cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.14288/1.0397561
title: Data from: Herbarium specimens reveal increasing herbivory over the past century

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Predicting how ecological interactions will respond to global change is a major challenge. Plants and their associated insect herbivores compose much of macroscopic diversity, yet how their interactions have been altered by recent environmental change remains underexplored. To address this gap, we quantified herbivory on herbarium specimens of four plant species with records extending back 112 years. Our study focused on the northeastern US, where temperatures have increased rapidly over the last few decades. This region also represents a range of urban development, a form of global change that has shown variable effects on herbivores in the past studies. Herbarium specimens collected in the early 2000s were 23% more likely to be damaged by herbivores than those collected in the early 1900s. Herbivory was greater following warmer winters and at low latitudes, suggesting that climate warming may drive increasing insect damage over time. In contrast, human population densities were negatively associated with herbivore damage. To explore whether changes in insect occurrence or abundance might explain shifts in herbivory, we used insect observational records to build climate occupancy models for lepidopteran herbivores (butterflies and moths) of our focal plant species. These models show that higher winter temperatures were associated with higher probability of insect herbivore presence, while urbanization was associated with reduced probability of herbivore presence, supporting a link between insect herbivore occurrence and herbivory mediated through environment. Synthesis. Using a temporal record of plant herbivory that spans over a century, we show that both temperature and urbanization influence insect damage to plants, but in very different ways. Our results indicate that damage to plants by insect herbivores will likely continue to increase through time in the northeastern US as global temperatures rise, but that urbanization may disrupt local effects of winter warming on herbivory by excluding certain herbivores. These changes may scale to shape ecosystem processes that are driven by herbivory, including plant productivity.
DOI: 10.14288/1.0397569
title: Data from: Rethinking phylogenetic comparative methods

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;As a result of the process of descent with modification, closely related species tend to be similar to one another in a myriad different ways. In statistical terms, this means that traits measured on one species will not be independent of traits measured on others. Since their introduction in the 1980s, phylogenetic comparative methods (PCMs) have been framed as a solution to this problem. In this paper, we argue that this way of thinking about PCMs is deeply misleading. Not only has this sowed widespread confusion in the literature about what PCMs are doing but has led us to develop methods that are susceptible to the very thing we sought to build defenses against --- unreplicated evolutionary events. Through three Case Studies, we demonstrate that the susceptibility to singular events is indeed a recurring problem in comparative biology that links several seemingly unrelated controversies. In each Case Study we propose a potential solution to the problem. While the details of our proposed solutions differ, they share a common theme: unifying hypothesis testing with data-driven approaches (which we term ``phylogenetic natural history'') to disentangle the impact of singular evolutionary events from that of the factors we are investigating. More broadly, we argue that our field has, at times, been sloppy when weighing evidence in support of causal hypotheses. We suggest that one way to refine our inferences is to re-imagine phylogenies as probabilistic graphical models; adopting this way of thinking will help clarify precisely what we are testing and what evidence supports our claims.
DOI: 10.14288/1.0397579
title: Data from: Form–function relationships in a marine foundation species depend on scale: a shoot to global perspective from a distributed ecological experiment

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Form-function relationships in plants underlie their ecosystem roles in supporting higher trophic levels through primary production, detrital pathways, and habitat provision. For widespread, phenotypically-variable plants, productivity may differ not only across abiotic conditions, but also from distinct morphological or demographic traits. A single foundation species, eelgrass (Zostera marina), typically dominates north temperate seagrass meadows, which we studied across 14 sites spanning 32-61° N latitude and two ocean basins. Body size varied by nearly two orders of magnitude through this range, and was largest at mid-latitudes and in the Pacific Ocean. At the global scale, neither latitude, site-level environmental conditions, nor body size helped predict productivity (relative growth rate 1-2% d-1 at most sites), suggesting a remarkable capacity of Z. marina to achieve similar productivity in summer. Furthermore, among a suite of stressors applied within sites, only ambient leaf damage reduced productivity; grazer reduction and nutrient addition had no effect on eelgrass size or growth. Scale-dependence was evident in different allometric relationships within and across sites for productivity and for modules (leaf count) relative to size. Z. marina provides a range of ecosystem functions related to both body size (habitat provision, water flow) and growth rates (food, carbon dynamics). Our observed decoupling of body size and maximum production suggests that geographic variation in these ecosystem functions may be independent, with a future need to resolve how local adaptation or plasticity of body size might actually enable more consistent peak productivity across disparate environmental conditions.
DOI: 10.14288/1.0397585
title: Data from: Sociality influences cultural complexity

