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Updated: Jun 24, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Correlation between Ka/Ks and Ks is related to substitution model and evolutionary lineage
Jun Li1, Zhang Zhang, Søren Vang
1Beijing Genomics Institute, Shenzhen, Building Complex, BeiShan Industrial Zone, Yantian District, Shenzhen, 518083, China. junli@genomics.org.cn
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.
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