GeoCAT – an open source tool for rapid Red List assessments
Volume 9 Number 1 - January 2012
Steven Bachman and Justin Moat
Plants and the Red List
The IUCN Red List is well known to many as the most authoritative source of information on extinction risk for the world’s organisms. The annual release highlights the familiar creatures: the polar bear, the orang-utan, the rhino, the gorilla - the celebrity species of the conservation world. And each year we are reminded again that many species are slipping toward extinction, usually as a result of pressures from human activities. But when was the last time you remember a species of plant being mentioned? All too often plants fall under the radar when it comes to the Red List, although they are being assessed and they are as threatened as the ‘better known’ groups such as mammals (see the Sampled Red List Index – Plants Under Pressure a global assessment 2010). So why is there such a shortfall? The sheer number of species, in comparison to the number of available scientists, is the main problem. There are as many as 380,000 species of plants presently known and around a thousand new species are described as new to science every year 1. There are more species in a single family of plants such as grasses (Poaceae) than there are all known mammals (5,488). With that in mind it is no wonder that so far only around 4% of the world’s flora have been assigned a category of threat on the global Red List. Although significant activity on Red Listing for plants is taking place around the world, often in botanic gardens, the sheer scale of the task is daunting.
“Only around 4% of the world’s plants have been assessed for their conservation status at the global level”
Despite attempts from the botanical community to accelerate the production of Red List assessments, such as the ambitious Target 2 of the Global Strategy for Plant Conservation 2 ‘an assessment of conservation status of all known plant species’ we are still falling short. The implications of this are very significant. How can we even begin to focus our resources into practical conservation effort if we don’t know where or what to focus on? The good news is that progress is being made. Not only is raw information on plants becoming increasingly available through data sharing platforms such as the Global Biodiversity Information Facility (GBIF), but automated and semi-automated tools are now available to allow scientists and experts to harness that data to answer important questions like – how endangered is my species? With these powerful analytic tools we can more rapidly assess species and more effectively prioritise conservation action. With the development of tools such as GeoCAT, the target of assessing all species may just become more achievable.Introducing GeoCAT
The Royal Botanic Gardens, Kew has long been associated with the Red List process, being key players in the development of the original Red Data books of endangered plants and continuing with major contributions of plant assessments to the present day Red List. The Geographical Information Systems (GIS) Unit at Kew has a more specific interest in the application of GIS techniques for Red List assessment, in particular the geographic components of an assessment. Innovations within the field of GIS over the last few decades have allowed for the first time the production of tools to aid Red List assessment such as the CAT (Conservation Assessment Tools) project 3. Released in 2007, CAT is an extension to the ArcView GIS software system and allows automatic calculation of measures used in Red List assessment. With the recent explosion of web mapping innovations such as Google Earth and Google Maps it was clear that these conservation tools needed to be brought into this new era, which led to the development of GeoCAT.
GeoCAT is a rapid assessment tool that utilises primary plant occurrence data to produce measurements relating to the geographic range of a species. These are then compared with the IUCN Red List categories and criteria and provide evidence to support a full Red List assessment. It is important to note that it is an expert driven system i.e. it is assumed that the user of the tool has good knowledge of the species being assessed as well as a thorough understanding of the Red List categories and criteria (IUCN 2001).
Geographic range measures used in the Red List
One aspect of Red Listing that has been particularly challenging so far is the calculation of geospatial measurements included in the criteria – in other words criteria related to the geography of a species. Geospatial aspects of the Red List criteria mostly relate to Criterion B - Geographic Range, but also appear as elements throughout the other categories A – D. Two different measures of geographic range: extent of occurrence (EOO) and area of occupancy (AOO) are used in the Red List criteria. Extent of occurrence (EOO) is a measure of the geographic range size of a species. IUCN guidelines suggest a minimum convex polygon (MCP) can be used to calculate this value. A MCP is defined as the smallest polygon in which no internal angle exceeds 180˚ and contains all sites of occurrence. This value represents the spread of risk for a species such that species with a large extent will be more robust to threatening processes. An alternative approach for depicting a species range is to show the area where a species occurs or area of occupancy (AOO). A simple way to measure this value is to overlay the distribution with a grid and sum the area of square grid cells the species occupies.
