cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.145mg74
title: Data from: Sperm head abnormalities are associated with excessive omega-6 fatty acids in two finch species feeding on sunflower seeds

description: In a rapidly changing world, it is important to understand how urban
 environments impact wildlife. For example, supplementary feeding of birds,
 though well‐intended, might have unexpected negative effects on the health
 of individual animals. Sunflower seeds are commonly provided in garden
 bird feeders, but they contain high levels of linoleic acid (LA), an
 omega‐6 polyunsaturated fatty acid (PUFA). Omega‐6 PUFAs are associated
 with increased oxidative stress, which can damage cell membranes, and in
 particular sperm cells. We assessed the level of LA in the blood of two
 seed‐eating finch species, greenfinches Chloris chloris and hawfinches
 Coccothraustes coccothraustes, caught in 2015 and 2017 in environments
 with direct access to sunflower seed feeders (Norway), and compared these
 with the level of LA in a smaller number of individuals sampled in 2015 in
 a rural area with low incidence of sunflower seed feeders (Czech
 Republic). Furthermore, we investigated the relationship between the
 proportion of LA in the blood (as well as the proportion of 10 other fatty
 acids) and sperm quality (the frequency of sperm head abnormalities and
 sperm swimming speed). We found that both finch species, but particularly
 greenfinches caught near feeders, exhibited levels of LA that were
 considerably higher than those previously reported for other wild birds.
 We also found that the proportion of LA was positively correlated with the
 frequency of abnormal sperm heads (sperm missing the acrosome), while
 there was no significant effect of fatty acid composition on sperm
 swimming speed. Our results indicate that the sperm quality of finches may
 be negatively affected by a high intake of sunflower seeds, adding to a
 growing body of research showing that supplementary feeding may have
 detrimental side effects for urban animals. This is particularly relevant
 for the greenfinch, which is currently affected by disease and population
 declines.
description: Fatty acid and damage
 dataSperm damage rates and
 fatty acid for greenfinches and hawfinches, including accession number at
 the Natural History Museum of OsloFinchesDamageData.csvSingle cell VCL dataVelocity data for all single sperm cellssinglecellVCLdata.csvFatty acid data for six bird speciesFatty acid data for six bird species, including accession numbers at the Natural History Museum of OsloSixSpeciesFAs.csv
DOI: 10.5061/dryad.16837bf
title: Data from: The distributions of morphologically specialized hummingbirds coincide with floral trait matching across an Andean elevational gradient

description: Morphological trait matching between species affects resource partitioning
 in mutualistic systems. Yet, the determinants of spatial variation in
 trait matching remain largely unaddressed. Here, we generate a hypothesis
 that is based on the geographical distributions of species morphologies.
 To illustrate our hypothesis, as a study system we use hummingbirds in the
 tropical Andes. Hummingbirds with specialized morphologies (i.e. long or
 curved bills) may forage on flowers that are inaccessible to hummingbirds
 with generalized bill morphologies (i.e. small-to-medium-sized bills with
 no curvature), yet the vast majority of hummingbirds have generalized bill
 morphologies. Thus, we propose that trait matching across space is
 determined by the distribution of morphological specialists. In the Andes,
 we observe the richness of specialized hummingbird morphotypes to peak at
 high and low elevations. Therefore, we hypothesize that trait matching
 should be most influential in predicting pairwise interactions at high and
 low elevations. We illustrate our hypothesis by field observations along
 an elevational gradient in Podocarpus National Park (Ecuador). Using
 Bayesian hierarchical modelling of interaction frequencies in combination
 with network analyses, we found that hummingbirds at high and low
 elevations contributed to resource partitioning by foraging on
 morphologically close-matching flowers. Moreover, at high and low
 elevations, hummingbirds with specialized morphologies showed a stronger
 tendency to visit close-matching flowers than morphological
 non-specialists did. In contrast, at mid-elevations, hummingbirds were not
 attracted to morphologically close-matching flowers. These results suggest
 that the spatial distribution of specialized morphotypes determines trait
 matching and the partitioning of interactions within hummingbird-plant
 communities.
description: Hummingbird-plant
 InteractionsInteractions.xlsxPlant abundancesHummingbird abundancesPlant morphologies
DOI: 10.5061/dryad.sq7072h
title: Data from: Cats under cover: habitat models indicate a high dependency on woodlands by Atlantic Forest felids

