Biology subjects

Eggers, V. K.

Publications and source records attributed to Eggers, V. K..

3 recordsLinked to original sources

bioRxiv2026

Re-inventing sex: A W chromosome and a path out of parthenogenesis for Bunonema nematodes

Sex chromosomes are deeply conserved in some organisms but remarkably labile in others. Here we describe the evolution of a novel sex chromosome in the nematode Bunonema JU3390, a species with an autosome-derived genomic segment currently functioning as a female-limited W chromosome. We propose this neo sex chromosome system evolved to escape lethal structural mutations accumulated during a period of parthenogenesis, demonstrating the role of evolutionary contingency in this rapid re-invention of sex.

evolutionary biology↗

bioRxiv2025

Outcrossing Complicates Mutation Purging by Trapping Single Nucleotide Polymorphisms in Structural Variant Mutations

Classical mutational theories centered on single nucleotide polymorphisms suggest that outcrossing enhances the purging of deleterious mutations by promoting recombination. However, larger structural variants, such as insertions, deletions, and inversions, can suppress recombination and create linkage blocks. Using experimental evolution and whole-genome long- and short-read sequencing, we characterized structural and nucleotide mutation landscapes in three Caenorhabditis elegans strains following repeated mutagen exposure and recovery. We found substantial strain-specific differences in structural variant accumulation and mutation retention. The strain with the highest outcrossing propensity exhibited the greatest structural variant burden and a higher fraction of single nucleotide polymorphisms within structural variant intervals. Consistent with this pattern, our population genetic simulations showed that structural variants can persist more readily under higher outcrossing rates. Together, these results indicate that structural variant architecture may influence mutation retention dynamics and highlight strain-specific constraints on purging following mutagenesis in C. elegans.

bioinformatics↗

bioRxiv2024

Regulatory logic and transposable element dynamics in nematode worm genomes

Genome sequencing has revealed a tremendous diversity of transposable elements (TEs) in eukaryotes but there is little understanding of the evolutionary processes responsible for TE diversity. Non-autonomous TEs have lost the machinery necessary for transposition and rely on closely related autonomous TEs for critical proteins. We studied two mathematical models of TE regulation, one assuming that both autonomous tranposons and their non-autonomous relatives operate under the same regulatory logic, competing for transposition resources, and one assuming that autonomous TEs self-attenuate transposition while non-autonomous transposons continually increase, parasitizing their autonomous relatives. We implemented these models in stochastic simulations and studied how TE regulatory relationships influence transposons and populations. We found that only outcrossing populations evolving with Parasitic TE regulation resulted in stable maintenance of TEs. We tested our model predictions in Caenorhabditis genomes by annotating TEs in two focal families, autonomous LINEs and their non-autonomous SINE relatives and the DNA transposon Mutator. We found broad variation in autonomous - non-autonomous relationships and rapid mutational decay in the sequences that allow non-autonomous TEs to transpose. Together, our results suggest that individual TE families evolve according to disparate regulatory rules that are relevant in the early, acute stages of TE invasion.

evolutionary biology↗