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.     

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.     

ConR: An R package to assist large‐scale multispecies preliminary conservation assessments using distribution data

The Red List Categories and the accompanying five criteria developed by the International Union for Conservation of Nature (IUCN) provide an authoritative and comprehensive methodology to assess the conservation status of organisms. Red List criterion B, which principally uses distribution data, is the most widely used to assess conservation status, particularly of plant species. No software package has previously been available to perform large‐scale multispecies calculations of the three main criterion B parameters [extent of occurrence (EOO), area of occupancy (AOO) and an estimate of the number of locations] and provide preliminary conservation assessments using an automated batch process. We developed ConR, a dedicated R package, as a rapid and efficient tool to conduct large numbers of preliminary assessments, thereby facilitating complete Red List assessment. ConR (1) calculates key geographic range parameters (AOO and EOO) and estimates the number of locations sensu IUCN needed for an assessment under criterion B; (2) uses this information in a batch process to generate preliminary assessments of multiple species; (3) summarize the parameters and preliminary assessments in a spreadsheet; and (4) provides a visualization of the results by generating maps suitable for the submission of full assessments to the IUCN Red List. ConR can be used for any living organism for which reliable georeferenced distribution data are available. As distributional data for taxa become increasingly available via large open access datasets, ConR provides a novel, timely tool to guide and accelerate the work of the conservation and taxonomic communities by enabling practitioners to conduct preliminary assessments simultaneously for hundreds or even thousands of species in an efficient and time‐saving way.     

The use of spatial ecological modelling as a tool for improving the assessment of geographic range size of threatened species

We analysed endemic threatened tree and reptile species of Socotra Island (Yemen), characterised by different ecological requirements and spatial distribution, in order to evaluate the usefulness of spatial ecological modelling in the estimation of species extent of occurrence (EOO) and area of occupancy (AOO). Point occurrences for the entire species range were used to model their spatial distribution by Random Forest (RF) and Generalised Linear Model (GLM). For each species the suitability area (SA) was obtained by applying the 0% omission error criterion on the probability map, and compared or integrated with EOO and AOO area obtained by topological methods such as the minimum convex polygon (MCP), α-hull and 2 km × 2 km grid.RF showed a lower prediction error than GLM. Higher accuracy was achieved for species with higher number of occurrences and narrower ecological niche. SA was always greater than AOO measured with the 2 km × 2 km grid method. SA was greater than EOO, measured by both MCP and α-hull methods, for species with localised distribution, while it was smaller for widely distributed species. EOO-α-hull area was equal or smaller than that calculated by MCP depending on the spatial distribution of species. AOO measured considering the SA within the EOO-MCP was greater than that measured using the standard 2 km × 2 km grid. Conversely, AOO calculated considering the suitable area within the EOO-α-hull showed variable results, being smaller or greater than the 2 km × 2 km grid AOO depending on the ecological niche and spatial distribution of species. According to our results, SEM does not provide an effective alternative to topological methods for the estimate of EOO and AOO. However, it may be considered a useful tool to estimate AOO within the boundaries of EOO measured by the α-hull method, because it reduces some potential sources of inconsistency and bias.     

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.     

A standardized set of metrics to assess and monitor tree invasions

Scientists, managers, and policy-makers need functional and effective metrics to improve our understanding and management of biological invasions. Such metrics would help to assess progress towards management goals, increase compatibility across administrative borders, and facilitate comparisons between invasions. Here we outline key characteristics of tree invasions (status, abundance, spatial extent, and impact), discuss how each of these characteristics changes with time, and examine potential metrics to describe and monitor them. We recommend quantifying tree invasions using six metrics: (a) current status in the region; (b) potential status; (c) the number of foci requiring management; (d) area of occupancy (AOO) (i.e. compressed canopy area or net infestation); (e) extent of occurrence (EOO) (i.e. range size or gross infestation); and (f) observations of current and potential impact. We discuss how each metric can be parameterised (e.g. we include a practical method for classifying the current stage of invasion for trees following Blackburn’s unified framework for biological invasions); their potential management value (e.g. EOO provides an indication of the area over which management is needed); and how they can be used in concert (e.g. combining AOO and EOO can provide insights into invasion dynamics; and we use potential status and threat together to develop a simple risk analysis tool). Based on these metrics, we propose a standardized template for reporting tree invasions that we hope will facilitate cross-species and inter-regional comparisons. While we feel this represents a valuable step towards standardized reporting, there is an urgent need to develop more consistent metrics for impact and threat, and for many specific purposes additional metrics are still needed (e.g. detectability is required to assess the feasibility of eradication).     

