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Table 2 Summary of parameter estimates and likelihood scores for the model of best fit showing evidence of positive selection

From: Colon cancer associated genes exhibit signatures of positive selection at functionally significant positions

Gene Model lnL Parameter Estimates Positive Selection BEB Positively Selected Sites
Lineage-Specific Analyses
Euarchontoglires Ancestral Branch
STK11 modelA −8602.921472 p0 = 0.93299, p1 = 0.05633, p2 = 0.01007, p3 = 0.00061 ω0 = 0.03346, ω1 = 1.00000, ω2 = 197.90897 Yes 3 > 0.50, 1 > 0.95, 0 > 0.99
Primate Ancestral Branch
CDH1 modelA −16658.03484 p0 = 0.75454, p1 = 0.23453, p2 = 0.00834, p3 = 0.00259 ω0 = 0.05683, ω1 = 1.00000, ω2 = 10.20516 Yes 9 > 0.50, 1 > 0.95, 0 > 0.99
Hominidae Ancestral Branch
STK11 modelA −8601.056009 p0 = 0.93574, p1 = 0.05920, p2 = 0.00476, p3 = 0.00030 ω0 = 0.03323, ω1 = 1.00000, ω2 = 44.31709 Yes 3 > 0.50, 2 > 0.95, 1 > 0.99
VHL modelA −4263.853291 p0 = 0.73748, p1 = 0.25109, p2 = 0.00853, p3 = 0.00290 ω0 = 0.05985, ω1 = 1.00000, ω2 = 220.34533 Yes 1 > 0.50, 0 > 0.95, 0 > 0.99
Chimpanzee Extant Branch
TSC2 modelA −42659.27711 p0 = 0.90352, p1 = 0.09434, p2 = 0.00194, p3 = 0.00020 ω0 = 0.04404, ω1 = 1.00000, ω2 = 190.09480 Yes 6 > 0.50, 2 > 0.95, 2 > 0.99
VHL modelA −4262.098043 p0 = 0.73571, p1 = 0.25251, p2 = 0.00877, p3 = 0.00301 ω0 = 0.05976, ω1 = 1.00000, ω2 = 262.72662 Yes 3 > 0.50, 0 > 0.95, 0 > 0.99
Gorilla Extant Branch
MSH2 modelA −19485.4338 p0 = 0.92233, p1 = 0.06298, p2 = 0.01375, p3 = 0.00094 ω0 = 0.06427, ω1 = 1.00000, ω2 = 999.00000 Yes 46 > 0.50, 34 > 0.95, 18 > 0.99
TSC2 modelA −42569.22884 p0 = 0.89862, p1 = 0.08796, p2 = 0.01222, p3 = 0.00120 ω0 = 0.04339, ω1 = 1.00000, ω2 = 999.00000 Yes 27 > 0.50, 14 > 0.95, 12 > 0.99
MSH6 modelA −34009.90221 p0 = 0.78382, p1 = 0.18418, p2 = 0.02591, p3 = 0.00609 ω0 = 0.06974, ω1 = 1.00000, ω2 = 999.00000 Yes 46 > 0.50, 34 > 0.95, 18 > 0.99
ATM modelA −69374.08393 p0 = 0.80673, p1 = 0.17971, p2 = 0.01109, p3 = 0.00247 ω0 = 0.09745, ω1 = 1.00000, ω2 = 999.00000 Yes 48 > 0.50, 23 > 0.95, 19 > 0.99
Orangutan Extant Branch
TSC1 modelA −24068.71106 p0 = 0.79963, p1 = 0.18828, p2 = 0.00978, p3 = 0.00230 ω0 = 0.08020, ω1 = 1.00000, ω2 = 999.00000 Yes 13 > 0.50, 6 > 0.95,5 > 0.99
TSC2 modelA −42673.92339 p0 = 0.90414, p1 = 0.09295, p2 = 0.00263, p3 = 0.00027 ω0 = 0.04433, ω1 = 1.00000, ω2 = 40.47366 Yes 9 > 0.50, 0 > 0.95, 0 > 0.99
Marmoset Extant Branch
TSC2 modelA −42616.04524 p0 = 0.89841, p1 = 0.09019, p2 = 0.01035, p3 = 0.00104 ω0 = 0.04325, ω1 = 1.00000, ω2 = 235.10448 Yes 38 > 0.50, 9 > 0.95
MSH6 modelA −34009.90221 p0 = 0.78382, p1 = 0.18418, p2 = 0.02591, p3 = 0.00609 ω0 = 0.06974, ω1 = 1.00000, ω2 = 999.00000 Yes 45 > 0.50, 16 > 0.95, 12 > 0.99
VHL modelA −4262.443441 p0 = 0.72045, p1 = 0.22453, p2 = 0.04195, p3 = 0.01307 ω0 = 0.05886, ω1 = 1.00000, ω2 = 90.26952 Yes 10 > 0.50, 0 > 0.95, 0 > 0.99
ATM modelA −69583.23068 p0 = 0.81640, p1 = 0.18148, p2 = 0.00173, p3 = 0.00038 ω0 = 0.09939, ω1 = 1.00000, ω2 = 46.82466 Yes 2 > 0.50, 0 > 0.95, 0 > 0.99
Muridae Ancestral Branch
