Rerooting the evolutionary tree of malaria parasites

Proceedings of the National Academy of Sciences of the United States of America

Volumn 108, Issue 32, 2011, Pages 13183-13187

  Outlaw, Diana C ^a   Ricklefs, Robert E ^b  

^a MISSISSIPPI STATE UNIVERSITY   (United States)

^b UNIVERSITY OF MISSOURI ST LOUIS   (United States)

Author keywords

Bayes factors; Parasite diversification; Plasmodiidae

Indexed keywords

ARTICLE; BAYES THEOREM; HAEMOPROTEUS; HEPATOCYSTIS; LEUCOCYTOZOON; MOLECULAR CLOCK; NONHUMAN; PARAHAEMOPROTEUS; PARASITE VECTOR; PHYLOGENETIC TREE; PHYLOGENETIC TREE CONSTRUCTION METHOD; PHYLOGENETIC TREE ROOT; PLASMODIUM; POLYCHROMOPHILUS; PRIORITY JOURNAL;

ANIMALS; BAYES THEOREM; CYTOCHROMES B; EVOLUTION, MOLECULAR; LIKELIHOOD FUNCTIONS; MALARIA; MODELS, GENETIC; PARASITES; PHYLOGENY;

AVES; DIPTERA; HAEMOPROTEUS; HAEMOSPORIDA; LEUCOCYTOZOON; MAMMALIA; PLASMODIUM (APICOMPLEXA); PLASMODIUM PARASITES; VERTEBRATA;

EID: 80051960846     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1109153108     Document Type: Article

References (33)

1. Garnham P.C.C. (1966) Malaria Parasites and Other Haemosporidia (Blackwell Scientific, Oxford).
2. Valkiunas G. (2005) Avian Malaria Parasites and Other Haemosporidia (CRC Press, Boca Raton, FL).
3. Duval L., et al. (2007) Multiple host-switching of Haemosporidia parasites in bats. Malar J 6:157.
4. Chasar A., et al. (2009) Prevalence and diversity patterns of avian blood parasites in degraded African rainforest habitats. Mol Ecol 18:4121-4133.
5. Beadell J.S., et al. (2009) Host associations and evolutionary relationships of avian blood parasites from West Africa. Int J Parasitol 39:257-266.
6. Ishtiaq F., et al. (2007) Prevalence and diversity of avian hematozoan parasites in Asia: A regional survey. J Wildl Dis 43:382-398. (Pubitemid 47342982)
7. Bensch S., Hellgren O., Pérez-Tris J. (2009) MalAvi: A public database of malaria parasites and related haemosporidians in avian hosts based on mitochondrial cytochrome b lineages. Mol Ecol Resour 9:1353-1358.
8. Ricklefs R.E., Fallon S.M. (2002) Diversification and host switching in avian malaria parasites. Proc Biol Sci 269:885-892. (Pubitemid 34518130)
9. Huelsenbeck J.P., Bollback J.P., Levine A.M. (2002) Inferring the root of a phylogenetic tree. Syst Biol 51:32-43. (Pubitemid 35169406)
10. Esposito A., et al. (2008) FRET imaging of hemoglobin concentration in Plasmodium falciparum-infected red cells. PLoS ONE 3:e3780.
11. Rosenthal P.J., Meshnick S.R. (1996) Hemoglobin catabolism and iron utilization by malaria parasites. Mol Biochem Parasitol 83:131-139. (Pubitemid 27062385)
12. Escalante A.A., Freeland D.E., Collins W.E., Lal A.A. (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. (Pubitemid 28326077)
13. Perkins S.L., Schall J.J. (2002) A molecular phylogeny of malarial parasites recovered from cytochrome b gene sequences. J Parasitol 88:972-978. (Pubitemid 35278746)
14. Farris J.S. (1972) Estimating phylogenetic trees from distance matrices. Am Nat 106:645-668.
15. Hess P.N., De Moraes Russo C.A. (2007) An empirical test of the midpoint rooting method. Biol J Linn Soc 92:669-674. (Pubitemid 350221975)
16. Maddison W.P., Donoghue M.J., Maddison D.R. (1984) Outgroup analysis and parsimony. Syst Zool 33:88-103.
17. Boykin L.M., Kubatko L.S., Lowrey T.K. (2010) Comparison of methods for rooting phylogenetic trees: A case study using Orcuttieae (Poaceae: A case study using Orcuttieae (PoaceaeChloridoideae). Mol Phylogenet Evol 54:687-700.
18. Renner S.S., Grimm G.W., Schneeweiss G.M., Stuessy T.F., Ricklefs R.E. (2008) Rooting and dating maples (Acer) with an uncorrelated-rates molecular clock: Implications for North American/Asian disjunctions. Syst Biol 57:795-808.
19. Martinsen E.S., Perkins S.L., Schall J.J. (2008) 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.
20. Megali A., Yannic G., Christe P. (2011) Disease in the dark: Molecular characterization of Polychromophilus murinus in temperate zone bats revealed a worldwide distribution of this malaria-like disease. Mol Ecol 20:1039-1048.
21. Outlaw D.C., Ricklefs R.E. (2010) Comparative gene evolution in haemosporidian (Apicomplexa) parasites of birds and mammals. Mol Biol Evol 27:537-542.
22. Bergsten J. (2005) A review of long-branch attraction. Cladistics 21:163-193.
23. Felsenstein J. (2004) Inferring Phylogenies (Sinauer Associates, Sunderland, MA).
24. Kolaczkowski B., Thornton J.W. (2009) Long-branch attraction bias and inconsistency in Bayesian phylogenetics. PLoS ONE 4:e7891.
25. Valkiunas G., et al. (2007) Linkage between mitochondrial cytochrome b lineages and morphospecies of two avian malaria parasites, with a description of Plasmodium (Novyella) ashfordi sp. nov. Parasitol Res 100:1311-1322. (Pubitemid 46450550)
26. Ricklefs R.E., Outlaw D.C. (2010) A molecular clock for malaria parasites. Science 329:226-229.
27. Poinar G., Jr. (2005) Plasmodium dominicana n. sp. (Plasmodiidae: Haemospororida) from Tertiary Dominican amber. Syst Parasitol 61:47-52.
28. Poinar G., Jr., Telford S.R., Jr. (2005) Paleohaemoproteus burmacis gen. n., sp. n. (Haemospororida: Plasmodiidae) from an Early Cretaceous biting midge (Diptera: Plasmodiidae) from an Early Cretaceous biting midge (DipteraCeratopogonidae). Parasitology 131:79-84.
29. Drummond A.J., Rambaut A. (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214.
30. Stamatakis A., Hoover P., Rougemont J. (2008) A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol 57:758-771.
31. Rambaut A., Drummond A.J. (2007) Tracer version 1.4. Available from http://beast.bio.ed.ac.uk/Tracer.
32. Shimodaira H., Hasegawa M. (1999) Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 16:1114-1116. (Pubitemid 29368141)
33. Swofford D. (2003) PAUP*4.0: Phylogenetic Analysis Using Parsimony*and Other Methods (Sinauer Associates, Sutherland, MA).