cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5683/sp2/ls5rlf
title: Data from: A review of riverine ecosystem service quantification: research gaps and recommendations

description: Abstract1.Increasing demand for benefits provided by riverine ecosystems threatens their sustainable provision. The ecosystem service concept is a promising avenue to inform riverine ecosystem management, but several challenges have prevented the application of this concept. 2.We quantitatively assess the field of riverine ecosystem services’ progress in meeting these challenges. We highlight conceptual and methodological gaps, which have impeded integration of the ecosystem service concept into management. 3.Across 89 relevant studies, 33 unique riverine ecosystem services were evaluated, for a total of 404 ecosystem service quantifications. Studies quantified between one and 23 ecosystem services, although the majority (55%) evaluated three or less. Among studies that quantified more than one service, 58% assessed interactions between services. Most studies (71%) did not include stakeholders in their quantification protocols, and 34% developed future scenarios of ecosystem service provision. Almost half (45%) conducted monetary valuation, using 16 methods. Only 9% did not quantify or discuss uncertainties associated with service quantification. The indicators and methods used to quantify the same type of ecosystem service varied. Only 3% of services used indicators of capacity, flow, and demand in concert. 4.Our results suggest indicators, data sources, and methods for quantifying riverine ecosystem services should be more clearly defined and accurately represent the service they intend to quantify. Furthermore, more assessments of multiple services across diverse spatial extents and of riverine service interactions are needed, with better inclusion of stakeholders. Addressing these challenges will help riverine ecosystem service science inform river management. 5.Synthesis and applications. The ecosystem service concept has great potential to inform riverine ecosystem management and decision making processes. However, this review of riverine ecosystem service quantification uncovers several remaining research gaps, impeding effective use of this tool to manage riverine ecosystems. We highlight these gaps and point to studies showcasing methods that can be used to address them.
DOI: 10.5683/sp2/edgsvs
title: Data from: A simple approach for maximizing the overlap of phylogenetic and comparative data

description: AbstractBiologists are increasingly using curated, public data sets to conduct phylogenetic comparative analyses. Unfortunately, there is often a mismatch between species for which there is phylogenetic data and those for which other data are available. As a result, researchers are commonly forced to either drop species from analyses entirely or else impute the missing data. A simple strategy to improve the overlap of phylogenetic and comparative data is to swap species in the tree that lack data with ‘phylogenetically equivalent’ species that have data. While this procedure is logically straightforward, it quickly becomes very challenging to do by hand. Here, we present algorithms that use topological and taxonomic information to maximize the number of swaps without altering the structure of the phylogeny. We have implemented our method in a new R package phyndr, which will allow researchers to apply our algorithm to empirical data sets. It is relatively efficient such that taxon swaps can be quickly computed, even for large trees. To facilitate the use of taxonomic knowledge, we created a separate data package taxonlookup; it contains a curated, versioned taxonomic lookup for land plants and is interoperable with phyndr. Emerging online data bases and statistical advances are making it possible for researchers to investigate evolutionary questions at unprecedented scales. However, in this effort species mismatch among data sources will increasingly be a problem; evolutionary informatics tools, such as phyndr and taxonlookup, can help alleviate this issue.
DOI: 10.5683/sp2/lx4mvp
title: Data from: A stochastic model for predicting age and mass at maturity of insects

description: AbstractVariation in age and mass at maturity is commonly observed in populations, even among individuals with the same genetic and environmental backgrounds. Accounting for such individual variation with a stochastic model is important for estimating optimal evolutionary strategies and for understanding potential trade-offs among life history traits. However, most studies employ stochastic models that are either phenomenological or account for variation in only one life history trait. We propose a model based on the developmental biology of the moth Manduca sexta that accounts for stochasticity in two key life history traits, age and mass at maturity. The model is mechanistic, describing feeding behavior and common insect developmental processes including the degradation of juvenile hormone prior to molting. We derive a joint probability density function for the model and explore how the distribution of age and mass at maturity is affected by different parameter values. We find that the joint distribution is generally non-normal and highly sensitive to parameter values. In addition, our model predicts previously observed effects of temperature change and nutritional quality on the expected values of insect age and mass. Our results highlight the importance of integrating multiple sources of stochasticity into life history models.
DOI: 10.5683/sp2/j1dsdn
title: Data from: A target enrichment method for gathering phylogenetic information from hundreds of loci: an example from the Compositae

