cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.td2g2/1
title: seed_metadata

description: Animal-dispersed seeds were collected by seed traps and by recovery from mist-netted birds in the area of Monteverde, Costa Rica, during 2012 and 2013.  Seeds were cleaned and stored dry.  Photos can be accessed at the urls indicated in the accompanying data file, or at this url: http://web.colby.edu/jstone/


Seeds were collected at four sites:
Monteverde Cloud Forest Reserve (10°18.296’, 84°47.761’), 1535 m.a.s.l. Lower montane wet forest, late successional.
Monteverde Community (10°18.053’, 84°48.565’) 1420 m.a.s.l., Premontane wet forest, early successional.
Bajo del Tigre Reserve (10°18.328’, 84°48.878’) 1366 m.a.s.l.  Premontane moist forest, early successional
San Luis de Monteverde (10°17.072’, 84°47.976’) 1155 m.a.s.l.  Premontane wet forest, late successional.


The database shows the seed ID, its size and description, the source (seed trap versus collection from a particular mist-netted bird species), the site, date, and identification.  

It also provides a column explaining the basis for the identification.
Voucher indicates locally collected voucher, with plant identified by local expert, during 2012-13
Murray voucher indicates voucher collected in the higher elevation areas during the 1980’s-1990’s, identified by local experts, and stored by Greg Murray in alcohol.
Photo identifications provided by Alice Boyle (http://aliceboyle.net/Seeds/SeedPhotos.html) or by Phytoimages.si.edu
DOI: 10.5061/dryad.v3p2g/1
title: Body mass and offspring counts

description: Body mass and reproductive success (offspring counts) of 113 house mice living in semi-natural enclosures. Designation of  replicate population (n = 10), initial study (n = 3), and litter identifiers are provided. Each row represents an individual mouse.
DOI: 10.17632/67tyxkj4sh.1
title: Lunar images using Earthshine telescopes

description: Images of the Moon taken with a small automatic telescope operated from Mauna Loa in the period 2011-2012. Image detector was a 16-bit Andor CCD camera, allowing capture of the bright side and dark side in the same image. Terrestrial Albedo can be derived by analysis of the images.
DOI: 10.5061/dryad.12b0h/1
title: Demography_LifeHistories

description: Life histories values for each species and site, as obtained from the parameterization carried out in studies that used the model SORTIE. The data include growth at full light (Growth-L), defined as the time (in years) needed for a sapling with DBH= 1cm to become an adult (DBH=7.5 cm) when light = 100%; growth in shade (Growth-D), as the time (in years) needed for a sapling with DBH= 1cm to become an adult
(DBH=7.5 cm) when light = 1%; and survival in shade (Surv-D), defined as the 5-year survivorship of a sapling with DBH = 1cm when light = 1%. The data source of each value can be found in Appendix S2 in the manuscript.
DOI: 10.5061/dryad.12b0h/2
title: Functional_Traits

description: Functional trait values for each of the 48 study species, including 23 evergreen and 25 deciduous. Traits include Leaf mass area (LMA), photosynthetic capacity per unit leaf mass (Amass), Leaf N content per unit mass (Nmass), Leaf P content per unit mass (Pmass), Leaf lifespan (LL), Leaf length (Llength), seed mass (SeM), wood density (WD) ad maximum tree height (MaxH).
DOI: 10.5061/dryad.2275g/1
title: TRANSFORMING WATER PLOS ONE DATASET 11.19.16
DOI: 10.5061/dryad.24767/1
title: Eurypterida nexus file

description: Nexus file for phylogenetic analysis of Eurypterida
DOI: 10.5061/dryad.24767/2
title: Supporting Information - Data Matrix

description: Spreadsheet file including character matrix for Eurypterida including inferred ancestors and the character list.
DOI: 10.5061/dryad.380n3/1
title: GAk32 transcriptome annotation

