cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.98c6c
title: Data from: Biogenic silica accumulation varies across tussock tundra plant functional type

description: 1. Silica (SiO2) accumulation by terrestrial vegetation is an important
 component of the biological silica cycle because it improves overall plant
 fitness and influences export rates of silica from terrestrial to marine
 systems. However, most research on silica in plants has focused on
 agricultural and forested ecosystems, and knowledge of terrestrial silica
 cycling in the Arctic, as well as the potential impacts of climate change
 on the silica cycle is severely lacking. 2. We quantified biogenic silica
 (BSi) accumulation in above and belowground portions of three moist acidic
 tundra (MAT) sites spanning a 300 km latitudinal gradient in central and
 northern Alaska, USA. We also examined plant silica accumulation across
 three main tundra types found in the Arctic (MAT, moist non-acidic tundra
 (MNT), and wet sedge tundra (WST)). 3. BSi concentrations in live
 Eriophorum vaginatum, a tussock-forming sedge that is the foundation
 species of tussock tundra, were not significantly (p&lt;0.05)
 different across the three main sites. Concentrations of BSi in live
 aboveground tissue were highest in the graminoid species (0.55 ± 0.07 %
 BSi in sedges from WST, and 0.27 ± 0.01% in E. vaginatum across the three
 MAT sites). Both inter-tussock tundra species and shrubs contained
 substantially lower BSi concentrations than E. vaginatum. 4. Our results
 have implications for how shifts in vegetation cover associated with
 climatic warming may alter silica storage in tussock tundra vegetation.
 Our calculations suggest that shrub expansion via warming will increase
 BSi storage in Arctic land plants due to the higher biomass associated
 with shrub tundra, whereas conversion of tussock tundra to WST via
 permafrost thaw would produce the opposite effect in the terrestrial plant
 BSi pool. Such changes in the size of the terrestrial vegetation silica
 reservoir could have direct consequences for the rates and timing of
 silica delivery to receiving waters in the Arctic.
description: AbovegroundMaterial_NutrientConcentrationsConcentrations of biogenic silica (as %SiO2 by dry weight), and nutrient ratios of Si:C and Si:N in aboveground material of tussocks (E. vaginatum) in MAT and MNT plots, plus aboveground material of gramminoids found in the WST. Values from each individual plot at each site.Abv_5.30.17.csvBlwgrnd_TussockBiogenic silica concentrations (as %SiO2 by dry weight) of belowground plant material in the tussocks for each core, at each depth, at the three MAT and one MNT site.Blwgrnd_BSi_InterTussBiogenic silica concentrations (as %SiO2 by dry weight) of belowground plant material in the inter-tussocks for each core, at each depth, at the three MAT and one MNT site.Blwgrnd_InterTuss_5.30.17.csvBlwgrnd_WST_5.30.17Biogenic silica concentrations (as %SiO2 by dry weight) of belowground plant material for each core, at each depth, at the WST site.
DOI: 10.5061/dryad.k580m37
title: Data from: Capacity to support predators scales with habitat size

description: Habitat reduction could drive biodiversity loss if the capacity of food
 webs to support predators is undermined by habitat-size constraints on
 predator body size. Assuming that (i) available space restricts predator
 body size, (ii) mass-specific energy needs of predators scale with their
 body size, and (iii) energy availability scales with prey biomass, we
 predicted that predator biomass per unit area would scale with habitat
 size (quarter-power exponent) and prey biomass (three-quarter–power
 exponent). We found that total predator biomass scaled with habitat size
 and prey resources as expected across 29 New Zealand rivers, such that a
 unit of habitat in a small ecosystem supported less predator biomass than
 an equivalent unit in a large ecosystem. The lower energetic costs of
 large body size likely mean that a unit of prey resource supports more
 biomass of large-bodied predators compared to small-bodied predators.
 Thus, contracting habitat size reduces the predator mass that can be
 supported because of constraints on predator body size, and this may be a
 powerful mechanism exacerbating reductions in biodiversity due to habitat
 loss.
description: Predator prey ratio
 dataset.csv file with variable
 names in first row and units in second row. Columns are variables and rows
 are sitesPredprey ratio Analysis
 dataset_upload.csv
DOI: 10.5061/dryad.t8344
title: Data from: Reduction in the cumulative effect of stress-induced inbreeding depression due to intra-generational purging in Drosophila melanogaster

