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. DaviesKeping Ma, W. John Kress

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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.

源语言	英语
文章编号	15127
期刊	Scientific Reports
卷	5
DOI	https://doi.org/10.1038/srep15127
出版状态	已出版 - 12 10月 2015
已对外发布	是

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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, 文章 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",

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}

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, 卷 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 - http://www.scopus.com/inward/record.url?scp=84943799223&partnerID=8YFLogxK

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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