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Free Content Simple phylogenetic tree searches easily "succeed" with large matrices of single genes

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Here we show with both extensive real and simulated data that rigorous and time-intensive approaches, including parsimony, maximum likelihood and Bayesian methods, to reconstructing large phylogenetic trees are unwarranted with small amounts of data (i.e., single or small numbers, 2–3 genes) because they actually produce trees with scores that are shorter or otherwise less optimal than the model tree or trees produced with larger amounts of data. Furthermore they also fail to obtain consistently more correct groups than simple parsimony methods, leaving the latter to be preferred. When numbers of variable sites are limited relative to numbers of taxa sampled, simpler swapping strategies perform as well as much more rigorous methods. We caution against confidence in any results based on small data sets, even if (or especially if) there have been thorough analyses. Analyses of such data sets for exploratory purposes should rely on simple search strategies and not use excessive branch swapping or time.


Document Type: Short Communication

Affiliations: 1: Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, U.K. 2: Department of Botany, University of Florida, Gainesville, Florida 32611, U.S.A. 3: Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611, U.S.A. 4: 829 Pine Hall Road, State College, Pennsylvania 16801-3008, U.S.A.

Publication date: August 1, 2006

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