description: Four Neotropical small and medium felids—the ocelot, jaguarundi, margay
 and southern tiger cat—have overlapping geographic distributions in the
 endangered Atlantic Forest. Local studies show that these felids avoid
 areas with high human impact, but the three smaller ones use
 human-modified areas more frequently than do ocelots. To understand how
 landscape changes affect the habitat distribution of these four felids in
 the Atlantic Forest of Argentina, we used maximum entropy models to
 analyze the effect of environmental and anthropogenic factors. We
 estimated niche breadth and overlap among these felids. The conversion of
 the native forest to land uses without trees was the most important
 variable that determined the habitat distribution of the four species. For
 all four species the optimal habitat covered less than 1/3 of the study
 area and corresponds mainly to the native forest areas. Nearly 50 percent
 of these areas had some level of protection. The niche width was higher
 for the small felids than for ocelots. Niche overlap was high for all
 species pairs, but higher among the small felids and lower for each of
 these with the ocelot. The four felids were negatively affected by native
 forest loss, with ocelots being more sensitive than the smaller felids.
 The conversion of unprotected forest areas to other types of land uses
 would imply a greater habitat loss for these felids. The protection of
 current remnants of Atlantic Forest in Argentina is important for the
 long-term conservation of the four felids.
description: Cruz et al 2019-
 Presence dataPresence data for four
 small and medium felids of the Atlantic Forest of Argentina. These data
 were obtained through the following sampling methods: camera-trap records
 from the authors’ own and colleagues’ systematic and non-systematic
 surveys, roadkills, reliable sightings (i.e. animals seen by experts or a
 photograph allowing identification by experts), and feces identified by
 DNA analyses.
DOI: 10.5061/dryad.kq27n36
title: Data from: Physical linkage and mate preference generate linkage disequilibrium for behavioral isolation in two parapatric crickets

description: Behavioral isolation is a potent barrier to gene flow and a source of
 striking diversity in the animal kingdom. However, it remains unclear if
 the linkage disequilibrium (LD) between sex-specific traits required for
 behavioral isolation results mostly from physical linkage between signal
 and preference loci or from directional mate preferences. Here, we test
 this in the field crickets Gryllus rubens and G. texensis. These closely
 related species diverged with gene flow and have strongly diverged songs
 and preference functions for the mate calling song rhythm. We map
 quantitative trait loci for signal and preference traits (pQTL) as well as
 for gene expression associated with these traits (eQTL). We find strong,
 positive genetic covariance between song traits and between song and
 preference. Our results show that this is in part explained by incomplete
 physical linkage: although both linked pQTL and eQTL couple male and
 female traits, major effect loci for different traits were never on the
 same chromosome. We suggest that the finely-tuned, highly divergent
 preference functions are likely an additional source of LD between male
 and female traits in this system. Furthermore, pleiotropy of gene
 expression presents an underappreciated mechanism to link sexually
 dimorphic phenotypes.
description: vcf_unfilteredeach VCF file contains the unfiltered SNPs (output from GATK) for each backcross family including parents and grandparents. For nomenclature please see supplemental figure S1 and for ID information see the VCF_IDs spreadsheetVCF_idsSample IDs and information.Gryllus QTL pedigreeIDs of backcrossed individuals and their parentageGryllusQTLpedigree.txtMale PhenotypesPhenotypic data from the backcrossed malesGryllusQTLmalePhenotypes.txtFemale PhenotypesPhenotypic data from the backcrossed femalesGryllusQTLfemalePhenotypes.txtfemale QTL objectr/QTL object for female data (this has the genotypes, linkage map, and phenotypes; requires package r/QTL)femaleQTLobject.Rdatamale QTL objectr/QTL object for male data (this has the genotypes, linkage map, and phenotypes; requires package r/QTL)maleQTLobject.Rdatamale eQTL objectQTL object for the imported read counts ($abundance = TPM scales read counts, $counts = raw read counts, $length = transcript length) for males (requires package tximport)GryllusEQTL_maleReadCounts.RDatafemale eQTL objectQTL object for the imported read counts ($abundance = TPM scales read counts, $counts = raw read counts, $length = transcript length) for females (requires package tximport).GryllusEQTL_femaleReadCounts.RData
DOI: 10.5281/zenodo.18350478
title: KEYS_BRAND7_50F_3_23C_0k_EDLC_single
DOI: 10.5281/zenodo.18350477
title: KEYS_BRAND7_50F_3_23C_0k_EDLC_single
DOI: 10.5061/dryad.3hv23t3
title: Data from: Reductions in body size of benthic macroinvertebrates as a precursor of the Early Toarcian (Early Jurassic) extinction event in the Lusitanian Basin, Portugal

