Additional Table 6: Complete set of Paml results for all models tested, LRTs are given beneath each table, results are shown on a gene by gene basis.
(a) Complete set of estimates for Adam2 from codeml:
Model / P / Estimates of parameters / Positivelyselected sites
M0 : one ratio / 1 / w = 0.3874 / None
Site-specific:
M1:Neutral / 2 / p0= 0.58406, w0<1 / Not allowed
M2:Selection / 4 / p0=0.54635, p1= 0.38914
(p2= 0.06451), w0<1, w1 = 1, w2 = 5.14527 / NEB: 45>0.50, 18>0.95
5>0.99 BEB: 59>0.50,
18>0.95 5>0.99
M3:Discrete(K = 2) / 3 / p0= 0.59766, (p1= 0.40234)
w0= 0.11485,w1= 1.08488 / NEB:303> 0.50, 201>0.95, 159>0.99
M3:Discrete(K = 3) / 5 / p0=0.46598, p1= 0.44659, (p2= 0.08744)
w0=0.06444, w1=0.67760, w2= 3.49724 / NEB: 304>0.50 201>0.95, 159>0.99
M7: Beta / 2 / p= 0.32715, q= 0.47096 / Not allowed
M8: Beta&Omega > 1 / 4 / p0=0.92632 , p =0.37637 , q = 0.60688
(p1=0.07368 ), w =3.94326 / NEB: 51>0.50,22>0.95, 6>0.99 BEB: 45>0.50, 15>0.95, 5>0.99
M8a: Beta&Omega = 1 / 3 / p0=0.69927, p =0.63216, q =2.94862
(p1=0.30073 ), w = 1 / Not allowed
Branch-specific: Human
Model A / 4 / p0 = 0.55158, p1 =0.39114,
(p2 = 0.03352 , p3 = 0.02377), w0 = 0.10557 w1 = 1, w2 = 3.40857 / NEB: 1>0.50, 0>0.95, 0>0.99 BEB: 1>0.50, 0>0.95, 0>0.99
Model A null / 3 / p0 = 0.50204 , p1 =0.35622,
(p2 = 0.08291 , p3 = 0.05883), w0 = 0.10555, w1 = 1, w2 = 1 / Not allowed
Model B / 5 / p0 = 0.55732, p1 = 0.37303,
(p2 = 0.04173 ,p3 = 0.02793),
w0 = 0.11517, w1 = 1.08741, w2 = 3.25405 / NEB: 1>0.50, 0>0.95, 0>0.99
Branch-specific: Chimp
Model A / 4 / p0 = 0.42038, p1 = 0.29767,
(p2 = 0.16507, p3 = 0.11689),
w0 = 0.10516 , w1 = 1, w2 =1.58791 / NEB: 5>0.50, 0>0.95, 0>0.99 BEB: 5>0.50, 0>0.95, 0>0.99
Model A null / 3 / p0 = 0.34053 , p1 = 0.24107,
(p2 = 0.24497, p3 = 0.17342),
w0 = 0.10518, w1 = 1, w2 = 1 / Not allowed
Model B / 5 / p0 = 0.38462, p1 = 0.25656,
(p2 = 0.21524, p3 = 0.14358),
w0 = 0.11500, w1 =1.08919 , w2 = 1.35250 / NEB: 5>0.50
Branch-specific: Macaque
Model A / 4 / p0 = 0.52835, p1 =0.37595 ,
(p2 = 0.05591, p3 = 0.03979), w0 = 0.10376, w1 = 1, w2 =1.71397 / NEB: 9>0.50
BEB: 2>0.50
Model A null / 3 / p0 = 0.49793, p1 = 0.35442 ,
(p2 = 0.08625 , p3 = 0.06139), w0 =0.10375 , w1 = 1, w2 = 1 / Not allowed
Model B / 5 / p0 = 0.52879 , p1 =0.35559, (p2 =0.06913 , p3 = 0.04649),
w0 = 0.11307, w1 = 1.08474, w2 = 1.42198 / NEB: 9>0.50
Branch-specific: Mouse
Model A / 4 / p0 = 0.58406, p1 = 0.41594,
(p2 = 0, p3 = 0), w0 = 0.10547, w1 = 1, w2 = 1 / NEB: None, BEB: None
Model A null / 3 / p0 = 0.58406, p1 =0.41594,
