PDR 2012, 34(3) 263-270 DOI:   10.3724/SP.J.1143.2012.11173  ISSN: 2095-0845 CN: 53-1217/Q

Current Issue | Archive | Search                                                            [Print]   [Close]
Information and Service
This Article
Supporting info
Service and feedback
Email this article to a colleague
Add to Bookshelf
Add to Citation Manager
Cite This Article
Email Alert
DNA barcoding
Phylogenetic reconstruction
Plant community
Dinghushan forest dynamics plot
Subtropical forests
PEI Nan-Cai
Article by Pei, N. C.

Building a Subtropical Forest Community Phylogeny Based on Plant DNA Barcodes from Dinghushan Plot

 PEI  Nan-Cai

Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China


 Reconstructing phylogenies at the community scale remains a fundamental but important work for current researches related to plant systematics, which can be facilitated due to the arising of plant DNA barcodes. We sampled, sequenced, and employed matK, rbcL and psbAtrnH to generate a multilocus barcode for 20ha Dinghushan subtropical forest dynamics plot, with 183 angiosperm species belonging to 110 genera (51 families from 24 orders) in South China. Compared to the twolocus barcode (rbcL+matK , and rbcL+psbAtrnH), the supermatrix of three barcode loci discriminated most of closed related taxa and generated a betterresolved community phylogeny utilizing an unconstraint approach in the Dinghushan plot, providing a first case that a subtropical forest plot with similarly limited taxon sampling with fewer orders and families could also provide significant congruence to the overall angiosperm phylogeny.

Keywords DNA barcoding   Phylogenetic reconstruction   Plant community   Dinghushan forest dynamics plot   Subtropical forests  
Received 2011-12-02 Revised  Online: 2012-01-17 
DOI: 10.3724/SP.J.1143.2012.11173
Corresponding Authors:
About author:


