Genomic Gigantism is not Associated with Reduced Selection Efficiency in Neotropical Salamanders

Abstract

Genome size variation in eukaryotes has myriad effects on organismal biology from the genomic to whole-organism level. Large genome size may be associated with lower selection efficiency because lower effective population sizes allow fixation of deleterious mutations via genetic drift, increasing genome size and decreasing selection efficiency. Because of a hypothesized negative relationship between genome size and recombination rate per base pair, increased genome size could also increase the effect of linked selection in the genome, decreasing the efficiency with which natural selection can fix or remove mutations. We used a transcriptomic dataset of 15 and a subset of six Neotropical salamander species ranging in genome size from 12 to 87 pg to study the relationship between genome size and efficiency of selection. We estimated dN/dS of salamanders with small and large genomes and tested for relaxation of selection in the larger genomes. Contrary to our expectations, we did not find a significant relationship between genome size and selection efficiency or strong evidence for higher dN/dS values in species with larger genomes for either species set. We also found little evidence for relaxation of selection in species with larger genomes. A positive correlation between genome size and range size (a proxy of population size) in this group disagrees with predictions of stronger drift in species with larger genomes. Our results highlight the complex interactions between the many forces shaping genomic variation in organisms with genomic gigantism.

Size evolution of gigantic genomes suggests stochastic outcomes of transposable element/host silencing interactions

“…How do TE activity and permissive TE silencing interact to shape genome expansion in gigantic genomes?¾ Deletion rate can drive genome size evolution, but we see no evidence that it differs across these salamander genome sizes. Variation in the strength of genetic drift can also drive genome size evolution, but salamanders do not show patterns consistent with drift-mediated genome expansion (Rios-Carlos, et al 2024). Thus, we focus on TE proliferation.…”