A new method of obtaining ancient genomic data without damaging source material has been developed by researchers at the University of Otago, creating new opportunities for museums and archaeological collections around the world.
“Ancient DNA doesn’t have to be destructive,” says lead author Lachie Scarsbrook. “Our new method allows the reconstruction of the genetic whakapapa without destroying the very bone that has held its secrets for thousands of years.”
The research, published in the international journal Molecular ecologypresents a new method of obtaining genomic data from small vertebrate remains that causes no visible damage to the underlying bone.
“This will not only facilitate analyzes on materials in museum collections that are either too small to be destructively sampled, but also more rare and valuable materials, both culturally and scientifically,” Scarsbrook said.
The study, undertaken while Mr Scarsbrook was completing a Master of Science in the Department of Zoology, used contemporary and extinct populations of Hoplodactyl geckos as a case study, and represents the first mitochondrial genomes obtained for any New Zealand lizard.
The newly sequenced DNA data allowed researchers to understand and show how tectonic activity, climate change and human impact have influenced Duvaucel’s gecko (Hoplodactylus duvauceli) regional populations in New Zealand.
“The deep divisions between the North Island and South Island populations reflect long-term isolation prior to the formation of the Cook Strait, while the South Island populations exhibit geographically consistent genetic breaks with maximum ice cover at the height of the last ice age,” says Scarsbrook.
“The significant loss of genetic diversity in the North and South Island populations is testimony to the impact of humans and introduced predators. Our research has significant and direct impacts on the conservation management of Duvaucel’s gecko. “
Study supervisor and co-author Dr. Nic Rawlence of the Otago Paleogenetics Laboratory
says that one result of this research is that knowledge of New Zealand geckos at the time of human arrival is now a clean slate.
“It was previously thought that you could only tell the bones of different gecko species apart based on their size, but surprisingly CT scans and ancient DNA have shown that we can actually tell different geckos apart using only the shape – size was thrown out with the bathwater,” says Dr. Rawlence.
“It turns out size doesn’t matter after all, which means what we know about New Zealand geckos at the time of human arrival is now a paleontological clean slate.”
Currently completing his PhD with the Paleogenomics and Bioarchaeology Research Network at the University of Oxford, Mr Scarsbrook says the research also addresses the process involved in scientific progress.
“We first attempted to obtain mitochondrial genomes using a different method, and after months in the lab we failed to produce usable data.”
“After going back to the drawing board and making a few tweaks, we’ve achieved our goal, which just goes to show that persistence in the face of failure is essential if you want to help advance science.”
Dr Rawlence says the ongoing research program will use these new techniques to reconstruct the lost ecological history of New Zealand geckos and skinks (where size-based identifications have confounded scientists), frogs and tuatara, in partnership with the Department of Conservation and M? ori iwi.
“The long-term preservation of finished specimens is a major concern for curators around the world, so what Lachie has developed will not only unlock molecular secrets, but potentially vast swathes of natural history and archaeological collections at scale. worldwide for similar genetic analysis.”
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