description: Annotation of the GAK32 (Ganges accession) de novo assembly.  Annotation was performed using the Trinotate pipeline.  Ortholog clustering was performed using OrthoFinder.  Ortholog groups and the corresponding A. thaliana TAIR codes have been combined with the Trinotate annotation.
DOI: 10.5061/dryad.380n3/10
title: Python code - taxonomic group

description: Python code to extract the taxonomic group after blast search.
DOI: 10.5061/dryad.380n3/2
title: LCk32 transcriptome annotation

description: Annotation of the LCK32 (La Calamine accession) de novo assembly.  Annotation was performed using the Trinotate pipeline.  Ortholog clustering was performed using OrthoFinder.  Ortholog groups and the corresponding A thaliana TAIR codes have been combined with the Trinotate annotation.
DOI: 10.5061/dryad.380n3/3
title: LEk32 transcriptome annotation

description: Annotation of the LEK32 (Lellingen accession) de novo assembly.  Annotation was performed using the Trinotate pipeline.  Ortholog clustering was performed using OrthoFinder.  Ortholog groups and the corresponding A thaliana TAIR codes have been combined with the Trinotate annotation.
DOI: 10.5061/dryad.380n3/4
title: MPk32 transcriptome annotation

description: Annotation of the MPK32 (Monte Prinzera accession) de novo assembly.  Annotation was performed using the Trinotate pipeline.  Ortholog clustering was performed using OrthoFinder.  Ortholog groups and the corresponding A thaliana TAIR codes have been combined with the Trinotate annotation.
DOI: 10.5061/dryad.380n3/5
title: Fasta files of ortholog groups

description: A zip archive containing the fasta files of the protein sequences clustered into ortholog groups by OrthoFinder.
DOI: 10.5061/dryad.3c6d2/1
title: Cleaned White Dataset

description: Data from McKechnie & Wolf (2004) and White et al. (2006) matched to our complete phylogeny (857 species). Data columns include lnBMR (log standard metabolic rate from White et al. 2006 and McKechnie & Wolf 2004, temperature corrected using the Arrhenius equation to 293.15 K); lnMass (log mass in grams, from White et al. 2006 and McKechnie & Wolf 2004); lnMass2 (squared log mass in grams); lnGS (log genome size in c-values. From the animal genome size database) and endo (Indicator variable for endothermy, applied to birds and mammals).
DOI: 10.5061/dryad.3c6d2/2
title: Cleaned vertebrate phylogeny

description: Phylogeny used in analyses of trait evolution. Produced by combining published megaphylogenies including birds (Jetz et al. 2012), squamates (Pyron and Burbrink 2014), amphibians (Pyron and Wiens 2011) and fish (Rabosky et al. 2013). Mammals were constructed using Bininda-Emonds et al. 2007, Meredith et al. 2011 and phylogenies from the OpenTree of life database (Hinchliff et al. 2015) using the pipeline described in the manuscript. Trees were connected using dates from the timetree of life (Hedges et al. 2006) for the 5 major clades.
DOI: 10.5061/dryad.3c6d2/3
title: Cleaned Kolokotrones dataset

description: Cleaned dataset from Kolokotrones et al. (2010) matched to our mammalian phylogeny. Columns are: lnBMR (log standard metabolic rate in mlO2h^-1 from Kolokotrones et al. 2010); lnMass (log body mass in grams from Kolokotrones et al. 2010); lnMass2 (squared log body mass in grams); TempK (body temperature^-1 in Kelvins^-1 from Kolokotrones et al. 2010, and the Pantheria database, Jones et al. 2009 when absent from Kolokotrones et al. 2010).
DOI: 10.5061/dryad.3c6d2/4
title: Cleaned Kolokotrones phylogeny

description: Our mammal phylogeny produced using our OpenTree pipeline (described in the full vertebrate phylogeny and manuscript) matched to the Kolokotrones dataset.
DOI: 10.5061/dryad.511ms/1
title: The effect of temperature on Drosophila hybrid fitness: data files

description: This directory includes the raw counts for the genetic maps of hybrid inviability in mel/sim and mel/san F1 hybrid females at 18ºC.The file also includes all code to replicate the analyses in Miller and Matute (2016).
DOI: 10.5061/dryad.58416/3
title: ExampleSimulationCall

description: This is a plain text file that contains a script for running a set of simulations in Mathematica.
DOI: 10.5061/dryad.5q6s3/1
title: weight and prey

description: Latency to attack prey and average weight gained in the experiment that links prey attack and weight gain in groups of adult spiders.
DOI: 10.5061/dryad.5q6s3/2
title: boldness - Keystone identity

description: Boldness and weight at the beginning and end of the experiment for all individuals.
DOI: 10.5061/dryad.5q6s3/3
title: Prey trials - keystone identity

description: Latency to attack prey and identity of individual attacking.
DOI: 10.5061/dryad.8091q/1
title: adult_worm_and_eight_miracidia_stringent_filter

description: vcf comprised of stringently filtered variants found from ddRADseq in S. japonicum adult worm and eight miracidia samples.
DOI: 10.5061/dryad.8091q/2
title: mircidia_only_stringent_filter

description: vcf comprised of stringently filtered variants found from ddRADseq in 8 S. japonicum miracidia samples.
DOI: 10.5061/dryad.8091q/3
title: miracidia_missing25_stringent_filter

description: vcf comprised of variants found in ddRADseq in at least 75% of eight S. japonicum miracidia.
DOI: 10.5061/dryad.8091q/4
title: miracidia_only_loose_filter

description: vcf comprised of loosely filtered variants from ddRADseq of eight S japonicum miracidia
DOI: 10.5061/dryad.9mj14/1
title: data_reefmonitoring

description: Coral Reef Monitoring (1 year, central Red Sea); find details in the the README.txt
DOI: 10.5061/dryad.b56d4/1
title: Raw Argos data of arctic foxes from Bylot Island

description: This dataset contains the Argos locations of arctic foxes tracked from July 2007 to May 2013 (66 individuals, 97 fox-years); the file is provided in txt format. More information is provided in the joined ReadMe file.
DOI: 10.5061/dryad.c471f/1
title: Datasets and tree files accompanying publication about Asgard archaea.

description: Bins, tree files for figures and phylogenetic datasets and results (sequence selection as fasta, alignments and trimmed alignments, tree files) for the publication about Asgard archaea.
DOI: 10.5061/dryad.cg385/1
title: Pore size distribution of HNM and FNJ supports
DOI: 10.5061/dryad.cg385/2
title: Porosities of HNM support obtained under different pressing pressures before sintering
DOI: 10.5061/dryad.cg385/3
title: XRD patterns of HNM support obtained at different sintering temperatures
DOI: 10.5061/dryad.cg385/4
title: XRD patterns of HNM support, zeolite seeds and zeolite membranes
DOI: 10.5061/dryad.d8d7n/1
title: Individual measurements of house crickets in cohorts with different starting densities

description: The data file includes the raw data of the study ("Metabolic theory predicts animal self-thinning"), with individual measurements of the body mass (mg) of house crickets, in cohorts of different starting densities, as time progresses and density declines in most cohorts.
DOI: 10.5061/dryad.fd548/1
title: Signal-to-noise Ratio measurements for Incilius luetkenii calls

description: Column A shows five transcripts described in the paper (1-5). Column B shows the number of speakers (1, 5, or 10 simulated toads). Column C shows distance between the loudspeakers and the microphone, in meters. Column D shows the frequency of the calls, either their natural frequency, or one of three transposed frequencies (Low, Mid, or High). Column E shows the measured Signal-to-noise Ratio, and Column F shows the square root transformed SNR values.
DOI: 10.5061/dryad.gb424/1
title: Questionnaire Data - All 14Feb17
DOI: 10.5061/dryad.h2162/1
title: effects of density and diversity on primrose communities

description: Please see the associated metadata tab for descriptions of individual columns. These data derive from an experimental manipulation of genotypic diversity and density in common evening primrose.
DOI: 10.5061/dryad.j14r5/1
title: Keskin_AmpliconSequencingFis1TA

description: A pool of plasmids containing Fis1p TA mutations in a Gal4-sfGFP-Fis1 fusion protein and constructed using degenerate primers was cultured in strain MaV203 for four generations in SC-Trp medium, SC-Ura medium, or SMM-Trp-His medium containing 0 mM, 5 mM, 10 mM, or 20 mM 3-AT. Plasmids present under each culture condition were then recovered from 10 OD600 units of cells. Primers 882 (TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGGTAGAGGATAAGATCCAGAAGGAAAC) and 883 (GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCATAAGAAATTCGCTTATTTAGAAGTG) were used to amplify the genomic region encoding the Fis1p TA from each plasmid pool. Using the provided PCR products, next-generation, paired-end sequencing was performed by Microsynth (Balgach, Switzerland) on a MiSeq Nano (2x150v2). GZIP-compressed FASTQ files and a commercial sequencing report are found in the associated ZIP file.
DOI: 10.5061/dryad.k6636/1
title: Zip folder of Nemo simulation inputs and output data.

description: This zip folder contains scripts for generating input files for the modified version of Nemo described in text and available on Github, and requires the aNEMOne R package also described in text and on Github. Output stats files from Nemo are also included which are summary statistics over the whole landscape through time for each simulation. These can be used to generate all of the expansion rate results. Files within the "ind_seln" folders contain output data on individual fitness values across the landscape at a given point in time. These can be used to generate all of the fitness results and spatial-specific information. Files within the "Quanti" folder contain output data on genotypes across all loci for every individual across the landscape at a given time point. These can be used to generate the values of effect size differences in the two-patch models. There is also a folder labeled "Compiled_SimulationResults" which contains the relevant calculations from all of the above described output file sets.
DOI: 10.5061/dryad.k7797/1
title: High fidelity- EPP in plover species_RawData

description: This file contains the raw microsatellite data for twelve populations and eight species of plover. Details of the microsatellite markers and PCR conditions can be found in the paper.
DOI: 10.5061/dryad.kp3fv.1/1.1
title: Bird data

description: Total number of individuals of each bird species recorded along each 250-m transect per year. Rowname - row identification including the transect code and the bird census year. Transect - transect code; Farmland_area - low- or high-intensity farmland area; Year - bird census year; Date - bird census date; Recorder - recorder's name.
DOI: 10.5061/dryad.kp3fv.1/2.1
title: Bird categories

description: Bird species categorization according to their habitat affinities and conservation status. Species - species scientific name; All_species – All species: bird species recorded except aquatic birds because they were excluded from analyses; Farmland - Farmland birds: species associated with all farmland habitat types (e.g., arable fields, permanent crops, hedgerows); Steppe - Steppe birds: a subset of farmland birds that are rare or absent outside open grassland habitats; SPEC1-3 - Species of European Conservation Concern (SPEC1-3).
DOI: 10.5061/dryad.kp3fv.1/3.1
title: Habitat data

description: Rowname - row identification including the transect code and the time period (T0: 1995-1997, T1: 2010-2012). Transect - Transect code; Farmland_area - low- or high-intensity farmland area; Time_period - 1995-1997 or 2010-2012; woodland - percentage cover by holm woods (Quercus rotundifolia) with &gt;30% tree cover and shrub understory, old eucalyptus plantations with understory, and tree lines; open_woodland - percentage cover by holm woods with &gt;30% tree cover and grassy understory, young plantations without understory; shrubland - percentage cover by shrublands without trees or with scattered trees; streams - percentage cover by streams with vegetation (herbs, shrubs or trees); water_bodies - percentage cover by ponds and reservoirs; arable_land_with_scattered_trees - percentage cover by annual crops with scattered trees (&lt;30% tree cover); annual_dry_crops_and_fallows - percentage cover by non-irrigated annual crops (dry cereals (e.g. wheat, barley) and legumes) in rotation with ploughed fields, stubbles and fallows usually grazed by sheep or cattle; permanent_pastures - percentage cover by grassy vegetation grazed by sheep or cattle; annual_irrigated_crops - percentage cover by irrigated annual crops (corn and sunflower); permanent_crops - percentage cover by permanent irrigated and non-irrigated crops (olive groves and vineyards); human_structures - percentage cover by buildings and asphalt roads; PR_nat - natural habitats richness (no); AREA_MN_nat - mean patch area of natural habitats (ha); ED_nat - edge density of natural habitats (m2/ha); PR_crop - crop richness (no); AREA_MN_crop - mean patch area of crops (ha); ED_crop - edge density of crops (m2/ha).
DOI: 10.5061/dryad.kp3fv.1/4.1
title: Transect coordinates

description: Transect - transect code; X - XX coordinate of the transect centroid (UTM WGS 84); Y - YY coordinate of the transect centroid (UTM WGS 84); Farmland_area - low- or high-intensity farmland area.
DOI: 10.5061/dryad.m17c8.1
title: Data from: Biostratigraphy and geometric morphometrics of conchostracans (Crustacea, Branchiopoda) from the Late Triassic fissure deposits of Cromhall Quarry, UK
DOI: 10.5061/dryad.m17c8.2
title: Data from: Biostratigraphy and geometric morphometrics of conchostracans (Crustacea, Branchiopoda) from the Late Triassic fissure deposits of Cromhall Quarry, UK
DOI: 10.5061/dryad.m17c8.2/1.2
title: Data files 1-3, 5-8

description: Specimen and data lists
DOI: 10.5061/dryad.m17c8.2/2.2
title: Data file 4

description: Supplementary figures
DOI: 10.5061/dryad.n04pb/1
title: Landscape and Insect Community Dataset

description: The dataset is arranged with rows separated by research site and year, with columns of data. The dataset consists of the following columns of data: research site ID (Farm ID), research year (Year; 1=2012, 2=2013), the area of the potato field sampled as a research site in square meters (FieldArea) initial number of plants infected (InitialInfected), the final number of plants infected (FinalInfected), the difference in the number of plants infected (Infected; FinalInfected-InitialInfected), the number of plants sampled (NPlants), the number of times the plants were sampled throughout the season (NSamples), the number of insect traps collected throughout the season (NTraps), the  number of aphids collected throughout the season (Naphids), the number of aphids collected throughout the season that were identified to species or genera (NAphidsID), aphid species richness (NAphidSpp, meaning the count of aphid species collected throughout the season), the interpolated aphid species richness (AphidRichness), the Shannon diversity of the aphid community (ShannonDiversity), the number of coccinellids collected throughout the season (PredatorAbundance), the coccinellid species richness (Predator Richness, meaning the count of coccinellid species found throughout the season), the percentage of unmanaged land within a 500 m radius of the site (Nat500), the percentage of unmanaged land within a 1000 m radius of the site (Nat1000) the percentage of unmanaged land within a 1500 m radius of the site (Nat1500), the percentage of cropland within a 500 m radius of the site (Ag500), the percentage of cropland within a 1000 m radius of the site (Ag1000), and the percentage of cropland within a 1500m radius of the site (Ag1500).
DOI: 10.5061/dryad.n816r/1
title: American_eel_annotation_files

description: Included is a compressed file containing a gff annotation file as well as blast results for all CDS regions.
DOI: 10.5061/dryad.q5t5s/1
title: Waxholm Rat Calculation Template

description: This template will help you to translate pixel co-ordinates of cells identified from microscopy images to Waxholm co-ordinates. In needs to be used in conjunction with the AlignNii image anchoring tool, which aligns 2d histological images in the 3d MRI Waxholm rat brain. Access to this tool can be requested from Jan Bjaalie (j.g.bjaalie@medisin.uio.no).
DOI: 10.5061/dryad.s56rq/1
title: MUVC AL_721 DICOM

description: Medical CT data of adult Alligator mississippiensis scanned at 600µm slice thickness.
DOI: 10.5061/dryad.s56rq/2
title: MUVC AL_623 DICOM

description: microCT data of a juvenile American alligator (Alligator mississippiensis) scanned on a Siemens Inveon MicroCT at 21µm.
DOI: 10.5061/dryad.t8q1g/1
title: program_codes_of_abc_for_Dipteronia161207
DOI: 10.5061/dryad.t8q1g/2
title: Dipteronia dyeriana-cpSSRs
DOI: 10.5061/dryad.t8q1g/3
title: Dipteronia dyeriana-nSSRs
DOI: 10.5061/dryad.tv40b/1
title: Rohwer et al_data_21 July

description: Excel file with all data used in analyses presented in the paper.
DOI: 10.5061/dryad.0kh67/1
title: List of plant species and traits

description: Table S1. Summary of fruit display traits from plant species in a subtropical Andean montane forest of NW Argentina (Southern Yungas). Fruit consumption is a relative frequency of fruit consumption for each plant species by the community of fruit-eating birds (see Methods); Nc (not consumption) indicates fruit species that are not usually eaten by birds , while a hyphen indicates species eaten by birds but without data in our databases. Fruit size is the mean fresh-fruit mass expressed in grams. Fruit colour type is described as it is perceived by humans (i.e., related to hue). Fruit chromatic contrast (ΔS) is expressed in unities of just noticeable difference (JND) between the fruit and the corresponding leaves of the species (background) (see Methods). Fruit exposure has two categories: Exposed (pendulums, erect and terminals) and Unexposed (sessile fruits and fruits that are not exposed away from the contiguous foliage). Fruit aggregation expresses the mean number of fruit in discrete and differentiable groups. Fruit crop size is the mean number of fruits of each plant species, classified into five categories: 1 (1-10 fruits), 2 (11-100), 3 (101-1000), 4 (1001-10000) and 5 ( &gt;10000). See Methods for details. Plant systematics follows Instituto de Botánica Darwinion (2015).
DOI: 10.5061/dryad.0kh67/2
title: Methods for collection and analysis for data on fruit reflectance

description: Methods for collection and analysis for data on fruit reflectance.
DOI: 10.5061/dryad.0kh67/3
title: Bases and criteria for fruit consumption data

description: The first step in the multi-step process we used to make raw data on fruit consumption comparable, consisted in the delimitation of datasets that were homogeneous with respect to their geographic location, forest type, collection date and sampling technique. This entailed, on the one hand, the split of some large raw datasets (e.g. covering various types of forests, or more than one season) and, on the other, the grouping of similar opportunistic records from different sources in a same dataset.
DOI: 10.5061/dryad.0kh67/4
title: Competing models in the GLM procedure

description: Competing models in the GLM procedure to determine the importance of fruit conspicuousness on fruit consumption by birds.
DOI: 10.5061/dryad.13410/1
title: Invasion experiment data

description: Data collected from experimental laboratory invasions of the bean beetle Callosobruchus maculatus. Data show the post-dispersal densities of beetles in each patch of the one-dimensional invasion array. Columns (in order) are date, start time, end time, population ID, generation (1-10), treatment (0 = spatially sorted, 1 = shuffled), array_patch (the patch number in the dispersal array), array_shift (the cumulative number of patches that the invasion has been shifted towards 0 each generation to ensure that the invasion would fit in the spatial extent of the array), invasion_patch (array_patch + array_shift), N_females (number of females in each patch), N_males (number of males in each patch), N_unsexed (number of unsexed beetles in each patch), and notes.