cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fj852/12
title: Petrie Science 2018 Fig 2C

description: Data collected for results shown in figure 2C, see notes within the file and the manuscript for further guidance.
DOI: 10.5061/dryad.gj651/10
title: Informatics resource citation counts (2009)

description: The number of 'awareness', 'usage' and total citations for informatics resource publications up to the year 2009.
DOI: 10.5061/dryad.gj651/11
title: Informatics resource citation counts (2010)

description: The number of 'awareness', 'usage' and total citations for informatics resource publications up to the year 2010.
DOI: 10.5061/dryad.gj651/12
title: Informatics resource citation counts (2011)

description: The number of 'awareness', 'usage' and total citations for informatics resource publications up to the year 2011.
DOI: 10.5061/dryad.gj651/13
title: Informatics resource citation counts (2012)

description: The number of 'awareness', 'usage' and total citations for informatics resource publications up to the year 2012.
DOI: 10.5061/dryad.gj651/14
title: Informatics resource citation counts (2013)

description: The number of 'awareness', 'usage' and total citations for informatics resource publications up to the year 2013.
DOI: 10.5061/dryad.gj651/15
title: Informatics resource citation counts (2014)

description: The number of 'awareness', 'usage' and total citations for informatics resource publications up to the year 2014.
DOI: 10.5061/dryad.gj651/16
title: Informatics resource citation counts (2015)

description: The number of 'awareness', 'usage' and total citations for informatics resource publications up to the year 2015.
DOI: 10.5061/dryad.gj651/17
title: Informatics resource uIndex values (2000)

description: uIndex values for informatics resource publications up to the year 2000.
DOI: 10.5061/dryad.gj651/18
title: Informatics resource uIndex values (2001)

description: uIndex values for informatics resource publications up to the year 2001.
DOI: 10.5061/dryad.hv8qm00/1
title: mouse_trapping_data

description: This file contains all the data collected from trapped mice and was used in the analysis
DOI: 10.5061/dryad.k6tp614/1
title: Fig2a
DOI: 10.5061/dryad.k6tp614/2
title: Fig2b
DOI: 10.5061/dryad.k6tp614/3
title: Fig3cminus150kHz
DOI: 10.5061/dryad.k6tp614/4
title: Fig3cplus150kHz
DOI: 10.5061/dryad.k6tp614/5
title: Fig4a
DOI: 10.5061/dryad.k6tp614/6
title: Fig4b
DOI: 10.5061/dryad.k6tp614/7
title: Fig4c
DOI: 10.5061/dryad.pd612qp/2
title: SCR.BERNOULLI.PAB.WOLVERINE

description: JAGS model file to run the wolverine analysis associated with the WOLVERINE.Rdata file.
DOI: 10.5061/dryad.qn037tk/1
title: Enbody_Behavioral_Ecology_2018_Testosterone_Raw_Data

description: Raw testosterone data (plasma testosterone levels) to be processed by Androgens_Comparative.Rmd.
DOI: 10.5061/dryad.qn037tk/2
title: Enbody_Behavioral_Ecology_2018_Experimental_Response_Mount_Data

description: Raw data for analyzing response to simulated territorial intrusions by White-shouldered Fairywrens (Malurus alboscapulatus). Can be processed by Mount_Analysis_Revised.Rmd.
DOI: 10.5061/dryad.qn037tk/3
title: Enbody_Behavioral_Ecology_2018_Experimental_Response_YesOrNo_Mount_Data

description: Data for analyzing if White-shouldered Fairywrens responded to simulated territorial intrusions (binary 1 or 0). To be processed by Mount_Analysis_Revised.Rmd.
DOI: 10.5061/dryad.qn037tk/4
title: Enbody_Behavioral_Ecology_2018_Rscript_Testosterone_Data

description: An R markdown file (easily opened in RStudio) for analyzing raw testosterone data (in Enbody_WSFW_androgens.csv). Requires local installation of several R packages.
DOI: 10.5061/dryad.qn037tk/5
title: Enbody_Behavioral_Ecology_2018_RScript_Experimental_Response_Mount_Data

description: An R Markdown file (easily opened in R studio) for analyzing response to simulated territorial intrusions by White-shouldered Fairywrens (data in Enbody_WSFW_mount_responses_revised_renamed.csv and binresp2.csv).
DOI: 10.5061/dryad.05s45/1
title: Sorby2017_ArtemiaThermalToleranceData

