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Random roots and lineage sorting.
MedLine Citation:
PMID:  22445448     Owner:  NLM     Status:  Publisher    
Lineage sorting has been suggested as a major force in generating incongruent phylogenetic signal when multiple gene partitions are examined. The degree of lineage sorting can be estimated using the coalescent process and simulation studies have also pointed to a major role for incomplete lineage sorting as a factor in phylogenetic inference. Some recent empirical studies point to an extreme role for this phenomenon with up to 50-60% of all informative genes showing incongruence as a result of lineage sorting. Here, we examine seven large multi-partition genome level data sets over a large range of taxonomic representation. We took the approach of examining outgroup choice and its impact on tree topology, by swapping outgroups into analyses with successively larger genetics distances to the ingroup. Our results indicate a linear relationship of outgroup distance with incongruence in the data sets we examined suggesting a strong random rooting effect. In addition, we attempted to estimate the degree of lineage sorting in several large genome level data sets by examining triads of very closely related taxa. This exercise resulted in much lower estimates of incongruent genes that could be the result of lineage sorting, with an overall estimate of around 10% of the total number of genes in a genome showing incongruence as a result of true lineage sorting. Finally we examined the behavior of likelihood and parsimony approaches on the random rooting phenomenon. Likelihood tends to stabilize incongruence as outgroups get further and further away from the ingroup. In one extreme case, likelihood overcompensates for sequence divergence but increases random rooting causing long branch repulsion.
Jeffrey A Rosenfeld; Ansel Payne; Robert Desalle
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2012-3-14
Journal Detail:
Title:  Molecular phylogenetics and evolution     Volume:  -     ISSN:  1095-9513     ISO Abbreviation:  -     Publication Date:  2012 Mar 
Date Detail:
Created Date:  2012-3-26     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  9304400     Medline TA:  Mol Phylogenet Evol     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Copyright Information:
Copyright © 2012 Elsevier Inc. All rights reserved.
IST/High Performance and Research Computing, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103, USA; American Museum of Natural History, Sackler Institute for Comparative Genomics, New York, NY 10024, USA.
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