Plant DNA Barcodes Can Accurately Estimate Species Richness in Poorly Known Floras

Craig Costion,Mark Harrington,Hugh Cross,Andrew Ford,Darren Crayn,Andrew Lowe,Jack Anthony Gilbert

doi:10.1371/journal.pone.0026841

Abstract

BackgroundWidespread 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.Methodology/Principal FindingsHere 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/SignificanceWe 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.

Highlights

Much of the world’s plant diversity is concentrated in recognized biodiversity hotspots [1] containing a high percentage of endemic plant species under threat of extinction
Conclusions/Significance: 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
We show that 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

Summary

Introduction

Much of the world’s plant diversity is concentrated in recognized biodiversity hotspots [1] containing a high percentage of endemic plant species under threat of extinction. Since these hyper-diverse floras are vulnerable to the increasing threats from human activities, methods that enable rapid identification and quantification of species are needed to aid conservation efforts [2,3]. DNA barcoding has the potential to provide an alternative means of estimating species richness without high level expertise in field identification skills and in a much shorter time frame. 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

Methods

Results

Discussion

Conclusion