Influence of Effective Population Size on Genes under Varying Levels of Selection Pressure

Abstract

The ratio of diversities at amino acid changing (nonsynonymous) and neutral (synonymous) sites (ω = πN/πS) is routinely used to measure the intensity of selection pressure. It is well known that this ratio is influenced by the effective population size (Ne) and selection coefficient (s). Here, we examined the effects of effective population size on ω by comparing protein-coding genes from Mus musculus castaneus and Mus musculus musculus—two mouse subspecies with different Ne. Our results revealed a positive relationship between the magnitude of selection intensity and the ω estimated for genes. For genes under high selective constraints, the ω estimated for the subspecies with small Ne (M. m. musculus) was three times higher than that observed for that with large Ne (M. m. castaneus). However, this difference was only 18% for genes under relaxed selective constraints. We showed that the observed relationship is qualitatively similar to the theoretical predictions. We also showed that, for highly expressed genes, the ω of M. m. musculus was 2.1 times higher than that of M.m. castaneus and this difference was only 27% for genes with low expression levels. These results suggest that the effect of effective population size is more pronounced in genes under high purifying selection. Hence the choice of genes is important when ω is used to infer the effective size of a population.

Effect of genetic drift on determinants of protein evolution

“…A number of studies have provided empirical evidence for this prediction and the influence of drift on the reduction of the efficacy of negative [12,13] and positive [14,15] selection has been well documented. A previous study showed that the effect of N e is more pronounced in highly expressed genes compared to the lowly expressed genes [16]. In the current study we investigated the other dimension: whether the effect of gene expression (and three other determinants) on protein evolution is more pronounced in species/populations with large N e compared to those with small N e .…”

Deleterious mutation load in the admixed mice population

“…To investigate this, we obtained the whole genome data of Mus musculus castaneus and Mus musculus musculus and their hybrid or admixed populations. We specifically selected these because the subspecies M. m. musculus and M. m. castaneus have population sizes of 60,000-120,000 and 200,000-400,000, respectively (Salcedo et al, 2007;Geraldes et al, 2008), and previous studies have found a much higher mutational load in the former compared to that observed in the latter (Phifer-Rixey et al, 2012;Subramanian, 2018). We estimated the dN/dS ratios and the proportion of deleterious nonsynonymous SNVs (nSNVs) for the admixed mouse population and compared them with those of their parental populations.…”

The complete mitochondrial genome of Calidris tenuirostris (Charadriiformes: Scolopacidae)

“…However, few studies attempted to reveal why some species from Charadriiformes are endangered by analyzing the genetic feature (Liu et al. 2018 ; Subramanian 2018 ). Thus, it is necessary to figure out the genetic structure and phylogenetic relationship, which may facilitate understand the fitness and selective pressure of great knot.…”

“…Recently, many studies focus on the habitat ecology, migratory phenology and behavior to try to explain the terrible situation (Peng et al 2015;Tan et al 2018). However, few studies attempted to reveal why some species from Charadriiformes are endangered by analyzing the genetic feature (Liu et al 2018;Subramanian 2018). Thus, it is necessary to figure out the genetic structure and phylogenetic relationship, which may facilitate understand the fitness and selective pressure of great knot.…”