The use of DNA barcoding as a tool for the conservation biogeography of subtropical forests in China

• Published in: Diversity & distributions Vol. 21; no. 2; pp. 188 - 199
• Main Authors: Liu, Juan, Yan, Hai-Fei, Newmaster, Steven G., Pei, Nancai, Ragupathy, Subramanyam, Ge, Xue-Jun
• Format: Journal Article
• Language: English
• Published: Oxford Blackwell Publishing Ltd 01.02.2015; John Wiley & Sons Ltd; John Wiley & Sons, Inc
• Subjects: Biodiversity; Biodiversity assessments; BIODIVERSITY RESEARCH; Biogeography; Conservation biology; Deoxyribonucleic acid; DNA; Forests; large genera; rbcL + ITS2; rbcL + matK; spatial scale; species resolution
• ISSN: 1366-9516; 1472-4642
• DOI: 10.1111/ddi.12276

Aim Rapid and accurate species identification is the foundation for biodiversity assessment. DNA barcoding has been shown to be an effective tool to overcome the taxonomic impediment to facilitate biodiversity conservation in temperate forests. However, this tool has rarely been considered for use in tropical forests. This study aims to investigate the utility and species resolution of DNA barcoding in a subtropical region. Location The Dinghushan National Nature Reserve (DNNR) in China. Methods A DNA barcoding database was constructed for 531 trees present in the DNNR. We used a phylogenetic method (neighbour-joining trees) and sequence similarity (all-to-all BLASTn searches) to evaluate the utility and species resolution of five DNA barcode regions (rbcL, matK, ITS, ITS2 and trnH-psbA), both singly and in combinations of two or three region. Results The combination of rbcL + matK + ITS had the highest species resolution (94.19%). However, when considering the difficulty of sequence recoverability, rbcL + ITS2 performed best (64.64%). Species resolution for large genera containing more than two species was substantially lower than that for small genera with one and two species per genus. Local small spatial scales (1-ha quadrats) resulted in moderately improved species resolution (70.82% for rbcL + ITS2) compared to larger spatial scales (20 and 1133 ha). We document incongruent signals between nuclear and cpDNA regions and the challenges associated with barcoding large genera inherent to subtropical floras. Main conclusions This study considerably expands the global DNA barcode database for subtropical trees. Based on cost-effectiveness and the trade-off between sequence recovery and species resolution, we suggest that the rbcL + ITS2 barcode combination is an effective tool for documenting plant diversity in the DNNR. This study also sheds some light on the limitations and challenges for the application of barcoding to conservation biogeography in subtropical forests.