TSC1 modelA −24126.17894 p0 = 0.80995, p1 = 0.18416, p2 = 0.00481, p3 = 0.00109 ω0 = 0.08293, ω1 = 1.00000, ω2 = 999.00000 Yes 1 > 0.59, 0 > 0.95, 0 > 0.99
Murinae Ancestral Branch
SDHC modelA −3846.690164 p0 = 0.87666, p1 = 0.08131, p2 = 0.03846, p3 = 0.00357 ω0 = 0.15340, ω1 = 1.00000, ω2 = 253.61375 Yes 9 > 0.50, 2 > 0.95, 1 > 0.99
MSH6 modelA −34190.13821 p0 = 0.79911, p1 = 0.19671, p2 = 0.00335, p3 = 0.00082 ω0 = 0.07057, ω1 = 1.00000, ω2 = 126.22513 Yes 3 > 0.50, 1 > 0.95, 0 > 0.99
Rat Extant Branch
MADH4 modelA −6092.186945 p0 = 0.93360, p1 = 0.01536, p2 = 0.05021, p3 = 0.00083 ω0 = 0.01379, ω1 = 1.00000, ω2 = 102.33013 Yes 24 > 0.50, 11 > 0.95, 10 > 0.99
NF1 modelA −37750.29866 p0 = 0.96609, p1 = 0.02476, p2 = 0.00892, p3 = 0.00023 ω0 = 0.02265, ω1 = 1.00000, ω2 = 999.00000 Yes 39 > 0.50, 10 > 0.95, 10 > 0.99
Guinea pig Extant Branch
TSC1 modelA −24116.58577 p0 = 0.80206, p1 = 0.18611, p2 = 0.00961, p3 = 0.00223 ω0 = 0.08093, ω1 = 1.00000, ω2 = 284.22603 Yes 9 > 0.50, 4 > 0.95, 0 > 0.99
NF1 modelA −37849.50819 p0 = 0.97375, p1 = 0.02506, p2 = 0.00116, p3 = 0.00003 ω0 = 0.02414, ω1 = 1.00000, ω2 = 171.64068 Yes 3 > 0.50, 1 > 0.95, 0 > 0.99
Rabbit Extant Branch
MLH1 modelA −19516.63525 p0 = 0.80595, p1 = 0.18541, p2 = 0.00703, p3 = 0.00162 ω0 = 0.05262, ω1 = 1.00000, ω2 = 7.52747 Yes 5 > 0.05, 3 > 0.95, 0 > 0.99
MUTYH modelA −15911.6175 p0 = 0.61027, p1 = 0.37605, p2 = 0.00846, p3 = 0.00522 ω0 = 0.07703, ω1 = 1.00000, ω2 = 998.99697 Yes 5 > 0.50, 4 > 0.95, 3 > 0.99
SDHC modelA −3822.683246 p0 = 0.57771, p1 = 0.06636, p2 = 0.31926, p3 = 0.03667 ω0 = 0.12047, ω1 = 1.00000, ω2 = 3.59059 Yes 51 > 0.50, 10 > 0.95, 8 > 0.99
ATM modelA −69582.95152 p0 = 0.81572, p1 = 0.18045, p2 = 0.00313, p3 = 0.00069 ω0 = 0.09930, ω1 = 1.00000, ω2 = 7.41594 Yes 6 > 0.50, 0 > 0.95, 0 > 0.99
BHD modelA −13523.51719 p0 = 0.90728, p1 = 0.05930, p2 = 0.03137, p3 = 0.00205 ω0 = 0.02817, ω1 = 1.00000, ω2 = 6.50017 Yes 10 > 0.50, 7 > 0.95, 1 > 0.99
Site-specific Analyses
CDH1 m8 −16589.88768 p = 0.21848, p0 = 0.99291, p1 = 0.00709, q = 0.80842 ω=4.53766 Yes 15 > 0.5, 1 > 0.95, 0 > 0.99
PMS1 m8 −26480.39761 p = 0.61337, p0 = 0.93580, p1 = 0.06420, q = 1.93110 ω=1.32691 Yes 25 > 0.50, 1 > 0.95, 0 > 0.99
PMS2 m8 −27449.3651 p = 0.29104, p0 = 0.91064, p1 = 0.08936, q = 1.31619 ω=1.28855 Yes 37 > 0.50, 1 > 0.95, 0 > 0.99
MUTYH m8 −15797.6226 p = 0.37255, p0 = 0.97242, p1 = 0.02758, q = 1.00900 ω=2.44412 Yes 18 > 0.5, 1 > 0.95, 0 > 0.99
TP53 m8 −8688.19126 p = 0.40362, p0 = 0.94645, p1 = 0.05355, q = 1.77507 ω=1.97385 Yes 13 > 0.5, 3 > 0.95, 0 > 0.99
  1. The model of best fit is summarized below for those genes with evidence of positive selection. The lineage-specific results for each lineage tested from the Euarchontoglires ancestor to modern lineages are shown in the top panel and the site-specific results are shown in the bottom panel. The model abbreviations are as per main text. P refers to the number of free parameters estimated in that model. BEB = Bayes Empirical Bayes estimations. The number of positively selected sites identified can be found the final column, sites are separated by the posterior probability cutoffs of 0.50, 0.95, and 0.99.