Biodiversity Data Journal :
Software Description
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Corresponding author: Steven Bachman (s.bachman@kew.org)
Academic editor: Pedro Cardoso
Received: 02 Oct 2019 | Accepted: 18 Nov 2019 | Published: 23 Jan 2020
© 2020 Steven Bachman, Barnaby Walker, Sara Barrios, Alison Copeland, Justin Moat
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Bachman S, Walker BE, Barrios S, Copeland A, Moat J (2020) Rapid Least Concern: towards automating Red List assessments. Biodiversity Data Journal 8: e47018. https://doi.org/10.3897/BDJ.8.e47018
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The IUCN Red List of Threatened SpeciesTM (hereafter the Red List) is an important global resource for conservation that supports conservation planning, safeguarding critical habitat and monitoring biodiversity change (
One reason for this lack of species coverage is that a manual and relatively time-consuming procedure is usually employed to assess and document species. A recent update of Red List documentation standards (
We present a web application, Rapid Least Concern, that addresses the challenge of accelerating the generation and documentation of Least Concern Red List assessments. Rapid Least Concern utilises open-source datasets, such as the Global Biodiversity Information Facility (GBIF) and Plants of the World Online (POWO) through a simple web interface. Initially, the application is intended for use on plants, but it could be extended to other groups, depending on the availability of equivalent datasets for these groups.
Rapid Least Concern users can assess a single species or upload a list of species that are assessed in a batch operation. The batch operation can either utilise georeferenced occurrence data from GBIF or occurrence data provided by the user. The output includes a series of CSV files and a point map file that meet the minimum data requirements for a Least Concern Red List assessment (
We outline the knowledge gap this application aims to fill and describe how the application works. We demonstrate a use-case for Rapid Least Concern as part of an ongoing initiative to complete a global Red List assessment of all native species for the United Kingdom Overseas Territory of Bermuda.
Red List, Least Concern, Non-threatened, plants, automation, GBIF, Plants of the World Online, Bermuda
The global Red List is incomplete, with plants, fungi and invertebrates representing the major gaps in coverage. Despite major efforts to document the Red List status of plants (
To speed up the assessment process, we can adopt a two-stage strategy: prioritisation and automation. Prioritisation is necessary because ongoing and intensifying threats to biodiversity (
To ensure that the assessor network can focus primarily on threatened species, we need user-friendly tools to both prioritise and automate the assessment of the remaining pool of 'Not Evaluated' plant species. The first step is to apply a triage approach that classifies species into those likely to be threatened and those likely non-threatened. Secondly, for the non-threatened species, the assessments should be automatically generated.
Prioritisation:
Several approaches to prioritise plant species for assessments have shown a high level of accuracy (> 96%) when predicting non-threatened species, especially those that incorporate some measure of geographic range (see
Automatic generation of Least Concern assessments:
The second stage is to fully document those species identified as Least Concern. All Red List assessments require three elements: the assessment category, supporting documentation and a distribution map (
SIS Connect - bridging raw data and the Red List
All published assessments on the Red List are drawn from an underlying database called the Species Information Service. Until recently, supporting documentation for Red List assessments had to be entered into SIS manually. The recent development of SIS Connect (http://connect.iucnredlist.org/) has enabled batch transfer of assessments to SIS. Batch transfer requires preparation of a compressed file containing multiple CSV files that collectively make up the raw data of Red List assessments. After registering and logging in to SIS Connect, the user can upload the compressed file, which is then subject to validation checks. If approved by the Red List Unit and subsequently reviewed by the relevant Red List Authority, the assessments represented in the batch file can be processed for publication on the Red List.
Rapid documentation of Least Concern plants for the Red List
Can be applied worldwide across all plants. Case study from Bermuda.
The Rapid Least Concern user interface can be accessed from the following link: https://spbachman.shinyapps.io/rapidLC. From the home page, the user can choose the single or batch species workflow, access the quick-start video tutorials or access the user manual via the help tab (Suppl. material
Single species workflow:
The single species workflow requires the user to enter a plant species name in the binomial form i.e. Genus species into the text input box on the left side panel (Fig.
The GBIF Occurrence API is then accessed via the GBIF usageKey using the selected plant name to query all georeferenced occurrence records that do not have a geospatial issue. A parameter to determine the upper limit for the number of occurrences can be set using the slider widget where a minimum of 1,000 and maximum of 10,000 occurrences are permitted with a default of 3,000 occurrences. Clicking the 'Run analysis!' button will initiate a spatial query of the occurrence records within the native range, such that all non-native occurrence records are excluded from any further analysis. The occurrence records and native range are visualised on a base map (Fig.
Field | Description | LC Threshold |
EOO | Extent of occurrence. Calculated as the area (km2) of a minimum convex polygon of all extant occurrence points within the native range. | 30,000 km2 |
AOO | Area (km2) calculated by summing the number of occupied cells based on occurrence points within the native range by the area of the cells. A grid of 10 km x 10 km cells was used to account for georeference error as opposed to the standard 2 x 2 km reference scale. A single occupied cell would return an AOO value of 100 km2 | 3,000 km2 |
RecordCount | The number of unique georeferenced occurrence records within the native range. | 75 |
TDWGCount | The number of Level 3 TDWG regions in which the species occur across its native range. | 5 |
POWO_ID | Unique ID for Plants of the World Online | |
full_name | Binomial | |
warning | Indicates a problem with analysis e.g. no points in GBIF | |
leastConcern | Indicates whether the species meets or exceeds all the LC thresholds. | TRUE/FALSE |
It should be noted that the application primarily uses range-based parameters to determine Least Concern status, which, although shown to be good predictors of threat status (
The 'Run analysis!' button also initiates the generation of several data tables that form the basis of the minimum required documentation for a Least Concern assessment (
Batch species workflow:
The batch species workflow offers the option to apply the single species workflow to multiple species at once. Instead of entering a name, the user can upload a CSV file containing multiple names. The batch analysis runs an initial test of the name against POWO and returns a report on the number of name matches or names recognised by POWO as synonyms. Any names not matched to POWO or listed as synonyms are excluded from further analysis. Again, the parameter of GBIF occurrence record limit can be set and then the analysis returns a table of results comprising the same statistics as for the single species workflow: extent of occurrence (EOO), area of occupancy (AOO), number of occurrence records and number of TDWG Level 3 regions for each species.
