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 Plasmodium vivax (Molecular Biology and Evolution (2008) 25,6, (1192-1198) DOI: 10.1093/molbev/msn069);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 Plasmodium vivax

Molecular Biology and Evolution

Volumn 25, Issue 6, 2008, Pages 1192-1198

  Roy, Scott William ^a   Irimia, Manuel ^b  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b UNIVERSITY OF BARCELONA   (Spain)

Author keywords

Apicomplexan evolution; Parasite evolution; Phylogenetic methods; Rare genomic characters

Indexed keywords

MITOCHONDRIAL RNA; RIBOSOME RNA; RNA; RNA, MITOCHONDRIAL;

ARTICLE; CLADISTICS; EVOLUTIONARY ADAPTATION; GENE DELETION; GENE LOCUS; GENE LOSS; GENE SEQUENCE; GENOME ANALYSIS; INTRON; MALARIA; MITOCHONDRIAL GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PARASITE VIRULENCE; PHYLOGENY; PLASMODIUM FALCIPARUM; PLASMODIUM GALLINACEUM; PLASMODIUM VIVAX; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; ANIMAL; CLASSIFICATION; GENETICS; GENOME; HUMAN; MALARIA FALCIPARUM; METABOLISM; MITOCHONDRIAL GENOME; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PARASITOLOGY; RNA GENE; RNA SPLICING; SPLICEOSOME;

AVES; MAMMALIA; PLASMODIUM FALCIPARUM; PLASMODIUM GALLINACEUM; PLASMODIUM VIVAX; PRIMATES;

ANIMALS; BASE SEQUENCE; EVOLUTION, MOLECULAR; GENES, RRNA; GENOME, MITOCHONDRIAL; GENOME, PROTOZOAN; HUMANS; INTRONS; MALARIA, FALCIPARUM; MALARIA, VIVAX; MOLECULAR SEQUENCE DATA; PLASMODIUM FALCIPARUM; PLASMODIUM VIVAX; RNA; RNA SPLICING; RNA, RIBOSOMAL; SEQUENCE DELETION; SPLICEOSOMES;

EID: 44649136815     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msn191     Document Type: Erratum

References (33)

