Persistent gene flow suggests an absence of reproductive isolation in an African antelope speciation model

African antelope diversity is a globally unique vestige of a much richer
world-wide Pleistocene megafauna. Despite this, the evolutionary processes
leading to the prolific radiation of African antelopes are not well
understood. Here, we sequenced 145 whole genomes from both subspecies of
the waterbuck, an African antelope believed to be in the process of
speciation. We investigated genetic structure and population divergence
and found evidence of a mid-Pleistocene separation on either side of the
eastern Great Rift Valley, consistent with vicariance caused by a rain
shadow along the so-called ‘Kingdon’s Line’. However, we also found
pervasive evidence of not only isolated and recent, but also widespread
historical gene flow across the Rift Valley barrier. By inferring the
genome-wide landscape of variation among subspecies, we found 14 genomic
regions of elevated differentiation, including a locus that may be related
to each subspecies’ distinctive coat pigmentation pattern. We investigated
these regions as candidate speciation islands. However, we observed no
significant reduction in gene flow in these regions, nor any indications
of selection against hybrids. Altogether, these results suggest a pattern
whereby climatically driven vicariance is the most important process
driving the African antelope radiation, and suggest that reproductive
isolation may not set in until very late in the divergence process.