Global genomic diversity of the selfing nematode <i>Caenorhabditis tropicalis</i> correlates with geography

Self-fertilization reduces genetic diversity compared to outcrossing and hypothetically decreases the ability to adapt to diverse environments. Among Caenorhabditis nematodes, self-fertilization evolved three times independently in Caenorhabditis elegans, Caenorhabditis briggsae, and the more recently discovered Caenorhabditis tropicalis. To survey C. tropicalis genetic relatedness, the influence of geography and niche on species-wide variation, and the signatures of selection, we collected 785 wild strains, sequenced their genomes, and identified 622 distinct genotypes (isotypes). In contrast to C. elegans and C. briggsae, C. tropicalis relatedness shows substantial association with geography and no transcontinental selective sweeps or broadly sampled isotypes. Populations from the Hawaiian Islands or Taiwan harbor more genetic variation than populations from the Caribbean or Americas, suggesting a Pacific species origin similar to other members of the Elegans subclade. Punctuated genomic regions of extreme genetic variation pervade the genome. These hyper-divergent regions (HDRs) comprise less than 6% of the reference genome despite harboring 73% of all variant sites on average and are enriched for genes likely involved in environmental adaptation. HDRs represent a shared genomic feature of self-fertilizing Caenorhabditis nematodes despite their independent evolutionary origins and suggest a mechanism to explain worldwide distributions despite low species-wide levels of genetic variation.

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Publication Details

Journal
Genetics
Published
2026-07-28
DOI
https://doi.org/10.1093/genetics/iyag196
Primary Topic
Genetics, Aging, and Longevity in Model Organisms
Type
article
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article

Global genomic diversity of the selfing nematode Caenorhabditis tropicalis correlates with geography

Daehan Lee, Asher D. Cutter, Stefan Zdraljevic, Clotilde Gimond et al.
Genetics
Genetics, Aging, and Longevity in Model Organisms
article

Global genomic diversity of the selfing nematode Caenorhabditis tropicalis correlates with geography

Daehan Lee, Asher D. Cutter, Stefan Zdraljevic, Clotilde Gimond, Viet Dai Dang, Loraina A. Stinson, Kathryn S. Evans, Daniel E. Cook, Gaotian Zhang, Mu-En Chen, Matthew V. Rockman, Robyn E. Tanny, Timothy A. Crombie, Ayeh Khorshidian, Nicolas D. Moya, Erik C. Andersen, Nicole M. Roberto, Ryan McKeown, Charlie Gosse, Christian Braendle, Bowen Wang, John Wang, L O'Connor, Clayton Dilks, Lewis Stevens, Marie-Anne Félix, Michael E G Sauria, Claire Buchanan
article en

Abstract

Self-fertilization reduces genetic diversity compared to outcrossing and hypothetically decreases the ability to adapt to diverse environments. Among Caenorhabditis nematodes, self-fertilization evolved three times independently in Caenorhabditis elegans, Caenorhabditis briggsae, and the more recently discovered Caenorhabditis tropicalis. To survey C. tropicalis genetic relatedness, the influence of geography and niche on species-wide variation, and the signatures of selection, we collected 785 wild strains, sequenced their genomes, and identified 622 distinct genotypes (isotypes). In contrast to C. elegans and C. briggsae, C. tropicalis relatedness shows substantial association with geography and no transcontinental selective sweeps or broadly sampled isotypes. Populations from the Hawaiian Islands or Taiwan harbor more genetic variation than populations from the Caribbean or Americas, suggesting a Pacific species origin similar to other members of the Elegans subclade. Punctuated genomic regions of extreme genetic variation pervade the genome. These hyper-divergent regions (HDRs) comprise less than 6% of the reference genome despite harboring 73% of all variant sites on average and are enriched for genes likely involved in environmental adaptation. HDRs represent a shared genomic feature of self-fertilizing Caenorhabditis nematodes despite their independent evolutionary origins and suggest a mechanism to explain worldwide distributions despite low species-wide levels of genetic variation.

Genetics
Florida Institute of Technology (US), Northwestern University (US), Centre National de la Recherche Scientifique (FR), National Taiwan Normal University (TW), Johns Hopkins University (US), Inserm (FR), University of Toronto (CA), Johns Hopkins Medicine (US), Wellcome Sanger Institute (GB), Research Center for Applied Science, Academia Sinica (TW), Institute of Sociology, Academia Sinica (TW), Institut de Biologie Valrose (FR), Institut de Biologie de l'École Normale Supérieure (FR), Biodiversity Research Center, Academia Sinica (TW), New York Genome Center (US), Vietnam Academy of Science and Technology (VN), Academia Sinica (TW), Sungkyunkwan University (KR)
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Openalex Percentile: Top 13%
Genetics, Aging, and Longevity in Model Organisms
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