description: AbstractPremise of the study: The Compositae (Asteraceae) are a large and diverse family of plants, and the most comprehensive phylogeny to date is a meta-tree based on 10 chloroplast loci that has several major unresolved nodes. We describe the development of an approach that enables the rapid sequencing of large numbers of orthologous nuclear loci to facilitate efficient phylogenomic analyses. Methods and Results: We designed a set of sequence capture probes that target conserved orthologous sequences in the Compositae. We also developed a bioinformatic and phylogenetic workflow for processing and analyzing the resulting data. Application of our approach to 15 species from across the Compositae resulted in the production of phylogenetically informative sequence data from 763 loci and the successful reconstruction of known phylogenetic relationships across the family. Conclusions: These methods should be of great use to members of the broader Compositae community, and the general approach should also be of use to researchers studying other families.
DOI: 10.5683/sp2/mjiqv2
title: Data from: A test of hybrid growth disadvantage in wild, free-ranging species pairs of threespine sticklebacks (Gasterosteus aculeatus) and its implications for ecological speciation

description: AbstractEcological speciation is the evolution of reproductive isolation as a direct or indirect consequence of divergent natural selection. Reduced performance of hybrids in nature is thought to be an important process by which natural selection can favour the evolution of assortative mating and drive speciation. Benthic and limnetic sympatric species of threespine stickleback (Gasterosteus aculeatus) are adapted to alternative trophic niches (bottom browsing versus open water planktivory, respectively) and reduced feeding performance of hybrids is thought to have contributed to the evolution of reproductive isolation. We tested this “hybrid-disadvantage hypothesis” by inferring growth rates from otoliths sampled from wild, free-ranging benthic, limnetic, and hybrid sticklebacks from two lakes. There were significant differences in growth rate between lakes, life-history stages, and among years (maximum P = 0.02), as well as interactions between most factors, but not between hybrid and parental species sticklebacks in most comparisons. Our results provide little evidence of a growth disadvantage in hybrid sticklebacks when free-ranging in nature. While trophic ecology per se may contribute less to ecological speciation than envisioned, it may act in concert with other aspects of stickleback biology, such as interactions with parasites, predators, competitors and/or sexual selection, to present strong multifarious selection against hybrids.
DOI: 10.5683/sp2/yppic6
title: Data from: A test of the effects of timing of a pulsed resource subsidy on stream ecosystems

description: AbstractSpatial resource subsidies can alter bottom-up and top-down forces of community regulation across ecosystem boundaries. Most subsidies are temporally variable, and recent theory has suggested that consumer-resource dynamics can be stabilized if the peak timing of a subsidy is desynchronized with that of prey productivity in the recipient ecosystem. However, magnitude of consumer responses per se could depend on the subsidy timing, which may be a critical component for community dynamics and ecosystem processes. The aim of this study was to test (1) whether a recipient consumer (cutthroat trout) responds differently to a resource subsidy occurring early in its growing season than to a subsidy occurring late in the season, and, if this is the case, (2) whether the timing-dependent consumer response has cascading effects on communities and ecosystem functions in streams. To test those hypotheses, we conducted a large-scale field experiment, in which we directly manipulated the timing of augmentation of the terrestrial invertebrates that enter stream (i.e., peak timing of June-August vs. August-October), keeping constant the total amounts of the invertebrates entered. We found large increases in the individual growth rate and population biomass of the cutthroat trout, in response to the early resource pulse, but not to the late pulse. This timing-dependent consumer response cascaded down to reduce benthic invertebrates and leaf break-down rate, and increased water nutrient concentrations. Furthermore, the early resource pulse resulted in higher maturity rate of the cutthroat trout in the following spring, demonstrating the importance of the subsidy timing on long-term community dynamics via the consumer's numerical response. Our results emphasize the need to acknowledge timing-dependent consumer responses in understanding the effects of subsidies on communities and ecosystem processes. Elucidating the mechanisms by which consumers effectively exploit pulsed subsidies is an important avenue to better understand community dynamics in spatially coupled ecosystems.
DOI: 10.5683/sp2/adgsbj
title: Data from: A test of the umbrella species approach in restored floodplain ponds.

description: Abstract1.The umbrella species approach, where conservation actions targeted for one or a group of species should benefit the broader community, may provide an effective framework to guide habitat restoration. This requires congruence in the response of umbrella and co-occurring species to environmental stress and recovery, and the identification of potential mechanisms by which co-occurring species benefit from conservation of an umbrella species. 2.Past evaluations of this approach have considered only the presence/absence of umbrella species. In addition to presence/absence, we quantified abundance and biomass of both umbrella and co-occurring species to support a more quantitative evaluation of species co-occurrence. Floodplain ponds are restored in British Columbia and the Pacific Northwest to benefit coho salmon Oncorhynchus kisutch, a presumptive umbrella species. To test its effectiveness as an umbrella species, we assessed the relationships between species richness, abundance and biomass of aquatic vertebrates, including vertebrates of conservation concern (“listed”), and benthic invertebrates and the abundance and biomass of juvenile coho. We used ordination to evaluate relationships between species’ abundance and biomass and environmental attributes. 3.Positive relationships were identified between coho abundance and biomass and species richness, abundance and biomass of fish and listed species. These relationships were negative for benthic invertebrates. Listed species were located close to coho in ordinations, suggesting they respond to similar environmental features while benthic invertebrates clustered away from coho. 4.Synthesis and applications. We found that where our umbrella species coho is most productive, so are other listed species and fish in general, a relationship that would not have been evident had we evaluated species richness alone. We also reported strong relationships between some environmental features manipulated in the habitat restoration and the presence and productivity of coho and co-occurring species. Our study demonstrates the umbrella species approach has potential to guide habitat restoration when there is congruence in the response of umbrella and co-occurring species to environmental attributes that can be manipulated in the restoration. Where this is possible, one can use restoration designed for one or several umbrella species and successfully restore habitats that are viable for other species, including listed species.
DOI: 10.5683/sp2/8kbh8e
title: Data from: Acceleration and novelty: community restoration speeds recovery and transforms species composition in Andean cloud forest

description: AbstractCommunity-based tropical forest restoration projects, often promoted as a win-win solution for local communities and the environment, have increased dramatically in number in the past decade. Many such projects are underway in Andean cloud forests, which, given their extremely high biodiversity and history of extensive clearing, are understudied. This study investigates the efficacy of community-based tree-planting projects to accelerate cloud forest recovery, as compared to unassisted natural regeneration. This study takes place in northwest Andean Ecuador, where the majority of the original, highly diverse cloud forests have been cleared, in five communities that initiated tree-planting projects to restore forests in 2003. In 2011, we identified tree species along transects in planted forests (n = 5), naturally regenerating forests (n = 5), and primary forests (n = 5). We also surveyed 120 households about their restoration methods, tree preferences, and forest uses. We found that tree diversity was higher in planted than in unplanted secondary forest, but both were less diverse than primary forests. Ordination analysis showed that all three forests had distinct species compositions, although planted forests shared more species with primary forests than did unplanted forests. Planted forests also contained more animal-dispersed species in both the planted canopy and in the unplanted, regenerating understory than unplanted forests, and contained the highest proportion of species with use value for local people. While restoring forest increased biodiversity and accelerated forest recovery, restored forests may also represent novel ecosystems that are distinct from the region's previous ecosystems and, given their usefulness to people, are likely to be more common in the future.
DOI: 10.5683/sp2/ks38pk
title: Data from: Accelerometers can measure total and activity-specific energy expenditure in free-ranging marine mammals only if linked to time-activity budgets

description: AbstractEnergy expenditure is an important component of foraging ecology, but is extremely difficult to estimate in free-ranging animals and depends on how animals partition their time between different activities during foraging. Acceleration data have emerged as a new way to determine energy expenditure at a fine scale but this needs to be tested and validated in wild animals. This study investigated whether vectorial dynamic body acceleration (VeDBA) could accurately predict the energy expended by marine predators during a full foraging trip. We also aimed to determine whether the accuracy of predictions of energy expenditure derived from acceleration increased when partitioned by different types of at-sea activities (i.e. diving, transiting, resting and surface activities). To do so, we equipped 20 lactating northern (Callorhinus ursinus) and 20 lactating Antarctic fur seals (Arctocephalus gazella) with GPS, time-depth recorders and tri-axial accelerometers and obtained estimates of field metabolic rates using the doubly labelled water (DLW) method. VeDBA was derived from tri-axial acceleration, and at-sea activities (diving, transiting, resting and surface activities) were determined using dive depth, tri-axial acceleration and travelling speed. We found that VeDBA did not accurately predict the total energy expended by fur seals during their full foraging trips (R2 = 0·36). However, the accuracy of VeDBA as a predictor of total energy expenditure increased significantly when foraging trips were partitioned by activity and when activity-specific VeDBA was paired with time-activity budgets (R2 = 0·70). Activity-specific VeDBA also accurately predicted the energy expenditures of each activity independent of each other (R2 &gt; 0·85). Our study confirms that acceleration is a promising way to estimate energy expenditures of free-ranging marine mammals at a fine scale never attained before. However, it shows that it needs to be based on the time-activity budgets that make up foraging trips rather than being derived as a single measure of VeDBA applied to entire foraging trips. Our activity-based method provides a cost-effective means to accurately calculate energy expenditures of fur seals using acceleration and time-activity budgets, that can be transfered to studies on other species.
DOI: 10.5683/sp2/wklmjv
title: Data from: Acid secretion by the boring organ of the burrowing giant clam, Tridacna crocea

