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Mol Phylogenet Evol. 2014 Feb;71:142-8. doi: 10.1016/j.ympev.2013.11.013. Epub 2013 Dec 6.

Sampling strategies for improving tree accuracy and phylogenetic analyses: a case study in ciliate protists, with notes on the genus Paramecium.

Author information

  • 1Key Laboratory of Ecology and Environment Science in Guangdong Higher Education, School of Life Science, South China Normal University, Guangzhou 510631, China; Laboratory of Protozoology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
  • 2Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario NIG 2W1, Canada.
  • 3Laboratory of Protozoology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
  • 4Key Laboratory of Ecology and Environment Science in Guangdong Higher Education, School of Life Science, South China Normal University, Guangzhou 510631, China. Electronic address: xlin@scnu.edu.cn.
  • 5Laboratory of Protozoology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China. Electronic address: wsong@ouc.edu.cn.

Abstract

In order to assess how dataset-selection for multi-gene analyses affects the accuracy of inferred phylogenetic trees in ciliates, we chose five genes and the genus Paramecium, one of the most widely used model protist genera, and compared tree topologies of the single- and multi-gene analyses. Our empirical study shows that: (1) Using multiple genes improves phylogenetic accuracy, even when their one-gene topologies are in conflict with each other. (2) The impact of missing data on phylogenetic accuracy is ambiguous: resolution power and topological similarity, but not number of represented taxa, are the most important criteria of a dataset for inclusion in concatenated analyses. (3) As an example, we tested the three classification models of the genus Paramecium with a multi-gene based approach, and only the monophyly of the subgenus Paramecium is supported.

Copyright © 2013 Elsevier Inc. All rights reserved.

KEYWORDS:

Ciliophora; Missing data; Multi-gene; Paramecium; Phylogeny

PMID:
24315865
[PubMed - indexed for MEDLINE]
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