title: Phylogeography of the African buffalo based on mitochondrial and Y-chromosomal loci: Pleistocene origin and population expansion of the Cape buffalo subspecies.
abstract: Population genetics and phylogeography of the African buffalo (Syncerus caffer) are inferred from genetic diversity at mitochondrial D-loop hypervariable region I sequences and a Y-chromosomal microsatellite. Three buffalo subspecies from different parts of Africa are included. Nucleotide diversity of the subspecies Cape buffalo at hypervariable region I is high, with little differentiation between populations. A mutation rate of 13-18% substitutions/million years is estimated for hypervariable region I. The nucleotide diversity indicates an estimated female effective population size of 17 000-32 000 individuals. Both mitochondrial and Y-chromosomal diversity are considerably higher in buffalo from central and southwestern Africa than in Cape buffalo, for which several explanations are hypothesized. There are several indications that there was a late middle to late Pleistocene population expansion in Cape buffalo. This also seems to be the period in which Cape buffalo evolved as a separate subspecies, according to the net sequence divergence with the other subspecies. These two observations are in agreement with the hypothesis of a rapid evolution of Cape buffalo based on fossil data. Additionally, there appears to have been a population expansion from eastern to southern Africa, which may be related to vegetation changes. However, as alternative explanations are also possible, further analyses with autosomal loci are needed.
authors.affiliation: Wageningen University, Department of Environmental Sciences, Tropical Nature Conservation and Vertebrate Ecology Group, Bornsesteeg 69, 6708 PD Wageningen, The Netherlands. vanhooft@cml.leidenuniv.nl
authors.forename: W F
authors.initials: WF
authors.lastname: Van Hooft
authors.forename: A F
authors.initials: AF
authors.lastname: Groen
authors.forename: H H T
authors.initials: HH
authors.lastname: Prins
mesh_terms: D000349:Africa; D000818:Animals; D005075:Biological Evolution; D002020:Buffaloes / Q000235:genetics*; D004272:DNA, Mitochondrial / Q000032:analysis / Q000235:genetics*; D005260:Female; D005828:Genetics, Population; D006239:Haplotypes; D008297:Male; D018895:Microsatellite Repeats; D010802:Phylogeny; D014998:Y Chromosome / Q000235:genetics*
chemical_list: D004272:DNA, Mitochondrial