cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jd2s1
title: Data from: A general-purpose spatial survey design for collaborative science and monitoring of global environmental change: the global grid

description: Recent guidance on environmental modeling and global land-cover validation
 stresses the need for a probability-based design. Additionally, spatial
 balance has also been recommended as it ensures more efficient sampling,
 which is particularly relevant for understanding land use change. In this
 paper I describe a global sample design and database called the Global
 Grid (GG) that has both of these statistical characteristics, as well as
 being flexible, multi-scale, and globally comprehensive. The GG is
 intended to facilitate collaborative science and monitoring of land
 changes among local, regional, and national groups of scientists and
 citizens, and it is provided in a variety of open source formats to
 promote collaborative and citizen science. Since the GG sample grid is
 provided at multiple scales and is globally comprehensive, it provides a
 universal, readily-available sample. It also supports uneven probability
 sample designs through filtering sample locations by user-defined strata.
 The GG is not appropriate for use at locations above ±85° because the
 shape and topological distortion of quadrants becomes extreme near the
 poles. Additionally, the file sizes of the GG datasets are very large at
 fine scale (resolution ~600 m × 600 m) and require a 64-bit integer
 representation.
description: README for Global Grid
 DatasetGG_CSV_L2_L13_201605277z archive (2.4GB) of text files in CSV format containing the Global Grid for levels 2 thru 13. Please see README file for further information on naming conventions and variables included in the files.GGe_L147z archive (3.8GB) in CSV format containing the Global Grid for eastern hemisphere, level 14.GGw_L147z archive (3.8GB) in CSV format containing the Global Grid for western hemisphere, level 14.GG_KML_201606037z archive (1.3MB) in KML format containing the Global Grid for eastern and western hemispheres at level 10 that represents terrestrial (land) locations stratified across the urban to rural gradient used in Figure 3 of Theobald 2016 paper.
DOI: 10.5061/dryad.42pg7
title: Data from: Contrasting responses of pre- and post-copulatory traits to variation in mating competition

description: 1. Original sperm competition theory assumed that males trade expenditure
 on searching for mates for expenditure on the ejaculate, and predicted
 that males should increase their expenditure on the ejaculate in response
 to increased risk of competition. A recent extension of this theory has
 modeled pre-copulatory expenditure in terms of direct contest competition,
 and predicts that when the gains from marginal investment in weaponry are
 large, males might be expected to allocate resources to armaments even at
 the expense of the ejaculate. 2. Here we examine socially cued plasticity
 in allocation to pre- (body condition) and post-copulatory (testes mass)
 traits in a male dimorphic beetle, Onthophagus taurus, where major males
 fight for access to females and minor males obtain reproductive success
 via sperm competition. Both male morphs were either reared in social
 isolation or exposed to rivals during the period of sexual maturation
 following adult emergence. 3. Testes mass was found to be insensitive to
 social cues of future mating competition for both major and minor males.
 Major males allocated more to body condition when exposed to rivals, a
 response expected for a species in which the outcome of dyadic contests
 strongly affect male reproductive success. In contrast, minor male
 allocation to condition was insensitive to social cues. 4. Our data
 illustrate how socially cued plasticity in pre- and post-copulatory traits
 can depend on the relative importance of these episodes of selection for
 individual male fitness. In O. taurus dung beetles, males strategically
 adjusted the amount of resources they allocated to winning pre-copulatory
 contests over access to females. Strategic allocation to pre-copulatory
 contest competition did not come at a cost to male investment in sperm
 competition, suggesting that males may trade investment into contest
 competition against some other life history trait, such as longevity. The
 lack of plasticity in testes size suggests that selection from sperm
 competition may be a relatively constant feature of this species mating
 system.
description: Morphological
 measurements made from male dung beetles reared under different social
 conditionsExcel spreadsheet
 containing body mass, size and testes and soma mass, and their log10
 transformed values. Data are provided for males reared under high or low
 competition environments, and males are identified as major (horned) or
 minor (hornless) males. Five outlying data points are
 highlighted.Simmons & Buzatto
 2013.xlsx
DOI: 10.5061/dryad.r0j3s
title: Data from: Biotic invasion, niche stability, and the assembly of regional biotas in deep time: comparison between faunal provinces

