Molecular evolution of toothed whale genes reveals adaptations to echolocating in different environments

BMC Genomics

Table 2 Codeml branch, site, and branch-site models with significant results for the gene TMC1. The hypotheses H1-H4 are outlined in table 4. lnL = log-likelihood; LRT = likelihood ratio test; np = number of free parameters; df = degrees of freedom; ω = omega; a model = alternative model

TMC1 - branch, site, and branch-site codeml models
Model (hypothesis)	Toothed whale test branches	lnL	LRT	np	df	p-value	ω
Two ratio (H1a)	Ancestral	-5,241.08	9.764	88	1	0.0017	0.101
One ratio		-5,245.97	9.764	87	1	0.0017	0.101	0.235
Two ratio (H1b)	Extant	-5,242.92	6.092	88	1	0.0135	0.107
One ratio		-5,245.97	6.092	87	1	0.0135	0.107	0.213
Two ratio (H3)	Oceanic	-5,243.10	5.738	88	1	0	0.115
One ratio		-5,245.97	5.738	87	1	0	0.115	0.295
Two ratio (H4)	Coastal	-5,243.50	4.925	88	1	0.0264	0.121
One ratio		-5,245.97	4.925	87	1	0.0264	0.121	0.515
Site model 1	None	-5,195.18	5.768	88	2	0.0559	proportion	0.890	0.103	0.007
Site model 2	None	-5,192.30	5.768	90	2	0.0559	ω value	0.019	1.000	4.466
Site model 7	None	-5,195.40	6.687	88	2	0.0353	proportion	0.792	0.099	0.099	0.010
Site model 8	None	-5,192.06	6.687	90	2	0.0353	ω value	< 0.0201	0.208	0.867	3.915
A model (H1b)	Extant	-5,189.40	8.281	90	1	0.004
							proportion	0.891	0.095	0.013	0.001
							background ω	0.018	1.000	0.018	1.000
Null (H1b)		-5,193.54		89			foreground ω	0.018	1.000	9.827	9.827
A model (H4)	Coastal	-5,187.13	14.307	90	1	0.0001
							proportion	0.887	0.110	0.003	0.000
							background ω	0.016	1.000	0.016	1.000
Null (H4)		-5,194.29		89			foreground ω	0.016	1.000	149.076	149.076

ISSN: 1471-2164