Bernstein, M. R. | bioRxiv Science

bioRxiv2025

Variation in inbreeding depression within and among Caenorhabditis species

Outbreeding populations harbor large numbers of recessive deleterious alleles that reduce the fitness of inbred individuals, and this inbreeding depression potentially shapes the evolution of mating systems, acting as a counterweight to the inherent selective advantage of self-fertilization. The population biological factors that influence inbreeding depression are numerous and often difficult to disentangle. We investigated the utility of obligately-outcrossing (gonochoristic) Caenorhabditis nematodes as models for inbreeding depression. By systematically inbreeding lines from ten populations and tracking line extinction, we found that inbreeding depression is universal but highly variable among species and populations. Inbreeding depression was detected across the life cycle, from mating to embryo production to embryonic viability and larval growth, and reciprocal crosses implicated female-biased effects. In most cases, the surviving inbred lines have dramatically reduced fitness, but the variance among inbred lines is substantial and compatible with the idea that inbreeding depression need not be an obstacle to the evolution of selfing in these worms. Populations of some species, including Caenorhabditis becei, exhibited modest inbreeding depression and could be tractable laboratory models for gonochoristic Caenorhabditis.

evolutionary biology↗

bioRxiv2018

Tightly-linked antagonistic-effect loci underlie polygenic demographic variation in C. elegans

Recent work has provided strong empirical support for the classic polygenic model for trait variation. Population-based findings suggest that most regions of genome harbor variation affecting most traits. This view is hard to reconcile with the experience of researchers who define gene functions using mutagenesis, comparing mutants one at a time to the wild type. Here, we use the approach of experimental genetics to show that indeed, most genomic regions carry variants with detectable effects on complex traits. We used high-throughput phenotyping to characterize demography as a multivariate trait in growing populations of Caenorhabditis elegans sensitized by nickel stress. We show that demography under these conditions is genetically complex in a panel of recombinant inbred lines. We then focused on a 1.4-Mb region of the X chromosome. When we compared two near isogenic lines (NILs) that differ only at this region, they were phenotypically indistinguishable. When we used additional NILs to subdivide the region into fifteen intervals, each encompassing ~0.001 of the genome, we found that eleven of intervals have significant effects. These effects are often similar in magnitude to those of genome-wide significant QTLs mapped in the recombinant inbred lines but are antagonized by the effects of variants in adjacent intervals. Contrary to the expectation of small additive effects, our findings point to large-effect variants whose effects are masked by epistasis or linkage disequilibrium between alleles of opposing effect.

genetics↗