Molecular Biology and Evolution, Vol 13, 1159-1166, Copyright © 1996 by Society for Molecular Biology and Evolution
LM Bowe and CW dePamphilis
RNA editing is a ubiquitous phenomenon affecting most mitochondrial and
chloroplast, and some nuclear genomes, where mutations in genomic DNA are
"corrected" in the mRNA during transcriptional processing. Most editing in
plants and animals corrects T-to-C substitutions at nonsynonymous first or
second base positions, and the overall effect is an mRNA and protein
sequence that differs from that predicted by the DNA. It has been suggested
that genomic sequences that undergo editing should not be used in
phylogenetics. We contend that editing will have little or no effect on
DNA-based phylogenetic reconstruction because it is an intrinsic
transcriptional process that does not affect the historical information in
the DNA sequence. The only effect of editing on protein-coding DNA should
be an increase in the rate of T-to-C transitions. Here we test the effects
of RNA editing on phylogenetic reconstruction, using two data sets with
high levels of editing, plant coxII and coxIII. Even with high levels of
editing, phylogenies based on DNA and edited mRNA are virtually identical.
The two types of sequences should not be used in the same analysis,
however, because the particular forms of the gene will tend to group
together. We also examine the effects of processed paralogs--a term
proposed for mRNA sequences that are reverse transcribed and reinserted
into the genome as intact gene sequences. Processed paralogs result in a
distinct and under-appreciated source of conflict among gene trees because
of RNA editing. Analyses with unidentified processed paralogs may yield
incorrect phylogenies, and the sequences may evolve at different rates if
the gene has been transferred from one genetic compartment (nuclear,
mitochondrial, chloroplast) to another. Although RNA editing itself is not
a problem in phylogenetic reconstruction, analyses should not combine mRNAs
with DNAs, and processed paralogs should be either excluded or analyzed
with caution.
ORIGINAL ARTICLE
Effects of RNA editing and gene processing on phylogenetic reconstruction
Vanderbilt University, Nashville, Tennessee 37235, USA. bowelm@ctrvax.vanderbilt.edu
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