cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jh57v4n/1
title: Selaginella spore sizes, habitat LAI and NPP

description: This is a  comma-delimited file containing data on the megaspore and microspore volumes of 114 species of Selaginella (Selaginellaceae) along with the minimum, mean, and maximum leaf area index (LAI) and minimum, mean, and maximum net primary productivity (NPP, g carbon assimilation/m^2/day) of the habitat where each species occurs.
DOI: 10.5061/dryad.m6383tr/1
title: Cape Race_final SNP data
DOI: 10.5061/dryad.m6383tr/10
title: Cape Race wild populations in captivity_obs_freq(mortality_by_sex_by_pop)
DOI: 10.5061/dryad.m6383tr/2
title: Cape Race_microsatellite data_from 2009 to 2015_with additional popns
DOI: 10.5061/dryad.m6383tr/3
title: Cape Race brook trout_female_eggsize_wild and captive
DOI: 10.5061/dryad.m6383tr/4
title: Cape Race brook trout_female_fecundity_wild and captive
DOI: 10.5061/dryad.m6383tr/5
title: Cape Race survival_progeny of captive born adults in a common hatchery environment
DOI: 10.5061/dryad.m6383tr/6
title: Cape Race wild population survival in captivity to one year 2011 and 2014
DOI: 10.5061/dryad.m6383tr/7
title: Cape Race wild population survival in captivity_egg to yolk absorption_2011 and 2014_six populations
DOI: 10.5061/dryad.m6383tr/8
title: Cape Race wild populations in captivity_lengthalltimeallpop
DOI: 10.5061/dryad.m89k18s/4
title: Maronde_oxidative stress & fledging probability
DOI: 10.5061/dryad.m89k18s/5
title: Maronde_proportion_caterpillar
DOI: 10.5061/dryad.r99v2gh/1
title: Data Dryad-Zhou et al.-JEcol

description: Original data for root traits of co-existing herbaceous species in temperate steppes
DOI: 10.5061/dryad.017vp2q/1
title: Middleton Welling et al. UK butterfly traits

description: This spreadsheet details the available trait data for UK butterflies from six representative sources. Each trait source is coded on a separate sheet. Detailed trait descriptions and references for each source are provided within the spreadsheet itself on a supplementary sheet.
DOI: 10.5061/dryad.0st06f0/2
title: Phylogenetic tree
DOI: 10.5061/dryad.12r74m2/1
title: Thorpe et al. 2018. Chytrid possitives from the Western Ghats. GE Distribution  Table

description: Tabulated positive results for amphibians infected with the pathogenic fungus Batrachochytrium dendrobatidis found in the northern Western Ghats, south west India. Amphibian samples from species complexes that are poorly resolved are shown as 'cf' as molecular confirmation of identity was not available at the time of upload.
DOI: 10.5061/dryad.1802hj0/1
title: Trichostrongylus worm counts

description: Data of Trichostrongylus colubriformis adult worm counts through time post initial infection in individual singly infected and Haemonchus contortus coinfected sheep.
DOI: 10.5061/dryad.1802hj0/2
title: Haemonchus worm counts

description: Haemonchus contortus adult and arrested larval worm counts through time since first infection in individual singly infected sheep and sheep coinfected with Trichostrongylus colubriformis.
DOI: 10.5061/dryad.1802hj0/3
title: Jejunal histology

description: Jejunal histology - cell counts and scores per villus crypt unit, through time, from individual sheep from four treatment groups. Uninfected controls, infected with Haemonchus contortus only, infected with Trichostrongylus retortaeformis only or coinfected with both parasites.
DOI: 10.5061/dryad.1802hj0/4
title: Abomasal histology

description: Abomasal histology - cell counts and scores per villus crypt unit, through time, from individual sheep from four treatment groups. Uninfected controls, infected with Haemonchus contortus only, infected with Trichostrongylus retortaeformis only or coinfected with both parasites.
DOI: 10.5061/dryad.1802hj0/5
title: Anti-Trichostrongylus IgG1 titres

