Abstract:
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.
