Closely-related taxa influence woody species discrimination via DNA barcoding: evidence from global forest dynamics plots

Sci Rep. 2015 Oct 12:5:15127. doi: 10.1038/srep15127.

Abstract

To determine how well DNA barcodes from the chloroplast region perform in forest dynamics plots (FDPs) from global CTFS-ForestGEO network, we analyzed DNA barcoding sequences of 1277 plant species from a wide phylogenetic range (3 FDPs in tropics, 5 in subtropics and 5 in temperate zone) and compared the rates of species discrimination (RSD). We quantified RSD by two DNA barcode combinations (rbcL + matK and rbcL + matK + trnH-psbA) using a monophyly-based method (GARLI). We defined two indexes of closely-related taxa (Gm/Gt and S/G ratios) and correlated these ratios with RSD. The combination of rbcL + matK averagely discriminated 88.65%, 83.84% and 72.51% at the local, regional and global scales, respectively. An additional locus trnH-psbA increased RSD by 2.87%, 1.49% and 3.58% correspondingly. RSD varied along a latitudinal gradient and were negatively correlated with ratios of closely-related taxa. Successes of species discrimination generally depend on scales in global FDPs. We suggested that the combination of rbcL + matK + trnH-psbA is currently applicable for DNA barcoding-based phylogenetic studies on forest communities.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chloroplasts / genetics
  • Climate
  • DNA Barcoding, Taxonomic / methods*
  • DNA, Plant / genetics*
  • Endoribonucleases / genetics
  • Forests
  • Gene Expression
  • Genetic Loci
  • Histidine-tRNA Ligase / genetics
  • Nucleotidyltransferases / genetics
  • Photosystem II Protein Complex / genetics
  • Phylogeny*
  • Ribulose-Bisphosphate Carboxylase / genetics
  • Sequence Analysis, DNA
  • Species Specificity
  • Trees / classification
  • Trees / genetics*

Substances

  • DNA, Plant
  • Photosystem II Protein Complex
  • Nucleotidyltransferases
  • mRNA maturase
  • Endoribonucleases
  • RbcL protein, plastid
  • Ribulose-Bisphosphate Carboxylase
  • Histidine-tRNA Ligase