New inferences from tree shape: Numbers of missing taxa and population growth rates

Systematic Biology

Volumn 51, Issue 6, 2002, Pages 881-888

  Pybus, O G ^a   Rambaut, A ^a   Holmes, E C ^a   Harvey, P H ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Coalescent; Extinction; Flavivirus; Macroevolution; Speciation; Taxon sampling

Indexed keywords

ANIMALIA; FLAVIVIRUS;

EID: 0036964355     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/10635150290102582     Document Type: Conference Paper

References (39)

1. AVISE, J. C. 2000. Phylogeography. The history and formation of species. Harvard Univ. Press, Cambridge, Massachusetts.
2. BARRACLOUGH, T. G., A. P. VOGLER, AND P. H. HARVEY. 1998. Revealing the factors that promote speciation. Philos. Trans. R. Soc. Lond. B 353:241-249.
3. COX, D. R., AND P. A. W. LEWIS. 1966. The statistical analysis of series of events. Methuen, London.
4. DRUMMOND, A. J., G. K. NICHOLLS, A. G. RODRIGO, AND W. SOLOMON. 2002. Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161:1307-1320.
5. FELSENSTEIN, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17:368-376.
6. GRIFFITHS, R. C., AND S. TAVARÉ. 1994. Sampling theory for neutral alleles in a varying environment. Philos. Trans. R. Soc. Lond. B 344:403-410.
7. HARVEY, P. H., A. J. LEIGH BROWN, J. MAYNARD SMITH, AND S. NEE (eds.). 1996. New uses for new phylogenies. Oxford Univ. Press, Oxford, U.K.
8. HASEGAWA, M., H. KISHINO, AND T. YANO. 1985. Dating the human-ape split by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
9. HOLMES, E. C., S. NEE, A. RAMBAUT, G. P. GARNETT, AND P. H. HARVEY. 1995. Revealing the history of infectious disease epidemics through phylogenetic trees. Philos. Trans. R. Soc. Lond. B. 349:33-40.
10. HUELSENBECK, J. P., B. LARGET, AND D. SWOFFORD. 2000. A compound Poisson process for relaxing the molecular clock. Genetics 154:1879-1892.
11. HUELSENBECK, J. P., F. RONQUIST, R. NIELSEN, AND J. P. BOLLBACK. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310-2314.
12. KAPLAN, N. L., T. DARDEN, AND R. R. HUDSON. 1988. The coalescent process in models with selection. Genetics 120:819-829.
13. KINGMAN, J. F. C. 1982. On the genealogy of large populations. J. Appl. Probab. 19A:27-43.
14. KIRKPATRICK, M., AND M. SLATKIN. 1993. Searching for evolutionary pattern in the shape of a phylogenetic tree. Evolution 47:1171-1181.
15. KRONE, S. M., AND C. NEUHAUSER. 1997. Ancestral processes with selection. Theor. Popul. Biol. 51:210-237.
16. KUHNER, M. K., J. YAMATO, AND J. FELSENSTEIN. 1998. Maximum likelihood estimation of growth rates based on the coalescent. Genetics 149:429-434.
17. KUNO, G., J. GWONG-JEN, K. CHANG, R. TSUCHIYA, N. KARABATSOS, AND C. B. CROPP. 1998. Phylogeny of the genus Flavivirus. J. Virol. 72:73-83.
18. MONATH, T. P., AND F. X. HEINZ. 1996. Flaviviruses. Pages 961-1034 in Fields virology, 3rd edition (B. N. Fields, D. M. Knipe, and P. M. Howley, eds.). Lippincott-Raven, Philadelphia.
19. MOOERS, A. Ø., AND S. B. HEARD. 1997. Inferring evolutionary process from phylogenetic tree shape. Q. Rev. Biol. 72:31-54.
20. NEE, S., E. C. HOMES, R. M. MAY, AND P. H. HARVEY. 1994a. Extinction rates can be estimated from molecular phylogenies. Philos. Trans. R. Soc. Lond. B 344:77-82.
21. NEE, S., R. M. MAY, AND P. H. HARVEY. 1994b. The reconstructed evolutionary process. Philos. Trans. R. Soc. Lond. B 344:305-311.
22. NEE, S., A. Ø. MOOERS, AND P. H. HARVEY. 1992. Tempo and mode of evolution revealed from molecular phylogenies. Proc. Natl. Acad. Sci. USA 89:8322-8326.
23. PURVIS, A., S. NEE, AND P. H. HARVEY. 1995. Macroevolutionary inferences from primate phylogeny. Proc. R. Soc. Lond. B 260:329-333.
24. PYBUS, O. G., M. A. CHARLESTON, S. GUPTA, A. RAMBAUT, E. C. HOLMES, AND P. H. HARVEY. 2001. The epidemic behaviour of the hepatitis C virus. Science 292:2323-2325.
25. PYBUS, O. G., AND P. H. HARVEY. 2000. Testing macroevolutionary models using incomplete molecular phylogenies. Proc. R. Soc. Lond. B 267:2267-2272.
26. PYBUS, O. G., E. C. HOLMES, AND P. H. HARVEY. 1999. The mid-depth method and HIV-1: A practical approach for testing hypotheses of viral epidemic history. Mol. Biol. Evol. 16:953-959.
27. RAMBAUT, A., P. H. HARVEY, AND S. NEE. 1997. End-Epi: An application for inferring phylogenetic and population dynamical processes from molecular sequences. Comput. Appl. Biosci. 13:303-306.
28. RAUP, D. M., S. J. GOULD, T. J. M. SCHOPF, AND D. SIMBERLOFF. 1973. Stochastic models of phylogeny and the evolution of diversity. J. Geol. 81:525-542.
29. SANDERSON, M. J. 1994. Reconstructing the history of evolutionary processes using maximum likelihood. Pages 13-26 in Molecular evolution of physiological processes (D. M. Fambrough, ed.). Rockerfeller Univ. Press, New York.
30. SANDERSON, M. J. 1997. A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol. 14:1218-1232.
31. SANDERSON, M. J., AND M. J. DONOGHUE. 1994. Shifts in diversification rate with the origin of the angiosperms. Science 264:1590-1593.
32. SCHLUTER, D. 2000. The ecology of adaptive radiation. Oxford Univ. Press, Oxford, U.K.
33. SLATKIN, M., AND R. R. HUDSON. 1991. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129:555-562.
34. SLOWINSKI, J., AND C. GUYER. 1989. Testing the stochasticity of patterns of organismal diversity: An improved null model. Am. Nat. 134:907-921.
35. SWOFFORD, D. L. 2000. PAUP,* version 4: Phylogenetic analysis using parsimony (*and other methods). Sinauer, Sunderland, Massachusetts.
36. THORNE, J. L., H. KISHINO, AND I. S. PAINTER. 1998. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15:1647-1657.
37. Walter Reed Biosystematics Unit. 2001. 2001 Systematic Catalog of Culicidae. Available from http:/wrbi.si.edu.
38. WEISS, G., AND A. VON HAESELER. 1998. Inference of population history using a likelihood approach. Genetics 149:1539-1546.
39. ZINK, R. M., AND J. B. SLOWINSKI. 1995 Evidence from molecular systematics for decreased avian diversification in the Pleistocene epoch. Proc. Natl. Acad. Sci. USA 92:5832-5835.