Understanding how species’ thermal limits have evolved across the tree of life is central to predicting species’ responses to climate change. Here, using experimentally-derived estimates of thermal tolerance limits for over 2000 terrestrial and aquatic species, we show that most of the variation in thermal tolerance can be attributed to a combination of adaptation to current climatic extremes, and the existence of evolutionary ‘attractors’ that reflect either boundaries or optima in thermal tolerance limits. Our results also reveal deep-time climate legacies in ectotherms, whereby orders that originated in cold paleoclimates have presently lower cold tolerance limits than those with warm thermal ancestry. Conversely, heat tolerance appears unrelated to climate ancestry. Cold tolerance has evolved more quickly than heat tolerance in endotherms and ectotherms. If the past tempo of evolution for upper thermal limits continues, adaptive responses in thermal limits will have limited potential to rescue the large majority of species given the unprecedented rate of contemporary climate change.
BackgroundInaccurate estimates of phylogenetic signal may mislead interpretations of many ecological and evolutionary processes, and hence understanding where potential sources of uncertainty may lay has become a priority for comparative studies. Importantly, the sensitivity of phylogenetic signal indices and their associated statistical tests to incompletely resolved phylogenies and suboptimal branch-length information has been only partially investigated.MethodsHere, we use simulations of trait evolution along phylogenetic trees to assess whether incompletely resolved phylogenies (polytomic chronograms) and phylogenies with suboptimal branch-length information (pseudo-chronograms) could produce directional biases in significance tests (p-values) associated with Blomberg et al.’s K and Pagel’s lambda (λ) statistics, two of the most widely used indices to measure and test phylogenetic signal. Specifically, we conducted pairwise comparisons between the p-values resulted from the use of “true” chronograms and their degraded counterparts (i.e. polytomic chronograms and pseudo-chronograms), and computed the frequency with which the null hypothesis of no phylogenetic signal was accepted using “true” chronograms but rejected when using their degraded counterparts (type I bias) and vice versa (type II bias).ResultsWe found that the use of polytomic chronograms in combination with Blomberg et al.’s K resulted in both, clearly inflated estimates of phylogenetic signal and moderate levels of type I and II biases. More importantly, pseudo-chronograms led to high rates of type I biases. In contrast, Pagel’s λ was strongly robust to either incompletely resolved phylogenies and suboptimal branch-length information.ConclusionsOur results suggest that pseudo-chronograms can lead to strong overestimation of phylogenetic signal when using Blomberg et al.’s K (i.e. high rates of type I biases), while polytomies may be a minor concern given other sources of uncertainty. In contrast, Pagel’s λ seems strongly robust to either incompletely resolved phylogenies and suboptimal branch-length information. Hence, Pagel’s λ may be a more appropriate alternative over Blomberg et al.’s K to measure and test phylogenetic signal in most ecologically relevant traits when phylogenetic information is incomplete.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-017-0898-y) contains supplementary material, which is available to authorized users.
According to the competitive exclusion principle, species with low competitive abilities should be excluded by more efficient competitors, and yet they generally remain as rare species. Here, we describe the positive and negative spatial association networks of 326 disparate assemblages, showing a general organization pattern that simultaneously supports the primacy of competition and the persistence of rare species. Abundant species monopolize negative associations in about 90% of the assemblages. Contrarily, rare species are mostly involved in positive associations, forming small network modules. Simulations suggest that positive interactions among rare species and microhabitat preferences are the most likely mechanisms underpinning this pattern and rare species persistence. The
A large body of research shows that biodiversity loss can reduce ecosystem functioning, thus providing support for the conservation of biological diversity  . Much of the evidence for this relationship is drawn from biodiversity-ecosystem functioning experiments (hereafter: biodiversity experiments), in which biodiversity loss is simulated by randomly assembling communities of varying species diversity, and ecosystem functions are measured  . This random assembly has led some ecologists to question the relevance of biodiversity experiments to real-world ecosystems, where community assembly may often be non-random and influenced by external drivers, such as climate or land-use intensification  . Despite these repeated criticisms, there has been no comprehensive, quantitative assessment of how experimental and real-world plant communities really differ, and whether these differences invalidate the experimental results. Here, we compare data from two of the largest and longest-running grassland biodiversity experiments globally (Jena Experiment, Germany; BioDIV, USA) to related real-world grassland plant communities in terms of their taxonomic, functional, and phylogenetic diversity and functional-trait composition. We found that plant communities of biodiversity experiments have greater variance in these compositional features than their real-world counterparts, covering almost all of the variation of the real-world communities (82-96%) while also containing community types that are not currently observed in the real world. We then re-analysed a subset of experimental data that included only ecologically-realistic communities, i.e. those comparable to real-world communities. For ten out of twelve biodiversity-ecosystem functioning relationships, biodiversity effects did not differ significantly between the full dataset of biodiversity experiments and the ecologically-realistic subset of experimental communities. This demonstrates that the results of biodiversity experiments are largely insensitive to the inclusion/exclusion of unrealistic communities. By bridging the gap between experimental and real-world studies, these results demonstrate the validity of inferences from biodiversity experiments, a key step in translating their results into specific recommendations for real-
Dominants are key species shaping ecosystem functioning. Plant dominance is typically 25 assessed on aboveground appearance but aboveground-belowground dominance of 26 individual species may not scale proportionally. This is especially important in biomes 27where most biomass is allocated belowground, and includes areas accounting for >60% 28 of biomes' land cover worldwide.
