The evolutionary history of the European rabbit (Oryctolagus cuniculus):: major patterns of population differentiation and geographic expansion inferred from protein polymorphism

The patterns of population differentiation and geographical expansion of the European rabbit (Oryctolagus cuniculus) remain largely unknown. Using gene frequency data for 20 polymorphic protein loci (102 alleles), we investigated the evolutionary history of the rabbit through the analysis of 13 representative populations and the use of both the neighbor-joining (NJ) and the unweighted pair-group method with arithmetic mean (UPGMA) trees. We also conducted a separate analysis comparing one domestic and one wild population with previously published results. Our data indicate that an ancient split separated southwestern Iberian populations from all others, including domestic breeds, and that this division may have corresponded to the emergence of the subspecies O.c. algirus and O.c. cuniculus. Separation times between the two major groups of populations were estimated with Nei's genetic distance and were found to be highly discrepant with the mtDNA divergence estimate. The southwestern Iberian populations (algirus group) are more polymorphic than northern populations (cuniculus group), the latter displaying more than simply a subset of southern alleles. These results are thus compatible with the isolation of a marginal population or with a smaller long-term population size in the north. The high degree of genetic differentiation between the two subspecies allows the reconstruction of rabbit geographical expansion. France, Britain and other European countries. as well as Australia, were colonized by animals belonging to the cuniculus group, from which domestic breeds are exclusively derived. In contrast, Azorean island populations represent an expansion of the algirus group and show evidence of a strong bottleneck effect.