Phylogenetic informativeness reconciles ray-finned fish molecular divergence times

Table 2 Best-fit nucleotide substitution models and partition strategies identified by PartitionFinder and peaks of phylogenetic informativeness for nDNA

Subset	Best model	Subset partitions	Subset sites	PI peak/slope
1	GTR + I + G	Plag_2, SH3PX3_2, SREB2_2, ZIC1_1	1-691\3, 2785-3497\3, 3500-4636\3, 5323-6194\3	180/-1.24e-04
2	SYM + G	*Plag_3, ptr_1, SREB2_3*	2-691\3, 692-1405\3, 3498-4636\3	62/-7.79e-03
3	HKY + I + G	Plag_1, TBR1_3, TBR1_1, glyt_1	3-691\3, 4638-5321\3, 4639-5321\3, 6197-7024\3	85/-1.29e-03
4	GTR + I + G	ptr_2, myh6_2	693-1405\3, 7027-7769\3	128/-3.82e-05
5	GTR + I + G	*ptr_3, glyt_3, myh6_3*	694-1405\3, 6196-7024\3, 7025-7769\3	70/-4.70e-03
6	SYM + I + G	RAG1_2, RAG1_1	1406-2784\3, 1408-2784\3	70/-1.46e-03
7	GTR + I + G	RAG1_3, TBR1_2	1407-2784\3, 4637-5321\3	245/-3.34e-05
8	GTR + I + G	*SH3PX3_3, myh6_1*	2786-3497\3, 7026-7769\3	62/-1.93e-03
9	K80 + I + G	*SH3PX3_1, SREB2_1*	2787-3497\3, 3499-4636\3	58/-3.40e-03
10	K80 + G	ZIC1_3	5322-6194\3	66/-4.55e-04
11	K80 + I + G	ZIC1_2, glyt_2	5324-6194\3, 6195-7024\3	163/-8.90e-06

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.

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