description: Environmental stress generally exacerbates the harmful effects of
 inbreeding and it has been proposed that this could be exploited in
 purging deleterious alleles from threatened inbred populations. However,
 understanding what factors contribute to variability in the strength of
 inbreeding depression (ID) observed across adverse environmental
 conditions remains a challenge. Here, we examined how the nature and
 timing of stress affects ID and the potential for purging using inbred and
 outbred Drosophila melanogaster larvae exposed to biotic (larval
 competition, bacteria infection) and abiotic (ethanol, heat) stressors
 compared with unstressed controls. ID was measured during (larval
 survival) and after (male mating success) stress exposure. The level of
 stress imposed by each stressor was approximately equal, averaging a 42%
 reduction in outbred larval survival relative to controls. All stressors
 induced on average the same ID, causing a threefold increase in lethal
 equivalents for larval survival relative to controls. However,
 stress-induced ID in larval success was followed by a 30% reduction in ID
 in mating success of surviving males. We propose that this fitness
 recovery is due to ‘intragenerational purging’ whereby fitness
 correlations facilitate stress-induced purging that increases the average
 fitness of survivors in later life history stages. For biotic stressors,
 post-stress reductions in ID are consistent with intragenerational
 purging, whereas for abiotic stressors, there appeared to be an
 interaction between purging and stress-induced physiological damage. For
 all stressors, there was no net effect of stress on lifetime ID compared
 with unstressed controls, undermining the prediction that stress enhances
 the effectiveness of population-level purging across generations.
description: Data Average Fitness
 Measureskey to terminology in
 file: set = 1/2; population 1= Galante Winery 2= Mayo Winery; LCI = laval
 competitive index; MCI = male competitive index. Cum Fitness = Cumulative
 fitness. Each value is the average across replicate
 vialsDryad
 Data Lethal Equivalents.csv
DOI: 10.5061/dryad.m8q88
title: Data from: Androgens predict parasitism in female meerkats: a new perspective on a classic trade-off

description: The immunocompetence handicap hypothesis posits that androgens in males
 can be a ‘double-edged sword’, actively promoting reproductive success,
 while also negatively impacting health. Because there can be both
 substantial androgen concentrations in females and significant androgenic
 variation among them, particularly in species portraying female social
 dominance over males or intense female–female competition, androgens might
 also play a role in mediating female health and fitness. We examined this
 hypothesis in the meerkat (Suricata suricatta), a cooperatively breeding,
 social carnivoran characterized by aggressively mediated female social
 dominance and extreme rank-related reproductive skew. Dominant females
 also have greater androgen concentrations and harbour greater parasite
 loads than their subordinate counterparts, but the relationship between
 concurrent androgen concentrations and parasite burdens is unknown. We
 found that a female's faecal androgen concentrations reliably
 predicted her concurrent state of endoparasitism irrespective of her
 social status: parasite species richness and infection by Spirurida
 nematodes, Oxynema suricattae, Pseudandrya suricattae and coccidia were
 greater with greater androgen concentrations. Based on gastrointestinal
 parasite burdens, females appear to experience the same trade-off in the
 costs and benefits of raised androgens as do the males of many species.
 This trade-off presumably represents a health cost of sexual selection
 operating in females.
description: Dataset
DOI: 10.5061/dryad.8f61v
title: Data from: A new subfamily LIP of the major intrinsic proteins

