Abstract
Conservationists face challenges when managing behaviourally cryptic, long-lived, endangered species that persist across fragmented populations. Limited data on life history, ecology, and population trends complicate decisions surrounding the prioritisation of funding and management effort. With relatively little field work, conservation genomics provides a means to infer key population parameters, such as size, structure, and connectivity. Crucially, genomic data also reveal patterns of genetic diversity and inbreeding, which are correlated with population fitness and adaptability. Genomic assessments are vital when undertaking translocations to establish new populations or induce gene flow. Since translocations often involve small, isolated populations, genetic drift and inbreeding may threaten their long-term viability by reducing genetic diversity and amplifying the expression of deleterious alleles.
Exemplifying these global issues are threatened Leiopelma frogs, whose management is hindered by extreme longevity, behavioural crypsis, and dependence on specific habitat features. I aimed to support their conservation management by 1) developing a minimally-invasive sampling technique to obtain DNA; and 2) investigating the long-term genetic viability of small, isolated populations of Hamilton’s frogs (Leiopelma hamiltoni), including those founded by past translocation efforts.
Genomic research on Leiopelma has lagged behind other endemic herpetofauna, partly because traditional sampling methods such as toe-clipping and euthanasia raise cultural and ethical concerns. Buccal swabbing is a minimally invasive alternative that involves collecting mucosal cells from the mouth. I demonstrated buccal swabbing as an effective genetic sampling technique for Hochstetter’s frogs (Leiopelma hochstetteri) and Hamilton’s frogs. A duplicate swabbing method allowed Leiopelma to recover from potential heat stress between two short sampling periods, with the second swab yielding approximately twice as much DNA as the first. DNA from buccal swabs was representative of the entire genome, albeit fragmented compared to DNA from toe-clips.
Management decisions for Leiopelma, including translocations of the critically endangered Hamilton’s frog, were implemented prior to the routine application of genomics in conservation management, risking a rapid loss of genetic diversity. I analysed buccal swabs alongside toe-clips utilising genotyping-by-sequencing to produce a single-nucleotide polymorphism dataset for Hamilton’s frog. My findings revealed that, although translocations have not yet had detectable genetic impacts, overall, Hamilton’s frog has depauperate genetic diversity and is highly inbred. Remarkably, I found that the smaller natural population on Takapourewa (about 250 frogs) has significantly higher genetic diversity and lower inbreeding than the larger Te Pākeka population (estimated at 19,000–34,000 frogs). Takapourewa frogs maintained a higher historical population size throughout the formation of the Marlborough Sounds than Te Pākeka, which has influenced contemporary genetic diversity. These results provide strong, direct support for genetic rescue as a potential future management intervention.
Collectively, I highlight the value of genomic data for conserving behaviourally cryptic species. Sampling of small frogs could shift toward buccal swabbing as standard practice, facilitating future genomic research in Leiopelma, particularly where field studies cannot reliably infer long-term population trends. Further, my Hamilton’s frog case study underscores the need to critically evaluate the management implications of genomic data and interrogate how patterns of genetic diversity and population structure arise in endangered species.