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Analysis of long-term trends in abundance of animal populations provides insights into population dynamics. Population growth rates are the emergent interplay of inter alia fertility, survival, and dispersal. However, the density feedbacks operating on some vital rates (“component feedback”) can be decoupled from density feedbacks on population growth rates estimated using abundance time series (“ensemble feedback”). Many of the mechanisms responsible for this decoupling are poorly understood, thereby questioning the validity of using logistic-growth models versus vital rates to infer long-term population trends. To examine which conditions lead to decoupling, we simulated age-structured populations of long-lived vertebrates experiencing component density feedbacks on survival. We then quantified how imposed stochasticity in survival rates, density-independent mortality (catastrophes, harvest-like removal of individuals) and variation in carrying capacity modified the ensemble feedback in abundance time series simulated from age-structured populations. The statistical detection of ensemble density feedback from census data was largely unaffected by density-independent processes. Long-term population decline caused from density-independent mortality was the main mechanism decoupling the strength of component versus ensemble density feedbacks. Our study supports the use of simple logistic-growth models to capture long-term population trends, mediated by changes in population abundance, when survival rates are stochastic, carrying capacity fluctuates, and populations experience moderate catastrophic mortality over time.

Studies examining the underlying causes of the distributions of species and their future trajectories under climate change have benefitted from the accumulation of measurements of thermal tolerance across the tree of life. However, gaps in the global coverage of heat-tolerance data for ectotherms persist on four critical fronts. First, most large-scale analyses treat heat tolerance as a fixed species trait despite that population-level variation can equal or exceed cross-species variation. Second, terrestrial non-arthropod invertebrates and aquatic ectotherms other than bony fish have been poorly sampled, particularly in boreal and tropical regions, the Indian Ocean and the mesopelagic-deep ocean. Third, the study of climate impacts on the heat tolerance of terrestrial ectotherms has often neglected the interaction of environmental temperatures with water availability. And fourth, the mechanisms driving the dependence of heat tolerance on oxygen supply-demand remain largely unknown. We contend that filling those data and knowledge gaps requires novel strategies for the ecophysiological sampling of the range of understudied populations and species that occupy the length of climatic gradients globally. Such developments are essential for comprehensively predicting species responses to climate change across aquatic and terrestrial biomes.

In the summer of 2012, two fires affected Mediterranean ecosystems in the eastern Iberian Peninsula. The size of these fires was at the extreme of the historical variability (megafires). Animals are traditionally assumed to recolonize from source populations outside of the burned area (exogenous regeneration) while plants recover from endogenous regeneration (resprouting and seeding). However, there is increasing evidence of in situ fire survival in animals. To evaluate the effect of large-scale fires on biodiversity and the mechanism of recovery, in 2013, we set up 12 plots per fire, covering burned vegetation at different distances from the fire perimeter and unburned vegetation. In each plot, we followed the postfire recovery of arthropods, reptiles (including some of their parasites), and plants for 2 to 5 years. Here we present the resulting database (POSTDIV) of taxon abundance. POSTDIV totals 19,906 records for 457 arthropod taxa (113,681 individuals), 12 reptile taxa (503 individuals), 4 reptile parasites (234 individuals), and 518 plant taxa (cover-abundance). We provide examples in the R language to query the database., In the summer of 2012, two fires affected Mediterranean ecosystems in the eastern Iberian Peninsula. The size of these fires was at the extreme of the historical variability (megafires). Animals are traditionally assumed to recolonize from source populations outside of the burned area (exogenous regeneration) while plants recover from endogenous regeneration (resprouting and seeding). However, there is increasing evidence of in situ fire survival in animals. To evaluate the effect of large-scale fires on biodiversity and the mechanism of recovery, in 2013, we set up 12 plots per fire, covering burned vegetation at different distances from the fire perimeter and unburned vegetation. In each plot, we followed the postfire recovery of arthropods, reptiles (including some of their parasites), and plants for 2 to 5 years. Here we present the resulting database (POSTDIV) of taxon abundance. POSTDIV totals 19,906 records for 457 arthropod taxa (113,681 individuals), 12 reptile taxa (503 individuals), 4 reptile parasites (234 individuals), and 518 plant taxa (cover-abundance). We provide examples in the R language to query the database., In the summer of 2012, two fires affected Mediterranean ecosystems in the eastern Iberian Peninsula. The size of these fires was at the extreme of the historical variability (megafires). Animals are traditionally assumed to recolonize from source populations outside of the burned area (exogenous regeneration) while plants recover from endogenous regeneration (resprouting and seeding). However, there is increasing evidence of in situ fire survival in animals. To evaluate the effect of large-scale fires on biodiversity and the mechanism of recovery, in 2013, we set up 12 plots per fire, covering burned vegetation at different distances from the fire perimeter and unburned vegetation. In each plot, we followed the postfire recovery of arthropods, reptiles (including some of their parasites), and plants for 2 to 5 years. Here we present the resulting database (POSTDIV) of taxon abundance. POSTDIV totals 19,906 records for 457 arthropod taxa (113,681 individuals), 12 reptile taxa (503 individuals), 4 reptile parasites (234 individuals), and 518 plant taxa (cover-abundance). We provide examples in the R language to query the database.

