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.     

Genetic variation across species' geographical ranges: the central-marginal hypothesis and beyond

There is growing interest in quantifying genetic population structure across the geographical ranges of species to understand why species might exhibit stable range limits and to assess the conservation value of peripheral populations. However, many assertions regarding peripheral populations rest on the long-standing but poorly tested supposition that peripheral populations exhibit low genetic diversity and greater genetic differentiation as a consequence of smaller effective population size and greater geographical isolation relative to geographically central populations. We reviewed 134 studies representing 115 species that tested for declines in within-population genetic diversity and/or increases in among-population differentiation towards range margins using nuclear molecular genetic markers. On average, 64.2% of studies detected the expected decline in diversity, 70.2% of those that tested for it showed increased differentiation and there was a positive association between these trends. In most cases, however, the difference in genetic diversity between central and peripheral population was not large. Although these results were consistent across plants and animals, strong taxonomic and biogeographical biases in the available studies call for a cautious generalization of these results. Despite the large number of studies testing these simple predictions, very few attempted to test possible mechanisms causing reduced peripheral diversity or increased differentiation. Almost no study incorporated a phylogeographical framework to evaluate historical influences on contemporary genetic patterns. Finally, there has been little effort to test whether these geographical trends in putatively neutral variation at marker loci are reflected by quantitative genetic trait variation, which is likely to influence the adaptive potential of populations across the geographical range.     

Evolutionary patterns in the geographic range size of Atlantic Forest plants

Species’ geographic range size is arguably the single most important predictor of vulnerability to extinction and a key metric in ecology. Despite this, patterns of specific variation in range size and their underlying reasons are still poorly understood. For example, hypotheses on how evolutionary history affects range size have scarcely been tested. To address these questions, we focused on Brazil's Atlantic Forest flora, one of the most species-rich in the world, relatively well-known and highly threatened. We investigated whether and how lineages’ diversification rate, number of species and age are associated with species’ geographic range size. We estimated the extent of occurrence and area of occupancy of each of 13 283 plant species native to the Atlantic Forest region based on over 500 000 unique records. We used phylogenetic least squares and logistic regressions to analyze how the predictors affect the geographic range size. On average, the higher the diversification rate and number of species in the lineage, the smaller the species range size and the higher the proportion of species with vulnerably small range size. Lineage age showed no clear effect on average range size. The results support our expectations that dynamics of diversification and taxonomic richness considerably affect the species range size. Finally, this work reveals poorly known patterns of range size variation and some of the mechanisms driving variation in range size and vulnerability to extinction.     

Understanding bias in geographic range size estimates

Aim Estimates of geographic range size derived from natural history museum specimens are probably biased for many species. We aim to determine how bias in these estimates relates to range size. Location We conducted computer simulations based on herbarium specimen records from localities ranging from the southern United States to northern Argentina. Methods We used theory on the sampling distribution of the mean and variance to develop working hypotheses about how range size, defined as area of occupancy (AOO), was related to the inter‐specific distribution of: (1) mean collection effort per area across the range of a species (MC); (2) variance in collection effort per area across the range of a species (VC); and (3) proportional bias in AOO estimates (PBias: the difference between the expected value of the estimate of AOO and true AOO, divided by true AOO). We tested predictions from these hypotheses using computer simulations based on a dataset of more than 29,000 herbarium specimen records documenting occurrences of 377 plant species in the tribe Bignonieae (Bignoniaceae). Results The working hypotheses predicted that the mean of the inter‐specific distribution of MC, VC and PBias were independent of AOO, but that the respective variance and skewness decreased with increasing AOO. Computer simulations supported all but one prediction: the variance of the inter‐specific distribution of VC did not decrease with increasing AOO. Main conclusions Our results suggest that, despite an invariant mean, the dispersion and symmetry of the inter‐specific distribution of PBias decreases as AOO increases. As AOO increased, range size was less severely underestimated for a large proportion of simulated species. However, as AOO increased, range size estimates having extremely low bias were less common.     

