Phylogeography of the African buffalo based on mitochondrial and Y-chromosomal loci: Pleistocene origin and population expansion of the Cape buffalo subspecies

Authors

  • W. F. Van Hooft,

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    1. Wageningen University, Department of Environmental Sciences, Tropical Nature Conservation and Vertebrate Ecology Group, Bornsesteeg 69, 6708 PD Wageningen, The Netherlands,
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  • A. F. Groen,

    1. Wageningen University, Department of Animal Sciences, Animal Breeding and Genetics Group, PO Box 338, 6700 AH Wageningen, The Netherlands
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  • H. H. T. Prins

    1. Wageningen University, Department of Environmental Sciences, Tropical Nature Conservation and Vertebrate Ecology Group, Bornsesteeg 69, 6708 PD Wageningen, The Netherlands,
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W. F. van Hooft. ‡Present address: Leiden University, Centre of Environmental Science, PO Box 9518, 2300 RA Leiden, The Netherlands. Fax: + 31 71 5275587; E-mail: vanhooft@cml.leidenuniv.nl

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.

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