Probabilistic Analysis Indicates Discordant Gene Trees in Chloroplast Evolution |
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Authors: | Claus Vogl Jonathan Badger Paul Kearney Ming Li Michael Clegg Tao Jiang |
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Institution: | (1) Department of Computer Science, University of California, Riverside, CA 92521, USA,;(2) Department of Computer Science, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada,;(3) Department of Computer Science, University of California, Santa Barbara, CA 93106, USA,;(4) Department of Botany and Plant Sciences, University of California, Riverside, CA 92521-0124, USA, |
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Abstract: | Abstract
Analyses of whole-genome data often reveal that some genes have evolutionary histories that diverge from the majority phylogeny
estimated for the entire genome. We present a probabilistic model that deals with heterogeneity among gene trees, implement
it via the Gibbs sampler, and apply it to the plastid genome. Plastids and their genomes are transmitted as a single block
without recombination, hence homogeneity among gene trees within this genome is expected. Nevertheless, previous work has
revealed clear heterogeneity among plastid genes (e.g., Delwiche and Palmer 1996). Other studies, using whole plastid genomes
of various algae and land plants, found little additional heterogeneity (Martin et al. 1998; Adachi et al. 2000). We augment
the earlier studies by using a data set of 14 taxa: 6 land plants, 2 green algae, a diatom, 2 red algae and a cryptophyte,
the cyanelle of the glaucocystophyte Cyanophora, and the blue–green alga Synechocystis as an outgroup. Contrary to the earlier analyses, we cannot find even a single, dominant consensus tree. Therefore, we formulate
a probabilistic model that divides the genes into two sets: those that follow the consensus tree and those that have independent
gene trees. No particular tree is supported by more than three-fourths of the genes. But the set of genes that follows a certain
tree is fairly independent of data processing and the method of analysis. With one possible exception, we find no evidence
for collinear or functionally related genes to follow similar trees. The phylogenetic pattern also seems independent of bias
in amino acid composition. Among possible explanations for the observed phenomenon, the hypothesis that different genes have
different covarion structures is difficult to assess. But gene duplication may be possible through the inverted or direct
repeat regions, while horizontal gene transfer seems less likely. In contrast to green algae and land plants, inverted repeat
regions in red algae and in Cyanophora show abundant differences among the copies. Thus, genes may get duplicated when they are recruited into the inverted repeat
region and one of the two copies may be lost after leaving the inverted repeat region. |
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Keywords: | Chloroplast Phylogeny Gene duplication Probabilistic model Gibbs sampling |
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