description: Anti-Trichostrongylus IgG1 titre through time for individual sheep  from three groups, uninfected controls, singly infected with Trichostrongylus colubriformis or coinfected with Trichostrongylus colubriformis and Haemonchus contortus
DOI: 10.5061/dryad.1802hj0/6
title: Anti-Haemonchus IgG1 titres

description: Anti-Haemonchus contortus IgG1 titre through time for individual sheep from three groups, 1) uninfected controls, 2) singly infected with Haemonchus contortus  or 3) coinfected with Haemonchus contortus and Trichostrongylus colubriformis.
DOI: 10.5061/dryad.1r634nj/1
title: Chevrinais_SupplementaryInformation_review1

description: 3 figures, one table, one list of phylogenetic characters
DOI: 10.5061/dryad.2k6v37j/1
title: Homer Output

description: Chip-Seq for H3K27me3 was performed on wild type (wt) male, wt female, and trophoblast-specific Ogt knock out (ko) male and female placental chromatin.  Due to hardware failure, raw reads for this experiment were lost.  This data package contains the output from our downstream analysis using Homer.
DOI: 10.5061/dryad.5d5g47g/1
title: ctenizid_loci_raw_fasta

description: Raw fasta alignment files for all AHE loci
DOI: 10.5061/dryad.5d5g47g/2
title: ctenizidae

description: Final concatenated matrix of all loci in phylip format
DOI: 10.5061/dryad.6524f.2
title: Data from: HiMAP: robust phylogenomics from highly multiplexed amplicon sequencing
DOI: 10.5061/dryad.6524f.2/1.2
title: amplicon_alignments_nt

description: amplicon alignments in nucleotide space
DOI: 10.5061/dryad.6524f.2/2.2
title: amplicon_alignments_pep

description: amplicon alignments in peptide space
DOI: 10.5061/dryad.6524f.2/3.2
title: ASTRAL_INPUT_all_raxml_genetrees

description: input trees for ASTRAL analysis
DOI: 10.5061/dryad.6524f.2/4.2
title: ASTRAL_INPUT_CONFIG_spp_indsRmvd

description: config file for ASTRAL analysis
DOI: 10.5061/dryad.6524f.2/5.2
title: EXABAYES_INPUT_CONFIG_config

description: config file for EXABAYES analysis
DOI: 10.5061/dryad.6524f.2/6.2
title: FigureS1-S6

description: Supplemental figures S1-S6
DOI: 10.5061/dryad.6524f.2/7.2
title: Full_HiMAP_part01_input

description: full input for HiMAP part01
DOI: 10.5061/dryad.6524f.2/8.2
title: Full_HiMAP_part02_input

description: full input for HiMAP part02
DOI: 10.5061/dryad.6d1qm1j/1
title: tt.for.dryad
DOI: 10.5061/dryad.7cr0c76/11
title: BEAST dating analysis -- chloroplast data, lognormal prior

description: BEAST analysis of the chloroplast genome with a lognormal calibration prior. For analytical details see the manuscript. Tip labels for all taxa newly sampled in this analysis, Linnaean binomials were used. For all taxa sampled in previous work, sample codes were used to match voucher references in other works; for these refer to Folk et al., Systematic Biology, 66(3): 320–337; refer also to the associated Dryad deposition, https://doi.org/10.5061/dryad.cd546 (in which see Online Appendix 1).
DOI: 10.5061/dryad.7cr0c76/12
title: BEAST dating analysis -- chloroplast data, truncated normal prior

description: BEAST analysis of the chloroplast genome with a truncated normal calibration prior. For analytical details see the manuscript. Tip labels for all taxa newly sampled in this analysis, Linnaean binomials were used. For all taxa sampled in previous work, sample codes were used to match voucher references in other works; for these refer to Folk et al., Systematic Biology, 66(3): 320–337; refer also to the associated Dryad deposition, https://doi.org/10.5061/dryad.cd546 (in which see Online Appendix 1).
DOI: 10.5061/dryad.7cr0c76/13
title: BEAST dating analysis -- nuclear data, lognormal prior

