Table 3.

Branch models and branch-site test for W-linked branches

Gene	Species		Branch model test	Branch model test	Branch-site test
name	included1	ω	(ω=1) likelihood ratio	(ω=0) likelihood ratio	(ω =1) likelihood ratio
HINT1W	G, M, T	1.10	0.05	3697.05**	0.05
CHD1W	G, A, T	0.14	94.45**	7012.15**	0.00
RASA1W	G, A, M, T	0.09	31.33**	1386.95**	0.00
KCMF1W	G, A, T	0.22	35.49**	5674.71**	0.22
MIER3W	G, A, T	0.24	17.97**	167.25**	0.00
SPINW	G, A, M, T	0.09	28.45**	1749.98**	0.00
HNRNPKW	G, A, T	0.03	108.75**	84.21**	0.03
VCPW	G, A, T	0.03	25.58**	19.13**	0.16
ZFRW	G, A, T	0.18	27.16**	173.50**	0.00
NIPBLW	G, A, T	0.05	44.08**	63.91**	0.00
NIPBLW	G, M, T	0.03	38.40**	343.5**	0.00
UBAP2W	G, M, T	0.15	6.19*	354.82**	0.00
ATP5A1W	G, M, T	0.09	16.54**	650.83**	3.58*
MADH2W	G, M, T	0.06	22.37**	333.50**	0.01
UBE2R2W	G, A, T	0.04	15.03**	17.39**	0.00
ZSWIM6W	G, A, T	0.25	11.25**	128.88**	0.00

¹G = G. gallus, M = M. gallopavo, A = A. platyrhynchos, T = T. guttata.

^**P-value < 0.01.

^*P-value < 0.05.

Likelihood values for each model and the gene IDs are listed in Table S4. Significant likelihood ratios are in bold.