cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5683/sp2/ytmpnq
title: Data from: Low levels of hybridization across two contact zones among three species of woodpeckers (Sphyrapicus sapsuckers)

description: AbstractThree species of closely related woodpeckers (sapsuckers; Sphyrapicus) hybridize where they come into contact, presenting a rare ‘λ‐shape’ meeting of hybrid zones. Two of the three arms of this hybrid zone are located on either side of the Interior Plateau of British Columbia, Canada bordering the foothills of the Coast Mountains and the Rocky Mountains. The third arm is located in the eastern foothills of the Rocky Mountains. The zones of hybridization present high variability of phenotypes and alleles in relatively small areas and provide an opportunity to examine levels of reproductive isolation between the taxa involved. We examined phenotypes (morphometric traits and plumage) and genotypes of 175 live birds across the two hybrid zones. We used the Genotyping By Sequencing (GBS) method to identify 180 partially diagnostic single nucleotide polymorphisms (SNPs) to generate a genetic hybrid index (GHI) for each bird. Phenotypically diverged S. ruber and S. nuchalis are genetically closely related, while S. nuchalis and S. varius have similar plumage but are well separated at the genetic markers studied. The width of both hybrid zones is narrower than expected under neutrality, and analyses of both genotypes and phenotypes indicate that hybrids are rare in the hybrid zone. Rarity of hybrids indicates assortative mating and/or some form of fitness reduction in hybrids, which might maintain the species complex despite close genetic distance and introgression. These findings further support the treatment of the three taxa as distinct species.
DOI: 10.5683/sp2/ajaokn
title: Data from: Lowland biotic attrition revisited: body size and variation among climate change ‘winners’ and ‘losers’

description: AbstractThe responses of lowland tropical communities to climate change will critically influence global biodiversity but remain poorly understood. If species in these systems are unable to tolerate warming, the communities—currently the most diverse on Earth—may become depauperate (‘biotic attrition’). In response to temperature changes, animals can adjust their distribution in space or their activity in time, but these two components of the niche are seldom considered together. We assessed the spatio-temporal niches of rainforest mammal species in Borneo across gradients in elevation and temperature. Most species are not predicted to experience changes in spatio-temporal niche availability, even under pessimistic warming scenarios. Responses to temperature are not predictable by phylogeny but do appear to be trait-based, being much more variable in smaller-bodied taxa. General circulation models and weather station data suggest unprecedentedly high midday temperatures later in the century; predicted responses to this warming among small-bodied species range from 9% losses to 6% gains in spatio-temporal niche availability, while larger species have close to 0% predicted change. Body mass may therefore be a key ecological trait influencing the identity of climate change winners and losers. Mammal species composition will probably change in some areas as temperatures rise, but full-scale biotic attrition this century appears unlikely.
DOI: 10.5683/sp2/ogn6oi
title: Data from: Lythrum salicaria common garden under Neogalerucella herbivory

description: AbstractWe transplanted1088 seedlings of the invasive perennial plant Lythrum salicaria (purple loosestrife), from 136 maternal families sourced from 17 populations in the region around Ottawa, Canada, into a common garden containing 4 plots. The 17 populations differed in their prior exposure to the biocontrol agent Neogalerucella spp. leaf beetles (naïve = no prior exposure; recent = secondary colonization, ~5-15 years; release = sites of biocontrol release, ~20 years ago). Plants were planted in a wetland containing other Lythrum plants and experienced ambient (but significant) herbivory by Neogalerucella spp. leaf beetles. We measured herbivory, plant size and biomass over a period of 3.5 years; see the publication for more details. This experiment used the same seed material as a previously published greenhouse study by Stastny & Sargent 2017 (see below). Additional datasets, such as the proportion and phenology of flowering individuals, leaf size, stem and meristem numbers, etc., are available upon request.
DOI: 10.5683/sp2/woigqf
title: Data from: Macroevolutionary synthesis of flowering plant sexual systems

description: AbstractSexual system is a key determinant of genetic variation and reproductive success, affecting evolution within populations and within clades. Much research in plants has focused on evolutionary transitions away from the most common state of hermaphroditism and toward the rare state of dioecy (separate sexes). Rather than transitions predominantly toward greater sexual differentiation, however, evolution may proceed in the direction of lesser sexual differentiation. We analyzed the macroevolutionary dynamics of sexual system in angiosperm genera that contain both dioecious and non-dioecious species. Our phylogenetic analyses encompass a total of 2145 species from 40 genera. Overall, we found little evidence that rates of sexual system transitions are greater in any direction. Counting the number of inferred state changes revealed a mild prevalence of transitions away from hermaphroditism and away from dioecy, toward states of intermediate sexual differentiation. We identify genera in which future studies of sexual system evolution might be especially productive, and we discuss how integrating genetic or population-level studies of sexual system could improve the power of phylogenetic comparative analyses. Our work adds to the evidence that different selective pressures and constraints act in different groups, helping maintain the variety of sexual systems observed among plants.
DOI: 10.5683/sp2/iszbru
title: Data from: Making pore choices: repeated regime shifts in stomatal ratio