(p2 = 0, p3 = 0), w0 = 0.10547, w1 = 1, w2 = 1 / Not allowed
Model B / 5 / p0 = 0.43939, p1 = 0.29554,
(p2 = 0.15848, p3 =0.10659),
w0 = 0.11674, w1 = 1.10607, w2 =0 / NEB: None
Branch-specific: Primates
Model A / 4 / p0 = 0.58406, p1 =0.41594,
(p2 = 0, p3 = 0), w0 = 0.10547 , w1 = 1, w2 = 1 / NEB: None, BEB: None
Model A null / 3 / p0 =0.58406, p1 = 0.41594,
(p2 = 0, p3 = 0), w0 = 0.10547, w1 = 1, w2 = 1 / Not allowed
Model B / 5 / p0 = 0.59766 , p1 = 0.40234,
(p2 = 0.00, p3 = 0),
w0 = 0.11485 , w1 = 1.08489, w2 = 0 / NEB: None
Branch-specific: Rodents
Model A / 4 / p0 = 0.58406, p1 = 0.41594,
(p2 = 0.00, p3 = 0.00), w0 = 0.10547, w1 = 1, w2 = 1 / NEB: None, BEB: None
Model A null / 3 / p0 = 0.58406, p1 = 0.41594,
(p2 = 0, p3 = 0), w0 = 0.10547, w1 = 1, w2 = 1 / Not allowed
Model B / 5 / p0 = 0, p1 = 0, (p2 = 0.59733, p3 = 0.40267),
w0 =0.12205, w1 =1.18934, w2 = 0.04224 / NEB: None
Likelihood Ratio Tests for adam2:
Comparison / Null Model lnL/ Alt Model lnL
/ df / Adjusted deltaL
/ Critical Value
/ Significant?
Site Analysis
m0 v m3Discrtk2
/ -15264.16288 / -14752.16817 / 2 / 1023.989412 / 5.99 / YES
m3Discrtk2 v m3Discrtk3
/ -14752.16817 / -14678.25281 / - / 73.915361 / 1 / YES
m1Neutral v m2Selection
/ -14753.10507 / -14691.90877 / 2 / 122.392612 / 5.99 / YES
m7 v m8
/ -14739.14385 / -14670.28361 / 2 / 137.72048 / 5.99 / YES
m8a v m8
/ -14724.947 / -14670.28361 / 1 / 109.326792 / 2.71 / YES
Branch Analysis
Human :
ModelA v m1Neutral / -14752.9021 / -14753.10507 / 2 / 0.405958 / 5.99 / NO
ModelA v ModelAnull / -14752.9021 / -14753.105075 / 1 / 0.40596 / 3.84 / NO
ModelB v m3Discrtk2 / -14751.911362 / -14752.16817 / 2 / 0.513624 / 5.99 / NO
Chimp :
ModelA v m1Neutral / -14751.74232 / -14753.10507 / 2 / 2.725508 / 5.99 / NO
ModelA v ModelAnull / -14751.74232 / -14751.771550 / 1 / 0.05846 / 3.84 / NO
ModelB v m3Discrtk2 / -14750.726249 / -14752.16817 / 2 / 2.88385 / 5.99 / NO
Macaque :
ModelA v m1Neutral / -14751.49307 / -14753.10507 / 2 / 3.224012 / 5.99 / YES
ModelA v ModelAnull / -14751.49307 / -14751.550205 / 1 / 0.114274 / 3.84 / NO
ModelB v m3Discrtk2 / -14750.57921 / -14752.16817 / 2 / 3.17792 / 5.99 / NO
Mouse :
ModelA v m1Neutral / -14753.105074 / -14753.10507 / 2 / 0 / 5.99 / NO
ModelA v ModelAnull / -14753.105074 / -14753.105075 / 1 / 2E-06 / 3.84 / NO
ModelB v m3Discrtk2 / -14751.045525 / -14752.16817 / 2 / 2.245298 / 5.99 / NO
Primates :
ModelA v m1Neutral / -14753.105075 / -14753.10507 / 2 / 2E-06 / 5.99 / NO
ModelA v ModelAnull / -14753.105075 / -14753.105074 / 1 / 2E-06 / 3.84 / NO
