1
|
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.
Collapse
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
| |
Collapse
|
2
|
Shackleton JD, Follows MJ, Thomas PJ, Omta AW. The Mid-Pleistocene Transition: a delayed response to an increasing positive feedback? CLIMATE DYNAMICS 2022; 60:4083-4098. [PMID: 37292246 PMCID: PMC10244291 DOI: 10.1007/s00382-022-06544-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 10/14/2022] [Indexed: 06/10/2023]
Abstract
Glacial-interglacial cycles constitute large natural variations in Earth's climate. The Mid-Pleistocene Transition (MPT) marks a shift of the dominant periodicity of these climate cycles from ∼ 40 to ∼ 100 kyr. Recently, it has been suggested that this shift resulted from a gradual increase in the internal period (or equivalently, a decrease in the natural frequency) of the system. As a result, the system would then have locked to ever higher multiples of the external forcing period. We find that the internal period is sensitive to the strength of positive feedbacks in the climate system. Using a carbon cycle model in which feedbacks between calcifier populations and ocean alkalinity mediate atmospheric CO2 , we simulate stepwise periodicity changes similar to the MPT through such a mechanism. Due to the internal dynamics of the system, the periodicity shift occurs up to millions of years after the change in the feedback strength is imposed. This suggests that the cause for the MPT may have occurred a significant time before the observed periodicity shift.
Collapse
Affiliation(s)
- J. D. Shackleton
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - M. J. Follows
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - P. J. Thomas
- Department of Mathematics, Applied Mathematics and Statistics, Case Western Reserve University, Cleveland, OH 44106 USA
| | - A. W. Omta
- Department of Earth, Environmental, and Planetary Sciences, Case Western Reserve University, Cleveland, OH 44106 USA
| |
Collapse
|
3
|
Thomas NC, Bradbury HJ, Hodell DA. Changes in North Atlantic deep-water oxygenation across the Middle Pleistocene Transition. Science 2022; 377:654-659. [PMID: 35926027 DOI: 10.1126/science.abj7761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The oxygen concentrations of oceanic deep-water and atmospheric carbon dioxide (pCO2) are intrinsically linked through organic carbon remineralization and storage as dissolved inorganic carbon in the deep sea. We present a high-resolution reconstruction of relative changes in oxygen concentration in the deep North Atlantic for the past 1.5 million years using the carbon isotope gradient between epifaunal and infaunal benthic foraminifera species as a proxy for paleo-oxygen. We report a significant (>40 micromole per kilogram) reduction in glacial Atlantic deep-water oxygenation at ~960 thousand to 900 thousand years ago that coincided with increased continental ice volume and a major change in ocean thermohaline circulation. Paleo-oxygen results support a scenario of decreasing deep-water oxygen concentrations, increased respired carbon storage, and a reduction in glacial pCO2 across the Middle Pleistocene Transition.
Collapse
Affiliation(s)
- Nicola C Thomas
- Department of Earth Science, University of Cambridge, Cambridge, UK
| | | | - David A Hodell
- Department of Earth Science, University of Cambridge, Cambridge, UK
| |
Collapse
|