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   PID: hpt/lnx 1.9.0-cur 2019-01-08   
   TID: hpt/lnx 1.9.0-cur 2019-01-08   
    Surprises in sea turtle genes could help them adapt to a rapidly   
   changing world    
      
     Date:   
         February 7, 2023   
     Source:   
         University of Massachusetts Amherst   
     Summary:   
         Around 100 million years ago, a group of land-dwelling turtles   
         took to the oceans, eventually evolving into the sea turtles that   
         we know today.   
      
         However, the genetic foundations that have enabled them to thrive   
         in oceans throughout the world have remained largely unknown.   
      
      
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   FULL STORY   
   ==========================================================================   
   Around 100 million years ago, a group of land-dwelling turtles took   
   to the oceans, eventually evolving into the sea turtles that we know   
   today. However, the genetic foundations that have enabled them to   
   thrive in oceans throughout the world have remained largely unknown. In   
   research recently published in the Proceedings of the National Academy of   
   Sciences, an international team of 48 researchers led by the University   
   of Massachusetts Amherst in collaboration with the Leibniz Institute for   
   Zoo and Wildlife Research and the Vertebrate Genome Project revealed an   
   incredibly detailed genetic map of two species - - green and leatherback   
   turtles -- which is packed with surprises that might hold the key to   
   their survival in a rapidly changing world.   
      
      
   ==========================================================================   
   A single species' genome contains the genetic set of instructions used   
   to build that species, and sequencing any species' genome is an enormous   
   amount of work.   
      
   This is akin to translating an entire library into a language   
   that scientists can read and has only been possible in the last few   
   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 researcher in environmental   
   conservation at UMass Amherst and the lead author of the new research,   
   "these pieces of genetic information weren't precisely mapped out. It   
   was as if you walked into a library and found 100,000 pages lying   
   on the floor."  To more precisely catalogue the turtles' genomes,   
   the international team turned to new technologies including long read   
   sequencing -- a technique recently named 2022 Method of the Year by   
   the journal Nature. This has made it possible to sequence genomes from   
   virtually any living species and to do so with far more accuracy than was   
   previously possible. Sequencing of the turtles' genomes was performed   
   both at Rockefeller University, in the Vertebrate Genome Laboratory   
   (VGL), led by Erich Jarvis, who chairs the VGP, and Olivier Fedrigo who   
   is director of the VGL, and at the Max Planck Institute of Molecular   
   Cell Biology and Genetics by Eugene Myers -- all coauthors on the new   
   study. "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 Bentley and his co-authors had correctly organized and annotated   
   the genetic data, they started finding surprises. 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 those differences that make them unique,"   
   says Lisa Komoroske, professor of environmental conservation at UMass   
   and one of the paper's two senior authors. And it's those differences   
   that may hold the key to each species' long-term survival, especially   
   considering that populations of both greens and leatherbacks have seen   
   precipitous declines due to human activity.   
      
   It turns out that green turtles have evolved more genes dedicated   
   to immunity, suggesting an immune system that is better prepared for   
   new pathogens, as well as more olfactory receptors -- they have better   
   senses of smell. The leatherback genome also shows that they lower genetic   
   diversity and have historically 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 conservation biologists   
   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 Bentley and Komoroske spent in the turtles'   
   genomes, the more it became clear that much of the genetic differences   
   between the two species is to be found, not on the macrochromosomes,   
   but on what was once considered to be "genetic junk": microchromosomes,   
   or small genetic bits that seem not to exist in mammals but are   
   characteristic of avian and reptilian genomes. "We found most of   
   the divergences between the green and the leatherbacks on these   
   microchromosomes," says Camila Mazzoni, a researcher at the Leibniz   
   Institute for Zoo and Wildlife Research and the study's other senior   
   author, "and our work feeds into the growing scholarship 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 organizations like   
   the Vertebrate Genome Project and NOAA Fisheries' 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, Max Planck   
   Institute of Molecular Cell Biology and Genetics, National Institutes   
   of Health, Howard Hughes Medical Institute, Vertebrate Genomes Project,   
   Sanger Institute, Sa~o Paolo Research Foundation, German Federal Ministry   
   of Education and Research, Generalitat de Catalunya, la Caixa Foundation,   
   Vienna Science and Technology Fund, City of Vienna, Welsh Government   
   Se^r Cymru II, European Union's Horizon 2020 research and innovation   
   program under the Marie Skłodowska-Curie grant, the Florida Sea   
   Turtle Grants Program, and individual international donors.   
      
       * RELATED_TOPICS   
             o Plants_&_Animals   
                   # Evolutionary_Biology # Biology # Endangered_Animals   
             o Earth_&_Climate   
                   # Environmental_Policy # Environmental_Awareness #   
                   Sustainability   
             o Fossils_&_Ruins   
                   # Evolution # Origin_of_Life # Early_Humans   
       * RELATED_TERMS   
             o Sea_turtle o Turtle o Snapping_turtle o Ocean o Dinosaur o   
             Antarctic_ice_sheet o Frog_zoology o Tortoise   
      
   ==========================================================================   
   Story Source: Materials provided by   
   University_of_Massachusetts_Amherst. Note: Content may be edited for   
   style and length.   
      
      
   ==========================================================================   
   Journal Reference:   
      1. Blair P. Bentley, Toma's Carrasco-Valenzuela, Elisa K. S. Ramos,   
         Harvinder Pawar, Larissa Souza Arantes, Alana Alexander, Shreya M.   
      
         Banerjee, Patrick Masterson, Martin Kuhlwilm, Martin Pippel,   
         Jacquelyn Mountcastle, Bettina Haase, Marcela Uliano-Silva, Giulio   
         Formenti, Kerstin Howe, William Chow, Alan Tracey, Ying Sims,   
         Sarah Pelan, Jonathan Wood, Kelsey Yetsko, Justin R. Perrault,   
         Kelly Stewart, Scott R. Benson, Yaniv Levy, Erica V. Todd,   
         H. Bradley Shaffer, Peter Scott, Brian T.   
      
         Henen, Robert W. Murphy, David W. Mohr, Alan F. Scott, David   
         J. Duffy, Neil J. Gemmell, Alexander Suh, Sylke Winkler, Franc,oise   
         Thibaud-Nissen, Mariana F. Nery, Tomas Marques-Bonet, Agostinho   
         Antunes, Yaron Tikochinski, Peter H. Dutton, Olivier Fedrigo,   
         Eugene W. Myers, Erich D.   
      
         Jarvis, Camila J. Mazzoni, Lisa M. Komoroske. Divergent sensory and   
         immune gene evolution in sea turtles with contrasting demographic   
         and life histories. Proceedings of the National Academy of Sciences,   
         2023; 120 (7) DOI: 10.1073/pnas.2201076120   
   ==========================================================================   
      
   Link to news story:   
   https://www.sciencedaily.com/releases/2023/02/230207161248.htm   
      
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