Table 1 Analysis of positive selection in PeuLAC family genes in P. euphratica using a branch-site PAML model

Branch-site Model	-ln L	2△ (ln L)	P-value	Parameter estimates	Positively selected sites
Dataset I: all PeuLACs (40 sequences)
Branch F
Null	6929.287611			ω₀ = 0.11, ω₁ = 1.0, ω₂ = 1.0
Alternative	6922.843499	12.89	<0.001	ω₀ = 0.11, ω₁ = 1.0, ω₂ = 999.000	22Y (0.990); 65S (0.999); 85S (0.993); 92D (0.993*)
Branch D
Null	6931.431556			ω₀ = 0.11, ω₁ = 1.0, ω₂ = 1.0
Alternative	6920.259594	22.34	<0.001	ω₀ = 0.11, ω₁ = 1.0, ω₂ = 999.000
Dataset II: clade VI (3 sequences)
Branch (terminal branch of PeuLAC2)
Null	4739.621196			ω₀ = 0.06, ω₁ = 1.0, ω₂ = 1.0
Alternative	4736.546196	6.15	=0.013	ω₀ = 0.07, ω₁ = 1.0, ω₂ = 88.382	170S (0.867); 240G (0.856); 277S (0.824); 396K (0.842); 432S (0.832); 483K (0.890)
Dataset III: clade IV (9 sequences)
Branch a
Null	5541.400987			ω₀ = 0.07, ω₁ = 1.0, ω₂ = 1.0
Alternative	5534.424466	13.95	<0.001	ω₀ = 0.07, ω₁ = 1.0, ω₂ = 13.415
Branch b
Null	5537.882645			ω₀ = 0.06, ω₁ = 1.0, ω₂ = 1.0
Alternative	5532.622033	10.52	<0.001	ω₀ = 0.07, ω₁ = 1.0, ω₂ = 4.560
Branch e
Null	5555.958312			ω₀ = 0.07, ω₁ = 1.0, ω₂ = 1.0
Alternative	5549.757667	12.40	<0.001	ω₀ = 0.08, ω₁ = 1.0, ω₂ = 998.990
Branch d
Null	5556.551602			ω₀ = 0.08, ω₁ = 1.0, ω₂ = 1.0
Alternative	5549.891034	13.32	<0.001	ω₀ = 0.08, ω₁ = 1.0, ω₂ = 998.997
Branch g
Null	5557.376628			ω₀ = 0.08, ω₁ = 1.0, ω₂ = 1.0
Alternative	5553.172610	8.41	<0.001	ω₀ = 0.08, ω₁ = 1.0, ω₂ = 119.419

Note: Codons identified by PAML as under positive selection along with Bayesian (BEB) analysis posterior probability for sites with P > 0.80 under branch-site models (*, 0.99 > P > 0.80; **, P > 0.99)

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