Table 2.

Genome-Wide Model Family Ranking

	Data/Count	Rank
		1	2	3	4	5	6	7	8	9	10
AIC best model	Mammal	TIM3	TrN	TPM3uf	GTR	HKY	TIM2	TIM1	TPM2uf	TVM	TPM1uf
	10	15.09	12.69	10.39	9.08	9.03	8.37	7.43	4.14	2.81	2.63
	Vertebrate	GTR	TIM2	TIM3	TrN	TIM1	TVM	TPM3uf
	7	28.29	20.73	12.96	7.61	4.26	3.53	3.01
	Drosophila	TIM2	GTR	TIM3	TrN	TIM1	TVM
	6	28.84	23.2	12.83	9.17	4.98	2.1
AIC 95% CI	Mammal	TIM3	GTR	TrN	TIM2	TIM1	TPM3uf	HKY	TVM	TPM2uf	TPM1uf
		59.34	52.69	51.02	49.43	47.84	41.81	36.01	35.27	34.86	33.48
	Vertebrate	GTR	TIM2	TIM3	TIM1	TrN	TVM	TPM3uf	TPM2uf	HKY	TPM1uf
		32.98	24.7	21.31	15.81	15.37	13.5	10.07	9.95	6.43	5.92
	Drosophila	GTR	TIM2	TIM3	TrN	TIM1	TVM	TPM2uf	TPM3uf	HKY	SYM
		34.95	30.39	24.29	19.68	18.04	11.26	9.89	8.59	6.49	6.31
AIC best model LP mammal	Low LP	TrN	HKY	TIM3	TIM1	TPM3uf	TPM1uf	TIM2	TPM2uf	TrNef	TIM2ef
	12	22.44	14.82	9.56	7.48	5.54	5.12	5.12	4.02	2.35	1.39
	Mid LP	TIM3	TrN	TPM3uf	TIM2	HKY	GTR	TPM2uf	TPM1uf	TIM1	TVM
	10	17.31	14.13	11.08	9.83	9.14	7.34	4.02	3.46	3.19	2.77
	High LP	GTR	TVM	TIM3	TPM3uf	TPM2uf	TIM2	TrN
	7	25.09	15.7	14.98	12.27	5.05	4.15	3.79

Note.—The set of model families with 1) the highest representation under the best model, 2) the 95% CI, or 3) the best model for different subsets of the mammal set varying in both alignment length and pairwise nucleotide diversity (“Best Model LP Mammal”) are shown ranked by their frequency (as a percentage) in each of the three sets of species (labels under the “Data” column, first and second main rows) or low, median, and high values of LP (labels under the “Data” column, third main row). Only the first ten ranks shown, and where the best model is considered (first and third main rows), only the minimum number of families required to explain at least 80% of all genes were considered (numbers under the “Count” column).