ModelB v m3Discrtk2 / -14752.168174 / -14752.16817 / 2 / 0 / 5.99 / NO
Rodents :
ModelA v m1Neutral / -14753.10508 / -14753.10507 / 2 / 2E-06 / 5.99 / NO
ModelA v ModelAnull / -14753.10508 / -14753.105075 / 1 / 0 / 3.84 / NO
ModelB v m3Discrtk2 / -14735.53025 / -14752.16817 / 2 / 33.27585 / 5.99 / YES
(b) Complete set of estimates for Catsper1_Exon1 from codeml:
selected sites
M0 : one ratio
/ 1 / w = 0.9438 / NEB: None, BEB: None
Site-specific:
M1:Neutral /
2 /
p0=0.23061 , w0<1 / Not allowed
M2:Selection / 4 / p0= 0.18411, p1= 0.65127
(p2=0.16462 ), w0<1, w1 = 1, w2 = 3.17328
/ NEB: 40>0.50, 4>0.95 BEB: 46>0.50, 4>0.95
M3:Discrete(K = 2) / 3 / p0=0.39805 , (p1=0.60195 )
w0=0.24359, w1= 1.71676
/ NEB: 0>0.50
M3:Discrete(K = 3) / 5 / p0= 0.23088, p1=0.67010, (p2=0.09902)
w0= 0.09268, w1=1.17408, w2= 3.90174
/ NEB : 209>0.50, 186>0.95, 130>0.99
M7: Beta / 2 / p= 0.06046, q=0.01243
/ Not allowed
M8: Beta&Omega > 1 / 4 / p0=0.82736, p =0.13661, q = 0.03850
(p1= 0.17264), w = 3.13071 / NEB: 45>0.50, 4>0.95 BEB : 97>0.50 7>0.95, 1>0.99
M8a: Beta&Omega = 1 / 3 / p0=0.23129 , p =7.73621 , q = 99.00000
(p1= 0.76871), w = 1 / Not allowed
Branch-specific: Human
Model A / 4 / p0 = 0, p1 = 0,
(p2 = 0.23266, p3 = 0.76734),
w0 =0.06615, w1 = 1, w2 = 1.56616 / NEB: 363>0.50,464>0.95, 363>0.99 BEB: 4>0.50
Model A null / 3 / p0 = 0, p1 =0,
(p2 = 0.23273 , p3 = 0.76727), w0 = 0.06621 , w1 = 1, w2 = 1 / Not allowed
Model B / 5 / p0 = 0, p1 =0, (p2 = 0.38629, p3 =0.61371 ),
w0 = 0.22474, w1 = 1.69600 , w2 = 1.61272 / NEB : 363>0.50, 63>0.95, 363>0.99
Branch-specific: Chimp
Model A / 4 / p0 = 0.18928, p1 = 0.63150,
(p2 = 0.04133, p3 = 0.13789),
w0 = 0.07031, w1 = 1, w2 = 1.41789 / NEB: 0>0.50 BEB: 0>0.50
Model A null / 3 / p0 = 0.18928, p1 = 0.63150,
(p2 = 0.04133 , p3 = 0.13789),
w0 = 0.07031, w1 = 1, w2 = 1 / Not allowed
Model B / 5 / p0 = 0.31752, p1 = 0.48018 , (p2 = 0.08052, p3 = 0.12177),
w0 = 0.24359, w1 = 1.71676, w2 = 1.20375 / NEB: 0>0.50
Branch-specific: Macaque
Model A / 4 / p0 = 0.21476, p1 = 0.71515,
(p2 = 0.01619 , p3 = 0.05390),
w0 = 0.06853, w1 = 1, w2 = 5.27750 / NEB: 1>0.50
BEB: 1>0.50
Model A null / 3 / p0 = 0.22902, p1 = 0.76401,
(p2 = 0.00161, p3 = 0.00536),
w0 = 0.07024 , w1 = 1, w2 = 1 / Not allowed
Model B / 5 / p0 = 0.39054 , p1 = 0.59232,
(p2 = 0.00681 , p3 = 0.01033),
w0 = 0.24184, w1 =1.71382, w2 = 5.16526 / NEB: 0>0.50
Branch-specific: Gorilla
Model A / 4 / p0 = 0.23061, p1 = 0.76939,
(p2 = 0, p3 = 0), w0 = 0.07031,
w1 = 1, w2 = 1 / NEB: None BEB: None
