cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6gf28/1
title: S1_VarData

description: Compiled table of evolved variants used to produce Figure 1. Columns refer to sample number (sample_number), whether the clone had evolved in a population with or without the plasmid (plasmid_trt, pQBR57 = plasmid-containing, plasmid- = plasmid free), with or without the other species (cul, ss = single-species, co=co-culture), the level of mercury treatment (mer, in µg/g), replicate (rep), species (spc, Pf = P. fluorescens, Pp = P. putida), whether the clone was carrying a plasmid (plasmid, P = plasmid+, T = contained Tn5042 but not the plasmid, 0 = contained neither plasmid nor Tn5042), the chromosome in which the variant was detected (chr, numbers are as the EMBL database with AM181176 referring to the P. fluorescens SBW25 chromosome, AE015451 to the P. putida KT2440 chromosome and LN713926 referring to pQBR57), the position of the variant (position and position.1, where the variant is a SNV/indel these numbers are identical and refer to the first base in question, where the variant is a TE insertion these numbers refer to the boundaries of the direct repeat caused on insertion, where the variant is a duplication or deletion these numbers refer to the start and end of the event respectively), the target gene (target, where the target it intergenic the upstream and downstream genes are given, separated by a dash), the type of mutation (type, either SNV/indel, or, if a TE insertion, the name of the TE), and the predicted effect of the mutation (effect, as determined by snpEff).
DOI: 10.5061/dryad.6gf28/2
title: S2_Hg_transfer_data

description: Comma-separated values formatted file containing data presented in Figure 2. Columns refer to replicate (rep), transfer number (transfer), antibiotic marker of the donor strain (donor_marker), mercury treatment in µg/g soil (mercury), and the estimated densities of donors and recipients with and without plasmid in cfu/g soil.
DOI: 10.5061/dryad.7mg3h/1
title: All data
DOI: 10.5061/dryad.9m5h0/7
title: ParseDups_ODBv9.1.pl

description: Perl script that uses an OrthoDB v9.1 tab delimited file to identify EOGs with a certain number of genes per species, which was used to identify genes that were duplicated in A. mellifera but single copy in every other species in the Apoidea.

ie. perl parse_full_orthodb9v1_byStuff.pl ODB_v9.1_input.txt 7460.1.1,	7461.1.1,	7462.1.1,	7463.1.1,	30195.1.1,	88501.1.1,	132113.1.1,	143995.1.1,	166423.1.1,	178035.1.1,	516756.1.1,	597456.1.1 ODB_v9.1_output.txt

Further details on how to run the script can be found in the file.
DOI: 10.5061/dryad.9m5h0/8
title: Apoidea_DupRates.txt

description: Text file with 10 bees in the Apoidea, along with the number of species-specific duplicates, divergence time, duplication rate, and social state. Divergence time was taken from Cardinal and Danforth (2013). Social State was determined from Kapheim et al. (2015).
DOI: 10.5061/dryad.9m5h0/9
title: README

description: Read me text.
DOI: 10.5061/dryad.bt651/1
title: Supplementary_Data_July_29_2017_

description: T1 Metatherian fossil dataset
T2 Bibliographical references for datasets
T3 Correlations between time bin length, number of genera and number of sites
T4 Preservation, Origination and Extinction Rates
T5 Coverage and sampling target
T6 Prolific sites list
T7 South American diversity curve calculated by SQS method with target set to 0 0.3
DOI: 10.5061/dryad.bt651/2
title: Supplementary_Text_1

description: R code for Metatheria Diversity Curves using Classic Rarefaction
DOI: 10.5061/dryad.bt651/3
title: Supplementary_Text_2

description: R code for Metatheria Diversity Curves using SQS
DOI: 10.5061/dryad.c1b4h/1
title: Dataset S1. List of Red Sea and Mediterranean bivalve species used in the analyses.

description: List of bivalve species reported from shelf depths in the Mediterranean Sea and the Red Sea, their alien status in the Mediterranean, body size, and taxonomic and functional affiliation.
DOI: 10.5061/dryad.c1b4h/2
title: Dataset S2. Body size of Lessepsian bivalves in their native and invaded range.

