Conservation Genetics of the Critically Endangered Riverine Rabbit, Bunolagus monticularis: Structured Populations and High mtDNA Genetic Diversity

The riverine rabbit, Bunolagus monticularis, is regarded critically endangered. This endemic South African leporid is believed to have extremely low population numbers, and was traditionally thought to be confined to a small region within the Nama Karoo and Succulent Karoo biomes. Recent discoveries of the species at lower altitudes in the Fynbos biome, however, question many of the broadly accepted ideas of the past. The newly defined distribution limits provide an opportunity to assess genetic relatedness across two altitudinally delimited populations providing data that are critical for the development of future conservation efforts, and assessment of the species’ IUCN red list status. We analyzed the degree of geographic genetic structure and mtDNA diversity in Bunolagus using control region sequences from 70 individuals (12 subpopulations) sampled between 1947-2020 across the species’ range. A TCS haplotype network, pairwise AMOVA analysis, and average sequence divergences among subpopulations, all provide genetic support for the recognition of a previously defined Northern and Southern population separated by a semi-permeable geographic barrier comprising unsuitable rocky habitat. Bayesian Skyline analyses link a decline in Bunolagus population numbers to the last glacial maximum but, importantly, the haplotype networks suggest that the Northern and Southern populations responded differently to these paleoclimatic changes. The Northern population, presently confined to the Nama Karoo biome, reflects the effects of fragmentation and survival in refugia in times of increasing aridity, followed by dispersal during more mesic periods. The Southern population, which is mostly confined to Fynbos, exhibits a more stable demographic profile. Surprisingly, given the accepted view of critically low population numbers, Bunolagus exhibits high mtDNA haplotypic diversity underscoring the need for subpopulation connectivity in maintaining genetic diversity through time. We argue that its successful conservation is contingent on reducing human transformation of their habitat and, importantly, protection of sufficient connectivity throughout the species’ range.