Hoplodactylus duvaucelii sequencing reads (FastQ) - modern, historic and ancient

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 and mainland
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.