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(American Journal of Botany. 2008;95:871-884.) doi: 10.3732/ajb.2007310 © 2008 Botanical Society of America, Inc.

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Phylogenetic analyses of two mitochondrial metabolic genes sampled in parallel from angiosperms find fundamental interlocus incongruence¹

Biological Sciences, Northern Illinois University, DeKalb, Illinois USA 60115-2861

ABSTRACT

Plant molecular phylogeneticists have supported an analytical approach of combining loci from different genomes, but the combination of mitochondrial sequences with chloroplast and nuclear sequences is potentially problematic. Low substitution rates in mitochondrial genes should decrease saturation, which is especially useful for the study of deep divergences. However, individual mitochondrial loci are insufficiently informative, so that combining congruent loci is necessary. For this study atp1 and cox1 were selected, which are of similar lengths, encode components of the respiratory pathway, and generally lack introns. Thus, these genes might be expected to have similar functional constraints, selection pressures, and evolutionary histories. Strictly parallel sampling of 52 species was achieved as well as six additional composite terminals with representatives from the major angiosperm clades. However, analyses of the separate loci produced strongly incongruent topologies. The source of the incongruence was investigated by validating sequences with questionable affinities, excluding RNA-edited nucleotides, deleting taxa with unexpected phylogenetic associations, and comparing different phylogenetic methods. However, even after potential artifacts were addressed and sites and taxa putatively associated with conflict were excluded, the resulting gene trees for the two mitochondrial loci were still substantially incongruent by all measures examined. Therefore, combining these loci in phylogenetic analysis may be counterproductive to the goal of fully resolving the angiosperm phylogeny.

Key Words: angiosperms • atp1 • cox1 • incongruence • mitochondrion • phylogenetics

Received for publication 28 September 2007. Accepted for publication 14 May 2008.

FOOTNOTES

¹ The authors thank Y.-L. Qiu, University of Michigan, Ann Arbor and D. Les, University of Connecticut, Storrs for donating DNA extracts. The authors thank A. Hackman and T. Russell, Northern Illinois University, for technical assistance and Mark Simmons and three anonymous reviewers for valuable comments on the paper. This work was supported in part by the Plant Molecular Biology Center, Northern Illinois University.

² Author for correspondence (e-mail: t80mrd1{at}wpo.cso.niu.edu), phone: 815-753-7806, fax: 815-753-7855

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