GENEALOGY-DNA-L ArchivesArchiver > GENEALOGY-DNA > 2005-06 > 1119881837
Subject: PubMed abstract: mtDNA tree
Date: Mon, 27 Jun 2005 10:17:17 EDT
This 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.
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,
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]