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A simple covarion‐based approach to analyse nucleotide substitution rates
Author(s) -
Siltberg J.,
Liberles D. A.
Publication year - 2002
Publication title -
journal of evolutionary biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.289
H-Index - 128
eISSN - 1420-9101
pISSN - 1010-061X
DOI - 10.1046/j.1420-9101.2002.00416.x
Subject(s) - nonsynonymous substitution , biology , phylogenetic tree , substitution (logic) , synonymous substitution , selection (genetic algorithm) , negative selection , evolutionary biology , positive selection , tree (set theory) , phylogenetics , substitution method , gene , genetics , computational biology , codon usage bias , mathematics , machine learning , combinatorics , computer science , telecommunications , genome , programming language
Using the ratio of nonsynonymous to synonymous nucleotide substitution rates ( K a / K s ) is a common approach for detecting positive selection. However, calculation of this ratio over a whole gene combines amino acid sites that may be under positive selection with those that are highly conserved. We introduce a new covarion‐based method to sample only the sites potentially under selective pressure. Using ancestral sequence reconstruction over a phylogenetic tree coupled with calculation of K a / K s ratios, positive selection is better detected by this simple covarion‐based approach than it is using a whole gene analysis or a windowing analysis. This is demonstrated on a synthetic dataset and is tested on primate leptin, which indicates a previously undetected round of positive selection in the branch leading to Gorilla gorilla .