description: AbstractEcologically important traits do not evolve without limits. Instead, evolution is constrained by the set of available and viable phenotypes. In particular, natural selection may only favour a narrow range of adaptive optima constrained within selective regimes. Here, I integrate data with theory to test whether selection explains phenotypic constraint. A global database of 599 plant species from 94 families shows that stomatal ratio, a trait affecting photosynthesis and defence against pathogens, is highly constrained. Most plants have their stomata on the lower leaf surface (hypostomy), but species with half their stomata on each surface (amphistomy) form a distinct mode in the trait distribution. A model based on a trade-off between maximizing photosynthesis and a fitness cost of upper stomata predicts a limited number of adaptive solutions, leading to a multimodal trait distribution. Phylogenetic comparisons show that amphistomy is the most common among fast-growing species, supporting the view that CO2 diffusion is under strong selection. These results indicate that selective optima stay within a relatively stable set of selective regimes over macroevolutionary time.
DOI: 10.5683/sp2/qhkyfl
title: Data from: Mandated data archiving greatly improves access to research data

description: AbstractThe data underlying scientific papers should be accessible to researchers both now and in the future, but how best can we ensure that these data are available? Here we examine the effectiveness of four approaches to data archiving: no stated archiving policy, recommending (but not requiring) archiving, and two versions of mandating data deposition at acceptance. We control for differences between data types by trying to obtain data from papers that use a single, widespread population genetic analysis, STRUCTURE. At one extreme, we found that mandated data archiving policies that require the inclusion of a data availability statement in the manuscript improve the odds of finding the data online almost 1000-fold compared to having no policy. However, archiving rates at journals with less stringent policies were only very slightly higher than those with no policy at all. We also assessed the effectiveness of asking for data directly from authors and obtained over half of the requested datasets, albeit with ∼8 d delay and some disagreement with authors. Given the long-term benefits of data accessibility to the academic community, we believe that journal-based mandatory data archiving policies and mandatory data availability statements should be more widely adopted.
DOI: 10.5683/sp2/ixl3u7
title: Data from: Mandible allometry in extant and fossil Balaenopteridae (Cetacea: Mammalia): the largest vertebrate skeletal element and its role in rorqual lunge-feeding

description: AbstractRorqual whales (crown Balaenopteridae) are unique among aquatic vertebrates in their ability to lunge-feed. During a single lunge, rorquals rapidly engulf a large volume of prey-laden water at high speed, which they then filter to capture suspended prey. Engulfment biomechanics are mostly governed by the coordinated opening and closing of the mandibles at large gape angles, which differentially exposes the floor of the oral cavity to oncoming flow. Mouth area in rorquals is delimited by unfused bony mandibles that form kinetic linkages to each other and with the skull. The relative scale and morphology of these skeletal elements have profound consequences for the energetic efficiency of foraging in these gigantic predators. Here we performed a morphometric study of rorqual mandibles using a dataset derived from a survey of museum specimens. Across adult specimens of extant balaenopterids, mandibles range in size from ~1-6 m in length, and at their upper limit they represent the single largest osteological element of any vertebrate, living or extinct. Our analyses determined that rorqual mandibles exhibit positive allometry, whereby the relative size of these mandibles becomes greater with increasing body size. These robust scaling relationships allowed us to predict mandible length for fragmentary remains (e.g., incomplete and/or fossil specimens), as we demonstrated for two partial mandibles from the latest Miocene of California, U.S.A., and for mandibles from previously described fossil balaenopterids. Furthermore, we showed the allometry of mandible length to body size in extant mysticetes, which hints at fundamental developmental constraints in mysticetes despite their ecomorphologic differences in the feeding styles. Lastly, we outlined how our findings can be used to test hypotheses about the antiquity and evolution of lunge-feeding.
DOI: 10.5683/sp2/fxiueh
title: Data from: Mapping the fitness landscape of gene expression uncovers the cause of antagonism and sign epistasis between adaptive mutations

