Phylogeny and adaptive evolution of the brain-development gene microcephalin (MCPH1) in cetaceans

McGowen, Michael R; Montgomery, Stephen H; Clark, Clay; Gatesy, John

doi:10.1186/1471-2148-11-98

BMC Ecology and Evolution

Table 1 Results for site model analyses using the species tree derived from multiple sources [39–42]

From: Phylogeny and adaptive evolution of the brain-development gene microcephalin (MCPH1) in cetaceans

		Avg.	Prop. sites	ω sites with	Sites under positive selection
Model	-ln L	ω	ω > 1	ω > 1	(p > 0.95, BEB)
All mammals:
M1a	15880.84	0.757
M2a	15869.046	0.858	0.07	2.063	362
M8	15863.642	0.829	0.14	1.721	112, 132, 172, 205, 209, 247, 362
M8a	15877.044	0.737
M1a v. M2a: df = 2, -2ΔlnL = 23.587, p < 0.001
M8 v. M8a: df = 1, -2ΔlnL = 26.804, p < 0.001
All cetaceans:
M1a	3913.4037	0.7975
M2a	3903.628	0.9548	0.021	6.767	89, 362
M8	3903.6499	0.9458	0.072	6.564	89, 362
M8a	3913.4114	0.8017
M1a v. M2a: df = 2, -2ΔlnL = 19.551, p < 0.001
M8 v. M8a: df = 1, -2ΔlnL = 19.523, p < 0.001
All odontocetes:
M1a	3519.5486	0.7351
M2a	3514.0255	0.9211	0.046	4.583	89
M8	3514.0265	0.923	0.045	4.635	89, 195
M8a	3519.5486	0.7351
M1a v. M2a: df = 2, -2ΔlnL = 11.046, p < 0.001
M8 v. M8a: df = 1, -2ΔlnL = 11.044, p < 0.001
All delphinids:
M1a	2251.6189	0.548
M2a	2236.8709	0.9868	0.028	14.257	20, 89, 195
M7	2251.7481	0.5
M8	2236.871	0.9887	0.045	14.308	20, 89, 195
M8a	2251.6189	0.5479
M1a v. M2a: df = 2, -2ΔlnL = 29.496, p < 0.001
M8 v. M8a: df = 1, -2ΔlnL = 29.496, p < 0.001
All mysticetes:
M1a	1690.448	1
M2a	1688.2783	1.5764	0.014	41.761	None
M8	1690.448	1.5764	0.014	41.757	None
M8a	1690.448	1
M1a v. M2a: df = 2, -2ΔlnL = 4.339, p = 0.114
M8 v. M8a: df = 1, -2ΔlnL = 0, p = 1.0
All primates:
M1a	5103.5715	0.6245
M2a	5098.7948	0.728	0.065	2.608	None
M8	5098.9315	0.7297	0.132	2.13	209, 309
M8a	5103.5982	0.6244
M1a v. M2a: df = 2, -2ΔlnL = 9.553, p = 0.008
M8 v. M8a: df = 1, -2ΔlnL = 9.333, p = 0.005
No cetaceans/primates:
M1a	8990.4108	0.7309
M2a	8987.9053	0.8132	0.059	2.17	None
M8	8980.7366	0.7764	0.117	1.82589	None
M8a	8986.2851	0.7017
M1a v. M2a: df = 2, -2ΔlnL = 5.011, p = 0.082
M8 v. M8a: df = 1, -2ΔlnL = 11.010, p = 0.002

Each data set is listed separately with models, likelihood score (-lnL), average ω, the proportion of sites in the site class with ω > 1, the ω estimate for the site class with ω > 1, and the specific sites with ω > 1 using the Bayes empirical Bayes (BEB) procedure. Likelihood ratio tests for site models are also shown below for each data set with degrees of freedom (df), likelihood ratio (-2ΔlnL), and p-value. Statistically significant p-values are shown in bold.

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ISSN: 2730-7182

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