Principal component analysis (PCA) is a powerful tool for the analysis of population structure, a genetic property that is essential to understand the evolutionary processes driving biological diversification and (pre)historical colonizations, migrations and extinctions. In the current era of high- throughput sequencing technologies, population structure can be quantified from scores of genetic markers across hundreds to thousands of genomes. However, these big genomic datasets pose substantial computing and analytical challenges.We present the r package smartsnp for fast and user- friendly computation of PCA on single-nucleotide polymorphism (SNP) data. Inspired by the current field- standard software EIGENSOFT, smartsnp includes appropriate SNP scaling for genetic drift and allows projection of ancient samples onto a modern genetic space while also providing permutation- based multivariate tests for population differences in genetic diversity (both location and dispersion).Our extensive benchmarks show that smartsnp's PCA is 2– 4 times faster than EIGENSOFT's SMARTPCA algorithm across a wide range of sample and SNP sizes. All four smartsnp functions (smart_pca, smart_permanova, smart_permdisp and smart_mva) process datasets with up to 100 samples and 1 million simulated SNPs in less than 30 s and accurately recreate previously published SMARTPCA of ancient- human and wolf genotypes.The package smartsnp provides fast and robust multivariate ordination and hypothesis testing for big genomic data that is also suitable for ancient and low- coverage modern DNA. The simple implementation should appeal to biological conservation, evolutionary, ecological and (palaeo)genomic researchers, and be useful for phenotype, ancestry and lineage studies.

Quantifying intraspecific variation in heat tolerance is critical to understand how species respond to climate change. In a previous study, we recorded variability in critical thermal maxima (CT) by 3 °C among populations of small Iberian lizard species, which could substantially influence predictions of climate-driven activity restriction. Here, we undertake experiments to examine whether we could reproduce similar levels of heat-tolerance variability in response to water deficit. We hypothesized that deprivation of drinking water should increase variability in CT between populations more than deprivation of food under the theoretical expectation that the variation of the more limiting resource must trigger stronger variation in physiological performance. We measured CT after manipulating availability of live prey and drinking water in two populations of an arid and a mesic lizard species from the Iberian Peninsula. We quantified a mean CT across all studied lizards of 44.2 °C ± 0.2 SE for the arid species and 41.7 °C ± 0.3 SE for the mesic species. Using multimodel inference, we found that water deprivation (combined with food supply) caused population differences in CT by 3 to 4 °C which were two to three times wider than population differences due to food deprivation (combined with water supply) or to food and water provision. To highlight the need for more thermo-hydroregulatory research, we examined bias in research effort towards thermal versus hydric environmental effects on heat tolerance through a systematic literature review. We show that environmental temperature has been used five times more frequently than precipitation in ecological studies of heat tolerance of terrestrial species. Studies linking thermal tolerance of ectotherms to the interplay of air temperature and water availability are needed in the face of projected increases in aridity and drought in the 21st century, because the balance of body temperature and water resources are functionally

