Li Jun, Zhang Zhang, Vang Søren, Yu Jun, Wong Gane Ka-Shu, Wang Jun
Beijing Genomics Institute, Shenzhen, Building Complex, BeiShan Industrial Zone, Yantian District, Shenzhen, 518083, China.
J Mol Evol. 2009 Apr;68(4):414-23. doi: 10.1007/s00239-009-9222-9. Epub 2009 Mar 24.
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.
2005年，怀科夫及其同事使用LPB93算法在几个数据集中描述了Ka/Ks与Ks之间惊人的强相关性。这一发现表明，在使用Ka/Ks比率测量选择强度的方式上，可能会发生范式转变。我们使用六种不同算法对三个跨物种直系同源数据集进行了Ka和Ks的计算，发现算法和谱系之间存在高度可变的相关性。基于GY-HKY替代模型的算法比基于K2P和JC69替代模型的算法表现出较弱的正相关或较强的负相关。即使一种算法在温血谱系中显示出Ka/Ks与Ks之间存在正相关，在冷血谱系中也可能不显示相关性。这种与算法和进化谱系相关的相关性表明，在全基因组选择强度分析中仅使用一种Ka和Ks算法得出结论时需要格外谨慎。我们的结果表明，目前用于计算Ka和Ks的算法存在缺陷，需要改进。
