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

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

Chinese Academy of Forestry
Smithsonian Institution
Chinese Academy of Sciences
University of Maryland, College Park
Flora Conservation Department
Oregon State University
National Museum of Natural Science, Taiwan
National Taiwan University
Nanyang Technological University
University of Puerto Rico
National Dong Hwa University

Research output: Contribution to journal › Article › peer-review

26 Scopus citations

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 (G m/G t 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.

Original language	English
Article number	15127
Journal	Scientific Reports
Volume	5
DOIs	https://doi.org/10.1038/srep15127
State	Published - 12 Oct 2015
Externally published	Yes

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Pei, N., Erickson, D. L., Chen, B., Ge, X., Mi, X., Swenson, N. G., Zhang, J. L., Jones, F. A., Huang, C. L., Ye, W., Hao, Z., Hsieh, C. F., Lum, S., Bourg, N. A., Parker, J. D., Zimmerman, J. K., McShea, W. J., Lopez, I. C., Sun, I. F., ... Kress, W. J. (2015). Closely-related taxa influence woody species discrimination via DNA barcoding: Evidence from global forest dynamics plots. Scientific Reports, 5, Article 15127. https://doi.org/10.1038/srep15127

@article{5ba1f0f399a64edf928e6b770914f6a5,

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 (G m/G t 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.",

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

year = "2015",

month = oct,

day = "12",

doi = "10.1038/srep15127",

language = "英语",

volume = "5",

journal = "Scientific Reports",

issn = "2045-2322",

publisher = "Nature Research",

}

Pei, N, Erickson, DL, Chen, B, Ge, X, Mi, X, Swenson, NG, Zhang, JL, Jones, FA, Huang, CL, Ye, W, Hao, Z, Hsieh, CF, Lum, S, Bourg, NA, Parker, JD, Zimmerman, JK, McShea, WJ, Lopez, IC, Sun, IF, Davies, SJ, Ma, K & Kress, WJ 2015, 'Closely-related taxa influence woody species discrimination via DNA barcoding: Evidence from global forest dynamics plots', Scientific Reports, vol. 5, 15127. https://doi.org/10.1038/srep15127

TY - JOUR

T1 - Closely-related taxa influence woody species discrimination via DNA barcoding

T2 - Evidence from global forest dynamics plots

AU - Pei, Nancai

AU - Erickson, David L.

AU - Chen, Bufeng

AU - Ge, Xuejun

AU - Mi, Xiangcheng

AU - Swenson, Nathan G.

AU - Zhang, Jin Long

AU - Jones, Frank A.

AU - Huang, Chun Lin

AU - Ye, Wanhui

AU - Hao, Zhanqing

AU - Hsieh, Chang Fu

AU - Lum, Shawn

AU - Bourg, Norman A.

AU - Parker, John D.

AU - Zimmerman, Jess K.

AU - McShea, William J.

AU - Lopez, Ida C.

AU - Sun, I. Fang

AU - Davies, Stuart J.

AU - Ma, Keping

AU - Kress, W. John

PY - 2015/10/12

Y1 - 2015/10/12

N2 - 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 (G m/G t 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.

AB - 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 (G m/G t 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.

UR - https://www.scopus.com/pages/publications/84943799223

U2 - 10.1038/srep15127

DO - 10.1038/srep15127

M3 - 文章

C2 - 26456472

AN - SCOPUS:84943799223

SN - 2045-2322

VL - 5

JO - Scientific Reports

JF - Scientific Reports

M1 - 15127

ER -

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

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