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Baker DN, Abueg L, Escalona M, Farquharson KA, Lanyon JM, Le Duc D, Schöneberg T, Absolon D, Sims Y, Fedrigo O, Jarvis ED, Belov K, Hogg CJ, Shapiro B. A chromosome-level genome assembly for the dugong (Dugong dugon). J Hered 2024; 115:212-220. [PMID: 38245832 PMCID: PMC10936554 DOI: 10.1093/jhered/esae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/16/2024] [Indexed: 01/22/2024] Open
Abstract
The dugong (Dugong dugon) is a marine mammal widely distributed throughout the Indo-Pacific and the Red Sea, with a Vulnerable conservation status, and little is known about many of the more peripheral populations, some of which are thought to be close to extinction. We present a de novo high-quality genome assembly for the dugong from an individual belonging to the well-monitored Moreton Bay population in Queensland, Australia. Our assembly uses long-read PacBio HiFi sequencing and Omni-C data following the Vertebrate Genome Project pipeline to reach chromosome-level contiguity (24 chromosome-level scaffolds; 3.16 Gbp) and high completeness (97.9% complete BUSCOs). We observed relatively high genome-wide heterozygosity, which likely reflects historical population abundance before the last interglacial period, approximately 125,000 yr ago. Demographic inference suggests that dugong populations began declining as sea levels fell after the last interglacial period, likely a result of population fragmentation and habitat loss due to the exposure of seagrass meadows. We find no evidence for ongoing recent inbreeding in this individual. However, runs of homozygosity indicate some past inbreeding. Our draft genome assembly will enable range-wide assessments of genetic diversity and adaptation, facilitate effective management of dugong populations, and allow comparative genomics analyses including with other sirenians, the oldest marine mammal lineage.
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Affiliation(s)
- Dorothy Nevé Baker
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Linelle Abueg
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Katherine A Farquharson
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, NSW, Australia
| | - Janet M Lanyon
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Diana Le Duc
- Institute of Human Genetics, University Medical Center Leipzig, Leipzig, Germany
| | - Torsten Schöneberg
- Medical Faculty, Rudolf Schönheimer Institute of Biochemistry, University of Leipzig, Leipzig, Germany
- School of Medicine, University of Global Health Equity, Kigali, Rwanda
| | - Dominic Absolon
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Ying Sims
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | | | - Erich D Jarvis
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, United States
- Howard Hughes Medical Institute, Chevy Chase, MD, United States
| | - Katherine Belov
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, NSW, Australia
| | - Carolyn J Hogg
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, NSW, Australia
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
- Howard Hughes Medical Institute, Chevy Chase, MD, United States
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Hautier L, Gomes Rodrigues H, Ferreira-Cardoso S, Emerling CA, Porcher ML, Asher RJ, Portela Miguez R, Delsuc F. From teeth to pad: tooth loss and development of keratinous structures in sirenians. Proc Biol Sci 2023; 290:20231932. [PMID: 38018114 PMCID: PMC10685118 DOI: 10.1098/rspb.2023.1932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/03/2023] [Indexed: 11/30/2023] Open
Abstract
Sirenians are a well-known example of morphological adaptation to a shallow-water grazing diet characterized by a modified feeding apparatus and orofacial morphology. Such adaptations were accompanied by an anterior tooth reduction associated with the development of keratinized pads, the evolution of which remains elusive. Among sirenians, the recently extinct Steller's sea cow represents a special case for being completely toothless. Here, we used μ-CT scans of sirenian crania to understand how motor-sensor systems associated with tooth innervation responded to innovations such as keratinized pads and continuous dental replacement. In addition, we surveyed nine genes associated with dental reduction for signatures of loss of function. Our results reveal how patterns of innervation changed with modifications of the dental formula, especially continuous replacement in manatees. Both our morphological and genomic data show that dental development was not completely lost in the edentulous Steller's sea cows. By tracing the phylogenetic history of tooth innervation, we illustrate the role of development in promoting the innervation of keratinized pads, similar to the secondary use of dental canals for innervating neomorphic keratinized structures in other tetrapod groups.
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Affiliation(s)
- Lionel Hautier
- Institut des Sciences de l’Évolution, Université Montpellier, CNRS, IRD, EPHE, Montpellier 34095, France
- Mammal Section, Life Sciences, Vertebrate Division, The Natural History Museum, London, UK
| | - Helder Gomes Rodrigues
- Centre de Recherche en Paléontologie—Paris (CR2P), UMR CNRS 7207, Muséum National d'Histoire Naturelle, Sorbonne Université, Paris, France
| | - Sérgio Ferreira-Cardoso
- Institut des Sciences de l’Évolution, Université Montpellier, CNRS, IRD, EPHE, Montpellier 34095, France
| | | | - Marie-Lou Porcher
- Institut des Sciences de l’Évolution, Université Montpellier, CNRS, IRD, EPHE, Montpellier 34095, France
| | - Robert J. Asher
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Roberto Portela Miguez
- Mammal Section, Life Sciences, Vertebrate Division, The Natural History Museum, London, UK
| | - Frédéric Delsuc
- Institut des Sciences de l’Évolution, Université Montpellier, CNRS, IRD, EPHE, Montpellier 34095, France
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Kersten O, Star B, Krabberød AK, Atmore LM, Tørresen OK, Anker-Nilssen T, Descamps S, Strøm H, Johansson US, Sweet PR, Jakobsen KS, Boessenkool S. Hybridization of Atlantic puffins in the Arctic coincides with 20th-century climate change. SCIENCE ADVANCES 2023; 9:eadh1407. [PMID: 37801495 PMCID: PMC10558128 DOI: 10.1126/sciadv.adh1407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 09/06/2023] [Indexed: 10/08/2023]
Abstract
The Arctic is experiencing the fastest rates of global warming, leading to shifts in the distribution of its biota and increasing the potential for hybridization. However, genomic evidence of recent hybridization events in the Arctic remains unexpectedly rare. Here, we use whole-genome sequencing of contemporary and 122-year-old historical specimens to investigate the origin of an Arctic hybrid population of Atlantic puffins (Fratercula arctica) on Bjørnøya, Norway. We show that the hybridization between the High Arctic, large-bodied subspecies F. a. naumanni and the temperate, smaller-sized subspecies F. a. arctica began as recently as six generations ago due to an unexpected southward range expansion of F. a. naumanni. Moreover, we find a significant temporal loss of genetic diversity across Arctic and temperate puffin populations. Our observations provide compelling genomic evidence of the impacts of recent distributional shifts and loss of diversity in Arctic communities during the 20th century.
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Affiliation(s)
- Oliver Kersten
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Anders K. Krabberød
- Section for Genetics and Evolutionary Biology (Evogene), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Lane M. Atmore
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Ole K. Tørresen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | | | | | - Hallvard Strøm
- Norwegian Polar Institute, Fram Centre, Langnes, Tromsø, Norway
| | | | - Paul R. Sweet
- American Museum of Natural History, New York, NY, USA
| | - Kjetill S. Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Sanne Boessenkool
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
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