Document Detail


Identifying a species tree subject to random lateral gene transfer.
MedLine Citation:
PMID:  23340439     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
A major problem for inferring species trees from gene trees is that evolutionary processes can sometimes favour gene tree topologies that conflict with an underlying species tree. In the case of incomplete lineage sorting, this phenomenon has recently been well-studied, and some elegant solutions for species tree reconstruction have been proposed. One particularly simple and statistically consistent estimator of the species tree under incomplete lineage sorting is to combine three-taxon analyses, which are phylogenetically robust to incomplete lineage sorting. In this paper, we consider whether such an approach will also work under lateral gene transfer (LGT). By providing an exact analysis of some cases of this model, we show that there is a zone of inconsistency when majority-rule three-taxon gene trees are used to reconstruct species trees under LGT. However, a triplet-based approach will consistently reconstruct a species tree under models of LGT, provided that the expected number of LGT transfers is not too high. Our analysis involves a novel connection between the LGT problem and random walks on cyclic graphs. We have implemented a procedure for reconstructing trees subject to LGT or lineage sorting in settings where taxon coverage may be patchy and illustrate its use on two sample data sets.
Authors:
Mike Steel; Simone Linz; Daniel H Huson; Michael J Sanderson
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2013-1-19
Journal Detail:
Title:  Journal of theoretical biology     Volume:  -     ISSN:  1095-8541     ISO Abbreviation:  J. Theor. Biol.     Publication Date:  2013 Jan 
Date Detail:
Created Date:  2013-1-23     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  0376342     Medline TA:  J Theor Biol     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Copyright Information:
Copyright © 2013. Published by Elsevier Ltd.
Affiliation:
Allan Wilson Centre for Molecular Ecology and Evolution, University of Canterbury, Christchurch, New Zealand. Electronic address: mathmomike@gmail.com.
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