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The performance of phylogenetic algorithms in estimating haplotype genealogies with migration
JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift)
 
ID 974005
Author(s) Salzburger, Walter; Ewing, Greg B; Von Haeseler, Arndt
Author(s) at UniBasel Salzburger, Walter
Year 2011
Title The performance of phylogenetic algorithms in estimating haplotype genealogies with migration
Journal Molecular ecology
Volume 20
Number 9
Pages / Article-Number 1952-63
Keywords haplotype genealogy, maximum likelihood, maximum parsimony, neighbour-joining, networks
Abstract

Genealogies estimated from haplotypic genetic data play a prominent role in various biological disciplines in general and in phylogenetics, population genetics and phylogeography in particular. Several software packages have specifically been developed for the purpose of reconstructing genealogies from closely related, and hence, highly similar haplotype sequence data. Here, we use simulated data sets to test the performance of traditional phylogenetic algorithms, neighbour-joining, maximum parsimony and maximum likelihood in estimating genealogies from nonrecombining haplotypic genetic data. We demonstrate that these methods are suitable for constructing genealogies from sets of closely related DNA sequences with or without migration. As genealogies based on phylogenetic reconstructions are fully resolved, but not necessarily bifurcating, and without reticulations, these approaches outperform widespread 'network' constructing methods. In our simulations of coalescent scenarios involving panmictic, symmetric and asymmetric migration, we found that phylogenetic reconstruction methods performed well, while the statistical parsimony approach as implemented in TCS performed poorly. Overall, parsimony as implemented in the PHYLIP package performed slightly better than other methods. We further point out that we are not making the case that widespread 'network' constructing methods are bad, but that traditional phylogenetic tree finding methods are applicable to haplotypic data and exhibit reasonable performance with respect to accuracy and robustness. We also discuss some of the problems of converting a tree to a haplotype genealogy, in particular that it is nonunique.

Publisher Blackwell
ISSN/ISBN 0962-1083
edoc-URL http://edoc.unibas.ch/dok/A5849102
Full Text on edoc No
Digital Object Identifier DOI 10.1111/j.1365-294X.2011.05066.x
PubMed ID http://www.ncbi.nlm.nih.gov/pubmed/21457168
ISI-Number WOS:000289522400015
Document type (ISI) Journal Article
 
   

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02/05/2024