Chen, H.-y. | Search bioRxiv

bioRxiv2026

Transgenerational inheritance is variable across Caenorhabditis worms

Transgenerational epigenetic inheritance (TEI) allows organisms to express heritable responses to environmental stresses, and can potentially contribute to adaptive evolution. The microbivorous model organism Caenorhabditis elegans is perhaps the best example, as it can learn to avoid pathogenic Pseudomonas bacteria and transmit this learned avoidance to its offspring. However, the extent to which TEI is widespread in nature remains unclear, and therefore our understanding of the generality of this response is limited. To address this, we conducted the first comparative study of TEI across five Caenorhabditis nematode worm species (C. kamaaina, C. elegans, C. tropicalis, C. remanei and C. briggsae). These species differ in RNA interference competence and in the degree of sequence homology between Caenorhabditis worm genes and bacterial RNAs, two factors thought to influence epigenetic responses. We examined transgenerational avoidance of P. vranovensis, a pathogen that reduces fitness in all five species tested. In addition to C. elegans, we found that C. remanei also exhibited transgenerational avoidance of P. vranovensis, whereas neither learning nor inheritance was observed in the other three species. In addition, parental exposure to P. vranovensis also conferred a transgenerational survival benefit upon pathogen encounter in C. elegans, C. remanei and C. tropicalis. Our findings show that TEI of pathogen avoidance extends beyond C. elegans but is not a general response across Caenorhabditis species. This shows that TEI is a species-specific response and highlights the need to understand TEI alongside other responses to environmental variability.

evolutionary biology↗

bioRxiv2021

Mutationathon: towards standardization in estimates of pedigree-based germline mutation rates

In the past decade, several studies have estimated the human per-generation germline mutation rate using large pedigrees. More recently, estimates for various non-human species have been published. However, methodological differences among studies in detecting germline mutations and estimating mutation rates make direct comparisons difficult. Here, we describe the many different steps involved in estimating pedigree-based mutation rates, including sampling, sequencing, mapping, variant calling, filtering, and how to appropriately account for false-positive and false-negative rates. For each step, we review the different methods and parameter choices that have been used in the recent literature. Additionally, we present the results from a "Mutationathon", a competition organized among five research labs to compare germline mutation rate estimates for a single pedigree of rhesus macaques. We report almost a two-fold variation in the final estimated rate among groups using different post-alignment processing, calling, and filtering criteria and provide details into the sources of variation across studies. Though the difference among estimates is not statistically significant, this discrepancy emphasizes the need for standardized methods in mutation rate estimations and the difficulty in comparing rates from different studies. Finally, this work aims to provide guidelines for computational and statistical benchmarks for future studies interested in identifying germline mutations from pedigrees.

evolutionary biology↗