Genome-scale phylogeny and the detection of systematic biases

Phillips, Matthew J., Delsuc, Frederic, & Penny, David (2004) Genome-scale phylogeny and the detection of systematic biases. Molecular Biology and Evolution, 21(7), pp. 1455-1458.

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Abstract

Phylogenetic inference from sequences can be misled by both sampling (stochastic) error and systematic error (nonhistorical signals where reality differs from our simplified models). A recent study of eight yeast species using 106 concatenated genes from complete genomes showed that even small internal edges of a tree received 100% bootstrap support. This effective negation of stochastic error from large data sets is important, but longer sequences exacerbate the potential for biases (systematic error) to be positively misleading. Indeed, when we analyzed the same data set using minimum evolution optimality criteria, an alternative tree received 100% bootstrap support. We identified a compositional bias as responsible for this inconsistency and showed that it is reduced effectively by coding the nucleotides as purines and pyrimidines (RY-coding), reinforcing the original tree. Thus, a comprehensive exploration of potential systematic biases is still required, even though genome-scale data sets greatly reduce sampling error.

Impact and interest:

260 citations in Scopus
250 citations in Web of Science®
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ID Code: 59863
Item Type: Journal Article
Refereed: Yes
Additional Information: Articles free to read on journal website after 12 months
DOI: 10.1093/molbev/msh137
ISSN: 1537-1719
Divisions: Current > Schools > School of Earth, Environmental & Biological Sciences
Current > QUT Faculties and Divisions > Science & Engineering Faculty
Copyright Owner: Copyright 2004 Oxford Univeristy Press
Deposited On: 10 May 2013 02:35
Last Modified: 05 Feb 2015 05:38

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