cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5f1t0/1
title: Floral and fitness measures (seeds set and seeds sired) of Polemonium brandegeei pollinated by Ruby-Throated Hummingbirds (Archilochus colubris)

description: Floral traits measured from greenhouse raised plants.  Floral measurements are fully described in the methods of the manuscript.
DOI: 10.5061/dryad.5sk8g/1
title: RRM_optimization

description: RRM_Optimization: datasets. CS_ini.ini: Circuitscape template option file; fst.txt: Genetic data from Rogic et al. (2013); landscape7.asc: Land use raster with 7 classes; patches_centroids_100.asc: Mice population raster. workdir (EMPTY). Example.R: Main script to run the optimization. function_library.R: My function library. It is called from theExample.R script.
DOI: 10.5061/dryad.64fs5/1
title: PARENT_OFFSPRINGDATA

description: Here are genotypes of mother queen, her offspring and their father (spermatheca)
DOI: 10.5061/dryad.64fs5/2
title: POPULATIONDATA

description: Here are microsatellite genotypes from all the individuals collected from the hybrid population during time 1996 - 2011.
DOI: 10.5061/dryad.7m6kg/17
title: Fig. 4a: ROM 59658 – Nectocaris pteryx from the Burgess Shale

description: Part, under crossed polars
DOI: 10.5061/dryad.7m6kg/18
title: Fig. 4a: ROM 59658 – Nectocaris pteryx from the Burgess Shale

description: Part, direct illumination
DOI: 10.5061/dryad.7m6kg/23
title: Fig. 4b: ROM 60079 – Nectocaris pteryx from the Burgess Shale

description: Counterpart, direct illumination
DOI: 10.5061/dryad.85223/1
title: Figure 2, 3 & 5 data

description: Data used in Table 1 and Figures 2, 3 and 5 were derived from published papers obtained from Web of Knowledge search strings about brush management. These searches yielded 1350 unique papers published in refereed journals which were distilled to 364 papers that report quantitative responses to brush management. This database was further refined to 59 papers that directly quantified herbaceous production after brush management and these papers contribute the data shown in Figures 2, 3 and 5. Brush management was defined as mechanical, herbicide, fire, or treatments in combination and excluded studies that were confounded by continued sheep or cattle grazing on treatment sites. Of those 59 papers, 18 provided mean changes in herbaceous production with error on both control and treatment sites. Data from these 18 papers were used to generate Figures 2 and 3. Among those in the database of 1350 papers were 46 papers that directly measured changes in herbaceous diversity after brush management. Of those 46 papers, 29 provided mean changes in diversity (richness or Shannon diversity) with error on both control and treatment sites. Data from these papers were used to generate Figure 5. When multiple tables or figures are listed they represent data reported by site or year and were averaged in our dataset. Data originally published in figure format was quantified using Adobe Illustrator CS6 or DataThief III.
DOI: 10.5061/dryad.943j7/1
title: Supplement-Eocene abundance data

description: Species-level abundance data from 106 Lower and Middle Eocene stations, assigned to genera and families.
DOI: 10.5061/dryad.943j7/2
title: Supplement-Plio-Pleistocene abundance data

description: Species-level abundance in 48 Pliocene and Pleistocene stations, assigned to genera and families.
DOI: 10.5061/dryad.9tb73/1
title: FRUBASE dataset

description: The FRUBASE database, a huge dataset of fleshy fruit traits compiled from bibliographic references and my own work. Data are provided for more than 1000 plant species from all around the world. The FRUBASE package accompanies: Jordano, P. 1995. Angiosperm fleshy fruits and seed dispersers: a comparative analysis of adaptation and constraints in plant-animal interactions. American Naturalist 145: 163-191. It contains a copy of the main data file used for this paper, as well as other accompanying files (see below). Nomenclature and taxonomic arrangement follows Stevens, P. F. (2001 onwards). Angiosperm Phylogeny Website. Version 8, June 2007. http://www.mobot.org/MOBOT/research/APweb/. This scheme follows: A.P.G. [= Angiosperm Phylogeny Group] II. 2003. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II. Bot. J. Linnean Soc. 141: 399-436. Also see https://github.com/pedroj/FRUBASE.
DOI: 10.5061/dryad.f8j02/1
title: SI Exploring the Conditions Under Which Division of Labor Evolves

description: In this section of the paper, we presented an additional experiment performed using the Avida digital evolution software in which we vary the environmental conditions and explore whether or not division of labor will evolve. 

