Comparative phylogeography of hairy-nosed wombats (Lasiorhinus spp.) reveals long-term low mitochondrial DNA diversity in the critically endangered northern hairy-nosed wombat (L. krefftii)

The northern hairy-nosed wombat (Lasiorhinus krefftii, NHNW) is critically endangered following major range and population declines during the 20th century, resulting in a population bottleneck of ~30 individuals in the 1980s. Understanding the population history, impact of extirpations, range contraction and the bottleneck in this species is critical to contextualising ongoing efforts to understand and manage surviving genetic diversity. We generated mtDNA genomes from contemporary and historical samples of the NHNW from the extant and two extirpated populations and compared mtDNA diversity and phylogeography to the closely related southern hairy-nosed wombat (L. latifrons, SHNW) from southern Australia. The NHNW had very low mtDNA diversity, with shallow phylogeographic structure across its former range. A single mtDNA haplotype has been present in the extant population since at least 1937, suggesting a small long-term female effective population size and a possible pre-1937 bottleneck. In contrast SHNWs show four to five times higher mtDNA diversity and evidence of phylogeographic divergence across the Pleistocene Eyrean Barrier. Our results highlighted the need for further genomic analyses of the extant NHNW population, to estimate the extent of inbreeding and inbreeding depression and to help minimise loss of functional genetic diversity in this species.