APPENDIX 1

Substitution Models and Parameter Estimates

 

mtDNA data set:

Model selected:  GTR + G + I

-lnL = 16646.3379

Base frequencies:

            Freq A = 0.3833

            Freq C             = 0.3188

            Freq G = 0.1041

            Freq T             = 0.1939

Substitution model:

            Rate matrix

            R (a) [A-C]     = 2.4839

            R (b) [A-G]     = 11.0727

            R (c) [A-T]     = 3.1451

            R (d) [C-G]     = 0.7003

            R (e) [C-T]      = 19.7931

            R (f) [G-T]      = 1.0000

Among-site rate variation:

                        Gamma distribution shape parameter (G) = 0.8665

Proportion of invariable sites (I) = 04556

 

nNDNA data set:

Model selected:  K80 + G

-lnL = 960.3175

Equal base frequencies

Substitution model:

Ti/tv ratio = 2.6648

            Among-site rate variation:

                        Gamma distribution shape parameter = 0.2026

Proportion of invariable sites = 0

mtDNA + nDNA data set:

Model selected:  GTR + G + I

-lnL = 17842.4141

Base frequencies:

            Freq A = 0.3597

            Freq C             = 0.3020

            Freq G = 0.1358

            Freq T             = 0.2025

Substitution model:

            Rate matrix

            R (a) [A-C]     = 3.8467

            R (b) [A-G]     = 11.6527

            R (c) [A-T]     = 4.3039

            R (d) [C-G]     = 0.8898

            R (e) [C-T]      = 26.6143

            R (f) [G-T]      = 1.0000

Among-site rate variation:

                        Gamma distribution shape parameter = 0.8665

Proportion of invariable sites = 0.4556