绵刺属的分布区及其区系地理成分

绘制了绵刺属新的分布区图。阐明了该属的生态地理分布的基本特征和规律。确定了其区系地理成分为“阿拉善-东戈壁”成分。     

Coevolution between hosts and parasites with partially overlapping geographic ranges

Many host species interact with a specific parasite within only a fraction of their geographical range. Where host and parasite overlap geographically, selection may be reciprocal constituting a coevolutionary hot spot. Host evolution, however, may be driven primarily by selection imposed by alternative biotic or abiotic factors that occur outside such hot spots. To evaluate the importance of coevolutionary hot spots for host and parasite evolution, we analyse a spatially explicit genetic model for a host that overlaps with a parasite in only part of its geographical range. Our results show that there is a critical amount of overlap beyond which reciprocal selection leads to a coevolutionary response in the host. This critical amount of overlap depends upon the explicit spatial configuration of hot spots. When the amount of overlap exceeds this first critical level, host-parasite coevolution commonly generates stable allele frequency clines rather than oscillations. It is within this region that one of the primary predictions of the geographic mosaic theory is realized, and local maladaptation is prevalent in both species. Past a further threshold of overlap between the species oscillations do evolve, but allele frequencies in both species are spatially synchronous and local maladaptation is absent in both species. A consequence of such transitions between coevolutionary dynamics is that parasite adaptation is inversely proportional to the fraction of its host's range that it occupies. Hence, as the geographical range of a parasite increases, it becomes increasingly maladapted to the host. This suggests a novel mechanism through which the geographical range of parasites may be limited.     

Illuminating geographical patterns in species' range shifts

Species' range shifts in response to ongoing climate change have been widely documented, but although complex spatial patterns in species' responses are expected to be common, comprehensive comparisons of species' ranges over time have undergone little investigation. Here, we outline a modeling framework based on historical and current species distribution records for disentangling different drivers (i.e. climatic vs. nonclimatic) and assessing distinct facets (i.e. colonization, extirpation, persistence, and lags) of species' range shifts. We used extensive monitoring data for stream fish assemblages throughout France to assess range shifts for 32 fish species between an initial period (1980–1992) and a contemporary one (2003–2009). Our results provide strong evidence that the responses of individual species varied considerably and exhibited complex mosaics of spatial rearrangements. By dissociating range shifts in climatically suitable and unsuitable habitats, we demonstrated that patterns in climate‐driven colonization and extirpation were less marked than those attributed to nonclimatic drivers, although this situation could rapidly shift in the near future. We also found evidence that range shifts could be related to some species' traits and that the traits involved varied depending on the facet of range shift considered. The persistence of populations in climatically unsuitable areas was greater for short‐lived species, whereas the extent of the lag behind climate change was greater for long‐lived, restricted‐range, and low‐elevation species. We further demonstrated that nonclimatic extirpations were primarily related to the size of the species' range, whereas climate‐driven extirpations were better explained by thermal tolerance. Thus, the proposed framework demonstrated its potential for markedly improving our understanding of the key processes involved in range shifting and also offers a template for informing management decisions. Conservation strategies would greatly benefit from identifying both the geographical patterns and the species' traits associated with complex modifications of species' distributions in response to global changes.     

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.     

Effects of biotic interactions on modeled species' distribution can be masked by environmental gradients

A fundamental goal of ecology is to understand the determinants of species' distributions (i.e., the set of locations where a species is present). Competition among species (i.e., interactions among species that harms each of the species involved) is common in nature and it would be tremendously useful to quantify its effects on species' distributions. An approach to studying the large‐scale effects of competition or other biotic interactions is to fit species' distributions models (SDMs) and assess the effect of competitors on the distribution and abundance of the species of interest. It is often difficult to validate the accuracy of this approach with available data. Here, we simulate virtual species that experience competition. In these simulated datasets, we can unambiguously identify the effects that competition has on a species' distribution. We then fit SDMs to the simulated datasets and test whether we can use the outputs of the SDMs to infer the true effect of competition in each simulated dataset. In our simulations, the abiotic environment influenced the effects of competition. Thus, our SDMs often inferred that the abiotic environment was a strong predictor of species abundance, even when the species' distribution was strongly affected by competition. The severity of this problem depended on whether the competitor excluded the focal species from highly suitable sites or marginally suitable sites. Our results highlight how correlations between biotic interactions and the abiotic environment make it difficult to infer the effects of competition using SDMs.     

