**GENEALOGY-DNA-L Archives**

From:Subject:PubMed abstract: mtDNA treeDate:Mon, 27 Jun 2005 10:17:17 EDTThis is a theoretical article about the best way to construct a phylogenetic

tree. I'll put this one on my ToDo list -- I may skip the mathematical part,

but I'm curious to see what the mtDNA tree looks like.

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Mol Biol Evol. 2005 Feb;22(2):235-42. Epub 2004 Oct 13.

The MinMax Squeeze: guaranteeing a minimal tree for population data.

Holland BR, Huber KT, Penny D, Moulton V.

Allan Wilson Centre for Molecular Ecology and Evolution, Massey University,

New Zealand.

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.

PMID: 15483326 [PubMed - indexed for MEDLINE]

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Ann Turner

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