J Plant Ecol ›› 2016, Vol. 9 ›› Issue (2): 233-239.doi: 10.1093/jpe/rtv047

• Research Articles • Previous Articles     Next Articles

An updated megaphylogeny of plants, a tool for generating plant phylogenies and an analysis of phylogenetic community structure

Hong Qian1,* and Yi Jin2   

  1. 1 Research and Collections Center, Illinois State Museum, 1011 East Ash Street, Springfield, IL 62703, USA; 2 College of Life Sciences, Zhejiang University, Hangzhou 310058, China
  • Received:2014-11-05 Accepted:2015-05-30 Online:2015-06-15 Published:2016-03-24
  • Contact: Qian, Hong E-mail:hqian@museum.state.il.us

Abstract: Aims The aim of this article is 3-fold. First, we present an updated version of a published megaphylogeny of vascular plants that can be used in studies of plant ecology and biogeography. Second, we develop a tool that can be used by botanists and plant ecologists to generate phylogenetic hypotheses in three scenarios. Third, we use a set of regional assemblages of angiosperm trees in North America as a model system to evaluate the effect of differences in phylogenies generated using the three scenarios on the quantification of phylogenetic properties and the relationship between measures of phylogenetic properties and environment.
Methods The taxonomy and nomenclature of plant species in the megaphylogeny were standardized according to The Plant List (version 1.1). A tool for generating phylogenies was created using the R language. The robustness of derived phylogenies was evaluated using correlation and regression analyses.
Important findings An updated megaphylogeny of vascular plants (PhytoPhylo) and a tool for reconstructing phylogenies of seed plants (S.PhyloMaker) were generated. Our study shows that phylogenies generated by S.PhyloMaker using the PhytoPhylo megaphylogeny as a backbone are nearly as good as phylogeny resolved at the species level when using derived phylogenies to quantify phylogenetic properties (e.g. phylogenetic diversity and phylogenetic relatedness) of biological assemblages, and that S.PhyloMaker-generated phylogenies are robust for studies of community ecology and biogeography, particularly those seeking for patterns of phylogenetic properties along environmental gradients.

Key words: megatree, megaphylogeny, phylogenetic community ecology, phylogenetic metrics, phylogenetic tree, supertree, vascular plants

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[1] Ying Li;Kaijing Zuo;Kexuan Tang. A Survey of Functional Studies of the GH3 Gene Family in Plants[J]. Chin Bull Bot, 2008, 25(05): 507 -515 .
[2] Gu Tian-qing;Zhang Hui-miao and Lu jing-wen. Study on Biological Properties of Spirulina platensis Cultured with Industrial Waste, Water CO2 and Heat[J]. Chin Bull Bot, 1992, 9(02): 47 -52 .
[3] Suxia Xu;Liangsheng Wang;Qingyan Shu;Minghua Su;Qingyun Huang;Wenhui Zhang;Gongshe Liu . Progress of Study of the Biology of the Resource Plant Bougainvillea[J]. Chin Bull Bot, 2008, 25(04): 483 -490 .
[4] Xue Hong-wei;Wei Zhi-ming and Xu Zhi-hong. The Protoplast Culture and Genetic Transformation of Brassica oleracea[J]. Chin Bull Bot, 1995, 12(增刊): 7 -16 .
[5] Han Xian-zhong;Zhang Zhi-guo;Liu Hua and Zhao Li hong. Preliminary Research on the Growth Conditions of Adventitious Roots of GENTIANA MANSHUR CA[J]. Chin Bull Bot, 1990, 7(03): 49 -51 .
[6] ZHU Jing-Chun;WANG Tai and CHEN Ke-Cheng. Components and Functions of Ubiquitin System(I) - Components Recognition of Substrates and Protein Ubiquitination[J]. Chin Bull Bot, 1999, 16(03): 208 -218 .
[7] Fei Li;Yong Hu;Fan Wang;Zhen Zhang;Xianglin Liu;Sulan Bai;Yikun He. orting of early developmental non-hair cells in root by flow cytometry in Arabidopsis thaliana[J]. Chin Bull Bot, 2010, 45(04): 460 -465 .
[8] Jiang Gao-ming. A Study on the Historical Development Present Characteristics and Managements of the Urban Vegetation of Chengde City[J]. Chin Bull Bot, 1994, 11(04): 33 -38 .
[9] Zhang Hong-da and Zhong Ye-cong. Floristic analysis of Cycas L.[J]. Chin Bull Bot, 1995, 12(专辑): 11 -13 .
[10] CHANG Jie;GE Ying;FU Hua-Lin;YU Ming-Jian and CHEN Qi-Chang. A Study on the Morpho-Ecology of the Leaves of the Main Species in the Evergreen Broad-Leaved Forest Dominated by Cyclobalanopsis glauca[J]. Chin Bull Bot, 1998, 15(06): 59 -64 .