description: Biotic invasions in the fossil record provide natural experiments for
 testing hypotheses of niche stability, speciation, and the assembly and
 diversity of regional biotas. We compare ecologic parameters (preferred
 environment, occupancy, median abundance, rank abundance) of genera shared
 between faunal provinces during the Richmondian Biotic Invasion in the
 Late Ordovician on the Laurentian continent. Genera that spread from one
 faunal province to the other during the invasion (invading shared genera)
 have high Spearman rank correlations (&gt;0.5) in three of four
 ecologic parameters, suggesting a high level of niche stability among
 invaders. Genera that existed in both regions prior to and following the
 invasion (non-invading shared genera) have low correlations (&lt;0.3)
 and suggest niche shift between lineages that diverged at least 8 Myr
 earlier. Niche shift did not accumulate gradually over this time interval,
 but appears to have occurred in a pulse associated with the onset of the
 Taconic orogeny and the switch from warm-water to cool-water carbonates in
 southern Laurentia.
description: bighornc5_counts_PatzkowskyandHolland_2016_PaleobiologyThis file contains the collection counts for the Ordovician Horseshoe Mountain Member in the Bighorn Mountains, Wyoming.bighornc5_counts.csvbighornc5_factors_PatzkowskyandHolland_2016_PaleobiologyThis file contains the sample attributes for the Horseshoe Mountain Member collection counts.bighornc5_factors.csvC5CincyCounts_PatzkowskyandHolland_2016_PaleobiologyThis file contains the collection count data for the C5 sequence in the Cincinnatian type area.C5CincyCounts.csvsharedtaxa_ecol_param_PatzkowskyandHolland_2016_PaleobiologyThis file contains the ecological parameters shared between the Horseshoe Mountain Member in the Bighorn Mountains, WY and the C5 sequence in the Cincinnatian type area.sharedtaxa_ecol_param.csv
DOI: 10.5061/dryad.mf1ck
title: Data from: Impacts of degraded DNA on restriction enzyme associated DNA sequencing (RADSeq)

description: Degraded DNA from suboptimal field sampling is common in molecular
 ecology. However, its impact on techniques that use restriction site
 associated next-generation DNA sequencing (RADSeq, GBS) is unknown. We
 experimentally examined the effects of in situDNA degradation on data
 generation for a modified double-digest RADSeq approach (3RAD). We
 generated libraries using genomic DNA serially extracted from the muscle
 tissue of 8 individual lake whitefish (Coregonus clupeaformis) following
 0-, 12-, 48- and 96-h incubation at room temperature posteuthanasia. This
 treatment of the tissue resulted in input DNA that ranged in quality from
 nearly intact to highly sheared. All samples were sequenced as a
 multiplexed pool on an Illumina MiSeq. Libraries created from low to
 moderately degraded DNA (12–48 h) performed well. In contrast, the number
 of RADtags per individual, number of variable sites, and percentage of
 identical RADtags retained were all dramatically reduced when libraries
 were made using highly degraded DNA (96-h group). This reduction in
 performance was largely due to a significant and unexpected loss of raw
 reads as a result of poor quality scores. Our findings remained consistent
 after changes in restriction enzymes, modified fold coverage values (2- to
 16-fold), and additional read-length trimming. We conclude that starting
 DNA quality is an important consideration for RADSeq; however, the
 approach remains robust until genomic DNA is extensively degraded.
description: RadtagCounterPerl script that counts the number of RADtags in each*.matches file within a directorySNPCounterCounts the number of potential variable sites in a .vcf file generated by populations in the stacks programgenotypecounter.plperl script to determine how many genotype calls within the same individual are the same as the 0 hour muscle callcompressposition.plperl script to remove multiple entries for a variable site position and determine the total coverage of each positioncoveragecounter.plperl script to determine if a call in the 12, 48 or 96 file is present in the 0 file and if it is it determines the coverage at that position. The output is the average coverage per snp positionAdapterInfoThis file contains the internal and external adapters for each sample as well as the reverse compliment for the i7 tags.D1FastqFilesFastq files for the first restriction enzyme pair, EcoRI-NheID2FastqFilesFastq files for the second restriction enzyme pair, EcoRI-ClaISamplingInfoFile containing the treatment time, tissue type and restriction enzyme pair of each sample
DOI: 10.5061/dryad.d5h06
title: Data from: Warming affects different components of plant-herbivore interaction in a simplified community but not net interaction strength