How it works - calculating geographic range of species for Red List assessments
GeoCAT is driven by primary occurrence data. For hundreds of years botanists have been travelling to the ends of the earth to take cuttings from plants as scientific specimens. Herbarium specimens are verifiable records that show where and when a particular species was collected. By combining these records at the species level we immediately have an indication of the geographic range of a species and it is this data that GeoCAT analyses to determine the two measures of extent of occurrence (EOO) and area of occupancy (AOO). A benefit of GeoCAT is that as well as data being provided by the user e.g. from a database of their own specimens, it can also be imported from existing online sources such as GBIF and Flickr. The images in Flickr need to be labelled with the species name and ‘geotagged’ or ‘georeferenced’ i.e. assigned a latitude and longitude co-ordinate so we know where it was taken.
The data can be entered in three ways:
- Import from online sources - existing sources of primary data can be queried. By adding a search term e.g. a scientific name or a common name you can query two sources of online data: GBIF and Flickr. Any matching record that has been georeferenced can be added directly to the map editor.
- Upload your own data - where occurrence data has already been gathered, for example, in a specimen database or spreadsheet, it is possible to import this data directly to the map editor. Data simply needs to be converted to comma separated values format following a standard structure.
- Manual add - you may have specific knowledge regarding the distribution of a species. The user can add points directly to the map with a single click.
With data on the map the user can then edit by adjusting points, removing them and by examining the original data e.g. inspecting a Flickr image to see if it really is the species it is labelled as. From here, at the click of a button the analysis can be enabled. Based on the points on the map, the extent of occurrence (EOO) and area of occupancy (AOO) values are instantly calculated and the values are compared with the thresholds set in the IUCN Criteria. For example if the extent is less than 5,000 km2 then it meets the threshold for the Endangered (EN) category. From here a simple report can be generated and the data can be saved or exported to other formats such as KML for visualisation in other packages such as Google Earth. As mentioned previously it should be noted that this does not represent a full Red List assessment, it provides evidence that fulfils part of the criteria.
Impact and benefits
GeoCAT is a good example of the innovative work presently being carried out in botanic gardens, in this case to directly support plant conservation. Specifically GeoCAT provides the potential to speed up the Red Listing process for plants and offers hope that global targets such as the Global Strategy for Plant Conservation may be reached. By utilising existing data it is an evidence based approach that can be used immediately as much occurrence data is already available. The tool is open and free to use so there are no restrictions in terms of accessibility aside from a connection to the internet. It provides a platform that can be built on in the future to make other aspects of the Red List criteria automated. In short, it could be the first step towards a fully automated data-driven Red List assessment. Perhaps then we will see plants in the spotlight for the next edition of the Red List.
Bachman S., Moat J., Hill A.W., de la Torre J., Scott B. 2011 Supporting Red List threat assessments with GeoCAT: geospatial conservation assessment tool. ZooKeys 150: 117–126 doi: 10.3897/zookeys.150.210
Brummitt, N. ,Bachman., S.P. Moat, J. 2008 Using the Red List as a barometer for plant diversity. Endangered Species Research. doi: 10.3354/esr0013
IUCN (2001) IUCN Red List Categories and Criteria: Version 3.1. IUCN Species Survival Commission. IUCN, Gland, Switzerland and Cambridge, UK: 30 p
Plants under pressure a global assessment. The first report of the IUCN Sampled Red List Index for Plants. Royal Botanic Gardens, Kew, UK. 2010
Steve Bachman and Justin Moat
Royal Botanic Gardens Kew,
Surrey TW9 3AB,