Mol Biol Evol. 2026 Aug 12:msag202. doi: 10.1093/molbev/msag202
Population structure and punctuated genomic hyper-diversity in Caenorhabditis briggsae
Nicolas D Moya1, Bowen Wang1, Robyn E Tanny1, Michael E G Sauria1, Lance M O’Connor1, Ayeh Khorshidian1, Ryan McKeown2, Charlie Gosse3, Clayton M Dilks2, Timothy A Crombie2,4, Gaotian Zhang2,3, Emha Rais5, Lise Frézal3, Viet Dai Dang6,7, Elkana Haryoso5, Mia P Devi5, Clotilde Gimond8, Daniel E Cook2, Jung-Chen Hsu6, Amanda O Shaver1, Stefan Zdraljevic2, Aurélien Richaud3, Tongshu Wen9, Aatira Mehraj10, Sharanya H10, Karthick Raja Arulprakasam10, Emily J Koury2, Nicole M Roberto2, Etta S Schaye1, Varsha Singh10,11, Hagus Tarno5, Michael Ailion12, Annalise B Paaby13, Zhongying Zhao9, Asher D Cutter14, John Wang6, Matthew V Rockman15, Marie-Anne Félix3, Christian Braendle8, Erik C Andersen1
Affiliations
1Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA.
2Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA.
3Institut de Biologie de l’Ecole Normale Supérieure, CNRS, Inserm, Paris, 75005, France.
4Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL, 32901, USA.
5Department of Pests and Disease, Faculty of Agriculture, University of Brawijaya, JL Veteran Malang, Malang, East Java 65145, Indonesia.
6Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan.
7Southern Institute of Ecology, Institute of Applied Material Science, Vietnam Academy of Science and Technology, Ho Chi Minh, Vietnam.
8Université Côte d’Azur, CNRS, Inserm, IBV, Nice, 06108, France.
9Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China.
10Indian Institute of Science, Bengaluru, 2H88+R9, India.
11Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, Scotland, DD1 5EH, UK.
12Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.
13School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
14Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, M5S3B2, Canada.
15Department of Biology and Center for Genomics & Systems Biology, New York University, New York, NY, 10003, USA.
Abstract
Comparative genomics provides a powerful framework to uncover the molecular and evolutionary mechanisms that shape genetic diversity, revealing how shared or lineage-specific processes influence their evolutionary trajectories. The nematode Caenorhabditis briggsae is distributed world-wide and is a comparative model to Caenorhabditis elegans in the biology of development, cellular mechanisms, neurobiology, complex trait mappings, and evolution. Following massive collection efforts by the nematode research community, we present the isolation of over 1,900 wild strains and analyses of genome sequences that catalog over six million single-nucleotide and insertion-deletion variants. These resources provide a powerful means to interrogate the causal genetic bases of phenotypic variation. Additionally, we describe C. briggsae population structure and discover new, genetically distinct groups within this primarily self-fertilizing species, including groups of highly related strains sampled across entire continents. We leverage expansive genetic variation to decipher the effects of linkage and selection on the distribution of genetic diversity across the genome and across geographic regions. Within the species, we find genomic regions with extremely high levels of genetic variation similar to hyper-divergent regions found in C. elegans and other species. These regions harbor new genes and variation enriched for environmental sensing and pathogen responses. Based on comparisons to the outbreeding sister species Caenorhabditis nigoni, we conclude that long-term balancing selection has maintained substantial functional variation, likely associated with ecological variation, within C. briggsae since its divergence from an outbreeding ancestor. Overall, this massive strain resource enables future comparative genetics studies, including genome-wide association study contrasts between Caenorhabditis species.