The widespread observation that heat tolerance is less variable than cold tolerance (‘cold-tolerance asymmetry’) leads to the prediction that species exposed to temperatures near their thermal maxima should have reduced evolutionary potential for adapting to climate warming. However, the prediction is largely supported by species-level global studies based on single estimates of both physiological metrics per taxon. We ask whether cold-tolerance asymmetry holds for Iberian lizards after accounting for intraspecific variation in critical thermal maxima (CT) and minima (CT). To do so, we quantified CT and CT for 58 populations of 15 Iberian lizard species (299 individuals). Then, we randomly selected one population from each study species (population sample = 15 CT and CT values), tested for differences between the variance of both thermal metrics across species, and repeated the test for thousands of population samples as if we had undertaken the same study thousands of times, each time sampling one different population per species (as implemented in global studies). The ratio of variances in CT to CT across species varied up to 16-fold depending on the populations chosen. Variance ratios show how much CT departs from the cross-species mean compared to CT, with a unitary ratio indicating equal variance of both thermal limits. Sampling one population per species was six times more likely to result in the observation of greater CT variance (‘heat-tolerance asymmetry’) than cold-tolerance asymmetry. The probability of obtaining the data (given the null hypothesis of equal variance being true) was twice as likely for cases of cold-tolerance asymmetry than for the opposite scenario. Range-wide, population-level studies that quantify heat and cold tolerance of individual species are urgently needed to ascertain the global prevalence of cold-tolerance asymmetry. While broad latitudinal clines of cold tolerance have been strongly supported, heat tolerance might respond to sm

Genetic data are a crucial and exponentially growing resource across all biological sciences, yet curated databases are scarce. The widespread occurrence of sequence and (meta)data errors in public repositories calls for comprehensive improvements of curation protocols leading to robust research and downstream analyses. We collated and curated all available GenBank cytochrome-b sequences for amphibians, a benchmark marker in this globally declining vertebrate clade. The Amphibia’s Curated Database of Cytochrome-b (ACDC) consists of 36,514 sequences representing 2,309 species from 398 genera (median = 2 with 50% interquartile ranges of 1–7 species/genus). We updated the taxonomic identity of >4,800 sequences (ca. 13%) and found 2,359 (6%) conflicting sequences with 84% of the errors originating from taxonomic misidentifications. The database (accessible at https:// doi.org/10.6084/m9.figshare.9944759) also includes an R script to replicate our study for other loci and taxonomic groups. We provide recommendations to improve genetic-data quality in public repositories and flag species for which there is a need for taxonomic refinement in the face of increased rate of amphibian extinctions in the Anthropocene.

The widespread observation that heat tolerance is less variable than cold tolerance (‘cold-tolerance asymmetry’) leads to the prediction that species exposed to temperatures near their thermal maxima should have reduced evolutionary potential for adapting to climate warming. However, the prediction is largely supported by species-level global studies based on single estimates of both physiological metrics per taxon. We ask if cold-tolerance asymmetry holds for Iberian lizards after accounting for intraspecific variation in critical thermal maxima (CTmax) and minima (CTmin). To do so, we quantified CTmax and CTmin for 58 populations of 15 Iberian lizard species (299 individuals). Then, we randomly selected one population from each study species (population sample = 15 CTmax and CTmin values), tested for variance homoscedasticity across species, and repeated the test for thousands of population samples as if we had undertaken the same study thousands of times, each time sampling one different population per species. The ratio of variances in CTmax to CTmin across species varied up to 16-fold depending on the populations chosen. Variance ratios show how much CTmax departs from the cross-species mean compared to CTmin, with a unitary ratio indicating equal variance of both thermal limits. Sampling one population per species was six times more likely to result in the observation of greater CTmax variance (‘heat-tolerance asymmetry’) than cold-tolerance asymmetry. The null hypothesis of equal variance was twice as likely for cases of cold-tolerance asymmetry than for the opposite scenario. Range-wide, population-level studies that quantify heat and cold tolerance of individual species are urgently needed to ascertain the global prevalence of cold-tolerance asymmetry. While broad latitudinal clines of cold tolerance have been strongly supported, heat tolerance might respond to smaller-scale climatic and habitat factors hence go unnoticed in global studies. Studies investig

