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MBE Advance Access published online on September 8, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msj005
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Published by Oxford University Press 2005.
Accepted August 25, 2005

Research Article

Heterotachy and Tree Building: A Case Study with Plastids and Eubacteria

Peter Lockhart 1*, Phil Novis 2, Brook G. Milligan 3, Jamie Riden 1, Andrew Rambaut 4, and Tony Larkum 5

1 The Allan Wilson Centre, Institute of Molecular BioSciences, Massey University, Palmerston North, New Zealand
2 Manaaki Whenua - Landcare Research, P.O. Box 69, Gerald St, Lincoln 8152, New Zealand
3 Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA
4 Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
5 Sydney University Biological Informatics and Technology Centre, Building A08, School of Biological Sciences, University of Sydney, NSW 2006, Australia

* To whom correspondence should be addressed.
Peter Lockhart, E-mail: p.j.lockhart{at}massey.ac.nz


  Abstract

The nature of heterotachy at the centre of recent controversy over the relative performance of tree building methods is different from the form of heterotachy that has been inferred in empirical studies. The latter have suggested that proportions of variable sites (pvar) vary amongst orthologues and amongst paralogues. However, the strength of this inference, describing what may be one of the most important evolutionary properties of sequence data, has remained weak. Consequently, other models of sequence evolution have been proposed to explain some long branch attraction problems that could be attributed to differences in pvar. For an empirical case with plastid and eubacterial RNA polymerase sequences, we confirm using capture-recapture estimates and simulations that pvar can differ amongst orthologues in anciently diverged evolutionary lineages. We find that parsimony and a least squares distance method, that implements an overly simple model of sequence evolution, are susceptible to long branch attraction induced by this form of heterotachy. Although homogenous maximum likelihood inference was found to be robust to model misspecification in our specific example, we caution against assuming that it will always be so.

Keywords: Heterotachy; covarion evolution; long branch attraction; plastid origins.
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