## 2 The Domestication Process of the Rabbit and the Origin of the Genetic Diversity in this Species  
Using morphometric analyses and molecular markers (starting from biochemical markers and then by analyzing mitochondrial DNA and nuclear genome differences), two subspecies of wild European rabbits have been described: _O. c. algirus_ (originally spread in the southwest of the Iberian Peninsula) and _O. c. cuniculus_ (originally distributed in the northeastern regions of the Iberian Peninsula and South of France [7; 8; 9; 10; 11; 12; 13]). At the molecular level, these two subspecies were first reported to carry two separated mitochondrial DNA (mtDNA) lineages (clades A and B) that have about 4.5% nucleotide differences [8; 9; 12; 13]. Differences between these two subspecies were subsequently also clearly evidenced at the nuclear DNA level (e.g., [10; 14; 15]. The phylogeographic pattern of these wild European rabbit populations suggests that the two groups remained isolated for a certain time and evolved independently. Climatic-generated barriers were probably determined by the glacial dynamics in the Iberian Peninsula that occurred during the Quaternary ice-ages. When glacial barriers later disappeared the two groups expanded their previously confined distribution areal, creating a sort of transversal line of diluted overlapping and gradual separation that goes from the North-East to the South-West of this peninsula [14]. As a consequence of the related population genetic histories, the subspecies of the mtDNA clade A maintained more genetic diversity than the subspecies of the other clade [12; 13]. A reduced level of genetic diversity observed in the South of France populations is the result of bottlenecks due to the origin of these populations from the contiguous Iberian _O. c. cuniculus_ populations [9; 12; 13; 15; 16]. In historical time, wild populations of European rabbit expanded in the North of France and North of Europe by means of human translocation activities that mainly started during the Middle Age and continued over the subsequent centuries [17; 18]. The domestication process relied on the genetic stock constituted by the subspecies _O. c. cuniculus_ that first colonized France and then other regions of the North of Europe. Animal domestication can be usually described with a gradual morphological, biological, and behavioral modification of the animals in one or more populations, and a few domestication pathways have been proposed [19]. The domestication pathway that could better describe what probably occurred in the rabbit is the directed pathway that, in the case of this species, cannot be simply derived by few events. This model does not involve any preliminary steps of habituation to the humans or preliminary management of the animals and directly begins with the capture of wild forms with the aim to control their reproduction and manage their breeding [20; 21; 22]. It is however not completely clear if preliminary habituation to anthropogenic environments and human derived management conditions of the wild genetic pool could have, at least in part, contributed to shape and lead the domestication process of the rabbit. Domestic rabbits carry a subset of the B mitotypes (B1 is the most frequent) also identified in the wild rabbit populations of the North-East Iberia and South-West of France, demonstrating that the domestication of this species was based on the wild populations that were present in France [9; 23; 24]. The domestication processes produced another reduction of genetic diversity that, however, was stronger than that observed during the transition from the Iberian to the French wild rabbits [15; 16; 25].