description: Upper thermal limits of individual Artemia
DOI: 10.5061/dryad.07nd0hc/1
title: Trierweiler_2011_2012_CO2_P_Mo_growth_data

description: Seedling growth and fixation data collected from our CO2, P, Mo fertilization experiment. See README file for complete documentation.
DOI: 10.5061/dryad.07nd0hc/2
title: Trierweiler_2011_CO2_P_Mo_CN_data

description: Leaf tissue measurements of %N, %C and C:N  from our CO2, P, Mo fertilization experiment. See README file for complete documentation.
DOI: 10.5061/dryad.10rn5/1
title: Mielke et al_ESM_code

description: Code for the statistical analysis of kinematic data using a hierarchical Bayesian generalized linear model as described in Mielke et al. "Motion analysis of non-model organisms using a hierarchical model: Influence of setup enclosure size on gait parameters of Swinhoe’s striped squirrels as a test case".
DOI: 10.5061/dryad.10rn5/2
title: Mielke et al_ESM_data

description: A table containing all data to reproduce the analysis as described in Mielke et al. "Motion analysis of non-model organisms using a hierarchical model: Influence of setup enclosure size on gait parameters of Swinhoe’s striped squirrels as a test case".
DOI: 10.5061/dryad.682dc/1
title: I. Tables 3-11 results of ANOVA and Tukey-Kramer tests for flight parameters by species

description: Tables 3–11:  results of ANOVA and Tukey-Kramer tests for flight parameters by species. From "Moving like a model: mimicry of hymenopteran flight trajectories by clearwing moths of Southeast Asian rainforests" Skowron Volponi, Marta, McLean, Donald, Volponi, Paolo, Dudley, Robert
DOI: 10.5061/dryad.682dc/2
title: II. R code. Flight trajectories calculations

description: This is a complete R code used for flight trajectory analysis described in "Moving like a model: mimicry of hymenopteran flight trajectories by clearwing moths of Southeast Asian rainforests" Skowron Volponi, Marta, McLean, Donald, Volponi, Paolo, Dudley, Robert
DOI: 10.5061/dryad.682dc/3
title: III. Calculated flight trajectories parameters

description: Complete calculated parameters of all analysed flight trajectories in study "Moving like a model: mimicry of hymenopteran flight trajectories by clearwing moths of Southeast Asian rainforests" Skowron Volponi, Marta, McLean, Donald, Volponi, Paolo, Dudley, Robert
DOI: 10.5061/dryad.682dc/4
title: IV. Minimums, maximums and means of calculated variables

description: Minimums, maximums and means of calculated variables from "Moving like a model: mimicry of hymenopteran flight trajectories by clearwing moths of Southeast Asian rainforests" Skowron Volponi, Marta, McLean, Donald, Volponi, Paolo, Dudley, Robert
DOI: 10.5061/dryad.6q6r5/1
title: Individual Microsatellite Genotypes and Geographic Coordinates

description: First column represents unique individual identifier with population abbreviation. WA=White Oak 2013, WB=White Oak 2014, WO=White Oak 2015, see paper for additional abbreviations. Individuals whose identifier ends with a letter are females who were attracted to the male with the same number without the letter suffix (for example, LL-10A is the first female who was attracted to male LL-10). Column headings show the name of the loci/marker used.
DOI: 10.5061/dryad.6q6r5/2
title: Sex Ratios

description: Includes sex ratios and length of time where female trapping occurred at several different leks
DOI: 10.5061/dryad.6q6r5/3
title: Male Mass Data

description: Includes data on male mass and lek size
DOI: 10.5061/dryad.6q6r5/4
title: Male Size Data

description: Spreadsheet of male mass, size, and lek size
DOI: 10.5061/dryad.6q6r5/5
title: 2009-2015 female attractions

