Phylogeny of Asian primate malaria parasites inferred from apicoplast genome-encoded genes with special emphasis on the positions of Plasmodium vivax and P. fragile

Gene

Volumn 450, Issue 1-2, 2010, Pages 32-38

  Mitsui, Hideya ^a,b   Arisue, Nobuko ^c   Sakihama, Naoko ^d   Inagaki, Yuji ^a   Horii, Toshihiro ^c   Hasegawa, Masami ^b   Tanabe, Kazuyuki ^d   Hashimoto, Tetsuo ^a  

^a UNIVERSITY OF TSUKUBA   (Japan)

^b GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

^c OSAKA UNIVERSITY   (Japan)

^d OSAKA UNIVERSITY   (Japan)

Author keywords

Codon substitution model; Combined molecular phylogeny; Model comparison; Plasmodium fragile; Plasmodium vivax

Indexed keywords

ELONGATION FACTOR TU; ENDOPEPTIDASE CLP; LARGE SUBUNIT RIBOSOMAL RNA; SMALL SUBUNIT RIBOSOMAL RNA;

APICOPLAST; ARTICLE; ASIA; CONTROLLED STUDY; GENE AMPLIFICATION; GENE SEQUENCE; GENOME; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLASMODIUM; PLASMODIUM COATNEYI; PLASMODIUM CYNOMOLGI; PLASMODIUM FIELDI; PLASMODIUM FRAGILE; PLASMODIUM GONDERI; PLASMODIUM HYLOBATI; PLASMODIUM INUI; PLASMODIUM KNOWLESI; PLASMODIUM SIMIOVALE; PLASMODIUM VIVAX; PRIMATE; PRIORITY JOURNAL; PROTOZOAL GENETICS;

ANIMALS; GENETIC MARKERS; HUMANS; MALARIA; PHYLOGENY; PLASMODIUM; PLASMODIUM VIVAX; PRIMATES;

CERCOPITHECIDAE; PLASMODIUM COATNEYI; PLASMODIUM CYNOMOLGI; PLASMODIUM FIELDI; PLASMODIUM FRAGILE; PLASMODIUM GONDERI; PLASMODIUM HYLOBATI; PLASMODIUM KNOWLESI; PLASMODIUM SIMIOVALE; PLASMODIUM VIVAX; PRIMATES;

EID: 72449210137     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2009.10.001     Document Type: Article

References (38)

