Historical Population Declines Prompted Significant Genomic Erosion​ in the Northern and Southern White Rhinoceros (​ <i>Ceratotherium simum</i>)

Abstract

Large vertebrates are extremely sensitive to anthropogenic pressures, and their populations are declining fast. The white rhinoceros (​Ceratotherium simum) is a paradigmatic case: this African megaherbivore suffered a remarkable population reduction in the last 150 years due to human activities. The two white rhino subspecies, the Northern (NWR) and the Southern white rhino (SWR), however, underwent opposite fates: the NWR vanished quickly after the onset of the decline, while the SWR recovered after a severe bottleneck. Such demographic events are predicted to have an erosive effect at the genomic level, linked to increased genetic drift and inbreeding. However, there is little empirical data available with which to reconstruct the subtleties of such processes. We therefore generated a whole-genome, temporal dataset consisting of 52 re-sequenced white rhino genomes, that represents both subspecies at two time windows throughout the past ~ 170 years. Our data not only reveals previously unknown population substructure within both subspecies, but allowed us to quantify the genomic erosion they underwent, with post-bottleneck white rhinos showing significantly lower levels of heterozygosity and higherinbreeding coefficients than pre-bottleneck individuals. Moreover, the effective population size (N​e​) has suffered a decrease of two and three orders of magnitude in the NWR and SWR, respectively. Our data provides empirical support for theoretical predictions about the genomic consequences ofshrinking populations, which is relevant for understanding the process of population extinction. Furthermore, our findings have the potential to inform tailored management approaches for the conservation of the remaining white rhinos.