Positive Selection of Squalene Synthase in Cucurbitaceae Plants

Table 2

Parameter estimation and likelihood ratio tests for the site model.

Model		Estimate of parameters		RT pairs				Positively selected sites
M0: one ratio	112		-29891.94
M3: discrete	116	,	-28662.22	M0/M3	4	2459.44	0.001	None
		,
		,
M1a: neutral	113	,	-29207.98	M1a/M2a	2	0.00	1.000	None
		,
M2a: selection	115	,	-29207.98
		,
		,
M7: beta	113	, q = 1.95163	-28621.19	M7/M8	2	11187.62	0.001	2G, 14F, 22M, 26N, 33Q, 42T, 59Q, 60P, 86E, 95I, 99R, 109S, 133E, 189S, 196S, 200S, 250V, 265I, 277L, 354T, 357L, 369Q, 372L, 378L, 380V, 381V, 382R, 383S, 384E, 385P, 386I, 389P, 390T, 391L, 394I, 406L, 407S, 408A, 409K, 410R, 411F, 412P, 414N, 416S, 417M (all were )
M8: beta & ω	115	, ,	-34215.80
		,

lnL: loglikelihood; LRT: likelihood ratio test; : average dN/dS ratio for sites subject to positive selection. and : shape parameters for the beta distribution of ω; , , and : proportions of codons subject to purifying selection, neutral evolution, and positive selection, respectively; : degrees of freedom; : twice the loglikelihood difference of the models compared. Selection analysis by site models was performed using CodeML implemented in PAML. Bold values indicate and . Significant tests at 1% cut-off, ; .