Model A null / 3 / p0 = 0.23061, p1 =0.76939 ,
(p2 = 0, p3 = 0), w0 = 0.07031 ,
w1 = 1, w2 = 1 / Not allowed
Model B / 5 / p0 = 0.15064, p1 = 0.22748 ,
(p2 = 0.24775, p3 = 0.37413),
w0 = 0.24771, w1 =1.75003, w2 =0 / NEB: None
Branch-specific: Cercopithecidae
Model A / 4 / p0 = 0.23061, p1 = 0.76939 ,
(p2 = 0, p3 = 0), w0 = 0.07031
w1 = 1, w2 = 1 / NEB: None BEB: None
Model A null / 3 / p0 = 0.23061 , p1 = 0.76939,
(p2 = 0 p3 = 0), w0 = 0.07031,
w1 = 1, w2 = 1 / Not allowed
Model B / 5 / p0 = 0.30816, p1 = 0.46799,
(p2 = 0.08888, p3 = 0.13497),
w0 = 0.24692, w1 = 1.74843, w2 = 0 / NEB: None
Branch-specific: Hominidae
Model A / 4 / p0 = 0.18623, p1 = 0.61846,
(p2 = 0.04520 , p3 = 0.15011), w0 = 0.06844, w1 = 1, w2 = 1 / NEB: None BEB: None
Model A null / 3 / p0 = 0.18623, p1 = 0.61846,
(p2 = 0.04520, p3 = 0.15011),
w0 = 0.06844, w1 = 1, w2 = 1 / Not allowed
Model B / 5 / p0 = 0.08972, p1 = 0.13965,
(p2 = 0.30143, p3 = 0.46920),
w0 = 0.24130 , w1 = 1.78475, w2 = 0.12024 / NEB: None
Likelihood Ratio Tests for Catsper1_Exon1:
Comparison / Null Model lnL/ Alt Model lnL
/ df / Adjusted deltaL
/ Critical Value
/ Significant?
Site Analysis
m0 v m3Discrtk2
/ -5308.477759 / -5257.816479 / 2 / 101.32256 / 5.99 / YES
m3Discrtk2 v m3Discrtk3
/ -5257.816479 / -5253.104026 / - / 4.712453 / 1 / YES
m1Neutral v m2Selection
/ -5267.435019 / -5253.234859 / 2 / 28.40032 / 5.99 / YES
m7 v m8
/ -5267.801857 / -5253.289195 / 2 / 29.025324 / 5.99 / YES
m8a v m8
/ -5267.447975 / -5253.289195 / 1 / 28.31756 / 2.71 / YES
Branch Analysis
Human
ModelA v m1Neutral / -5266.312655 / -5267.435019 / 2 / 2.244728 / 5.99 / NO
ModelA v ModelAnull / -5266.312655 / -5266.399601 / 1 / 0.173892 / 3.84 / NO
ModelB v m3Discrtk2 / -5256.816869 / -5257.816479 / 2 / 1.99922 / 5.99 / NO
Chimp
ModelA v m1Neutral / -5267.435029 / -5267.435019 / 2 / 2E-05 / 5.99 / NO
ModelA v ModelAnull / -5267.435029 / -5267.435027 / 1 / 4E-06 / 3.84 / NO
ModelB v m3Discrtk2 / -5257.816492 / -5257.816479 / 2 / 2.6E-05 / 5.99 / NO
Macaque
ModelA v m1Neutral / -5267.252488 / -5267.435019 / 2 / 0.365062 / 5.99 / NO
ModelA v ModelAnull / -5267.252488 / -5267.4349 / 1 / 0.364824 / 3.84 / NO
ModelB v m3Discrtk2 / -5257.80282 / -5257.816479 / 2 / 0.027318 / 5.99 / NO
Gorilla
ModelA v m1Neutral / -5267.435019 / -5267.435019 / 2 / 0 / 5.99 / NO
ModelA v ModelAnull / -5267.435019 / -5267.435019 / 1 / 0 / 3.84 / NO
ModelB v m3Discrtk2 / -5256.669264 / -5257.816479 / 2 / 2.29443 / 5.99 / NO
Hominidae
ModelA v m1Neutral / -5267.334989 / -5267.435019 / 2 / 0.20006 / 5.99 / NO