1. Andersson SG, Kurland CG. 1998. Reductive evolution of resident genomes. Trends Microbiol. 6:263-268.
2. Corredor V, Enea V. 1993. Plasmodial ribosomal RNA as phylogenetic probe: a cautionary note. Mol Biol Evol. 10:924-926.
3. Darby AC, Cho NH, Fuxelius HH, Westberg J, Andersson SG. 2007. Intracellular pathogens go extreme: genome evolution in the Rickettsiales. Trends Genet. 23:211-220.
4. Dávalos LM, Perkins SL. 2008. Saturation and base composition bias explain phylogenomic conflict in Plasmodium. Genomics.
5. Escalante AA, Ayala FJ. 1994. Phylogeny of the malarial genus Plasmodium, derived from rRNA gene sequences. Proc Natl Acad Sci USA. 91:11373-11377.
6. Escalante AA, Barrio E, Ayala FJ. 1995. Evolutionary origin of human and primate malarias: evidence from the circumsporozoite protein gene. Mol Biol Evol. 12:616-626.
7. Escalante AA, Freeland DE, Collins WE, Lal AA. 1998. The evolution of primate malaria parasites based on the gene encoding cytochrome b from the linear mitochondrial genome. Proc Natl Acad Sci USA. 95:8124-8129.
8. Escalante AA, Goldman IF, De Rijk P, De Wachter R, Collins WE, Qari SH, Lal AA. 1997. Phylogenetic study of the genus Plasmodium based on the secondary structure-based alignment of the small subunit ribosomal RNA. Mol Biochem Parasitol. 90:317-321.
9. Frugoli JA, McPeek MA, Thomas TL, McClung CR. 1998. Intron loss and gain during evolution of the catalase gene family in angiosperms. Genetics. 149:355-365.
10. Garnham PCC. 1966. Malaria parasites and other Haemosporidia. Oxford: Blackwell.
11. Hagner S, Misof B, Maier W, Kampen H. 2007. Bayesian analysis of new and old malaria parasite DNA sequence data demonstrates the need for more phylogenetic signal to clarify the descent of Plasmodium falciparum. Parasitol Res. 101:493-503.
12. Hugall AF, Foster R, Lee MS. 2007. Calibration choice, rate smoothing, and the pattern of tetrapod diversification according to the long nuclear gene RAG-1. Syst Biol. 56:543-563.
13. Hughes AL. 1991. Circumsporozoite protein genes of malaria parasites (Plasmodium spp.): evidence for positive selection on immunogenic regions. Genetics. 127:345-353.
14. Leclerc MC, Hugot JP, Durand P, Renaud F. 2004. Evolutionary relationships between 15 Plasmodium species from new and old world primates (including humans): an 18S rDNA cladistic analysis. Parasitol. 129:677-684.
15. Martinsen ES, Perkins SL, Schall JJ. 2007. A three-genome phylogeny of malaria parasites (Plasmodium and closely related genera): evolution of life-history traits and host switches. Mol Phylogenet Evol. 47:261-273.
16. McCutchan TF, Dame JB, Miller LH, Barnwell J. 1984. Evolutionary relatedness of Plasmodium species as determined by the structure of DNA. Science. 225:808-811.
17. McCutchan TF, Kissinger JC, Touray MG, Rogers MJ, Li J, Sullivan M, Braga EM, Krettli AU, Miller LH. 1996. Comparison of circumsporozoite proteins from avian and mammalian malarias: biological and phylogenetic implications. Proc Natl Acad Sci USA. 93:11889-11894.
18. Mu J, Joy DA, Duan J, et al. (11 co-authors). 2005. Host switch leads to emergence of Plasmodium vivax malaria in humans. Mol Biol Evol. 22:1686-1693.
19. Nguyen H, Yoshihama M, Kenmochi N. 2005. New maximum likelihood estimators for eukaryotic intron evolution. PLoS Comput Biol. 1:e79.
20. Nguyen HD, Yoshihama M, Kenmochi N. 2007. The evolution of spliceosomal introns in alveolates. Mol Biol Evol. 24:1093-1096.
21. Niu D-K, Hou W-R, Li S-W. 2005. mRNA-mediated intron losses: evidence from extraordinarily large exons. Mol Biol Evol. 22:1475-1481.
22. Perkins SL, Schall JJ. 2002. A molecular phylogeny of malarial parasites recovered from cytochrome b gene sequences. J Parasitol. 88:972-978.
23. Qari SH, Shi YP, Pieniazek NJ, Collins WE, Lal AA. 1996. Phylogenetic relationship among the malaria parasites based on small subunit rRNA gene sequences: monophyletic nature of the human malaria parasite, Plasmodium falciparum. Mol Phylogenet Evol. 6:157-165.
24. Reisz RR, Müller J. 2004. Molecular timescales and the fossil record: a paleontological perspective. Trends Genet. 20:237-241.
25. Rokas A, Holland PWH. 2000. Rare genomic changes as a tool for phylogenetics. Trends Ecol Evol. 15:454-459.
26. Roy SW, Gilbert W. 2005a. Resolution of a deep animal divergence by the pattern of intron conservation. Proc Natl Acad Sci USA. 102:4403-4408.
27. Roy SW, Gilbert W. 2005b. The pattern of intron loss. Proc Natl Acad Sci USA. 102:713-718.
28. Roy SW, Hartl DL. 2006. Very little intron loss/gain in Plasmodium: intron loss/gain mutation rates and intron number. Genome Res. 16:750-756.
29. Roy SW, Irimia M. 2008. Rare genomic characters do not support Coelomata: intron loss/gain. Mol Biol Evol. 25:620-623.
30. Roy SW, Penny D. 2006. Large-scale intron conservation and order-of-magnitude variation in intron loss/gain rates in apicomplexan evolution. Genome Res. 16:1270-1275.
31. Venkatesh B, Ning Y, Brenner S. 1999. Late changes in spliceosomal introns define clades in vertebrate evolution. Proc Natl Acad Sci USA. 96:10267-10271.
32. Waters AP, Higgins DG, McCutchan TF. 1991. Plasmodium falciparum appears to have arisen as a result of lateral transfer between avian and human hosts. Proc Natl Acad Sci USA. 88:3140-3144.
33. Zheng J, Rogozin IB, Koonin EV, Przytycka TM. 2007. Support for the Coelomata clade of animals froma rigorous analysis of the pattern of intron conservation. Mol Biol Evol. 24:2583-2592.