TABLE 3.

Test of selection among lineages using revised branch-site model A and test 2 as implemented in PAML 315 (see materialsandmethods)

	Parameter estimates
Model A		Site class	p	ω0 background	ω1 foreground	Ln likelihood, LRT test 2	Selected codon, posterior P
Domestic cat lineage	κ = 2.0844	0	0.42368	0.27811	0.27811	−1618.646	K125R (0.943)
		1	0.57024	1	1	−1623.128 (Null)
		2a	0.00259	0.27811	74.02392
		2b	0.00349	1	74.02392	LRT = 8.965, P < 0.1
Asian leopard cat lineage	κ = 2.04134	0	0.11785	0.12684	0.12684	−1622.952
		1	0.18680	1	1	−1622.952 (Null)
		2a	0.26899	0.12684	1
		2b	0.42637	1	1	LRT = 0, NS
Ocelot lineagea	κ = 2.04608	0	0.38217	0.21098	0.21098	−1623.179
		1	0.61783	1	1	−1623.179 (Null)
		2a	0.00000	0.21098	1
		2b	0.00000	1	1	LRT = 0, NS
Puma lineage	κ = 1.99378	0	0	0.16775	0.16775	−1618.396	S6R**	M97R**
		1	0	1	1	−1621.544 (Null)	V14A**	A161D**
		2a	0.49690	0.16775	999.000		Q18P**	M187V*
		2b	0.50310	1	999.000	LRT = 6.295, P > 0.01	V25A**	A213P**
							R46G*	Y223C*
							V75M**
Lynx lineage	κ = 2.0609	0	0.39158	0.22067	0.22067	−1621.591
		1	0.57691	1	1	−1623.132 (Null)
		2a	0.01235	0.22067	84.78123
		2b	0.01816	1	84.78123	LRT = 3.082, NS
Caracal lineage	κ = 2.04609	0	0.38216	0.21097	0.21097	−1623.179
		1	0.31784	1	1	−1623.179 (Null)
		2a	0	0.21097	1
		2b	0	1	1	LRT = 0, NS
Bay cat lineage	κ = 2.04401	0	0	0.22458	0.22458	−1622.007
		1	0	1	1	−1623.139 (Null)
		2a	0.40068	0.22458	277.069
		2b	0.59932	1	277.069	LRT = −2.263, NS
Panthera lineagea	κ = 2.04609	0	0.38216	0.21097	0.21097	−1623.179
		1	0.61784	1	1	−1623.179 (Null)
		2a	0	0.21097	1
		2b	0	1	1	LRT = 0, NS

κ, transition/transversion ratio; NS, not significant results of Ln likelihood-ratio test; ω₀, background ratio of d_N/d_S; ω₁, lineage-specific ratio of d_N/d_S. *Posterior P > 0.95%, **Posterior P > 0.99%.

^aNeofelis nebulosa and Leopardus pardalis were omitted due to frameshift mutations incompatible with PAML.