Within this file, the treatments are: 

a. unlimited resources
b. mutations occur during individual replication
c. migration rate of 10%

We used the shannon column to compute the information in the text.
DOI: 10.5061/dryad.f8j02/2
title: SI Intrinsic Task-Switching Costs

description: In this section of the paper, we presented an additional experiment performed using the Avida digital evolution software in which we limited the number of types of tasks available in the environment to 3, while maintaining the same resources levels, and resource requirements for replication (1000 units) as our other experiments. Within this file, the treatments are: e1000-3more. 1000 resources, 0 task-switching costs. d1000-3more. 1000 resources, 25 task-switching costs. e1000-3-more. 1000 resources, 50 task-switching costs. We used the shannon column to compute the information in the text.
DOI: 10.5061/dryad.fd31n/6
title: Env_assoc_sample_list

description: - Subpopulation of origin for samples in Env_assoc_SNP_table.txt and Env_assoc_subpop_data.txt. Each subpopulation represents a sampling location. D = dune, N = nondune, I = intermediate.
DOI: 10.5061/dryad.h02b3/12
title: Python modules required for dNCalcs_tBLASTx_clustal_ORF.py
DOI: 10.5061/dryad.h02b3/5
title: Python script for protein prediction and ka/ks calculations
DOI: 10.5061/dryad.h02b3/6
title: Python script for comparing duplicates

description: Includes selection of random sequence pairs.
DOI: 10.5061/dryad.h02b3/7
title: Python script for identifying duplicate pairs in Salmo salar
DOI: 10.5061/dryad.h02b3/8
title: Python script for carrying out a reciprocal BLAST search
DOI: 10.5061/dryad.m466f/18
title: hybridization_analysis

description: "hybridization_analysis.R" is a text file containing R code for replicating the analysis to detect hybridization based on inter-individual distances.  It was created in Emacs Speaks Statistics but can be opened in any text editor.  When executed in R, the working directory will need to contain the files in this data archive.
DOI: 10.5061/dryad.m466f/20
title: mean_distances

description: Mean pairwise genetic distances between the 579 samples analyzed.  These distances were calculated using the meandistance.matrix function in the R package "polysat" version 0.1, using the Bruvo.distance measure.  Each file contains a square matrix with row names and column names (sample names), as produced by the write.csv function in R version 2.11 under default parameters.
DOI: 10.5061/dryad.m466f/21
title: parviflorus

description: Samples in the "parviflorus" analysis group.
DOI: 10.5061/dryad.m466f/30
title: spectabilis

description: Samples in the "spectabilis" analysis group.
DOI: 10.5061/dryad.m466f/31
title: uncutcultivated

description: Samples in the "cultivated" analysis group with the "uncut" trnK allele (maternally derived from R. ursinus).
DOI: 10.5061/dryad.m466f/32
title: uncut_Structure

description: "uncut_Structure.txt" is a tab-delimited file containing genotypes for all individuals in the hybridization study with the "uncut" trnK chloroplast allele, formatted for the software Structure 2.3.3.  The file contains a row of marker names and a row of recessive allele symbols (all of them -9, the missing data symbol, to indicate allele copy number ambiguity), followed by the rows containing the genotypes.  The ploidy of the file is 8, so each individual is represented by eight rows.  The first column contains labels (sample names for each individual) and the second column contains numbers indicating population identity, corresponding to "LatOrder" in "species_chloroplast_latlong.csv".  This file was generated using the R package "polysat" version 0.1.
DOI: 10.5061/dryad.m466f/33
title: ursinus

