Non-destructive method for obtaining data from ancient DNA developed during a gecko study at the University of Otago

A University of Otago researcher has developed a non-destructive method to get data from ancient DNA, after initially spending fruitless months using another method to try to get information from bones of geckos.

“We first attempted to obtain mitochondrial genomes using a different method, and after months in the lab we failed to produce usable data,” said researcher Lachie Scarsbrook.

“After going back to the drawing board and making some changes, we achieved our goal, which just goes to show that persistence in the face of failure is key if you want to contribute to scientific progress.”

A Duvaucel gecko.

Delwyn Dickey / Stuff

A Duvaucel gecko.

The work was done while Scarsbrook was completing an MSc in the university’s zoology department and used contemporary, extinct populations of Hoplodactylus geckos as a case study. These were the first mitochondrial genomes obtained for any New Zealand lizard, the university said.

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“Ancient DNA doesn’t have to be destructive,” Scarsbrook said. “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 new method of obtaining genomic data from the remains of small vertebrates, in a way that causes no visible damage to the underlying bone, is presented in a journal article Molecular ecology.

“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,” Scarbrook said.

Lachie Scarsbrook.

University of Otago

Lachie Scarsbrook.

Using the newly sequenced DNA data, the researchers were able to show how tectonic activity, climate change and human impact had influenced Duvaucel’s gecko (Hoplodactylus duvauceli) populations.

According to the Department of Conservation, Duvaucel geckos are endemic to New Zealand and are the largest living lizard in that country and one of the largest geckos in the world. They can measure up to 161 mm from the tip of the snout to the vent and a total length of up to 320 mm.

Duvaucel’s geckos can live for over 40 years and were once widespread across much of New Zealand, but are now largely confined to the Cook Strait Islands, including Mana Island, and off the east coast of the North Island.

Scarsbrook, who is currently working on a doctorate, said the research had direct impacts on Duvaucel’s gecko conservation management.

His supervisor and co-author of the study, Dr Nic Rawlence of the Otago Paleogenetics Laboratory, said it was believed that the bones of different gecko species could be distinguished based on their size.

Dr. Nic Rawlence, Director of the Paleogenetics Laboratory at the University of Otago

University of Otago

Dr. Nic Rawlence, Director of the Paleogenetics Laboratory at the University of Otago

But research has shown that size doesn’t matter and that different gecko species can be distinguished from each other based on shape alone, Rawlence said.

This meant that what was known about New Zealand geckos at the time of human arrival was a “paleontological clean slate”.

The new techniques would be used to reconstruct the lost ecological history of New Zealand geckos and skinks (where size-based identifications have confused scientists), frogs and tuatara.

“The long-term preservation of finished specimens is a major concern for conservators around the world,” Rawlence said.

“So what Lachie has developed will not just unlock molecular secrets, but potentially vast swathes of natural history and archaeological collections globally for similar genetic analysis.”

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