Anna Rönnfeldt¹, Katrin Schifferle¹, Valén Holle¹, Juliano Sarmento Cabral^2,3, Dylan Craven^4,5, Tiffany Knight^6,7,8,9, Hanno Seebens¹⁰, Patrick Weigelt¹¹, Damaris Zurell¹

1. University of Potsdam, Institute of Biochemistry and Biology, Am Neuen Palais 10, 14469 Potsdam, Germany
2. School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
3. Ecological Modelling, Bonner Institute for Organismal Biology - Dept. of Plant Biodiversity, University of Bonn, Bonn, Germany
4. GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Camino La Pirámide 5750, Huechuraba, Santiago, Chile
5. Data Observatory Foundation, ANID Technology Center No. DO210001, Eliodoro Yáñez 2990, 7510277, Providencia, Santiago, Chile
6. Department of Species Interaction Ecology, Helmholtz Centre for Environmental Research – UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
7. German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany
8. Institute of Biology, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle (Saale), Germany
9. Department of Science and Conservation, National Tropical Botanical Garden, Kalāheo, HI, USA
10. Department of Animal Ecology & Systematics, Justus Liebig University, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
11. Department of Environmental Science, Radboud Institute for Biological and Environmental Sciences (RIBES), Radboud University, Heyendaalseweg 135, 6525AJ Nijmegen, The Netherlands

This repository contains R scripts for matching global occurrence data for 3963 non-native plants species from the PaciFLora data set with a biogeographic status. The workflow integrates three complementary data sources to classify each occurrence as native, non-native, contradictory, or unknown. It's output provides a harmonised dataset as base for further analyses, facilitating comparative studies on topics such as the distribution and establishment potential of non-native species, or regional characteristics of their non-native ecological niches.

The workflow was conceptualised and implemented by Anna Rönnfeldt, Katrin Schifferle, Valén Holle, and Damaris Zurell.

This study was supported by the German Research Foundation DFG (grant no. ZU 361/3-1 to DZ).

These data have to be downloaded to reproduced this workflow:

• the species list from the PaciFLora data set. It lists 3963 vascular plant species known to occur as naturalised species on the Pacific Islands
• spatial data corresponding to level 3 tdwg regions
• GloNAF data for the status assignment

script 0_prep_species_list

A species list based on the PaciFLora data set is prepared. In addition to the original PaciFLora names, two additional columns are appendet with alternative ways of writing names of hybrid species.

scripts 1_download_bien, 1_download_gbif

Two scripts to download occurrence data from BIEN and GBIF. We downloaded occurrence data in June 2023.

script 2_data_preparation

The downloaded occurrence records from the two sources were then cleaned to remove duplicates and occurrences with erroneous time stamps or coordinates, and harmonised to combine them into one data set at a 1 km resolution.

scripts 3_status_GIFT, 3_status_GloNAF, 3_status_WCVP

The main source for information on the invasion status (native, introduced, contradictory or unknown) of a species occurrence is the World Checklist of Vascular Plants (WCVP) at the base resolution of level 3 of tdwg. To close data gaps, two additional sources were used: Global Inventory of Floras and Traits (GIFT) and Global Naturalized Alien Flora (GloNAF). As the three sources used different terminology to describe the biogeographic invasion status, we harmonised the terminology as native or introduced.
There are three scripts, each handling the status assignment based on one of the three data sources.

script 4_resolve_status_conflicts

Merging the status information from these three sources resulted in some conflicts. If the sources that caused the conflict referred to areas of different sizes (e.g., Honshu and Japan), the status from the source referring to the smaller area is used. If the sources refer to the same area size, two cirteria can be used to deal with conflicts:

• Criterion 1: All sources are weighted equally. Occurrences with conflicts in the status assignment get the status contradictory.
• Criterion 2: Status information provided by WCVP is preferred, because it has been targeted towards the level 3 resolution of tdwg.

scripts

data
├── download_bien
├── download_gbif
├── status_assignment
├── GloNAF 
├── spatial_data

• R version 4.2.2 (2022-10-31 ucrt)
• Platform: x86_64-w64-mingw32/x64 (64-bit)
• Running under: Windows 10 x64 (build 19045)
• Attached packages: [1] BIEN_1.26 [2] conflicted_1.2.0.9000 [3] CoordinateCleaner_3.0.1 [4] doParallel_1.0.17 [5] fasterize_1.0.4 [6] foreach_1.5.2 [7] GIFT_1.0.0 [8] lcvplants_2.1.0 [9] rgbif_3.7.5 [10] rWCVP_1.2.4 [11] sf_1.0-16 [12] taxize_0.9.100 [13] tibble_3.2.1 [14] tidyverse_2.0.0 [15] terra_1.7-78 [16] units_0.8-5