Testing models of evolution

Web document 7.7. Output file from the ModelTest program in which 56 models of nucleotide substitution were evaluated.

The input consisted of 11 myoglobin coding sequences that were first executed using PAUP software.

Testing models of evolution - Modeltest 3.7

Facultad de Biologia, Universidad de Vigo,

Campus Universitario, 36310 Vigo, Spain

_______________________________________________________________

Thu Jul 26 11:12:11 2007

OS = Macintosh (Sioux console)

Input format: PAUP* scores file

Run settings:

Using the standard AIC (not the AICc)

Not using branch lengths as parameters

Including all models in model-averaging calculations

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* *

* HIERARCHICAL LIKELIHOD RATIO TESTS (hLRTs) *

* *

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Confidence level = 0.01

Equal base frequencies

Null model = JC -lnL0 = 2343.2463

Alternative model = F81 -lnL1 = 2337.7295

2(lnL1-lnL0) = 11.0337 df = 3

P-value = 0.011545

Ti=Tv

Null model = JC -lnL0 = 2343.2463

Alternative model = K80 -lnL1 = 2306.5754

2(lnL1-lnL0) = 73.3418 df = 1

P-value = <0.000001

Equal Ti rates

Null model = K80 -lnL0 = 2306.5754

Alternative model = TrNef -lnL1 = 2303.4163

2(lnL1-lnL0) = 6.3184 df = 1

P-value = 0.011949

Equal Tv rates

Null model = K80 -lnL0 = 2306.5754

Alternative model = K81 -lnL1 = 2306.3589

2(lnL1-lnL0) = 0.4331 df = 1

P-value = 0.510469

Equal rates among sites

Null model = K80 -lnL0 = 2306.5754

Alternative model = K80+G -lnL1 = 2242.7925

2(lnL1-lnL0) = 127.5659 df = 1

Using mixed chi-square distribution

P-value = <0.000001

No Invariable sites

Null model = K80+G -lnL0 = 2242.7925

Alternative model = K80+I+G -lnL1 = 2242.4980

2(lnL1-lnL0) = 0.5889 df = 1

Using mixed chi-square distribution

P-value = 0.221429

Model selected: K80+G

-lnL = 2242.7925

K = 2

Base frequencies:

Equal frequencies

Substitution model:

Ti/tv ratio = 1.5819

Among-site rate variation

Proportion of invariable sites = 0

Variable sites (G)

Gamma distribution shape parameter = 0.4545

PAUP* Commands Block: If you want to implement the previous estimates as likelihod settings in PAUP*, attach the next block of commands after the data in your PAUP file:

Likelihood settings from best-fit model (K80+G) selected by hLRT in Modeltest 3.7 on Thu Jul 26 11:12:11 2007

]

BEGIN PAUP;

Lset Base=equal Nst=2 TRatio=1.5819 Rates=gamma Shape=0.4545 Pinvar=0;

END;

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* *

* AKAIKE INFORMATION CRITERION (AIC) *

* *

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Model selected: TrN+G

-lnL = 2228.6187

K = 6

AIC = 4469.2373

Base frequencies:

freqA = 0.2573

freqC = 0.2642

freqG = 0.2980

freqT = 0.1805

Substitution model:

Rate matrix

R(a) [A-C] = 1.0000

R(b) [A-G] = 2.2635

R(c) [A-T] = 1.0000

R(d) [C-G] = 1.0000

R(e) [C-T] = 5.0391

R(f) [G-T] = 1.0000

Among-site rate variation

Proportion of invariable sites = 0

Variable sites (G)

Gamma distribution shape parameter = 0.4433

PAUP* Commands Block: If you want to implement the previous estimates as likelihod settings in PAUP*, attach the next block of commands after the data in your PAUP file:

Likelihood settings from best-fit model (TrN+G) selected by AIC in Modeltest 3.7 on Thu Jul 26 11:12:11 2007

]

BEGIN PAUP;

Lset Base=(0.2573 0.2642 0.2980) Nst=6 Rmat=(1.0000 2.2635 1.0000 1.0000 5.0391) Rates=gamma Shape=0.4433 Pinvar=0;

END;

* MODEL SELECTION UNCERTAINTY : Akaike Weights

Model -lnL K AIC delta weight cumWeight

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TrN+G 2228.6187 6 4469.2373 0.0000 0.3517 0.3517

