Computational protocol: The global distribution of bamboos: assessing correlates of introduction and invasion

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Protocol publication

[…] We categorized the presence of a species in a given country or region as native or non-native (or introduced) based on distribution data from Kew’s GrassBase and cross-referenced with . These two data sources provide a complete inventory of the taxonomy and distribution of bamboos that was needed to establish native and introduced ranges. We defined these categories using the compendium of concepts in invasion science proposed by . Species were listed as ‘non-native’ or ‘introduced’ when their presence in a region is due to human activity. Note that our records do not distinguish between successful introductions (where species have established and are still present today) and failed introductions (where species no longer occur in that region)—they simply reflect the presence of a species in a given region at some point in time. We classified a subset of ‘non-native’ species as ‘invasive’. Invasive species are ‘naturalized plants that produce reproductive offspring often in large numbers at a considerable distance from parent plants…’ (). Records of bamboos being listed as invasive were found either through the databases mentioned above, or through an independent literature search. References for invasions came from a combination of peer-reviewed literature and official government reports, which were then cross-checked to validate claims that species were ‘invasive’ following the criteria of [see ].To conceptualize and display the flows of introduced and invasive species between and within different biogeographic regions around the world, we used circos visualization from the R package ‘circlize’ (). [...] The exchange of species and the rates of invasion are rarely random, but often have distinct patterns that are influenced by a number of factors, some human-mediated and others related to the evolutionary history of species. Within particular groups this can lead to ′taxonomic selectivity′. In the case of bamboo, forestry and horticulture have been the main drivers of introductions, and this has led to the preferential selection of taxa. To test whether introductions and invasions have been random, we used Fisher’s exact test to analyse differences between numbers of introduced compared with non-introduced species, and the number of invasive compared with non-invasive species across genera, lineages (i.e. neotropical woody), and introduced countries.If certain bamboo traits are important to invasion success, and if these traits reflect evolutionary history, then we would expect the phylogeny to indicate ′taxonomic selectivity′, with only certain lineages becoming invasive. Much work has been done on reviewing this phenomenon to improve the prediction of extinctions. Studies have found that extinctions within taxonomic groups in birds, mammals and plants tend not to be randomly distributed across phylogenies but are concentrated in particular high-risk clades (; ). This is arguably due to phylogenetically conserved life-history traits or ecology (; ; ; ). There is evidence to suggest this is also true with invasiveness across taxa (; ; ; ; ). We explore this for bamboos by testing the phylogenetic signal of status (introduced/invasive) and other correlates of introduction and invasion. To do this we collated genetic data for one chloroplast gene region (maturase K; matK) for all taxa with available data in the online GenBank repository (ncbi.nlm.nih.gov) for phylogeny reconstruction. Where possible, GenBank accessions denoted as ‘voucher’ specimens were used. Our final dataset comprised 124 taxa (including two non-bamboo grass species Bromus interruptus & Trisetum spicatum as outgroup taxa). DNA sequence data were combined and aligned in the BioEdit version 7.0.5.3 () and were edited manually. Flanking regions were trimmed to avoid excessive missing data. Our final DNA alignment consisted of 860 characters and contained three gaps ranging between 1 and 6 base pairs. A Bayesian inference phylogeny was reconstructed using Mr Bayes v 3.2 (). jModelTestv2.13 () and the Akaike information criterion () determined the best fit model for our data as the GTR + I +G model. The Bayesian model was run for 1.5 million generations sampling every 1000th generation and a consensus tree was built, discarding the first 25 % of trees as burn-in. Posterior probabilities (PP) were calculated using a majority rule consensus method to assess tree topology support.To test whether continuous traits (culm dimensions) are phylogenetically clustered or over-dispersed, we used Blomberg’s K statistic with a null hypothesis of Brownian Motion Model (). We also tested for phylogenetic signal of other variables, i.e. introduction and invasion frequency (the number of countries a species has been introduced to or become invasive), and propagule pressure (using the frequency of cultivars as a proxy; see below) using Pagel’s λ (lambda) which uses transformation of the branch lengths assuming Brownian motion (). Both analyses were done using the R packages ‘phytools’ and function Phylosig.R () Species traits, status and cultivar diversity per species were mapped onto the phylogeny to visualise patterns using the R package ‘adephylo’ () [see ]. We used the D statistic () to test for phylogenetic signal and strength of binary traits. This method tests whether traits are randomly assigned across the phylogeny tips (when D equals 0), and whether they are clustered (D equals 1) under a Brownian threshold model. We carried out two tests: one for introduction status (introduced/not introduced) across the whole phylogeny; in the second, we used a tree trimmed to include only introduced bamboos and tested invasion status (invasive/not invasive). This was done using the R package Caper with function phylo.d (). Introduction effort and utility : Many species of bamboo have had cultivars developed for improving their utility and value. We suggest that cultivar diversity associated with species could provide a proxy and quantitative means to measure their popularity and utility. Cultivars are cultivated plant varieties that are developed through selective breeding, genetic manipulations such as polyploidization and hybridization. They are often distinctive, uniform and stable and retain key characteristics when propagated (). Cultivar diversity likely corresponds with propagation frequency and will, therefore, be an important determinant of the probability of introduction, as well as invasion success.As there is no officially accredited list of bamboo cultivars, we used the list compiled by based on the 1995 International Code of Nomenclature for Cultivated Plants (ICNCP). To assess the relationship between introduction status and the number of cultivars developed we used a generalized linear model with a Poisson error structure with number of cultivars as the response variable and status as a predictor variable. As a proxy of introduction effort, we used the number of regions into which a species has been introduced. We tested for this using a generalized linear model with a Poisson error structure with the number of regions a species has been introduced to as a predictor variable and the number of regions a species is invasive in as a response variable. […]

Pipeline specifications

Software tools Circos, circlize, PHYSIG, BioEdit, Phytools, adephylo
Applications Phylogenetics, Genome data visualization
Organisms Homo sapiens