Abstract Detail

Systematics Section/ASPT

Morris, Ashley [1], Leonard, O. Rayne [1], Shafer, Haden [2], Schorr, Mark [3], Kovach, Margaret [3], Shaw, Joey [4].

Variation in noncoding chloroplast DNA regions at the lowest taxonomic levels: Tortoise and Hare IV and beyond.

Choosing an appropriate genetic marker for phylogeny reconstruction is challenging, particularly in closely related taxa or intraspecific studies, in which divergence times are expected to be recent. In plants, the chloroplast genome has been the tool of choice for such studies due to the ease with which both coding and noncoding regions can be amplified with near universal primers, as well as for its uniparental mode of inheritance, which simplifies analyses over biparentally inherited nuclear loci. However, species-level and intraspecific studies often suffer from insufficient resolution due to a lack of variable genetic markers. Previous work in the Tortoise and Hare (TH) series of papers has identified a number of noncoding chloroplast DNA (NC-cpDNA) regions that have relatively high numbers of potentially informative characters averaged across angiosperms. In TH4, we surveyed 178 publications from the plant phylogeography literature between 2007 and 2013 to determine which markers were used and how that compares to recommendations from the TH series. We then compared 25 congeneric pairs of plastomes representing the breadth of angiosperm lineages to test previous findings of TH2 and TH3 in the context of more publicly available data. The results of the literature review indicate that 69% of studies used cpDNA sequence data, with the average number of regions used ranging from two to three. The majority of top performing NC-cpDNA regions from the TH series were used infrequently in the reviewed papers. Through whole plastome comparisons, we identified several regions as being consistently variable across angiosperm lineages. However, our pairwise comparisons show that top performing NC-cpDNA regions vary among lineages. Since the publication of TH4, we have expanded our sampling of basal angiosperm plastomes with an emphasis on Illicium to further assess variability of NC-cpDNA regions within clades. Several of the most variable regions across Illicium overlap with the angiosperm-wide top performers identified in TH4, and the top performing NC-cpDNA regions varied between Old and New World clades within Illicium. These findings further support the conclusions of TH4 that there is no ‘holy grail’ NC-cpDNA region, and all new studies should consider comparative plastomics or a comparison of the top TH regions as a tool for targeting the best markers in their respective clades. Additional work is underway in Illicium to assess actual phylogenetic utility of whole plastome datasets relative to a subset of selected markers.

1 - Middle Tennessee State University, Department Of Biology, 1500 Greenland Drive, Box 60, Murfreesboro, TN, 37132, USA
2 - University of Tennessee at Chattanooga, Department of Biological and Environmental Science, Dept 2653, 615 McCallie Avenue, Chattanooga, TN, 37403-2598, USA
3 - University of Tennessee at Chattanooga, Dept 2653, 615 McCallie Avenue, Chattanooga, TN, 37403-2598, United States
4 - University Of Tennessee At Chattanooga, Department Of Biological And Envoronmental Science, Dept 2653, 615 Mccallie Avenue, Chattanooga, TN, 37403-2598, USA

Keywords:
plastome
chloroplast
comparative plastomics
basal angiosperms
Illicium
Phylogeography.

Presentation Type: Oral Paper:Papers for Sections
Session: 33
Location: Salon 10/The Shaw Conference Centre
Date: Tuesday, July 28th, 2015
Time: 10:30 AM
Number: 33010
Abstract ID:741
Candidate for Awards:None