Skip Navigation


MBE Advance Access originally published online on March 2, 2005
Molecular Biology and Evolution 2005 22(5):1161-1164; doi:10.1093/molbev/msi123
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (PDF) Freely available
Right arrow All Versions of this Article:
22/5/1161    most recent
msi123v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (33)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Spencer, M.
Right arrow Articles by Roger, A. J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Spencer, M.
Right arrow Articles by Roger, A. J.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oupjournals.org

Letter

Likelihood, Parsimony, and Heterogeneous Evolution

Matthew Spencer*,{dagger}, Edward Susko* and Andrew J. Roger{dagger}

* Department of Mathematics and Statistics and {dagger} Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada

E-mail: matts{at}mathstat.dal.ca.

Evolutionary rates vary among sites and across the phylogenetic tree (heterotachy). A recent analysis suggested that parsimony can be better than standard likelihood at recovering the true tree given heterotachy. The authors recommended that results from parsimony, which they consider to be nonparametric, be reported alongside likelihood results. They also proposed a mixture model, which was inconsistent but better than either parsimony or standard likelihood under heterotachy. We show that their main conclusion is limited to a special case for the type of model they study. Their mixture model was inconsistent because it was incorrectly implemented. A useful nonparametric model should perform well over a wide range of possible evolutionary models, but parsimony does not have this property. Likelihood-based methods are therefore the best way to deal with heterotachy.

Key Words: Heterotachy • mixture models • likelihood • consistency • simulation


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Mol Biol EvolHome page
B. Kolaczkowski and J. W. Thornton
A Mixed Branch Length Model of Heterotachy Improves Phylogenetic Accuracy
Mol. Biol. Evol., June 1, 2008; 25(6): 1054 - 1066.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
H.-C. Wang, M. Spencer, E. Susko, and A. J. Roger
Testing for Covarion-like Evolution in Protein Sequences
Mol. Biol. Evol., January 1, 2007; 24(1): 294 - 305.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
G. Baele, J. Raes, Y. Van de Peer, and S. Vansteelandt
An Improved Statistical Method for Detecting Heterotachy in Nucleotide Sequences
Mol. Biol. Evol., July 1, 2006; 23(7): 1397 - 1405.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
M. Turmel, C. Otis, and C. Lemieux
The Chloroplast Genome Sequence of Chara vulgaris Sheds New Light into the Closest Green Algal Relatives of Land Plants
Mol. Biol. Evol., June 1, 2006; 23(6): 1324 - 1338.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
D. H. Huson and D. Bryant
Application of Phylogenetic Networks in Evolutionary Studies
Mol. Biol. Evol., February 1, 2006; 23(2): 254 - 267.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
P. Lockhart, P. Novis, B. G. Milligan, J. Riden, A. Rambaut, and T. Larkum
Heterotachy and Tree Building: A Case Study with Plastids and Eubacteria
Mol. Biol. Evol., January 1, 2006; 23(1): 40 - 45.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
S. R. Gadagkar and S. Kumar
Maximum Likelihood Outperforms Maximum Parsimony Even When Evolutionary Rates Are Heterotachous
Mol. Biol. Evol., November 1, 2005; 22(11): 2139 - 2141.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
J. Leebens-Mack, L. A. Raubeson, L. Cui, J. V. Kuehl, M. H. Fourcade, T. W. Chumley, J. L. Boore, R. K. Jansen, and C. W. dePamphilis
Identifying the Basal Angiosperm Node in Chloroplast Genome Phylogenies: Sampling One's Way Out of the Felsenstein Zone
Mol. Biol. Evol., October 1, 2005; 22(10): 1948 - 1963.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.