cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5683/sp2/hepit0
title: Data from: Using experimentation to understand the 10-year snowshoe hare cycle in the boreal forest of North America

description: Abstract1. Population cycles have long fascinated ecologists from the time of Charles Elton in the 1920s. The discovery of large population fluctuations in undisturbed ecosystems challenged the idea that pristine nature was in a state of balance. The 10-year cycle of snowshoe hares (Lepus americanus Erxleben) across the boreal forests of Canada and Alaska is a classic cycle, recognized by fur traders for more than 300 years. 2. Since the 1930s ecologists have investigated the mechanisms that might cause these cycles. Proposed causal mechanisms have varied from sunspots to food supplies, parasites, diseases, predation, and social behaviour. Both the birth rate and the death rate change dramatically over the cycle. Social behaviour was eliminated as a possible cause because snowshoe hares are not territorial and do not commit infanticide. 3. Since the 1960s large-scale manipulative experiments have been used to discover the major limiting factors. Food supply and predation quickly became recognized as potential key factors causing the cycle. Experiments adding food and restricting predator access to field populations have been decisive in pinpointing predation as the key mechanism causing these fluctuations. 4. The immediate cause of death of most snowshoe hares is predation by a variety of predators, including the Canada lynx (Lynx canadensis Kerr). The collapse in the reproductive rate is not due to food shortage as was originally thought, but is a result of chronic stress from predator chases. 5. Five major issues remain unresolved. First, what is the nature of the predator-induced memory that results in the prolonged low phase of the cycle? Second, why do hare cycles form a travelling wave, starting in the centre of the boreal forest in Saskatchewan and travelling across western Canada and Alaska? Third, why does the amplitude of the cycle vary greatly from one cycle to the next in the same area? Fourth, do the same mechanisms of population limitation apply to snowshoe hares in eastern North American or in similar ecosystems across Siberia? Finally, what effect will climatic warming have on all the above issues? The answers to these questions remain for future generations of biologists to determine.
DOI: 10.5683/sp2/tgdqio
title: Data from: Using fuzzy logic to determine the vulnerability of marine species to climate change

description: AbstractMarine species are being impacted by climate change and ocean acidification, although their level of vulnerability varies due to differences in species' sensitivity, adaptive capacity and exposure to climate hazards. Due to limited data on the biological and ecological attributes of many marine species, as well as inherent uncertainties in the assessment process, climate change vulnerability assessments in the marine environment frequently focus on a limited number of taxa or geographic ranges. As climate change is already impacting marine biodiversity and fisheries, there is an urgent need to expand vulnerability assessment to cover a large number of species and areas. Here, we develop a modelling approach to synthesize data on species-specific estimates of exposure, and ecological and biological traits to undertake an assessment of vulnerability (sensitivity and adaptive capacity) and risk of impacts (combining exposure to hazards and vulnerability) of climate change (including ocean acidification) for global marine fishes and invertebrates. We use a fuzzy logic approach to accommodate the variability in data availability and uncertainties associated with inferring vulnerability levels from climate projections and species' traits. Applying the approach to estimate the relative vulnerability and risk of impacts of climate change in 1074 exploited marine species globally, we estimated their index of vulnerability and risk of impacts to be on average 52 ± 19 SD and 66 ± 11 SD, scaling from 1 to 100, with 100 being the most vulnerable and highest risk, respectively, under the ‘business-as-usual' greenhouse gas emission scenario (Representative Concentration Pathway 8.5). We identified 157 species to be highly vulnerable while 294 species are identified as being at high risk of impacts. Species that are most vulnerable tend to be large-bodied endemic species. This study suggests that the fuzzy logic framework can help estimate climate vulnerabilities and risks of exploited marine species using publicly and readily available information.
DOI: 10.5683/sp2/d7uckc
title: Data from: Using genetic relatedness to understand heterogeneous distributions of urban rat-associated pathogens

description: AbstractUrban Norway rats (Rattus norvegicus) carry several pathogens transmissible to people. However, pathogen prevalence can vary across fine spatial scales (i.e., by city block). Using a population genomics approach, we sought to describe rat movement patterns across an urban landscape, and to evaluate whether these patterns align with pathogen distributions. We genotyped 605 rats from a single neighborhood in Vancouver, Canada and used 1,495 genome-wide single nucleotide polymorphisms to identify parent-offspring and sibling relationships using pedigree analysis. We resolved 1,246 pairs of relatives, of which only 1% of pairs were captured in different city blocks. Relatives were primarily caught within 33 meters of each other leading to a highly leptokurtic distribution of dispersal distances. Using binomial generalized linear mixed models we evaluated whether family relationships influenced rat pathogen status with the bacterial pathogens Leptospira interrogans, Bartonella tribocorum, and Clostridium difficile, and found that an individual’s pathogen status was not predicted any better by including disease status of related rats. The spatial clustering of related rats and their pathogens lends support to the hypothesis that spatially restricted movement promotes the heterogeneous patterns of pathogen prevalence evidenced in this population. Our findings also highlight the utility of evolutionary tools to understand movement and rat-associated health risks in urban landscapes.
DOI: 10.5683/sp2/lk4ibl
title: Data from: Validation of an algorithm for identifying MS cases in administrative health claims datasets