description: Body size data for Brachidontes pharaonis and Pinctada imbricata radiata from multiple sites across their native (Red Sea and NW Indian Ocean) and invaded range (Mediterranean Sea and Suez Canal).
DOI: 10.5061/dryad.cc2tc/1
title: Janes et al. (2017). The K=2 conundrum. Review data and simulations.

description: The zip file contains the raw meta-analysis/review data and all data associated with the simulations and STRUCTURE runs.
DOI: 10.5061/dryad.d6q6b/1
title: Working Master Data Sheets

description: Raw data used for GLMM analysis.
DOI: 10.5061/dryad.f4m6k/1
title: SOC stocks, soil properties, topographical attributes and vegetation characteristics of a tropical montane landscape

description: Please see ReadMe file.
DOI: 10.5061/dryad.h21v2.1/6.1
title: Candidate genes for UV floral patterning

description: List of candidate genes under the four proportional UV pigmentation QTL matched against the Arabidopsis thaliana TAIR10 protein database using blastp (e &lt; e-20; Lamesch et al., 2011). Filtered specifically for proteins with WD or bHLH functional domains or part of the MYB or UDP-glycotransferase families. Column headers: which (filtered functional category), HaName (id of Helianthus annuus mRNA), AtName (best Arabidopsis thaliana hit), evalue (match value), chr (Helianthus annuus chromosome number), program (maker for this analysis), type (all genes in this analysis), start (start of gene in basepairs), end (end of gene in basepairs), score (NA), strand (+ or -), phase (NA), ID (internal id), Name (internal name), followed by functional annotation of that protein.
DOI: 10.5061/dryad.h9f3c/1
title: Byrne_et_al_data_readme

description: Information about contents of data files for tagging, fate, and harvest information.
DOI: 10.5061/dryad.h9f3c/2
title: Byrne_et_al_Mako_Tagging_Fate_data

description: Tagging information and ultimate fate of all mako sharks in this study.Can be used to recreate survival analysis
DOI: 10.5061/dryad.h9f3c/3
title: Byrne_et_al_Harvest_data

description: Information on all harvest events
DOI: 10.5061/dryad.jn6vn/2
title: Dorsal landmarks

description: TPS with the dorsal landmarks position. Landmarks are already scaled. Individuals are identified with their FC code.
DOI: 10.5061/dryad.jn6vn/3
title: Lateral Landmarks

description: TPS with the lateral landmarks position. Landmarks are already scaled. Individuals are identified with their FC code.
DOI: 10.5061/dryad.kq30q/1
title: RazoBelmanetal_(2017) Journal of Ecology 2017-0005

description: All data on volatile organic compounds (VOCs) emitted from Acacia branches (sheet 1), extrafloral nectar (EFN) secretion (sheet 2), data on EFN secretion and VOC emission from the same branches that were used in Fig. 3 (sheet 3), results of the behavioural assays of ant queens in the cage (sheet 4) and in the olfactometer (sheet 5) and data of the inhibition assays using natural bacterial pathogens (sheet 6).
DOI: 10.5061/dryad.n7n71/10
title: Detailed Methods

description: Microsoft Word file that describes laboratory and computational approaches.
DOI: 10.5061/dryad.n7n71/11
title: Scripts

description: Please see ReadMe file.
DOI: 10.5061/dryad.n7n71/7
title: Data Files

description: Please see ReadMe file.
DOI: 10.5061/dryad.n7n71/8
title: Tree Files

description: Please see ReadMe file.
DOI: 10.5061/dryad.n7n71/9
title: Dating Analyses

description: Please see ReadMe file.
DOI: 10.5061/dryad.pk84p/5
title: VIDEO 5-Agonistic interaction in Anolis proboscis-part I

description: Agonistic Interaction. Bite attempts, rostral appendage lifting, displays with half dewlap extensions and low push-ups. Pushes with the tip of the snout and a bite in the throat of one of the males are observed.
DOI: 10.5061/dryad.pk84p/6
title: VIDEO 6-Agonistic interaction in Anolis proboscis-part II