关于IUCN和WWF联合植物保护研究计划工作的成就和今后的任务

植物是人类和动物生活所必需,由于缺乏长远规划的目标,无计划的滥用已导致许多植物灭绝或陷入濒临灭绝的境地。为此,IUCN—WWF联合建立了“植物保护研究计划”,并把其列入他们各自工作的重点。主要工作内容有下列各项:1)传播信息宣传群众;2)建立必要的植物保护的工作条件:3)植物遗传资源的保护:4)野生经济植物的保护:5)加强植物园开展植物保护的工作条件:6)促进植物丰富的国家开展植物保护工作。     

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.     

Ecological assessment of vegetation from a nature reserve using regional reference data and indicator scores

A method is presented for ecological assessment of botanical sample data from a nature reserve network. The approach uses regional floristic survey data for a specific biotope as a context for spatial and temporal comparison. Assessments are based upon floristic similarity to reference vegetation types and indicator scores that summarise multivariate plant species data in relation to important environmental gradients. The approach was implemented as a software tool using floristic survey data for soligenous mires in a UK region. Plant community monitoring data were assessed against reference communities from this regional baseline to illustrate the potential advantages of the method. These include; (a) allowing links to be made between multivariate plant species data and measurements of environmental drivers, (b) providing realistic assessments of spatial and temporal differences because comparisons are against typical values of indicator scores for the region, (c) providing the scope for setting realistic criteria for vegetation monitoring.     

对IUCN红色名录等级中"Vulnerable"一词翻译的商榷

根据IUCN Red List Categories and Criteria(V3.1),作者认为把"Vulnerable"翻译成"渐危"和"易危"不十分准确,容易混淆和误导,建议把其翻译成"低危"。     

Population dynamics can be more important than physiological limits for determining range shifts under climate change

Evidence is accumulating that species' responses to climate changes are best predicted by modelling the interaction of physiological limits, biotic processes and the effects of dispersal‐limitation. Using commercially harvested blacklip (Haliotis rubra) and greenlip abalone (Haliotis laevigata) as case studies, we determine the relative importance of accounting for interactions among physiology, metapopulation dynamics and exploitation in predictions of range (geographical occupancy) and abundance (spatially explicit density) under various climate change scenarios. Traditional correlative ecological niche models (ENM) predict that climate change will benefit the commercial exploitation of abalone by promoting increased abundances without any reduction in range size. However, models that account simultaneously for demographic processes and physiological responses to climate‐related factors result in future (and present) estimates of area of occupancy (AOO) and abundance that differ from those generated by ENMs alone. Range expansion and population growth are unlikely for blacklip abalone because of important interactions between climate‐dependent mortality and metapopulation processes; in contrast, greenlip abalone should increase in abundance despite a contraction in AOO. The strongly non‐linear relationship between abalone population size and AOO has important ramifications for the use of ENM predictions that rely on metrics describing change in habitat area as proxies for extinction risk. These results show that predicting species' responses to climate change often require physiological information to understand climatic range determinants, and a metapopulation model that can make full use of this data to more realistically account for processes such as local extirpation, demographic rescue, source‐sink dynamics and dispersal‐limitation.     