description: Reduction of body size is a common response of organisms to environmental
 stress. Studying the Early Toarcian succession in the Lusitanian Basin of
 Portugal, we tested whether the shell size of benthic marine communities
 of bivalves and brachiopods changed at and prior to the global,
 warming-related Toarcian Oceanic Anoxic Event (T-OAE). Statistical
 analyses of shell size over time show that the mean shell size of
 communities decreased significantly prior to the T-OAE. This trend is
 distinct in brachiopods and is caused by larger-sized species becoming
 less abundant over time, whereas it is not significant in bivalves,
 suggesting a decoupled response to environmental stress. Reductions in
 shell size precede the decline in standardized sample-level species
 richness associated with the Early Toarcian extinction event. Such
 decreases in the shell size of marine invertebrates, well before the onset
 of biodiversity change, suggest that reductions in body size more
 generally may be a precursor of a subsequent loss of species and turnover
 at the community-level caused by climate change. Sedimentological evidence
 is against hypoxia as a driver of extinction and preceding size decrease
 in the brachiopod fauna in the studied succession, although low oxygen
 levels are widely held responsible for elevated Early Toarcian extinction
 rates globally. Reduction of mean shell size in brachiopods but stasis in
 bivalves is difficult to explain with ocean acidification because
 experimental work shows that brachiopods can be resilient to lowered pH,
 albeit long-term metabolic costs and potential evolutionary adaptations
 are unknown. Rising Early Toarcian temperatures in the Lusitanian Basin
 seem to be a plausible factor in both diversity decline associated with
 the T-OAE as well as the preceding reductions in mean shell size because
 thermal tolerances in modern bivalves are among the highest within marine
 invertebrates.
description: Shell size measurements
 of bivalves/brachiopods from Fonte Coberta/RabacalPiazzaetal_Appendix_FINAL.xlsx
DOI: 10.5061/dryad.1c05010
title: Data from: Perceived shift of the centres of contracting and expanding optic flow fields: different biases in the lower-right and upper-right visual quadrants

description: We studied differences in localizing the centres of flow in radially
 expanding and contracting patterns in different regions of the visual
 field. Our results suggest that the perceived centre of a peripherally
 viewed expanding pattern is shifted towards the fovea relative to that of
 a contracting pattern, but only in the lower right and upper right visual
 quadrants and when a single speed gradient with appropriate overall speeds
 of the trajectories of the moving dots was used. The biases were not
 systematically related to differences of sensitivity to optic flow in
 different quadrants. Further experiments demonstrated that the biases were
 likely due to a combination of two effects: an advantage of global
 processing in favor of the lower visual hemifield and a hemispheric
 asymmetry in attentional allocation in favor of motion-induced spatial
 displacement in the right visual hemifield. The bias in the lower right
 visual quadrant was speed gradient-sensitive and could be reduced to a
 non-significant level with the usage of multiple speed gradients, possibly
 due to a special role of the lower visual hemifield in extracting global
 information from the multiple speed gradients. A holistic processing on
 multiple speed gradients, rather than a predominant processing on a single
 speed gradient, was likely adopted. In contrast, the perceived bias in the
 upper right visual quadrant was overall speed-sensitive and could be
 reduced to a non-significant level with the reduction of the overall
 speeds of the trajectories. The implications of these results for
 understanding motion-induced spatial illusions are discussed.
description: Experiment_Results
DOI: 10.5061/dryad.37rq624
title: Data from: Geographic space, relief, and soils predict plant community patterns of Asteraceae in rupestrian grasslands, Brazil

