ArticleGenome biology and evolution2011
Significant selective constraint at 4-fold degenerate sites in the avian genome and its consequence for detection of positive selection.
Article in Genome biology and evolution, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed.
- Genetic diversity analysis and core collection construction of Macadamia spp. from Yunnan using fourfold degenerate SNP sites.BMC plant biology · 2026Article
- Patterns of Change in Nucleotide Diversity Over Gene Length.Genome biology and evolution · 2024Article
- Detection of evolutionary conserved and accelerated genomic regions related to adaptation to thermal niches inEcology and evolution · 2024Article
- Draft genome of six Cuban Anolis lizards and insights into genetic changes during their diversification.BMC ecology and evolution · 2022Article
- Controlling for Variable Transposition Rate with an Age-Adjusted Site Frequency Spectrum.Genome biology and evolution · 2022Article
- Selection on Accessible Chromatin Regions in Capsella grandiflora.Molecular biology and evolution · 2021Article
- Population genetic models of GERP scores suggest pervasive turnover of constrained sites across mammalian evolution.PLoS genetics · 2020Article
- A Study of Faster-Z Evolution in the Great Tit (Parus major).Genome biology and evolution · 2020Article
- Population genomics of parallel evolution in gene expression and gene sequence during ecological adaptation.Scientific reports · 2018Article
- Hybridization and gene flow in the mega-pest lineage of moth,Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- GC Content of Early Metazoan Genes and Its Impact on Gene Expression Levels in Mammalian Cell Lines.Genome biology and evolution · 2018Article
- Determinants of the Efficacy of Natural Selection on Coding and Noncoding Variability in Two Passerine Species.Genome biology and evolution · 2017Article
- Direct estimate of the rate of germline mutation in a bird.Genome research · 2016Article
- Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.Science (New York, N.Y.) · 2014Article
- Genomic identification and characterization of the pseudoautosomal region in highly differentiated avian sex chromosomes.Nature communications · 2014Article
- Highly variable recombinational landscape modulates efficacy of natural selection in birds.Genome biology and evolution · 2014Article
- Kr/Kc but not dN/dS correlates positively with body mass in birds, raising implications for inferring lineage-specific selection.Genome biology · 2014Article
- Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition.Genome biology · 2014Article
- Strong purifying selection at synonymous sites in D. melanogaster.PLoS genetics · 2013Article
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3 authors.
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Abstract
A major conclusion from comparative genomics is that many sequences that do not code for proteins are conserved beyond neutral expectations, indicating that they evolve under the influence of purifying selection and are likely to have functional roles. Due to the degeneracy of the genetic code, synonymous sites within protein-coding genes have previously been seen as "silent" with respect to function and thereby invisible to selection. However, there are indications that synonymous sites of vertebrate genomes are also subject to selection and this is not necessarily because of potential codon bias. We used divergence in ancestral repeats as a neutral reference to estimate the constraint on 4-fold degenerate sites of avian genes in a whole-genome approach. In the pairwise comparison of chicken and zebra finch, constraint was estimated at 24-32%. Based on three-species alignments of chicken, turkey, and zebra finch, lineage-specific estimates of constraint were 43%, 29%, and 24%, respectively. The finding of significant constraint at 4-fold degenerate sites from data on interspecific divergence was replicated in an analysis of intraspecific diversity in the chicken genome. These observations corroborate recent data from mammalian genomes and call for a reappraisal of the use of synonymous substitution rates as neutral standards in molecular evolutionary analysis, for example, in the use of the well-known d(N)/d(S) ratio and in inferences on positive selection. We show by simulations that the rate of false positives in the detection of positively selected genes and sites increases several-fold at the levels of constraint at 4-fold degenerate sites found in this study.
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