Nestedness and niche‐based species loss in moorland plant communities

Communities in isolated habitat patches surrounded by inhospitable matrices often form a nested subset pattern. However, the underlying causal mechanisms and conservation implications of nestedness in regional communities remain controversial. The nested ranks of species in a nested species‐by‐site matrix may reflect a gradient of species vulnerability to extinction or of colonization ability. However, nestedness analysis has rarely been used to explore determinants of species rank; consequently, little is known of underpinning mechanisms. In this study, we examined nestedness in moorland plant communities widely interspersed within the subalpine zone of northern Japan. Moorland sites differed in area (1000–160 000 m²) and were naturally isolated from one another to various extents within an inhospitable forest matrix. We also determined whether site characteristics (physical and morphometric measures) and species characteristics (niche position and breadth, based on species’ traits) are related to nestedness. Moorland plant communities in the study area were significantly nested. The pH and moorland kernel density (proxy for spatial clustering of moorlands around the focal site) were the most important predictors of moorland site nested rank in a nestedness matrix. Niche breadths of species (measured as variation in leaf mass area and height) predicted species’ nested ranks. Selective environmental tolerances imposed by environmental harshness and selective extinction caused by declines in site carrying capacities probably account for the nested subset pattern in moorland plant communities. The nested rank of species in the nestedness matrix can therefore be translated into the potential order of species loss explainable by species niche breadths (based on variation in functional traits). Complementary understanding of the determinants of site ranking and species ranking in the nestedness matrix provides powerful insight into ecological processes underlying nestedness and into the ways by which communities are assembled or disassembled by such processes.     

Historical drivers of extinction risk: using past evidence to direct future monitoring

Global commitments to halt biodiversity decline mean that it is essential to monitor species'' extinction risk. However, the work required to assess extinction risk is intensive. We demonstrate an alternative approach to monitoring extinction risk, based on the response of species to external conditions. Using retrospective International Union for Conservation of Nature Red List assessments, we classify transitions in the extinction risk of 497 mammalian carnivores and ungulates between 1975 and 2013. Species that moved to lower Red List categories, or remained Least Concern, were classified as ‘lower risk''; species that stayed in a threatened category, or moved to a higher category of risk, were classified as ‘higher risk''. Twenty-four predictor variables were used to predict transitions, including intrinsic traits (species biology) and external conditions (human pressure, distribution state and conservation interventions). The model correctly classified up to 90% of all transitions and revealed complex interactions between variables, such as protected areas (PAs) versus human impact. The most important predictors were: past extinction risk, PA extent, geographical range size, body size, taxonomic family and human impact. Our results suggest that monitoring a targeted set of metrics would efficiently identify species facing a higher risk, and could guide the allocation of resources between monitoring species'' extinction risk and monitoring external conditions.     

The Muni-Pomadze Ramsar site

The Coastal Wetlands Management Project (CWMP), funded by the Global Environment Facility and implemented by the Ghana Wildlife Department, seeks to preserve the ecological integrity of coastal lagoons that serve as important sites for migratory waterbirds. This report describes the geomorphology, hydrology, soils, water chemistry, and vegetation of the Muni-Pomadze Ramsar site. Muni lagoon is a saline, shallow water lagoon separated from the sea by a sand bar which may be breached occasionally. The bulk of the rainfall in the catchment evaporates or flows as surface runoff into three streams that empty into Muni lagoon. Open water in the lagoon varies seasonally from 100 ha in the dry season to over 1000 ha in the wet season. The natural flora of the site can be divided into four main types; flood plain (including mangrove and wetland vegetation), dune vegetation, riverine vegetation, and terrestrial vegetation on elevated ground. The latter consists of a combination of grasslands, thickets, and Eucalyptus plantations. Fifty-three percent of the site is classified as natural vegetation. An additional 32.5% is agricultural land and 12.6% is residential area for the 11 communities within the site. The main source of employment are farming or fishing. The area surrounding Muni lagoon is used extensively for bushmeat hunting and as the tribal hunting grounds of the Efutu people. Apart from the global importance of the Muni-Pomadze site for biodiversity, management of the site is further justified by its considerable potential for development as an income-generating and educational nature reserve with an eco-cultural theme, managed by the local communities in partnership with the governmental and non-governmental conservation agencies.     

