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

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.

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)

“…All SNPs were manually examined in Tablet and SNPs on edges of indels and repetitive regions were excluded. Annotations of the S. haliakalae reference genome were transferred to the locations of the SNPs for comparisons of variability with the most commonly used plastid regions for phylogenetic analyses (Shaw et al, 2005;Shaw et al, 2007). We compared the levels of chloroplast genome diversity among the six genomes by identifying unique, variable positions, which we refer to as potentially informative characters (PICs) (Shaw et al, 2005;Shaw et al, 2007).…”

“…Annotations of the S. haliakalae reference genome were transferred to the locations of the SNPs for comparisons of variability with the most commonly used plastid regions for phylogenetic analyses (Shaw et al, 2005;Shaw et al, 2007). We compared the levels of chloroplast genome diversity among the six genomes by identifying unique, variable positions, which we refer to as potentially informative characters (PICs) (Shaw et al, 2005;Shaw et al, 2007). Note that the definition of PIC used here excludes indels and inversions, which have been included in other studies of locus variability (Shaw et al, 2005;Shaw et al, 2007).…”

“…We compared the levels of chloroplast genome diversity among the six genomes by identifying unique, variable positions, which we refer to as potentially informative characters (PICs) (Shaw et al, 2005;Shaw et al, 2007). Note that the definition of PIC used here excludes indels and inversions, which have been included in other studies of locus variability (Shaw et al, 2005;Shaw et al, 2007).…”

“…Phylogenies of the Hawaiian mints have been reconstructed from datasets composed of commonly used DNA sequence markers, including cpDNA and nuclear ribosomal 5S non-transcribed spacer and external transcribed spacer regions (Lindqvist and Albert, 2002;Roy et al, 2013), which are rapidly evolving in many other species (Baldwin and Markos, 1998;Shaw et al, 2005;Small et al, 1998), but they fail to resolve relationships among the Hawaiian mints. A similar pattern of low genetic diversity has been noted in other recent radiations of Hawaiian plants (Appelhans et al, 2014;Baldwin and Sanderson, 1998;Cronk et al, 2005;Givnish et al, 2009;Givnish et al, 2013).…”

Population demographic history of a temperate shrub, Rhododendron weyrichii (Ericaceae), on continental islands of Japan and South Korea

“…Two cpDNA and eight nDNA regions were sequenced in order to detect DNA polymorphisms. Two cpDNA loci ( trnG intron and rpl36 ‐ rps8 ) were PCR‐amplified from four individuals per population using universal primers (Kress, Wurdack, Zimmer, Weigt, & Janzen, 2005; Shaw et al., 2005). For the eight nDNA loci, primers developed for other Ericaceous species (C16 and C22 [Wei, Fu, & Arora, 2005], EST39, EST65, EST121, and EST136 [De Keyser, De Riek, & Van Bockstaele, 2009], PHYB and PHYE [Ikeda & Setoguchi, 2010]) were used for PCR amplification of seven or eight individuals per population (Table S1).…”