Computational protocol: High risk of plant invasion in the understory of eucalypt plantations in South China

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Protocol publication

[…] We applied four indices, namely, species richness, phylogenetic diversity, Shannon’s index () and Pielou’s evenness index (), to assess plant diversity in eucalypt plantations and contrast vegetation. To calculate phylogenetic diversity, we constructed a phylogeny tree with all of the recorded species by using the topology of “Phylomatic tree R20120829 for plants” ( and adjusted the branch length with the estimated age of important nodes. The branch length of the phylogeny tree was calculated by using Phylocom (version 4.2). Shannon’s index where Pi is the proportion of individuals that belong to the ith species in the plot and s denotes the total number of species in the same plot. Pielou’s evenness index where H is Shannon’s index, S is the total number of species within a plot and ln (S) denotes the maximum value of H. Importance value where Ci is the coverage of the ith species, C is the total coverage of all species within a plot, Di is the number of the ith species, D is the total individual number of all species, Fi is the frequency of the ith species in the subplots and F is the total frequency of all species within a plot.The importance value of each recorded species within each plot was calculated as the average of relative coverage, relative density and relative frequency in the community (). The importance value of each family within each plot was calculated by using a similar method as species importance, with the coverage and number of each family calculated as the sum of species’ values in which each family belongs to. The importance of invasive species within each plot was calculated as the sum of importance for all invasive species within a plot. The diversity indices, importance values and other statistics were calculated by using R version 3.1.2 with the package “vegan” (version 2.2–1). […]

Pipeline specifications

Software tools Phylomatic, Phylocom, vegan
Application Phylogenetics
Diseases Pulmonary Fibrosis