description: Background: Proteins of the major intrinsic protein (MIP) family, or
 aquaporins, have been detected in almost all organisms. These proteins are
 important in cells and organisms because they allow for passive
 transmembrane transport of water and other small, uncharged polar
 molecules. Results: We compared the predicted amino acid sequences of 20
 MIPs from several algae species of the phylum Heterokontophyta (Kingdom
 Chromista) with the sequences of MIPs from other organisms. Multiple
 sequence alignments revealed motifs that were homologous to functionally
 important NPA motifs and the so-called ar/R-selective filter of
 glyceroporins and aquaporins. The MIP sequences of the studied chromists
 fell into several clusters that belonged to different groups of MIPs from
 a wide variety of organisms from different Kingdoms. Two of these proteins
 belong to Plasma membrane intrinsic proteins (PIPs), four of them belong
 to GlpF-like intrinsic proteins (GIPs), and one of them belongs to a
 specific MIPE subfamily from green algae. Three proteins belong to the
 unclassified MIPs, two of which are of bacterial origin. Eight of the
 studied MIPs contain an NPM-motif in place of the second conserved
 NPA-motif typical of the majority of MIPs. The MIPs of heterokonts within
 all detected clusters can differ from other MIPs in the same cluster
 regarding the structure of the ar/R-selective filter and other generally
 conserved motifs. Conclusion: We proposed placing nine MIPs from
 heterokonts into a new group, which we have named the LIPs (large
 intrinsic proteins). The possible substrate specificities of the studied
 MIPs are discussed.
description: all_MIPsPhylogenetic tree of 212 MIP sequences constructed using the neighbour joining (NJ) method and the Jones-Taylor-Thornton (JTT) evolutionary modeldiatom_greenA phylogenetic tree was constructed using the neighbour joining (NJ) method and the Jones-Taylor-Thornton (JTT) evolutionary model
DOI: 10.5061/dryad.12111
title: Data from: Assessing among-lineage variability in phylogenetic imputation of functional trait datasets

description: Phylogenetic imputation has recently emerged as a potentially powerful
 tool for predicting missing data in functional traits datasets. As such,
 understanding the limitations of phylogenetic modelling in predicting
 trait values is critical if we are to use them in subsequent analyses.
 Previous studies have focused on the relationship between phylogenetic
 signal and clade-level prediction accuracy, yet variability in prediction
 accuracy among individual tips of phylogenies remains largely unexplored.
 Here, we used simulations of trait evolution along the branches of
 phylogenetic trees to show how the accuracy of phylogenetic imputations is
 influenced by the combined effects of (1) the amount of phylogenetic
 signal in the traits and (2) the branch length of the tips to be imputed.
 Specifically, we conducted cross-validation trials to estimate the
 variability in prediction accuracy among individual tips on the
 phylogenies (hereafter “tip-level accuracy”). We found that under a
 Brownian motion model of evolution (BM, Pagel's λ = 1), tip-level
 accuracy rapidly decreased with increasing tip branch-lengths, and only
 tips of approximately 10% or less of the total height of the trees showed
 consistently accurate predictions (i.e. cross-validation R-squared
 &gt; 0.75). When phylogenetic signal was weak, the effect of tip
 branch-length was reduced, becoming negligible for traits simulated with λ
 &lt; 0.7, where accuracy was in any case low. Our study shows that
 variability in prediction accuracy among individual tips of the phylogeny
 should be considered when evaluating the reliability of phylogenetically
 imputed trait values. To address this challenge, we describe a Monte
 Carlo-based method that allows one to estimate the expected tip-level
 accuracy of phylogenetic predictions for continuous traits. Our approach
 identifies gaps in functional trait datasets for which phylogenetic
 imputation performs poorly, and will help ecologists to design more
 efficient trait collection campaigns by focusing resources on lineages
 whose trait values are more uncertain.
description: Phylogeny used for the
 empirical analysisSpecies-level
 time-calibrated molecular phylogeny of DNA including the 69 European and
 North American tree species used in the empirical analysis of the study
 (subset of a higher-rank phylogeny including 889 European and North
 American tree species, see Appendix 2 in Supplementary
 Material)Phylogeny.txt
DOI: 10.5061/dryad.2m9r762
title: Data from: Historical contingency and productivity effects on food-chain length

description: Food-chain length (FCL) is a fundamental ecosystem attribute, integrating
 information on both food web composition and ecosystem processes. It
 remains untested whether FCL also reflects the history of community
 assembly known to affect community composition and ecosystem functioning.
 Here, we performed microcosm experiments with a copepod (top predator),
 two ciliate species (intermediate consumers), and bacteria (producers),
 and modified the sequence of species introduction into the microcosm at
 four productivity levels to jointly test the effects of historical
 contingency and productivity on FCL. FCL increased when the top predator
 was introduced last; thus, the trophic position of the copepod reflected
 assembly history. A shorter FCL occurred at the highest productivity
 level, probably because the predator switched to feeding at the lower
 trophic levels because of the abundant basal resource. Thus, we present
 empirical evidence that FCL was determined by historical contingency,
 likely caused by priority effects, and by productivity.
description: Doi&Hillebrand-FCL-dataThe data used in this study, experimental setup (inputted pellet mass and species sequence), the number of individuals in the species at the final day (28 days) of the experiment, food-chain length (FCL) from d15N of copepod, and copepod biomass.
DOI: 10.5061/dryad.j0r8127
title: Data from: Quantifying the dark data in museum fossil collections as palaeontology undergoes a second digital revolution