description: Samples in the "ursinus" analysis group.
DOI: 10.5061/dryad.m466f/34
title: rubus_photos1

description: Photographs of plants sampled at sites ARC, ARP, BBG, and BWP.  Sample IDs can be seen within the images.  Image format is .jpg.
DOI: 10.5061/dryad.m466f/35
title: rubus_photos2

description: Photographs of plants at sites CMB, CSR, CSP, and CFX.  Sample IDs are shown within the images.  Images are in .jpg format.
DOI: 10.5061/dryad.nd2mb/7
title: Supplementary Figure 7

description: Comparison betweeen diversity trends using 0.5My bins and 1My bins (bold: with 1My bins, thin: with 0.5My bins). A. Range-through diversity in whole-fauna data. B. Range-through diversity in subsampled Neptune dataset (black: UW; grey: SQS). The quotas for 1My-bins subsampling are 20 collections for UW and 0.70 for SQS.
DOI: 10.5061/dryad.qc297/2
title: DATA TABLE 2 Early survival of focal snails

description: Measurements of early survival of inbred and outbred focal snails assessed under controlled laboratory conditions. For column abbreviations see data sheet 'DATA TABLE 2 Legend'.
DOI: 10.5061/dryad.s2479/1
title: microsatellite_data_Remon_et_al_PLOS_ONE_2013

description: Excel with microsatellite data from Iberolacerta populations used in this work
DOI: 10.5061/dryad.s2479/2
title: DL_cytb_final_Remon_et_al_PLOS_ONE_2013

description: Concatenated mitochondrial DNA sequences of control region and cytochrome b, for the different populations of Iberolacerta analyzed in this work.
DOI: 10.5061/dryad.sh53j/4
title: 4_longevity

description: Longevity data for male and female crickets as analysed in the section Postzygotic barriers in the Results section and depicted in Figure 4.
DOI: 10.5061/dryad.t66c7/1
title: Microsatellite data (17 loci) for 38 population samples of Malagasy Rattus rattus

description: L1: title; L2-18: locus names; individual genotypes in a "Genepop" format. Population samples are separated by "pop" and labelled according the 4 first letters of the individual code.
DOI: 10.5061/dryad.t66c7/2
title: Input datafile for the main DIYABC analyses of the paper: microsatellite and D-loop data for two Madagascan population samples

description: L1: title; L2-18: locus names; individual genotypes (Genepop format) for two population samples of Madagascar: DIE (Diego Suarez), north Madagascar,  and MAN (Mandena), south of Madagascar
DOI: 10.5061/dryad.t66c7/3
title: Code for Diyabc analyses

description: Reference table associated with the file DieMan_Dloop.txt and containing the code for scenarios, chosen prior distributions and summary statistics
DOI: 10.5061/dryad.t66c7/4
title: Assembly_Dloop

description: D-loop final sequence assembly for the 36 haplotypes found in Malagasy R. rattus
DOI: 10.5061/dryad.td20f/1
title: Garrick_et_al_MolEcol_DRYAD
DOI: 10.5061/dryad.v0v83/1
title: FlycatcherGenotype

description: These are the genotype files of collared flycatcher used for linkage analysis. Please see README.txt for more details.
DOI: 10.5061/dryad.v84n1/1
title: morphology data

description: morpho_data.txt: input file for morphometric analyses. Column 1: specimen voucher, Column2: Laboratory analyses ID, Column 3: Ecotype (Coastal or Pelagic), Column 4: Sex (Female, Male or Undetermined), Column 5: L1 = total body length, Columns 6 to 14: Ratio R(n) of each measurement L(n) on the total body length (L1)
DOI: 10.5061/dryad.v84n1/2
title: stable isotope data

description: stable_isotope_data.txt: input file for stable isotope analyses. Column 1: specimen voucher, Column 2: Laboratory analyses ID, Column 3: Ecotype (Coastal or Pelagic), Column 4: Sex (Female, Male or Undetermined), Column 5: Sulfur stable isotope values, Column 6: Carbon stable isotope values, Column7: Nitrogen stabe isotope values
DOI: 10.5061/dryad.vv2c1/1
title: Data from Drolet et al 2014

