Table 2 Nucleotide diversity in human and ape P. vivax lineages.

*P. vivax* genome	Locus	Length (bp)	Human *P. vivax**			Ape *P. vivax**			Ape/human ratio ^†	Distance to *P. cynomolgi* ^‡
			No.	π ( × 10⁻³)^§	Ratio ^\|\|	No.	π ( × 10⁻³)^§	Ratio ^\|\|		Distance	Ratio ^\|\|
Mitochondrial	cox1; cytb	2,443	138	0.75	1.0	62	1.02	1.0	1.4	0.012	1.0
Nuclear	ldh	679	114	1.58	2.1	42	14.07	13.8	8.9	0.161	13.5
Nuclear	asl	838	97	1.45	1.9	21	12.78	12.5	8.8	0.197	16.5
Nuclear	crk2	666	134	0.54	0.7	32	25.92	25.4	49.9	0.081	6.8
Nuclear	β-tub	684	81	0.81	1.1	12	11.85	11.6	14.6	0.161	13.5
Apicoplast	clpC	574	70	0.34	0.5	21	1.99	2.0	5.9	0.024	2.0

^*All human parasite sequences were derived using SGA methods from a global sampling of P. vivax strains (Supplementary Table 5), except for five completely sequenced reference genomes from the database (Salvador I, Brazil I, Mauritania I, North Korea and India VII). Ape P. vivax sequences were also derived by SGA from faecal and blood samples of wild-living and sanctuary apes (Supplementary Table 3).
^†Ratio of nucleotide diversity (π) values in ape and human parasites.
^‡Average distance between P. vivax and the orthologous sequences from P.cynomolgi.
^§Nucleotide diversity (π). Human and ape sequences were compared over the same length of sequence.
^||Diversity (or distance) value expressed relative to that for mtDNA.

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