DOI: 10.5061/dryad.k6djh9wd3
title: Naturalization of introduced plants is driven by life-form-dependent cultivation biases

description: Aims: Most naturalized plants are escapees from cultivation. Inventories
 of cultivated introduced species thus offer unique, still underutilized,
 opportunities to assess naturalization drivers of introduced plants. We
 used a comprehensive inventory of 13,718 introduced species cultivated in
 China’s botanical gardens to test which species characteristics
 distinguish the 739 species that have naturalized. Locations: China.
 Methods: We used generalized linear models to test whether the
 naturalization of cultivated introduced plants in China is associated with
 functional traits, propagule pressure, environmental niche, and
 introduction history. To test direct and indirect effects of those
 variables and their relative importance in driving naturalization, we used
 structural equation models. Results: We showed that species were more
 likely to naturalize when they originate from the Americas, are more
 widely cultivated, and have a longer residence time. Moreover, species
 were more likely to naturalize if they have a good environmental match,
 are short-lived herbs, are predominantly propagated from seeds, and, in
 the case of herbs, are relatively tall compared to other herbs. Part of
 the latter effects are mediated by how these variables relate to
 propagule-pressure proxies, and this varies among short-lived herbs,
 long-lived herbs and woody plants. Main conclusions: Naturalization is
 partly driven by life-form-dependent cultivation biases.
description: Details of the methods are provided in the associated
 publication.
description: ### Data and R code for "Naturalization of alien plants is driven by
 life-form-dependent cultivation biases" Prepared by Bi-Cheng Dong 13
 October 2023 This README file lists and describes the files used for the
 analyses involved in the manuscript, "Naturalization of alien plants
 is driven by life-form-dependent cultivation biases", by Bi-Cheng
 Dong, Qiang Yang, Nicole L. Kinlock, Robin Pouteau, Petr Pyšek, Patrick
 Weigelt, Fei-Hai Yu, and Mark van Kleunen, published in *Diversity and
 Distributions*. Please see the manuscript itself and the Supporting
 Information for additional details regarding this analysis. ### Files
 included ### Dataset of introduced taxa cultivated in China’s botanical
 gardens * **checklist\_nat.pla\_in\_China.updated20230523.csv**: this is
 the main dataset used in all analyses at the country scale. Each row is a
 seed plant taxon introduced to China listed in Lin et al. (2019).
 Associated data on functional traits, propagule pressure, environmental
 niche, and introduction history are also provided for each taxon. The
 columns in the dataset are listed below. NA in the cell means data not
 available. The CSV file is UTF-8 encoded. *
 **checklist\_nat.pla\_in\_provinces.of.China.updated20230523.csv**: this
 is the main dataset used in all analyses at the province scale. The
 columns in the dataset are listed below. NA in the cell means data not
 available. The CSV file is UTF-8 encoded. ### R code used to conduct
 analyses All R code has been compressed into a single ZIP file
 (**cultivated\_introduced\_plants\_in\_China.zip**). *
 **20230523Fig1\_native\_range\_resampling\_test.R**: the randomization
 test for continents of origin, also including Figure 1; *
 **20230523Table1.and.Appendix.table2.and.Fig2\_GLMs.lowercase.R**: the
 separate GLMs and the GLM with interaction between life form and max.
 height, including Figure 2; *
 **20230523piecewiseSEMs.with.correaltions.R**: piecewise SEMs with
 correlations. Figure 3 was manually made, using
 [diagrams.net](http://diagrams.net/) (formerly [draw.io](http://draw.io/))
 software ([https://app.diagrams.net/](https://app.diagrams.net/)). *
 **20230523Appendix.Tables1and3\_phylo\_GLMs.R**: separate phylogenetic
 GLMs and the phylogenetic GLM with interaction between life form and max.
