Abstract
Advances in sequencing and chromosome-scale assembly have brought non-model animals into focus, deepening our understanding of genome and chromosome evolution. Here, we present the waterbuck (Kobus ellipsiprymnus) as an emerging model antelope for studying population dynamics and chromosome evolution. Waterbuck evolutionary history has been shaped by both climatic and geographic changes, as well as structural chromosome changes, principally Robertsonian (Rb) fusions. To provide new insights into waterbuck evolution, we generated a chromosome-level genome assembly for the species using PacBio HiFi and Hi-C sequencing. We further leveraged museum collections to perform whole genome sequencing (WGS) of 24 historical specimens. Combined with a previous WGS dataset (n = 119), this represents the largest study of waterbuck populations to date and reveals previously unrecognised population structure and gene flow between waterbuck populations, alongside several regions of high genomic differentiation between the two recognised subspecies. Notably, several differentiation hotspots occur near the centromeres of fixed and polymorphic Rb fusions, exhibiting signatures of low recombination and local population structure. These regions contain genes involved in development, fertility, and recombination. Our findings underscore the value of chromosome-level genome assemblies, the critical role of historical collections in capturing fine-scale population structure and gene flow in species with wide-ranging distributions, and the potential evolutionary impacts of Rb fusions on genomic differentiation and recombination landscapes.