description: Agonistic Interaction 2. ‘Agonistic’ display, bite attempts, rostral appendage lifting, tail movements, displays with half dewlap extensions and low push-ups, and jaw locking can be observed.
DOI: 10.5061/dryad.pv583/1
title: A Drosophila Model for Developmental Nicotine Exposure_DATA

description: This Excel file includes all the data used to generate the figures in the associated manuscript. The first Tab in the spreadsheet is an Index Tab with information about which set of data corresponds to which panel in which figure in the manuscript. Each Tab has data for a single type of experiment. The experiment type is the label of the Tab. At the top of each worksheet there is a short description of what the experiment tested, information about abbreviations used for that set of data, and any additional analyses particular to those data. Additional information can be found in the README file.
DOI: 10.5061/dryad.q6h2n/1
title: Sample info

description: Sample descriptions and id.
DOI: 10.5061/dryad.q6h2n/2
title: tag primers

description: Tag primers used in the pyrosequencing with corresponding samples and sequencing plate id.
DOI: 10.5061/dryad.q6h2n/3
title: Pyrosequencing plate 1

description: fasta, qual and sff file from pyrosequencing plate 1.
DOI: 10.5061/dryad.q6h2n/4
title: pyrosequencing plate 2

description: fasta, qual and sff file from pyrosequencing plate 2.
DOI: 10.5061/dryad.q6h2n/5
title: Pyrosequencing plate 3

description: fasta, qual and sff file from pyrosequencing plate 3.
DOI: 10.5061/dryad.q6h2n/6
title: Pyrosequencing plate 4

description: fasta, qual and sff file from pyrosequencing plate 4.
DOI: 10.5061/dryad.rq560/15
title: Imaging Data - Part 12

description: Calcium imaging data recorded during head-fixed awake in vivo two-photon imaging experiments. Data is designed to be read by corresponding figure code at https://github.com/losonczylab/Zaremba_NatNeurosci_2017.
DOI: 10.5061/dryad.rq560/16
title: Imaging Data - Part 13

description: Calcium imaging data recorded during head-fixed awake in vivo two-photon imaging experiments. Data is designed to be read by corresponding figure code at https://github.com/losonczylab/Zaremba_NatNeurosci_2017.
DOI: 10.5061/dryad.rq560/17
title: Imaging Data - Part 14

description: Calcium imaging data recorded during head-fixed awake in vivo two-photon imaging experiments. Data is designed to be read by corresponding figure code at https://github.com/losonczylab/Zaremba_NatNeurosci_2017.
DOI: 10.5061/dryad.rq560/18
title: Imaging Data - Part 15

description: Calcium imaging data recorded during head-fixed awake in vivo two-photon imaging experiments. Data is designed to be read by corresponding figure code at https://github.com/losonczylab/Zaremba_NatNeurosci_2017.
DOI: 10.5061/dryad.rq560/19
title: Imaging Data - Part 16

description: Calcium imaging data recorded during head-fixed awake in vivo two-photon imaging experiments. Data is designed to be read by corresponding figure code at https://github.com/losonczylab/Zaremba_NatNeurosci_2017.
DOI: 10.5061/dryad.t5pv8/1
title: submit Dryad data
DOI: 10.5061/dryad.t8t25/6
title: Flight-initiation-distance, age, and sampling interval data

description: Flight-initiation distance measurements, age, and sampling interval of 99 individuals used in 'Personality-matching habitat choice, rather than behavioural plasticity, is a likely driver of a phenotype-environment covariance'.
DOI: 10.17632/k29djg6sy5.1
title: Data for: When the human spirit helps? The moderating role of somatization on the association between Olympic game viewing and the will-to-live

description: The moderating role of somatization on the association between Olympic game viewing and WTL
DOI: 10.17632/k29djg6sy5.2
title: Data for: When the human spirit helps? The moderating role of somatization on the association between Olympic game viewing and the will-to-live

description: The moderating role of somatization on the association between Olympic game viewing and WTL
DOI: 10.5061/dryad.14v89/1
title: TAGS

