cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8br13
title: Data from: Individual growth as a non-dietary determinant of the isotopic niche metrics

description: 1. Quantitative analytical approaches for isotopic niche analysis in the
 trophic diversity studies are proliferating rapidly; however, the
 assumptions behind the isotopic niche applications are rarely tested. One
 of the main assumptions is independence of the niche metrics and
 physiological status of the animals. The aim of this experimental study
 was to test the relationship between growth and Layman’s metrics of
 isotopic niche in consumers eating the same food but in different
 quantities and growing at different rates. 2. Based on research indicating
 that individual variability in isotopic fractionation increases under
 suboptimal conditions, I hypothesized that a group of consumers
 originating from the same population and exposed to food limitation would
 have greater estimates of the niche breadth and diversity as a result of
 higher inter-individual variability in growth rate and stable isotope
 signatures than in non-limiting feeding conditions. This hypothesis was
 tested using Baltic mysids Neomysis integer fed isotopically uniform diet
 under laboratory conditions and analyzing individual growth and stable
 isotope signature in concert. 3. As hypothesized, mysid growth rate was a
 significant negative predictor of most niche metrics. These effects were
 related to both increased inter-individual variability and higher trophic
 fractionation in malnourished animals, whereas in actively growing mysids
 lower fractionation was observed together with lower values for niche
 size, isotopic range and trophic diversity. 4. These findings challenge
 how we interpret the intrapopulation isotopic variance and evaluate
 isotopic evidence of individual specialization and call for integrated
 approaches for isotopic niche and growth assessment.
description: Experimental data on
 growth, mortality, elemental composition and stable isotope
 compositionIndividual data on
 survival, growth, %C, %N, C:N, d13C and d15N in Neomysis integer fed
 Artemia in different amounts.experimental.data.csv
DOI: 10.5061/dryad.62517nb
title: Data from: Carnivory maintains cranial dimorphism between males and females: evidence for niche divergence in extant Musteloidea

description: The evolution and maintenance of sexual dimorphism has long been
 attributed to sexual selection. Niche divergence, however, serves as an
 alternative but rarely tested selective pressure also hypothesized to
 drive phenotypic disparity between males and females. We reconstructed
 ancestral social systems and diet and used Ornstein-Uhlenbeck (OU)
 modeling approaches to test whether niche divergence is stronger than
 sexual selection in driving the evolution of sexual dimorphism in cranial
 size and bite force across extant Musteloidea. We found that multi-peak OU
 models favored different dietary regimes over social behavior and that the
 greatest degree of cranial size and bite force dimorphism were found in
 terrestrial carnivores. Because competition for terrestrial vertebrate
 prey is greater than other dietary groups, increased cranial size and bite
 force dimorphism reduces dietary competition between the sexes. In
 contrast, neither dietary regime nor social system influenced the
 evolution of sexual dimorphism in cranial shape. Furthermore, we found
 that the evolution of sexual dimorphism in bite force is influenced by the
 evolution of sexual dimorphism in cranial size rather than cranial shape.
 Overall, our results highlight niche divergence as an important mechanism
 that maintains the evolution of sexual dimorphism in musteloids.
description: Raw
 dataSexual dimorphism
 metrics of cranial size, cranial shape, and bite force.Dryad_data.csv
DOI: 10.5061/dryad.364pj
title: Data from: Flight-induced changes in gene expression in the Glanville fritillary butterfly

description: Insect flight is one of the most energetically demanding activities in the
 animal kingdom, yet for many insects flight is necessary for reproduction
 and foraging. Moreover, dispersal by flight is essential for the viability
 of species living in fragmented landscapes. Here, working on the Glanville
 fritillary butterfly (Melitaea cinxia), we use transcriptome sequencing to
 investigate gene expression changes caused by 15 min of flight in two
 contrasting populations and the two sexes. Male butterflies and
 individuals from a large metapopulation had significantly higher peak
 flight metabolic rate (FMR) than female butterflies and those from a small
 inbred population. In the pooled data, FMR was significantly positively
 correlated with genome-wide heterozygosity, a surrogate of individual
 inbreeding. The flight experiment changed the expression level of 1513
 genes, including genes related to major energy metabolism pathways,
 ribosome biogenesis and RNA processing, and stress and immune responses.
 Males and butterflies from the population with high FMR had higher basal
 expression of genes related to energy metabolism, whereas females and
 butterflies from the small population with low FMR had higher expression
 of genes related to ribosome/RNA processing and immune response. Following
 the flight treatment, genes related to energy metabolism were generally
 down-regulated, while genes related to ribosome/RNA processing and immune
 response were up-regulated. These results suggest that common molecular
 mechanisms respond to flight and can influence differences in flight
 metabolic capacity between populations and sexes.
description: sample
 informationInformation on the
 samples used in the study, including sample origin, sex, phenotypic
 measurements (pupal and adult weight, flight metabolic rate), treatments,
 and GEO accession numbers for two libraries used in RNA-seq
 analysis.sample_information.txt
DOI: 10.5517/ccdc.csd.cc2p7v0t
title: CCDC 2480186: Experimental Crystal Structure Determination

