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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 (? =??N/?S) 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 ? 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 ? estimated for genes. For genes under high selective constraints, the ? 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 ? 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 ? is used to infer the effective size of a population.

SUBMITTER: Subramanian S

PROVIDER: S-EPMC5841380 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature

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

Subramanian Sankar S

Genome biology and evolution 20180301 3

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 reveale ...[more]

PMID: 29608718

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Project description:The Lundehund is an old dog breed with remarkable anatomical features including polydactyly in all four limbs and extraordinary flexibility of the spine. We genotyped 28 Lundehund using the canine Illumina high density beadchip to estimate the effective population size (Ne) and inbreeding coefficients as well as to identify potential regions of positive selection. The decay of linkage disequilibrium was slow with r2=0.95 in 50 kb distance. The last 7-200 generations ago, Ne was at 10-13. An increase of Ne was noted in the very recent generations with a peak value of 19 for Ne at generation 4. The FROH estimated for 50-, 65- and 358-SNP windows were 0.87, 087 and 0.81, respectively. The most likely estimates for FROH after removing identical-by-state segments due to linkage disequilibria were at 0.80-0.81. The extreme loss of heterozygosity has been accumulated through continued inbreeding over 200 generations within a probably closed population with a small effective population size. The mean inbreeding coefficient based on pedigree data for the last 11 generations (FPed=0.10) was strongly biased downwards due to the unknown coancestry of the founders in this pedigree data. The long-range haplotype test identified regions with genes involved in processes of immunity, olfaction, woundhealing and neuronal development as potential targets of selection. The genes QSOX2, BMPR1B and PRRX2 as well as MYOM1 are candidates for selection on the Lundehund characteristics small body size, increased number of digits per paw and extraordinary mobility, respectively. The objectives of the present study were to genotype 28 Lundehund using the canine Illumina high density beadchip (Illumina, San Diego, CA, USA) to estimate the effective population size (Ne) from data on linkage disequilibria (LD). We identified runs of homozygosity (ROH) as regions with a local loss of genetic variation. Inbreeding coefficients were calculated on the basis of pedigree data (FPed) and genotype information (FROH, FIS) to compare the results of these different methods for this population. We applied the long-range haplotype test to search for potential selective sweeps.

Dataset Information

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

Publications

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

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