APG III, 2009. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III[J]. Botanical Journal of the Linnean Society, 161 (2): 105—121
Burns JH, Strauss SY, 2011. More closely related species are more ecologically similar in an experimental test[J]. Proceedings of the National Academy of Sciences of the United States of America, 108 (13): 5302—5307
Cadotte MW, Davies TJ, Regetz J et al., 2010. Phylogenetic diversity metrics for ecological communities: integrating species richness, abundance and evolutionary history[J]. Ecology Letters, 13 (1): 96—105
CBOL Plant Working Group, 2009. A DNA barcode for land plants[J]. Proceedings of the National Academy of Sciences of the United States of America, 106 (31): 12794—12797
China Plant BOL Group, 2011. Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants[J]. Proceedings of the National Academy of Sciences of the United States of America, 108 (49): 19641—19646
Chisholm RA, Pacala SW, 2010. Niche and neutral models predict asymptotically equivalent species abundance distributions in highdiversity ecological communities[J]. Proceedings of the National Academy of Sciences of the United States of America, 107 (36): 15821—15825
Cooper N, Jetz W, Freckleton RP, 2010. Phylogenetic comparative approaches for studying niche conservatism[J]. Journal of Evolutionary Biology, 23: 2529—2539
Doyle JJ, Doyle JL, 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue[J]. Phytochemical Bulletin, 19: 11—15
Duarte LdS, 2011. Phylogenetic habitat filtering influences forest nucleation in grasslands[J]. Oikos, 120 (2): 208—215
Feng G (冯刚), Zhang J L (张金龙), Pei N C (裴男才) et al., 2011. Comparison of phylobetadiversity indices based on community data from Gutianshan forest plot[J]. Chinese Science Bulletin (科学通报), 56 (34): 2857—2864
Gonzalez MA, Roger A, Courtois EA et al., 2010. Shifts in species and phylogenetic diversity between sapling and tree communities indicate negative density dependence in a lowland rain forest[J]. Journal of Ecology, 98 (1): 137—146
Heath TA, Hedtke SM, Hillis DM, 2008. Taxon sampling and the accuracy of phylogenetic analyses[J]. Journal of Systematics and Evolution, 46 (3): 239—257
Hebert PDN, Cywinska A, Ball SL et al., 2003. Biological identifications through DNA barcodes[J]. Proceedings of the Royal Society of London Series BBiological Sciences, 270 (1512): 313—321
Holdaway RJ, Richardson SJ, Dickie IA et al., 2011 Species and communitylevel patterns in fine root traits along a 120 000year soil chronosequence in temperate rain forest[J]. Journal of Ecology, 99 (4): 991—1000
Hollingsworth PM, Graham SW, Little DP, 2011. Choosing and using a plant DNA barcode[J]. PLoS ONE, 6 (5): e19254
Janzen DH, Hallwachs W, Blandin P et al., 2009. Integration of DNA barcoding into an ongoing inventory of complex tropical biodiversity[J]. Molecular Ecology Resources, 9: 1—26
Khanuja SPS, Shasany AK, Darokar MP et al., 1999. Rapid isolation of DNA from dry and fresh samples of plants producing large amounts of secondary metabolites and essential oils[J]. Plant Molecular Biology Reporter, 17: 1—7
Kooyman R, Rossetto M, Cornwell W et al., 2011. Phylogenetic tests of community assembly across regional to continental scales in tropical and subtropical rain forests[J]. Global Ecology and Biogeography, 20 (5): 707—716
Kress WJ, Erickson DL, 2007. A twolocus global DNA barcode for land plants: the coding rbcL gene complements the noncoding trnHpsbA spacer region[J]. PLoS ONE, 2 (6): e508
Kress WJ, Erickson DL, 2012. DNA Barcodes: Methods and Protocols[M]. Berlin: Humana Press
Kress WJ, Erickson DL, Jones FA et al., 2009. Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama[J]. Proceedings of the National Academy of Sciences of the United States of America, 106 (44): 18621—18626
Kress WJ, Erickson DL, Swenson NG et al., 2010. Advances in the use of DNA barcodes to build a community phylogeny for tropical trees in a Puerto Rican forest dynamics plot[J]. PLoS ONE, 5 (11): e15409
Kress WJ, Wurdack KJ, Zimmer EA et al., 2005. Use of DNA barcodes to identify flowering plants[J]. Proceedings of the National Academy of Sciences of the United States of America, 102 (23): 8369—8374
Losos JB, 2011. Seeing the Forest for the Trees: The Limitations of Phylogenies in Comparative Biology[J]. The American Naturalist, 177 (6): 709—727
Maddison WP, Maddison DR, 2007. Mesquite: a modular system for evolutionary analysis Version 2.0[OL]. http://mesquiteproject.org
Miller M, Holder M, Vos R et al., 2009 The CIPRES Portals. http://www.phylo.org/sub_sections/portal
Niu KC (牛克昌), Liu YN (刘怿宁), Shen ZH (沈泽昊) et al., 2009. Community assembly: the relative importance of neutral theory and niche theory[J]. Biodiversity Science (生物多样性), 17 (6): 579—593
Pei NC (裴男才), 2011. Phylogenetic community ecology and trait evolution of lower subtropical forest in Dinghushan[PhD Thesis] (鼎湖山南亚热带森林系统发育群落生态学与性状进化研究) Guangzhou: Graduate University of the Chinese Academy of Sciences
Pei NC (裴男才), Zhang JL (张金龙), Mi XC (米湘成) et al., 2011. Plant DNA barcodes promote the development of phylogenetic community ecology[J]. Biodiversity Science (生物多样性), 19 (3): 284—294
Pei N, Lian JY, Erickson DL et al., 2011. Exploring treehabitat associations in a Chinese Subtropical Forest Plot using a molecular phylogeny generated from DNA barcode Loci[J]. PLoS One, 6 (6): e21273
Rambaut A, 1996. SeAl: sequence alignment editor. http://evolve.zoo.ox.ac.uk/
Stamatakis A, 2006. RAxMLVIHPC: Maximum likelihoodbased phylogenetic analyses with thousands of taxa and mixed models[J]. Bioinformatics, 22 (21): 2688—2690
Swenson NG, 2009. Phylogenetic resolution and quantifying the phylogenetic diversity and dispersion of communities[J]. PLoS ONE, 4 (2): e4390
Swenson NG, AngladaCordero P, Barone JA, 2011. Deterministic tropical tree community turnover: evidence from patterns of functional beta diversity along an elevational gradient[J]. Proceedings of the Royal Society B, 278: 877—884
Valentini A, Pompanon F, Taberlet P, 2009. DNA barcoding for ecologists[J]. Trends in Ecology & Evolution, 24 (2): 110—117
Webb CO, 2000. Exploring the phylogenetic structure of ecological communities: an example for rain forest trees[J]. The American Naturalist, 156 (2): 145—155
Webb CO, Ackerly DD, McPeek MA et al., 2002. Phylogenies and community ecology[J]. Annual Review of Ecology and Systematics, 33: 475—505
Webb CO, Donoghue MJ, 2005. Phylomatic: tree assembly for applied phylogenetics[J]. Molecular Ecology Notes, 5 (1): 181—183
Ye WH (叶万辉), Cao HL (曹洪麟), Huang ZL (黄忠良) et al., 2008. Community structure of a 20hm2 lower subtropical evergreen broadleaved forest plot in Dinghushan, China[J]. Journal of Plant Ecology (植物生态学报), 32 (2): 274—286
Zhang SB, Slik JWF, Zhang JL et al., 2011. Spatial patterns of wood traits in China are controlled by phylogeny and environment[J]. Global Ecology and Biogeography, 20 (2): 241—250

Similar articles
2.OU Guang-Long1 , 2 , PENG Ming-Chun1 , HE Zhao-Rong1, WANG Chong-Yun1 , WANG Hao-Bo1 , XIANG Ling1.Quantitative Classification of Plant Communities on the Northern Part of Gaoligong Mountains by TWINSPAN[J]. PDR, 2008,30(6): 679-687
3. YANG Zhen-Yan-1, 2 , ZHANG Ling-1.Screening Potential DNA Barcode Regions in Amomum (Zingiberaceae)[J]. PDR, 2010,32(05): 393-
4. DIAO Yue-Mei-1、2, ZHANG Ling-1.Using DNA Barcoding in Genus Tacca (Dioscoreaceae)[J]. PDR, 2011,33(6): 674-682
5. DU Fang, XU Fang.Gene Flow Dependent Introgression and Species Delimitation[J]. PDR, 2012,34(3): 257-262

Comment for this article:

Copyright by PDR