Mapped read data and files and scripts from: Vicariance followed by secondary gene flow in a young gazelle species complex

Grant’s gazelles have recently been proposed to be a species complex
comprising three highly divergent mtDNA lineages (Nanger granti, N. notata
and N. petersii). The three lineages have non-overlapping distributions in
East Africa, but without any obvious geographical divisions, making them
an interesting model for studying the early stage evolutionary dynamics of
allopatric speciation in detail. Here we use genomic data obtained by
restriction site-associated (RAD) sequencing of 106 gazelle individuals to
shed light on the evolutionary processes underlying Grant's gazelle
divergence, to characterize their genetic structure and to assess the
presence of gene flow between the main lineages in the species complex. We
date the species divergence to 134,000 years ago, which is recent in
evolutionary terms. We find population subdivision within N. granti, which
coincides with the previously suggested two subspecies, N.g. granti and
N.g. robertsii. Moreover, these two lineages seem to have hybridized in
Masai Mara. Perhaps more surprisingly given their extreme genetic
differentiation, N. granti and N. petersii also show signs of prolonged
admixture in Mkomazi, which we identified as a hybrid population most
likely founded by allopatric lineages coming into secondary contact.
Despite the admixed composition of this population, elevated X-chromosomal
differentiation suggests that selection may be shaping the outcome of
hybridization in this population. Our results therefore provide detailed
insights into the processes of allopatric speciation and secondary contact
in a recently radiated species complex.