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 investig..., , , # Persistent gene flow suggests an absence of reproductive isolation in an African antelope speciation model

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## Description of data

SB.waterbuck.MinorR2.SupplementaryFile.pdf ---Supplementary information of methods details and Supplementary Figures/Tables

SupplementaryTable2.xlsx (on Dryad) ---Samples inclusion after different steps of sample filtering.

SupplementaryFigure16.pdf---Plot of Fst between two subspecies and variation in local topological relationships between two subspecies using TWISST, pairwise diversity, Tajimas D, and the pattern of localized linkage disequilibrium (LD) for defassa waterbuck (orange) and common waterbuck (light purple) of all 11 chromosomes where differentiation islands were found.

SupplementaryFigure18.pdf---Plot of F st within all 14 outlying F st windows and its surrounding genomic region, together with its annotated protein coding genes.

SupplementaryFigure20.pdf---No signatures for reduced gene flow in 14 differentiation islands.

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