title: Chloroplast DNA sequence utility for the lowest phylogenetic and phylogeographic inferences in angiosperms: the tortoise and the hare IV.
abstract: OBJECTIVE
  Noncoding chloroplast DNA (NC-cpDNA) sequences are the staple data source of low-level phylogeographic and phylogenetic studies of angiosperms. We followed up on previous papers (tortoise and hare II and III) that sought to identify the most consistently variable regions of NC-cpDNA. We used an exhaustive literature review and newly available whole plastome data to assess applicability of previous conclusions at low taxonomic levels.
  
  
  METHODS
  We aligned complete plastomes of 25 species pairs from across angiosperms, comparing the number of genetic differences found in 107 NC-cpDNA regions and matK. We surveyed Web of Science for the plant phylogeographic literature between 2007 and 2013 to assess how NC-cpDNA has been used at the intraspecific level.
  
  
  RESULTS
  Several regions are consistently the most variable across angiosperm lineages: ndhF-rpl32, rpl32-trnL((UAG)), ndhC-trnV((UAC)), 5'rps16-trnQ((UUG)), psbE-petL, trnT((GGU))-psbD, petA-psbJ, and rpl16 intron. However, there is no universally best region. The average number of regions applied to low-level studies is ∼2.5, which may be too little to access the full discriminating power of this genome.
  
  
  CONCLUSIONS
  Plastome sequences have been used successfully at lower and lower taxonomic levels. Our findings corroborate earlier works, suggesting that there are regions that are most likely to be the most variable. However, while NC-cpDNA sequences are commonly used in plant phylogeographic studies, few of the most variable regions are applied in that context. Furthermore, it appears that in most studies too few NC-cpDNAs are used to access the discriminating power of the cpDNA genome.
authors.affiliation: Department of Biological and Environmental Sciences, University of Tennessee at Chattanooga, Chattanooga, Tennessee 37403 USA Botanical Research Institute of Texas, Fort Worth, Texas USA.
authors.forename: Joey
authors.initials: J
authors.lastname: Shaw
authors.affiliation: Department of Biological and Environmental Sciences, University of Tennessee at Chattanooga, Chattanooga, Tennessee 37403 USA.
authors.forename: Hayden L
authors.initials: HL
authors.lastname: Shafer
authors.affiliation: Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee 37132 USA.
authors.forename: O Rayne
authors.initials: OR
authors.lastname: Leonard
authors.affiliation: Department of Biological and Environmental Sciences, University of Tennessee at Chattanooga, Chattanooga, Tennessee 37403 USA.
authors.forename: Margaret J
authors.initials: MJ
authors.lastname: Kovach
authors.affiliation: Department of Biological and Environmental Sciences, University of Tennessee at Chattanooga, Chattanooga, Tennessee 37403 USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Schorr
authors.affiliation: Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee 37132 USA.
authors.forename: Ashley B
authors.initials: AB
authors.lastname: Morris
mesh_terms: D000818:Animals; D002736:Chloroplasts / Q000235:genetics; D018742:DNA, Chloroplast / Q000737:chemistry / Q000235:genetics*; D034621:Hares; D007438:Introns / Q000235:genetics; D019684:Magnoliopsida / Q000235:genetics*; D058974:Phylogeography
chemical_list: D018742:DNA, Chloroplast
keywords: DNA barcode; chloroplast; intergenic spacer; intraspecific; intron; noncoding cpDNA; phylogeography; plastid region; plastome; tortoise and hare