description: Related Article: Zongsu Han, Kun-Yu Wang, Jiatong Huo, Wenyue Cui, Zhaoyi Liu, Yihao Yang, Rong-Ran Liang, Wei Shi, Hong-Cai Zhou|2026|J.Am.Chem.Soc.|||doi:10.1021/jacs.5c20085
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5061/dryad.7q3n51j
title: Data from: Colonization across gradients of risk and reward: nutrients and predators generate species-specific responses among aquatic insects

description: 1. Predation risk and resource abundance are two primary characteristics
 that determine species abundances and community composition. Colonizing
 organisms should attempt to minimize the risk of mortality and maximize
 growth through selection of patches with the highest expected fitness.
 However, maximizing fitness across multiple gradients of patch quality
 involves accurate cue assessment, integration, and behavioral responses
 that consider multiple factors that affect fitness simultaneously. 2. Our
 goal was to simultaneously and factorially assess the effects of predation
 risk and resource abundance among an assemblage of aquatic insects to
 determine the relative importance of each factor, and whether the two
 factors interact to affect colonization, oviposition, and community
 assembly. 3. We conducted a field mesocosm experiment in which we crossed
 predator density (0, 1, 2 fish, Fundulus chrysotus) with supplemental
 nutrient abundance (0, 4, 8 g rabbit chow) in a 3 × 3 factorial design. We
 then assayed colonization by natural populations of aquatic beetles and
 oviposition by Culex mosquitoes. 4. We observed species-specific
 responses, with many species avoiding fish and some selecting habitats
 with more nutrients. Nutrients and predator presence only interactively
 affected oviposition by Culex mosquitoes, and the effect of fish presence
 exceeded that of nutrients in all but one analysis. 5. Our results
 illustrate the primacy of predation risk in generating colonization
 patterns and structuring communities in aquatic habitats, but that
 colonization responses to variation in multiple components of patch
 quality are often species-specific. Simultaneous assessments of multiple
 aspects of patch quality allow for the determination of potential
 interactions among cue sources and the relative importance of various
 patch characteristics to colonizers.
description: Pintar et al. 2018 Funct
 Ecol dataData from Pintar,
 Matthew R., Jason R. Bohenek, Lauren L. Eveland, and William J.
 Resetarits, Jr. 2018. Colonization across gradients of risk and reward:
 nutrients and predators generate species-specific responses among aquatic
 insects. Functional Ecology. See the README for details about the data
 file contents.
DOI: 10.5061/dryad.nn2j150
title: Data from: Delaying conservation actions matters for species vulnerable to climate change

description: 1. Most climate change adaptation efforts emphasize where to implement
 management actions, whereas timing remains largely overlooked. The rate of
 modern climate change introduces urgency in evaluating whether delaying
 conservation actions compromises their efficacy for reaching important
 conservation targets. 2. We evaluated the importance of multiple climate
 change adaptation strategies including timing of actions on preventing
 extinctions for a threatened climate-sensitive species, the Eastern
 Massasauga rattlesnake (Sistrurus catenatus). We parameterised a
 range-wide population viability analysis model that integrated climate
 change vulnerability components of sensitivity, exposure, and adaptive
 capacity. We related demographic sensitivities to drought events and
 human-modified land cover to assess vulnerability to future climate
 change. Using simulations, we assessed the efficacy and trade-offs
 associated with alternative climate adaptation strategies aimed at
 maximizing the number of future populations including when to initiate
 conservation actions, duration of management, number of managed
 populations, and local management effectiveness. 3. Population-level
 projections under future climate change scenarios revealed a broad-scale
 pattern of range contraction in the southwestern portion of the current
 range. Along the extinction gradient, we identified demographic
 strongholds and refugia critical for population persistence under climate
 change as well as populations at high risk of extinction and candidates
 for climate change adaptation actions. 4. In the context of future climate
 change, the timing of conservation actions was crucial; acting earlier
 maximised chances of achieving conservation targets. Even considering
 uncertainty in climate change projections, delaying actions was less
 efficient and introduced undesirable trade-offs including the need to
 implement conservation actions for longer or targeting more populations to
 achieve a similar conservation target. 5. Synthesis and applications. Our
 findings highlight how acting quickly reduces risk and improves outcomes
 for a highly vulnerable species under future climate change. Climate
 change vulnerability assessments for species and ecosystems require
 translation of model-based outputs into tractable information for climate
 change adaptation planning. Quantifying trade-offs associated with the
 multi-dimensional decision space of species conservation and management is
 a critical step in climate change adaptation.
description: Data from: Delaying
 conservation actions matters for species vulnerable to climate
 changezipped folder contains 2
 files: a csv file containing Eastern Massasauga Rattlesnake survival data
 and environmental covariates, and R code to perform simulations evaluating
 trade-offs between climate change adaptation decision points for
 conservation of threatened species.Naujokaitis-Lewis_etal_JAppEco_SuppInfo.zip
DOI: 10.5061/dryad.085jj60
title: Data from: How quantitative is metabarcoding: a meta-analytical approach

