Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.

Science 30 June 2000:
Vol. 288. no. 5475, pp. 2349 - 2350
DOI: 10.1126/science.288.5475.2349
Prev | Table of Contents | Next

Reports

Accommodating Phylogenetic Uncertainty in Evolutionary Studies

John P. Huelsenbeck, 1* Bruce Rannala, 2 John P. Masly 1

Many evolutionary studies use comparisons across species to detect evidence of natural selection and to examine the rate of character evolution. Statistical analyses in these studies are usually performed by means of a species phylogeny to accommodate the effects of shared evolutionary history. The phylogeny is usually treated as known without error; this assumption is problematic because inferred phylogenies are subject to both stochastic and systematic errors. We describe methods for accommodating phylogenetic uncertainty in evolutionary studies by means of Bayesian inference. The methods are computationally intensive but general enough to be applied in most comparative evolutionary studies.

1 Department of Biology, University of Rochester, Rochester, NY 14627, USA.
2 Department of Medical Genetics, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
*   To whom correspondence should be addressed. E-mail: johnh{at}brahms.biology.rochester.edu

Read the Full Text


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Developmental patterns in anatomy are shared among separate evolutionary origins of stem succulent and storage root-bearing growth habits in Adenia (Passifloraceae).
D. J. Hearn (2009)
Am. J. Botany 96, 1941-1956
   Abstract »    Full Text »    PDF »
A Bayesian approach for evaluating the impact of historical events on rates of diversification.
B. R. Moore and M. J. Donoghue (2009)
PNAS 106, 4307-4312
   Abstract »    Full Text »    PDF »
Fast, accurate and simulation-free stochastic mapping.
V. N Minin and M. A Suchard (2008)
Phil Trans R Soc B 363, 3985-3995
   Abstract »    Full Text »    PDF »
Accounting for Phylogenetic Uncertainty in Biogeography: A Bayesian Approach to Dispersal-Vicariance Analysis of the Thrushes (Aves: Turdus).
J. A. A. Nylander, U. Olsson, P. Alstrom, and I. Sanmartin (2008)
Syst Biol 57, 257-268
   Abstract »    Full Text »    PDF »
Multistate Characters and Diet Shifts: Evolution of Erotylidae (Coleoptera).
R. A. B. Leschen and T. R. Buckley (2007)
Syst Biol 56, 97-112
   Abstract »    Full Text »    PDF »
A Bayesian Approach for Discriminating Among Alternative Inheritance Hypotheses in Plant Polyploids: The Allotetraploid Origin of Genus Borderea (Dioscoreaceae).
P. Catalan, J. G. Segarra-Moragues, M. Palop-Esteban, C. Moreno, and F. Gonzalez-Candelas (2006)
Genetics 172, 1939-1953
   Abstract »    Full Text »    PDF »
Inference and Analysis of the Relative Stability of Bacterial Chromosomes.
E. P. C. Rocha (2006)
Mol. Biol. Evol. 23, 513-522
   Abstract »    Full Text »    PDF »
Under-parameterized Model of Sequence Evolution Leads to Bias in the Estimation of Diversification Rates from Molecular Phylogenies.
L. J. Revell, L. J. Harmon, and R. E. Glor (2005)
Syst Biol 54, 973-983
   Full Text »    PDF »
Ascoma morphology is homoplaseous and phylogenetically misleading in some pyrenocarpous lichens.
I. Schmitt, G. Mueller, and H. T. Lumbsch (2005)
Mycologia 97, 362-374
   Abstract »    Full Text »    PDF »
Molecular phylogeny of parmotremoid lichens (Ascomycota, Parmeliaceae).
O. Blanco, A. Crespo, P. K. Divakar, J. A. Elix, and H. T. Lumbsch (2005)
Mycologia 97, 150-159
   Abstract »    Full Text »    PDF »
Trends in Morphological Evolution in Homobasidiomycetes Inferred Using Maximum Likelihood: A Comparison of Binary and Multistate Approaches.
D. S. Hibbett (2004)
Syst Biol 53, 889-903
   Abstract »    Full Text »    PDF »
Phylogenetic relationships of Gomphillaceae and Asterothyriaceae: evidence from a combined Bayesian analysis of nuclear and mitochondrial sequences.
R. Lucking, B. L. Stuart, and H. T. Lumbsch (2004)
Mycologia 96, 283-294
   Abstract »    Full Text »    PDF »
Inducible Expression, Enzymatic Activity, and Origin of Higher Plant Homologues of Bacterial RelA/SpoT Stress Proteins in Nicotiana tabacum.
R. M. Givens, M.-H. Lin, D. J. Taylor, U. Mechold, J. O. Berry, and V. J. Hernandez (2004)
J. Biol. Chem. 279, 7495-7504
   Abstract »    Full Text »    PDF »
Phylogeny of the lichen genus Placopsis and its allies based on Bayesian analyses of nuclear and mitochondrial sequences.
I. Schmitt, H. T. Lumbsch, and U. Sochting (2003)
Mycologia 95, 827-835
   Abstract »    Full Text »    PDF »
Bayes or Bootstrap? A Simulation Study Comparing the Performance of Bayesian Markov Chain Monte Carlo Sampling and Bootstrapping in Assessing Phylogenetic Confidence.
M. E. Alfaro, S. Zoller, and F. Lutzoni (2003)
Mol. Biol. Evol. 20, 255-266
   Abstract »    Full Text »    PDF »
TESTING PHYLOGENETIC HYPOTHESES WITH STRATIGRAPHY AND MORPHOLOGY--A COMMENT ON SMITH (2000).
(2002)
Journal of Paleontology 76, 590-593
Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology.
J. P. Huelsenbeck, F. Ronquist, R. Nielsen, and J. P. Bollback (2001)
Science 294, 2310-2314
   Abstract »    Full Text »    PDF »


To Advertise     Find Products

Science. ISSN 0036-8075 (print), 1095-9203 (online)