Lineage-specific positive selection at the merozoite surface protein 1 (msp1) locus of Plasmodium vivax and related simian malaria parasites

Table 1 Topology difference between the mitochondrial genome tree and msp1 trees.

		Mitochondrial genome^a		msp1 ^b
	Topology of the ML best tree	Δli^c	p-value^d	Δli^c	p-value^d
mitochondrial genome	(((((Pcy,Pvi),(Phy,Pin)),Pfi),(Pco,Pkn)),Pfr,Pgo)	(-14380.5)		-23.6	0.041
msp1 all sites msp1 codon 1 + 2	((((Pcy,Pfi),((Pco,Pkn),Pfr)),(Phy,Pin)),Pvi,Pgo) ((((Pcy,Pfi),((Pco,Pkn),Pfr)),(Phy,Pin)),Pvi,Pgo)	-42.1 -42.1	0.003 0.003	(-28818.3) (-28818.3)
msp1 codon 3	((((Pcy,(Pfi,Pvi)),(Phy,Pin)),(Pco,Pkn)),Pfr,Pgo)	-9.4	0.333	-23.4	0.030

^a The mitochondrial genome sequences were applied to each of the 3 msp1 trees (msp1 all sites, msp1 codon 1 + 2, and msp1 codon 3), and topology difference was evaluated using the PAML software package [52].
^b The msp1 sequences were applied to each of the mitochondrial genome tree and the msp1 codon 3 tree, and topology difference was evaluated.
^c Log-likelihood difference of the alternative tree against the best tree.
^d p-values are obtained with the Shimodaira-Hasegawa test [51].

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