Molecular evolution and phylogenetics of rodent malaria parasites

BMC Evolutionary Biology

Volumn 12, Issue 1, 2012, Pages

  Ramiro, Ricardo S ^a   Reece, Sarah E ^a   Obbard, Darren J ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

Divergence time; Molecular evolution; Phylogeny; Plasmodium; Rodent malaria; Species delimitation

Indexed keywords

DIVERGENCE; GENOTYPE; HOST-PARASITE INTERACTION; MALARIA; MOLECULAR ANALYSIS; NUMERICAL MODEL; PARASITOLOGY; PHYLOGENETICS; PHYLOGENY; POLYMORPHISM; POPULATION STRUCTURE; RODENT;

PLASMODIUM BERGHEI; PLASMODIUM CHABAUDI; PLASMODIUM VINCKEI; PLASMODIUM YOELII; RODENTIA;

PROTOZOAL DNA; PROTOZOAL PROTEIN;

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; GENOTYPE; HOST PARASITE INTERACTION; MALARIA; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PARASITOLOGY; PHYLOGENY; PHYSIOLOGY; PLASMODIUM; PLASMODIUM BERGHEI; PLASMODIUM CHABAUDI; PLASMODIUM YOELII; RODENT; TIME;

ANIMALS; BAYES THEOREM; DNA, PROTOZOAN; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENOTYPE; HOST-PARASITE INTERACTIONS; MALARIA; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLASMODIUM; PLASMODIUM BERGHEI; PLASMODIUM CHABAUDI; PLASMODIUM YOELII; PROTOZOAN PROTEINS; RODENTIA; SEQUENCE ANALYSIS, DNA; TIME FACTORS;

MLCS; MLOWN;

EID: 84868712208     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-12-219     Document Type: Article

References (51)