description: AbstractHow do adapting populations navigate the tensions between the costs of gene expression and the benefits of gene products to optimize the levels of many genes at once? Here we combined independently-arising beneficial mutations that altered enzyme levels in the central metabolism of Methylobacterium extorquens to uncover the fitness landscape defined by gene expression levels. We found strong antagonism and sign epistasis between these beneficial mutations. Mutations with the largest individual benefit interacted the most antagonistically with other mutations, a trend we also uncovered through analyses of datasets from other model systems. However, these beneficial mutations interacted multiplicatively (i.e., no epistasis) at the level of enzyme expression. By generating a model that predicts fitness from enzyme levels we could explain the observed sign epistasis as a result of overshooting the optimum defined by a balance between enzyme catalysis benefits and fitness costs. Knowledge of the phenotypic landscape also illuminated that, although the fitness peak was phenotypically far from the ancestral state, it was not genetically distant. Single beneficial mutations jumped straight toward the global optimum rather than being constrained to change the expression phenotypes in the correlated fashion expected by the genetic architecture. Given that adaptation in nature often results from optimizing gene expression, these conclusions can be widely applicable to other organisms and selective conditions. Poor interactions between individually beneficial alleles affecting gene expression may thus compromise the benefit of sex during adaptation and promote genetic differentiation.
DOI: 10.5683/sp2/0wx7zv
title: Data from: Mapping the imprint of biotic interactions on β-diversity

description: AbstractInvestigating how trophic interactions influence the β-diversity of meta-communities is of paramount importance to understanding the processes shaping biodiversity distribution. Here, we apply a statistical method for inferring the strength of spatial dependencies between pairs of species groups. Using simulated community data generated from a multi-trophic model, we showed that this method can approximate biotic interactions in multi-trophic communities based on β-diversity patterns across groups. When applied to soil multi-trophic communities along an elevational gradient in the French Alps, we found that fungi make a major contribution to the structuring of β-diversity across trophic groups. We also demonstrated that there were strong spatial dependencies between groups known to interact specifically (e.g. plant-symbiotic fungi, bacteria-nematodes) and that the influence of environment was less important than previously reported in the literature. Our method paves the way for a better understanding and mapping of multi-trophic communities through space and time.
DOI: 10.5683/sp2/hksfan
title: Data from: Maternal provisioning is structured by species’ competitive neighborhoods

description: AbstractDifferential maternal provisioning of offspring in response to environmental conditions has been argued as ‘the missing link’ in plant life histories. Although empirical evidence suggests that maternal provisioning responses to abiotic conditions are common, there is little understanding of how differences in maternal provisioning manifest in response to competition. Frequency manipulations are commonly employed in ecological studies to assess the strength of interspecific competition, relative to intraspecific competition, and we used frequency manipulations to test how competition in two soil moisture environments affects maternal provisioning of seed mass. Specifically, for 15 pairs comprised from 25 annual plant species that occur in California, we varied the relative frequencies of conspecific to heterospecific competitors from 90% (intraspecific competition) to 10% (interspecific competition). We found that conspecific frequency affected maternal provisioning (seed mass) in 12 of the 25 species (8 significantly (P&lt;0.05), four marginally significantly (P&lt;0.07)), and that these responses included both increased (5 species) and decreased (6 species) seed mass, as well as one species with opposing directions of response to conspecific frequency that depended on the soil moisture environment. Conspecific frequency also affected per capita fecundity (seed number) for 17 of the 25 species (15 significantly (P&lt;0.05), two marginally significantly (P&lt;0.09)), which generally decreased seed number as conspecific frequency increased. The direction and magnitude of frequency-dependent seed mass depended on the identity of the competitor, even among species whose fecundity was not affected by competitor identity; the latter finding reveals competitive differences among species that would otherwise appear to be competitively equivalent. Our research demonstrates how species responses to different competitive environments manifest through maternal provisioning, and that these responses alter previous estimates of environmentally-determined maternal provisioning and reproductive output; future study is needed to understand their combined effects on population and community dynamics.
DOI: 10.5683/sp2/48vvbr
title: Data from: Maternal stress has divergent effects on gene expression patterns in the brains of male and female threespine stickleback

description: AbstractMaternal stress can have long-term effects on neurodevelopment that can influence offspring performance and population evolutionary trajectories. To examine the mechanistic basis for these neurodevelopmental effects of maternal stress, we used RNA-seq to assess differential gene expression across the brain transcriptome of adult male and female threespine stickleback (Gasterosteus aculeatus) from stressed and unstressed mothers. We identified sexually divergent effects of maternal stress on the brain transcriptome. In males, genes that were up-regulated by maternal stress were enriched for processes involved in synaptic function and organization and steroid hormone mediated signaling pathways, whereas in females genes that were up-regulated by maternal stress were enriched for processes involved in protein translation and metabolic functions. The expression of several genes involved in the hypothalamic-pituitary-interrenal response to stress and epigenetic processes such as the regulation of DNA methylation patterns and miRNAs increased in males and not in females. These data suggest that maternal stress has markedly different effects on cellular pathways in the brains of male and female offspring of mothers that are exposed to stress, which could have important implications when assessing the long-term ecological and evolutionary impacts of stress across generations.
DOI: 10.5683/sp2/xxwhzt
title: Data from: Measuring agreement among experts in classifying camera images of similar species

