Scientists unveil the highest quality map of sea turtles’ genomes – their future may lie in their evolutionary history
In a paper recently published in the scientific journal “Proceedings of the National Academy of Sciences”, an international team of scientists revealed an incredibly detailed genetic map of two species – green and leatherback sea turtles. This will, for the first time, elucidate the genetic foundations that have enabled the once land-dwelling turtles to thrive in oceans throughout the world. Around 100 million years ago, their ancestors turned to the oceans, eventually evolving into the sea turtles that we know today. Knowing the genetic background of this remarkable adaptation may prove crucial for their conservation in current times of rapid environmental change.
The mapping of the genomes of the green sea turtle (Chelonia mydas) and the leatherback sea turtle (Dermochelys coriacea) is the result of a collaborative, international effort led by the Leibniz Institute for Zoo and Wildlife Research (Leibniz-IZW) and the University of Massachusetts Amherst (UMass) in collaboration with the Vertebrate Genomes Project. “We have assembled two of the most complete reptile genomes up until now, representing two ancient families of sea turtles”, says Camila Mazzoni, one of the two senior authors and group leader of Evolutionary and Conservation Genomics at the Leibniz-IZW and the Berlin Center for Genomics in Biodiversity Research (BeGenDiv).
Sequencing any species genome is an enormous amount of work, akin to translating that entire library into a language that scientists can read, and has only been possible in the last two decades. For green sea turtles, a draft genome, including approximately 100,000 pieces of genetic information, has been available since 2013, “but” says Blair Bentley, a postdoctoral scientist at the Department of Environmental Conservation at UMass Amherst and the lead author of the new paper, “these 100,000 pieces of genetic information weren’t precisely mapped out. It was as if you walked into a library and found 100,000 books lying on the floor.”
To more precisely catalogue the turtles’ genomes, the international team turned to new technologies including Pacbio long read sequencing – an innovation recently named 2022 Method of the Year (https://www.nature.com/articles/s41592-022-01759-x). This has made it possible to sequence genomes from virtually any living species, and to do so with far more accuracy than previously possible. Sequencing of the turtles’ genomes was performed at Rockefeller University in the Vertebrate Genome Laboratory (VGL), led by Erich Jarvis and Olivier Fedrigo, and at the Max Planck Institute of Molecular Cell Biology and Genetics led by Eugene Myers, all co-authors on the new publication. “These advances allowed us to do the equivalent of shelving everything according to the Dewey Decimal System so that we can begin to understand how everything fits together”, says Bentley.
Once the genomes were complete, several surprises were unveiled by the combined efforts of the research groups of Mazzoni and Lisa Komoroske, Professor of Environmental Conservation at UMass and the paper’s other senior author. The first is that, though greens and leatherbacks diverged from a common ancestor about 60 million years ago, their genomes are remarkably similar. Similar, but not the same. “It’s these differences that make them unique,” says Komoroske. And it is these differences that may hold the key to each species’ survival, especially considering that populations of both greens and leatherbacks have seen recent precipitous declines because of human activity.
It turns out that green turtles have evolved to have more genes dedicated to immunity, suggesting an immune system that is better prepared for new pathogens, as well as more olfactory receptors – they have a better sense of smell. The leatherback genome also shows that historically they have had lower population levels. “This is both a blessing and a curse,” says Komoroske, “because it means that, while leatherbacks are a resilient species, there isn’t much genetic diversity for them to evolve to meet the challenges of their rapidly changing environment.” Insights such as these will help conservationists make more informed decisions about how best to protect these animals as they face the challenges of adapting to our rapidly changing planet.
Furthermore, the more time Mazzoni and Komoroske research groups and collaborators spent on the turtle genomes, the more it became clear that much of the genetic differences between the two species is not found on the large chromosomes, which comprise more than 80% of the sea turtle genomes, but on the microchromosomes, or small genetic bits that do not to exist in mammals but are characteristic of avian and reptilian genomes. “We found most of the divergences between the green and the leatherback sea turtle on these microchromosomes,” says Mazzoni. “Our work feeds into the growing scholarly knowledge on the importance of microchromosomes in vertebrate evolution.”
“The only way we could do this work at all was through an incredible collaborative network that brought scientists from different fields together, with organisations such as the Vertebrate Genomes Project, the Israeli Sea Turtle Rescue Center and the NOAA Southwest Fisheries Science Center, supported by funders from around the world,” says Komoroske. Indeed, the research was supported by the National Science Foundation, National Oceanic and Atmospheric Administration, National Research Council, National Institutes of Health, the Vertebrate Genomes Project, the Max Planck Institute of Molecular Cell Biology and Genetics, CONICYT-DAAD, the Sanger Institute, the São Paulo Research Foundation, the German Federal Ministry of Education and Research, Generalitat de Catalunya, la Caixa Foundation, Vienna Science and Technology Fund, City of Vienna, Welsh Government Sêr Cymru II, European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant, the Florida Sea Turtle Grants Program, and individual international donors.
Bentley BP, Carrasco-Valenzuela T, Ramos EKS, Pawar H, Arantes LS, Alexander A, Banerjee SM, Masterson P, Kuhlwilm M, Pippel M, Mountcastle J, Haase B, Uliano-Silva M, Formenti G, Howe K, Chow W, Tracey A, Sims Y, Pelan S, Wood J, Kelsey Yetsko, Perrault JR, Stewart K, Benson SR, Levy T, Todd EV, Shaffer HB, Scott P, Henen BT, Murphy RW, Mohr DW, Scott AF, Duffy DJ, Gemmell NJ, Suh A, Winkler S, Thibaud-Nissen F, Nery MF, Marques-Bonet T, Antunes A, Tikochinski Y, Dutton PH, Fedrigo O, Myers EW, Jarvis ED, Mazzoni CJ, Komoroske LM (2023): Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories. PNAS 120 (7) e2201076120. DOI: 10.1073/pnas.2201076120
Leibniz Institute for Zoo and Wildlife Research (Leibniz-IZW)
in the Forschungsverbund Berlin e.V.
Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
Research Group Leader in Evolutionary and Conservation Genomics at the Department of Evolutionary Genetics at Leibniz-IZW
Core scientist at Berlin Center for Genomics in Biodiversity Research (BeGenDiv)
phone: +49(0)30 5168315 and +49(0)30 83859961
phone: +49(0)30 5168121
University of Massachusetts (UMass) Amherst
Department of Environmental Conservation
160 Holdsworth Way, Amherst, MA 01003-9285
Assistant Professor, Environmental Conservation