Extensive Population Structure Highlights an Apparent Paradox of Stasis in the Impala (Aepyceros melampus)

Impalas are unusual among bovids because they have remained morphologically similar over millions of years—a phenomenonreferred to as evolutionary stasis. Here, we sequenced 119 whole genomes from the two extant subspecies of impala, the common(Aepyceros melampus melampus) and black-faced (A. m. petersi) impala. We investigated the evolutionary forces working withinthe species to explore how they might be associated with its evolutionary stasis as a taxon. Despite being one of the most abundantbovid species, we found low genetic diversity overall, and a phylogeographic signal of spatial expansion from southern to easternAfrica. Contrary to expectations under a scenario of evolutionary stasis, we found pronounced genetic structure between andwithin the two subspecies with indications of ancient, but not recent, gene flow. Black-faced impala and eastern African commonimpala populations had more runs of homozygosity than common impala in southern Africa, and, using a proxy for genetic load,we found that natural selection is working less efficiently in these populations compared to the southern African populations.Together with the fossil record, our results are consistent with a fixed-optimum model of evolutionary stasis, in which impalasin the southern African core of the range are able to stay near their evolutionary fitness optimum as a generalist ecotone species,whereas eastern African impalas may struggle to do so due to the effects of genetic drift and reduced adaptation to the local hab-itat, leading to recurrent local extinction in eastern Africa and re-colonisation from the South.