Molecular Biology and Evolution, Vol 16, 286-297, Copyright © 1999 by Society for Molecular Biology and Evolution
RD Reed and FA Sperling
In this study, we explored how the concept of the process partition may be
applied to phylogenetic analysis. Sequence data were gathered from 23
species and subspecies of the swallowtail butterfly genus Papilio, as well
as from two outgroup species from the genera Eurytides and Pachliopta.
Sequence data consisted of 1,010 bp of the nuclear protein- coding gene
elongation factor-1 alpha (EF-1 alpha) as well as the entire sequences (a
total of 2,211 bp) of the mitochondrial protein- coding genes cytochrome
oxidase I and cytochrome oxidase II (COI and COII). In order to examine the
interaction between the nuclear and mitochondrial partitions in a combined
analysis, we used a method of visualizing branch support as a function of
partition weight ratios. We demonstrated how this method may be used to
diagnose error at different levels of a tree in a combined
maximum-parsimony analysis. Further, we assessed patterns of evolution
within and between subsets of the data by implementing a multipartition
maximum-likelihood model to estimate evolutionary parameters for various
putative process partitions. COI third positions have an estimated average
substitution rate more than 15 times that of EF-1 alpha, while COII third
positions have an estimated average substitution rate more than 22 times
that of EF-1 alpha. Ultimately, we found that although the mitochondrial
and nuclear data were not significantly incongruent, homoplasy in the
fast-evolving mitochondrial data confounded the resolution of basal
relationships in the combined unweighted parsimony analysis despite the
fact that there was relatively strong support for the relationships in the
nuclear data. We conclude that there may be shortcomings to the methods of
"total evidence" and "conditional combination" because they may fail to
detect or accommodate the type of confounding bias we found in our data.
ORIGINAL ARTICLE
Interaction of process partitions in phylogenetic analysis: an example from the swallowtail butterfly genus Papilio
Department of Environmental Science, Policy, and Management, University of California, Berkeley, USA. reed@u.arizona.edu
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