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Archaeological and ethnohistorical evidence suggests a link between a population's size and structure, and the diversity or sophistication of its toolkits or technologies. Addressing these patterns, several evolutionary models predict that both the size and social interconnectedness of populations can contribute to the complexity of its cultural repertoire. Some models also predict that a sudden loss of sociality or of population will result in subsequent losses of useful skills/technologies. Here, we test these predictions with two experiments that permit learners to access either one or five models (teachers). Experiment 1 demonstrates that naive participants who could observe five models, integrate this information and generate increasingly effective skills (using an image editing tool) over 10 laboratory generations, whereas those with access to only one model show no improvement. Experiment 2, which began with a generation of trained experts, shows how learners with access to only one model lose skills (in knot-tying) more rapidly than those with access to five models. In the final generation of both experiments, all participants with access to five models demonstrate superior skills to those with access to only one model. These results support theoretical predictions linking sociality to cumulative cultural evolution.
DOI: 10.14288/1.0397594
title: Data from: The genetics of adaptation to discrete heterogeneous environments: frequent mutation or large-effect alleles can allow range expansion

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Range expansions are complex evolutionary and ecological processes. From an evolutionary standpoint, a populations' adaptive capacity can determine the success or failure of expansion. Using individual-based simulations, we model range expansion over a two-dimensional, approximately continuous landscape. We investigate the ability of populations to adapt across patchy environmental gradients and examine how the effect sizes of mutations influence the ability to adapt to novel environments during range expansion. We find that genetic architecture and landscape patchiness both have the ability to change the outcome of adaptation and expansion over the landscape. Adaptation to new environments succeeds via many mutations of small effect or few of large effect, but not via the intermediate between these cases. Higher genetic variance contributes to increased ability to adapt, but an alternative route of successful adaptation can proceed from low genetic variance scenarios with alleles of sufficiently large effect. Steeper environmental gradients can prevent adaptation and range expansion on both linear and patchy landscapes. When the landscape is partitioned into local patches with sharp changes in phenotypic optimum, the local magnitude of change between subsequent patches in the environment determines the success of adaptation to new patches during expansion.
DOI: 10.14288/1.0397600
title: Data from: Adenosine receptors mediate the hypoxic ventilatory response but not the hypoxic metabolic response in the naked mole rat during acute hypoxia

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Naked mole rats are the most hypoxia-tolerant mammals identified; however, the mechanisms underlying this tolerance are poorly understood. Using whole-animal plethysmography and open-flow respirometry, we examined the hypoxic metabolic response (HMR), hypoxic ventilatory response (HVR) and hypoxic thermal response in awake, freely behaving naked mole rats exposed to 7% O2 for 1 h. Metabolic rate and ventilation each reversibly decreased 70% in hypoxia (from 39.6 ± 2.9 to 12.1 ± 0.3 ml O2 min−1 kg−1, and 1412 ± 244 to 417 ± 62 ml min−1 kg−1, respectively; p &lt; 0.05), whereas body temperature was unchanged and animals remained awake and active. Subcutaneous injection of the general adenosine receptor antagonist aminophylline (AMP; 100 mg kg−1, in saline), but not control saline injections, prevented the HVR but had no effect on the HMR. As a result, AMP-treated naked mole rats exhibited extreme hyperventilation in hypoxia. These animals were also less tolerant to hypoxia, and in some cases hypoxia was lethal following AMP injection. We conclude that in naked mole rats (i) hypoxia tolerance is partially dependent on profound hypoxic metabolic and ventilatory responses, which are equal in magnitude but occur independently of thermal changes in hypoxia, and (ii) adenosine receptors mediate the HVR but not the HMR.
DOI: 10.14288/1.0397603
title: Data from: Testing a “genes-to-ecosystems” approach to understanding aquatic-terrestrial linkages