description: Global warming impacts natural communities through effects on performance
 of individual species and through changes in the strength of interactions
 between them. While there is a body of evidence of the former, we lack
 experimental evidence on potential changes in interaction strengths.
 Knowledge about multispecies interactions is fundamental to understand the
 regulation of biodiversity and the impact of climate change on
 communities. This study investigated the effect of warming on a simplified
 community consisting of three species: rosy apple aphid Dysaphis
 plantaginea feeding on plantain, Plantago lanceolata, and a heterospecific
 neighbouring plant species, perennial ryegrass, Lolium perenne. The aphid
 does not feed on L. perenne. The experimental design consisted of
 monocultures and mixtures of L. perenne and P. lanceolata at three
 temperature levels. We did not find indication for indirect temperature
 effects on D. plantaginea through changes in leaf nitrogen or relative
 water content. However, experimental warming affected the life history
 traits of the aphid directly, in a non-linear manner. Aphids performed
 best at moderate warming, where they grew faster and had a shorter
 generation time. In spite of the increased population growth of the aphids
 under warming, the herbivory rates were not changed and consequently the
 plant–herbivore interaction was not altered under warming. This suggests
 reduced consumption rates at higher temperature. Also plant competition
 affected the aphids but through an interaction with temperature. We
 provide proof-of-concept that net interactions between plants and
 herbivores should not change under warming despite direct effects of
 warming on herbivores when plant–plant interaction are considered. Our
 study stresses the importance of indirect non–trophic interactions as an
 additional layer of complexity to improve our understanding of how trophic
 interactions will alter under climate change.
description: Aphid and plant
 performanceThis datafile contains
 raw data that were used in the accompanied manuscript. One sheet contains
 the results for effects of temperature and plant composition on aphid
 performance growing on Plantago lanceolata. The other sheets contain the
 results for effects of temperature, plant composition and aphid
 infestation on plant performance.Data Van De Velde et al.
 2016.xlsx
DOI: 10.5061/dryad.hg5473q
title: Data from: Body size shifts influence effects of increasing temperatures on ectotherm metabolism

