Pan-African genetic structure in the African buffalo (Syncerus caffer): investigating intraspecific divergence.

The African buffalo (Syncerus caffer) exhibits extreme morphological variability, which has led to controversies about the validity and taxonomic status of the various recognized subspecies. The present study aims to clarify these by inferring the pan-African spatial distribution of genetic diversity, using a comprehensive set of mitochondrial D-loop sequences from across the entire range of the species. All analyses converged on the existence of two distinct lineages, corresponding to a group encompassing West and Central African populations and a group encompassing East and Southern African populations. The former is currently assigned to two to three subspecies (S. c. nanus, S. c. brachyceros, S. c. aequinoctialis) and the latter to a separate subspecies (S. c. caffer). Forty-two per cent of the total amount of genetic diversity is explained by the between-lineage component, with one to seventeen female migrants per generation inferred as consistent with the isolation-with-migration model. The two lineages diverged between 145 000 to 449 000 years ago, with strong indications for a population expansion in both lineages, as revealed by coalescent-based analyses, summary statistics and a star-like topology of the haplotype network for the S. c. caffer lineage. A Bayesian analysis identified the most probable historical migration routes, with the Cape buffalo undertaking successive colonization events from Eastern toward Southern Africa. Furthermore, our analyses indicate that, in the West-Central African lineage, the forest ecophenotype may be a derived form of the savanna ecophenotype and not vice versa, as has previously been proposed. The African buffalo most likely expanded and diverged in the late to middle Pleistocene from an ancestral population located around the current-day Central African Republic, adapting morphologically to colonize new habitats, hence developing the variety of ecophenotypes observed today.

Examples of probable host-pathogen co-adaptation/co-evolution in isolated farmed animal populations in the mountainous regions of North Vietnam.

In Vietnam, for a number of specific geographical and historical reasons, the mountainous areas have preserved an exceptional diversity of wild and domestic animal species of high socioeconomic interest. This endemic genetic diversity fosters a rapid response to environmental change in mostly isolated local communities and, in particular, fosters the constant adaptation of ecosystems common to humans and farmed and wild animal populations and pathogens. During a 2-year study carried out in several mountainous regions of North Vietnam near the Chinese border, we surveyed 1697 breeders in 249 villages and gathered 5815 biological samples among the four main domesticated species of food animals: chickens, cattle, buffaloes, and goats. Serological analyses were carried out by ELISA on 726 sera in order to assess the prevalence of antibodies specific to two major diseases suspected to be present in the region: avian influenza (AI) and peste des petits ruminants (PPR). The results reported here reveal the presence of antibodies specific to AI, but not the H5N1 highly pathogenic strain, and the presence of antibodies specific to PPR, confirming that this disease, never previously described in Southeast Asia, is present in this region, with no mortality and little or no evidence of clinical cases. These are probably situations of co-evolutive epidemiological equilibrium between pathogen populations, which may have lost their virulence, and animal populations that have acquired genetic resistances over generations, either naturally or through genetic introgression from related wild species better adapted to such pathogens. These results suggest the need for more research, both short-term and, more globally, long-term.