Phylogenetic imputation has recently emerged as a potentially powerful tool for predicting missing data in functional traits datasets. As such, understanding the limitations of phylogenetic modelling in predicting trait values is critical if we are to use them in subsequent analyses. Previous studies have focused on the relationship between phylogenetic signal and clade‐level prediction accuracy, yet variability in prediction accuracy among individual tips of phylogenies remains largely unexplored. Here, we used simulations of trait evolution along the branches of phylogenetic trees to show how the accuracy of phylogenetic imputations is influenced by the combined effects of 1) the amount of phylogenetic signal in the traits and 2) the branch length of the tips to be imputed. Specifically, we conducted cross‐validation trials to estimate the variability in prediction accuracy among individual tips on the phylogenies (hereafter ‘tip‐level accuracy’). We found that under a Brownian motion model of evolution (BM, Pagel't λ = 1), tip‐level accuracy rapidly decreased with increasing tip branch‐lengths, and only tips of approximately 10% or less of the total height of the trees showed consistently accurate predictions (i.e. cross‐validation R‐squared >0.75). When phylogenetic signal was weak, the effect of tip branch‐length was reduced, becoming negligible for traits simulated with λ < 0.7, where accuracy was in any case low. Our study shows that variability in prediction accuracy among individual tips of the phylogeny should be considered when evaluating the reliability of phylogenetically imputed trait values. To address this challenge, we describe a Monte Carlo‐based method that allows one to estimate the expected tip‐level accuracy of phylogenetic predictions for continuous traits. Our approach identifies gaps in functional trait datasets for which phylogenetic imputation performs poorly, and will help ecologists to design more efficient trait collection campaigns by focusing resources on lineages whose trait values are more uncertain.
Aim To reconstruct the historical assembly of the eudicot flora of Mediterranean sierras by examining compositional (CBD), phylogenetic (PBD) and functional (FBD) beta diversity between elevational belts among disjunct mountain ranges (sierras), and relating these measures of turnover to environmental and geographical distances. Location Baetic ranges, Andalusia, southern Spain. Methods We compiled eudicot species and subspecies (‘entities’) checklists for three elevational belts within each of eight sierras of Andalusia (‘sites’) and tested for non‐random patterns of PBD and FBD of all entities and of endemic entities separately among sites between and within sierras. Multiple regression on distance matrices was used to determine the respective contribution of climate, lithology and geographical distance to CBD, PBD and FBD. Finally, we decomposed PBD into the turnover and nestedness components of beta diversity, and quantified the phylogenetic diversity (PD) within sites. Results The observed PBD and FBD among elevational belts within sierras for all entities were generally higher than expected based on their respective null distributions, whereas CBD among elevational belts within sierras was similar or even lower than between sierras. In contrast, the observed PBD and FBD for endemics were non‐significant in most of the comparisons. Temperature‐related variables best explained patterns of CBD, PBD and FBD for all entities, whereas lithology and geographical distance were the main drivers of endemic CBD. The observed PBD among elevational belts within sierras was mainly attributable to differences in PD rather than ‘true’ turnover. Main conclusions There is strong structuring of plant lineages along elevational gradients in the Baetic range, probably due to habitat filtering acting on life forms and character syndromes that show strong phylogenetic signal. The differentiation of the endemic flora that contributed to the emergence of this western Mediterranean biodiversity hotspot was probably driven by geographical isolation and/or by repeated specialization to contrasting lithologies.
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