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

TLDR

Chloroplast DNA, especially the widely used noncoding regions trnL‑trnF and trnK/matK, is a key source for plant phylogenetics but often lacks resolution at low taxonomic levels, and selecting appropriate cpDNA regions is hampered by limited knowledge of their evolutionary rate heterogeneity. The study aimed to determine whether predictable rate heterogeneity exists among 21 noncoding cpDNA regions useful for low‑level phylogenetic analysis. The authors tested rate heterogeneity by sequencing three species from each of ten groups across eight major seed‑plant lineages. They found that a survey of as few as three taxa can predict the phylogenetic informativeness of a cpDNA region and that rate heterogeneity exists among noncoding cpDNA regions.

Abstract

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.