Ancient mitochondrial genomes recovered from small vertebrate bones
through minimally destructive DNA extraction: phylogeography of the New
Zealand gecko genus Hoplodactylus.
Abstract
Methodological and technological improvements are continually
revolutionizing the field of ancient DNA. Most ancient DNA extraction
methods require the partial (or complete) destruction of finite museum
specimens, which disproportionately impacts small or fragmentary
subfossil remains, and future analyses. We present a minimally
destructive ancient DNA extraction method optimized for small vertebrate
remains. We applied these methods to detect lost mainland genetic
diversity in the large New Zealand diplodactylid gecko genus
Hoplodactylus, which is presently restricted to predator-free island
sanctuaries. We present the first mitochondrial genomes for New Zealand
diplodactylid geckos, recovered from 19 modern, six historic/archival
(1898 to 2011) and 16 Holocene Hoplodactylus duvaucelii sensu latu
specimens, and one modern Woodworthia sp. specimen. No obvious damage
was observed in post-extraction micro-CT reconstructions. All ‘large
gecko’ specimens examined from extinct populations were found to be
conspecific with extant Hoplodactylus species, suggesting their large
relative size evolved only once in the New Zealand diplodactylid
radiation. Phylogenetic analyses of Hoplodactylus samples recovered two
genetically (and morphologically) distinct North and South Island
clades, probably corresponding to distinct species. Finer
phylogeographic structuring within Hoplodactylus spp. highlighted the
impacts of Late-Cenozoic biogeographic barriers, including the opening
and closure of Pliocene marine straits, fluctuations in size and
suitability of glacial refugia, and eustatic sea-level change. Recent
mainland extinction obscured these signals from the modern tissue
derived data. These results highlight the utility of minimally
destructive DNA extraction in genomic analyses of less well studied
small vertebrate taxa, and the conservation of natural history
collections.