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;A ‘genes-to-ecosystems’ approach has been proposed as a novel avenue for integrating the consequences of intraspecific genetic variation with the underlying genetic architecture of a species in order to shed light on the relationships among hierarchies of ecological organization (genes [RIGHTWARDS ARROW] individuals [RIGHTWARDS ARROW] communities [RIGHTWARDS ARROW] ecosystems). However, attempts to identify genes with major effect on the structure of communities and/or ecosystem processes have been limited and a comprehensive test of this approach has yet to emerge. Here, we present an interdisciplinary field study that integrated a common garden containing different genotypes of a dominant, riparian tree, Populus trichocarpa, and aquatic mesocosms to determine how intraspecific variation in leaf litter alters both terrestrial and aquatic communities and ecosystem functioning. Moreover, we incorporate data from extensive trait screening and genome-wide association studies estimating the heritability and genes associated with litter characteristics. We found that tree genotypes varied considerably in the quality and production of leaf litter, which contributed to variation in phytoplankton abundances, as well as nutrient dynamics and light availability in aquatic mesocosms. These ‘after-life’ effects of litter from different genotypes were directly comparable to the responses of terrestrial communities associated with the living foliage. We found that multiple litter traits corresponding with aquatic community and ecosystem responses differed in their heritability. Moreover, the underlying genetic architecture of these traits was complex, and many genes contributed only a small portion to phenotypic variation. Our results provide further evidence that genetic variation is a key component of aquatic-terrestrial linkages, but challenges the ability to predict community or ecosystem responses based on the actions of one or a few genes.
DOI: 10.14288/1.0397620
title: Data from: Isotopic variation ccross the Audubon’s-myrtle warbler hybrid zone

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Differences in seasonal migratory behaviours are thought to be an important component of reproductive isolation in many organisms. Stable isotopes have been used with success in estimating the location and qualities of disjunct breeding and wintering areas. However, few studies have used isotopic data to estimate the movements of hybrid offspring in species that form hybrid zones. Here, we use stable hydrogen to estimate the wintering locations and migratory patterns of two common and widespread migratory birds, Audubon's (Setophaga auduboni) and myrtle (S. coronata) warblers, as well as their hybrids. These two species form a narrow hybrid zone with extensive interbreeding in the Rocky Mountains of British Columbia and Alberta, Canada, which has been studied for over four decades. Isotopes in feathers grown on the wintering grounds or early on migration reveal three important patterns: (1) Audubon's and myrtle warblers from allopatric breeding populations winter in isotopically different environments, consistent with band recovery data and suggesting that there is a narrow migratory transition between the two species, (2) most hybrids appear to overwinter in the south-eastern USA, similar to where myrtle warblers are known to winter, and (3) some hybrid individuals, particularly those along the western edge of the hybrid zone, show Audubon's-like isotopic patterns. These data suggest there is a migratory divide between these two species, but that it is not directly coincident with the centre of the hybrid zone in the breeding range. We interpret these findings and discuss them within the context of previous research on hybrid zones, speciation and migratory divides.
DOI: 10.14288/1.0397623
title: Data from: Assessment of plasma proteomics biomarker’s ability to distinguish benign from malignant lung nodules

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Background: Lung nodules are a diagnostic challenge, with an estimated yearly incidence of 1.6 million in the United States. This study evaluated the accuracy of an integrated proteomic classifier in identifying benign nodules in patients with a pretest probability of cancer (pCA) ≤ 50%. Methods: A prospective, multicenter observational trial of 685 patients with 8- to 30-mm lung nodules was conducted. Multiple reaction monitoring mass spectrometry was used to measure the relative abundance of two plasma proteins, LG3BP and C163A. Results were integrated with a clinical risk prediction model to identify likely benign nodules. Sensitivity, specificity, and negative predictive value were calculated. Estimates of potential changes in invasive testing had the integrated classifier results been available and acted on were made. Results: A subgroup of 178 patients with a clinician-assessed pCA ≤ 50% had a 16% prevalence of lung cancer. The integrated classifier demonstrated a sensitivity of 97% (CI, 82-100), a specificity of 44% (CI, 36-52), and a negative predictive value of 98% (CI, 92-100) in distinguishing benign from malignant nodules. The classifier performed better than PET, validated lung nodule risk models, and physician cancer probability estimates (P &lt; .001). If the integrated classifier results were used to direct care, 40% fewer procedures would be performed on benign nodules, and 3% of malignant nodules would be misclassified. Conclusions: When used in patients with lung nodules with a pCA ≤ 50%, the integrated classifier accurately identifies benign lung nodules with good performance characteristics. If used in clinical practice, invasive procedures could be reduced by diverting benign nodules to surveillance. Trial Registry: ClinicalTrials.gov; No.: NCT01752114; URL: www.clinicaltrials.gov).
DOI: 10.14288/1.0397635
title: Data from: Mutational effects depend on ploidy level: all else is not equal