TrN+I+G 2228.1694 7 4470.3389 1.1016 0.2027 0.5544

TIM+G 2228.3206 7 4470.6411 1.4038 0.1743 0.7287

GTR+G 2226.8057 9 4471.6113 2.3740 0.1073 0.8360

TIM+I+G 2227.8782 8 4471.7563 2.5190 0.0998 0.9359

GTR+I+G 2226.4597 10 4472.9194 3.6821 0.0558 0.9916

HKY+G 2234.6826 5 4479.3652 10.1279 0.0022 0.9939

SYM+G 2234.2625 6 4480.5249 11.2876 0.0012 0.9951

HKY+I+G 2234.3298 6 4480.6597 11.4224 0.0012 0.9963

K81uf+G 2234.4517 6 4480.9033 11.6660 0.0010 0.9973

TVM+G 2232.9568 8 4481.9136 12.6763 0.0006 0.9979

SYM+I+G 2234.0093 7 4482.0186 12.7812 0.0006 0.9985

K81uf+I+G 2234.0986 7 4482.1973 12.9600 0.0005 0.9991

TVM+I+G 2232.6309 9 4483.2617 14.0244 0.0003 0.9994

TVMef+G 2237.3064 5 4484.6128 15.3755 0.0002 0.9995

TrN+I 2236.7471 6 4485.4941 16.2568 0.0001 0.9996

TVMef+I+G 2237.0334 6 4486.0669 16.8296 7.79e-05 0.9997

TrNef+G 2240.0940 3 4486.1880 16.9507 7.33e-05 0.9998

TIMef+G 2239.3413 4 4486.6826 17.4453 5.73e-05 0.9998

TIM+I 2236.6038 7 4487.2075 17.9702 4.41e-05 0.9999

TrNef+I+G 2239.8000 4 4487.6001 18.3628 3.62e-05 0.9999

TIMef+I+G 2239.0437 5 4488.0874 18.8501 2.84e-05 1.0000

K80+G 2242.7925 2 4489.5850 20.3477 1.34e-05 1.0000

K81+G 2242.0952 3 4490.1904 20.9531 9.91e-06 1.0000

GTR+I 2236.4111 9 4490.8223 21.5850 7.23e-06 1.0000

K80+I+G 2242.4980 3 4490.9961 21.7588 6.63e-06 1.0000

K81+I+G 2241.7944 4 4491.5889 22.3516 4.93e-06 1.0000

HKY+I 2244.0312 5 4498.0625 28.8252 1.94e-07 1.0000

K81uf+I 2243.9150 6 4499.8301 30.5928 8.00e-08 1.0000

TVM+I 2243.6582 8 4503.3164 34.0791 1.40e-08 1.0000

SYM+I 2247.6377 6 4507.2754 38.0381 1.93e-09 1.0000

TrNef+I 2250.9824 3 4507.9648 38.7275 1.37e-09 1.0000

TIMef+I 2250.3979 4 4508.7959 39.5586 9.04e-10 1.0000

TVMef+I 2250.3684 5 4510.7368 41.4995 3.42e-10 1.0000

K80+I 2253.7705 2 4511.5410 42.3037 2.29e-10 1.0000

K81+I 2253.2083 3 4512.4165 43.1792 1.48e-10 1.0000

F81+G 2278.2764 4 4564.5527 95.3154 7.06e-22 1.0000

F81+I+G 2278.0466 5 4566.0933 96.8560 3.27e-22 1.0000

JC+G 2284.4009 1 4570.8018 101.5645 3.10e-23 1.0000

JC+I+G 2284.1919 2 4572.3838 103.1465 1.41e-23 1.0000

F81+I 2287.1672 4 4582.3345 113.0972 9.71e-26 1.0000

JC+I 2294.1985 1 4590.3970 121.1597 1.72e-27 1.0000

GTR 2289.9819 8 4595.9639 126.7266 1.07e-28 1.0000

TrN 2294.6165 5 4599.2329 129.9956 2.08e-29 1.0000

TIM 2294.4741 6 4600.9482 131.7109 8.82e-30 1.0000

SYM 2295.6414 5 4601.2827 132.0454 7.46e-30 1.0000

TVMef 2298.7981 4 4605.5962 136.3589 8.63e-31 1.0000

TVM 2296.5637 7 4607.1274 137.8901 4.02e-31 1.0000

HKY 2301.3118 4 4610.6235 141.3862 6.99e-32 1.0000

TrNef 2303.4163 2 4610.8325 141.5952 6.30e-32 1.0000

K81uf 2301.1807 5 4612.3613 143.1240 2.93e-32 1.0000

TIMef 2303.1917 3 4612.3833 143.1460 2.90e-32 1.0000

K80 2306.5754 1 4615.1509 145.9136 7.27e-33 1.0000

K81 2306.3589 2 4616.7178 147.4805 3.32e-33 1.0000

F81 2337.7295 3 4681.4590 212.2217 0.00e+00 1.0000

JC 2343.2463 0 4686.4927 217.2554 0.00e+00 1.0000

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-lnL: Negative log likelihod

K: Number of estimated parameters

IC: Information Criterion

delta: Information difference

weight: Information weight

cumWeight: Cumulative information weight

* MODEL AVERAGING AND PARAMETER IMPORTANCE (using Akaike Weights)

Including all 56 models

Model-averaged

Parameter Importance estimates

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fA 0.9977 0.2582

fC 0.9977 0.2626

fG 0.9977 0.2972

fT 0.9977 0.1820

TiTv 0.0034 1.6297

rAC 0.1661 1.4251

rAG 0.9938 2.4551

rAT 0.1661 0.9237

rCG 0.1661 1.7305

rCT 0.9938 5.4920

pinv(I) 0.0002 0.4778

alpha(G) 0.6387 0.4442

pinv(IG) 0.3611 0.2031

alpha(IG) 0.3611 0.7231

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Values have been rounded.

(I): averaged using only +I models.

(G): averaged using only +G models.

(IG): averaged using only +I+G models.

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Program is done.

Time processing: 0.03137 seconds

If you need help type '-?' in the command line of the program.