Invasion
Alien flora are accumulating steadily in China over the last 80 years
(2025, iScience)
Analysis 1: Temporal analysis of alien flora accumulation (based on the minimum residence time (MRT) of the alien plant species)
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Fitting nonlinear functions (fitting, compare, plot)
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Segmented regression (breakpoint estimation, plot, linear regression model to identify temporal trend)
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Bootstrap procedure (prediction of temporal trend in the future)
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Analysis 2: Comparative analysis (compare the MRT values across categories of biotic and abiotic variables)
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Descriptive statistics
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Check for normality (Shapiro-Wilk test) and homogeneity of variance (Levene test)
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Compare (Kruskal-Wallis H test, post hoc Dunn test, ART ANOVA: non-parametric alternative of 2-way ANOVA)
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Analysis 3: Identify the variables’ influence on MRT
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Testing for phylogenetic signals (Blomberg's K and Pagel's λ)
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Univariate regression: logistic regression for variables having no phylogenetic signals, phylogenetic generalised least squares (PGLS) for variables with phylogenetic signals
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Multivariate regression: Phylogenetic path analysis (PPA)
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LASSO regression: Identification of variables' categories that can influence the MRT
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Implications for biological invasion of non-native plants for sale in the world's largest online market
(2024, Conservation Biology)
Analysis 1: Comparison of variables between categories (between the alien species offered for sale and not offered for sale in Chinese online marketplaces) Script
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Descriptive statistics (summarySE)
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Check for normality (Shapiro-Wilk test) and homogeneity of variance (Levene test)
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Compare and effect size estimation (Wilcox test and t-test, post hoc Dunn test)
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Subset data based on criteria
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Analysis 2: Regression analysis (identify variables’ influence on the sale availability of alien plant species of three invasion categories) Script
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Fitting a generalised linear model (glm: binomial logistic regression)
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Plot regression results using the sjPlot package
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Analysis 3: Structural equation modelling (identify variables’ direct and indirect influence on the sale availability of alien plant species of three invasion categories) Script
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Using the lavaan package
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Plot result using the semPlot package
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Spatio-temporal pattern of cross-continental invasion: Evidence of climatic niche shift and predicted range expansion provide management insights for smooth cordgrass (2022, Ecological Indicators)
Analysis 1: Testing spatial niche conservatism (COUE framework) and the environmental analogy between native and non-native ranges
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Using the ecospat package
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Calculating niche overlap, niche similarity, and niche equivalency
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Quantify niche dynamics and plot centroid shift
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MESS analysis
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Analysis 2: Estimate and compare the rate of spread between the three regions of the species’ introduced range
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Custom script
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Fitting the exponential growth model
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Estimating slope and confidence intervals
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Different factors influence naturalisation and invasion processes – A case study of Indian alien flora provides management insights (2021, Journal of Environmental Management)
Analysis 1: Comparison of minimum residence time (MRT) between invasion categories
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Descriptive statistics (summarise function)
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Check for normality (Shapiro-Wilk test) and homogeneity of variance (Levene test)
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Compare (ANOVA, Tukey's HSD, Shapiro-Wilk test, Dunn test)
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Analysis 2: Imputation of missing data
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Visualisation of missing data
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Imputation using the missForest package
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Standardisation of variables
Analysis 3: Logistic regression
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Testing the effects of the biotic and abiotic variables on invasion success (invasive aliens-1, casual aliens-0)
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Analysis 4: Phylogenetic analysis
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Making a phylogenetic tree (V.PHYLOMAKER package), and pruning the tree to genus level
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Testing for phylogenetic signals (Blomberg's K and Pagel's λ), PHYTOOLS package
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Phylogeography
Glacial vicariance and oceanic circulation shape population structure of the coastal legume Derris trifoliata in the Indo-West Pacific (2022, American Journal of Botany)
Analysis 1: Determine the relationship of genetic differentiation with geographic (IBD), environmental (IBE), and resistance (IBR) distances
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Partial Mantel test
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Multiple Regression on Distance Matrices (MRM)
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VIF analysis using the usdm package
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Compute Euclidean distances between points
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Deciphering the global phylogeography of a coastal shrub (Scaevola taccada) reveals the influence of multiple forces on contemporary population structure (2021, Journal of Systematics and Evolution)
Analysis 1: Identify genetic clusters and describe the relationships between them
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Discriminant analysis of principal components
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Contrasting Phylogeographic Patterns in Lumnitzera Mangroves Across the Indo-West Pacific (2021, Frontiers in Plant Science)
Analysis 1: To estimate population differentiation based on cpDNA sequence data
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Hedrick’s G/ST estimation
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Prominent genetic structure across native and introduced ranges of Pluchea indica, a mangrove associate, as revealed by
microsatellite markers (2020, Journal of Plant Ecology)
Analysis 1: To investigate the genetic structure (by integrating the spatial information in the clustering algorithm)
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Assess clustering pattern and plotting (GENELAND package)
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Going with the flow: analysis of population structure reveals high gene flow shaping invasion pattern and inducing range expansion of Mikania micrantha in Asia (2020, Annals of Botany)
Analysis 1: To assess the relationship of genetic differentiation with isolation by distance, environment and resistance surfaces
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Generalized Dissimilarity Modeling analysis in R to model how genetic differentiation changes with environmental conditions and geographic distance (GDM package)
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Native exotic relationships in plant communities: the role of exotic dominance in framing community composition (2017, Ecological Research)
Analysis 1: Likelihood ratio test for equality of Poisson means
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To compare native species richness between sites invaded by two invasive species, either alone or in combination. The number of native species in a site was assumed to follow a Poisson distribution with mean depending on the presence or absence of the two focal species and their joint occurrence.
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