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Closely-related taxa influence woody species discrimination via DNA barcoding: evidence from global forest dynamics plots.
Pei, Nancai; Erickson, David L; Chen, Bufeng; Ge, Xuejun; Mi, Xiangcheng; Swenson, Nathan G; Zhang, Jin-Long; Jones, Frank A; Huang, Chun-Lin; Ye, Wanhui; Hao, Zhanqing; Hsieh, Chang-Fu; Lum, Shawn; Bourg, Norman A; Parker, John D; Zimmerman, Jess K; McShea, William J; Lopez, Ida C; Sun, I-Fang; Davies, Stuart J; Ma, Keping; Kress, W John.
Affiliation
  • Pei N; State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, PR China.
  • Erickson DL; Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, PR China.
  • Chen B; Department of Botany, MRC-166, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington, DC 20013-7012, USA.
  • Ge X; State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, PR China.
  • Mi X; Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, PR China.
  • Swenson NG; South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China.
  • Zhang JL; State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China.
  • Jones FA; Department of Biology, University of Maryland, College Park, MD 20742, USA.
  • Huang CL; Flora Conservation Department, Kadoorie Farm and Botanic Garden, Lam Kam Road, Tai Po, N.T., Hong Kong.
  • Ye W; Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR, 97331, USA.
  • Hao Z; Laboratory of Molecular Phylogenetics, Department of Biology, National Museum of Natural Science, Taichung, Taiwan.
  • Hsieh CF; South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China.
  • Lum S; State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, PR China.
  • Bourg NA; Institute of Ecology and Evolutionary Biology, National Taiwan University, Roosevelt Road 1, Taipei, Taiwan.
  • Parker JD; National Institute of Education of Nanyang Technological University, Singapore 637616.
  • Zimmerman JK; Smithsonian Conservation Biology Institute, Front Royal, VA, USA.
  • McShea WJ; Smithsonian Environmental Research Center, Edgewater, Maryland, USA.
  • Lopez IC; Institute for Tropical Ecosystem Studies, University of Puerto Rico, San Juan Puerto Rico, 00936-8377, USA.
  • Sun IF; Smithsonian Conservation Biology Institute, Front Royal, VA, USA.
  • Davies SJ; Department of Botany, MRC-166, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington, DC 20013-7012, USA.
  • Ma K; Department of Natural Resources and Environmental Studies, National Dong Hwa University, Hualien, Taiwan.
  • Kress WJ; Center for Tropical Forest Science-Forest Global Earth Observatory, Smithsonian Tropical Research Institute, P.O. Box 37012, Washington, DC 20013-7012, USA.
Sci Rep ; 5: 15127, 2015 Oct 12.
Article in En | MEDLINE | ID: mdl-26456472
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.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Phylogeny / Trees / DNA, Plant / DNA Barcoding, Taxonomic Type of study: Incidence_studies / Prognostic_studies Language: En Journal: Sci Rep Year: 2015 Document type: Article
Fulltext
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Phylogeny / Trees / DNA, Plant / DNA Barcoding, Taxonomic Type of study: Incidence_studies / Prognostic_studies Language: En Journal: Sci Rep Year: 2015 Document type: Article