Population and conservation genomics of the world's rarest hyena species, the brown hyena (Parahyena brunnea)

Abstract

With an estimated population size of less than 10,000 individuals worldwide, the brown hyena (Parahyaena brunnea) has been listed as near threatened by the IUCN. Despite this rank, studies involving DNA analyses of the brown hyena are limited. Little consideration has been focussed towards population structure within the brown hyena, which could provide valuable insights about its evolutionary history and aid in conservation efforts of the species. Here we report both mitochondrial and nuclear genomes of wild-caught brown hyena individuals from across southern Africa. Mitochondrial DNA shows little to no phylogeographic structure, whereas low-coverage nuclear genomes reveal several potential sub-populations. Moreover, we find that brown hyenas harbour the lowest genetic diversity for a species on both the mitochondrial and nuclear level when compared to a number of mammalian species for which such information is currently available. Our data also reveal that at least on the nuclear DNA level, this low diversity could be the result of a continuous and ongoing decline in effective population size that started about one million years ago and dramatically accelerated towards the end of the Pleistocene. Moreover, our findings also show that the correlation between genetic diversity and the perceived risk of extinction is not particularly strong, since many species with higher genetic diversity than the brown hyena are considered to be at greater risk of extinction. Taken together, our results have important implications for the conservation status and conservation approaches of the brown hyena.