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

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Abstract

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.

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Availability of Data and Material

All sequence data are available through Genbank – MZ871373 - MZ871442. DNA extracted from the material is housed in the private collection of the Evolutionary Genomics Group at Stellenbosch University, South Africa. Four frozen fibroblasts cells represented by MZ871373 - MZ871376 have been deposited at the National Biobank Facility at the South African National Biodiversity Institute, Pretoria.

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Acknowledgements

Material was provided by landowners and the interested public under auspices and permitting of the Riverine Rabbit Working Group, CapeNature, Northern Cape Environmental Affairs and Nature Conservation, the Amathole Museum, and the Endangered Wildlife Trust Drylands Conservation Programme. Vicky Ahlmann, Bonnie Schumann, Cobus Theron, Guy Palmer, Insauf de Vries, Corne Claasen, Zoe Woodgate, and Jan Humann are especially acknowledged for their sustained support over many years. Daryn Alpers is thanked for performing the DNA extractions on museum specimens. Funding was provided by Stellenbosch University and a National Research Foundation Grant to CAM.

Funding

Funding was provided by Stellenbosch University and a National Research Foundation Grant to CAM.

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Authors and Affiliations

  1. Evolutionary Genomics Group, Department of Botany and Zoology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa

    Conrad A. Matthee, Natalie de Wet & Terence J. Robinson

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  1. Conrad A. Matthee
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  2. Natalie de Wet
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  3. Terence J. Robinson
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Contributions

CAM: conceptualization, generation of data, data analyses, writing first draft, funding; NDW: generation of data, data analyses, editing of draft, approve final version; TJR: conceptualization, writing and editing of manuscript, approve final version.

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Correspondence to Conrad A. Matthee.

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Material was provided by landowners and the interested public under auspices and permitting of the Riverine Rabbit Working Group, CapeNature, Northern Cape Environmental Affairs and Nature Conservation, the Amathole Museum, and the Endangered Wildlife Trust Drylands Conservation Programme.

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All authors voluntary participated in conducting this research and had the full approval from Stellenbosch University.

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There are no conflicts of interest or competing interests associated with this work.

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Matthee, C.A., de Wet, N. & Robinson, T.J. Conservation Genetics of the Critically Endangered Riverine Rabbit, Bunolagus monticularis: Structured Populations and High mtDNA Genetic Diversity. J Mammal Evol 29, 137–147 (2022). https://doi.org/10.1007/s10914-021-09577-2

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