 height.; * **20230523Suppmentary\_materials\_GLMMs.R**: to test the
 effects of climatic suitability, cultivation status, and their interaction
 on naturalization per province, generalized linear mixed model (GLMM) with
 taxon and the provinces where the taxon was cultivated, as random factors,
 was used. ### Phylogenetic tree of taxa * **tree.tre**: the phylogenetic
 tree used in the phylogenetic GLMs and GLMM. ### Metadata for the main
 dataset * The columns in the first dataset
 (checklist\_nat.pla\_in\_China.updated20230523.csv) are as follows: *
 **Standardized\_names**: name of taxon, standardized using The Plant List
 (TPL); * **TPL\_Author**: Authority of the standardized names, provided by
 TPL; * **naturalized\_status**: has the taxon naturalized in China? (1 =
 naturalized, 0 = non-naturalized); * **bg\_num**: the number of botanical
 gardens in which the taxon was cultivated; * **chklst\_prov\_num**: the
 number of provinces in which the taxon was cultivated; *
 **ali\_new\_status**: has the taxon been for sale in Alibaba? (1 = yes, 0
 = no).; * **wcup\_eco\_use\_num**: the number of economic-use categories
 that the taxon had; * **hab\_suit\_mean**: the mean climatic suitability
 of the taxon across China (x1000), estimated by SDMs; *
 **new\_sum.L3.code**: the number of TDWG level-3 regions in which the
 taxon is considered native; * **min\_record\_year\_cvh**: the year of
 first record in the wild for the taxon with specimens in the Chinese
 Virtual Herbarium; * **residence\_time\_to\_2020**: the number of years
 since the taxon was first recorded in China (up until 2020); *
 **Life\_form\_new**: the life form of the taxon, categorized as
 short-lived herbaceous (1), long-lived herbaceous (2), or woody (3); *
 **LF\_data\_source**: source of life-form data; * **prop\_type**: the
 propagation mode that the taxon had, categorized as seed (1), vegetative
 (2), or both (3); * **prop\_data\_source**: source of propagation-mode
 data; * **Height\_max\_max**: max. height of the taxon, in meters; *
 **Height\_max\_data\_source\_tog**: source of max.-height data; *
 **tip.label**: label corresponding to the tips of the phylogenetic tree
 used in this analysis (**tree.tre**). Taxon names on the tree were
 standardized using the TPL backbone. * **tip.order**: the order of label
 corresponding to the tips of the phylogenetic tree used in this analysis.
 * **X1**: the TDWG level-1 region in which the taxon is considered native;
 Europe * **X2**: the TDWG level-1 region in which the taxon is considered
 native; Africa * **X3**: the TDWG level-1 region in which the taxon is
 considered native; Temperate Asia * **X4**: the TDWG level-1 region in
 which the taxon is considered native; Tropical Asia * **X5**: the TDWG
 level-1 region in which the taxon is considered native; Australasia *
 **X6**: the TDWG level-1 region in which the taxon is considered native;
 Pacific islands * **X7**: the TDWG level-1 region in which the taxon is
 considered native; Northern America * **X8**: the TDWG level-1 region in
 which the taxon is considered native; Southern America * **X9**: the TDWG
 level-1 region in which the taxon is considered native; Antarctic * The
 columns in the second dataset
 (**checklist\_nat.pla\_in\_provinces.of.China.updated20230523.csv**) are
 as follows: * **Standardized\_names**: name of taxon, standardized using
 The Plant List (TPL); * **prov.name.en**: name of province of China; *
 **prov\_code**: id of province of China; * **naturalized\_status\_China**:
 has the taxon naturalized in China? (1 = naturalized, 0 =
 non-naturalized); * **naturalized\_status\_prov**: has the taxon
 naturalized in one given province of China? (1 = naturalized, 0 =
 non-naturalized); * **prov\_planting\_status**: has the taxon been
 cultivated in one given province of China? (1 = yes, 0 = no); *
 **EMwmean\_mean**: the mean climatic suitability of the taxon in one given
 province of China (x1000), estimated by SDMs.