Phylogenetic analyses reveal molecular signatures associated with functional divergence among Subtilisin like Serine Proteases are linked to lifestyle transitions in Hypocreales

Table 4 Likelihood estimates of Proteinase K (S08.054) gene family for branch-site models in PAML

Branch- Site (Model)	np	Parameter estimates (Proportion p, omega ω)	lnL	LRT Pairs	2Δ lnL	df	P	Positively selected sites (BEB)
Nectriaceae (BS_{fix ω =1})	118	p ₀ = 0.65,p₁ = 0.33,p_2a = 0.003,p_2b = 0.001 ω₀₌ 0.123, ω₁ = 1.00b:ω_2a = 0.123, ω_2b = 1.000 f: ω_2a = 1.00, ω_2b = 1.00	−18857.30	BS_{fix ω =1}/ BS_{fix ω =0}	0	1	1
Nectriaceae (BS_{fix ω =0})	119	p ₀ = 0.39,p₁ = 0.20,p_2a=0.27, p_2b = 0.13,ω₀ = 0.123,ω₁ = 1.00, b:ω_2a = 0.123,ω_2b = 1.00 f: ω_2a = 2.09, ω_2b = 2.09	−18857.30
Cordycipitaceae/Clavicipitaceae (BS_{fix ω =1})	118	p ₀ = 0.66, p₁ = 0.33, p_2a = 0.00,p_2b = 0.00 ω₀₌0.123 ,ω₁ = 1.00, b:ω_2a = 0.123, ω_2b = 1.00 f: ω_2a = 1.00, ω_2b = 1.00	−18857.30	BS_{fix ω =1}/BS_{fix ω =0}	0	1	1
Cordycipitaceae/Clavicipitaceae (BS_{fix ω =0})	119	p ₀ = 0.66,p₁ = 0.33, p₂a = 0.00,p_2b = 0.00 ω₀₌ 0.123 ,ω₁ = 1.00,b:ω_2a = 0.123, ω_2b = 1.00 f: ω_2a = 1.00,ω_2b = 1.00	−18857.30
Ophiocordycipitaceae (BS_{fix ω =1})	118	p ₀ = 0.38,p₁ = 0.19,p_2a = 0.27,p_2b = 0.14 ω₀ = 0.12102,ω₁ = 1.00, b:ω_2a = 0.12, ω_2b = 1.00 f:ω_2a = 1.00,ω_2b = 1.00	−18849.02	BS_{fix ω =1}/ BS_{fix ω =0}	2.04	1	0.15
Ophiocordycipitaceae (BS_{fix ω =0})	119	p ₀ = 0.53,p₁ = 0.28,p_2a = 0.11,p_2b = 0.062 ω₀₌ 0.12 ,ω₁ = 1.00,b:ω_2a = 0.12,ω_2b = 1.00 f: ω _2a = 5.11,ω _2b = 5.11	−18848.00					69 S, 103 I

Selection analysis by branch-site models. BS: branch-site. lnL: log likelihood. LRT: likelihood ratio test. df: degrees of freedom. 2∆lnL: twice the log-likelihood difference of the models compared. The significant tests at 95 % cut off are labeled with*. Bold: P < 0.05

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