Table 2.

ML of Trees under Different Partitioning Schemes.

Data Set	Partitioning Scheme	Topological Constraint	Number of Partitions	Substitution Model	Number of Parameters	Ln L	AIC	ΔAIC
All genes	Unpartitioned (one partition)	None	1	GTR	8	−787,773	1,575,562	62,885
	PartitionFinder (six partitions)	On one partition tree	6	GTR	48	−758,061	1,516,219	3,349
	Gene/codon-position (41 partitions)	On one partition tree	41	GTR	328	−756,379	1,513,414	737
	Gene/codon-position (41 partitions)	On six partition tree	41	GTR	328	−756,272	1,513,199	522
	PartitionFinder (six partitions)	On 41 partition tree	6	GTR	48	−758,010	1,516,116	3,439
	Gene/codon-position (41 partitions)	None	41	GTR	328	−756,010	1,512,677	n/a
	PartitionFinder (six partitions)	On one partition tree	6	GTR	48	−758,061	1,516,219	3,542
Protein-coding genes	Unpartitioned (one partition)	None	1	GTR	8	−684,161	1,368,339	34,473
	Gene/codon-position (39 partitions)	On 1 partition tree	39	GTR	312	−666,834	1,334,219	425
	PartitionFinder (5 partitions)	None	5	GTR	40	−668,480	1,337,039	3,173
	Gene/codon-position (39 partitions)	On five partition tree	39	GTR	312	−666,678	1,333,981	115
	PartitionFinder (five partitions)	On 39 partition tree	5	GTR	40	−668,523	1,337,127	3,261
	Gene/codon-position (39 partitions)	None	39	GTR	312	−666,621	1,333,866	n/a
	PartitionFinder (five partitions)	On one partition tree	5	GTR	40	−668,567	1,337,213	3,347

Note.—Trees were obtained under no partitioning, under the six- or five-partition schemes selected by PartitionFinder, and by the maximum number of partitions tested (partitioning by gene and codon position). Each of the resulting trees was then assessed for their likelihood under the alternative models. Note the comparatively small difference in likelihood (ΔAIC) under each partitioning scheme regardless of the model used in the tree search.