description: BEAST analysis of the nuclear genes with a lognormal calibration prior. For analytical details see the manuscript. Tip labels for all taxa newly sampled in this analysis, Linnaean binomials were used. For all taxa sampled in previous work, sample codes were used to match voucher references in other works; for these refer to Folk et al., Systematic Biology, 66(3): 320–337; refer also to the associated Dryad deposition, https://doi.org/10.5061/dryad.cd546 (in which see Online Appendix 1).
DOI: 10.5061/dryad.7cr0c76/14
title: BEAST dating analysis -- nuclear data, truncated normal prior

description: BEAST analysis of the nuclear genes with a truncated normal calibration prior. For analytical details see the manuscript. Tip labels for all taxa newly sampled in this analysis, Linnaean binomials were used. For all taxa sampled in previous work, sample codes were used to match voucher references in other works; for these refer to Folk et al., Systematic Biology, 66(3): 320–337; refer also to the associated Dryad deposition, https://doi.org/10.5061/dryad.cd546 (in which see Online Appendix 1).
DOI: 10.5061/dryad.7cr0c76/15
title: Predicted niche occupancy profiles -- narrow-buffer models

description: Predicted niche occupancy profiles for narrow-buffer models. These are CSV files where the second column represents the variable value for a left-hand bin break-point, and the third column represents the weight for the bin to the right of this. For variable numbering see the translation table in this deposition. Each file represents one variable for one species.
DOI: 10.5061/dryad.7cr0c76/16
title: Predicted niche occupancy profiles -- wide-buffer models

description: Predicted niche occupancy profiles for wide-buffer models. These are CSV files where the second column represents the variable value for a left-hand bin break-point, and the third column represents the weight for the bin to the right of this. For variable numbering see the translation table in this deposition. Each file represents one variable for one species.
DOI: 10.5061/dryad.7cr0c76/17
title: Predicted niche occupancy profiles -- distance-buffer models

description: Predicted niche occupancy profiles for distance-buffer models. These are CSV files where the second column represents the variable value for a left-hand bin break-point, and the third column represents the weight for the bin to the right of this. For variable numbering see the translation table in this deposition. Each file represents one variable for one species.
DOI: 10.5061/dryad.7cr0c76/18
title: Model suitability ASC files -- narrow-buffer models

description: Model suitability rasters for narrow-buffer models from Maxent. These were the rasters used for predicted niche occupancy calculations.
DOI: 10.5061/dryad.8hq75j7/1
title: Ant Community Composition of selectively logged forest, Kakamega Forest, Kenya

description: Data originally collected in the field in Kakamega forest, Kenya. Ants were sampled via pitfall traps and winkler leaf litter sampling. Data represent species identity and occurrence data for all ant species sampled in Kakamega forest (.xlsx format)
DOI: 10.5061/dryad.b1c58f8/8
title: Snake_PairsOutput

description: Full Pairs output for Snake Range. Output from site and trapline analyses are both contained in this file.
DOI: 10.5061/dryad.b1c58f8/9
title: Toiyabe_PairsOutput

description: Full Pairs output for Toiyabe Range. Output from site and trapline analyses are both contained in this file.
DOI: 10.5061/dryad.f25c87j/1
title: Data from: Thirdhand smoke uptake to aerosol particle in the indoor environment

description: This file includes data used to produce Figures 1, 2, 3, SI1, SI2, SI3 for the manuscript.
DOI: 10.5061/dryad.f8c0c8h/1
title: Razgour2018_DDI_GLMM_R_scripts

description: R scripts for running the GLMMs for the fine-scale analysis of the effect of water body characteristics on bat activity, species richness and the activity of the three potentially competing Pipistrellus species.
DOI: 10.5061/dryad.f8c0c8h/2
title: Razgour2018_DDI_Maxent_model_outputs

description: Species distribution modelling (Maxent) outputs for all desert bats.
DOI: 10.5061/dryad.gb90p1c/1
title: Statistical Supplement

description: This is the Rcode and output from that code for the statistical analyses reported in this paper.
DOI: 10.5061/dryad.h4c25/1
title: raw data
DOI: 10.5061/dryad.hs20gv7/1
title: Data-from-Kuusk-et-al-Functional_Ecology-2018-Leaf-structural-and-photosynthetic-characteristics-in three-conifer-species

