Functional divergence of the NIP III subgroup proteins involved altered selective constraints and positive selection

Table 2 Results of positive selection analysis using a variety of codon substitution models

Model	Omega distribution	lnL	2Δℓ	Positively selected sites^a,b
M0 (one ratio)	ω = 0.197	-13752.4		None
M3 (discrete)	0.97% sites: ω = 1.85; 99.03% sites: 0.01<ω < 0.80	-13171.3	1162.2 (M3 vs M0) p < < 0.01	28T, 77S
M7 (β)	ω = 0.243	-13181.8		Not allowed
M8 (β+ω > 1)	1.72% sites: ω = 1.54; 98.28% sites: 0.0004<ω < 0.76	-13176.7	10.2 (M8 vs M7) p < 0.01	28T, 30P, 38A, 77S, 245M

Note: ^a, Codon sites under positive selection that are estimated using the program CODEML implemented in the PAML package v4.4. Asterisk (*) denotes posterior probability > 0.95.
^b, Codon (amino acid) positions presented above are based on the rice OsNIP2;1 gene.

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