description: Represents number of female attractions by each male on several different leks
DOI: 10.5061/dryad.7cr0c76/43
title: Binned-probabilities 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 normalized binned-probabilities maps.
DOI: 10.5061/dryad.7cr0c76/44
title: Binned-probabilities 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 normalized binned-probabilities maps.
DOI: 10.5061/dryad.7cr0c76/45
title: Binned-probabilities suitability prediction for California Heuchera MRCA: Last interglacial, 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 interglacial (120k-140k years ago), using narrow-buffer models and normalized binned-probabilities maps.
DOI: 10.5061/dryad.7cr0c76/46
title: Binned-probabilities suitability prediction for Mitella MRCA: Holocene climatic optimum, wide-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 wide-buffer models and normalized binned-probabilities maps.
DOI: 10.5061/dryad.7cr0c76/47
title: Binned-probabilities suitability prediction for California Heuchera MRCA: Holocene climatic optimum, wide-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 wide-buffer models and normalized binned-probabilities maps.
DOI: 10.5061/dryad.7cr0c76/48
title: Binned-probabilities suitability prediction for Mitella MRCA: Last Glacial Maximum, wide-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 wide-buffer models and normalized binned-probabilities maps.
DOI: 10.5061/dryad.7cr0c76/49
title: Binned-probabilities suitability prediction for California Heuchera MRCA: Last Glacial Maximum, wide-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 wide-buffer models and normalized binned-probabilities maps.
DOI: 10.5061/dryad.7cr0c76/50
title: Binned-probabilities suitability prediction for Mitella MRCA: Last interglacial, wide-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 wide-buffer models and normalized binned-probabilities maps.
DOI: 10.5061/dryad.7n3df16/10
title: SI_Archive_S10

description: Checking Mnat_13309 to confirm identiy as Ago3 with M. bellicosus de novo data.
(1_checking_trin_mbel.txt; Format: plain text)
(2_trin_ago3_vs_dmel; Format: plain text)
(pfam_domains_ago3_contig.txt; Format: plain text)
(protocol.txt; Format: plain text)
(Trinity_contig.fa; FASTA-Format)
(workflow.docx; Format: MS Word)
DOI: 10.5061/dryad.7n3df16/6
title: SI_Archive_S6

description: Full results of Orthofinder inferring orthologs between M. natalensis and D. melanogaster.
(OrthoFinder_OrthologousGroups_all_results_MNAT_DMEL.txt; Format: plain text)
Identified single copy orthologs (OrthoFinder) between M. natalensis and D. melanogaster.
(OrthoFinder_OrthologousGroups_single_copy_MNAT_DMEL.txt; Format: plain text)
DOI: 10.5061/dryad.7n3df16/7
title: SI_Archive_S7

description: DEG lists for caste wise comparison
(DEG_caste.csv; Format: csv)
DOI: 10.5061/dryad.7n3df16/8
title: SI_Archive_S8

description: Annotations obtained from InterProScan, Pfam and Dfam
Interproscan
(interproscan.tsv; Format: tsv)
Pfam
(pfam.out; Format: plain text)
Dfam
(dfam.out; Format: plain text)
DOI: 10.5061/dryad.7n3df16/9
title: SI_Archive_S9

description: Masked multiple sequence alignment for tree inference.
AGO1-3/Piwi/Aub set (ALICUT_ago1-3-piwi-aub.ginsi.vsm.fas; FASTA format)
DOI: 10.5061/dryad.7n53r7f/1
title: data capture dates and energy stores

description: There are seven columns: 1. "energystores_capture": This is a numeric variable and it provides the individual energy stores at capture, estimated as detailed in eqn. 2 of the paper. 2. "Age.ad": This is a factor with two levels, i.e., "young" and "old". In autumn, "young" means 1st calendar year bird and "old" means that the individual was older than "young". In spring, "young" means 2nd calendar year bird and "old" means that the individual was older than "young". 3. "Sex": This is a factor with two levels. "1" says that the bird was a male and "2" that it was a female. 4. "subsp": This is a factor with two levels. "leu" says that the bird belonged to the leucorhoa subspecies of the northern wheatear and "oen" says that the bird belonged to the oenanthe subspecies of the northern wheatear. 5. “season”: This variable indicates whether the bird was caught in spring or autumn. 6. “year”: This variable indicates the year in which the bird was caught. 7. “jd”: This is the day of year of capture with 1 Jan is 1.
DOI: 10.5061/dryad.7s3m38n/1
title: Gene expression data
DOI: 10.5061/dryad.7s3m38n/2
title: Heart rates
DOI: 10.5061/dryad.7s3m38n/3
title: Measured and calculated seawater carbonate chemistry variables
DOI: 10.5061/dryad.db901.1
title: Data from: Toward a periodic table of niches, or exploring the lizard niche hypervolume
DOI: 10.5061/dryad.db901.1/1.1
title: C1-Appendix

description: 134 lizard species with data on 50 niche dimensions including habitat, anatomy, diet, life history, metabolism, and defense. Four other variables (semi arboreal, semi fossorial, crepuscular, and mixed foraging mode) were scored with double entries. Multivariate analyses capture 61.7 % of the total variance in the first 3 dimensions. Lizard niches appear to be tightly constrained.
DOI: 10.5061/dryad.db901.2
title: Data from: Toward a periodic table of niches, or exploring the lizard niche hypervolume
DOI: 10.5061/dryad.db901.2/1.2
title: C1-Appendix

description: 134 lizard species with data on 50 niche dimensions including habitat, anatomy, diet, life history, metabolism, and defense. Four other variables (semi arboreal, semi fossorial, crepuscular, and mixed foraging mode) were scored with double entries. Multivariate analyses capture 61.7 % of the total variance in the first 3 dimensions. Lizard niches appear to be tightly constrained.
DOI: 10.5061/dryad.dg8q0.1
title: Data from: Dating the species network: allopolyploidy and repetitive DNA evolution in American daisies (Melampodium sect. Melampodium, Asteraceae)
DOI: 10.5061/dryad.dg8q0.1/1.1
title: Dryad_Repo_for_Submission.tar

description: A compressed archive of nexus alignments, Beast XML files and MCC trees from the analyses performed in this study. The subfolders are clearly labeled to indicate file and analysis type associated with each file.
DOI: 10.5061/dryad.dg8q0.2
title: Data from: Dating the species network: allopolyploidy and repetitive DNA evolution in American daisies (Melampodium sect. Melampodium, Asteraceae)
DOI: 10.5061/dryad.dg8q0.2/1.2
title: Dryad_Repo_for_Submission.tar

description: A compressed archive of nexus alignments, Beast XML files and MCC trees from the analyses performed in this study. The subfolders are clearly labeled to indicate file and analysis type associated with each file.
DOI: 10.5061/dryad.dg8q0.2/2.2
title: Supplementary Information
DOI: 10.5061/dryad.g7v1b/1
title: Supplementary Tables & Figures
DOI: 10.5061/dryad.gj651/19
title: Informatics resource uIndex values (2002)

description: uIndex values for informatics resource publications up to the year 2002.
DOI: 10.5061/dryad.gj651/20
title: Informatics resource uIndex values (2003)

description: uIndex values for informatics resource publications up to the year 2003.
DOI: 10.5061/dryad.gj651/21
title: Informatics resource uIndex values (2004)

description: uIndex values for informatics resource publications up to the year 2004.
DOI: 10.5061/dryad.gj651/22
title: Informatics resource uIndex values (2005)

description: uIndex values for informatics resource publications up to the year 2005.
DOI: 10.5061/dryad.gj651/23
title: Informatics resource uIndex values (2006)

description: uIndex values for informatics resource publications up to the year 2006.
DOI: 10.5061/dryad.gj651/24
title: Informatics resource uIndex values (2007)

description: uIndex values for informatics resource publications up to the year 2007.
DOI: 10.5061/dryad.gj651/25
title: Informatics resource uIndex values (2008)

description: uIndex values for informatics resource publications up to the year 2008.
DOI: 10.5061/dryad.gj651/26
title: Informatics resource uIndex values (2009)

description: uIndex values for informatics resource publications up to the year 2009.
DOI: 10.5061/dryad.gj651/27
title: Informatics resource uIndex values (2010)

description: uIndex values for informatics resource publications up to the year 2010.
DOI: 10.5061/dryad.k04q2kd/1
title: Barents Sea food webs

description: The excel file contains 25 food webs of the Barents Sea. Sheet 1: Species names; Sheet 2. Subregion-by-species matrix; Sheet 3: Pairwise list of trophospecies interactions; Sheet 4: The Barents Sea metaweb.
DOI: 10.5061/dryad.k6tp614/10
title: FigS1c_exp
DOI: 10.5061/dryad.k6tp614/8
title: FigS1a_exp
DOI: 10.5061/dryad.k6tp614/9
title: FigS1b_exp
DOI: 10.5061/dryad.qn037tk/6
title: Enbody_RStudio_Project