description: AbstractThe giant clam Tridacna crocea, native to Indo-Pacific coral reefs, is noted for its unique ability to bore fully into coral rock and is a major agent of reef bioerosion. However, T. crocea’s mechanism of boring has remained a mystery despite decades of research. By exploiting a new, two-dimensional pH-sensing technology and manipulating clams to press their presumptive boring tissue (the pedal mantle) against pH-sensing foils, we show that this tissue lowers the pH of surfaces it contacts by more than 2 pH units below seawater pH day and night. Acid secretion is likely mediated by vacuolar-type H+-ATPase, which we demonstrate (by immunofluorescence) is abundant in the pedal mantle outer epithelium. Our discovery of acid secretion solves this decades-old mystery and reveals that, during bioerosion, T. crocea can liberate reef constituents directly to the soluble phase, rather than producing sediment alone as earlier assumed.
DOI: 10.5683/sp2/pvjfke
title: Data from: Adaptation to elevated CO2 in different biodiversity contexts

description: AbstractIn the absence of migration, species persistence depends on adaption to a changing environment, but whether and how adaptation to global change is altered by community diversity is not understood. Community diversity may prevent, enhance or alter how species adapt to changing conditions by influencing population sizes, genetic diversity and/or the fitness landscape experienced by focal species. We tested the impact of community diversity on adaptation by performing a reciprocal transplant experiment on grasses that evolved for 14 years under ambient and elevated CO2, in communities of low or high species-richness. Using biomass as a fitness proxy, we find evidence for local adaptation to elevated CO2, but only for plants assayed in a community of similar diversity to the one experienced during the period of selection. Our results indicate that the biological community shapes the very nature of the fitness landscape within which species evolve in response to elevated CO2.
DOI: 10.5683/sp2/k69ktm
title: Data from: Adaptation with gene flow across the landscape in a dune sunflower

description: AbstractIsolation by adaptation increases divergence at neutral loci when natural selection against immigrants reduces the rate of gene flow between different habitats. This can occur early in the process of adaptive divergence and is a key feature of ecological speciation. Despite the ability of isolation by distance and other forms of landscape resistance to produce similar patterns of neutral divergence within species, few studies have used landscape genetics to control for these other forces. We have studied the divergence of Helianthus petiolaris ecotypes living in active sand dunes and adjacent non-dune habitat, using landscape genetics approaches, such as circuit theory and multiple regression of distance matrices, in addition to coalescent modelling. Divergence between habitats was significant, but not strong, and was shaped by isolation by distance. We expected that increased resistance due to patchy and unfavourable habitat in the dunes would contribute to divergence. Instead, we found that landscape resistance models with lower resistance in the dunes performed well as predictors of genetic distances among subpopulations. Nevertheless, habitat class remained a strong predictor of genetic distance when controlling for isolation by resistance and isolation by distance. We also measured environmental variables at each site and confirmed that specific variables, especially soil nitrogen and vegetation cover, explained a greater proportion of variance in genetic distance than did landscape or the habitat classification alone. Asymmetry in effective population sizes and numbers of migrants per generation was detected using coalescent modelling with Bayesian inference, which is consistent with incipient ecological speciation being driven by the dune habitat.
DOI: 10.5683/sp2/7idtpn
title: Data from: Adaptive divergence along environmental gradients in a climate-change-sensitive mammal

description: AbstractIn the face of predicted climate change, a broader understanding of biotic responses to varying environments has become increasingly important within the context of biodiversity conservation. Local adaptation is one potential option, yet remarkably few studies have harnessed genomic tools to evaluate the efficacy of this response within natural populations. Here we show evidence of selection driving divergence of a climate change-sensitive mammal, the American pika (Ochotona princeps), distributed along elevation gradients at its northern range margin in the Coast Mountains of British Columbia (BC), Canada. We employed amplified fragment length polymorphism-based genomic scans to conduct genome-wide searches for candidate loci among populations inhabiting varying environments from sea-level to 1500m. Using a highly stringent approach to outlier locus detection, we identified 68 candidate loci putatively under selection (out of a total 1509 screened), 15 of which displayed significant associations with environmental variables including annual precipitation and maximum summer temperature. These candidate loci may represent important targets for predicting pika responses to climate change and informing novel approaches to wildlife conservation in a changing world.