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An Empirical Test for Branch-Specific Positive Selection
- Publication Year :
- 2008
- Publisher :
- Genetics Society of America, 2008.
-
Abstract
- The use of phylogenetic analysis to predict positive selection specific to human genes is complicated by the very close evolutionary relationship with our nearest extant primate relatives, chimpanzees. To assess the power and limitations inherent in use of maximum-likelihood (ML) analysis of codon substitution patterns in such recently diverged species, a series of simulations was performed to assess the impact of several parameters of the evolutionary model on prediction of human-specific positive selection, including branch length and dN/dS ratio. Parameters were varied across a range of values observed in alignments of 175 transcription factor (TF) genes that were sequenced in 12 primate species. The ML method largely lacks the power to detect positive selection that has occurred since the most recent common ancestor between humans and chimpanzees. An alternative null model was developed on the basis of gene-specific evaluation of the empirical distribution of ML results, using simulated neutrally evolving sequences. This empirical test provides greater sensitivity to detect lineage-specific positive selection in the context of recent evolutionary divergence.
- Subjects :
- Most recent common ancestor
Genetics
Genome
Phylogenetic tree
Null model
Molecular Sequence Data
Context (language use)
Biology
Investigations
Empirical distribution function
Evolution, Molecular
Phylogenetics
Animals
Humans
Human genome
Computer Simulation
Selection, Genetic
Codon
Phylogeny
Transcription Factors
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Accession number :
- edsair.doi.dedup.....4f1837d1d8ee6f3230412572c5e4eefa