, we have genotyped 500 Murciano Granadina goats with the Goat SNP50BeadChip and we have performed supervised ADMIXTURE analysis using as reference populations (i) A Spanish breed, (ii) A Swiss cosmopolitan breed and (iii) North African breeds: Moroccan, Egyptian, Algerian and Sudanese. We have found that the African introgression of Murciano-Granadina goats has its roots in Morocco, with an average percentage of about 4% and a range between 0-12%. In contrast, goats from other Northern African countries did not contribute alleles to Murciano-Granadina goats in a significant way. The presence of a Moroccan genetic component in Murciano-Granadina goats could be due to the conquest of Spain by Berber troops, originally from the Maghreb, who stayed in the Iberian Peninsula for eight centuries. However, other alternative historical scenarios making possible the gene flow between Moroccan and Spanish goat populations could be also involved. In study 3, we were interested in characterizing the mitochondrial variation of local Sardinian cattle breeds (Sarda, Sardo Bruna and Sardo Modicana) to determine its magnitude as well as the presence of an African genetic signature. By doing so, we have observed a significant genetic differentiation between the three Sardinian breeds. Moreover, by constructing a Median Joining Network based on sequences from Sardinian cattle, a typical 'star-like' conformation likely produced by a founder effect was observed. We made a second Median Joining Network including mitochondrial sequences from cattle of African, Italian, Spanish and Asian origin to identify their relationship with other cattle breeds. This analysis revealed the presence of the T3 haplogroup (typically European) in the Sarda breed, and of the T1 and T1'2'3' haplogroups in the Sarda and Sardo Bruna breeds. The identification in Sardinian cattle of haplogroup T1, characteristic of African taurine breeds, may reflect the occurrence of an African introgression event. Such event could have occurred through direct exchanges of bovines between North Africa and Sardinia or indirectly through trade with Mediterranean populations already introgressed with African cattle. Such scenario is plausible given that Sardinia is located at the crossroads of many maritime trading routes traversing the Mediterranean Sea.