title: Closely-related taxa influence woody species discrimination via DNA barcoding: evidence from global forest dynamics plots.
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.
authors.affiliation: State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, PR China.|Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, PR China.
authors.forename: Nancai
authors.initials: N
authors.lastname: Pei
authors.affiliation: Department of Botany, MRC-166, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington, DC 20013-7012, USA.
authors.forename: David L
authors.initials: DL
authors.lastname: Erickson
authors.affiliation: State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, PR China.|Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, PR China.
authors.forename: Bufeng
authors.initials: B
authors.lastname: Chen
authors.affiliation: South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China.
authors.forename: Xuejun
authors.initials: X
authors.lastname: Ge
authors.affiliation: State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China.
authors.forename: Xiangcheng
authors.initials: X
authors.lastname: Mi
authors.affiliation: Department of Biology, University of Maryland, College Park, MD 20742, USA.
authors.forename: Nathan G
authors.initials: NG
authors.lastname: Swenson
authors.affiliation: Flora Conservation Department, Kadoorie Farm and Botanic Garden, Lam Kam Road, Tai Po, N.T., Hong Kong.
authors.forename: Jin-Long
authors.initials: JL
authors.lastname: Zhang
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR, 97331, USA.
authors.forename: Frank A
authors.initials: FA
authors.lastname: Jones
authors.affiliation: Laboratory of Molecular Phylogenetics, Department of Biology, National Museum of Natural Science, Taichung, Taiwan.
authors.forename: Chun-Lin
authors.initials: CL
authors.lastname: Huang
authors.affiliation: South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China.
authors.forename: Wanhui
authors.initials: W
authors.lastname: Ye
authors.affiliation: State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, PR China.
authors.forename: Zhanqing
authors.initials: Z
authors.lastname: Hao
authors.affiliation: Institute of Ecology and Evolutionary Biology, National Taiwan University, Roosevelt Road 1, Taipei, Taiwan.
authors.forename: Chang-Fu
authors.initials: CF
authors.lastname: Hsieh
authors.affiliation: National Institute of Education of Nanyang Technological University, Singapore 637616.
authors.forename: Shawn
authors.initials: S
authors.lastname: Lum
authors.affiliation: Smithsonian Conservation Biology Institute, Front Royal, VA, USA.
authors.forename: Norman A
authors.initials: NA
authors.lastname: Bourg
authors.affiliation: Smithsonian Environmental Research Center, Edgewater, Maryland, USA.
authors.forename: John D
authors.initials: JD
authors.lastname: Parker
authors.affiliation: Institute for Tropical Ecosystem Studies, University of Puerto Rico, San Juan Puerto Rico, 00936-8377, USA.
authors.forename: Jess K
authors.initials: JK
authors.lastname: Zimmerman
authors.affiliation: Smithsonian Conservation Biology Institute, Front Royal, VA, USA.
authors.forename: William J
authors.initials: WJ
authors.lastname: McShea
authors.affiliation: Department of Botany, MRC-166, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington, DC 20013-7012, USA.
authors.forename: Ida C
authors.initials: IC
authors.lastname: Lopez
authors.affiliation: Department of Natural Resources and Environmental Studies, National Dong Hwa University, Hualien, Taiwan.
authors.forename: I-Fang
authors.initials: IF
authors.lastname: Sun
authors.affiliation: Center for Tropical Forest Science-Forest Global Earth Observatory, Smithsonian Tropical Research Institute, P.O. Box 37012, Washington, DC 20013-7012, USA.
authors.forename: Stuart J
authors.initials: SJ
authors.lastname: Davies
authors.affiliation: State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China.
authors.forename: Keping
authors.initials: K
authors.lastname: Ma
authors.affiliation: Department of Botany, MRC-166, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington, DC 20013-7012, USA.
authors.forename: W John
authors.initials: WJ
authors.lastname: Kress
mesh_terms: D002736:Chloroplasts / Q000235:genetics; D002980:Climate; D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D018744:DNA, Plant / Q000235:genetics*; D004722:Endoribonucleases / Q000235:genetics; D065928:Forests; D015870:Gene Expression; D056426:Genetic Loci; D006643:Histidine-tRNA Ligase / Q000235:genetics; D009713:Nucleotidyltransferases / Q000235:genetics; D045332:Photosystem II Protein Complex / Q000235:genetics; D010802:Phylogeny; D012273:Ribulose-Bisphosphate Carboxylase / Q000235:genetics; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D014197:Trees / Q000145:classification / Q000235:genetics*
chemical_list: D018744:DNA, Plant; D045332:Photosystem II Protein Complex; D009713:Nucleotidyltransferases; C034038:mRNA maturase; D004722:Endoribonucleases; C101625:RbcL protein, plastid; D012273:Ribulose-Bisphosphate Carboxylase; D006643:Histidine-tRNA Ligase