Unlike the single workflow, the user can adjust the LC thresholds using the sliders on the left-hand side bar which will refresh the table of results. The user can then download the compressed folder containing CSV files for all species that met or exceeded the LC thresholds. In most tables, a separate row is added for each species, except for tables where there is a one-to-many relationship, (e.g. habitat), where a species can occur in multiple habitat types and each is recorded in a separate row. A results CSV file is also included in the download and includes the raw statistics for each species, whether or not it was LC, according to the thresholds and a note in the 'warning' column to explain any issues, for example, there were no georeferenced points from GBIF to carry out the area calculations.
An extension of the batch workflow allows users to upload their own occurrence data as they may already have a cleaned dataset prepared. The process is exactly the same as above, except the user uploads a CSV file with names alongside decimal latitude and longitude co-ordinates. In this scenario, the GBIF occurrence download is bypassed and the user occurrence points are used to calculate the spatial metrics.
Threshold values:
Although there are no defined thresholds to separate Near Threatened species from Least Concern species, the Red List guidelines indicate that an extent of occurrence (EOO) > 30,000 km2 and AOO > 3,000 km2 are not likely to trigger a threatened or Near Threatened category and hence can be classified as Least Concern (
In order to determine an appropriate threshold for each parameter, we carried out a sensitivity analysis using, as a validation dataset, a random set of 923 monocot species with complete, published Red List assessments from the Sampled Red List Index for Plants Project (
Sensitivity analysis to determine thresholds for Least Concern for each parameter: number of specimens, number of TDWG regions, extent of occurrence and area of occupancy. Vertical dashed line shows the chosen threshold (also reported in Table
The chosen thresholds listed in Table
Limitations
The batch species workflow currently processes up to 100 species at a time. Processing time can vary depending on the species and mostly on the number of occurrences per species. Batches of more than 100 species are not recommended because performance issues are encountered when dealing with sets of more than 100 species in the IUCN central database (SIS).
The coverage and accuracy of the underlying datasets used by Rapid Least Concern, such as GBIF and Plants of the World Online, will influence the results generated. Despite known gaps in coverage and quality (
Case study: Bermuda
We illustrate the utility of Rapid Least Concern with a use-case for the plants of the UK Overseas Territory of Bermuda. Bermuda has a sub-tropical climate and a total land mass of just 53 km². Bermuda’s Department of Environment and Natural Resources and the UK Overseas Territories team at the Royal Botanic Gardens, Kew have been collaborating to assess the global Red List status of Bermuda’s native plant species. This collaboration has resulted in ten endemic plant species assessed and published on the IUCN Red List. To prioritise the assessment of the remaining native flora and to generate Least Concern Red List assessments for the non-threatened taxa at global level, we applied Rapid Least Concern.
We queried the Plants of the World Online database to obtain a checklist of all native plants for Bermuda and cross-checked with Britton's (
We used the Rapid Least Concern batch species workflow and uploaded a list of the remaining 134 Not Evaluated species. We used default values for the upper limit of GBIF occurrences (3,000) and default thresholds to determine Least Concern (Table
Outcomes:
The overall proportion of species assessed at a global level increased from 38 (22%) to 147 (85%) (Fig.
Impact of Rapid Least Concern on overall proportion of species assessed for native plants in Bermuda. Number of species in each Red List category are shown prior to and after running Rapid Least Concern. Categories follow the IUCN Red List system: Extinct in the Wild (EW), Critically Endangered (CR), Endangered (EN), Vulnerable (VU), Near threatened (NT), Least Concern (LC), Data Deficient (DD) and Not Evaluated (NE). All species have been assessed at global level.
MIT License
Rapid Least Concern was written in the R programming language (
The application depends on the following R packages: raster (
This application is targeted towards any user wishing to assess and document Least Concern assessments of plants for the Red List. It should be particularly useful for members of the IUCN Species Survival Commission (SSC) Plant Specialist Groups and IUCN Red List partners. It may also be of use to conservation practitioners wishing to quickly prioritise species for further detailed assessments or deprioritise those likely to be non-threatened. Finally, it can be used to rapidly generate baseline data for potentially threatened species.
Many thanks to Malin Rivers at Botanic Gardens Conservation International (BGCI) and contributors to the Global Tree Assessment (GTA) workflow workshop, for providing the inspiration to develop this application. Thanks to Serene Hargreaves, Tarciso Leão, Cristina Lopez-Gallego, Jo Osborne, Domitilla Raimondo, Saba Rokni and Lize von Staden for providing feedback on earlier versions of the application. Thanks to Tim Wilkinson, John Iacona and James Crowe for technical feedback on application development and POWO names services. Robin Freeman provided help on an earlier version of code. Thanks to the IUCN Red List Unit - especially Craig Hilton-Taylor and Ackbar Joolia for feedback and advice regarding SIS Connect. Thanks to Martin Hamilton for his help with the UKOTs Species and Specimens Database. Thanks to Eimear Nic Lughadha for thoughtful comments that greatly improved an earlier version of the manuscript.
Rapid Least Concern User Guide.
List of native plant species in Bermuda. Includes Red List status if already assessed, predicted Red List status (LC or not LC) and final category decided after expert review.