description: Data from the expert opinion survey on probability of eradication of aquatic non-indigenous species. The first sheet presents the ranks assigned by experts for levels within factors and among factors; each row presents ranks assigned by an individual expert.The second and third sheets present the qualitative and quantitative (respectively) expert prediction for probability of eradication for real case studies. The information used in the model, and the model's prediction is presented for each case study. More details about the case studies can be found at http://dx.doi.org/10.5061/dryad.1rh77
DOI: 10.5879/bils/ga00001
title: Data from: Peacefully extreme - loss of combative strategies in the unstressed, sugar-xerophilic mould, Xeromyces bisporus

description: Annotation in GFF3-format for the draft genome of Xeromyces bisporus. Genome available for download at EMBL, accession nr. PRJEB6149.
DOI: 10.7925/drs1.ucdlib_32023
title: 18 Anne Street South, Dublin 2, Ireland

description: Consists of an orthorectified image of the structure in Adobe PhotoShop (PSD) format. The orthorectified image has been derived from one or more photographic images that are included as layers in the original Adobe PhotoShop (PSD) file. The composite and all other image layers have been extracted and saved in TIFF image files, and JPEG files in various resolutions have been derived from the flattened image layer to facilitate inspection.
description: Brickwork structure, 4 levels above ground.
description: Dublin City Council, Record of Protected Structures (2010), no. 184
description: Funded by an award from the Irish Research Council for Science, Engineering and Technology (IRCSET), Embark Initiative Postgraduate Scholarship, grant identifier RS/2011/435.
DOI: 10.7925/drs1.ucdlib_32027
title: 21 Wicklow Street, Dublin

description: Consists of an orthorectified image of the structure in Adobe PhotoShop (PSD) format. The orthorectified image has been derived from one or more photographic images that are included as layers in the original Adobe PhotoShop (PSD) file. The composite and all other image layers have been extracted and saved in TIFF image files, and JPEG files in various resolutions have been derived from the flattened image layer to facilitate inspection.
description: Brickwork structure, 4 levels above ground, constructed 1914.
description: Funded by an award from the Irish Research Council for Science, Engineering and Technology (IRCSET), Embark Initiative Postgraduate Scholarship, grant identifier RS/2011/435.
DOI: 10.7925/drs1.ucdlib_32029
title: 20 Anne Street South, Dublin 2, Ireland

description: Consists of an orthorectified image of the structure in Adobe PhotoShop (PSD) format. The orthorectified image has been derived from one or more photographic images that are included as layers in the original Adobe PhotoShop (PSD) file. The composite and all other image layers have been extracted and saved in TIFF image files, and JPEG files in various resolutions have been derived from the flattened image layer to facilitate inspection.
description: Brickwork structure, 4 levels above ground.
description: Dublin City Council, Record of Protected Structures (2010), no. 187
description: Funded by an award from the Irish Research Council for Science, Engineering and Technology (IRCSET), Embark Initiative Postgraduate Scholarship, grant identifier RS/2011/435.
DOI: 10.7925/drs1.ucdlib_32031
title: 22 Wicklow Street, Dublin

description: Consists of an orthorectified image of the structure in Adobe PhotoShop (PSD) format. The orthorectified image has been derived from one or more photographic images that are included as layers in the original Adobe PhotoShop (PSD) file. The composite and all other image layers have been extracted and saved in TIFF image files, and JPEG files in various resolutions have been derived from the flattened image layer to facilitate inspection.
description: Brickwork structure, 4 levels above ground, constructed 1911.
description: Funded by an award from the Irish Research Council for Science, Engineering and Technology (IRCSET), Embark Initiative Postgraduate Scholarship, grant identifier RS/2011/435.
DOI: 10.7925/drs1.ucdlib_32033
title: 24 Wicklow Street, Dublin 2, Ireland

