Biodiversity Science ›› 2013, Vol. 21 ›› Issue (6): 765-768.doi: 10.3724/SP.J.1003.2013.04133

• Orginal Article • Previous Article     Next Article

Canoco 5: a new version of an ecological multivariate data ordination program

Jiangshan Lai*()   

  1. State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093
  • Received:2013-05-31 Accepted:2013-08-22 Online:2013-12-02
  • Lai Jiangshan E-mail:lai@ibcas.ac.cn

Ordination of multidimensional data on community composition is one of the most important multivariate statistical methods used in biodiversity research. The aim of ordination is to visualize multidimensional data structure at a low-dimensional ordination space. Canoco is one of the most popular programs for ordination analysis and Canoco 4.5 was widely used for such analysis after its release in 2002, because of its simple user interface and powerful graphic tools. A new version of Cannoco, Canoco 5 was released in October 2012. This new version simplifies data entry, provides a better help system and graphics tools, simplifies steps of variation partitioning and significance tests, adds some new methods (e.g. PCNM, NMDS, association analysis of functional traits, etc.). This paper provides an overview of the major improvements to ??Canoco 5, and addresses important steps required for particular analyses.

Key words: variation partitioning, PCNM, NMDS, functional traits, phylogenetic

1 Borcard D, Legendre P (2002) All-scale spatial analysis of ecological data by means of principal coordinates of neighbour matrices.Ecological Modelling, 153, 51-68.
2 Legendre P, Borcard D, Peres-Neto PR (2005) Analyzing beta diversity: partitioning the spatial variation of community composition data.Ecological Monographs, 75, 435-450.
3 Legendre P, Borcard D, Peres-Neto PR (2008) Analyzing or explaining beta diversity? Comment.Ecology, 89, 3238-3244.
4 Lepx J, Smilauer P (2003) Multivariate Analysis of Ecological Data Using CANOCO. Cambridge University Press, Cambridge.
5 Petchey OL, Gaston KJ (2006) Functional diversity: back to basics and looking forward.Ecology Letters, 9, 741-758.
6 ter Braak CJF, Smilauer P (2002) CANOCO Reference Manual and CanoDraw for Windows User's Guide: Software for Canonical Community Ordination. Version 4.5. Microcomputer Power, Ithaca, New York.
7 ter Braak CJF, Smilauer P (2012) CANOCO Reference Manual and User's Guide: Software for Ordination. Version 5. Microcomputer Power Ithaca, New York.
8 von Wehrden H, Hanspach J, Bruelheide H, Wesche K (2009) Pluralism and diversity: trends in the use and application of ordination methods 1990-2007.Journal of Vegetation Science, 20, 695-705.
9 Zhang JT (张金屯) (2004) Quantitative Ecology (数量生态学). Science Press, Beijing. (in Chinese)
[1] Shitong Wang,Yaozhan Xu,Teng Yang,Xinzeng Wei,Mingxi Jiang. (2020) Impacts of microhabitats on leaf functional traits of the wild population of Sinojackia huangmeiensis . Biodiv Sci, 28(3): 277-288.
[2] CHAI Yong-Fu,XU Jin-Shi,LIU Hong-Yan,LIU Quan-Ru,ZHENG Cheng-Yang,KANG Mu-Yi,LIANG Cun-Zhu,WANG Ren-Qing,GAO Xian-Ming,ZHANG Feng,SHI Fu-Chen,LIU Xiao,YUE Ming. (2019) Species composition and phylogenetic structure of major shrublands in North China . Chin J Plant Ecol, 43(9): 793-805.
[3] QIN Hao,ZHANG Yin-Bo,DONG Gang,ZHANG Feng. (2019) Altitudinal patterns of taxonomic, phylogenetic and functional diversity of forest communities in Mount Guandi, Shanxi, China . Chin J Plant Ecol, 43(9): 762-773.
[4] XU Jin-Shi,CHAI Yong-Fu,LIU Xiao,YUE Ming,GUO Yao-Xin,KANG Mu-Yi,LIU Quan-Ru,ZHENG Cheng-Yang,JI Cheng-Jun,YAN Ming,ZHANG Feng,GAO Xian-Ming,WANG Ren-Qing,SHI Fu-Chen,ZHANG Qin-Di,WANG Mao. (2019) Community assembly, diversity patterns and distributions of broad-leaved forests in North China . Chin J Plant Ecol, 43(9): 732-741.
[5] Zhongdong Yu, Zhihe Yu, Shiyu Jin, Long Wang. (2019) Genetic diversity and toxin-producing characters of Aspergillus flavus from China . Biodiv Sci, 27(8): 842-853.
[6] FU Yi-Wen, TIAN Da-Shuan, WANG Jin-Song, NIU Shu-Li, ZHAO Ken-Tian. (2019) Patterns and affecting factors of nitrogen use efficiency of plant leaves and roots in Nei Mongol and Qinghai-Xizang Plateau grasslands . Chin J Plant Ecol, 43(7): 566-575.
[7] YAN Ya-Nan, YE Xiao-Qi, WU Ming, YAN Ming, ZHANG Xin-Li. (2019) Diversity and potassium-solubilizing activity of rhizosphere potassium-solubilizing bacteria of invasive Solidago canadensis . Chin J Plant Ecol, 43(6): 543-556.
[8] Gu Hanjiao, Zhang Cancan, Wang Jinsong, Shi Xuewen, Xia Ruixue, Liu Bin, Chen Fusheng, Bu Wensheng. (2019) Variation in basic morphological and functional traits of Chinese bamboo . Biodiv Sci, 27(6): 585-594.
[9] ZHAO Dan-Dan, MA Hong-Yuan, LI Yang, WEI Ji-Ping, WANG Zhi-Chun. (2019) Effects of water and nutrient additions on functional traits and aboveground biomass of Leymus chinensis . Chin J Plant Ecol, 43(6): 501-511.
[10] Chen Zhixiang, Yao Xueying, Stephen R. Downie, Wang Qizhi. (2019) Assembling and analysis of Sanicula orthacantha chloroplast genome . Biodiv Sci, 27(4): 366-372.
[11] CHENG Yi-Kang, ZHANG Hui, WANG Xu, LONG Wen-Xing, LI Chao, FANG Yan-Shan, FU Ming-Qi, ZHU Kong-Xin. (2019) Effects of functional diversity and phylogenetic diversity on the tropical cloud forest community assembly . Chin J Plant Ecol, 43(3): 217-226.
[12] Xie Lihong,Huang Qingyang,Cao Hongjie,Yang Fan,Wang Jifeng,Ni Hongwei. (2019) Leaf functional traits of Acer mono in Wudalianchi Volcano, China . Biodiv Sci, 27(3): 286-296.
[13] ZHANG Xi-Jin, SONG Kun, PU Fa-Guang, GAO Zhi-Wen, NI Tian-Pin, CHU Xing-Hang, WANG Ze-Ying, SHANG Kan-Kan, DA Liang-Jun. (2019) Study on compositions of parenchyma in twigs of woody saplings in Dabie Mountains, Anhui, China . Chin J Plant Ecol, 43(3): 238-244.
[14] Ruyun Zhang,Yanpeng Li,Yunlong Ni,Xujun Gui,Juyu Lian,Wanhui Ye. (2019) Intraspecific variation of leaf functional traits along the vertical layer in a subtropical evergreen broad-leaved forest of Dinghushan . Biodiv Sci, 27(12): 1279-1290.
[15] HE Yun-Yu, GUO Shui-Liang, WANG Zhe. (2019) Research progress of trade-off relationships of plant functional traits . Chin J Plant Ecol, 43(12): 1021-1035.
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed