Least concern to endangered: Applying climate change projections profoundly influences the extinction risk assessment for wild Arabica coffee

Arabica coffee (Coffea arabica) is a key crop in many tropical countries and globally provides an export value of over US$13 billion per year. Wild Arabica coffee is of fundamental importance for the global coffee sector and of direct importance within Ethiopia, as a source of harvestable income and planting stock. Published studies show that climate change is projected to have a substantial negative influence on the current suitable growing areas for indigenous Arabica in Ethiopia and South Sudan. Here we use all available future projections for the species based on multiple general circulation models (GCMs), emission scenarios, and migration scenarios, to predict changes in Extent of Occurrence (EOO), Area of Occupancy (AOO), and population numbers for wild Arabica coffee. Under climate change our results show that population numbers could reduce by 50% or more (with a few models showing over 80%) by 2088. EOO and AOO are projected to decline by around 30% in many cases. Furthermore, present‐day models compared to the near future (2038), show a reduction for EOO of over 40% (with a few cases over 50%), although EOO should be treated with caution due to its sensitivity to outlying occurrences. When applying these metrics to extinction risk, we show that the determination of generation length is critical. When applying the International Union for Conservation of Nature's Red list of Threatened Species (IUCN Red List) criteria, even with a very conservative generation length of 21 years, wild Arabica coffee is assessed as Threatened with extinction (placed in the Endangered category) under a broad range of climate change projections, if no interventions are made. Importantly, if we do not include climate change in our assessment, Arabica coffee is assessed as Least Concern (not threatened) when applying the IUCN Red List criteria.     

Using species distribution models for IUCN Red Lists of threatened species

Red Lists have been used for years globally and regionally in many countries to highlight species that need special attention because of the rarity or rapid decline of their populations. To ensure homogenized classification at the global and regional level, the International Union for Conservation of Nature (IUCN) defined categories of threat, and criteria to attribute the taxa to these categories. Nevertheless, the strict application of the criteria is not always straightforward, especially for invertebrates, because of the difficulties associated with precise estimates of the size and viability of their populations. This paper presents a method for the estimation of extent of occurrence (EOO) and area of occupancy (AOO) based on species distribution models using multivariate adaptive regression splines. To achieve this, presence data have been modeled against topographical and climatic explanatory variables. Predictions from the statistical distribution models have then been cut using the minimal convex hull around (EOO) or the watersheds in which (AOO) the species have really been observed in recent years. This allows us to delimit the EOO and AOO according to the IUCN criteria, and better take into account the ecological requirements of the species. Furthermore, the method allows for the use of historical data (e.g. from museum’s collections) and the direct comparison of historical and recent distributions of species. The method has been tested on six species of butterflies. The results show the possibility of using species distribution models to define the Red Lists status according to the IUCN guidelines, and shows that the results are consistent with previous Red Lists assessments.     

Scale dependency and area of occupancy: Tortula freibergii in north-west England

Abstract

Area of occupancy (AOO) is used commonly as a measure of species range size and the IUCN Red List Criteria provide thresholds of AOO for determining the extinction risk of species. Tortula freibergii is a rare moss globally and is considered to be a priority for conservation in the UK. This study provides the results of a comprehensive survey of the distribution of the species in north-west England, at a linear resolution of 0.5 km, which shows it to be considerably more widespread than understood previously. The data are used to create a 'species-area curve' that spans the scales of 0.1 to 10 km and examine how measures of AOO change according to the scale of measurement. AOO values declined sharply as the scale of measurement reduced, as a result of the linear and frequently fragmented distribution of the species. Implications for the application of the IUCN Red List Criteria and the monitoring of species are discussed.     

Redlistr: tools for the IUCN Red Lists of ecosystems and threatened species in R

The International Union for the Conservation of Nature (IUCN) Red List of ecosystems and Red List of threatened species are global standards for assessing risks of ecosystem collapse and species extinction. However, misconceptions of the Red List assessment process, along with its technically demanding nature, can result in the misapplication of their criteria, leading to inconsistent and potentially unreliable assessments. To address this problem, we developed redlistr, an R package aiding in the production of consistent species and ecosystem Red List assessments. Redlistr's features include methods to calculate 1) area from spatial data, 2) range size metrics, 3) rates of change of distributions or populations, and 4) distribution or population at another time from these rates. A key feature of the package is the systematic approach used to eliminate geometric uncertainty when estimating area of occupancy. Here, we develop two case studies to demonstrate the functionalities of redlistr with typical workflows for both species and ecosystems. Redlistr was developed to be accessible to users with a broad range of experience in programming for spatial and temporal data analysis, and sufficiently flexible to allow users to parameterise functions and select equations to fit their purposes. The package specifically aims to assist researchers and conservation practitioners to conduct robust and transparent risk assessments of ecosystems and species under the IUCN Red List criteria but is also useful for other studies requiring analyses of range size, area change and calculations of rates of change.     

The use of specimen information influences the outcomes of Red List assessments: the case of southern African plant specimens

Information contained on specimen labels of natural history collections is often the most reliable and available source of information to guide conservation decisions. When used for making IUCN Red List assessments, the inherent limitations associated with specimen information affect the assignment of Red List categories, and the case of the southern African plant Red Lists reflects this. Red List assessments that are based on specimen information can result in predictable outcomes, namely the tendency to assign the following categories: Data Deficient, Lower Risk-least concern, Vulnerable D2 or a threatened category using Criterion B. The reason for this is that specimen information satisfies distribution parameters of the IUCN system more readily than demographic parameters.     

A Revised Conservation Assessment of Dipterocarps in Sabah

Borneo has experienced a rapid decline in the extent of forest cover, which has reduced the amount of habitat available for many plant and animal species. The precise impact of habitat loss on the conservation status of dipterocarp trees is uncertain. We use three contrasting techniques, the extent of occurrence, area of occupancy and ecological niche models derived using maxent , in conjunction with a current land‐use map of Sabah, to derive estimates of habitat loss and infer a regional IUCN Red List conservation status for 33 Sabah dipterocarp species. Estimates of habitat loss differed significantly according to the methods employed and between species on different habitat types. Proportion of habitat loss determined from the ecological niche models varied from 21 percent for Shorea micans to 99.5 percent for Dipterocarpus lamellatus. Thirty‐two of the 33 dipterocarp species analyzed in this study would have their Sabah populations classified as Threatened (equal to a habitat loss of > 30%) under the A2 IUCN Red List criterion. Dipterocarps that occur in lowland forests have experienced greater habitat loss than upland/lower montane or ultramafic species. In addition, species with the lowest predicted area within their historic distributions had the highest proportion of habitat lost, which provides a rationale for targeting conservation effort on the species with narrow distributions. We recommend the ecological niche modeling approach as a rapid assessment tool for reconstructing species’ historic distributions during conservation assessments of tropical trees.     

A new method to estimate areas of occupancy using herbarium data

The World Conservation Union (IUCN) Red List of Threatened Species is an important instrument to evaluate the conservation status of living organisms. However, Red List assessors have been limited by the lack of reliable methods to calculate the area of occupancy (AOO) of species, which is an important parameter for red list assessments. Here we present a new practical method to estimate AOO based on herbarium specimen data: the Cartographic method by Conglomerates (CMC). This method, which combines elements from the Areographic and Cartographic methods previously used to calculate AOO, was tested with ten cactus species from the Chihuahuan Desert Region. The results derived from this novel procedure produced in average AOO calculations 3.5 and 5.5 smaller than the Areographic and Cartographic methods, respectively. The CMC takes into account the existence of disjunctions in the distribution range of the species, producing comparatively more accurate AOO estimations. Another advantage of the CMC is that it generates results more harmonic with the current Red List criteria. In contrast, the overestimated results of the Areographic and Cartographic methods tend to artificially categorize the species, even extremely narrow endemics, in lower endangerment status.     

Spatial ecology and conservation of the microendemic ovenbird Cipo Cinclodes (Cinclodes espinhacensis) from the Brazilian highlands

Birds in the genus Cinclodes are habitat specialists, with most restricted to the highlands of South America. The recently described Cipo Cinclodes (C. espinhacensis) is isolated in the southern Espinhaço Range of Brazil and is considered Endangered in Brazil and Near Threatened by the IUCN, but as a subspecies of Long‐tailed Cinclodes (C. pabsti). We examined the population and spatial ecology of Cipo Cinclodes at two geographic scales to improve our understanding of their basic biology and conservation status. We monitored 30 birds at Serra do Breu and found relatively large home ranges (mean = 9.3 ha), a density of paired adults of 0.09/ha, a male‐skewed adult sex ratio (males/total adults = 0.57) due to territories occupied by unpaired males, and long‐term site fidelity. Cipo Cinclodes used all habitat types available in our study area, including rocky outcrops, grasslands, and riparian areas, but habitat selection analyses revealed the importance of riparian areas for foraging and rocky outcrops for nesting. At the species distribution scale, we compiled known and novel recorded occurrence points and used them to calculate the extent of occurrence (EOO) and the area of occupancy (AOO). We used a Maxent species distribution model to generate a binary map to estimate upper limits for EOO (EOO around the model predicted area) and AOO (comprised by the model predicted area within the EOO). We obtained 41 locations, resulting in an EOO of 890.7 km² (up to 1748.7 km²) and an AOO of 100 km² (up to 327.5 km²). The global population is estimated to be between 880 and 2882 birds, which is concerning because small populations are at risk of extinction due to demographic stochasticity, genetic drift, and the interaction of these factors. As such, our results support the designation of Cipo Cinclodes as Endangered on the Brazilian red list.     

Optimal allocation of Red List assessments to guide conservation of biodiversity in a rapidly changing world

The IUCN Red List is the most extensive source of conservation status assessments for species worldwide, but important gaps in coverage remain. Here, we demonstrate the use of a spatial prioritization approach to efficiently prioritize species assessments to achieve increased and up‐to‐date coverage efficiently. We focus on freshwater fishes, which constitute a significant portion of vertebrate diversity, although comprehensive assessments are available for only 46% of species. We used marxan to identify ecoregions for future assessments that maximize the coverage of species while accounting for anthropogenic stress. We identified a set of priority regions that would help assess one‐third (ca 4000 species) of all freshwater fishes in need of assessment by 2020. Such assessments could be achieved without increasing current investment levels. Our approach is suitable for any taxon and can help ensure that species threat assessments are sufficiently complete to guide global conservation efforts in a rapidly changing world.     

Conservation study of endemic plants in serpentine landscapes: Antirrhinum rothmaleri (Plantaginaceae), a serpentinophyte with a restricted geographic distribution

Abstract

Assessing the conservation status of endemic species by monitoring population trends is one of the main aims of plant conservation studies. This article reports a detailed study of the distribution of Antirrhinum rothmaleri, a species endemic to the serpentine systems of Trás-os-Montes in NE Portugal (Lusitan-Duriensean biogeographical sector). The species' current distribution status, the size of its populations, and the threats it faces, measured according to International Union for Conservation of Nature (IUCN) 2008 Guidelines, were all assessed. The size estimates provided for the four confirmed populations were based on census data taken at the different sites. All censuses were performed by direct counting of all potentially reproductive individuals. Based on the present data, A. rothmaleri should be assigned a conservation status of “Critically Endangered” (CR). Its conservation status, according to the IUCN criteria, is mainly based on the narrow distribution, and on the area of occupancy (AOO) and extent of occurrence (EOO). The risk of extinction faced by the local populations is high due to their typically very small size. Suitable conservation strategies should be developed in order to preserve the species. The present study allowed us to characterize its distribution and population size, to collect and store ex situ the germplasm in the UIRGEMP/Banco Português de Germoplasma Vegetal, and to investigate its ecology. The conservation status of the species requires continued monitoring of the demography of its populations. Studies on the biology of the species are also needed in order to improve its management. The present results illustrate the need to protect serpentine landscapes, which contain a range of microhabitats inhabited byendemic plants.     

Supporting Red List threat assessments with GeoCAT: geospatial conservation assessment tool

GeoCAT is an open source, browser based tool that performs rapid geospatial analysis to ease the process of Red Listing taxa. Developed to utilise spatially referenced primary occurrence data, the analysis focuses on two aspects of the geographic range of a taxon: the extent of occurrence (EOO) and the area of occupancy (AOO). These metrics form part of the IUCN Red List categories and criteria and have often proved challenging to obtain in an accurate, consistent and repeatable way. Within a familiar Google Maps environment, GeoCAT users can quickly and easily combine data from multiple sources such as GBIF, Flickr and Scratchpads as well as user generated occurrence data. Analysis is done with the click of a button and is visualised instantly, providing an indication of the Red List threat rating, subject to meeting the full requirements of the criteria. Outputs including the results, data and parameters used for analysis are stored in a GeoCAT file that can be easily reloaded or shared with collaborators. GeoCAT is a first step toward automating the data handling process of Red List assessing and provides a valuable hub from which further developments and enhancements can be spawned.     

The desolation of Smaug: The human-driven decline of the Sungazer lizard (Smaug giganteus)

The Sungazer (Smaug giganteus) is a threatened lizard species endemic to the Highveld grasslands of South Africa. The species faces risks from habitat loss and fragmentation, and illegal harvesting for traditional medicine and the pet trade. Despite these threats, the current conservation status of the species was poorly validated. We visited 79 Sungazer populations recorded in 1978 to assess population change since the initial surveys, and surveyed an additional 164 sites to better define the distribution and estimate the current population size. We interrogated all known historical trade data of the species. One-third of Sungazer populations have been extirpated over the past 37 years. The distribution includes two allopatric populations, with the smaller Mpumalanga population experiencing a significantly higher decline. The species has an extent of occurrence (EOO) of 34 500 km², and an area of occupancy (AOO) of 1149 km². The interpreted distribution is 17 978 km², and just under 60% remains untransformed grassland. We estimate a population size of 677 000 mature individuals, down 48% from the estimated historical population, prior to commercial agricultural development. A total of 1194 live Sungazers were exported under permit from South Africa between 1985 and 2014, with a significant increase in numbers exported over the last decade. Without any evidence of captive breeding, we believe that these animals are all wild-caught. Based on the AOO, level of decline, fragmentation within the distribution and suspected level of exploitation, we recommend classification of the species as Vulnerable under IUCN Red List Criteria A2acd and B2ab(ii–v). The establishment of a protected area network, genetic research and further investigations into the pet and traditional medicine trades are urgently needed.     

长白山高山苔原带植物濒危现状及保护级别评估

通过野外调查、文献查阅、专家咨询及市场调查等手段获得长白山高山苔原带植物生存状况、分布数量的基本数据。在查阅文献的基础上,借助专家咨询构建了长白山高山苔原带植物受危等级、优先保护定量评估体系。该体系包含3个子系统,每个子系统下设不同指标共计12个。通过专家咨询法和层次分析法相结合的方法确定各子系统及各指标的权重。共评估植物94种,其中极危种3种,濒危种6种,易危种22种,近危种42种,无危种21种;在保护的缓急程度上,属于特级保护的有5种,一级保护的有6种,二级保护的有34种,三级保护的有30种,暂缓保护的有19种。评估结果与以往的红色名录进行了比较,一些从未列入红色目录的种类在本研究结果中有所体现。相反,有些曾被列入红色名录的物种在本次评估中被列为"无危"。对评估结果与以往红色名录之间产生差异种类及原因进行了讨论。     

Subpopulations,locations and fragmentation: applying IUCN red list criteria to herbarium specimen data

Despite the ecological and economic importance of plants, the majority of plant species and their conservation status are still poorly known. Based on the limited knowledge we have of many plant species, especially those in the tropics, the use of GIS techniques can give us estimates of the degree of population subdivision to be used in conservation assessments of extinction risk. This paper evaluates how best to use the IUCN Red List Categories and Criteria to produce effective and consistent estimates of subpopulation structure based on specimen data available in the herbaria around the world. We assessed population structure through GIS-based analysis of the geographic distribution of collections, using herbarium specimen data for 11 species of Delonix sensu lato. We used four methods: grid adjacency, circular buffer, Rapoport’s mean propinquity and alpha hull, to quantify population structure according to the terms used in the IUCN Red List: numbers of subpopulations and locations, and degree of fragmentation. Based on our findings, we recommend using the circular buffer method, as it is not dependent on collection density and allows points to be added, subtracted and/or moved without altering the buffer placement. The ideal radius of the buffer is debatable; however when dispersal characteristics of the species are unknown then a sliding scale, such as the 1/10th maximum inter-point distance, is the preferred choice, as it is species-specific and not sensitive to collection density. Such quantitative measures of population structure provide a rigorous means of applying IUCN criteria to a wide range of plant species that hitherto were inaccessible to IUCN classification.     

Measuring the fate of plant diversity: towards a foundation for future monitoring and opportunities for urgent action

Vascular plants are often considered to be among the better known large groups of organisms, but gaps in the available baseline data are extensive, and recent estimates of total known (described) seed plant species range from 200000 to 422000. Of these, global assessments of conservation status using International Union for the Conservation of Nature (IUCN) categories and criteria are available for only approximately 10000 species. In response to recommendations from the Conference of the Parties to the Convention on Biological Diversity to develop biodiversity indicators based on changes in the status of threatened species, and trends in the abundance and distribution of selected species, we examine how existing data, in combination with limited new data collection, can be used to maximum effect. We argue that future work should produce Red List Indices based on a representative subset of plant species so that the limited resources currently available are directed towards redressing taxonomic and geographical biases apparent in existing datasets. Sampling the data held in the world's major herbaria, in combination with Geographical Information Systems techniques, can produce preliminary conservation assessments and help to direct selective survey work using existing field networks to verify distributions and gather population data. Such data can also be used to backcast threats and potential distributions through time. We outline an approach that could result in: (i) preliminary assessments of the conservation status of tens of thousands of species not previously assessed, (ii) significant enhancements in the coverage and representation of plant species on the IUCN Red List, and (iii) repeat and/or retrospective assessments for a significant proportion of these. This would result in more robust Sampled Red List Indices that can be defended as more representative of plant diversity as a whole; and eventually, comprehensive assessments at species level for one or more major families of angiosperms. The combined results would allow scientifically defensible generalizations about the current status of plant diversity by 2010 as well as tentative comments on trends. Together with other efforts already underway, this approach would establish a firmer basis for ongoing monitoring of the status of plant diversity beyond 2010 and a basis for comparison with the trend data available for vertebrates.     

Improving the estimation of area of occupancy for IUCN Red List assessments by using a circular buffer approach

The area of occupancy (AOO) is one of the main measures used by IUCN to quantify range size for species. AOO represents the area of suitable habitat currently occupied by the taxon and is usually quantified by counting the number of occupied cells in a uniform grid that covers the entire range of a taxon. However, this methodology adds uncertainty by the location of the origin of the grid frame. In this communication paper, we tested the influence of the origin of the grid frame used to quantify AOO and found for Swiss bryophytes that 14 species (out of 1089) fall into a different Red List category when the origin of the grid frame was shifted. With this and theoretical examples we show that AOO quantified by circles around the occurrences (a circular buffer approach) would reduce uncertainty significantly because they are independent of the origin of a grid frame. A circular buffer approach to quantify AOO contribute thus to more robust and accurate Red Lists and its usage is in accordance with the IUCN criteria.     

Warning times for species extinctions due to climate change

Climate change is likely to become an increasingly major obstacle to slowing the rate of species extinctions. Several new assessment approaches have been proposed for identifying climate‐vulnerable species, based on the assumption that established systems such as the IUCN Red List need revising or replacing because they were not developed to explicitly consider climate change. However, no assessment approach has been tested to determine its ability to provide advanced warning time for conservation action for species that might go extinct due to climate change. To test the performance of the Red List system in this capacity, we used linked niche‐demographic models with habitat dynamics driven by a ‘business‐as‐usual’ climate change scenario. We generated replicate 100‐year trajectories for range‐restricted reptiles and amphibians endemic to the United States. For each replicate, we categorized the simulated species according to IUCN Red List criteria at annual, 5‐year, and 10‐year intervals (the latter representing current practice). For replicates that went extinct, we calculated warning time as the number of years the simulated species was continuously listed in a threatened category prior to extinction. To simulate data limitations, we repeated the analysis using a single criterion at a time (disregarding other listing criteria). Results show that when all criteria can be used, the Red List system would provide several decades of warning time (median = 62 years; >20 years for 99% of replicates), but suggest that conservation actions should begin as soon as a species is listed as Vulnerable, because 50% of replicates went extinct within 20 years of becoming uplisted to Critically Endangered. When only one criterion was used, warning times were substantially shorter, but more frequent assessments increased the warning time by about a decade. Overall, we found that the Red List criteria reliably provide a sensitive and precautionary way to assess extinction risk under climate change.     

The Sampled Red List Index for Plants,phase II: ground-truthing specimen-based conservation assessments

The IUCN Sampled Red List Index (SRLI) is a policy response by biodiversity scientists to the need to estimate trends in extinction risk of the world''s diminishing biological diversity. Assessments of plant species for the SRLI project rely predominantly on herbarium specimen data from natural history collections, in the overwhelming absence of accurate population data or detailed distribution maps for the vast majority of plant species. This creates difficulties in re-assessing these species so as to measure genuine changes in conservation status, which must be observed under the same Red List criteria in order to be distinguished from an increase in the knowledge available for that species, and thus re-calculate the SRLI. However, the same specimen data identify precise localities where threatened species have previously been collected and can be used to model species ranges and to target fieldwork in order to test specimen-based range estimates and collect population data for SRLI plant species. Here, we outline a strategy for prioritizing fieldwork efforts in order to apply a wider range of IUCN Red List criteria to assessments of plant species, or any taxa with detailed locality or natural history specimen data, to produce a more robust estimation of the SRLI.     

Developing conservation strategies for endemic tree species when faced with time and data constraints: <Emphasis Type="Italic">Boswellia</Emphasis> spp. on Socotra (Yemen)

Many endemic tree species have important scientific, ecological and economic value but the scarcity of information about their biological and ecological features makes it difficult to develop conservation strategies for them. A four-step approach is presented to address this problem, based on the analysis of data collected in a limited-duration field study: (1) Data collected are used to analyse the ecological niche, population structure and regeneration status of the species in question. (2) Several IUCN Red List (RL) parameters, useful for assessing the species’ risk of extinction, are measured, including population counts, number of locations, extent and area of occurrence. (3) The IUCN RL parameters are used together with the other information gathered to set preliminary conservation priorities. (4) The analysis of utilization pattern is used to develop conservation actions specific to the environmental and socio-economic context. To test the applicability of this approach Boswellia spp. of Socotra island were analysed. Ground-rooted species (B. ameero, B. elongata and B. socotrana) were the most abundant and widespread and, according to the spatial analysis, were characterised by a geo-altitudinal zonation. However, the Weibull functions fitted on their stem diameters, and the absence or presence of only a small number of saplings highlighted a poor regeneration status. In the absence of conservation actions, these species will probably be subject to a progressive decline because of uncontrolled grazing. Of the four cliff-rooted species, which grow in sites that are less accessible to livestock, two (B. popoviana and B. dioscorides) were of lower conservation priority and may become the most numerically abundant. Conversely, the other two (B. nana and B. bullata), which may be threatened by stochastic events because of their reduced populations and small number of locations, were considered of very high priority. Different conservation actions were then identified for each species. In particular, for Boswellia species producing gum, the conservation-through-use action was discussed as a potential option.