Ecography

Transforming the results of species distribution modelling from probabilities of or suitabilities for species occurrence to presences/absences needs a specific threshold. Even though there are many approaches to determining thresholds, there is no comparative study. In this paper, twelve approaches were compared using two species in Europe and artificial neural networks, and the modelling results were assessed using four indices: sensitivity, specificity, overall prediction success and Cohen's kappa statistic. The results show that prevalence approach, average predicted probability/suitability approach, and three sensitivity‐specificity‐combined approaches, including sensitivity‐specificity sum maximization approach, sensitivity‐specificity equality approach and the approach based on the shortest distance to the top‐left corner (0,1) in ROC plot, are the good ones. The commonly used kappa maximization approach is not as good as the afore‐mentioned ones, and the fixed threshold approach is the worst one. We also recommend using datasets with prevalence of 50% to build models if possible since most optimization criteria might be satisfied or nearly satisfied at the same time, and therefore it's easier to find optimal thresholds in this situation.

Accelerating climate and land‐use change are rapidly transforming Earth's biodiversity. While there is substantial evidence on the exposure and vulnerability of biodiversity to global change at the species level, the global exposure of intraspecific genetic diversity (GD) is still unknown. Here, we assess the exposure of mitochondrial GD to mid‐21st century climate and land‐use change in terrestrial mammal assemblages at grid‐cell and bioclimatic region scales under alternative narratives of future societal development. We used global predictions of mammal GD distribution based on thousands of georeferenced mitochondrial genes for hundreds of mammal species, the latest generation of global climate models from the ongoing sixth phase of the Coupled Model Intercomparison Project (CMIP6), and global future projections of land‐use prepared for CMIP6. We found that more than 50% of the genetically poorest geographic areas (grid‐cells), primarily distributed in tundra, boreal forests/taiga and temperate bioclimatic regions, will be exposed to mean annual temperature rise that exceeds 2°C compared to the baseline period under all considered future scenarios. We also show that at least 30% of the most genetically rich areas in tropical, subtropical and montane regions will be exposed to an increase of mean annual temperature > 2°C under less optimal scenarios. Genetic diversity in these rich regions is also predicted to be exposed to severe reductions of primary vegetation area and increasing human activities (an average loss of 5–10% of their total area under the less sustainable land‐use scenarios). Our findings reveal a substantial exposure of mammal GD to the combined effects of global climate and land‐use change. Meanwhile the post‐2020 conservation goals are overlooking genetic diversity, our study identifies both genetically poor and highly diverse areas severely exposed to global change, paving the road to better estimate the geography of biodiversity vulnerability to global change.

Variation in the spatial structure of communities in terms of species composition (beta diversity) is affected by different ecological processes, such as environmental filtering and dispersal limitation. Large rivers are known as barriers for species dispersal (riverine hypothesis) in tropical regions. However, when organisms are not dispersal limited by geographic barriers, other factors, such as climatic conditions and geographic distance per se, may affect species distribution. In order to investigate the relative contribution of major rivers, climate and geographic distance on Passeriformes beta diversity, we divided Amazonia into 549 grid cells (1° of latitude and longitude) and obtained data of species occurrence, climate and geographic position for each cell. Beta diversity was measured using taxonomic, phylogenetic and functional metrics of composition. The influence of climatic variables, geographic distance and rivers on these metrics was tested using regression analyses. Passerine beta diversity is characterized mainly by the change in species taxonomic identity and in phylogenetic lineages across climatic gradients and over geographic distance. However, species with similar traits are found throughout the entire Amazonia. The size of rivers was proportional to their effect on species composition. However, climate and geographic distance are relatively more important than rivers for Amazonian taxonomic and phylogenetic species composition.

The large ground‐dwelling bush cricket Decucus verrucivorus is widespread in continental Europe, but declining at the northern edge of its range This paper defines the species' habitat requirements in northern Europe by describing the distribution of each of the seven nymphal instars and adults in relation to vegetation structure within a chalk grassland in southern England First instars were strongly associated with short, sparse turf, reflecting the oviposition behaviour of females Subsequent early instars were also found in short, open turf, but at the fifth moult a distinct shift in distribution to dense grass tussocks occurred Late instars and adults were strongly associated with these structures, probably to avoid vertebrate predators Mean temperatures within tussocks were lower than in short turf, but these highly mobile stages actively thermoregulate by basking on the sides of tussocks In contrast, areas of short turf may be crucial for the development of the smaller and less mobile early instars and eggs It is concluded that a fine mosaic of closely‐grazed turf, dense tussocks and intermediate structures must be created and/or maintained at the species northern‐most sites, if its present distribution is not to contract