description: Data accompanying "Kuusk, V., Niinemets, Ü. & Valladares, F. (2018) Structural controls on photosynthetic capacity through juvenile-to-adult transition and needle aging in Mediterranean pines. Functional Ecology". All the the needle traits used (each data lines corresponds to an individual replicate measurement plant (juveniles) or branch (adults) that a grouped according to species, plant age and needle age
DOI: 10.5061/dryad.k0s6d62/1
title: Trait measures

description: This dataframe contains the data of all traits measured in replicate observations (Sheet 2) and at different time points during treatment (Sheet 1).
DOI: 10.5061/dryad.m6383tr/11
title: Cape Race wild populations in captivity_weightlengthallpop3
DOI: 10.5061/dryad.m6383tr/12
title: Cape Race wild populations in captivity_weightlengthallpop7
DOI: 10.5061/dryad.m6383tr/13
title: Cape Race wild populations in captivity_weightlengthallpop12
DOI: 10.5061/dryad.m6383tr/14
title: Cape Race_female_GSI_captive_wild
DOI: 10.5061/dryad.m6383tr/9
title: Cape Race wild populations in captivity_lengthweightallpop18months
DOI: 10.5061/dryad.mt78r/1
title: Appendix S1

description: Routine metabolic rate (RMR) and body mass of living fishes compiled from Froese & Pauly (2017) and Ferrón (2017).
DOI: 10.5061/dryad.p1t111n/1
title: Source code of Australian arid food web model

description: Source code in the R programming language developed to simulate the community dynamics in a multi-species food web model of the arid Australian ecosystem including 7 nodes: vegetation, European rabbit (Oryctolagus cuniculus), a generic small native mammal species, kangaroos (Macropus spp.), feral cat (Felis catus), fox (Vulpes vulpes), and dingo (Canis dingo).
DOI: 10.5061/dryad.v0108/1
title: Data used for results
DOI: 10.5061/dryad.1r634nj/2
title: Phylogenetic matrix of characters

description: Coding matrix
DOI: 10.5061/dryad.3gr233c/1
title: PCA input. cqn normalized and log2 transformed counts

description: Tab-delimited text file containing the cqn normalized and log2 transformed gene expression counts (using the conditional quantile normalization method) for 14,289 genes in 13 virginia opossum individuals. This normalized-transformed counts were used as input for the principal component analysis (PCA).
DOI: 10.5061/dryad.3gr233c/2
title: PCA results

description: Tab-delimited text file containing the results of the principal component analysis (PCA). It shows the loadings of 13 principal components (PC) for 14,289 genes. The genes are ordered by the loadings of PC1 from most negative to most positive.
DOI: 10.5061/dryad.3gr233c/3
title: WGCNA input. Phenotypic traits of Virginia opossum individuals

description: Tab-delimited text file with phenotypic trait measurements fro 13 Virginia opossum specimens that was used as input for the weighted gene coexpression network analysis (WGCNA). The traits that were used in the WGCNA analysis were  PTP (proportion of tail pigmentation), PEP (proportion of ear pigmentation) and PTO (proportion of toe pigmentation).
DOI: 10.5061/dryad.3gr233c/5
title: WGCNA input. Normalized-transformed counts for the differentially expressed genes

description: Tab-delimited text file containing the cqn normalized and log2 transformed counts (using the conditional quantile normalization method) for the 1,186 differentially expressed genes between pigmented and depigmented opossums. This normalized-transformed counts were used as input for the weighted gene coexpression network analysis (WGCNA).
DOI: 10.5061/dryad.59g2911/1
title: Scallop_all2012-2016_genopop-27pops

description: Genepop file with all scallops (adults and juveniles)
DOI: 10.5061/dryad.59g2911/2
title: Scallop Environmental data

description: Environmental data for 27 scallop locations with latitude, longitude and corresponding cartesian coordinates. Data includes averaged annual maximum and minimum and seasonally averaged temperature and salinity from the sea surface (SST, SSS) and bottom (BT, BS) for all scallop sites between 2011 and 2015.
DOI: 10.5061/dryad.6524f.1
title: Data from: HiMAP: robust phylogenomics from highly multiplexed amplicon sequencing
DOI: 10.5061/dryad.6524f.2/10.2
title: PARTITIONFINDER_INPUT_CONFIG_partition_finder_nt

