Population structure and punctuated genomic hyper-diversity in Caenorhabditis briggsae
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 leveraged 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.
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BibTeX
@article{moya2026population,
title = {{Population structure and punctuated genomic hyper-diversity in Caenorhabditis briggsae}},
author = {Nicolas Moya and Bowen Wang and Robyn Tanny and Michael Sauria and Lance O’connor and Ayeh Khorshidian and Ryan Mckeown and Charlie Gosse and Clayton Dilks and Timothy Crombie and Gaotian Zhang and Emha Rais and Lise Frézal and Viet Dai Dang and Elkana Haryoso and Mia Devi and Clotilde Gimond and Daniel Cook and Jung-Chen Hsu and Amanda Shaver and Stefan Zdraljevic and Aurélien Richaud and Tongshu Wen and Aatira Mehraj and Sharanya H and Karthick Raja Arulprakasam and Emily Koury and Nicole Roberto and Etta Schaye and Varsha Singh and Hagus Tarno and Michael Ailion and Annalise Paaby and Zhongying Zhao and Asher Cutter and John Wang and Matthew Rockman and Marie-Anne Félix and Christian Braendle and Erik Andersen},
journal = {Molecular Biology and Evolution},
year = {2026},
month = aug,
doi = {10.1093/molbev/msag202},
url = {https://hal.science/hal-05784281v1},
note = {CC BY-NC 4.0},
}
RIS
TY - JOUR
TI - Population structure and punctuated genomic hyper-diversity in Caenorhabditis briggsae
AU - Nicolas Moya
AU - Bowen Wang
AU - Robyn Tanny
AU - Michael Sauria
AU - Lance O’connor
AU - Ayeh Khorshidian
AU - Ryan Mckeown
AU - Charlie Gosse
AU - Clayton Dilks
AU - Timothy Crombie
AU - Gaotian Zhang
AU - Emha Rais
AU - Lise Frézal
AU - Viet Dai Dang
AU - Elkana Haryoso
AU - Mia Devi
AU - Clotilde Gimond
AU - Daniel Cook
AU - Jung-Chen Hsu
AU - Amanda Shaver
AU - Stefan Zdraljevic
AU - Aurélien Richaud
AU - Tongshu Wen
AU - Aatira Mehraj
AU - Sharanya H
AU - Karthick Raja Arulprakasam
AU - Emily Koury
AU - Nicole Roberto
AU - Etta Schaye
AU - Varsha Singh
AU - Hagus Tarno
AU - Michael Ailion
AU - Annalise Paaby
AU - Zhongying Zhao
AU - Asher Cutter
AU - John Wang
AU - Matthew Rockman
AU - Marie-Anne Félix
AU - Christian Braendle
AU - Erik Andersen
PY - 2026
DA - 2026/08/01
JO - Molecular Biology and Evolution
DO - 10.1093/molbev/msag202
UR - https://hal.science/hal-05784281v1
AB - 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 leveraged 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.
SN - 0737-4038
SN - 1537-1719
ER -