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Table 1 Best-fit nucleotide substitution models and partition strategies identified by PartitionFinder and peaks of phylogenetic informativeness for mtDNA

From: Phylogenetic informativeness reconciles ray-finned fish molecular divergence times

Subset

Best model

Subset partitions

Subset sites

PI peak/slope

1

GTR + I + G

nd5_1, cytb_1, nd2_1, atp8_3

1-1145\3, 1832-2008\3, 6610-7665\3, 7668-9522\3

91/-3.61E-03

2

GTR + I + G

cytb_2, coi_2

2-1145\3, 2010-3562\3

116/-2.60E-04

3

GTR + I + G

cytb_3,nd5_3

3-1145\3, 7667-9522\3

72/-9.25E-03

4

GTR + I + G

nd5_2,atp8_1,nd2_2,atp6_1

1146-1831\3, 1833-2008\3, 6611-7665\3, 7666-9522\3

87/-2.36E-03

5

GTR + I + G

coiii_2,atp6_2,atp8_2

1147-1831\3, 1834-2008\3, 4255-5637\3

72/-4.74E-03

6

GTR + I + G

coiii_3,coiii_1,atp6_3

1148-1831\3, 4254-5637\3, 4256-5637\3

77/-4.85E-03

7

SYM + I + G

coi_1

2009-3562\3

106/-3.56E-04

8

GTR + G

coii_3,coi_3

2011-3562\3, 3565-4253\3

72/-7.35E-03

9

SYM + I + G

nd1_1,coii_1

3563-4253\3, 5638-6609\3

145/-3.25E-04

10

GTR + I + G

nd1_2,coii_2

3564-4253\3, 5639-6609\3

217/-4.80E-05

11

HKY + I + G

nd1_3

5640-6609\3

72/-4.29E-03

12

HKY + I + G

nd2_3

6612-7665\3

62/-4.75E-03

13

GTR + I + G

nd6_2

9523-10061\3

116/-2.23E-04

14

GTR + I + G

nd6_1,nd6_3

9524-10061\3, 9525-10061\3

72/-2.56E-03

  1. Values following underscores after the gene name indicate first, second, or third codon positions. Subset sites correspond to the order of genes in the concatenated alignment. Peak of the PI profiles are indicated in millions of years. Slope values correspond to the slope of a chord joining the peak of profile and the midpoint of the profile between the peak and the root of the tree. Bolded partitions indicate partitions removed for subsequent analysis.