Research addressing the effects of global warming on the distribution and persistence of species generally assumes that population variation in thermal tolerance is spatially constant or overridden by interspecific variation. Typically, this rationale is implicit in sourcing one critical thermal maximum (CTmax) population estimate per species to model spatiotemporal cross‐taxa variation in heat tolerance. Theory suggests that such an approach could result in biased or imprecise estimates and forecasts of impact from climate warming, but limited empirical evidence in support of those expectations exists. We experimentally quantify the magnitude of intraspecific variation in CTmax among lizard populations, and the extent to which incorporating such variability can alter estimates of climate impact through a biophysical model. To do so, we measured CTmax from 59 populations of 15 Iberian lizard species (304 individuals). The overall median CTmax across all individuals from all species was 42.8°C and ranged from 40.5 to 48.3°C, with species medians decreasing through xeric, climate‐generalist and mesic taxa. We found strong statistical support for intraspecific differentiation in CTmax by up to a median of 3°C among populations. We show that annual restricted activity (operative temperature > CTmax) over the Iberian distribution of our study species differs by a median of >80 hr per 25‐km2 grid cell based on different population‐level CTmax estimates. This discrepancy leads to predictions of spatial variation in annual restricted activity to change by more than 20 days for six of the study species. Considering that during restriction periods, reptiles should be unable to feed and reproduce, current projections of climate‐change impacts on the fitness of ectotherm fauna could be under‐ or over‐estimated depending on which population is chosen to represent the physiological spectra of the species in question. Mapping heat tolerance over the full geographical ranges of sin

The scientific evidence for anthropogenic climate change is empirically settled, but communicating it to nonscientific audiences remains challenging. To be explicit about the state of knowledge on climate science, the Intergovernmental Panel on Climate Change (IPCC) has adopted a vocabulary that ranks climate findings through certainty-calibrated qualifiers of confidence and likelihood. In this article, we quantified the occurrence of knowns and unknowns about "The Physical Science Basis" of the IPCC's Fifth Assessment Report by counting the frequency of calibrated qualifiers. We found that the tone of the IPCC's probabilistic language is remarkably conservative (mean confidence is medium, and mean likelihood is 66%-100% or 0-33%), and emanates from the IPCC recommendations themselves, complexity of climate research, and exposure to politically motivated debates. Leveraging communication of uncertainty with overwhelming scientific consensus about anthropogenic climate change should be one element of a wider reform, whereby the creation of an IPCC outreach working group could enhance the transmission of climate science to the panel's audiences.

The study of palaeo-chronologies using fossil data provides evidence for past ecological and evolutionary processes, and is therefore useful for predicting patterns and impacts of future environmental change. However, the robustness of inferences made from fossil ages relies heavily on both the quantity and quality of available data. We compiled Quaternary non-human vertebrate fossil ages from Sahul published up to 2013. This, the FosSahul database, includes 9,302 fossil records from 363 deposits, for a total of 478 species within 215 genera, of which 27 are from extinct and extant megafaunal species (2,559 records). We also provide a rating of reliability of individual absolute age based on the dating protocols and association between the dated materials and the fossil remains. Our proposed rating system identified 2,422 records with high-quality ages (i.e., a reduction of 74%). There are many applications of the database, including disentangling the confounding influences of hypothetical extinction drivers, better spatial distribution estimates of species relative to palaeo-climates, and potentially identifying new areas for fossil discovery.

The use of long-term population data to separate the demographic role of climate from density-modified demographic processes has become a major topic of ecological investigation over the last two decades. Although the ecological and evolutionary mechanisms that determine the strength of density feedbacks are now well understood, the degree to which climate gradients shape those processes across taxa and broad spatial scales remains unclear. Intuitively, harsh or highly variable environmental conditions should weaken compensatory density feedbacks because populations are hypothetically unable to achieve or maintain densities at which social and trophic interactions (e.g., competition, parasitism, predation, disease) might systematically reduce population growth. Here we investigate variation in the strength of compensatory density feedback, from long-term time series of abundance over 146 species of birds and mammals, in response to spatial gradients of broad-scale temperature precipitation variables covering 97 localities in 28 countries. We use informationtheoretic metrics to rank phylogenetic generalized least-squares regression models that control for sample size (time-series length) and phylogenetic non-independence. Climatic factors explained < 1% of the remaining variation in densityfeedback strength across species, with the highest non-control, model-averaged effect sizes related to extreme precipitation variables. We could not link our results directly to other published studies, because ecologists use contrasting responses, predictors and statistical approaches to correlate density feedback and climate - at the expense of comparability in a macroecological context. Censuses of multiple populations within a given species, and a priori knowledge of the spatial scales at which density feedbacks interact with climate, seem to be necessary to determine cross-taxa variation in this phenomenon. Despite the availability of robust modelling tools, the appropriate da