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.
Mol Biol Evol. 1994 Sep;11(5):725-36
[PMID:
7968486]
J Mol Evol. 1980 Dec;16(2):111-20
[PMID:
7463489]
Mol Biol Evol. 2006 Mar;23(3):530-40
[PMID:
16280543]
J Mol Evol. 1985;22(2):160-74
[PMID:
3934395]
Nat Rev Genet. 2006 Feb;7(2):98-108
[PMID:
16418745]
Mol Biol Evol. 1985 Mar;2(2):150-74
[PMID:
3916709]
Syst Biol. 2001 Aug;50(4):580-601
[PMID:
12116655]
Mol Biol Evol. 2004 Dec;21(12):2290-8
[PMID:
15329386]
Genomics Proteomics Bioinformatics. 2006 Aug;4(3):173-81
[PMID:
17127215]
Trends Genet. 2005 Jul;21(7):381-5
[PMID:
15946765]
Science. 2000 Nov 10;290(5494):1151-5
[PMID:
11073452]
Mol Biol Evol. 2000 Jan;17(1):32-43
[PMID:
10666704]
Mol Biol Evol. 1996 Jan;13(1):105-14
[PMID:
8583885]
Trends Genet. 2000 Jun;16(6):276-7
[PMID:
10827456]
Mol Biol Evol. 2007 Aug;24(8):1586-91
[PMID:
17483113]
J Mol Evol. 1993 Jan;36(1):96-9
[PMID:
8433381]
J Mol Evol. 1995 Jan;40(1):56-63
[PMID:
7714912]
Genomics Proteomics Bioinformatics. 2006 Nov;4(4):259-63
[PMID:
17531802]
Mol Biol Evol. 1986 Sep;3(5):418-26
[PMID:
3444411]
Curr Opin Genet Dev. 2001 Dec;11(6):642-6
[PMID:
11682307]
J Mol Evol. 1995 Feb;40(2):190-226
[PMID:
7699723]
BMC Evol Biol. 2007 Sep 21;7:168
[PMID:
17883872]
Mol Biol Evol. 1993 May;10(3):512-26
[PMID:
8336541]
Genome Res. 2003 Oct;13(10):2213-9
[PMID:
14525923]
Trends Ecol Evol. 2000 Dec 1;15(12):496-503
[PMID:
11114436]
Mol Biol Evol. 1993 Jan;10(1):186-204
[PMID:
8450755]
Proc Natl Acad Sci U S A. 1998 Mar 31;95(7):3708-13
[PMID:
9520431]
BMC Evol Biol. 2006 Jun 02;6:44
[PMID:
16740169]
