Ancient mitochondrial genomes recovered from small vertebrate bones through minimally destructive DNA extraction: Phylogeography of the New Zealand gecko genus Hoplodactylus

作者：Lachie Scarsbrook, Alexander J. F. Verry, Kerry Walton, Rodney A. Hitchmough, Nicolas J. Rawlence · 发表于：Molecular Ecology · 年份：2022 · DOI：10.1111/mec.16434 · 被引用次数：13 · 研究领域：Forensic and Genetic Research、Wildlife Ecology and Conservation、Species Distribution and Climate Change

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 this method to detect lost mainland genetic diversity in the large New Zealand diplodactylid gecko genus Hoplodactylus, which is presently restricted to predator-free island and mainland sanctuaries. We present the first mitochondrial genomes for New Zealand diplodactylid geckos, recovered from 19 modern, six historical/archival (1898-2011) and 16 Holocene Hoplodactylus duvaucelii sensu latu specimens, and one modern Woodworthia sp. specimen. No obvious damage was observed in post-extraction micro-computed tomography 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 phylogeographical structuring within Hoplodactylus spp. highlighted the impacts of Late Cenozoic biogeographical barriers, inc...