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(American Journal of Botany. 2005;92:142-166.)
© 2005 Botanical Society of America, Inc.

Systematics

The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis1

Joey Shaw2, Edgar B. Lickey, John T. Beck, Susan B. Farmer, Wusheng Liu, Jermey Miller, Kunsiri C. Siripun, Charles T. Winder, Edward E. Schilling and Randall L. Small

Department of Botany, 437 Hesler Biology, University of Tennessee, Knoxville, Tennessee 37996 USA

Chloroplast DNA sequences are a primary source of data for plant molecular systematic studies. A few key papers have provided the molecular systematics community with universal primer pairs for noncoding regions that have dominated the field, namely trnL-trnF and trnK/matK. These two regions have provided adequate information to resolve species relationships in some taxa, but often provide little resolution at low taxonomic levels. To obtain better phylogenetic resolution, sequence data from these regions are often coupled with other sequence data. Choosing an appropriate cpDNA region for phylogenetic investigation is difficult because of the scarcity of information about the tempo of evolutionary rates among different noncoding cpDNA regions. The focus of this investigation was to determine whether there is any predictable rate heterogeneity among 21 noncoding cpDNA regions identified as phylogenetically useful at low levels. To test for rate heterogeneity among the different cpDNA regions, we used three species from each of 10 groups representing eight major phylogenetic lineages of phanerogams. The results of this study clearly show that a survey using as few as three representative taxa can be predictive of the amount of phylogenetic information offered by a cpDNA region and that rate heterogeneity exists among noncoding cpDNA regions.

Key Words: angiosperms • cpDNA • intergenic spacers • introns • molecular systematics • noncoding chloroplast DNA • phylogeny • seed plants


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