1. Adachi J, Hasegawa M. Computer Science Monographs, No. 28, MOLPHY Version 2.3: Programs for Molecular Phylogenetics Based on Maximum Likelihood. 1996, The Institute of Statistical Mathematics, Tokyo.
2. Akaike H. Information theory and an extension of the maximum likelihood principle. Proceedings of the Second International Symposium on Information Theory. 1973, 267-281. Akademiai Kiado, Budapest. B.N. Petrov, F. Caski (Eds.).
3. Arisue N, Hirai M, Arai M, Matsuoka H, Horii T. Phylogeny and evolution of the SERA multigene family in the genus Plasmodium. J. Mol. Evol. 2007, 65:82-91.
4. Carlton J.M, et al. Comparative genomics of the neglected human malaria parasite Plasmodium vivax. Nature. 2008, 455:757-763.
5. Coatney GR, Collins WE, Warren M, Contacos PG. Plasmodium coatneyi. The Primate Malarias. 1971, 289-299. US Government Printing Office, Washington DC.
6. Creasey A, Mendis K, Carlton J, Williamson D, Wilson I, Carter R. Material inheritance of extrachromosomal DNA in malaria parasites. Mol. Biochem. Parasitol. 1994, 65:95-98.
7. Escalante A.A, et al. A monkey's tale: the origin of Plasmodium vivax as a human malaria parasite. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:1980-1985.
8. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 1985, 39:783-791.
9. Hasegawa M, Kishino H, Yano T. Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 1985, 22:160-174.
10. Hayakawa T, Culleton R, Otani H, Horii T, Tanabe K. Big bang in the evolution of extant malaria parasites. Mol. Biol. Evol. 2008, 25:2233-2239.
11. Inagaki Y, Roger AJ. Phylogenetic estimation under codon models can be biased by codon usage heterogeneity. Mol. Phylogenet. Evol. 2006, 40:428-434.
12. Inagaki Y, Nakajima Y, Sato M, Sakaguchi M, Hashimoto T. Gene sampling can bias multi-gene phylogenetic inferences: the relationship between red algae and green plants as a case study. Mol. Biol. Evol. 2009, 26:1171-1178.
13. Kishino H, Miyata T, Hasegawa M. Maximum likelihood inference of protein phylogeny and the origin of chloroplasts. J. M. Evol. 1990, 30:151-160.
14. Leclerc MC, Hugot JP, Durand P, Renaud F. Evolutionary relationships between 15 Plasmodium species from new and old world primates (including humans): an 18S rDNA cladistic analysis. Parasitology. 2004, 129:677-684.
15. Miyata T, Miyazawa S, Yasunaga T. Two types of amino acid substitutions in protein evolution. J. Mol. Evol. 1979, 12:219-236.
16. Mu J, et al. Host switch leads to emergence of Plasmodium vivax malaria in humans. Mol. Biol. Evol. 2005, 22:1686-1693.
17. Nishimoto Y, et al. Evolution and phylogeny of the heterogeneous cytosolic SSU rRNA genes in the genus Plasmodium. Mol. Phylogenet. Evol. 2008, 47:45-53.
18. Okamoto N, Janouškovec J, Chrudimský T, Lukeš J. Evolution of the apicoplast and its hosts: from heterotrophy to autotrophy and back again. Int. J. Parasitol. 2009, 39:1-2.
19. Okamoto N, Spurck TP, Goodman CD, McFadden GI. Apicoplast and mitochondrion in gametocytogenesis of Plasmodium falciparum. Eukaryot. Cell. 2009, 8:128-132.
20. Pain A, et al. The genome of the simian and human malaria parasite Plasmodium knowlesi. Nature. 2008, 455:799-803.
21. Perkins SL, Schall JJ. A molecular phylogeny of malarial parasites recovered from cytochrome b gene sequences. J. Parasitol. 2002, 88:972-978.
22. Pupko T, Huchon D, Cao Y, Okada N, Hasegawa M. Combining multiple data sets in a likelihood analysis: which models are the best?. Mol. Biol. Evol. 2002, 19:2294-2307.
23. Rathore D, Wahl AM, Sullivan M, McCutchan TF. A phylogenetic comparison of gene trees constructed from plastid, mitochondrial and genomic DNA of Plasmodium species. Mol. Biochem. Parasitol. 2001, 114:89-94.
24. Rodriguez F, Oliver JL, Marin A, Medina JR. The general stochastic model of nucleotide substitution. J. Theor. Biol. 1990, 142:485-501.
25. Sakihama N, Mitamura T, Kaneko A, Horii T, Tanabe K. Long PCR amplification of Plasmodium falciparum DNA extracted from filter paper blots. Exp. Parasitol. 2001, 97:50-54.
26. Schmidt HA, Strimmer K, Vingron M, von Haeseler A. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics. 2002, 18:502-504.
27. Shimodaira H, Hasegawa M. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics. 2001, 17:1246-1247.
28. Simodaira H. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 2002, 51:492-508.
29. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006, 22:2688-2690.
30. Stamatakis A, Ludwig T, Meier H. RAxML-III: a fast program for maximum likelihood-based inference of phylogenetic trees. Bioinformatics. 2005, 21:456-463.
31. Tanabe K, et al. Recent independent evolution of msp1 polymorphism in Plasmodium vivax and related simian malaria parasites. Mol. Biochem. Parasitol. 2007, 156:74-79.
32. Vargas-Serrato E, Corredor V, Galinski MR. Phylogenetic analysis of CSP and MSP-9 gene sequences demonstrates the close relationship of Plasmodium coatneyi to Plasmodium knowlesi. Infect. Genet. Evol. 2003, 3:67-73.
33. Williamson DH, Preiser PR, Moore PW, McCready S, Strath M, Wilson RJM. The plastid DNA of the malaria parasite Plasmodium falciparum is replicated by two mechanisms. Mol. Microbiol. 2002, 45:533-542.
34. Wilson R.J, et al. Complete gene map of the plastid-like DNA of the malaria parasite Plasmodium falciparum. J. Mol. Biol. 1996, 261:155-172.
35. Yang Z. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 1994, 39:306-314.
36. Yang Z. Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol. Evol. 1996, 11:367-372.
37. Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comp. Appl. Biosci. 1997, 13:555-556.
38. Yang Z, Nielsen R, Hasegawa M. Models of amino acid substitution and application to mitochondrial protein evolution. Mol. Biol. Evol. 1998, 15:1600-1611.