The phylogeography of three species of African bovids, the hartebeest (Alce
laphus buselaphus), the topi (Damaliscus lunatus), and the wildebeest (Conn
ochaetes taurinus), is inferred from sequence variation of 345 sequences at
the control region (d-loop) of the mtDNA. The three species are closely re
lated (tribe Alcelaphini) and share similar habitat requirements. Moreover,
their former distribution extended over Africa, as a probable result of th
e expansion of open grassland on the continent during the last 2.5 Myr. A c
ombination of population genetics (diversity and structure) and intraspecif
ic phylogeny (tree topology and relative branch length) methods is used to
substantiate scenarios of the species history. Population dynamics are infe
rred from the distribution of sequence pairwise differences within populati
ons. In the three species, there is a significant structuring of the popula
tions, as shown by analysis of molecular variance (AMOVA) pairwise and hier
archical differentiation estimations. In the wildebeest, a pattern of colon
ization from southern Africa toward east Africa is consistent with the asym
metric topology of the gene tree, showing a paraphyletic position of southe
rn lineages, as well as their relatively longer branch lengths, and is supp
orted by a progressive decline in population nucleotide diversity toward ea
st Africa. The phylogenetic pattern found in the topi and the hartebeest di
ffers from that of the wildebeest: lineages split into monophyletic clades,
and no geographical trend is detected in population diversity. We suggest
a scenario where these antelopes, previously with wide pan-African distribu
tions, became extinct except in a few refugia. The hartebeest, and probably
also the topi, survived in refugia north of the equator, in the east and t
he west, respectively, as well as one in the south. The southern refugium f
urthermore seems to have been the only place where the wildebeest has survi
ved.