description: We investigated the effects of geographic distance and environmental
 heterogeneity on Asteraceae communities in the rupestrian grasslands of
 the Espinhaço Range, southeastern Brazil. Asteraceae species composition
 and relative abundance were sampled in 21-1 ha plots distributed across
 park conservation units, comprising an environmental gradient in soils and
 relief (elevation and slope). We found high levels of heterogeneity
 overall in assemblages of herbaceous and woody Asteraceae species at the
 intermediate spatial scale of this study (10–100 km). We found that both
 relief and soil properties (texture and total exchangeable bases)
 explained significant proportions of variation in community composition,
 suggesting that definitions or expansions of conservation units should
 span the highest possible variability in observed relief and soil values.
 We also found that Asteraceae distribution exhibited strong spatial
 structure independent of environmental variation, reinforcing the need to
 consider conservation across larger areas. Considering the dystrophic
 character of the soils found in the Espinhaço Range and the few
 differences in the fertility observed between the sampling units, our
 results also support the hypothesis that plant distributions in the
 tropics are controlled by a hierarchy of environmental gradients, where
 variables such as relief and texture are only important in low-fertility
 soils. We suggest that Asteraceae could be a model family for conservation
 planning in other countries and regions because it is particularly well
 represented in open and montane areas of the Neotropics in general.
description: herbacious
 speciesThis file contains data
 of the herbacious species - composition and abundancenão.lenhosas.ago.2017.csvwoody species composition and abundanceThis file contais data of the Asteraceae woody species - composition and abundancelenhosas.ago.2017.csvenvironment dataThis file contains data of the environment: soils variables, slope, altitudeambiente.csvgeographic coordinatesThis file contains plot geographic coordinatesespaço.csv
DOI: 10.5061/dryad.37ts86v
title: Data from: Biomass consumption by surface fires across Earth's most fire prone continent

description: Landscape fire is a key but poorly understood component of the global
 carbon cycle. Predicting biomass consumption by fire at large spatial
 scales is essential to understanding carbon dynamics and hence how fire
 management can reduce greenhouse gas emissions and increase ecosystem
 carbon storage. An Australia‐wide field‐based survey (at 113 locations)
 across large‐scale macroecological gradients (climate, productivity and
 fire regimes) enabled estimation of how biomass combustion by surface fire
 directly affects continental‐scale carbon budgets. In terms of biomass
 consumption, we found clear trade‐offs between the frequency and severity
 of surface fires. In temperate southern Australia, characterised by less
 frequent and more severe fires, biomass consumed per fire was typically
 very high. In contrast, surface fires in the tropical savannas of northern
 Australia were very frequent but less severe, with much lower consumption
 of biomass per fire (about a quarter of that in the far south). When
 biomass consumption was expressed on an annual basis, biomass consumed was
 far greater in the tropical savannas (&gt;20 times that of the far
 south). This trade‐off is also apparent in the ratio of annual carbon
 consumption to net primary production (NPP). Across Australia's
 naturally vegetated land area, annual carbon consumption by surface fire
 is equivalent to about 11% of NPP, with a sharp contrast between temperate
 southern Australia (6%) and tropical northern Australia (46%). Our results
 emphasise that fire management to reduce greenhouse gas emissions should
 focus on fire prone tropical savanna landscapes, where the vast bulk of
 biomass consumption occurs globally. In these landscapes, grass biomass is
 a key driver of frequency, intensity and combustion completeness of
 surface fires, and management actions that increase grass biomass are
 likely to lead to increases in greenhouse gas emissions from savanna
 fires.
description: Murphy et al. fuels
 datasetFuels dataset used for
 analysis
DOI: 10.5061/dryad.6mh0sv3
title: Data from: Activation mechanism of ATP-sensitive K+ channels explored with real-time nucleotide binding