description: Consists of an orthorectified image of the structure in Adobe PhotoShop (PSD) format. The orthorectified image has been derived from one or more photographic images that are included as layers in the original Adobe PhotoShop (PSD) file. The composite and all other image layers have been extracted and saved in TIFF image files, and JPEG files in various resolutions have been derived from the flattened image layer to facilitate inspection.
description: Brickwork structure, 4 levels above ground.
description: Dublin City Council, Record of Protected Structures (2010), no. 8558
description: Funded by an award from the Irish Research Council for Science, Engineering and Technology (IRCSET), Embark Initiative Postgraduate Scholarship, grant identifier RS/2011/435.
DOI: 10.7925/drs1.ucdlib_32035
title: 27 Anne Street South, Dublin 2, Ireland

description: Consists of an orthorectified image of the structure in Adobe PhotoShop (PSD) format. The orthorectified image has been derived from one or more photographic images that are included as layers in the original Adobe PhotoShop (PSD) file. The composite and all other image layers have been extracted and saved in TIFF image files, and JPEG files in various resolutions have been derived from the flattened image layer to facilitate inspection.
description: Blockwork structure, 4 levels above ground, constructed ca. 1901.
description: Dublin City Council, Record of Protected Structures (2010), no. 194
description: Funded by an award from the Irish Research Council for Science, Engineering and Technology (IRCSET), Embark Initiative Postgraduate Scholarship, grant identifier RS/2011/435.
DOI: 10.5061/dryad.105c0/7
title: Hemocyanin F ortholog Group

description: Ortholog group F with Bayesian consensus trees
DOI: 10.5061/dryad.105c0/9
title: Hemocyanin All Paralog Concatenated

description: Concatenated data matrix of all hemocyanin paralogs with Bayesian consensus trees.
DOI: 10.5061/dryad.1k1ns/4
title: Lp02-AWE genome (GenBank format)

description: GenBank formatted file derived from editing NC_002942 (Legionella pneumophila subsp. pneumophila str. Philadelphia 1). Lp02 is a thymidine auxotroph, derived from Lp01 by trimethoprim selection. This sequence reflects the genome of the original Lp02 isolate in Alexander Ensminger's strain collection.
DOI: 10.5061/dryad.1p80f/1
title: pupfish shape

description: Procrustes residuals, source, sex, and centroid size data for 54 specimens of Cyprinodon pecosensis.  Data were collected from collections from the Museum of Southwestern Biology, University of New Mexico.  Accession numbers are as follows: Marsh sample: MSB 49238; Sinkhole sample: MSB 43612.
DOI: 10.5061/dryad.3c025/1
title: Sequences data matrix and trees

description: The original molecular data, and the results from ML, BI and BEAST analyses.
DOI: 10.5061/dryad.3c025/2
title: Body_length_Arg

description: The original body size data matrix
DOI: 10.5061/dryad.48s53/1
title: Data from: Evolution at a different pace: Distinctive phylogenetic patterns of cone snails from two ancient oceanic archipelagos

description: Combined data file: One fragment obtained with the universal primers 16Sar-L and 16Sbr-H (Palumbi, 1996), amplified a 472-base pair (bp) of the 16S rRNA gene in 115 specimens. The other fragment was obtained using C. guanche specific primers and amplified a 777-bp portion of the NADH dehydrogenase subunit 4 (NADH4) mitochondrial gene in 143 specimens. Additionally, a partial fragment (505 bp) of the internal transcribed spacer (ITS1) of nuclear-encoded ribosomal DNA was amplified in 129 specimens using C. guanche specific primers.
DOI: 10.5061/dryad.48s53/2
title: Data from: Evolution at a different pace: Distinctive phylogenetic patterns of cone snails from two ancient oceanic archipelagos

description: Mitochondrial fragment of 2,044 bp. This fragment includes the 3’ end of the 12S rRNA, the complete tRNA-Valine (Val), the 5’ portion of the 16S rRNA, and a partial sequence of the cytochrome b gene - cyt b
DOI: 10.5061/dryad.627ck/1
title: Capture and collection data

