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Sendell-Price AT, Tulenko FJ, Pettersson M, Kang D, Montandon M, Winkler S, Kulb K, Naylor GP, Phillippy A, Fedrigo O, Mountcastle J, Balacco JR, Dutra A, Dale RE, Haase B, Jarvis ED, Myers G, Burgess SM, Currie PD, Andersson L, Schartl M. Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks. Nat Commun 2023; 14:6628. [PMID: 37857613 PMCID: PMC10587355 DOI: 10.1038/s41467-023-42238-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 10/03/2023] [Indexed: 10/21/2023] Open
Abstract
Sharks occupy diverse ecological niches and play critical roles in marine ecosystems, often acting as apex predators. They are considered a slow-evolving lineage and have been suggested to exhibit exceptionally low cancer rates. These two features could be explained by a low nuclear mutation rate. Here, we provide a direct estimate of the nuclear mutation rate in the epaulette shark (Hemiscyllium ocellatum). We generate a high-quality reference genome, and resequence the whole genomes of parents and nine offspring to detect de novo mutations. Using stringent criteria, we estimate a mutation rate of 7×10-10 per base pair, per generation. This represents one of the lowest directly estimated mutation rates for any vertebrate clade, indicating that this basal vertebrate group is indeed a slowly evolving lineage whose ability to restore genetic diversity following a sustained population bottleneck may be hampered by a low mutation rate.
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Affiliation(s)
- Ashley T Sendell-Price
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE75123, Uppsala, Sweden
- Bioinformatics Research Technology Platform, University of Warwick, Coventry, UK
| | - Frank J Tulenko
- Australian Regenerative Medicine Institute, Monash University, Victoria, 3800, Australia
| | - Mats Pettersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE75123, Uppsala, Sweden
| | - Du Kang
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, 78666, USA
| | - Margo Montandon
- Australian Regenerative Medicine Institute, Monash University, Victoria, 3800, Australia
| | - Sylke Winkler
- Max-Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
| | - Kathleen Kulb
- Max-Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
| | - Gavin P Naylor
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Adam Phillippy
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health Bethesda, Bethesda, MD, 20892, USA
| | - Olivier Fedrigo
- Vertebrate Genome Laboratory, Rockefeller University, New York, NY, 10065, USA
| | - Jacquelyn Mountcastle
- Research Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA
| | - Jennifer R Balacco
- Research Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA
| | - Amalia Dutra
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health Bethesda, Bethesda, MD, 20892, USA
| | - Rebecca E Dale
- Australian Regenerative Medicine Institute, Monash University, Victoria, 3800, Australia
| | - Bettina Haase
- Vertebrate Genome Laboratory, Rockefeller University, New York, NY, 10065, USA
| | - Erich D Jarvis
- Vertebrate Genome Laboratory, Rockefeller University, New York, NY, 10065, USA
| | - Gene Myers
- Max-Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
- Center of Systems Biology Dresden, 01307, Dresden, Germany
| | - Shawn M Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health Bethesda, Bethesda, MD, 20892, USA.
| | - Peter D Currie
- Australian Regenerative Medicine Institute, Monash University, Victoria, 3800, Australia.
- EMBL Australia, Victorian Node, Monash University, Clayton, Victoria, 3800, Australia.
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE75123, Uppsala, Sweden.
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX77483, USA.
| | - Manfred Schartl
- Developmental Biochemistry, Theodor-Boveri Institute, Biocenter, University of Würzburg, 97074, Würzburg, Germany.
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