description: The response of ATP-sensitive K+ channels (KATP) to cellular metabolism is
 coordinated by three classes of nucleotide binding site (NBS). We used a
 novel approach involving labeling of intact channels in a native, membrane
 environment with a non-canonical fluorescent amino acid and measurement
 (using FRET with fluorescent nucleotides) of steady-state and
 time-resolved nucleotide binding to dissect the role of NBS2 of the
 accessory SUR1 subunit of KATP in channel gating. Binding to NBS2 was
 Mg2+-independent, but Mg was required to trigger a conformational change
 in SUR1. Mutation of a lysine (K1384A) in NBS2 that coordinates bound
 nucleotides increased the EC50 for trinitrophenyl-ADP binding to NBS2, but
 only in the presence of Mg2+, indicating that this mutation disrupts the
 ligand-induced conformational change. Comparison of nucleotide-binding
 with ionic currents suggests a model in which each nucleotide binding
 event to NBS2 of SUR1 is independent and promotes KATP activation by the
 same amount.
description: Puljung_data_sets
DOI: 10.5061/dryad.302bd95
title: Data from: Connectivity explains local ant community structure in a Neotropical forest canopy: a large-scale experimental approach

description: Understanding how habitat structure and resource availability affect local
 species distributions is a key goal of community ecology. Where habitats
 occur as a mosaic, variation in connectivity among patches influences both
 local species richness and composition, and connectivity is a key
 conservation concern in fragmented landscapes. Similarly, availability of
 limiting resources frequently determines species co-existence or
 exclusion. For primarily cursorial arthropods like ants, gaps between
 neighboring trees are a significant barrier to movement through the forest
 canopy. Competition for limited resources such as nest sites also promotes
 antagonistic interactions. Lianas (woody vines) connect normally isolated
 neighboring tree crowns and often have hollow stems inhabited by ants. We
 used two large-scale liana removal experiments to determine how
 connectivity and nest site availability provided by lianas affect arboreal
 ant species richness, species composition, and β-diversity in a lowland
 tropical forest in Panama. Removing lianas from a tree crown reduced ant
 species richness up to 35%, and disproportionately affected species that
 require large foraging areas. Adding artificial connectivity to trees
 mitigated the effects of liana removal. Ant colonization of artificial
 nests was higher (73% occupied) in trees without lianas vs. trees with
 lianas (28% occupied). However, artificial nests typically were colonized
 by existing polydomous, resident ant species. As a result, nest addition
 did not affect ant community structure. Collectively, these results
 indicate that lianas are important to the maintenance of arboreal ant
 diversity specifically by providing connectivity among neighboring tree
 crowns. Anticipated increases in liana abundance in this forest could
 increase the local (tree-level) species richness of arboreal ants, with a
 compositional bias toward elevating the density of broad-ranging
 specialist predators.
description: Adams et al Ecology 2019
 final data
DOI: 10.5061/dryad.v22901d
title: Data from: Differential resource consumption in leaf litter mixtures by native and non-native amphipods

description: Leaf litter processing is an essential ecosystem function in freshwater
 systems, since much of the carbon and nutrients moving through freshwater
 food webs come from the surrounding terrestrial ecosystems. Thus, it is
 important to understand how the species performing this function differ,
 especially because many native species are being replaced by non-native
 species in aquatic ecosystems. We used a field experiment to examine leaf
 consumption rates of two common shredding macroinvertebrates (the native
 Gammarus fossarum and the non-native Gammarus roeselii). Leaves from three
 species, varying in resource quality, were added both in leaf monocultures
 and as a three-species mixture. Biomass-adjusted daily consumption rates
 were similar between the two amphipod species, and each consumed
 nitrogen-rich alder leaves faster than oak or beech leaves. However,
 because adult G. roeselii are approximately twice the size of G. fossarum,
 this led to systematic, though nonsignificant, differences in consumption
 rates at the per-capita or population level. Furthermore, we found nuanced
 effects of decomposer identity on leaf decomposition in mixtures. Only G.
 roeselii showeding increased consumption of the preferred resource (alder)
 in the mixture, while G. fossarum consumed all leaves at the same
 proportional rates as in monocultures. This is an important distinction,
 as most measures of macroinvertebrate leaf shredding are made in the
 laboratory with only a single leaf resource available. Our results, based
 on a field experiment which could control the presence of dominant
 macroinvertebrates while still providing natural, biologically realistic
 context, suggests that even functionally-similar species may subtly shift
 ecosystem processes.
description: Little_Altermatt_Aquatic_Ecology_dataThis data is organized by experimental replicate, and includes the biomass of amphipods used in each replicate, as well as the biomass of leaf litter consumed in each replicate. Code to run the analyses and produce the figures based on this data is available at https://github.com/chelseajlittle/CAGE2