Unusual tandem expansion and positive selection in subgroups of the plant GRAS transcription factor superfamily

Wu, Ningning; Zhu, Yan; Song, Wanlu; Li, Yaxuan; Yan, Yueming; Hu, Yingkao

doi:10.1186/s12870-014-0373-5

BMC Plant Biology

Table 5 Parameters estimation and likelihood ratio tests for the branch-site models

From: Unusual tandem expansion and positive selection in subgroups of the plant GRAS transcription factor superfamily

Foreground branches	Estimates of parameter				positive selection sites (BEB) ⁴
Foreground branches	Site class ¹0	Site class 1	Site class 2a	Site class 2b	positive selection sites (BEB) ⁴
Group I	P0 = 0.50799	P1 = 0.05716	P2a = 0.39087	P2b = 0.04398	296Q,337A,397 K,407D,
	ω0(b)² = 0.13998	ω1(b) = 1.00000	ω2a(b) = 0.13998	ω2b(b) = 1.00000	412 L,415P,419H,446 T*,
	ω0(f)³ = 0.13998	ω1(f) = 1.00000	ω2a(f) = 3.03087	ω2b(f) = 3.03087	453 F*,457 L,464C,476E, 505 T,510Q,527A, 535 V
Group II	P0 = 0.63235	P1 = 0.07147	P2a = 0.26611	P2b = 0.03007	644 L*
	ω0(b) = 0.13987	ω1(b) = 1.00000	ω2a(b) = 0.13987	ω2b(b) = 1.00000
	ω0(f) = 0.13987	ω1(f) = 1.00000	ω2a(f) = 1.16777	ω2b(f) = 1.16777
Group III	P0 = 0.69273	P1 = 0.07803	P2a = 0.20604	P2b = 0.02321	None
	ω0(b) = 0.14005	ω1(b) = 1.00000	ω2a(b) = 0.14005	ω2b(b) = 1.00000
	ω0(f) = 0.14005	ω1(f) = 1.00000	ω2a(f) = 999.00000	ω2b(f) = 999.00000
Group IV	P0 = 0.86848	P1 = 0.04356	P2a = 0.08376	P2b = 0.00420	328Q, 368S*
	ω0(b) = 0.13026	ω1(b) = 1.00000	ω2a(b) = 0.13026	ω2b(b) = 1.00000
	ω0(f) = 0.13026	ω1(f) = 1.00000	ω2a(f) = 20.88429	ω2b(f) = 20.88429
Group V	P0 = 0.63670	P1 = 0.03187	P2a = 0.31563	P2b = 0.01580	296Q,303A,412 L*,418 F, 453 F,490 W,497D,508 L, 511R, 513A, 518 T*,
	ω0(b) = 0.12995	ω1(b) = 1.00000	ω2a(b) = 0.12995	ω2b(b) = 1.00000
	ω0(f) = 0.12995	ω1(f) = 1.00000	ω2a(f) = 1.56269	ω2b(f) = 1.56269
Group VI	P0 = 0.72413	P1 = 0.03621	P2a = 0.22825	P2b = 0.01141	448 K, 456 K, 515 K*
	ω0(b) = 0.12948	ω1(b) = 1.00000	ω2a(b) = 0.12948	ω2b(b) = 1.00000
	ω0(f) = 0.12948	ω1(f) = 1.00000	ω2a(f) = 1.26601	ω2b(f) = 1.26601
Group VII	P0 = 0.71371	P1 = 0.03569	P2a = 0.23866	P2b = 0.01194	297C*, 335S, 497D, 551R
	ω0(b) = 0.12951	ω1(b) = 1.00000	ω2a(b) = 0.12951	ω2b(b) = 1.00000
	ω0(f) = 0.12951	ω1(f) = 1.00000	ω2a(f) = 76.78801	ω2b(f) = 76.78801

Note: *p < 0.05 and **p < 0.01 (x ² test).
¹The sites in the sequence evolve according to the same process, the transition probability matrix is calculated only once for all sites for each branch.
²Background ω.
³Foreground ω.
⁴The number of amino acid sites estimated to have undergone positive selection; BEB: Bayes Empirical Bayes.

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