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Ploidy is predicted to influence adaptation directly, yet whether single mutations behave the same in different ploidy backgrounds has not been well studied. It has often been assumed theoretically that aside from dominance, selective parameters do not differ between cells of varying ploidy. Using the budding yeast Saccharomyces cerevisiae, I compared the effect size of 20 adaptive mutations in haploids and homozygous diploids and found, surprisingly, that the same mutations often had a much larger effect in haploids than homozygous diploids. This empirical result demonstrates that it cannot be assumed that mutations will have the same effect in haploids and homozygous diploids.
DOI: 10.14288/1.0397649
title: Data from: Decreases in beetle body size linked to climate change and warming temperatures

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;1. Body size is a fundamental ecological trait and is correlated with population dynamics, community structure and function, and ecosystem fluxes. Laboratory data from broad taxonomic groups suggest that a widespread response to a warming world may be an overall decrease in organism body size. However, given the myriad of biotic and abiotic factors that can also influence organism body size in the wild, it is unclear whether results from these laboratory assays hold in nature. 2. Here we use data sets spanning 30 to 100 years to examine whether the body size of wild-caught beetles has changed over time, whether body size changes are correlated with increased temperatures, and we frame these results using predictions derived from a quantitative review of laboratory responses of 22 beetle species to temperature. 3. We found that 95% of lab-reared beetles decreased in size with increased rearing temperature, with larger-bodied species shrinking disproportionately more than smaller-bodied beetles. In addition, the museum data sets revealed that larger-bodied beetle species have decreased in size over time, that mean beetle body size explains much of the interspecific variation in beetle responses to temperature, and that long-term beetle size changes are explained by increases in autumn temperature and decreases in spring temperature in this region. 4. Our data demonstrate that the relationship between body size and temperature of wild-caught beetles matches relatively well with results from laboratory studies, and that variation in this relationship is largely explained by interspecific variation in mean beetle body size. 5. This long-term beetle dataset is one of the most comprehensive arthropod body size datasets compiled to date, it improves predictions regarding the shrinking of organisms with global climate change, and together with the meta-analysis data, call for new hypotheses to explain why larger-bodied organisms may be more sensitive to temperature.
DOI: 10.14288/1.0397658
title: Data from: Assessing reproductive isolation using a contact zone between parapatric lake-stream stickleback ecotypes

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Ecological speciation occurs when populations evolve reproductive isolation as a result of divergent natural selection. This isolation can be influenced by many potential reproductive barriers, including selection against hybrids, selection against migrants, and assortative mating. How and when these barriers act and interact in nature is understood for relatively few empirical systems. We used a mark-recapture experiment in a contact zone between lake and stream three-spined sticklebacks (Gasterosteus aculeatus, Linnaeus) to evaluate the occurrence of hybrids (allowing inferences about reproductive isolation), the inter-annual survival of hybrids (allowing inferences about selection against hybrids), and the shift in lake-like versus stream-like characteristics (allowing inferences about selection against migrants). Genetic and morphological data suggest the occurrence of hybrids and no selection against hybrids in general, a result contradictory to a number of other studies of sticklebacks. However, we did find selection against more lake-like individuals, suggesting a barrier to gene flow from the lake into the stream. Combined with previous work on this system, our results suggest that multiple (most weakly and often asymmetric) barriers must be combining to yield substantial restrictions on gene flow. This work provides evidence of a reproductive barrier in lake-stream sticklebacks and highlights the value of assessing multiple reproductive barriers in natural contexts.
DOI: 10.14288/1.0397660
title: Data from: Indirect genetic effects underlie oxygen-limited thermal tolerance within a coastal population of chinook salmon

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;With global temperatures projected to surpass the limits of thermal tolerance for many species, evaluating the heritable variation underlying thermal tolerance is critical for understanding the potential for adaptation to climate change. We examined the evolutionary potential of thermal tolerance within a population of chinook salmon (Oncorhynchus tshawytscha) by conducting a full-factorial breeding design and measuring the thermal performance of cardiac function and the critical thermal maximum (CTmax) of offspring from each family. Additive genetic variation in offspring phenotype was mostly negligible, although these direct genetic effects explained 53% of the variation in resting heart rate (fH). Conversely, maternal effects had a significant influence on resting fH, scope for fH, cardiac arrhythmia temperature and CTmax. These maternal effects were associated with egg size, as indicated by strong relationships between the mean egg diameter of mothers and offspring thermal tolerance. Because egg size can be highly heritable in chinook salmon, our finding indicates that the maternal effects of egg size constitute an indirect genetic effect contributing to thermal tolerance. Such indirect genetic effects could accelerate evolutionary responses to the selection imposed by rising temperatures and could contribute to the population-specific thermal tolerance that has recently been uncovered among Pacific salmon populations.