Skip Navigation


MBE Advance Access originally published online on October 13, 2004
Molecular Biology and Evolution 2005 22(2):235-242; doi:10.1093/molbev/msi010
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (PDF) Freely available
Right arrow All Versions of this Article:
22/2/235    most recent
msi010v1
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 (3)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Holland, B. R.
Right arrow Articles by Moulton, V.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Holland, B. R.
Right arrow Articles by Moulton, V.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Molecular Biology and Evolution vol. 22 no. 2 © Society for Molecular Biology and Evolution 2005; all rights reserved.

Research Article

The MinMax Squeeze: Guaranteeing a Minimal Tree for Population Data

B. R. Holland*, K. T. Huber{dagger}, D. Penny* and V. Moulton{dagger}

* Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, New Zealand; {dagger} School of Computing Sciences, University of East Anglia, Norwich, United Kingdom

E-mail: b.r.holland{at}massey.ac.nz.

We report that for population data, where sequences are very similar to one another, it is often possible to use a two-pronged (MinMax Squeeze) approach to prove that a tree is the shortest possible under the parsimony criterion. Such population data can be in a range where parsimony is a maximum likelihood estimator. This is in sharp contrast to the case with species data, where sequences are much further apart and the problem of guaranteeing an optimal phylogenetic tree is known to be computationally prohibitive for realistic numbers of species, irrespective of whether likelihood or parsimony is the optimality criterion. The Squeeze uses both an upper bound (the length of the shortest tree known) and a lower bound derived from partitions of the columns (the length of the shortest tree possible). If the two bounds meet, the shortest known tree is thus proven to be a shortest possible tree. The implementation is first tested on simulated data sets and then applied to 53 complete human mitochondrial genomes. The shortest possible trees for those data have several significant improvements from the published tree. Namely, a pair of Australian lineages comes deeper in the tree (in agreement with archaeological data), and the non-African part of the tree shows greater agreement with the geographical distribution of lineages.

Key Words: lower bounds • parsimony • phylogeny estimation • human mtDNA


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
M. J. Pierson, R. Martinez-Arias, B. R. Holland, N. J. Gemmell, M. E. Hurles, and D. Penny
Deciphering Past Human Population Movements in Oceania: Provably Optimal Trees of 127 mtDNA Genomes
Mol. Biol. Evol., October 1, 2006; 23(10): 1966 - 1975.
[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.