Phylogenetic Analyses of Two Mitochondrial Metabolic Genes Sampled in Parallel from Angiosperms Find Fundamental Interlocus Incongruence
Date
2008Author
Duvall, Melvin R.
Robinson, J.W.
Mattson, J.G.
Moore, A.
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Show full item recordAbstract
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 insuffi ciently 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 affi nities, 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 confl ict 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.