Legend for Supplementary Figures online:
Supplementary Figure 1. Simplified life cycle of malaria parasites in human
hosts. The parasite’s development within mosquito vectors is not
represented. A few (5-20) haploid sporozoites are inoculated by bloodfeeding female Anopheles mosquitoes. After 30-60 min in the bloodstream,
these uninucleate extracellular stages penetrate hepatocytes and start
intense mitotic activity and nuclear division. The resulting mature,
multinucleate liver-stage schizont bursts within 9-16 days and releases
thousands of free merozoites, which are released into the bloodstream.
Within 1-2 min of release, merozoites invade red blood cells, where they
develop over 48 or 72 hours from early to late trophozoites and undergo a
further phase of mitotic division, which generates erythrocytic-stage
schizonts. When infected red blood cells rupture, each mature schizont
releases 8-32 merozoites, each of which invades new erythrocytes. After a
few cycles of asexual reproduction, some merozoites develop into sexual
stages known as gametocytes. When gametocytes are taken up by feeding
Anopheles mosquitoes, they mature into male and female gametes and unite to
form a zygote in the midgut of the vector. The zygote is the sole diploid
stage of malaria parasites; the only meiosis event during this life cycle
occurs within a few hours of zygote formation. This process generates
thousands of infective sporozoites, which migrate to the salivary glands of
mosquitoes.
Supplementary Figure 2. Comparison between nucleotide sequences of P.
reichenowi Msp-6 (assembled from data generated by the P. reichenowi genome
sequencing project) and the dimorphic lineages (K1 and 3D7) of P. falciparum
Msp-6. Note that the alignment of repetitive domains between species is
disturbed by the proliferation of different repeat units (see, for example,
the GAA GAA AAA ACA motif [underlined] in P. reichenowi Msp-6), indicated by
grey shading. Three blocks of sequence (15-, 24- and 129-bp long) present in
K1-type and P. reichenowi alleles are absent from 3D7-type alleles (see also
Figure 1 in the printed version of the paper). The following notation was
used to highlight some features of the aligned sequences: (a) black shading
shows nucleotide substitutions shared by P. reichenowi and one of the
dimorphic alleles of P. falciparum, (b) boldface italicised letters indicate
fixed differences between P. reichenowi and both P. falciparum alleles, (c)
boldface non-italicised letters indicate polymorphic sites within P.
falciparum lineages (nucleotides 295, 566 and 848), (d) lowercase letters
indicate a position (nucleotide 639) where P. falciparum lineages and P.
reichenowi all differ from each other, and (e) << and >> indicate repetitive
regions.
Supplementary Figure 3. Comparison of deduced amino acid sequences for P.
reichenowi Msp-3 (AF252287) and four allelic lineages of P. falciparum,
represented by the following isolates: (a) CSL2 (Thailand, U08852) and
FCC1/HN (China, AF188190), (b) K1 (Thailand, U08851), (c) D10 clone of FC27
(Papua New Guinea, L07944) and 3D7 clone of NF54 (presumably from Africa,
L28825). The following domains of MSP-3 (see also Figure 1 in the printed
version of the paper) are highlighted: (a) three blocks of Ala-X-X-Ala-X-X-X
heptad repeats (where Ala = alanine and X is any residue), grey shading
(residues 95-129, 138-166 and 190-218), (b) the glutamic acid (E)-rich
domain, black shading (residues 262-314), and (c) the putative leucine
zipper-like motif, light grey shading (residues 340-382). The D10 allele is
a mosaic of CSL2-type motifs (for example, residues 82-110) and 3D7-type
motifs (for example, residues 111-160). Bold italicized letters indicate
fixed differences between P. falciparum and P. reichenowi; codons with
synonymous nucleotide substitutions are underlined.
Supplementary Fig. 4. Critical values for the one-fourth rule.
n is the
number of individuals in the sample (or, in the case of balancing selection,
the number of allelic classes),  the mutation rate. For each pair of
parameters, we performed 10,000 coalescent simulations. For each simulation,
we calculated the ratio of the average genetic divergences 1) between pairs
of individuals whose last common ancestor is more recent than the last
common ancestor of the sample and 2) between pairs of individuals whose last
common ancestor is the last common ancestor of the sample.
which 95% of simulations yielded a higher ratio is given.
The value for