title: Correlation between Ka/Ks and Ks is related to substitution model and evolutionary lineage.
abstract: In 2005, Wyckoff and coworkers described a surprisingly strong correlation between Ka/Ks and Ks in several data sets using the LPB93 algorithm. This finding indicated the possibility of a paradigm shift in the way selection strength can be measured using the Ka/Ks ratio. We carried out a calculation of Ka and Ks using six different algorithms on three cross-species orthologous data sets and found a highly variable correlation among the algorithms and lineages. Algorithms based on the GY-HKY substitution model exhibit a weaker positive correlation or a stronger negative correlation than those based on the K2P and JC69 substitution model. Even if one algorithm shows a positive correlation between Ka/Ks and Ks in a warm-blooded lineage, it may show no correlation in a cold-blooded lineage. This algorithm-related and evolutionary lineage-related correlation indicates the need for great caution in drawing conclusions when using only one Ka and Ks algorithm in a genomewide analysis of selection strength. Our results indicated that currently used algorithms for Ka and Ks calculations are flawed and need improvements.
authors.affiliation: Beijing Genomics Institute, Shenzhen, Building Complex, BeiShan Industrial Zone, Yantian District, Shenzhen, 518083, China. junli@genomics.org.cn
authors.forename: Jun
authors.initials: J
authors.lastname: Li
authors.forename: Zhang
authors.initials: Z
authors.lastname: Zhang
authors.forename: Søren
authors.initials: S
authors.lastname: Vang
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
authors.forename: Gane Ka-Shu
authors.initials: GK
authors.lastname: Wong
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D000818:Animals; D003198:Computer Simulation; D004252:DNA Mutational Analysis; D003627:Data Interpretation, Statistical; D019143:Evolution, Molecular; D006801:Humans; D051379:Mice; D008957:Models, Genetic; D011110:Polymorphism, Genetic; D051381:Rats; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA