cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pq6p2
title: Data from: Large benefits to marine fisheries of meeting the 1.5°C global warming target

description: Translating the Paris Agreement to limit global warming to 1.5°C above
 preindustrial level into impact-related targets facilitates communication
 of the benefits of mitigating climate change to policy-makers and
 stakeholders. Developing ecologically relevant impact-related targets for
 marine ecosystem services, such as fisheries, is an important step. Here,
 we use maximum catch potential and species turnover as climate-risk
 indicators for fisheries. We project that potential catches will decrease
 by more than 3 million metric tons per degree Celsius of warming. Species
 turnover is more than halved when warming is lowered from 3.5° to 1.5°C
 above the preindustrial level. Regionally, changes in maximum catch
 potential and species turnover vary across ecosystems, with the biggest
 risk reduction in the Indo-Pacific and Arctic regions when the Paris
 Agreement target is achieved.
description: Data for fig. 1 -
 4These are the data used
 to plot figures 1 - 4 of the paper.Data.zip
DOI: 10.5061/dryad.hv223
title: Data from: Tracing the dynamics of gene transcripts after organismal death

description: In life, genetic and epigenetic networks precisely coordinate the
 expression of genes—but in death, it is not known if gene expression
 diminishes gradually or abruptly stops or if specific genes and pathways
 are involved. We studied this by identifying mRNA transcripts that
 apparently increase in relative abundance after death, assessing their
 functions, and comparing their abundance profiles through postmortem time
 in two species, mouse and zebrafish. We found mRNA transcript profiles of
 1063 genes became significantly more abundant after death of healthy adult
 animals in a time series spanning up to 96 h postmortem. Ordination plots
 revealed non-random patterns in the profiles by time. While most of these
 transcript levels increased within 0.5 h postmortem, some increased only
 at 24 and 48 h postmortem. Functional characterization of the most
 abundant transcripts revealed the following categories: stress, immunity,
 inflammation, apoptosis, transport, development, epigenetic regulation and
 cancer. The data suggest a step-wise shutdown occurs in organismal death
 that is manifested by the apparent increase of certain transcripts with
 various abundance maxima and durations.
description: MiceProbesParameters1. Columns: ProbeID, a, b, R2, CurveType. The CurveType refers to whether the best curve was Langmuir (LG) or Freundlich (F). The empirical parameters a and b in the Freundlich equation refer to the pre-exponent and the exponent (Y=a*Xb) respectively. The empirical parameters a and b in the Langmuir equation Y=Ymax*K*X/(1+K*X), where a = 1/(K*Ymax); b = 1/Ymax. The R2 refers to the fit of the empirical data to curve.FishProbesParameters1. Columns: ProbeID, a, b, R2, CurveType. The CurveType refers to whether the best curve was Langmuir (LG) or Freundlich (F). The empirical parameters a and b in the Freundlich equation refer to the pre-exponent and the exponent (Y=a*Xb) respectively. The empirical parameters a and b in the Langmuir equation Y=Ymax*K*X/(1+K*X), where a = 1/(K*Ymax); b = 1/Ymax. The R2 refers to the fit of the empirical data to curve.Mouse_liver_Log10_AllProfilesColumns: ProbeID, gene transcript abundances at postmortem stages 1 to 7.Mouse_brain_Log10_AllProfiles.txtColumns: ProbeID, gene transcript abundances at postmortem stages 1 to 7.Fish_Log10_AllProfilesColumns: ProbeID, gene transcript abundances at postmortem stages 1 to 10.MiceProbesSeqColumns: ProbeID, gene transcript abundances at postmortem stages 1 to 10.FishProbesSeqProbeIDs and DNA sequences.Gene_annotation_lit_refsMS Excel spreadsheet of zebrafish and mouse probe/gene annotations and functional categorizations: File_GenesLitRefs. Columns: microarray probe names, phylostrata, NCBI gene names, cluster, regulator, response, functional categorization fields 1 to 4, formal gene name, References.
DOI: 10.5061/dryad.v2p68
title: Data from: Quantifying uncertainty of taxonomic placement in DNA barcoding and metabarcoding

description: A crucial step in the use of DNA markers for biodiversity surveys is the
 assignment of Linnaean taxonomies (species, genus, etc.) to sequence
 reads. This allows the use of all the information known based on the
 taxonomic names. Taxonomic placement of DNA barcoding sequences is
 inherently probabilistic because DNA sequences contain errors, because
 there is natural variation among sequences within a species, and because
 reference data bases are incomplete and can have false annotations.
 However, most existing bioinformatics methods for taxonomic placement
 either exclude uncertainty, or quantify it using metrics other than
 probability. In this paper we evaluate the performance of the recently
 proposed probabilistic taxonomic placement method PROTAX by applying it to
 both annotated reference sequence data as well as to unknown environmental
 data. Our four case studies include contrasting taxonomic groups (fungi,
 bacteria, mammals and insects), variation in the length and quality of the
 barcoding sequences (from individually Sanger-sequenced sequences to short
 Illumina reads), variation in the structures and sizes of the taxonomies
 (800–130 000 species) and variation in the completeness of the reference
 data bases (representing 15–100% of known species). Our results
 demonstrate that PROTAX yields essentially unbiased probabilities of
 taxonomic placement, which means its quantification of species
 identification uncertainty is reliable. As expected, the accuracy of
 taxonomic placement increases with increasing coverage of taxonomic and
 reference sequence data bases, and with increasing ratio of genetic
 variation among taxonomic levels over within taxonomic levels. We conclude
 that reliable species-level identification from environmental samples is
 still challenging and that neglecting identification uncertainty can lead
 to spurious inference. A key aim for future research is the completion of
 taxonomic and reference sequence data bases and making these two types of
 data compatible.
description: Fungi
 OTUsFASTA file. Fungi ITS2
 region sequenced with 454 and clustered at 99% similarity threshold.
 Homopolymers of 454 reads converted into monomers. Cluster size included
 in FASTA ID of each OTU.fungimonomerOTU.faMammals OTUsFASTA file. Mammalian mt 16S rRNA derived from blood meals of 20.000 haematophagous leeches, sequenced by Illumina HiSeq 2000. OTU clustering with 98% similarity. Cluster size included in FASTA ID of each OTU.mammalsOTU.fa
DOI: 10.5061/dryad.ft64m
title: Data from: An integrated population model for bird monitoring in North America

description: Integrated population models (IPMs) provide a unified framework for
 simultaneously analyzing data sets of different types to estimate vital
 rates, population size, and dynamics; assess contributions of demographic
 parameters to population changes; and assess population viability.
 Strengths of an IPM include the ability to estimate latent parameters and
 improve the precision of parameter estimates. We present a hierarchical
 IPM that combines two broad-scale avian monitoring data sets; count data
 from the North American Breeding Bird Survey (BBS) and capture-recapture
 data from the Monitoring Avian Productivity and Survivorship (MAPS)
 program. These data sets are characterized by large numbers of sample
 sites and observers, factors capable of inducing error in the sampling and
 observation processes. The IPM integrates the data sets by modeling the
 population abundance as a first-order autoregressive function of the
 previous year's population abundance and vital rates. BBS counts were
 modeled as a log-linear function of the annual index of population
 abundance, observation effects (observer identity and first-survey-year),
 and overdispersion. Vital rates modeled included adult apparent survival,
 estimated from a transient Cormack-Jolly-Seber model using MAPS data, and
 recruitment (surviving hatched birds from the previous season + dispersing
 adults) estimated as a latent parameter. An assessment of the IPM
 demonstrated it could recover true parameter values from 200 simulated
 data sets. The IPM was applied to data sets (1992-2008) of two bird
 species, gray catbird (Dumetella carolinensis) and wood thrush (Hylocichla
 mustelina) in the New England/Mid-Atlantic coastal Bird Conservation
 Region of the USA. The gray catbird population was relatively stable
 (trend 0.4% yr−1), while the wood thrush population nearly halved (trend
 -4.5% yr−1) over the 17-yr study period. IPM estimates of population
 growth rates, adult survival, and detection and residency probabilities
 were similar and as precise as estimates from the stand-alone BBS and CJS
 models. A benefit of using the IPM was its ability to estimate the latent
 recruitment parameter. Annual growth rates for both species correlated
 more with recruitment than survival, and the relationship for wood thrush
 was stronger than for gray catbird. The IPM's unified modeling
 framework facilitates integration of these important data sets.
description: MAPS-17yr.dataCapture-recapture data from all MAPS stations over a 17-yr period.MAPS-stationsInformation on MAPS stations IDs.BBS-routesMetadata of Breeding Bird Survey routesBBS-AOU.dataAOU IDs of North American bird species.BBS-state.idsInformation on the IDs of BBS statesBBS-bcr.state-areaThe area of states in different BCR regions.
DOI: 10.5061/dryad.vh75r
title: Data from: History, geography, and host use shape genome-wide patterns of genetic variation in the redheaded pine sawfly (Neodiprion lecontei)

description: Divergent host use has long been suspected to drive population
 differentiation and speciation in plant-feeding insects. Evaluating the
 contribution of divergent host use to genetic differentiation can be
 difficult, however, as dispersal limitation and population structure may
 also influence patterns of genetic variation. In this study, we use
 double-digest restriction-associated DNA (ddRAD) sequencing to test the
 hypothesis that divergent host use contributes to genetic differentiation
 among populations of the redheaded pine sawfly (Neodiprion lecontei), a
 widespread pest that uses multiple Pinus hosts throughout its range in
 eastern North America. Because this species has a broad range and
 specializes on host plants known to have migrated extensively during the
 Pleistocene, we first assess overall genetic structure using model-based
 and model-free clustering methods, and identify three geographically
 distinct genetic clusters. Next, using a composite-likelihood approach
 based on the site frequency spectrum and a novel strategy for maximizing
 the utility of linked RAD markers, we infer the population topology and
 date divergence to the Pleistocene. Based on existing knowledge of Pinus
 refugia, estimated demographic parameters, and patterns of diversity among
 sawfly populations, we propose a Pleistocene divergence scenario for N.
 lecontei. Finally, using Mantel and partial Mantel tests, we identify a
 significant relationship between genetic distance and geography in all
 clusters, and between genetic distance and host use in two of three
 clusters. Overall, our results indicate that Pleistocene isolation,
 dispersal limitation, and ecological divergence all contribute to
 genome-wide differentiation in this species, and support the hypothesis
 that host use is a common driver of population divergence in
 host-specialized insects.
description: Data for Mantel and
 partial Mantel testsFolder containing files
 necessary for replicating Mantel and partial Mantel
 tests.IBD_IBE_partialMantels.zipData for demographic analyses using fastsimcoal2All datasets, template files, parameter files, and custom scripts needed to perform demographic analyses in fastsimcoal2, including: model choice, parameter estimation, bootstrapping, 2-population parameter estimation, and sensitivity analyses. Additional information on the input files and command lines required for each type of demographic analysis, and additional information on running custom scripts, can be found in ReadMe files within each folder.Demography_fastsimcoal2.zipPopulation structure analysis using ADMIXTUREPED and MAP files for population structure analysis in ADMIXTURE.PopulationStructureADMIXTURE.zipPopulation structure analysis using DAPCRAW file for analysis of population structure using DAPC.90_80_ropr_dapc.rawRaw VCF files.Raw VCF files exported from STACKS.VCF_files.zip
DOI: 10.5061/dryad.h1d1b
title: Data from: Causes of ecological gradients in leaf margin entirety: Evaluating the roles of biomechanics, hydraulics, vein geometry, and bud packing

description: PREMISE OF THE STUDY: A recent commentary by Edwards et al. (Am. J. Bot.
 103: 975–978) proposed that constraints imposed by the packing of young
 leaves in buds could explain the positive association between non-entire
 leaf margins and latitude but did not thoroughly consider alternative
 explanations. METHODS: We review the logic and evidence underlying six
 major hypotheses for the functional significance of marginal teeth,
 involving putative effects on (1) leaf cooling, (2) optimal support and
 supply of the areas served by major veins, (3) enhanced leaf-margin
 photosynthesis, (4) hydathodal function, (5) defense against herbivores,
 and (6) bud packing. KEY RESULTS: Theoretical and empirical problems
 undermine all hypotheses except the support–supply hypothesis, which
 implies that thinner leaves should have non-entire margins.
 Phylogenetically structured analyses across angiosperms, the El Yunque
 flora, and the genus Viburnum all demonstrate that non-entire margins are
 indeed more common in thinner leaves. Across angiosperms, the association
 of leaf thickness with non-entire leaf margins is stronger than that of
 latitude. CONCLUSION: We outline a synthetic model showing how
 biomechanics, hydraulics, vein geometry, rates of leaf expansion, and
 length of development within resting buds, all tied to leaf thickness,
 drive patterns in the distribution of entire vs. non-entire leaf margins.
 Our model accounts for dominance of entire margins in the tropics,
 Mediterranean scrub, and tundra, non-entire margins in cold temperate
 deciduous forests and tropical vines and early-successional trees, and
 entire leaf margins in monocots. Spinose-toothed leaves should be favored
 in short-statured evergreen trees and shrubs, primarily in Mediterranean
 scrub and related semiarid habitats.
description: GK_AJBZip file with data,
 trees, scripts and ReadMe file.
DOI: 10.5061/dryad.n0cf5
title: Data from: Prioritizing landscapes for restoration based on spatial patterns of ecosystem controls and plant-plant interactions

description: The widespread degradation of natural ecosystems requires cost-efficient
 restoration techniques that minimize risk and consider context-specific
 restoration conditions. However, meeting these demands can be difficult
 because information on ecosystem-level factors controlling vegetation and
 continuous spatial data on species interactions are often lacking. Using
 airborne LiDAR data from a Hawaiian dry forest, we delineated crowns and
 assessed the 3D structure of more than 700,000 shrubs and trees. We used
 Random Forest machine learning to assess the relative importance of
 resource availability, environmental conditions, and disturbance regimes
 on canopy density. We then modelled and scaled up plant–plant interactions
 (i.e. potential nursery effects) to landscape units using a LiDAR-derived
 Canopy Coalescence index (CC). We used the relative importance of
 ecosystem factors, canopy cover, and CC to prioritize landscapes for
 restoration. Here, we demonstrate a methodological framework that
 prioritizes landscapes in need of restoration (i.e. planting woody
 species) using two ecological perspectives: (1) ecosystem-level controls
 on remnant woody vegetation, and (2) potential interactions between
 established canopies and seedlings (e.g. nursery effect, competition). Our
 results highlight the heterogeneous nature of ecosystem-level drivers
 affecting forest structure along elevation gradients. Consequently, the
 degree of potential nursery interactions between established canopies and
 seedlings at the landscape-scale was context-specific. Synthesis and
 applications. Our study provides a methodological approach that
 prioritizes landscapes for restoration by identifying the main controls on
 tree spatial distribution and by inferring the favourable conditions for
 seedlings. This approach can guide land managers to define cost-efficient
 restoration strategies for large ecological areas.
description: Ecosystem-level drivers
 on canopy densityRemotely sensed data of
 crown density and environmental variables from a dry forest of Hawaii. See
 Barbosa & Asner; Prioritizing landscapes for restoration based on
 spatial patterns of ecosystem controls and plant–plant interactions.
 Journal of Applied EcologyData_for_JPE_Barbosa&Asner_Prioritizing landscapes for restoration.xlsx
DOI: 10.5061/dryad.cg250
title: Emergence patterns of novelty in European vegetation assemblages over the past 15 000 years

description: Plant communities are not stable over time and biological novelty is
 predicted to emerge due to climate change, the introduction of exotic
 species and land-use change. However, the rate at which this novelty may
 arise over longer time periods has so far received little attention. We
 reconstruct the emergence of novelty in Europe for a set of baseline
 conditions over the past 15 000 years to assess past rates of emergence
 and investigate underlying causes. The emergence of novelty is baseline
 specific and, during the early-Holocene, was mitigated by the rapid spread
 of plant taxa. Although novelty generally increases as a function of time,
 climate and human-induced landscape changes contributed to a non-linear
 post-glacial trajectory of novelty with jumps corresponding to periods of
 rapid changes. Emergence of novelty accelerated during the past 1000
 years. Historical cultural landscapes experienced a faster novelty
 development due to the contribution from anthropogenic land-cover changes.
description: EPD_Novelty_RoC_Data_and_RscriptsAll data were extracted from the European Pollen Database (EPD; http://www.europeanpollendatabase.net/) and the work of the data contributors and the EPD community is gratefully acknowledged. Please refer to the "readme.rtf" file for a more adequate description of the data and R scripts associated to this publication.
DOI: 10.15468/dl.rrvntw
title: Occurrence Download

description: A dataset containing 329277 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sporophila corvina"
 ]
}

 The dataset includes 329277 records from 107 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001450-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.bh213
title: Data from: ProtASR: an evolutionary framework for ancestral protein reconstruction with selection on folding stability

description: The computational reconstruction of ancestral proteins provides
 information on past biological events and has practical implications for
 biomedicine and biotechnology. Currently available tools for ancestral
 sequence reconstruction (ASR) are often based on empirical amino acid
 substitution models that assume that all sites evolve at the same rate and
 under the same process. However, this assumption is frequently violated
 because protein evolution is highly heterogeneous due to different
 selective constraints among sites. Here, we present ProtASR, a new
 evolutionary framework to infer ancestral protein sequences accounting for
 selection on protein stability. First, ProtASR generates site-specific
 substitution matrices through the structurally constrained mean-field
 substitution model (MF), which considers both unfolding and misfolding
 stability. We previously showed that MF models outperform empirical amino
 acid substitution models, as well as other structurally constrained
 substitution models, both in terms of likelihood and correctly inferring
 amino acid distributions across sites. In the second step, ProtASR adapts
 a well-established maximum-likelihood (ML) ASR procedure to infer
 ancestral proteins under MF models. A known bias of ML ASR methods is that
 they tend to overestimate the stability of ancestral proteins by
 under-estimating the frequency of deleterious mutations. We compared
 ProtASR under MF to two empirical substitution models (JTT and CAT),
 reconstructing the ancestral sequences of simulated proteins. ProtASR
 yields reconstructed proteins with less biased stabilities, which are
 significantly closer to those of the simulated proteins. Analysis of
 extant protein families suggests that folding stability evolves through
 time across protein families, potentially reflecting neutral fluctuation.
 Some families exhibit a more constant protein folding stability, while
 others are more variable. ProtASR is freely available from
 https://github.com/miguelarenas/protasr and includes detailed
 documentation and ready-to-use examples. It runs in seconds/minutes
 depending on protein length and alignment size.
description: Supplementary
 materialSupplementary
 materialProtASR_supmat_R1_6.pdfRaw dataRaw dataProtASR_Project_Data_2.zip
DOI: 10.5061/dryad.831g1
title: Data from: Phylogenomics provides new insight into evolutionary relationships and genealogical discordance in the reef-building coral genus Acropora

description: Understanding the genetic basis of reproductive isolation is a
 long-standing goal of speciation research. In recently diverged
 populations, genealogical discordance may reveal genes and genomic regions
 that contribute to the speciation process. Previous work has shown that
 conspecific colonies of Acropora that spawn in different seasons (spring
 and autumn) are associated with highly diverged lineages of the
 phylogenetic marker PaxC. Here, we used 10 034 single-nucleotide
 polymorphisms to generate a genome-wide phylogeny and compared it with
 gene genealogies from the PaxC intron and the mtDNA Control Region in 20
 species of Acropora, including three species with spring- and
 autumn-spawning cohorts. The PaxC phylogeny separated conspecific autumn
 and spring spawners into different genetic clusters in all three species;
 however, this pattern was not supported in two of the three species at the
 genome level, suggesting a selective connection between PaxC and
 reproductive timing in Acropora corals. This genome-wide phylogeny
 provides an improved foundation for resolving phylogenetic relationships
 in Acropora and, combined with PaxC, provides a fascinating platform for
 future research into regions of the genome that influence reproductive
 isolation and speciation in corals.
description: Raw DArT-seq
 dataDArT-seq genotypes for
 86 individuals of Acropora. These data include the raw sequences (~100 bp)
 for each of 10,034 loci, and show the position and variation of each
 single nucleotide polymorphism (SNP).Rosser et al_raw
 DArT-seq.xlsxPaxC sequence
 alignmentAligned DNA sequences
 from PaxC 46/47 intron, including indels, for 85 individuals of Acropora
 from Western Australia. Sequence length ~ 1067 bp. File is in FASTA
 format.PaxC_whole_seqs.txtControl Region (mtDNA) sequence alignmentAligned sequences of the mtDNA Control Region, including indels, for 84 individuals of Acropora from Western Australia. Sequence length ~1255 bp. File is in FASTA format.CR_whole_seqs.txt