Genetics. 2026 Jul 28:iyag196. doi: 10.1093/genetics/iyag196
Global genomic diversity of the selfing nematode Caenorhabditis tropicalis correlates with geography
Bowen Wang1, Nicolas D Moya1, Robyn E Tanny1, Michael E G Sauria1, Lance M O’Connor1, Ayeh Khorshidian1, Ryan McKeown2, Lewis Stevens3, Claire Buchanan2, Timothy A Crombie2,4, Clayton Dilks2, Kathryn S Evans2, Daniel E Cook2, Gaotian Zhang2,5, Loraina A Stinson2, Nicole M Roberto2, Daehan Lee2,6, Stefan Zdraljevic2, Charlie Gosse5, Clotilde Gimond7, Mu-En Chen8,9,10, Viet Dai Dang11, John Wang12, Asher D Cutter13, Matthew V Rockman14, Marie-Anne Félix5, Christian Braendle7, Erik C Andersen1
Affiliations
1Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA.
2Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA.
3Tree of Life, Wellcome Sanger Institute, Hinxton, CB10 1RQ, UK.
4Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL, 32901, USA.
5Institut de Biologie de l’Ecole Normale Supérieure, CNRS, Inserm, Paris, 75005, France.
6Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
7Université Côte d’Azur, CNRS, Inserm, IBV, Nice, 06108, France.
8Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115201, Taiwan.
9Department of Life Science, National Taiwan Normal University, Taipei, 116059, Taiwan.
10Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan.
11Institute of Advanced Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
12Biodiversity Research Center , Academia Sinica, Taipei, 115201, Taiwan.
13Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, M5S3B2, Canada.
14Department of Biology and Center for Genomics & Systems Biology, New York University, New York, NY, 10003, USA.
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.