description: Metabarcoding has been used in a range of ecological applications such as
 taxonomic assignment, dietary analysis, and the analysis of environmental
 DNA. However, after a decade of use in these applications there is little
 consensus on the extent to which proportions of reads generated
 corresponds to the original proportions of species in a community. To
 quantify our current understanding we conducted a structured review and
 meta-analysis. The analysis suggests that a weak quantitative relationship
 may exist between the biomass and sequences produced (slope =0.52 ±0.34,
 p&lt;0.01)), albeit it with a large degree of uncertainty. None of the
 tested moderators: sequencing platform type, the number of species used in
 a trial, or the source of DNA were able to explain the variance. Our
 current understanding of the factors affecting the quantitative
 performance of metabarcoding is still limited: additional research is
 required before metabarcoding can be confidently utilised for quantitative
 applications. Until then, we advocate the inclusion of mock communities
 when metabarcoding as this facilitates direct assessment of the
 quantitative ability of any given study.
description: Effect sizes, and
 confidence intervals for meta-analysisThis file contains all
 the effect sizes, confidence intervals, and grouping variables that were
 used in the meta-analysis.slopes_2.csv
DOI: 10.5061/dryad.b52n66j
title: Data from: A complex pattern of post-divergence expansion, contraction, introgression and asynchronous responses to Pleistocene climate changes in two Dipelta sister species from western China

description: The well-known vicariance and dispersal models dominate in understanding
 the allopatric pattern for related species and presume the simultaneous
 occurrence of speciation and biogeographic events. However, the formation
 of allopatry may postdate the species divergence. We examined this
 hypothesis using DNA sequence data from 3 chloroplast fragments and 5
 nuclear loci of Dipelta floribunda and D. yunnanensis, two shrub species
 with the circum Sichuan Basin distribution, combining the climatic niche
 modeling approach. The best-fit model supported by the approximate
 Bayesian computation (ABC) analysis indicated that, D. floribunda and D.
 yunnanensis diverged during the mid-Pleistocene period, consistent with
 the largest glacial period in the Qinghai-Tibet Plateau (QTP). The
 historically inter-specific gene flow was identified but seemed to have
 ceased after the last interglacial period (LIG), when the range of D.
 floribunda moved northward from the south of the Sichuan Basin. Further,
 populations of D. floribunda had expanded obviously in the north of the
 Sichuan Basin after the last glacial maximum (LGM). Relatively, the range
 of D. yunnanensis expanded before the LGM, reduced during the post-LGM
 especially in the north of the Sichuan Basin, reflecting the asynchronous
 responses of related species to the contemporary climate changes. Our
 results suggested that complex topography should be considered in
 understanding the distributional patterns even for closely related species
 and their demographic responses.
description: MG993626-MG994796all DNA sequencesMaxEnt input filesMaxEnt input files of Dipelta floribunda Maxim. and Dipelta yunnanensis FranchDFDY.csv
DOI: 10.5061/dryad.6d831
title: Data from: Environmental effects on fine-scale spatial genetic structure in four Alpine keystone forest tree species

description: Genetic responses to environmental changes take place at different spatial
 scales. While the effect of environment on the distribution of species’
 genetic diversity at large geographical scales has been the focus of
 several recent studies, its potential effects on genetic structure at
 local scales are understudied. Environmental effects on fine-scale spatial
 genetic structure (FSGS) were investigated in four Alpine conifer species
 (five to eight populations per species) from the eastern Italian Alps.
 Significant FSGS was found for 11 out of 25 populations. Interestingly, we
 found no significant differences in FSGS across species but great
 variation among populations within species, highlighting the importance of
 local environmental factors. Inter-annual variability in spring
 temperature had a small but significant effect on FSGS of Larix decidua,
 probably related to species-specific life-history traits. For Abies alba,
 Picea abies and Pinus cembra, linear models identified spring
 precipitation as a potentially relevant climate factor associated with
 differences in FSGS across populations; however, models had low
 explanatory power and were strongly influenced by a P. cembra outlier
 population from a very dry site. Overall, the direction of the identified
 effects is according to expectations, with drier and more variable
 environments increasing FSGS. Underlying mechanisms may include
 climate-related changes in the variance of reproductive success and/or
 environmental selection of specific families. This study provides new
 insights on potential changes in local genetic structure of four Alpine
 conifers in the face of environmental changes, suggesting that new
 climates, through altering FSGS, may also have relevant impacts on plant
 microevolution.
description: Environmental
 dataEnvironmental data used
 in models associating climate with fine-scale genetic structure
 (FSGS).Environmental_data_in.txt
DOI: 10.5061/dryad.d3d36
title: Data from: Temporal dynamics of direct reciprocal and indirect effects in a host-parasite network