Syntaxonomy of vegetation of Svjatoj Nos Peninsula,Lake Baikal 1. Non forest communities

Natural and semi-natural plant communities of Svjatoj Nos Peninsula on the East coast of Lake Baikal, Eastern Siberia, Russia, are classified and described using the methods of Braun-Blanquet phytosociology. A total of 48 associations and communities were recognized, comprising alpine tundra, subalpine forb vegetation, aquatic macrophyte vegetation, tall-herb and poor fens, mires, bogs, meadows, sand-dune and steppe vegetation. Twenty six syntaxa of ranks ranging from subassociation to class are described or validated for the first time. All communities are documented by phytosociological relevés.     

Plant communities,diversity and endemism of the Kula Volcano,Manisa, Turkey

Volcanoes often harbour specialized plant communities and shelter endemic plant species. Kula Volcano is one of 14 volcanoes in Turkey. Although this volcano is clearly a landmark of the Aegean region, only few botanical studies analysed the vegetation pattern at the Kula Volcano. None performed a phytosociological classification to delimit different plant communities. We applied a stratified random sampling design according to altitude and aspect and sampled 112 vegetation plots. We classified plant community types using a modified TWINSPAN analysis followed by the determination of diagnostic species based on φ coefficient fidelity values. Floristic relationships between plant community types were interpreted by ordination and ANOSIM analyses. Further, we used partial correlations of the ordination axes and environmental parameters in order to identify relationships between vegetation zonation and environment. We identified five major plant community types based on 85 diagnostic species. These plant community types were significantly correlated with altitude and aspect. Further, 13 endemic plant species were found from which one was endangered and one was classified as vulnerable according to International Union for Conservation of Nature (IUCN).     

30% land conservation and climate action reduces tropical extinction risk by more than 50%

Limiting climate change to less than 2°C is the focus of international policy under the climate convention (UNFCCC), and is essential to preventing extinctions, a focus of the Convention on Biological Diversity (CBD). The post-2020 biodiversity framework drafted by the CBD proposes conserving 30% of both land and oceans by 2030. However, the combined impact on extinction risk of species from limiting climate change and increasing the extent of protected and conserved areas has not been assessed. Here we create conservation spatial plans to minimize extinction risk in the tropics using data on 289 219 species and modeling two future greenhouse gas concentration pathways (RCP2.6 and 8.5) while varying the extent of terrestrial protected land and conserved areas from <17% to 50%. We find that limiting climate change to 2°C and conserving 30% of terrestrial area could more than halve aggregate extinction risk compared with uncontrolled climate change and no increase in conserved area.     

The ecological drivers and consequences of wildlife trade

Wildlife trade is a key driver of extinction risk, affecting at least 24% of terrestrial vertebrates. The persistent removal of species can have profound impacts on species extinction risk and selection within populations. We draw together the first review of characteristics known to drive species use – identifying species with larger body sizes, greater abundance, increased rarity or certain morphological traits valued by consumers as being particularly prevalent in trade. We then review the ecological implications of this trade-driven selection, revealing direct effects of trade on natural selection and populations for traded species, which includes selection against desirable traits. Additionally, there exists a positive feedback loop between rarity and trade and depleted populations tend to have easy human access points, which can result in species being harvested to extinction and has the potential to alter source–sink dynamics. Wider cascading ecosystem repercussions from trade-induced declines include altered seed dispersal networks, trophic cascades, long-term compositional changes in plant communities, altered forest carbon stocks, and the introduction of harmful invasive species. Because it occurs across multiple scales with diverse drivers, wildlife trade requires multi-faceted conservation actions to maintain biodiversity and ecological function, including regulatory and enforcement approaches, bottom-up and community-based interventions, captive breeding or wildlife farming, and conservation translocations and trophic rewilding. We highlight three emergent research themes at the intersection of trade and community ecology: (1) functional impacts of trade; (2) altered provisioning of ecosystem services; and (3) prevalence of trade-dispersed diseases. Outside of the primary objective that exploitation is sustainable for traded species, we must urgently incorporate consideration of the broader consequences for other species and ecosystem processes when quantifying sustainability.