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

Nancai Pei; David L Erickson; Bufeng Chen; Xuejun Ge; Xiangcheng Mi; Nathan G Swenson; Jin-Long Zhang; Frank A Jones; Chun-Lin Huang; Wanhui Ye; Zhanqing Hao; Chang-Fu Hsieh; Shawn Lum; Norman A Bourg; John D Parker; Jess K Zimmerman; William J McShea; Ida C Lopez; I-Fang Sun; Stuart J Davies; Keping Ma; W John Kress

doi:10.1038/srep15127

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.

Authors

Nancai Pei^{1

2}, David L Erickson³, Bufeng Chen^{1

2}, Xuejun Ge⁴, Xiangcheng Mi⁵, Nathan G Swenson⁶, Jin-Long Zhang⁷, Frank A Jones⁸, Chun-Lin Huang⁹, Wanhui Ye⁴, Zhanqing Hao¹⁰, Chang-Fu Hsieh¹¹, Shawn Lum¹², Norman A Bourg¹³, John D Parker¹⁴, Jess K Zimmerman¹⁵, William J McShea¹³, Ida C Lopez³, I-Fang Sun¹⁶, Stuart J Davies¹⁷, Keping Ma⁵, W John Kress³

Affiliations

¹ State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, PR China.
² Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, PR China.
³ Department of Botany, MRC-166, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington, DC 20013-7012, USA.
⁴ South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China.
⁵ State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China.
⁶ Department of Biology, University of Maryland, College Park, MD 20742, USA.
⁷ Flora Conservation Department, Kadoorie Farm and Botanic Garden, Lam Kam Road, Tai Po, N.T., Hong Kong.
⁸ Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR, 97331, USA.
⁹ Laboratory of Molecular Phylogenetics, Department of Biology, National Museum of Natural Science, Taichung, Taiwan.
¹⁰ State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, PR China.
¹¹ Institute of Ecology and Evolutionary Biology, National Taiwan University, Roosevelt Road 1, Taipei, Taiwan.
¹² National Institute of Education of Nanyang Technological University, Singapore 637616.
¹³ Smithsonian Conservation Biology Institute, Front Royal, VA, USA.
¹⁴ Smithsonian Environmental Research Center, Edgewater, Maryland, USA.
¹⁵ Institute for Tropical Ecosystem Studies, University of Puerto Rico, San Juan Puerto Rico, 00936-8377, USA.
¹⁶ Department of Natural Resources and Environmental Studies, National Dong Hwa University, Hualien, Taiwan.
¹⁷ Center for Tropical Forest Science-Forest Global Earth Observatory, Smithsonian Tropical Research Institute, P.O. Box 37012, Washington, DC 20013-7012, USA.

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