Natural variation and population genomics
The C. briggsae diversity survey paper is out in MBE, and the hyper-divergence story has changed. The preprint covered in 6 August digest has been published, retitled, ‘Population structure and punctuated genomic hyper-diversity in Caenorhabditis briggsae‘. Moya et al. compared whole-genome sequence from 1,972 wild strains, placed them into 713 isotypes, and catalogued over six million single-nucleotide and insertion-deletion variants. Hyper-divergent regions cover about 6% of an individual genome on average yet carry 31% of its SNVs. These regions are enriched for genes involved in environmental sensing and pathogen response.
Some change from the preprint version are worth mentioning. Using C. nigoni inbred lines as an outgroup, the authors find no detectable excess of alleles shared with C. nigoni inside HDRs relative to the genome as a whole. So, the hyper-divergent haplotypes do not predate speciation. Instead, these appear to have arisen at or near the split of the most diverged C. briggsae relatedness groups, and to have been retained by balancing selection acting on isolated groups, or by cross-breeding between them.
The largest regional isotype, NIC174, comprises 261 strains sampled across Europe. Assuming a minimum of ten generations per year, the authors estimate it diverged less than 100 years ago. This represents a single genome-wide haplotype spread by recent human activity, more extensive than the chromosome-scale sweeps known from European C. elegans isolates.
Moya et al. (2026) Molecular Biology and Evolution, Aug 12 (advance publication)
C. tropicalis relatedness actually tracks geography. The Wang et al. paper that was covered in August 3rd digest is now published as well. Authors collected 785 wild strains and resolved 622 isotypes. Unlike C. elegans and C. briggsae, C. tropicalis relatedness shows substantial association with geography, with no transcontinental selective sweeps and no broadly sampled isotypes. Hawaiian and Taiwanese populations carry more variation than Caribbean or American ones. HDRs occupy under 6% of the reference genome but hold 73% of all variant sites on average.
Wang et al. (2026), GENETICS iyag196
Genome evolution
Programmed DNA elimination (PDE) was present in the ancestor of Caenorhabditis, and most of the genus subsequently lost it. Stevens et al., a collaboration between Blaxter group (Wellcome Sanger Institute) and Sugimoto (Tohoku University) and Kikuchi (University of Tokyo) groups, sequenced 22 Caenorhabditis species. Nineteen gave the expected six chromosomes. Three early diverging species did not: C. auriculariae, C. monodelphis and C. parvicauda showed apparent haploid somatic counts of 15, 13 and 8. Germline assemblies for all three recovered six chromosomes homologous to the C. elegans set, confirming that the extra somatic pieces are products of precise, telomere-healed elimination during early embryogenesis.
The gene content analysis revealed many genes were eliminated in the three species: 1.2%, 0.5% and 0.7%, respectively; and most sit in multiple copies. The majority have no C. elegans counterpart at all. 80%, 65% and 69% of eliminated genes fall in orthogroups with no C. elegans representative. The comparative conclusion is that PDE is ancestral to the genus and was lost early, on the lineage leading to the Elegans group where C. briggsae and C. elegans both sit with the standard six somatic chromosomes.
Stevens et al. (2026), bioRxiv 2025.10.23.681605
Review
A synthesis of the three independent routes to self-fertility. Ellis and Pilgrim labs have written a review drawing together how hermaphroditism arose separately in C. elegans, C. briggsae and C. tropicalis, concentrating on the changes to sex determination in germ cells and on sperm activation.
Bobinski et al. (2026) Biology, MDPI press 15:876
Compiled from PubMed, bioRxiv, and other online sources. Corrections and additions are welcome.