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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.