Migratory connectivity is the degree to which populations are linked in space and time across the annual cycle. Low connectivity indicates mixing of populations while high connectivity indicates population separation in space or time. High migratory connectivity makes individual populations susceptible to local environmental conditions; therefore, evaluating migratory connectivity continuously across a species range is important for understanding differential population trends and revealing places and times contributing to these differences. The common nighthawk Chordeiles minor is a widespread, declining, long‐distance migratory bird. Variable population trends across the nighthawk breeding range suggest that knowledge of migratory connectivity is needed to direct conservation. We used GPS tags to track 52 individuals from 12 breeding populations. We estimated migratory connectivity as 0.29 (Mantel coefficient: 0 = no connectivity, 1 = full connectivity) between the breeding and wintering grounds. We then estimated migratory connectivity at every latitude (spatial connectivity) or day (temporal connectivity) of migration and smoothed those migratory connectivity estimates to produce continuous migratory connectivity ‘profiles'. Spatial and temporal connectivity were highest during migration through North America (around 0.3–0.6), with values generally around 0 in Central and South America due to mixing of populations along a common migratory route and similar migration timing across populations. We found local peaks in spatial and temporal connectivity during migration associated with crossing the Gulf of Mexico. We used simulations to estimate the probability that our method missed peaks (spatial: 0.12, temporal: 0.18) or detected false peaks (spatial: 0.11, temporal: 0.37) due to data gaps and showed that our approach remains useful even for sparse and/or sporadic location data. Our study presents a generalizable approach to evaluating migratory connectivity across the full annual cycle that can be used to focus migratory bird conservation towards places and times of the annual cycle where populations are more likely to be limited.

Identifying where animals come from during population recovery can help to understand the impacts of disturbance events and regimes on species distributions and genetic diversity. Alternative recovery processes for animal populations affected by fire include external recolonization, nucleated recovery from refuges, or in situ survival and population growth. We used simulations to develop hypotheses about ecological and genetic patterns corresponding to these alternative models. We tested these hypotheses in a study of the recovery of two small mammals, the Australian bush rat and the agile antechinus, after a large (> 50 000 ha), severe wildfire.

The abundance of both species was severely reduced by fire and recovered to near or above pre‐fire levels within two generations, yet we rejected a hypothesis of recovery by external recolonization. While the agile antechinus showed genetic evidence for far greater dispersal capacity than the bush rat, neither species showed gradients in abundance or genetic diversity with distance from unburnt forest during population recovery.

Population recovery was driven by local‐scale processes. However, the mechanisms differed between species, resulting from the spatial impacts of fire on habitat suitability. Agile antechinus populations recovered through population growth from in situ survivors. The bush rat followed a model of nucleated recovery, involving local recolonization from micro‐refuges in topographic drainage lines.

Nucleated recovery by the bush rat was associated with changes in dispersal, and fine‐scale patterns of genetic admixture. We identified increased dispersal by females during recovery, contrasting with male‐biased dispersal in unburnt forest. Such flexibility in dispersal can potentially increase recovery rates compared to expectations based on dispersal behavior within undisturbed populations.

Our study shows how the initial distribution of survivors, determined by fire effects on resource distribution, determines the subsequent scaling of population recovery patterns, and the sensitivity of population distribution and genetic diversity to changing disturbance regimes.

Understanding the ability of species to shift their distribution ranges in response to climate change is crucial for conservation biologists and resources managers. Although freshwater ecosystems include some of the most imperilled fauna worldwide, such range shifts have been poorly documented in streams and rivers and have never been compared to the current velocity of climate change. Based on national monitoring data, we examined the distributional changes of 32 stream fish species in France and quantified potential time lags in species responses, providing a unique opportunity to analyze range shifts over recent decades of warming in freshwater environments. A multi‐facetted approach, based on several range measures along spatial gradients, allowed us to quantify range shifts of numerous species across the whole hydrographic network between an initial period (1980–1992) and a contemporary one (2003–2009), and to contrast them to the rates of isotherm shift in elevation and stream distance. Our results highlight systematic species shifts towards higher elevation and upstream, with mean shifts in range centre of 13.7 m decade⁻¹ and 0.6 km decade⁻¹, respectively. Fish species displayed dispersal‐driven expansions along the altitudinal gradient at their upper range limit (61.5 m decade⁻¹), while substantial range contractions at the lower limit (6.3 km decade⁻¹) were documented for most species along the upstream–downstream gradient. Despite being consistent with the geographic variation in climate change velocities, these patterns reveal that the majority of stream fish have not shifted at a pace sufficient to track changing climate, in particular at their range centre where range shifts lag far behind expectation. Our study provides evidence that stream fish are currently responding to recent climate warming at a greater rate than many terrestrial organisms, although not as much as needed to cope with future climate modifications.

Diversity of most above‐ground organisms increases with decreasing latitude, but the biogeographical and macroecological diversity patterns of below‐ground animals have been poorly studied. We investigated the latitudinal diversity gradient in a primarily below‐ground living soil taxon, oribatid mites. Furthermore, oribatid mite species richness from islands and mainlainds was tested for correlation with the size of the respective area (island or mainland) to evaluate if their species–area relationships are similar to those of above‐ground taxa. The results suggest that for oribatid mites 1) diversity increases from the boreal to the warm temperate region but not further to the tropics, and 2) species–area relationships for islands and mainlands are similar to those of above‐ground taxa, but this is mainly caused by very small islands, such as Cocos islands, and very large islands, such as Madagascar. When these islands are excluded the species–area relationship strongly differs from those of typical islands. The results support the view that below‐ground animal taxa are generalists that inhabit wide niches. Most small islands have relatively rich oribatid mite faunas, supporting the observation that a large number of species can coexist in a small area (high α‐diversity).