description: A summary of tagged individuals. The variables DURATION_MAX and IDDI_MED were calculated from the behavior log returned by Argos satellites from SPLASH (Mk10a) transmitter tags produced by Wildlife Computers. The variable MASS_MED was calculated from models of body mass as a function of standard length. The variable MB derived from a variety of literature sources.
DOI: 10.5061/dryad.14v89/2
title: ARGOS

description: Location estimates and time stamps returned by Argos satellites from SPOT5 and SPLASH (Mk10a) tags produced by Wildlife Computers. Location error information derives from Argos Kalman filtering algorithm.
DOI: 10.5061/dryad.14v89/3
title: BEHAV

description: A log of dives and surface intervals returned by Argos satellites from SPLASH (Mk10a) transmitter tags produced by Wildlife Computers. Depths represent the maximum depth recorded on a dive, the duration of which was defined as the interval between successive dry measurements on the wet-dry sensor. Dives that did not exceed 15m was logged as Surface Time.
DOI: 10.5061/dryad.14v89/4
title: SERIES

description: A moderate resolution time series of time-depth recorder (TDR) measurements returned via Argos satellites from SPLASH (Mk10a) transmitter tags produced by Wildlife Computers.
DOI: 10.5061/dryad.14v89/5
title: TAT

description: Histograms representing the proportion of time a tag spent in 12 temperature bins define in 2C increments between 4C and 24C TAT histograms were returned by Argos satellites from SPOT5 tags produced by Wildlife Computers. TAT were collected in 6-hour sampling periods, and sampling periods were programmed to begin at 01:00, 07:00, 13:00, or 21:00 local time, so that the majority (&gt;80%) of sampling of each TAT histogram fell within either daytime or nighttime. TAT histograms that were translated into units of depth using the hydrographic data and interpolation methods detailed in Joyce et al. (2016).
DOI: 10.5061/dryad.14v89/6
title: PHYLO_DATA

description: A table of species used to implement a phylogenetic generalized least squares (PGLS) inter-specific comparative analysis. Aside from the five species tagged in this study maximum dive duration (Tmax) and inter-deep-dive interval (IDDI) as well as body mass (m) and myoglobin concentration ([Mb]) derive from literature-reported values or were extracted from supplemental materials.
DOI: 10.5061/dryad.14v89/7
title: Cetacean_Analysis_Import & Processing_0.6

description: R script importing and processing data files used in the analyses of presented in this paper.
DOI: 10.5061/dryad.1rd0m/10
title: Table S2

description: Regions removed from the alignment of DNA sequences and rationale for the removal.
DOI: 10.5061/dryad.1rd0m/11
title: Table S3

description: Primers used for PCR.
DOI: 10.5061/dryad.1rd0m/12
title: Table S4

description: Details of settings used in BEAST.
DOI: 10.5061/dryad.25b8f/10
title: CTmin_5d_8_23

description: CTmin_5d_8_23: 5day old flies developed at average temperature 23°C, with an amplitude of +/- 8°C and shifted as adults to opposite treatment regime, assayed for CTmin
DOI: 10.5061/dryad.25b8f/11
title: CTmax_9d_4_19

description: CTmax_9d_4_19: 9day old flies developed at average temperature 19°C, with an amplitude of +/- 4°C and shifted as adults to opposite temperature regime, assayed for CTmax
DOI: 10.5061/dryad.25b8f/12
title: CTmax_9d_4_23

description: CTmax_9d_4_23: 9day old flies developed at average temperature 23°C, with an amplitude of +/- 4°C and shifted as adults to opposite temperature regime, assayed for CTmax
DOI: 10.5061/dryad.25b8f/13
title: CTmin_9d_4_19

description: CTmin_9d_4_19: 9day old flies developed at average temperature 19°C, with an amplitude of +/- 4°C and shifted as adults to opposite temperature regime, assayed for CTmin
DOI: 10.5061/dryad.25b8f/14
title: CTmin_9d_4_23

description: CTmin_9d_4_23: 9day old flies developed at average temperature 23°C, with an amplitude of +/- 4°C and shifted as adults to opposite temperature regime, assayed for CTmin
DOI: 10.5061/dryad.25b8f/15
title: CTmax_9d_8_19

description: CTmax_9d_8_19: 9day old flies developed at average temperature 19°C, with an amplitude of +/- 8°C and shifted as adults to opposite temperature regime, assayed for CTmax
DOI: 10.5061/dryad.25b8f/16
title: CTmax_9d_8_23

description: CTmax_9d_8_23: 9day old flies developed at average temperature 23°C, with an amplitude of +/- 8°C and shifted as adults to opposite temperature regime, assayed for CTmax
DOI: 10.5061/dryad.25b8f/8
title: CTmax_5d_8_23

description: CTmax_5d_8_23: 5day old flies developed at average temperature 23°C, with an amplitude of +/- 8°C and shifted as adults to opposite treatment regime, assayed for CTmax
DOI: 10.5061/dryad.25b8f/9
title: CTmin_5d_8_19

description: CTmin_5d_8_19: 5day old flies developed at average temperature 19°C, with an amplitude of +/- 8°C and shifted as adults to opposite treatment regime, assayed for CTmin
DOI: 10.5061/dryad.2n430/1
title: Fruit production of Poulsenia armata

description: Data on annual fruit and seed production for Poulsenia armata at Los Tuxtlas forest, Mexico, from 2010 to 2012. Data includes tree tag, name of the plot and habitat type.
DOI: 10.5061/dryad.438q3/1
title: Viehman and Zydlewski 2017 Fish Count Data

description: This .csv file contains the two-year time series of the hourly counts of fish that were used in the publication, with corresponding tidal and diel stages.
DOI: 10.5061/dryad.68ff1/9
title: Subject Information

description: An XLS file containg basic information used to determine a subject's age at each session.
DOI: 10.5061/dryad.6gf28/3
title: S3_Tn5042_PP_Data

description: Comma-separated values formatted file containing data presented in Figure 3.  Columns refer to whether the population was evolved alone or in co-culture (cul, ss= single-species, co = co-culture), population (pop), transfer number (transfer), total clones tested (total_tested), total clones plasmid-free (free), total plasmid-containing clones with the focal Tn5042 insertion (p_focal_tn), total plasmid-free clones with the focal Tn5042 insertion (free_focal_tn), total plasmid-free clones with a different Tn5042 insertion (other_tn), and calculated frequencies of plasmid-free cells (free.f), plasmid-containing clones with the focal Tn5042 insertion (p_focal_tn.f), plasmid-free cells with the focal Tn5042 insertion (free_focal_tn.f), plasmid-free cells with a different Tn5042 insertion (other_tn.f), plasmid-free cells with no Tn5042 insertion (free_none.f) and plasmid-containing cells without the focal Tn5042 insertion (p_none.f)
DOI: 10.5061/dryad.6gf28/4
title: S4_Tn5042_PF_Data

description: Comma-separated values formatted file containing data presented in Figure 3. Columns refer to transfer number (transfer), total clones tested (total_tested), total clones plasmid-free (free), total plasmid-containing clones with the focal Tn5042 insertion (p_focal_tn), total plasmid-free clones with the focal Tn5042 insertion (free_focal_tn), total plasmid-free clones with a different Tn5042 insertion (other_tn), and calculated frequencies of plasmid-free cells (free.f), plasmid-containing clones with the focal Tn5042 insertion (p_focal_tn.f), plasmid-free cells with the focal Tn5042 insertion (free_focal_tn.f), plasmid-free cells with a different Tn5042 insertion (other_tn.f), plasmid-free cells with no Tn5042 insertion (free_none.f) and plasmid-containing cells without the focal Tn5042 insertion (p_none.f)
DOI: 10.5061/dryad.6gf28/5
title: ExtensiveGeneExchange_Scripts

description: Zip file (17 files) containing scripts representative of those used to generate data presented in the manuscript.
DOI: 10.5061/dryad.75r10/1
title: data file
DOI: 10.5061/dryad.9g5m2/1
title: Data I.D. Bos- Touwen clinical vignette study
DOI: 10.5061/dryad.bk760/1
title: figure1

