Insights into the genomics, evolution, and conservation of antelopes

Genomic advancements have increased the feasibility of generating chromosome-level genomes for non-model animals, enabling evolutionary and conservation related research of understudied species. Here, we focus on antelopes, in the ruminant subfamily Bovidae, and explore their chromosome evolution, 3D genome organisation, and population genomics. Antelopes have diploid chromosome numbers ranging between 2n = 30 and 2n = 60, predominantly due to Robertsonian fusions of acrocentric chromosomes. Additionally, some species have chromosome fusions that have remained polymorphic within species. One example of this is the waterbuck (Kobus ellipsiprymnus), with chromosome polymorphisms within and between two recognised subspecies, causing karyotypes of between 2n = 50 and 2n = 54. To explore inter- and intra-species genomics of antelopes we firstly sequenced and assembled a chromosome-level genome for the waterbuck using PacBio HiFi long-reads and Hi-C. We then extracted DNA and whole genome sequenced (WGS) 24 historical waterbuck samples and combined this with WGS data for 119 modern samples to explore the population genomics and chromosome rearrangements of waterbuck. Lastly, we combined the newly assembled waterbuck genome and Hi-C with published chromosome-level genomes and Hi-C data to investigate chromosome evolution and 3D genome organisation across antelopes. This study provides a highly contiguous and complete genome assembly for the waterbuck. At the population level we support previous studies by showing genomic differences between and within the two subspecies, with strong barriers to gene flow, but also varying degrees of admixture. We identified multiple regions of high genomic differentiation between the two subspecies, several of them near chromosome fusions, suggesting putative signatures of these rearrangements, with these regions containing genes that may be involved in speciation. Between species, we reconstructed the chromosomes of two bovid ancestors and explored chromosome fusions. We found that commonly fused chromosomes were not found to be located closer within the 3D genome organisation of the nucleus in species without the fusion. This was also the case for the polymorphic chromosome fusion in waterbuck. This study provides an overview of the genomics and evolution of antelopes, raising important questions on how we conserve species with variable karyotypes and in early speciation, and with ongoing hybridisation.