description: AbstractObjective: To develop a valid algorithm for identifying multiple sclerosis (MS) cases in administrative health claims (AHC) datasets. Methods: We used 4 AHC datasets from the Veterans Administration (VA), Kaiser Permanente Southern California (KPSC), Manitoba (Canada), and Saskatchewan (Canada). In the VA, KPSC, and Manitoba, we tested the performance of candidate algorithms based on inpatient, outpatient, and disease-modifying therapy (DMT) claims compared to medical records review using sensitivity, specificity, positive and negative predictive values, and interrater reliability (Youden J statistic) both overall and stratified by sex and age. In Saskatchewan, we tested the algorithms in a cohort randomly selected from the general population. Results: The preferred algorithm required ≥3 MS-related claims from any combination of inpatient, outpatient, or DMT claims within a 1-year time period; a 2-year time period provided little gain in performance. Algorithms including DMT claims performed better than those that did not. Sensitivity (86.6%–96.0%), specificity (66.7%–99.0%), positive predictive value (95.4%–99.0%), and interrater reliability (Youden J = 0.60–0.92) were generally stable across datasets and across strata. Some variation in performance in the stratified analyses was observed but largely reflected changes in the composition of the strata. In Saskatchewan, the preferred algorithm had a sensitivity of 96%, specificity of 99%, positive predictive value of 99%, and negative predictive value of 96%. Conclusions: The performance of each algorithm was remarkably consistent across datasets. The preferred algorithm required ≥3 MS-related claims from any combination of inpatient, outpatient, or DMT use within 1 year. We recommend this algorithm as the standard AHC case definition for MS.
DOI: 10.5683/sp2/uye3nz
title: Data from: Variation in body shape across species and populations in a radiation of Diaptomid copepods

description: AbstractInter and intra-population variation in morphological traits, such as body size and shape, provides important insights into the ecological importance of individual natural populations. The radiation of Diaptomid species (~400 species) has apparently produced little morphological differentiation other than those in secondary sexual characteristics, suggesting sexual, rather than ecological, selection has driven speciation. This evolutionary history suggests that species, and conspecific populations, would be ecologically redundant but recent work found contrasting ecosystem effects among both species and populations. This study provides the first quantification of shape variation among species, populations, and/or sexes (beyond taxonomic illustrations and body size measurements) to gain insight into the ecological differentiation of Diaptomids. Here we quantify the shape of five Diaptomid species (family Diaptomidae) from four populations each, using morphometric landmarks on the prosome, urosome, and antennae. We partition morphological variation among species, populations, and sexes, and test for phenotype-by-environment correlations to reveal possible functional consequences of shape variation. We found that intraspecific variation was 18-35% as large as interspecific variation across all measured traits. Interspecific variation in body size and relative antennae length, the two traits showing significant sexual dimorphism, were correlated with lake size and geographic location suggesting some niche differentiation between species. Observed relationships between intraspecific morphological variation and the environment suggest that divergent selection in contrasting lakes might contribute to shape differences among local populations, but confirming this requires further analyses. Our results show that although Diaptomid species differ in their reproductive traits, they also differ in other morphological traits that might indicate ecological differences among species and populations.
DOI: 10.5683/sp2/ywkgtx
title: Data from: Variation in offspring development is driven more by weather and maternal condition than predation risk

description: Abstract1. Variation in offspring development is expected to be driven by constraints on resource allocation between growth and maintenance (e.g., thermoregulation). Rapid post-natal development decreases predation risk, while inclement weather likely prolongs development. For taxa with parental care, parental behaviour may buffer offspring against some extrinsic drivers. 2. Using a 7-year dataset from an alpine population of horned lark Eremophila alpestris, a ground-nesting songbird in northern British Columbia, Canada, we investigated multiple potential drivers of variation in incubation and nestling development duration. 3. Using path analysis, we evaluated the direct effects of weather, predation risk, and parental care on offspring development, as well as, indirect developmental ‘carry-over’ effects of conditions during incubation on the nestling period. 4. Nestling period duration varied by nearly 100% (7–13 days) and incubation duration by 40% (10–14 days). Cold ambient temperatures late in the nestling period prolonged development by 1 day for every 2 days below 10°C; particularly when combined with heavy precipitation. Rapid nestling development was associated with high predation risk, and prolonging development incurred a nest survival cost (–2.3%/day). Females in good condition created nest environments that promoted rapid nestling development periods (average = 8–9 days) compared to poor condition females during harsh, early-season conditions (10–11 days), indicating buffering capabilities against environmental constraints. Incubation duration was only weakly correlated with fledging age (r = –0.21) suggesting minimal developmental carry-over effects. 5. Given high nest predation risk, immediate fitness benefits can be derived by overcoming environmental constraints and reducing development time. While predation risk was influential, inclement weather and maternal condition had stronger effects on within-population variation in development time. We highlight the importance of addressing multiple drivers of variation in key life-history traits and provide context for understanding life-history theory under changing environmental conditions.
DOI: 10.5683/sp2/abf5jf
title: Data from: Variation in parent-offspring kinship in socially monogamous systems with extra-pair reproduction and inbreeding

description: AbstractFemale extra-pair reproduction in socially monogamous systems is predicted to cause cuckolded socially-paired males to conditionally reduce paternal care, causing selection against extra-pair reproduction and underlying polyandry. However, existing models and empirical studies have not explicitly considered that cuckolded males might be related to their socially-paired female and/or to her extra-pair mate, and therefore be related to extra-pair offspring that they did not sire but could rear. Selection against paternal care, and hence against extra-pair reproduction, might then be weakened. We derive metrics that quantify allele-sharing between within-pair and extra-pair offspring and their mother and her socially-paired male in terms of coefficients of kinship and inbreeding. We use song sparrow (Melospiza melodia) paternity and pedigree data to quantify these metrics, and thereby quantify the joint effects of extra-pair reproduction and inbreeding on a brood's total allelic value to its socially-paired parents. Cuckolded male song sparrows were almost always detectably related to extra-pair offspring they reared. Consequently, although brood allelic value decreased substantially following female extra-pair reproduction, this decrease was reduced by within-pair and extra-pair reproduction among relatives. Such complex variation in kinship within nuclear families should be incorporated into models considering co-evolutionary dynamics of extra-pair reproduction, parental care and inbreeding.
DOI: 10.5683/sp2/rveqbi
title: Data from: Vertical partitioning between sister species of Rhizopogon fungi on mesic and xeric sites in an interior Douglas-fir forest

description: AbstractUnderstanding ectomycorrhizal fungal (EMF) community structure is limited by a lack of taxonomic resolution and autecological information. Rhizopogon vesiculosus and R. vinicolor (Basidiomycota) are morphologically and genetically related species. They are dominant members of interior Douglas-fir (Pseudotsuga menziesii var. glauca) EMF communities, but mechanisms leading to their coexistence are unknown. We investigated the microsite associations and foraging strategy of individual R. vesiculosus and R. vinicolor genets. Mycelia spatial patterns, pervasiveness and root colonization patterns of fungal genets were compared between Rhizopogon species and between xeric and mesic soil moisture regimes. Rhizopogon spp. mycelia were systematically excavated from the soil and identified using microsatellite DNA markers. Rhizopogon vesiculosus mycelia occurred at greater depth, were more spatially pervasive, and colonized more tree roots than R. vinicolor mycelia. Both species were frequently encountered in organic layers and between the interface of organic and mineral horizons. They were particularly abundant within microsites associated with soil moisture retention. The occurrence of R. vesiculosus shifted in the presence of R. vinicolor towards mineral soil horizons, where R. vinicolor was mostly absent. This suggests that competition and foraging strategy may contribute towards the vertical partitioning observed between these species. R. vesiculosus and R. vinicolor mycelia systems occurred at greater mean depths and were more pervasive in mesic plots compared to xeric plots. The spatial continuity and number of trees colonized by genets of each species did not significantly differ between soil moisture regimes.
DOI: 10.5683/sp2/rdfv9c
title: Data from: Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

description: AbstractThe ecological importance of viruses is now widely recognized, yet our limited knowledge of viral sequence space and virus-host interactions precludes accurate prediction of their roles and impacts. Here we mined publicly available bacterial and archaeal genomic datasets to identify 12,498 high‑confidence viral genomes linked to their microbial hosts. These data augment public datasets 10-fold, provide first viral sequences for 13 new bacterial phyla including ecologically abundant phyla, and help taxonomically identify 7-38% of 'unknown' sequence space in viromes. Genome- and network-based classification was largely consistent with accepted viral taxonomy and suggested that (i) 264 new viral genera were identified (doubling known genera) and (ii) cross-taxon genomic recombination is limited. Further analyses provided empirical data on extrachromosomal prophages and co‑infection prevalences, as well as evaluation of in silico virus-host linkage predictions. Together these findings illustrate the value of mining viral signal from microbial genomes.
DOI: 10.5683/sp2/po5ycv
title: Data from: Warming alters food web-driven changes in the CO2 flux of experimental pond ecosystems

