Naturalization of introduced plants is driven by life-form-dependent cultivation biases
Data files
Oct 16, 2023 version files 3.64 MB
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checklist_nat.pla_in_China.updated20230523.csv
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checklist_nat.pla_in_provinces.of.China.updated20230523.csv
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README.md
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tree.tre
Abstract
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.
README
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 (formerly draw.io) software (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.
Methods
Details of the methods are provided in the associated publication.