description: 1. Temporal variation in the direct and indirect influence that hosts and
 parasites exert on each other is still poorly understood. However,
 variation in species’ influence due to species and interactions turnover
 can have important consequences for host community dynamics and/or for
 parasite transmission dynamics, and eventually for the risk of zoonotic
 diseases. 2. We used data on a network of small mammals and their
 ectoparasites surveyed over six years to test hypotheses exploring (1) the
 temporal variability in direct and indirect influences species exert on
 each other in a community, and (2) the differences in temporal variability
 of direct/indirect influences between temporally persistent and temporally
 intermittent species. 3. We modelled the temporal variation in: (1) direct
 reciprocal influence between hosts and parasites (hosts providing
 resources to parasites and parasites exploiting the resources of hosts),
 using an asymmetry index; and (2) indirect influence among species within
 a community (e.g. facilitation of parasite infestation by other
 parasites), using betweenness centrality. We also correlated asymmetry and
 centrality to examine the relationship between them. 4. Network dynamics
 was determined by temporally persistent species but even those species had
 strong among-species heterogeneity in the temporal variation of the
 direct/indirect effects they exerted. In addition, there was a significant
 positive linear correlation between asymmetry and centrality. 5. We
 conclude that the temporal dynamics of host-parasite interactions is
 driven by temporally persistent hosts. However, even within this group of
 persistent species, some exhibit large temporal variation, such that the
 functional roles they play (e.g. in promoting parasite transmission)
 change over time. In addition, parasites having a large negative impact on
 hosts are also those facilitating the spread of other parasites through
 the entire host community. Our results provide new insights into community
 dynamics and can be applied in the management of antagonistic networks
 aimed at preventing disease outbreaks.
description: 6-year host-parasite
 network dataMatrices of fleas and
 gamasid mites collected from the bodies of small mammalian hosts in the
 vicinity of the city of Novosibirsk (Russia; 54°51'16.92"N, 83°
 6'24.48"E) during a six-year (1982-1987) survey. Matrix values
 are the mean abundance of an ectoparasite species on a host species, per
 year. Hosts are in rows, Ectoparasites are in columnsPilosof_et_al_2013_JAE.zip
DOI: 10.5061/dryad.n33g2
title: Data from: Linking species thermal tolerance to elevational range shifts in upland dung beetles

description: Climate warming has been proposed as the main cause of the recent range
 shifts seen in many species. Although species' thermal tolerances are
 thought to play a key role in determining responses to climate change,
 especially in ectotherms, empirical evidence is still limited. We
 investigate the connection between species' thermal tolerances,
 elevational range and shifts in the lower elevational limit of dung beetle
 species (Coleoptera, Aphodiidea) in an upland region in the northwest of
 England. We measured thermal tolerances in the laboratory, and used
 current and historical distribution data to test specific hypotheses about
 the area's three dominant species, particularly the species most
 likely to suffer from warming: Agollinus lapponum. We found marked
 differences between species in their minimum and maximum thermal tolerance
 and in their elevational range and patterns of abundance. Overall,
 differences in thermal limits among species matched the abundance patterns
 along the elevation gradient expected if distributions were constrained by
 climate. A. lapponum abundance increased with elevation and this species
 showed lower maximum and minimum thermal limits than Acrossus depressus,
 for which abundance declined with elevation. Consistent with lower
 tolerance to high temperature, we recorded an uphill retreat of the low
 elevation limit of A. lapponum (177 m over 57 years) in line with the
 increase in summer temperature observed in the region over the same
 period. Moreover, this species has been replaced at low and mid-elevations
 by the other two warm-tolerant species (A. depressus and Agrilinus ater).
 Our results provide empirical evidence that species' thermal
 tolerance constrains elevational ranges and contributes to explain the
 observed responses to climate warming. A mechanistic understanding of how
 climate change directly affects species, such as the one presented here,
 will provide a robust base to inform predictions of how individual species
 and whole assemblages may change in the future.
description: "Current"
 beetle distributions at Moor House NNR (2008 and 2013)Abundance and
 presence/absence data for dung beetle species at Moor House NNR in 2008
 and 2013 across elevation gradients from 300 m a.s.l.Current_distributions.csvThermal tolerance dataData from thermal tolerance testingThermal_tolerance.csv