description: AbstractEvidence shows the important role biota play in the carbon cycle, and strategic management of plant and animal populations could enhance CO2 uptake in aquatic ecosystems. However, it is currently unknown how management-driven changes to community structure may interact with climate warming and other anthropogenic perturbations to alter CO2 fluxes. Here we showed that under ambient water temperatures, predators (three-spined stickleback) and nutrient enrichment synergistically increased primary producer biomass, resulting in increased CO2 uptake by mesocosms in early dawn. However, a 3°C increase in water temperatures counteracted positive effects of predators and nutrients, leading to reduced primary producer biomass and a switch from CO2 influx to efflux. This confounding effect of temperature demonstrates that climate scenarios must be accounted for when undertaking ecosystem management actions to increase biosequestration.
DOI: 10.5683/sp2/hupmuy
title: Data from: Weak coordination between leaf structure and function among closely related tomato species

description: AbstractTheory predicts that natural selection should favor coordination between leaf physiology, biochemistry and anatomical structure along a functional trait spectrum from fast, resource-acquisitive syndromes to slow, resource-conservative syndromes. However, the coordination hypothesis has rarely been tested at a phylogenetic scale most relevant for understanding rapid adaptation in the recent past or for the prediction of evolutionary trajectories in response to climate change. We used a common garden to examine genetically based coordination between leaf traits across 19 wild and cultivated tomato taxa. We found weak integration between leaf structure (e.g. leaf mass per area) and physiological function (photosynthetic rate, biochemical capacity and CO2 diffusion), even though all were arrayed in the predicted direction along a ‘fast–slow’ spectrum. This suggests considerable scope for unique trait combinations to evolve in response to new environments or in crop breeding. In particular, we found that partially independent variation in stomatal and mesophyll conductance may allow a plant to improve water-use efficiency without necessarily sacrificing maximum photosynthetic rates. Our study does not imply that functional trait spectra, such as the leaf economics spectrum, are unimportant, but that many important axes of variation within a taxonomic group may be unique and not generalizable to other taxa.
DOI: 10.5683/sp2/j2zx8w
title: Data from: Weak habitat isolation in a threespine stickleback (Gasterosteus spp.) species pair

description: AbstractReproductive isolation is central to the study of speciation. Multiple isolating barriers may prevent species from hybridizing, although their individual strength and the interactions between them are rarely measured. We quantified habitat isolation in a recently diverged threespine stickleback species pair (Gasterosteus aculeatus complex) and controlled for any such interactions. Using enclosures in an outdoor pond, we confirm that males of the two species strongly prefer different nesting habitats: limnetic males build nests in open habitats, whereas benthic males nest under vegetation. However, forcing males to nest in their nonpreferred habitat did not reduce the probability of spawning by females. As a result, habitat isolation between the species is estimated to be weak. We compared the strength of habitat isolation estimated in the present study with estimates of other behavioural barriers using previously published data. We discovered that, although total mating isolation between the species is strong, the contributions of differences in body size and male nuptial colour are similarly individually weak. Instead, interactions with other, undetermined species-specific traits were responsible for most of the isolation resulting from differences in body size and, in benthics, colour. This is one of the first attempts to estimate individual isolating barriers at the same time as controlling for interactions.
DOI: 10.5683/sp2/qn6eil
title: Data from: When should we expect early bursts of trait evolution in comparative data? Predictions from an evolutionary food web model

description: AbstractConceptual models of adaptive radiation predict that competitive interactions among species will result in an early burst of speciation and trait evolution followed by a slowdown in diversification rates. Empirical studies often show early accumulation of lineages in phylogenetic trees, but usually fail to detect early bursts of phenotypic evolution. We use an evolutionary simulation model to assemble food webs through adaptive radiation, and examine patterns in the resulting phylogenetic trees and species' traits (body size and trophic position). We find that when foraging trade-offs result in food webs where all species occupy integer trophic levels, lineage diversity and trait disparity are concentrated early in the tree, consistent with the early burst model. In contrast, in food webs in which many omnivorous species feeding at multiple trophic levels, high levels of turnover of species' identities and traits tends to eliminate the early burst signal. These results suggest testable predictions about how the niche structure of ecological communities may be reflected by macroevolutionary patterns.