ModelA v ModelAnull / -5267.334989 / -5267.334989 / 1 / 0 / 3.84 / NO
ModelB v m3Discrtk2 / -5255.813942 / -5257.816479 / 2 / 4.005074 / 5.99 / NO
Cercopithecidae
ModelA v m1Neutral / -5267.435019 / -5267.435019 / 2 / 0 / 5.99 / NO
ModelA v ModelAnull / -5267.435019 / -5267.435019 / 1 / 0 / 3.84 / NO
ModelB v m3Discrtk2 / -5257.55949 / -5257.816479 / 2 / 0.513978 / 5.99 / NO
(c) Complete set of estimates for Catsper_Mammals from codeml:
selected sites
M0 : one ratio
/ 1 / w = 0.4109 / NEB: None BEB: None
Site-specific:
M1:Neutral /
2 /
p0=0.49925, w0<1 / Not allowed
M2:Selection / 4 / p0= 0.45323, p1= 0.42564
(p2=0.12113), w0<1, w1 = 1, w2 = 4.93971
/ NEB: 81>0.50, 18>0.95, 7>0.99 BEB: 85>0.50, 18>0.95 7>0.99
M3:Discrete(K = 2) / 3 / p0=0.54823, (p1= 0.45177)
w0=0.12061, w1= 1.37162
/ NEB: 0>0.50
M3:Discrete(K = 3) / 5 / p0= 0.35362, p1= 0.40982, (p2= 0.23656)
w0=0.03795, w1=0.54802, w2=2.56196
/ NEB: 180>0.50, 63>0.95, 32>0.99
M7: Beta / 2 / p=0.28339, q= 0.31193
/ Not allowed
M8: Beta&Omega > 1 / 4 / p0= 0.83315, p =0.34233, q = 0.51278
(p1=0.16685), w =3.26879 / NEB: 128>0.50, 27>0.95, 7>0.99 BEB: 124>0.50, 30>0.95, 8>0.99
M8a: Beta&Omega = 1 / 3 / p0=0.59360, p = 0.60936, q = 3.50222
(p1=0.40640), w = 1 / Not allowed
Branch-specific:Ferungulata
Model A / 4 / p0 = 0.48740, p1 =0.46800 , (p2 = 0.02276, p3 = 0.02185), w0 = 0.08841 ,
w1 = 1, w2 = 998.99981 / NEB: 13>0.50, 1>0.95 BEB : 5>0.50, 1>0.95
Model A null / 3 / p0 = 0.49037, p1 = 0.49065,
(p2 = 0.00948, p3 = 0.00949),
w0 = 0.08503, w1 = 1, w2 = 1 / Not allowed
Model B / 5 / p0 = 0.51692 , p1 = 0.42612,
(p2 =0.03122, p3 = 0.02574),
w0 = 0.12085, w1 = 1.37445, w2 = 0 / NEB : None
Branch-specific: Mouse
Model A / 4 / p0 = 0.45052 , p1 = 0.44724,
(p2 = 0.05131, p3 = 0.05093),
w0 = 0.08353 , w1 = 1, w2 = 1 / NEB: None BEB: None
Model A null / 3 / p0 = 0.45052, p1 = 0.44724,
(p2 = 0.05131, p3 = 0.05093),
w0 = 0.08353 , w1 = 1, w2 = 1 / Not allowed
Model B / 5 / p0 = 0.23435, p1 = 0.18155,
(p2 = 0.32913, p3 = 0.25497),
w0 = 0.12693, w1 = 1.50506, w2 = 0.24614 / NEB: None
Branch-specific: Rodents
Model A / 4 / p0 = 0.47315, p1 = 0.47238,
(p2 = 0.02726, p3 =0.02721), w0 = 0.08373, w1 = 1, w2 = 999 / NEB: 16>0.50
BEB: 11>0.50
Model A null / 3 / p0 = 0.46496 , p1 = 0.46638,
(p2 = 0.03428, p3 = 0.03438),
w0 = 0.08380, w1 = 1, w2 = 1 / Not allowed
Model B / 5 / p0 = 0.52986, p1 = 0.42545 ,
(p2 = 0.02478, p3 = 0.01990),
w0 = 0.12088, w1 = 1.38175, w2 = 999 / NEB: 12>0.50, 1>0.95
Likelihood Ratio Tests for Catsper1_Mammals: