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.
Highlights
The phylogeographic pattern of most of the savanna mammals distributed across Africa can be partitioned into two to four main lineages
As the taxonomic status of the subspecies is still subject to controversy, we defined each of the four putative subspecies as recognized by East [27] and Kingdon [26] and adopted by the IUCN (2004) as an ecophenotype, i.e., nanus ecophenotype, brachyceros ecophenotype, aequinoctialis ecophenotype and caffer ecophenotype (Cape buffalo from East and Southern Africa)
Inferences based on DNA data are somewhat hampered because of the time required for complete lineage sorting to occur, our data unequivocally show that the separation between S. c. brachyceros, S. c. nanus and S. c. aequinoctialis is not taxonomically equivalent to the split between all of these and S. c. caffer
Summary
The phylogeographic pattern of most of the savanna mammals distributed across Africa can be partitioned into two to four main lineages These lineages are typically associated with a WestCentral, Eastern, Southern and/or South-East African distribution. The vegetation changes associated with these climatic changes were probably the main driver of population expansions in savanna species during cool and dry phases, and population contraction during wet and warm phases [2]. The location of these refugia were purportedly in West, East, South and South-Western Africa [1,9,10,19,20]
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