Table.

Maximum Likelihood fits of 24 different nucleotide substitution models Mo

del Parameters BIC AICc lnL (+I) (+G) R f(A) f(T) f(C) f(G) r(AT) r(AC) r(AG) r(
TA) r(TC) r(TG) r(CA) r(CT) r(CG) r(GA) r(GT) r(GC)
T92+G60 4519.624 4014.775 -1947.278 n/a 0.05 6.50 0.347 0.347 0.153 0.153 0.020
0.009 0.135 0.020 0.135 0.009 0.020 0.307 0.009 0.307 0.020 0.009
T92+G+I61 4526.781 4013.521 -1945.647 0.13 0.05 6.54 0.347 0.347 0.153 0.153 0.0
20 0.009 0.135 0.020 0.135 0.009 0.020 0.307 0.009 0.307 0.020 0.009
HKY+G62 4531.278 4009.608 -1942.687 n/a 0.05 6.54 0.305 0.390 0.155 0.150 0.023
0.009 0.133 0.018 0.137 0.009 0.018 0.345 0.009 0.269 0.023 0.009
TN93+G63 4536.010 4005.929 -1939.844 n/a 0.05 6.55 0.305 0.390 0.155 0.150 0.022
0.009 0.185 0.017 0.093 0.009 0.017 0.233 0.009 0.375 0.022 0.009
HKY+G+I63 4537.016 4006.936 -1940.347 0.18 0.05 6.61 0.305 0.390 0.155 0.150 0.0
22 0.009 0.133 0.017 0.137 0.009 0.017 0.345 0.009 0.270 0.022 0.009
TN93+G+I64 4541.913 4003.423 -1937.587 0.18 0.05 6.62 0.305 0.390 0.155 0.150 0.
022 0.009 0.186 0.017 0.092 0.008 0.017 0.231 0.008 0.378 0.022 0.009
T9259 4557.601 4061.163 -1971.475 n/a n/a 6.24 0.347 0.347 0.153 0.153 0.021 0.0
09 0.134 0.021 0.134 0.009 0.021 0.306 0.009 0.306 0.021 0.009
T92+I60 4566.876 4062.027 -1970.904 0.03 n/a 6.24 0.347 0.347 0.153 0.153 0.021
0.009 0.134 0.021 0.134 0.009 0.021 0.306 0.009 0.306 0.021 0.009
GTR+G66 4566.941 4011.630 -1939.683 n/a 0.05 5.87 0.305 0.390 0.155 0.150 0.020
0.010 0.179 0.015 0.093 0.012 0.021 0.234 0.009 0.364 0.032 0.010
HKY61 4569.501 4056.241 -1967.007 n/a n/a 6.24 0.305 0.390 0.155 0.150 0.024 0.0
09 0.132 0.018 0.136 0.009 0.018 0.343 0.009 0.268 0.024 0.009
TN9362 4574.228 4052.558 -1964.162 n/a n/a 6.24 0.305 0.390 0.155 0.150 0.023 0.
009 0.178 0.018 0.097 0.009 0.018 0.244 0.009 0.362 0.023 0.009
TN93+I63 4574.407 4044.327 -1959.043 0.27 n/a 6.27 0.305 0.390 0.155 0.150 0.023
0.009 0.179 0.018 0.097 0.009 0.018 0.243 0.009 0.363 0.023 0.009
GTR+G+I67 4575.812 4012.092 -1938.910 0.06 0.05 5.89 0.305 0.390 0.155 0.150 0.0
20 0.010 0.180 0.015 0.093 0.012 0.021 0.233 0.009 0.365 0.032 0.010
HKY+I62 4578.628 4056.958 -1966.362 0.04 n/a 6.24 0.305 0.390 0.155 0.150 0.024
0.009 0.132 0.018 0.137 0.009 0.018 0.343 0.009 0.268 0.024 0.009
GTR65 4604.782 4057.882 -1963.812 n/a n/a 5.73 0.305 0.390 0.155 0.150 0.022 0.0
11 0.175 0.017 0.097 0.013 0.021 0.244 0.007 0.354 0.033 0.007
GTR+I66 4613.493 4058.182 -1962.959 0.05 n/a 5.73 0.305 0.390 0.155 0.150 0.022
0.011 0.175 0.017 0.097 0.013 0.021 0.244 0.007 0.354 0.033 0.008
K2+G59 4687.737 4191.298 -2036.543 n/a 0.05 6.29 0.250 0.250 0.250 0.250 0.017 0
.017 0.216 0.017 0.216 0.017 0.017 0.216 0.017 0.216 0.017 0.017
K2+G+I60 4696.784 4191.935 -2035.858 0.06 0.05 6.30 0.250 0.250 0.250 0.250 0.01
7 0.017 0.216 0.017 0.216 0.017 0.017 0.216 0.017 0.216 0.017 0.017
K258 4724.031 4236.003 -2059.899 n/a n/a 6.24 0.250 0.250 0.250 0.250 0.017 0.01
7 0.215 0.017 0.215 0.017 0.017 0.215 0.017 0.215 0.017 0.017
K2+I59 4732.778 4236.339 -2059.063 0.05 n/a 6.24 0.250 0.250 0.250 0.250 0.017 0
.017 0.215 0.017 0.215 0.017 0.017 0.215 0.017 0.215 0.017 0.017
JC+G58 4755.596 4267.568 -2075.682 n/a 0.05 0.50 0.250 0.250 0.250 0.250 0.083 0
.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083
JC+G+I59 4765.446 4269.007 -2075.397 0.02 0.05 0.50 0.250 0.250 0.250 0.250 0.08
3 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083
JC57 4791.720 4312.103 -2098.953 n/a n/a 0.50 0.250 0.250 0.250 0.250 0.083 0.08
3 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083
JC+I58 4801.086 4313.059 -2098.427 0.03 n/a 0.50 0.250 0.250 0.250 0.250 0.083 0
.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083
NOTE.-- Models with the lowest BIC scores (Bayesian Information Criterion) are c
onsidered to describe the substitution pattern the best. For each model, AICc va
lue (Akaike Information Criterion, corrected), Maximum Likelihood value (lnL), a
nd the number of parameters (including branch lengths) are also presented [1]. N
on-uniformity of evolutionary rates among sites may be modeled by using a discre
te Gamma distribution (+G) with 5 rate categories and by assuming that a certain
fraction of sites are evolutionarily invariable (+I). Whenever applicable, esti
mates of gamma shape parameter and/or the estimated fraction of invariant sites

are shown. Assumed or estimated values of transition/transversion bias (R) are s

hown for each model, as well. They are followed by nucleotide frequencies (f) an
d rates of base substitutions (r) for each nucleotide pair. Relative values of i
nstantaneous r should be considered when evaluating them. For simplicity, sum of
r values is made equal to 1 for each model. For estimating ML values, a tree to
pology was automatically computed. The analysis involved 30 nucleotide sequences
. Codon positions included were 1st+2nd+3rd+Noncoding. All positions containing
gaps and missing data were eliminated. There were a total of 1115 positions in t
he final dataset. Evolutionary analyses were conducted in MEGA5 [2].
Abbreviations: GTR: General Time Reversible; HKY: Hasegawa-Kishino-Yano; TN93: T
amura-Nei; T92: Tamura 3-parameter; K2: Kimura 2-parameter; JC: Jukes-Cantor.
1. Nei M. and Kumar S. (2000). Molecular Evolution and Phylogenetics. Oxford Uni
versity Press, New York.
2. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., and Kumar S. (2011).
MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolu
tionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution
28: 2731-2739.
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