Kelchner, Scot A. , Hansen, Shannalee C. .
A magic bullet? Comparison of chloroplast introns shows a strong difference in phylogenetic utility and a clear choice for grass systematics.
Many tasks in systematics can be addressed adequately by sequence analysis of one or a few DNA loci. Chloroplast noncoding regions have become principal targets for this purpose. Choice of which locus to use is often influenced by a regionís PIC ranking (PIC: potentially informative characters), as determined by comparative studies of chloroplast genome variation. A widespread assumption is that regions listed in the top Ďtierí (those with the highest PIC values) will offer the best chance of attaining a resolved, supported, and accurate phylogeny estimation. We tested this expectation with a comparative analysis of phylogenetic performance among a complete set of single copy chloroplast group II introns in bamboos (Poaceae: Bambusoideae). A corroborated chloroplast phylogeny of 14 bamboo genera was used to rank the eleven introns by accuracy, support, and degree of error. We found a remarkable discrepancy in evolutionary rates among introns and a lack of correlation between PIC value and phylogenetic performance across a variety of analytical frameworks. Our results confirm that PIC can be a poor predictor of a regionís phylogenetic utility. We identify two introns as superior targets and two as very poor targets for phylogenetic analysis of bamboo chloroplasts.
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1 - Idaho State University, Department of Biological Sciences, 921 South 8th Avenue, Stop 8007, Pocatello, ID, 83209-8007, USA
group II intron
noncoding chloroplast DNA
Presentation Type: Oral Paper:Papers for BSA Sections
Location: Cottonwood D/Snowbird Center
Date: Wednesday, July 29th, 2009
Time: 3:00 PM