description: Large-scale analysis of the fossil record requires aggregation of
 palaeontological data from individual fossil localities. Prior to
 computers these synoptic datasets were compiled by hand, a laborious
 undertaking that took years of effort and forced palaeontologists to make
 difficult choices about what types of data to tabulate. The advent of
 desktop computers ushered in palaeontology’s first digital revolution –
 online literature-based databases, such as the Paleobiology Database
 (PBDB). However, the published literature represents only a small
 proportion of the palaeontological data housed in museum collections.
 Although this issue has long been appreciated, the magnitude, and thus
 potential significance, of these so-called “dark data” has been difficult
 to determine. Here, in the early phases of a second digital revolution in
 palaeontology the digitization of museum collections – we provide an
 estimate of the magnitude of palaeontology’s dark data. Digitization of
 our nine institutions’ holdings of Cenozoic marine invertebrate
 collections from California, Oregon, and Washington in the United States
 reveals that they represent 23 times the number of unique localities than
 are currently available in the Paleobiology Database. These data, and the
 vast quantity of similarly untapped dark data in other museum collections,
 will when digitally mobilized enhance palaeontologists’ ability to make
 inferences about the patterns and processes of past evolutionary and
 ecological changes.
description: Supplementary_DataCounts of sites by county for Cenozoic fossil marine invertebrates used to create Figure 1, specifically the number of sites (collections) from the Paleobiology Database download, and the number of sites (localities) digitally mobilized from nine institutions of the EPICC TCN. The Paleobiology Database download was performed on November 10 2017 using the following query: http://paleobiodb.org/data1.2/colls/list.csv?datainfo&rowcount&interval=Cenozoic,Cenozoic&cc=US&envtype=marine&show=loc,paleoloc,strat,stratext,lith,geo,methods,resgroup,refattr,secref,ent,entname. The nine institutions are: Burke Museum of Natural History and Culture, University of Washington, Seattle, WA; California Academy of Sciences, San Francisco, CA; Natural History Museum of Los Angeles County, Los Angeles, CA; National Museum of Natural History, Smithsonian Institution, Washington, DC; Orange County Paleontological Collection, Fullerton, CA; Paleontological Research Institution, Ithaca, NY; University of Alaska Museum, University of Alaska, Anchorage, AK; University of California Museum of Paleontology, Berkeley, CA; University of Oregon Museum of Natural History, Eugene, OR. Data from both Paleobiology Database collections and museum collections were cleaned to remove terrestrial strata erroneously categorized as marine.
DOI: 10.5061/dryad.8180ph5
title: Data from: Landscape heterogeneity strengthens the relationship between β-diversity and ecosystem function