description: config file for PartitionFinder (nucleotide space)
DOI: 10.5061/dryad.6524f.2/11.2
title: PARTITIONFINDER_INPUT_CONFIG_partition_finder_pep

description: config file for PartitionFinder (peptide space)
DOI: 10.5061/dryad.6524f.2/12.2
title: POMO_INPUT_Teph3_878genes_cutInds100_cutGenes200

description: input file for POMO analysis
DOI: 10.5061/dryad.6524f.2/13.2
title: SVDQUARTETS_INPUT_Teph3_878genes_cutInds100_cutGenes200_svdq_noLog

description: input file for SVDquartets analysis
DOI: 10.5061/dryad.6524f.2/14.2
title: Tables_S1-S5

description: Supplemental tables S1-S5
DOI: 10.5061/dryad.6524f.2/15.2
title: Teph3_878genes_cutInds100_cutGenes200_Peptides

description: concatenated alignment (peptide space)
DOI: 10.5061/dryad.6524f.2/16.2
title: Teph3_878genes_cutInds100_cutGenes200

description: concatenated alignment (nucleotide space)
DOI: 10.5061/dryad.6524f.2/17.2
title: Dupuis_10.5061_dryad.6524f
DOI: 10.5061/dryad.6524f.2/9.2
title: OrthoMCL_input

description: full input for OrthoMCL
DOI: 10.5061/dryad.7cr0c76/19
title: Model suitability ASC files -- distance-buffer models

description: Model suitability rasters for distance-buffer models from Maxent. These were the rasters used for predicted niche occupancy calculations.
DOI: 10.5061/dryad.7cr0c76/20
title: Model suitability ASC files -- wide-buffer models

description: Model suitability rasters for wide-buffer models from Maxent. These were the rasters used for predicted niche occupancy calculations.
DOI: 10.5061/dryad.7cr0c76/21
title: Binary suitability prediction for Mitella MRCA: Holocene climatic optimum, narrow-buffer models

description: This is the suitability prediction for the MRCA of Mitella s.s. (Mitella nuda + Mitella diphylla) for the Holocene climatic optimum (6k years ago), using narrow-buffer models and binary maps.
DOI: 10.5061/dryad.7cr0c76/22
title: Variable numbering translate table

description: An excel sheet explaining variable numbering for ancestral reconstruction analyses. A column also describes the native units of these, which in some cases differ by a factor of 10 from publication figures in order to save space in ASCII representations.
DOI: 10.5061/dryad.7cr0c76/23
title: Binary suitability prediction for California Heuchera MRCA: Holocene climatic optimum, narrow-buffer models

description: This is the suitability prediction for the MRCA of the California Heuchera clade (Heuchera caespitosa, Heuchera abramsii, Heuchera elegans, Heuchera parishii, Heuchera hirsutissima) for the Holocene climatic optimum (6k years ago), using narrow-buffer models and binary maps.
DOI: 10.5061/dryad.7cr0c76/24
title: Binary suitability prediction for Mitella MRCA: Last Glacial Maximum, narrow-buffer models

description: This is the suitability prediction for the MRCA of Mitella s.s. (Mitella nuda + Mitella diphylla) for the Last Glacial Maximum (22k years ago), using narrow-buffer models and binary maps.
DOI: 10.5061/dryad.7cr0c76/25
title: Binary suitability prediction for California Heuchera MRCA: Last Glacial Maximum, narrow-buffer models

description: This is the suitability prediction for the MRCA of the California Heuchera clade (Heuchera caespitosa, Heuchera abramsii, Heuchera elegans, Heuchera parishii, Heuchera hirsutissima) for the Last Glacial Maximum (22k years ago), using narrow-buffer models and binary maps.
DOI: 10.5061/dryad.7cr0c76/26
title: Binary suitability prediction for Mitella MRCA: Last interglacial, narrow-buffer models

description: This is the suitability prediction for the MRCA of Mitella s.s. (Mitella nuda + Mitella diphylla) for the last interglacial (120k-140k years ago), using narrow-buffer models and binary maps.
DOI: 10.5061/dryad.82gj124/1
title: Robak_and_Richards_Zawacki_2018_data

