Multigenomic Delineation ofPlasmodiumSpecies of theLaveraniaSubgenus Infecting Wild-Living Chimpanzees and Gorillas

Abstract

Plasmodium falciparum, the major cause of malaria morbidity and mortality worldwide, is only distantly related to other human malaria parasites and has thus been placed in a separate subgenus, termed Laverania. Parasites morphologically similar to P. falciparum have been identified in African apes, but only one other Laverania species, Plasmodium reichenowi from chimpanzees, has been formally described. Although recent studies have pointed to the existence of additional Laverania species, their precise number and host associations remain uncertain, primarily because of limited sampling and a paucity of parasite sequences other than from mitochondrial DNA. To address this, we used limiting dilution polymerase chain reaction to amplify additional parasite sequences from a large number of chimpanzee and gorilla blood and fecal samples collected at two sanctuaries and 30 field sites across equatorial Africa. Phylogenetic analyses of more than 2,000 new sequences derived from the mitochondrial, nuclear, and apicoplast genomes revealed six divergent and well-supported clades within the Laverania parasite group. Although two of these clades exhibited deep subdivisions in phylogenies estimated from organelle gene sequences, these sublineages were geographically defined and not present in trees from four unlinked nuclear loci. This greatly expanded sequence data set thus confirms six, and not seven or more, ape Laverania species, of which P. reichenowi, Plasmodium gaboni, and Plasmodium billcollinsi only infect chimpanzees, whereas Plasmodium praefalciparum, Plasmodium adleri, and Pladmodium blacklocki only infect gorillas. The new sequence data also confirm the P. praefalciparum origin of human P. falciparum.

Out of Africa: origins and evolution of the human malaria parasites Plasmodium falciparum and Plasmodium vivax

“…2A summarizes the current knowledge concerning the geographic distribution and host species association of ape Laverania infections at over 100 field sites across sub-Saharan Africa (Kaiser et al, 2010; Liu et al, 2010a; De Nys et al, 2013; Boundenga et al, 2015; Liu et al, 2016). All chimpanzee subspecies, including western ( Pan troglodytes verus ), Nigeria-Cameroon ( Pan troglodytes ellioti ), central ( Pan troglodytes troglodytes ) and eastern ( Pan troglodytes schweinfurthii ) chimpanzees, as well as western lowland gorillas ( G. g. gorilla ) are endemically infected with Laverania parasites, with fecal detection rates ranging from 24% to 40% (Table 1).…”

“…All six Laverania spp. have been classified based on numerous SGA-derived organelle and nuclear gene sequences from many different field isolates (Liu et al, 2010a,, 2016). In addition, whole genome sequencing of P. reichenowi and P. gaboni parasites confirmed that they represent distinct species, with no evidence of interspecific hybridization (Otto et al, 2014; Sundararaman et al, 2016).…”

“…2A). SGA, which yields a proportional representation of all parasites present in a sample, failed to detect even minor fractions of parasites from the “wrong” species in more than 100 Laverania -infected apes (Liu et al, 2016). In contrast, host species specificity in captivity is not absolute (Duval et al, 2010; Pacheco et al, 2013), and so it will be of great interest to decipher to what extent host and/or vector biology contribute to host species restriction in the wild.…”

“…Diamonds in (B) indicate the capture sites of ape P. vivax infected sanctuary chimpanzees (black border) and gorillas (green border), respectively, and a star denotes the location where a European forester became infected with ape P. vivax (Prugnolle et al, 2013). Data were compiled from published (Kaiser et al, 2010; Liu et al, 2010a, 2014, 2016; De Nys et al, 2013; Paupy et al, 2013; Prugnolle et al, 2013; Boundenga et al, 2015) and unpublished studies (Table 1). The full names and locations of all sites are provided in Supplementary Table S1.…”

“…Asterisks at major nodes indicate bootstrap values ≥ 65%, and the scale bars represent (A, B) 0.01 nucleotide substitutions per site, or (C) 0.001 amino acid replacements per site, respectively. Sequences were combined from multiple studies (Kaiser et al, 2010; Krief et al, 2010; Liu et al, 2010a, 2016; Prugnolle et al, 2011). …”