description: Aim: Warmer temperatures directly increase metabolic rates of ectotherms,
 but temperature also indirectly affects metabolic rates. Higher
 temperatures result in smaller body sizes and associated decreases in
 metabolic rates, and it remains unknown whether this indirect effect of
 temperature increase could mitigate the direct positive effect of
 temperature on metabolic rate. Here, we assess whether temperature‐induced
 shifts in body size are likely to offset the direct influence of
 temperature on metabolic rate. Location: Global. Time period: 1940–2011.
 Major taxa studied: Ectotherms. Methods: We compiled literature‐derived
 data on mass and temperature for 109 ectotherm species raised at various
 constant temperatures. Using an allometric equation to estimate metabolic
 rate from size and temperature, we determined the body masses necessary
 for species to maintain constant metabolic rates under increased
 temperatures. We also calculated and compared (a) change in metabolic rate
 attributable to increased temperature where body size does not change with
 (b) change in metabolic rate including empirical size change. Results:
 Warmer temperatures resulted in increased metabolic rate estimates, but
 this was partly offset by decreased body sizes for the majority of
 species. For most species, observed decreases in body size at higher
 temperatures were insufficient to avoid metabolic rate increases. Main
 conclusions: Although the indirect effect of temperature on metabolic rate
 via body size is not sufficient to counterbalance the direct effect, it
 limits the magnitude of the increase in metabolic rate. Thus, in a warming
 climate, ectotherms are likely to experience increases in energy use that
 are smaller than anticipated. Given that metabolic rates have substantial,
 diverse impacts on individuals, populations, and ecosystems, these
 indirect effects of temperature change will have complex cascading effects
 on ecological communities, but the impacts of increases in metabolic rate
 of these varying magnitudes are unknown.
description: Data and
 CodeContains the four data
 files, two R scripts, and subfolder needed to replicate the analyses and
 figures in "Body size shifts influence effects of increasing
 temperatures on ectotherm metabolism". To do so, run first
 data_cleaning_MTEecto.R and then data_analysis_MTEecto_expanded.R using R
 version 3.4.1.data_and_code_Riemer_etal_2018.zip
DOI: 10.5061/dryad.gd077
title: Data from: How to best smash a snail: the effect of tooth shape on crushing load

description: Organisms that are durophagous, hard prey consumers, have a diversity of
 tooth forms. To determine why we see this variation, we tested whether
 some tooth forms break shells better than others. We measured the force
 needed with three series of aluminium tooth models, which varied in
 concavity and the morphology of a stress concentrating cusp, to break a
 shell. We created functionally identical copies of two intertidal snail
 shells: the thicker shelled Nucella ostrina and the more ornamented
 Nucella lamellosa using a three-dimensional printer. In this way, we
 reduced variation in material properties between test shells, allowing us
 to test only the interaction of the experimental teeth with the two shell
 morphologies. We found that for all tooth shapes, thicker shells are
 harder to break than the thinner shells and that increased ornamentation
 has no discernible effect. Our results show that for both shell
 morphologies, domed and flat teeth break shells better than cupped teeth,
 and teeth with tall or skinny cusps break shells best. While our results
 indicate that there is an ideal tooth form for shell breaking, we do not
 see this shape in nature. This suggests a probable trade-off between tooth
 function and the structural integrity of the tooth.
description: How to smash a
 snailExcel file containing
 force of initial failure data for three tooth model series
 (convex-concave, cusp - height, and cusp - width) for two snail shell
 morphologies (N ostrina and N lamellosa)
DOI: 10.5061/dryad.64732
title: Data from: The neural basis of risky choice with affective outcomes

