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Table 6 Best fitting evolutionary model for each codon position.

From: Molecular phylogeny and divergence times of Malagasy tenrecs: Influence of data partitioning and taxon sampling on dating analyses

   

Estimated by MODELTEST

Estimated by PAML

Gene

CP

Length

Ï€A

Ï€C

Ï€G

Best model

TRatio or Rmat

alpha

PInvar

PN

kappa

alpha

PN

ADRA2B

1

367

0.22

0.31

0.28

K81uf+I+Γ

(1.0 2.5 0.7 0.7 2.5)

1.04

0.36

1

1.05

0.34

1

 

2

367

0.19

0.30

0.21

GTR+Γ

(1.6 6.1 0.7 2.6 3.6)

0.24

0

2

1.18

0.20

2

 

3

367

0.10

0.42

0.32

TVM+Γ

(1.2 4.4 2.5 0.4 4.4)

2.56

0

3

1.96

1.78

3

AR

1

387

0.22

0.25

0.32

TIM+Γ

(1.0 4.5 0.5 0.5 3.0)

0.59

0

4

1.94

0.54

4

 

2

387

0.27

0.31

0.20

TVM+Γ

(1.2 2.9 0.7 1.8 2.9)

0.71

0

5

0.69

0.55

5

 

3

387

0.21

0.31

0.23

TIM+Γ

(1.0 5.4 0.7 0.7 4.4)

1.46

0

6

2.34

1.42

3

GHR

1

284

0.26

0.24

0.33

GTR+Γ

(2.1 3.9 0.9 1.1 2.8)

0.71

0

5

0.90

0.59

5

 

2

284

0.31

0.31

0.18

HKY+I+Γ

1.74

1.42

0.28

7

1.43

0.52

4

 

3

284

0.21

0.32

0.21

TIM+Γ

(1.0 6.0 0.8 0.8 3.8)

2.69

0

6

2.16

2.45

3

vWF

1

391

0.25

0.28

0.32

TVM+Γ

(1.7 3.4 1.1 1.3 3.4)

0.65

0

5

0.89

0.59

5

 

2

391

0.29

0.28

0.17

TrN+Γ+I

(1.0 5.6 1.0 1.0 4.3)

0.81

0.31

8

1.97

0.33

1

 

3

391

0.09

0.38

0.40

TVM+Γ

(2.5 9.9 5.6 0.8 9.9)

3.14

0

9

3.02

1.92

3

  1. Best models and parameters were found with the akaike criterion as implemented in MODELTEST 3.7 and with PAML, for each codon position of the four gene fragments. Codon positions with similar model and model parameters were regrouped into the same partition, which resulted in nine partitions when estimated by MODELTEST and five partitions when estimated by PAML. Codon positions were merged into the same partition when none of their model parameters (e.g., TRatio of position 1 compared to TRatio of position 2, PInvar 1 to PInvar 2, etc.) differed by more than 100%. For the parameters estimated by PAML we took also into account, to define the partitions, the rate of the various gamma low categories; these parameters are not included in this table. TRatio, transition/transversion ratio; Rmat, rate matrix; π, base frequency; PInvar, proportion of invariable sites; alpha, shape of gamma distribution; kappa, value of the transition/transversion ratio under the F84 model. CP stands for codon position and PN for partition number.
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BMC Ecology and Evolution

ISSN: 2730-7182

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