title: Plant DNA barcodes can accurately estimate species richness in poorly known floras.
abstract: BACKGROUND
  Widespread uptake of DNA barcoding technology for vascular plants has been slow due to the relatively poor resolution of species discrimination (∼70%) and low sequencing and amplification success of one of the two official barcoding loci, matK. Studies to date have mostly focused on finding a solution to these intrinsic limitations of the markers, rather than posing questions that can maximize the utility of DNA barcodes for plants with the current technology.
  
  
  RESULTS
  Here we test the ability of plant DNA barcodes using the two official barcoding loci, rbcLa and matK, plus an alternative barcoding locus, trnH-psbA, to estimate the species diversity of trees in a tropical rainforest plot. Species discrimination accuracy was similar to findings from previous studies but species richness estimation accuracy proved higher, up to 89%. All combinations which included the trnH-psbA locus performed better at both species discrimination and richness estimation than matK, which showed little enhanced species discriminatory power when concatenated with rbcLa. The utility of the trnH-psbA locus is limited however, by the occurrence of intraspecific variation observed in some angiosperm families to occur as an inversion that obscures the monophyly of species.
  
  
  CONCLUSIONS
  We demonstrate for the first time, using a case study, the potential of plant DNA barcodes for the rapid estimation of species richness in taxonomically poorly known areas or cryptic populations revealing a powerful new tool for rapid biodiversity assessment. The combination of the rbcLa and trnH-psbA loci performed better for this purpose than any two-locus combination that included matK. We show that although DNA barcodes fail to discriminate all species of plants, new perspectives and methods on biodiversity value and quantification may overshadow some of these shortcomings by applying barcode data in new ways.
authors.affiliation: Australian Centre for Ecology and Evolutionary Biology, University of Adelaide, Adelaide, South Australia, Australia. ccostion@googlemail.com
authors.forename: Craig
authors.initials: C
authors.lastname: Costion
authors.forename: Andrew
authors.initials: A
authors.lastname: Ford
authors.forename: Hugh
authors.initials: H
authors.lastname: Cross
authors.forename: Darren
authors.initials: D
authors.lastname: Crayn
authors.forename: Mark
authors.initials: M
authors.lastname: Harrington
authors.forename: Andrew
authors.initials: A
authors.lastname: Lowe
mesh_terms: D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D018744:DNA, Plant / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D010944:Plants / Q000145:classification / Q000235:genetics*; D014197:Trees / Q000145:classification / Q000235:genetics*
chemical_list: D018744:DNA, Plant; D010940:Plant Proteins
references.citation: Proc Natl Acad Sci U S A. 2009 Nov 3;106(44):18621-6
references.pmid: 19841276
references.citation: Trends Ecol Evol. 2007 Mar;22(3):148-55
references.pmid: 17129636
references.citation: Conserv Biol. 2008 Dec;22(6):1461-70
references.pmid: 18798854
references.citation: Proc Natl Acad Sci U S A. 2002 Feb 19;99(4):2067-71
references.pmid: 11854502
references.citation: PLoS One. 2010 Jul 13;5(7):e11533
references.pmid: 20644717
references.citation: Mol Ecol Resour. 2009 May;9 Suppl s1:130-9
references.pmid: 21564972
references.citation: Proc Natl Acad Sci U S A. 2008 Feb 26;105(8):2923-8
references.pmid: 18258745
references.citation: Mol Ecol Resour. 2010 May;10(3):421-30
references.pmid: 21565041
references.citation: Proc Natl Acad Sci U S A. 2009 Aug 4;106(31):12794-7
references.pmid: 19666622
references.citation: Proc Natl Acad Sci U S A. 2008 Apr 29;105(17):6350-5
references.pmid: 18436645
references.citation: Proc Natl Acad Sci U S A. 1999 Sep 28;96(20):11387-92
references.pmid: 10500186
references.citation: Mol Ecol Notes. 2007 May 1;7(3):355-364
references.pmid: 18784790
references.citation: Proc Natl Acad Sci U S A. 2006 Mar 7;103(10):3657-62
references.pmid: 16505365
references.citation: Mol Ecol. 2011 Mar;20(6):1289-302
references.pmid: 21255172
references.citation: Nature. 2007 Feb 15;445(7129):757-60
references.pmid: 17301791
references.citation: PLoS One. 2009 Oct 16;4(10):e7483
references.pmid: 19834612
references.citation: Mol Ecol Resour. 2009 May;9 Suppl s1:164-71
references.pmid: 21564975
references.citation: Science. 2006 Jul 7;313(5783):58-61
references.pmid: 16825561
references.citation: Mol Biol Evol. 2011 Oct;28(10):2731-9
references.pmid: 21546353
references.citation: Philos Trans R Soc Lond B Biol Sci. 2005 Oct 29;360(1462):1813-23
references.pmid: 16214740
references.citation: Nature. 2000 Feb 24;403(6772):853-8
references.pmid: 10706275
references.citation: Trends Ecol Evol. 2006 Jan;21(1):1-2
references.pmid: 16701459
references.citation: PLoS One. 2007 Jun 06;2(6):e508
references.pmid: 17551588
references.citation: Mol Ecol Resour. 2009 May;9 Suppl s1:172-80
references.pmid: 21564976