description: Both normative and many descriptive theories of decision making under risk
 are based on the notion that outcomes are weighted by their probability,
 with subsequent maximization of the (subjective) expected outcome.
 Numerous investigations from psychology, economics, and neuroscience have
 produced evidence consistent with this notion. However, this research has
 typically investigated choices involving relatively affect-poor, monetary
 outcomes. We compared choice in relatively affect-poor, monetary lottery
 problems with choice in relatively affect-rich medical decision problems.
 Computational modeling of behavioral data and model-based neuroimaging
 analyses provide converging evidence for substantial differences in the
 respective decision mechanisms. Relative to affect-poor choices,
 affect-rich choices yielded a more strongly curved probability weighting
 function of cumulative prospect theory, thus signaling that the
 psychological impact of probabilities is strongly diminished for
 affect-rich outcomes. Examining task-dependent brain activation, we
 identified a region-by-condition interaction indicating qualitative
 differences of activation between affect-rich and affect-poor choices.
 Moreover, brain activation in regions that were more active during
 affect-poor choices (e.g., the supramarginal gyrus) correlated with
 individual trial-by-trial decision weights, indicating that these regions
 reflect processing of probabilities. Formal reverse inference Neurosynth
 meta-analyses suggested that whereas affect-poor choices seem to be based
 on brain mechanisms for calculative processes, affect-rich choices are
 driven by the representation of outcomes’ emotional value and
 autobiographical memories associated with them. These results provide
 evidence that the traditional notion of expectation maximization may not
 apply in the context of outcomes laden with affective responses, and that
 understanding the brain mechanisms of decision making requires the domain
 of the decision to be taken into account.
description: BehavioralDataBehavioral data for all participantsS1fMRI data for subject 1S2fMRI data for subject 2S3fMRI data for subject 3S4fMRI data for subject 4S5fMRI data for subject 5S6fMRI data for subject 6S7fMRI data for subject 7S8fMRI data for subject 8S9fMRI data for subject 9S10fMRI data for subject 10S11fMRI data for subject 11S12fMRI data for subject 12S13fMRI data subject 13S14fMRI data subject 14S15fMRI data subject 15S16fMRI for subject 16S17fMRI data subject 17S18fMRI data subject 18S19fMRI data subject 19S20fMRI data subject 20S21fMRI data subject 21S22fMRI data subject 22S23fMRI data subject 23
DOI: 10.5061/dryad.4k0j7
title: Data from: The use of the nest for parental roosting and thermal consequences of the nest for nestlings and parents

description: At temperate latitudes, altricial birds and their nestlings need to handle
 night temperatures well below thermoneutrality during the breeding season.
 Thus, energy costs of thermoregulation might constrain nestling growth,
 and low nocturnal temperatures might require resources that parents could
 otherwise have invested into nestlings during the day. To manipulate
 parental work rate, we performed brood size manipulations in breeding
 marsh tits (Poecile palustris). Nest box temperatures were always well
 above ambient temperature and increased with increasing brood size. In
 line with predictions, a large majority of females (but no males) made use
 of this benign environment for roosting. Furthermore, females tending
 enlarged broods, thereby having to work harder during the day, reduced
 their body temperature at night. This might have reduced nocturnal energy
 expenditure. Our finding that a higher proportion of enlarged, as compared
 to control, females continued to use the nest box as roosting sites even
 after a simulated predation event despite increased vulnerability to
 predation, further highlighting the need for energy conservation in this
 group. High nest box attendance and reduced body temperature in
 brood-reduced females may indicate that these females prioritised
 self-maintenance by initiating other costly physiological adjustments,
 e.g. moult, when relieved from parental work. We suggest that the energy
 demand for defending homeothermy is an element of the general trade-off
 between current and future reproduction, i.e. between daytime investment
 in food provisioning and the potential short- and long-term costs of a
 reduction in body temperature and increased predation risk.
description: mainNest = Identity of nest
 box Idfemale = Identity of female Year = 1 denotes 2010 and 2 denotes 2011
 Date = The date of female body temperature measurement, 1 = 1 May Femtemp
 = Female body temperature Ambientnight = Ambient temperature during the
 night of female body temperature measurement Boxnight = The temperature
 within the nest box Day = The age of the nestlings when the female body
 temperature was measured Exp = Experimental category; 1 = enlarged, 2 =
 control, 3 = reduced broods Brood = Number of nestlings in the brood
 Femalemass = mass of the female at nestling age 14 days Femage = female
 age; 2 = a female in her second calendar year etc. Nestl mass = The mean
 mass of the nestlings in a brood Femaletars = tars of the female at
 nestling age 14 days Fem cond = Female condition estimated as the residual
 mass from the relationship between mass and tarsus length of the
 femalesinoutFemid = Female identity
 Year = 1 denotes 2010 and 2 denotes 2011 Exp = Experimental category; 1 =
 enlarged, 2 = control, 3 = reduced broods Inout = Denotes if the female is
 in or out of the box during the second night visit. 1 = in, 2 = out Age =
 female age; 2 = a female in her second calendar year etc. NestT = The
 temperature within the nest box