Sequencing the Genome of an Ancient Reptile

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Tuatara Reptile

The tuatara is the last surviving member of the reptilian order Rhynchocephalia, which once flourished globally in the age of the dinosaurs. Today, they live only in New Zealand. Among the creature’s unusual traits are exceptional longevity and a combination of bird and reptile characteristics that have made their position on the evolutionary tree a matter of uncertainty. Credit: ASU

New Zealand is home to an astonishingly rich web of life, with many indigenous plant and animal species found nowhere else on Earth. Even amid such exceptional biodiversity, however, the tuatara stands out as one of the most remarkable of New Zealand’s creatures.

Tuatara and related species flourished hundreds of millions of years ago, during the Mesozoic era, once inhabiting a landmass comprised of Africa, South America, Australia, Antarctica, the Indian subcontinent and the Arabian Peninsula — a supercontinent known as Gondwana.

In the ensuing millennia, tuatara have occupied their own solitary branch on the evolutionary tree, after diverging from snake and lizard ancestors some 250 million years ago. Today, tuatara is the only living member of the archaic reptilian order Rhynchocephalia.

The species is considered a living fossil and a genetic treasure trove for researchers like Arizona State University’s Melissa Wilson, a computational evolutionary biologist at the Biodesign Center for Mechanisms of Evolution and the Center for Evolution and Medicine, and associate professor at the School of Life Sciences.

Melissa Wilson

Melissa Wilson. Credit: ASU

In a new study, published in the journal Nature, Wilson joins an international team, led by Neil Gemmell, a geneticist at the department of anatomy, University of Otago, New Zealand, to help untangle the skein of tuatara’s outsized genome, which — at some 5 billion base pairs — is nearly twice that of humans and one of the largest vertebrate genomes on record. The new study highlights the peculiar architecture of the tuatara’s genetic composition and confirms the unique evolutionary status of this ancient reptile. 

“They’re as close to dragons as we have on this planet, because they are not closely related to any living reptiles,” Wilson said. “Unlike iguanas or Gila monsters or green anole lizards, tuatara are on this evolutionary branch all by themselves.”

This uniqueness makes unlocking the secrets of the tuatara challenging, as researchers have no analogous species suitable for comparison with this genomic outlier.

While tuatara represent the only extant member of Rhynchocephalia, they are a living relic of now-extinct stem reptiles from which the amniotes — dinosaurs, modern reptiles, birds and mammals — eventually evolved. Scientists believe tuatara can help fill in many pieces in the puzzle of amniote evolution.

Tuatara can live to more than 100 years of age, a biological feat likewise rooted in the animal’s unusual genome, which appears to be exceptionally effective in protecting them from disease and the ravages of age. The study also examined the genetic underpinnings of tuatara vision, smell and temperature regulation.

In addition to the large international team of researchers, the new study was conducted in close collaboration with the Ngātiwai, a Maori Indigenous tribe of Northland New Zealand, drawing on their particular knowledge of (and reverence for) the tuatara, which they consider a special treasure or “taonga.”

Gemmell cites the new study as providing a valuable template for future collaborative efforts with native communities. He stresses that one of the primary objectives of the new research is to assist long term conservation efforts and promote global awareness of the tuatara along with other endangered members of New Zealand’s spectacular ecosystem. Despite the country’s dizzying profusion of life, New Zealand is experiencing rapid biodiversity loss resulting from invasive species, habitat destruction and the effects of climate change.

For more on this research, read An Ancient Reptile in Peril: The Curious Genome of the Tuatara.

Reference: “The tuatara genome reveals ancient features of amniote evolution” by Neil J. Gemmell, Kim Rutherford, Stefan Prost, Marc Tollis, David Winter, J. Robert Macey, David L. Adelson, Alexander Suh, Terry Bertozzi, José H. Grau, Chris Organ, Paul P. Gardner, Matthieu Muffato, Mateus Patricio, Konstantinos Billis, Fergal J. Martin, Paul Flicek, Bent Petersen, Lin Kang, Pawel Michalak, Thomas R. Buckley, Melissa Wilson, Yuanyuan Cheng, Hilary Miller, Ryan K. Schott, Melissa D. Jordan, Richard D. Newcomb, José Ignacio Arroyo, Nicole Valenzuela, Tim A. Hore, Jaime Renart, Valentina Peona, Claire R. Peart, Vera M. Warmuth, Lu Zeng, R. Daniel Kortschak, Joy M. Raison, Valeria Velásquez Zapata, Zhiqiang Wu, Didac Santesmasses, Marco Mariotti, Roderic Guigó, Shawn M. Rupp, Victoria G. Twort, Nicolas Dussex, Helen Taylor, Hideaki Abe, Donna M. Bond, James M. Paterson, Daniel G. Mulcahy, Vanessa L. Gonzalez, Charles G. Barbieri, Dustin P. DeMeo, Stephan Pabinger, Tracey Van Stijn, Shannon Clarke, Oliver Ryder, Scott V. Edwards, Steven L. Salzberg, Lindsay Anderson, Nicola Nelson, Clive Stone and Ngatiwai Trust Board, 5 August 2020, Nature.
DOI: 10.1038/s41586-020-2561-9

Study co-author Clive Stone with the Ngatiwai Trust Board, Whangarei, New Zealand, said, “I think it is important we acknowledge some of the key Ngatiwai people that made this project possible — Nga Rangatira, Houpeke Piripi, Te Warihi Hetaraka and Hori Parata who guided us, informed us and inspired us to complete this journey.”

Wilson is also joined by co-author Shawn Rupp, a bioinformatics researcher in the Biodesign Center for Biocomputing, Security and Society and Marc Tollis, formerly with the Biodesign Institute, now a researcher at Northern Arizona University.





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