description: This file contains data on survival, body condition, Batrachochytrium dendrobatidis load, and Stenotrophomonas maltophilia load on Acris crepitans frogs involved in the experiment described in Robak & Richards-Zawacki (2018).
DOI: 10.5061/dryad.b8m8g7s/1
title: Landmark data for cichlid motion shapes

description: Landmark data for cichlid motion shapes. File is in .tps format, which can be opened in the tps series of morphometric programs as well as the package geomorph in R (with the readland.tps function). Note that scale is not provided in this file and must be implemented separately, with the "scale" factor in the accompanying "strike info.txt" file.
DOI: 10.5061/dryad.b8m8g7s/2
title: Sliding semilandmarks

description: File designating which cranial landmarks will be treated as "sliding semilandmarks" during shape alignment.
DOI: 10.5061/dryad.b8m8g7s/3
title: Feeding Strike Information

description: Table with information associated with each shape from feeding motions included in the "cichlid feeding LM.TPS" file.
DOI: 10.5061/dryad.b8m8g7s/4
title: Sample GM motion code

description: A sample of the code used to measure the magnitude of strike kinesis and kinematic efficiency. Files utilized in code: "cichlid feeding LM.TPS", "sliding_semi.txt", and "strike info.txt".
DOI: 10.5061/dryad.b8m8g7s/5
title: kinesis & standard errors (by individual)

description: Table of feeding kinesis averages and standard errors for each individual SPECIMEN analyzed in this study.
DOI: 10.5061/dryad.gb90p1c/2
title: stabilityRcode

description: R notebook used to generate the Statistical Supplement
DOI: 10.5061/dryad.gb90p1c/3
title: Data from moving slopes experiment

description: This is the dataset from experiments where each egg was placed on a surface then the slope gradually increased until the egg began to roll.
DOI: 10.5061/dryad.gb90p1c/4
title: Static slopes experiment comparing participants

description: This is a dataset to compare the ability of 12 naive subjects with a potentially biased subject (Jamie E Thompson; JET) in their ability to balance Razorbill and Commmon Murre eggs on surfaces with different slopes.
DOI: 10.5061/dryad.gb90p1c/5
title: Comparing stability on different slopes

description: This is the dataset from slope trials done by Jamie Thompson (JET) alone, to assess his ability to stabilize Razorbill and Common Murre eggs of different shapes on flat, sandpaper covered slopes of 20°, 30° and 40° above the horizontal.
DOI: 10.5061/dryad.gj651/1
title: Informatics resource citation counts (2000)

description: The number of 'awareness', 'usage' and total citations for informatics resource publications up to the year 2000.
DOI: 10.5061/dryad.gt8b5/1
title: Worker sterility - Code and data

description: Worker sterility - Code and data
DOI: 10.5061/dryad.mq2p20k/1
title: Flow_Data

description: Flow_Data.csv – Data produced from the Flow Experiment.

Fields:

pore_size – the filter pore size in µm. 

particle – the level of suspended particulate matter on the sampling day (high vs low). 

flow_rate – the user-input flow rate threshold value in L/min

replicate – the filter replicate number for each combination of flow_rate, particle, and pore size. 

vol_filtered – the volume of water filtered in Liters prior to the low-flow alarm.

minutes – the elapsed time between filtration initiation and the low-flow alarm (in minutes).
DOI: 10.5061/dryad.mq2p20k/2
title: Pressure_Data

description: Pressure_Data.csv – Data produced from the Pressure Experiment.

Fields:

pore_size – the filter pore size in µm. 

pressure – the user-input pressure threshold value in -psi.

filter_replicate – the filter replicate number for each combination of pressure and pore size.

SQ – The average calculated starting quantity (DNA copies/reaction) from 3 replicate qPCR reactions per sample. 

total_eDNA – The calculated total mudsnail eDNA per filter sample (DNA copies per filter).

vol_filtered – The volume of water filtered in Liters prior to system registering a low-flow alarm.

total_eDNA/L – Total eDNA captured per Liter of water filtered (DNA copies per Liter).