No signal of deleterious mutation accumulation in conserved gene sequences of extant asexual hexapods

Patterns of molecular evolution in a parthenogenic terrestrial isopod (Trichoniscus pusillus)

The "paradox of sex" refers to the question of why sexual reproduction is maintained in the wild, despite how costly it is compared to asexual reproduction. Because of these costs, one might expect nature to select for asexual reproduction, yet sex seems to be continually selected for. Multiple hypotheses have been proposed to explain this incongruence, including the niche differentiation hypothesis, the Red Queen hypothesis, and accumulation of harmful mutations in asexual species due to inefficient purifying selection. This study focuses on the accumulation of mutations in two terrestrial isopods, Trichoniscus pusillus, which has sexual diploid and parthenogenic triploid forms, and Hyloniscus riparius, an obligately sexual relative. We surveyed sex ratios of both species in an upstate New York population and obtained RNA-seq data from wild-caught individuals of both species to examine within- and between-species patterns of molecular evolution in protein-coding genes. The sex ratio and RNA-seq data together provide strong evidence that this T. pusillus population is entirely asexual and triploid, while the H. riparius population is sexual and diploid. Although all the wild T. pusillus individuals used for sequencing shared identical genotypes at nearly all SNPs, supporting a clonal origin, heterozygosity and SNP density were much higher in T. pusillus than in the sexually reproducing H. riparius. This observation suggests this parthenogenic lineage may have arisen via mating between two divergent diploid lineages. Between-species sequence comparisons showed no evidence of ineffective purifying selection in the asexual T. pusillus lineage, as measured by the ratio of nonsynonymous to synonymous substitutions (dN/dS ratios). Likewise, there was no difference between T. pusillus and H. riparius in the ratios of nonsynonymous to synonymous SNPs overall (pN/pS). However, pN/pS ratios in T. pusillus were significantly higher when considering only SNPs that may have arisen via recent mutation after the transition to parthenogenesis. Thus, these recent SNPs are consistent with the hypothesis that purifying selection is less effective against new mutations in asexual lineages, but only over long time scales. This system provides a useful model for future studies on the evolutionary tradeoffs between sexual and asexual reproduction in nature.

Novel genome sequence of Chinese cavefish (Triplophysa rosa) reveals pervasive relaxation of natural selection in cavefish genomes

All cavefishes, living exclusively in caves across the globe, exhibit similar phenotypic traits, including the characteristic loss of eyes. To understand whether such phenotypic convergence shares similar genomic bases, here we investigated genome-wide evolutionary signatures of cavefish phenotypes by comparing whole-genome sequences of three pairs of cavefishes and their surface fish relatives. Notably, we newly sequenced and generated a whole-genome assembly of the Chinese cavefish Triplophysa rosa. Our comparative analyses revealed several shared features of cavefish genome evolution. Cavefishes had lower mutation rates than their surface fish relatives. In contrast, the ratio of nonsynonymous to synonymous substitutions (ω) was significantly elevated in cavefishes compared to in surface fishes, consistent with the relaxation of purifying selection. In addition, cavefish genomes had an increased mutational load, including mutations that alter protein hydrophobicity profiles, which were considered harmful. Interestingly, however, we found no overlap in positively selected genes among different cavefish lineages, indicating that the phenotypic convergence in cavefishes was not caused by positive selection of the same sets of genes. Analyses of previously identified candidate genes associated with cave phenotypes supported this conclusion. Genes belonging to the lipid metabolism functional ontology were under relaxed purifying selection in all cavefish genomes, which may be associated with the nutrient-poor habitat of cavefishes. Our work reveals previously uncharacterized patterns of cavefish genome evolution and provides comparative insights into the evolution of cave-associated phenotypic traits.

Copper Chaperone for Superoxide Dismutase FoCCS1 in Frankliniella occidentalis May Be Associated with Feeding Adaptation after Host Shifting

Western flower thrips (Frankliniella occidentalis) pose a serious threat to the global vegetable and flower crop production. The regulatory mechanism for superoxide dismutase (SOD) in the feeding adaptation of F. occidentalis after host shifting remains unclear. In this study, the copper chaperone for SOD (CCS) and manganese SOD (MnSOD) genes in F. occidentalis were cloned, and their expression levels at different developmental stages was determined. The mRNA expression of FoCCS1 and FoMnSOD2 in F. occidentalis second-instar larvae and adult females of F₁, F₂, and F₃ generations was analyzed after shifting the thrips to kidney bean and broad bean plants, respectively. The F₂ and F₃ second-instar larvae and F₂ adult females showed significantly upregulated FoCCS1 mRNA expression after shifting to kidney bean plants. The F₁ second-instar larvae and F₂ adult females showed significantly upregulated FoCCS1 mRNA expression after shifting to broad bean plants. The RNA interference significantly downregulated the FoCCS1 mRNA expression levels and adult females showed significantly inhibited SOD activity after shifting to kidney bean and broad bean plants. F. occidentalis adult females subjected to RNA interference and released on kidney bean and broad bean leaves for rearing, respectively, significantly reduced the survival rate and fecundity. These findings suggest that FoCCS1 plays an active role in regulating the feeding adaptation ability of F. occidentalis after host shifting.