description: This zip file contains the R Studio project that holds all the scripts and data that are also separately uploaded here on Dryad. You can just open this and run it out of the box, without downloading the other files. However, you will still need to install the R packages that are loaded.
DOI: 10.5061/dryad.3h7q736/1
title: nitrogen and phosphorus conteens and N:P of different organs of different plant functional organs in forests
DOI: 10.5061/dryad.5b85783/1
title: Alignments

description: - Concatenated nucleotide alignment
- Concatenated protein alignment
- 1,105 exon alignments (protein and nucleotide)
- 1,721 exon alignments, with all nHmmer hits aligned
- 616 exon alignments of discarded loci, with only the best hit per locus   -8-model-species-alignments
DOI: 10.5061/dryad.5b85783/2
title: TreeFiles

description: See Appendix 1 in the Supplementary Appendix for the correspondence between these tree files and the figures in the paper.
DOI: 10.5061/dryad.5b85783/3
title: GGI-Constraint-Trees

description: Master constraint trees for all hypotheses tested. See Arcila et al. 2017 for a full tutorial of the GGI method.
DOI: 10.5061/dryad.5b85783/4
title: Scripts

description: Scripts used to extract markers from genomes/transcriptomes. There is a short tutorial included in the zip archive that explains the pipeline. Scripts are provided without warranty.
DOI: 10.5061/dryad.5b85783/5
title: MCMCTreeFiles

description: Files for running divergence time estimation in MCMCTree. See Supplementary Appendix for list of fossil calibrations and details on our three calibration schemes.
DOI: 10.5061/dryad.5b85783/6
title: BGI-Sequencing-Results

description: Assembly metrics from BGI-sequenced transcriptomes for Fish T1K
DOI: 10.5061/dryad.682dc/5
title: V. (x,y) coordinates of digitized flight trajectories

description: (x,y) coordinates of digitized flight trajectories from "Moving like a model: mimicry of hymenopteran flight trajectories by clearwing moths of Southeast Asian rainforests" Skowron Volponi, Marta, McLean, Donald, Volponi, Paolo, Dudley, Robert
DOI: 10.5061/dryad.748pd64/1
title: Occupancy data for Lower Keys marsh rabbits and free-ranging domestic cats from the Florida Keys

description: Detection data for marsh rabbits and domestic cats as well as covariates associated with each camera trap site.
DOI: 10.5061/dryad.7cr0c76/51
title: Binned-probabilities suitability prediction for California Heuchera MRCA: Last interglacial, wide-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 interglacial (120k-140k years ago), using wide-buffer models and normalized binned-probabilities maps.
DOI: 10.5061/dryad.7cr0c76/52
title: Binned-probabilities suitability prediction for Mitella MRCA: Holocene climatic optimum, distance-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 distance-buffer models and normalized binned-probabilities maps.
DOI: 10.5061/dryad.7cr0c76/53
title: Binned-probabilities suitability prediction for California Heuchera MRCA: Holocene climatic optimum, distance-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 distance-buffer models and normalized binned-probabilities maps.
DOI: 10.5061/dryad.7cr0c76/54
title: Binned-probabilities suitability prediction for Mitella MRCA: Last Glacial Maximum, distance-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 distance-buffer models and normalized binned-probabilities maps.
DOI: 10.5061/dryad.7cr0c76/55
title: Binned-probabilities suitability prediction for California Heuchera MRCA: Last Glacial Maximum, distance-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 distance-buffer models and normalized binned-probabilities maps.
DOI: 10.5061/dryad.7cr0c76/57
title: Binned-probabilities suitability prediction for California Heuchera MRCA: Last interglacial, distance-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 interglacial (120k-140k years ago), using distance-buffer models and normalized binned-probabilities maps.
DOI: 10.5061/dryad.7cr0c76/58
title: Simplified chloroplast genome phylogeny

description: This is a simplified version of Supplemental Figure S4, showing the most salient clades recovered with additional phylogenomic sampling.
DOI: 10.5061/dryad.7cr0c76/59
title: Chloroplast phylogenomic analysis -- best tree with bipartition frequencies

description: Analysis of all taxa (i.e., in some cases multiple accessions per species). 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.7cr0c76/60
title: Chloroplast phylogenomic analysis -- bootstrap trees

description: Analysis of all taxa (i.e., in some cases multiple accessions per species). 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).