Evidence that climate sets the lower elevation range limit in a high‐elevation endemic salamander

A frequent assumption in ecology is that biotic interactions are more important than abiotic factors in determining lower elevational range limits (i.e., the “warm edge” of a species distribution). However, for species with narrow environmental tolerances, theory suggests the presence of a strong environmental gradient can lead to persistence, even in the presence of competition. The relative importance of biotic and abiotic factors is rarely considered together, although understanding when one exerts a dominant influence on controlling range limits may be crucial to predicting extinction risk under future climate conditions. We sampled multiple transects spanning the elevational range limit of Plethodon shenandoah and site and climate covariates were recorded. A two‐species conditional occupancy model, accommodating heterogeneity in detection probability, was used to relate variation in occupancy with environmental and habitat conditions. Regional climate data were combined with datalogger observations to estimate the cloud base heights and to project future climate change impacts on cloud elevations across the survey area. By simultaneously accounting for species’ interactions and habitat variables, we find that elevation, not competition, is strongly correlated with the lower elevation range boundary, which had been presumed to be restricted mainly as a result of competitive interactions with a congener. Because the lower elevational range limit is sensitive to climate variables, projected climate change across its high‐elevation habitats will directly affect the species’ distribution. Testing assumptions of factors that set species range limits should use models which accommodate detection biases.     

The biogeography of plant reproduction: potential determinants of species' range sizes

Aim A major biogeographical hypothesis, the ‘niche‐breadth’ hypothesis, explains species range sizes based on the extent of a species’ niche (e.g. diversity of habitats occupied; range of environmental conditions tolerated). An alternative hypothesis explains range sizes using metapopulation theory (e.g. colonization dynamics; dispersal ability). Both niche breadth and colonization ability may be related to plant species’ reproductive characteristics. We evaluate both hypotheses by examining the relationship of plant range size to mating system and genomic structure (ploidy status). Location Western North America. Methods Using a data set of 60 taxa in the genus Clarkia (Onagraceae), we use three analytical techniques to examine the effect of reproductive characteristics on range size. We conduct cross‐species analyses of present‐day taxa to examine both mating system and polyploidy in relation to range size. We also conduct a phylogenetically independent contrasts analysis (using caic software) on the relationship of mating system to range size in diploid species. Third, we compare closely related taxon pairs that differ in mating system as an alternative method to control for phylogeny. Results Polyploid species have significantly larger ranges compared with diploid species. When considering only diploid taxa, no significant relationship is found for mating system in both cross‐species and phylogenetically independent contrasts analyses. The diploid pairwise analysis, comparing only the range sizes of direct sister taxa with alternative mating systems, does show a relationship, with outcrossing species having larger ranges than self‐fertilizing species. Main conclusions We argue that genetic diversity, colonization ability, or a combination of both factors may influence plant species’ range sizes. The significant pairwise analysis suggests that both the independent contrast and the cross‐species analysis may be confounded by polytomies of species at the terminal nodes of the phylogeny, indicating the importance of comparing the results of multiple analytical techniques. We propose that the range sizes of self‐fertilizing species have a bimodal distribution, obscuring the effect of mating system on range size, and that a broader survey of plant taxa will resolve the two modes from that of the outcrossing species. Lastly, polyploid species appear to show significantly larger range sizes than diploid species, irrespective of mating system.     

Increased seed dispersal potential towards geographic range limits in a Pacific coast dune plant

Dispersal may be favoured at geographic range edges by unstable population and metapopulation dynamics. However, dispersal may also evolve in response to geographic variation in other life-history traits, especially the mating system. Here, increased dispersal at range margins was tested for with a range-wide analysis of seed dispersal and mating system traits in Abronia umbellata, a plant endemic to Pacific coastal dunes of North America. Seeds disperse within winged anthocarps. Anthocarps from 34 populations varied widely in wing size (mass-corrected wing index). Wing index correlated negatively with threshold wind velocity for dispersal in wind tunnel tests, suggesting that wings facilitate tumbling over open sandy substrate. As predicted, wing index increased and threshold velocity decreased towards both range limits. Flower size, herkogamy and self-incompatibility declined towards range limits, indicating a shift to self-fertilization, and flower size and wing index correlated negatively. However, the increase in wing index towards range limits remained after statistically controlling flower size. These results are consistent with selection favouring dispersal at range margins. The evolutionary lability of dispersal across the range may affect the interaction between selection and gene flow in the establishment and maintenance of geographic range limits.