description: Geographic coordinates and number of bats captured/collected at sites in North American deserts
DOI: 10.5061/dryad.627ck/2
title: Community data

description: Community data matrices for each delimitation method for each desert
DOI: 10.5061/dryad.627ck/3
title: Tree files

description: Tree files used in phylogenetic community structure analyses and permuted trees used in sensitivity analyses
DOI: 10.5061/dryad.6t6k6/1
title: Cell densities, biovolume, and measures of diversity
DOI: 10.5061/dryad.6t6k6/2
title: Absorbance data and estimates of r, K, and N0
DOI: 10.5061/dryad.704g1/1
title: Trapping and PCR results for Tutuila, Aunu'u, Ofu, Olosega, and Ta'u islands villages
DOI: 10.5061/dryad.704g1/2
title: Trapping and PCR results for area in and around elementary school in Iliili village
DOI: 10.5061/dryad.7m6kg/21
title: Fig. 4b: ROM 60079 – Nectocaris pteryx from the Burgess Shale

description: ROM 60079, composite interference image of part and counterpart, showing coarse stripes and fine striations
DOI: 10.5061/dryad.7m6kg/22
title: Fig. 4b: ROM 60079 – Nectocaris pteryx from the Burgess Shale

description: Counterpart, crossed polars
DOI: 10.5061/dryad.7m6kg/31
title: Fig. 4d: ROM 60091 – Nectocaris pteryx from the Burgess Shale

description: Complete specimen; low angle light
DOI: 10.5061/dryad.7m6kg/32
title: Fig. 4d: ROM 60091 – Nectocaris pteryx from the Burgess Shale

description: Full specimen, crossed polars
DOI: 10.5061/dryad.7m6kg/75
title: Counterpart of ROM 61496 — Large morph of Nectocaris from the Burgess Shale

description: Images of the counterpart of ROM 61496; one (_271) under cross polars, the other (_265) in low angle light to highlight relief.
DOI: 10.5061/dryad.7st32/1
title: SM_A2_rawdata_full

description: Excel file with separate worksheets including: Raw visitation data, aggregate network, plant densities, and morphology classification matrices for plants and pollinators.
DOI: 10.5061/dryad.7st32/2
title: SM_A3_Rcode_rquantwebs

description: R code for the algorithm used to generate random interaction frequency matrices from the different probability models used in the study.
DOI: 10.5061/dryad.8h7k1/1
title: tapir_gh_uniq

description: This file presents the number of occurrences of each sequence (the trnL P6 loop) in the different faecal samples from tapirs.The sequences have been generated by the Illumina technology (Illumina/Solexa Genome Analyzer IIx).The sequences are sorted starting with the most repeated ones among all the samples.Data collection:  Fabrice Hibert, Pierre Taberlet, Jérôme Chave, Caroline Scotti-Saintagne, Daniel Sabatier , Cécile Richard-Hansen Contact author:     Fabrice Hibert (fabricenz@gmail.com)
DOI: 10.5061/dryad.8h7k1/2
title: tapir_itsSap_uniq

description: This fasta file presents the number of occurrences of each sequence (the first internal transcribed spacer (ITS1) of nuclear ribosomal DNA, for the Sapotaceae ) in the different faecal samples from tapirs.The sequences have been generated by the Illumina technology (Illumina/Solexa Genome Analyzer IIx).The sequences are sorted starting with the most repeated ones among all the samples.Data collection:  Fabrice Hibert, Pierre Taberlet, Jérôme Chave, Caroline Scotti-Saintagne, Daniel Sabatier , Cécile Richard-Hansen Contact author:     Fabrice Hibert (fabricenz@gmail.com)
DOI: 10.5061/dryad.8h7k1/3
title: tapir_gh_filtered
DOI: 10.5061/dryad.8h7k1/4
title: tapir_itsSap_filtered
DOI: 10.5061/dryad.943j7/3
title: Supplement-Eocene station data
DOI: 10.5061/dryad.943j7/4
title: Supplement-Plio-Pleistocene station data