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MBE Advance Access published online on March 21, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn069
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© 2008 The Authors
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

research article

Origins of Human Malaria: Rare Genomic Changes and Full Mitochondrial Genomes Confirm the Relationship of Plasmodium falciparum to Other Mammalian Parasites, but Complicate the Origins of P. vivax

Scott William Roy1 and Manuel Irimia2

1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
2 Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain

Corresponding author: SWR, telephone number: 301-496-8941, scottwroy{at}gmail.com

Received for publication January 5, 2008. Revision received February 27, 2008. Revision received March 11, 2008. Accepted for publication March 15, 2008.

Despite substantial work, the phylogeny of malaria parasites remains debated. The matter is complicated by concerns about patterns of evolution in potentially strongly selected genes as well as the extreme AT-bias of some Plasmodium genomes. Particularly contentious has been the position of the most virulent human parasite P. falciparum, whether grouped with avian parasites or within a larger clade of mammalian parasites. Here, we study three classes of rare genomic changes, as well as the sequences of mitochondrial rRNA genes. We report three lines of support for a clade of mammalian parasites: (i) we find no instances of spliceosomal intron loss in a hypothetical ancestor of P. falciparum and the avian parasite P. gallinaceum, suggesting against a close relationship between those species; (ii) we find four genomic mitochondrial indels supporting a mammalian clade, but none grouping P. falciparum with avian parasites; and (iii) slowly evolving mitochondrial rRNA sequences support a mammalian parasite clade with 100% posterior probability. We further report a large deletion in the mitochondrial LSU rRNA gene, which suggests a subclade including both African and Asian parasites within the clade of closely related primate malarias. This contrasts with previous studies that provided strong support for separate Asian and African clades, and reduces certainty about the historical and geographic origins of P. vivax. Finally, we find a lack of synapomorphic gene losses, suggesting a low rate of ancestral gene loss in Plasmodium.


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