1. Killick-Kendrick R, Peters W, Rodent Malaria London: Academic Press 1978
2. The contribution of Plasmodium chabaudi to our understanding of malaria. Stephens R, Culleton RL, Lamb TJ, Trends Parasitol 2012 28 2 73 82
3. Of mice and malaria mutants: unravelling the genetics of drug resistance using rodent malaria models. Carlton J, Hayton K, Cravo P, Walliker D, Trends Parasitol 2001 17 5 236 242 (Pubitemid 32422169)
4. The role of animal models for research on severe malaria. Craig AG, Grau GE, Janse C, Kazura JW, Milner D, Barnwell JW, Turner G, Langhorne J, Model HRMA, Plos Pathog 2012 8 2 1002401
5. Sexual development in plasmodium: lessons from functional analyses. Guttery DS, Holder AA, Tewari R, Plos Pathog 2012 8 1 1002404
6. Proteome analysis of separated male and female gametocytes reveals novel sex-specific biology. Khan S, Frankefayard B, Mair G, Lasonder E, Janse C, Mann M, Waters A, Cell 2005 121 5 675 687 (Pubitemid 40797591)
7. Molecular epidemiology of malaria. Conway DJ, Clin Microbiol Rev 2007 20 1 188 204 (Pubitemid 46167773)
8. Wilson DE, Reeder DM, Mammal Species of the World. A Taxonomic and Geographic Reference Baltimore: Johns Hopkins University Press 3 2005
9. Species tree inference in the age of genomics. Whelan NV, Trends Evol Biol 2011 3 1 23 28
10. Adaptive protein evolution at the Adh locus in Drosophila. McDonald JH, Kreitman M, Nature 1991 351 6328 652 654 (Pubitemid 21896661)
11. Bayesian inference of species trees from multilocus data. Heled J, Drummond A, Mol Biol Evol 2010 27 3 570
12. Delimiting species using multilocus data: diagnosing cryptic diversity in the southern cavefish, typhlichthys subterraneus (teleostei: amblyopsidae). Niemiller ML, Near TJ, Fitzpatrick BM, Evolution 2012 66 3 846 866
13. Big bang in the evolution of extant malaria parasites. Hayakawa T, Culleton R, Otani H, Horii T, Tanabe K, Mol Biol Evol 2008 25 10 2233 2239
14. The phylogeny of rodent malaria parasites: Simultaneous analysis across three genomes. Perkins SL, Sarkar IN, Carter R, Infect Genet Evol 2007 7 1 74 83 (Pubitemid 44858297)
15. Bayesian species delimitation using multilocus sequence data. Yang Z, Rannala B, P Natl Acad Sci USA 2010 107 20 9264 9269
16. A genealogical approach to quantifying lineage divergence. Cummings MP, Neel MC, Shaw KL, Evolution 2008 62 9 2411 2422
17. Evaluation of a bayesian coalescent method of species delimitation. Zhang C, Zhang D-X, Zhu T, Yang Z, Syst Biol 2011 60 6 747 761
18. Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus). Leache AD, Fujita MK, P Roy Soc B-Biol Sci 2010 278 1705 490 492
19. Phylogeny of the malarial genus Plasmodium, derived from rRNA gene sequences. Escalante AA, Ayala FJ, P Natl Acad Sci USA 1994 91 24 11373 11377 (Pubitemid 24356346)
20. A molecular clock for malaria parasites. Ricklefs RE, Outlaw DC, Science 2010 329 5988 226 229
21. Timing the origin of human malarias: the lemur puzzle. Pacheco MA, Battistuzzi FU, Junge RE, Cornejo OE, Williams CV, Landau I, Rabetafika L, Snounou G, Jones-Engel L, Escalante AA, BMC Evol Biol 2011 11 1 299
22. Asynchronous Colonization of Madagascar by the Four Endemic Clades of Primates, Tenrecs, Carnivores, and Rodents as Inferred from Nuclear Genes. Poux C, Madsen O, Marquard E, Vieites DR, de Jong WW, Vences M, Systematic Biology 2005 54 5 719 730 Doi 10.1080/10635150500234534 (Pubitemid 43142291)
23. Mammalian biodiversity on Madagascar controlled by ocean currents. Ali JR, Huber M, Nature 2010 463 7281 653 U680 Doi 10.1038/Nature08706
24. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Librado P, Rozas J, Bioinformatics 2009 25 11 1451 1452
25. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Tajima F, Genetics 1989 123 3 585 595 (Pubitemid 19274682)
26. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Nei M, Gojobori T, Mol Biol Evol 1986 3 5 418 426 (Pubitemid 16010523)
27. PAML 4: phylogenetic analysis by maximum likelihood. Yang ZZ, Mol Biol Evol 2007 24 8 1586 1591
28. Evidence of cross-contamination among laboratory lines of Plasmodium berghei. Saula AA, Prescott NN, Smitha F, Cheng Q, Walliker DD, Mol Biochem Parasitol 1997 84 1 143 147 (Pubitemid 27090515)
29. Estimating the genomewide rate of adaptive protein evolution in drosophila. Welch JJ, Genetics 2006 173 2 821 837 (Pubitemid 43945899)
30. The molecular epidemiology of parasite infections: Tools and applications. Lymbery AJ, Thompson RCA, Molecular and Biochemical Parasitology 2012 181 2 102 116
31. Phylogeny and biogeography of African Murinae based on mitochondrial and nuclear gene sequences, with a new tribal classification of the subfamily. Lecompte E, Aplin K, Denys C, Catzeflis F, Chades M, Chevret P, BMC Evol Biol 2008 8 199
32. High efficiency transfection of Plasmodium berghei facilitates novel selection procedures. Janse CJ, Franke-Fayard B, Mair GR, Ramesar J, Thiel C, Engelmann S, Matuschewski K, van Gemert GJ, Sauerwein RW, Waters AP, Mol Biochem Parasitol 2006 145 1 60 70 (Pubitemid 41691855)
33. Linkage maps from multiple genetic crosses and loci linked to growth-related virulent phenotype in Plasmodium yoelii. Li J, Pattaradilokrat S, Zhu F, Jiang H, Liu S, Hong L, Fu Y, Koo L, Xu W, Pan W, et al. P Natl Acad Sci USA 2011 108 31 374 382 10.1073/pnas.1102261108
34. Sulfadoxine-pyrimethamine resistance in the rodent malaria parasite Plasmodium chabaudi. Hayton K, Ranford-Cartwright LC, Walliker D, Antimicrobial Agents and Chemotherapy 2002 46 8 2482 2489 Doi 10.1128/Aac.46.8.2482-2489.2002 (Pubitemid 34793453)
35. The effect of variation in the effective population size on the rate of adaptive molecular evolution in eukaryotes. Gossmann TI, Keightley PD, Eyre-Walker A, Genome Biol Evol 2012 4 5 658 667
36. Falcipain-1, a Plasmodium falciparum cysteine protease with vaccine potential. Kumar A, Kumar K, Korde R, Puri SK, Malhotra P, Singh Chauhan V, Infect Immun 2007 75 4 2026 2034 (Pubitemid 46559472)
37. Within-host competition in genetically diverse malaria infections: parasite virulence and competitive success. Bell AS, De Roode JC, Sim D, Read AF, Evolution 2006 60 7 1358 1371 (Pubitemid 44795580)
38. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Hall TA, Nucleic Acids Symposium Series 1999 41 41 95 98
39. GARD: a genetic algorithm for recombination detection. Kosakovsky Pond S, Posada D, Gravenor M, Woelk C, Frost S, Bioinformatics 2006 22 24 3096
40. Automated phylogenetic detection of recombination using a genetic algorithm. Kosakovsky Pond S, Posada D, Gravenor M, Woelk C, Frost S, Mol Biol Evol 2006 23 10 1891
41. Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Delport W, Poon AFY, Frost SDW, Kosakovsky Pond SL, Bioinformatics 2010 26 19 2455 2457
42. Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Kosakovsky Pond SL, Delport W, Poon AFY, Frost SDW, Bioinformatics 2010 26 19 2455 2457
43. BEAST: Bayesian evolutionary analysis by sampling trees. Drummond, BMC Evol Biol 2007 7 1 214 214
44. The biology of rodent malaria with particular reference to Plasmodium vinckei vinckei Rodhain 1952. Bafort J, Ann Soc Belge Méd Trop 1971 51 1 5
45. Hierarchical comparative analysis of genetic and genitalic geographical structure: testing patterns of male and female genital evolution in the scarab beetle. Polihronakis M, Biol J Linn Soc 2009 96 135 149
46. Species delimitation in fungal endophyte diversity studies and its implications in ecological and biogeographic inferences. Gazis R, Rehner S, Chaverri P, Mol Ecol 2011 20 14 3001 3013
47. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Hasegawa M, Kishino H, Yano T, J Mol Evol 1985 22 2 160 174 (Pubitemid 16227864)
48. Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. Sánchez R, Serra F, Tárraga J, Medina I, Carbonell J, Pulido L, de María A, Capella-Gutíerrez S, Huerta-Cepas J, Gabaldón T, et al. Nucleic Acids Res 2011 39 Web Server issue 470 474
49. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Guindon S, Gascuel O, Syst Biol 2003 52 5 696 704 (Pubitemid 37365050)
50. jModelTest: phylogenetic model averaging. Posada D, Mol Biol Evol 2008 25 7 1253 1256 (Pubitemid 351882013)
51. Burnham KP, Anderson DR, Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach New York: Springer 2002