Abstract
While anthropogenic activity is driving major declines in global biodiversity, our understanding surrounding the number of species that exist on Earth remains remarkably incomplete, limiting our ability to accurately quantify and manage these losses. New Zealand is no exception to these trends. Despite over 90% of New Zealand’s reptiles being classified as ‘At Risk’ of extinction (or worse), almost half of the ~125 endemic species remain taxonomically unresolved. In particular, the skink fauna (family: Scincidae) has proved extremely challenging for scientists and taxonomists due to recent divergence, morphological similarities between species, and hybridisation, significantly complicating species management. Most of the taxonomic uncertainty can be attributed to a few particularly unresolved species complexes, some of which contain putative taxa that are highly threatened with extinction. Here, I carried out genotyping-by-sequencing, obtaining genome-wide single nucleotide polymorphism (SNP) data, to investigate the evolutionary history, genetic diversity, and population structure of two of New Zealand’s most poorly understood and threatened species groups: the cryptic skink (Oligosoma inconspicuum) species complex and the scree skink (O. waimatense) complex. For the cryptic skink complex I tested whether the putative taxa that form the complex were reciprocally monophyletic and accurately reflect the underlying genetic diversity. Further, I looked at the fine-scale diversity and structure of the morphologically unique and range-restricted South Westland populations. For the scree skink complex, I explored the complex’s phylogeographic history, and assessed where the putative species fall. Further, I elucidated how the closely related Otago skink (O. otagense) fits within this complex and tested whether it has hybridised with some members, as has been hypothesised in previous literature. In total, I collected 220 samples, covering a range of populations/species from both complexes. Tens of thousands of single nucleotide polymorphisms (SNPs) were obtained, and through various genomic analyses I was able to successfully characterise the evolutionary history and population structure of both complexes. The evolutionary history of the cryptic skink complex was revealed to be highly incongruent with the current species assignments, though significant geographic structure exists within the complex, possibly pointing to multiple cryptic lineages. Unexpectedly, the scree skink complex was found to comprise two distinct evolutionary lineages, which have subsequently diversified to form the complex as we know today, contradicting previous evidence of introgression. The Otago skink, previously thought to be sister to all scree skinks, was observed to be within the complex, being part of one of these distinct diversifications. My results also demonstrate that the two major known populations of alpine rock skink have evolved independently, and the scree skink (O. waimatense sensu stricto) represents two morphologically similar, yet evolutionarily, distinct lineages. These insights have already informed the national threat classification process for herpetofauna (assessed in 2025) and been incorporated directly into species management. Further, they provide a detailed dataset to inform future taxonomic descriptions of these vulnerable species. Even more significantly, my results have generated a phase-shift towards genomics-based species identification and management of New Zealand herpetofauna, ultimately enhancing how we preserve biodiversity at multiple biological scales.