Malaria parasite sequences from chimpanzee support the co-speciation hypothesis for the origin of virulent human malaria (Plasmodium falciparum)

Abstract

Phylogenetic analyses of the mitochondrial cytochrome b (cytb), apicoplast caseinolytic protease C (clpC), and 18S rRNA sequences of Plasmodium isolates from chimpanzees along with those of the virulent human malaria parasite P. falciparum showed that the common chimpanzee (Pan troglodytes) malaria parasites, assigned by Rich et al. (2009) to P. reichenowi, constitute a paraphyletic assemblage. The assumption that P. falciparum diverged from P. reichenowi as recently as 5000-50,000 years ago would require a rate of synonymous substitution/site/year in cytb and clpC on the order of 10(-5)-10(-6), several orders of magnitude higher than any known from eukaryotic organelle genomes, and would imply an unrealistically recent timing of the most recent common ancestor of P. falciparum mitochondrial genomes. The available data are thus most consistent with the hypothesis that P. reichenowi (in the strict sense) and P. falciparum co-speciated with their hosts about 5-7 million years ago.

Figure 1

ME tree of Plasmodium cytb sequences (477 aligned sites) based on the MCL distance. Clusters of P. falciparum and P. vivax sequences are condensed for ease of presentation; for accession numbers see Supplementary Table S1. Numbers on the branches are confidence levels of the standard-error test; only values ≥ 90% are shown.

Figure 2

ME tree of Plasmodium cytb sequences (477 aligned sites) based on the TN distance. Clusters of P. falciparum and P. vivax sequences are condensed for ease of presentation; for accession numbers see Supplementary Table S1. Numbers on the branches are confidence levels of the standard-error test; only values ≥ 90% are shown.

Figure 3

ME tree of Plasmodium cytb sequences, including those of Prugnolle et al. (2010; 349 aligned sites) based on the MCL distance. Clusters of P. falciparum and P. vivax sequences are condensed for ease of presentation; for accession numbers see Supplementary Table S1. Numbers on the branches are confidence levels of the standard-error test; only values ≥ 90% are shown.

Figure 4

ME tree of Plasmodium clpC sequences based on the MCL distance. Numbers on the branches are confidence levels of the standard-error test; only values ≥ 90% are shown.

Figure 5

ME tree of Plasmodium 18S rRNA sequences based on the MCL distance. Numbers on the branches are confidence levels of the standard-error test; only values ≥ 90% are shown.