description: AbstractCamera trapping and solicitation of wildlife images through citizen science have become common tools in ecological research. Such studies collect many wildlife images for which correct species classification is crucial; even low misclassification rates can result in erroneous estimation of the geographic range or habitat use of a species, potentially hindering conservation or management efforts. However, some species are difficult to tell apart, making species classification challenging - but the literature on classification agreement rates among experts remains sparse. Here, we measure agreement among experts in distinguishing between images of two similar congeneric species, bobcats (Lynx rufus) and Canada lynx (L. canadensis). We asked experts to classify the species in selected images to test whether the season, background habitat, time of day, and the visible features of each animal (e.g., face, legs, tail) affected agreement among experts about the species in each image. Overall, experts had moderate agreement (Fleiss’ kappa = 0.64), but experts had varying levels of agreement depending on these image characteristics. Most images (71%) had ≥1 expert classification of ‘unknown’, and many images (39%) had some experts classify the image as ‘bobcat’ while others classified it as ‘lynx’. Further, experts were inconsistent even with themselves, changing their classifications of numerous images when they were asked to reclassify the same images months later. These results suggest that classification of images by a single expert is unreliable for similar-looking species. Most of the images did obtain a clear majority classification from the experts, although we emphasize that even majority classifications may be incorrect. We recommend that researchers using wildlife images consult multiple species experts to increase confidence in their image classifications of similar sympatric species. Still, when the presence of a species with similar sympatrics must be conclusive, physical or genetic evidence should be required.
DOI: 10.5683/sp2/kakhh5
title: Data from: Measuring engagement in advance care planning: a cross-sectional multicentre feasibility study.

description: AbstractObjectives: To assess feasibility, acceptability, and clinical sensibility of a novel survey, the Advance Care Planning (ACP) Engagement Survey in various health care settings. Setting: A target sample of 50 patients from each of primary care, hospital, cancer care, and dialysis care settings. Participants: A convenience sample of patients without cognitive impairment who could speak and read English was recruited. Patients 50 years and older were eligible in primary care; patients 80 and older or 55 years and older with clinical markers of advanced chronic disease were recruited in hospital; patients aged 19 and older were recruited in cancer and renal dialysis centres. Outcomes: We assessed feasibility, acceptability and clinical sensibility of the ACP Engagement Survey using a 6-point scale. The ACP Engagement Survey measures ACP processes (knowledge, contemplation, self-efficacy, readiness) on 5-point Likert scales and actions (yes/no). Results: 196 patients (38 to 96 years old, 50.5% women) participated. Mean (±standard deviation) time to administer was 48.8 ±19.6 minutes. Mean acceptability scores ranged from 3.2±1.3 in hospital to 4.7±0.9 in primary care and mean relevance ranged from 3.5±1.0 in hospital to 4.9±0.9 in dialysis centres (p values &lt;0.001 for both). The mean process score was 3.1±0.6 and the mean action score was 11.2±5.6 (of a possible 25). Conclusions: The ACP Engagement Survey demonstrated feasibility and acceptability in out-patient settings, but was less feasible and acceptable among hospitalized patients due to length. A shorter version may improve feasibility. Engagement in ACP was low to moderate.
DOI: 10.5683/sp2/vfhw2x
title: Data from: Mechanisms of thermal adaptation and evolutionary potential of conspecific populations to changing environments

description: AbstractHeterogeneous and ever-changing thermal environments drive the evolution of populations and species, especially when extreme conditions increase selection pressure for traits influencing fitness. However, projections of biological diversity under scenarios of climate change rarely consider evolutionary adaptive potential of natural species. In this study, we tested for mechanistic evidence of evolutionary thermal adaptation among ecologically divergent redband trout populations (Oncorhynchus mykiss gairdneri) in cardiorespiratory function, cellular response and genomic variation. In a common garden environment, fish from an extreme desert climate had significantly higher critical thermal maximum (p&lt;0.05) and broader optimum thermal window for aerobic scope (&gt;3°C) than fish from cooler montane climate. In addition, the desert population had the highest maximum heart rate during warming (20% greater than montane populations), indicating improved capacity to deliver oxygen to internal tissues. In response to acute heat stress, distinct sets of cardiac genes were induced among ecotypes, which helps to explain the differences in cardiorespiratory function. Candidate genomic markers and genes underlying these physiological adaptations were also pinpointed, such as genes involved in stress response and metabolic activity (hsp40, ldh-b and camkk2). These markers were developed into a multi-variate model that not only accurately predicted critical thermal maxima, but also evolutionary limit of thermal adaptation in these specific redband trout populations relative to the expected limit for the species. This study demonstrates mechanisms and limitations of an aquatic species to evolve under changing environments that can be incorporated into advanced models to predict ecological consequences of climate change for natural organisms.