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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.