description: Consensus has emerged in the literature that increased biodiversity
 enhances the capacity of ecosystems to perform multiple functions.
 However, most biodiversity/ecosystem function studies focus on a single
 ecosystem, or on landscapes of homogenous ecosystems. Here we investigate
 how increased landscape-level environmental dissimilarity may affect the
 relationship between different metrics of diversity (α, β, or γ) and
 ecosystem function. We produced a suite of simulated landscapes, each of
 which contained four experimental outdoor aquatic mesocosms. Differences
 in temperature and nutrient conditions of the mesocosms allowed us to
 simulate landscapes containing a range of within-landscape environmental
 heterogeneities. We found that the variation in ecosystem functions was
 primarily controlled by environmental conditions, with diversity metrics
 accounting for a smaller (but significant) amount of variation in
 function. When landscapes were more homogeneous, α, β, and γ diversity was
 not associated with differences in primary production, and only γ was
 associated with changes in decomposition. In these homogeneous landscapes,
 differences in these two ecosystem functions were most strongly related to
 nutrient and temperature conditions in the ecosystems. However, as
 landscape-level environmental dissimilarity increased, the relationship
 between α, β, or γ and ecosystem functions strengthened, with β being a
 greater predictor of variation in decomposition at the highest levels of
 environmental dissimilarity than α or γ. We propose that when all
 ecosystems in a landscape have similar environmental conditions, species
 sorting is likely to generate a single community composition that is well
 suited to those environmental conditions, β is low, and the efficiency of
 diversity-ecosystem function couplings is similar across communities.
 Under this low β, the effect of abiotic conditions on ecosystem function
 will be most apparent. However, when environmental conditions vary among
 ecosystems, species sorting pressures is different among ecosystems,
 producing different communities among locations in a landscape. These
 conditions lead to stronger relationships between β and the magnitude of
 ecosystem functions. Our results illustrate that abiotic conditions and
 the homogeneity of communities influence ecosystem function expressed at
 the landscape-scale.
description: Data for Dryad Hammill
 et al EcologyAll the macro
 invertebrate, zooplankton, and ecosystem function data used in the Ecology
 Paper
DOI: 10.5061/dryad.46vm261
title: Data from: Committing to quantum resistance: a slow defence for Bitcoin against a fast quantum computing attack

description: Quantum computers are expected to have a dramatic impact on numerous
 fields, due to their anticipated ability to solve classes of mathematical
 problems much more efficiently than their classical counterparts. This
 particularly applies to domains involving integer factorisation and
 discrete logarithms, such as public key cryptography. In this paper we
 consider the threats a quantum-capable adversary could impose on Bitcoin,
 which currently uses the Elliptic Curve Digital Signature Algorithm
 (ECDSA) to sign transactions. We then propose a simple but slow
 commit--delay--reveal protocol, which allows users to securely move their
 funds from old (non-quantum-resistant) outputs to those adhering to a
 quantum-resistant digital signature scheme. The transition protocol
 functions even if ECDSA has already been compromised. While our scheme
 requires modifications to the Bitcoin protocol, these can be implemented
 as a soft fork.
description: Bitcoin UTXOs value
 analysisThis is a jupyter
 notebook used to extract the total number of Bitcoins that are protected
 by revealed public keys using the BlockSci tool. We run this notebook on a
 r4.2xlarge EC2 Amazon instance using the AMI (ami-0650807b) that BlockSci
 offers. BlockSci and the blockchain data are already provisioned there.
 For more details on using BlockSci or in case you wish to use this in
 another environment, please follow the instructions found on their github
 page: https://github.com/citp/BlockScirevealed
 UTXOS.ipynb
DOI: 10.5061/dryad.fn1q473
title: Data from: Does multiple paternity explain phenotypic variation among offspring in wild boar?

description: During pregnancy, littermates compete to extract maternal resources from
 the placenta. Unequal extraction of resources leads to developmental
 differences among offspring and thus within-litter variation in offspring
 mass. Because competition among littermates can be stronger among
 half-sibs, multiple paternity may represent an adaptive strategy allowing
 females to increase within-litter phenotypic variation among offspring
 when facing variable environments. Wild boar (Sus scrofa) females produce
 large litters with diversified offspring in terms of body mass.
 Additionally, multiple paternity within a litter has been observed in this
 promiscuous species. One can hypothesize that multiple paternity
 represents the mechanism by which females increase within-litter
 phenotypic variation. Combining long-term monitoring data with paternity
 analyses in a wild boar population, we tested whether the increase in the
 number of fathers within a litter explained the increase in within-litter
 variation in offspring mass observed in large litters. We showed that
 heavy females mated earlier during the rut, produced larger litters with a
 higher number of fathers and more variable fetus mass than lighter
 females. Within-litter variation of offspring mass increased with
 gestation stage and litter size, suggesting differential allocation of
 maternal resource among offspring in utero. However, we found only a weak
 paternal effect on offspring mass and no direct effect of the number of
 fathers on the within-litter variation in offspring mass. These results
 indicate that differential maternal allocation to offspring during
 pregnancy is unlikely related to paternal identity in this species.
description: Number of fathers within
 a litter and CV of fetus massThe first column
 corresponds to the estimated number of fathers within a litter. The second
 column corresponds to the coefficient of variation of fetus mass within a
 litter.Data_file.inp