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Peer-reviewedCC BY 4.0G3: Genes, Genomes, Genetics

The crabeater seal reference genome reveals hallmarks of persistently large effective population size and sustained population expansion in the World’s most abundant pinniped

  • Beril Yıldız1,2
  • Thomas Gelatt3
  • Luis A Hückstädt4,5,6
  • Daniel P Costa4,5
  • Michael Tift7
  • Jay Rotella8
  • Elizabeth Flesch8
  • Kaitlin Macdonald8
  • Nancy Chen9
  • Robert Garrott8
  • Mike E Goebel10,11
  • Jaume Forcada12
3 more authors
  • Thorsten Wachtmeister13
  • David L J Vendrami1,2,14
  • Joseph I Hoffman1,2,12,14
14 affiliations
  1. 1Department of Evolutionary Population Genetics, Faculty of Biology, Bielefeld University , 33501 Bielefeld ,
  2. 2Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University , 33615 Bielefeld ,
  3. 3Alaska Fisheries Science Center, National Oceanic and Atmospheric Administration , Seattle, WA ,
  4. 4Institute of Marine Science, University of California Santa Cruz , Santa Cruz, California ,
  5. 5Centre for Ecology and Conservation, College of Life and Environmental Science, University of Exeter , Penryn, Cornwall ,
  6. 6Sharjah Marine Science Research Centre, University of Khorfakkan , UAE
  7. 7Department of Biology and Marine Biology, University of North Carolina Wilmington , Wilmington, North Carolina ,
  8. 8Department of Ecology, Montana State University , P.O. Box 173460, Bozeman, MT 59717 ,
  9. 9Department of Ecology and Evolutionary Biology, University of California , Los Angeles, California ,
  10. 10Antarctic Ecosystem Research Division, Southwest Fisheries Science Center , NOAA Fisheries, La Jolla, California ,
  11. 11Institute of Marine Sciences, University of California Santa Cruz , Santa Cruz, California ,
  12. 12British Antarctic Survery, High Cross , Madingley Road, Cambridge CB3 OET ,
  13. 13Genomics & Transcriptomics Laboratory, Biologisch-Medizinisches Forschungszentrum, and West German Genome Center, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1 , 40225, Düsseldorf ,
  14. 14Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster , Bielefeld ,
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Abstract

Population genetic theory predicts that a species’ demographic history shapes patterns of genome-wide variation. However, conservation genomic studies have disproportionately focused on small or declining species, where low genetic diversity and inbreeding are major concerns, while highly abundant species have attracted comparatively less attention. Here, we investigate the crabeater seal (Lobodon carcinophaga) which, despite being one of the most numerous large mammals on Earth, remains largely uncharacterised in terms of its genomic diversity and demographic history. We assembled a high-quality crabeater seal reference genome from a combination of Illumina and PacBio HiFi reads, generating a 2.44 Gb assembly spanning 138 scaffolds with high completeness. To evaluate genomic diversity in a comparative context, we whole-genome resequenced 20 crabeater seals alongside 20 individuals each of three Antarctic phocids spanning a population size gradient: the Weddell seal (Leptopnychotes weddellii), leopard seal (Hydrurga leptonyx) and southern elephant seal (Mirounga leonina). Crabeater seals carried 61.5 million SNPs compared to 12–16 million in the other species and exhibited markedly higher nucleotide diversity and negligible genomic inbreeding. We observed an excess of rare alleles, with nearly half of all variants segregating at frequencies below 5%. Demographic reconstruction revealed persistently large effective population sizes over the past million years and sustained population expansion, paralleling inferred increases in Antarctic krill associated with sea-ice expansion during the late Pleistocene. This study provides a new genomic resource and sheds new light on the evolutionary dynamics of the world’s most abundant pinniped.

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Cite

BibTeXRIS
BibTeX
@article{yıldız2026crabeater,
  title = {{The crabeater seal reference genome reveals hallmarks of persistently large effective population size and sustained population expansion in the World’s most abundant pinniped}},
  author = {Beril Yıldız and Thomas Gelatt and Luis A Hückstädt and Daniel P Costa and Michael Tift and Jay Rotella and Elizabeth Flesch and Kaitlin Macdonald and Nancy Chen and Robert Garrott and Mike E Goebel and Jaume Forcada and Thorsten Wachtmeister and David L J Vendrami and Joseph I Hoffman},
  journal = {G3: Genes, Genomes, Genetics},
  year = {2026},
  month = oct,
  doi = {10.1093/g3journal/jkag294},
  url = {https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkag294/9005792},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - The crabeater seal reference genome reveals hallmarks of persistently large effective population size and sustained population expansion in the World’s most abundant pinniped
AU  - Beril Yıldız
AU  - Thomas Gelatt
AU  - Luis A Hückstädt
AU  - Daniel P Costa
AU  - Michael Tift
AU  - Jay Rotella
AU  - Elizabeth Flesch
AU  - Kaitlin Macdonald
AU  - Nancy Chen
AU  - Robert Garrott
AU  - Mike E Goebel
AU  - Jaume Forcada
AU  - Thorsten Wachtmeister
AU  - David L J Vendrami
AU  - Joseph I Hoffman
PY  - 2026
DA  - 2026/10/31
JO  - G3: Genes, Genomes, Genetics
DO  - 10.1093/g3journal/jkag294
UR  - https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkag294/9005792
AB  - Population genetic theory predicts that a species’ demographic history shapes patterns of genome-wide variation. However, conservation genomic studies have disproportionately focused on small or declining species, where low genetic diversity and inbreeding are major concerns, while highly abundant species have attracted comparatively less attention. Here, we investigate the crabeater seal (Lobodon carcinophaga) which, despite being one of the most numerous large mammals on Earth, remains largely uncharacterised in terms of its genomic diversity and demographic history. We assembled a high-quality crabeater seal reference genome from a combination of Illumina and PacBio HiFi reads, generating a 2.44 Gb assembly spanning 138 scaffolds with high completeness. To evaluate genomic diversity in a comparative context, we whole-genome resequenced 20 crabeater seals alongside 20 individuals each of three Antarctic phocids spanning a population size gradient: the Weddell seal (Leptopnychotes weddellii), leopard seal (Hydrurga leptonyx) and southern elephant seal (Mirounga leonina). Crabeater seals carried 61.5 million SNPs compared to 12–16 million in the other species and exhibited markedly higher nucleotide diversity and negligible genomic inbreeding. We observed an excess of rare alleles, with nearly half of all variants segregating at frequencies below 5%. Demographic reconstruction revealed persistently large effective population sizes over the past million years and sustained population expansion, paralleling inferred increases in Antarctic krill associated with sea-ice expansion during the late Pleistocene. This study provides a new genomic resource and sheds new light on the evolutionary dynamics of the world’s most abundant pinniped.
SN  - 2160-1836
ER  -