description: Best solution of planning units with a target of 10 without and with trophic weighting (= scaling 0.01-1). (a) red coloured areas show planning units (pu) selected in scenarios without trophic weighting (b) green coloured areas show planning units selected in scenarios with trophic weighting (c) difference in selected planning units with (green area) and without (red area) trophic weighting, grey coloured areas show planning units selected in both scenarios. Broad blue line indicates main stem; thin blue lines indicate tributaries of the Danube River.
DOI: 10.5061/dryad.bk760/2
title: Figure2

description: Effect of incorporating trophic level information and different weightings on average proportion of predator species per planning unit in chosen area. Average proportion of predator species for all planning units is indicated by orange line; Average proportion of predator species in chosen areas is shown for each target in runs without trophic information and for each target and weighting in runs with trophic information. Proportion of predator species for each target of runs without trophic information are drawn with thicker, solid lines and over all weightings, although no weighting was performed, to illustrate the difference between runs with trophic information, which are drawn with thinner, dashed lines. Trophic weighting is ratio highest to lowest with 3 being a weighting of 0.3-1, 4 being 0.25-1, 5 being 0.2-1, 6 being 0.15-1, 10 being 0.1-1, 20 being 0.05-1 and 100 being 0.01-1. a indicates significant difference (p &lt;0.001) between scenarios with the same target.
DOI: 10.5061/dryad.bk760/3
title: figure3

description: Effect of incorporating trophic level information and different weightings on average proportion of predator species per planning unit in unique chosen area. Average proportion of predator species for all planning units is indicated by orange line; Average proportion of predator species in chosen area unique to either runs without or with trophic information is shown for each target and each weighting. Proportion of predator species for runs without trophic information are drawn with thicker solid lines. Proportion of predator species for runs with trophic information are drawn with thinner dashed lines. Trophic weighting is ratio highest to lowest with 3 being a scaling of 0.3-1, 4 being 0.25-1, 5 being 0.2-1, 6 being 0.15-1, 10 being 0.1-1, 20 being 0.05-1 and 100 being 0.01-1. a and b indicate significant difference (p &lt; 0.001 and  p &lt; 0.05 respectively) between scenarios with the same target.
DOI: 10.5061/dryad.bk760/4
title: Appendix S1_ Species trophic level according to FishBase and assigned group

description: Species trophic level according to FishBase and assigned group
DOI: 10.5061/dryad.c063r/1
title: Supplementary File 1

description: Supplementary File 1. Species richness, clade ages, and stem and crown diversification rates for 72 families of squamates.
DOI: 10.5061/dryad.c063r/2
title: Supplementary File 2

description: Supplementary File 2. Species richness, clade ages, and stem and crown diversification rates for 505 genera of squamates.
DOI: 10.5061/dryad.c063r/3
title: Supplementary File 3

description: Supplementary File 3. Microhabitat data for all squamate species included in this study, including references.
DOI: 10.5061/dryad.c063r/4
title: Supplementary File 4

description: Supplementary File 4. Raw and logit-transformed data for proportional and strict proportions of microhabitat use for 72 squamate families.
DOI: 10.5061/dryad.c063r/5
title: Supplementary File 5

description: Supplementary File 5. Raw and logit-transformed data for strict proportions of microhabitat use and climatic distribution for 505 squamate genera
DOI: 10.5061/dryad.c063r/6
title: Supplementary File 6

description: Supplementary File 6. Climatic distribution for all squamate species analyzed in this study.
DOI: 10.5061/dryad.cr43m/1
title: Diet.lion.leo

description: Data used to estimate dietary breadth and overlap for lions and leopards in the Sabi Sand Game Reserve, South Africa, from 2013 to 2015.
DOI: 10.5061/dryad.cr43m/2
title: GLMM.lion.risk

description: Data used in generalised linear mixed models assessing the probability of leopard occurrence (presence/absence) in relation to habitat type and the long-term risk of encountering lions in the Sabi Sand Game Reserve, South Africa, in 2015.