cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.n5h13/4
title: Analysis files

description: Each tab contains file used to execute statistical test performed in JMP.
DOI: 10.5061/dryad.n5h13/5
title: COI Sequencer file

description: Sequences used for identification.  Raw .ab1 files edited and aligned using Sequencher software.
DOI: 10.5061/dryad.p5614/1
title: Data PONE-D-14-18420

description: This is an excel file containing the data underlying the results described in each manuscript. This file contains 11 spreadsheets, containing the raw data of 1) Dyrk1A protein levels, 2) MWM performance, 3) CFC performance, 4) Rotarod Performance, 5) Open Field performance, 6) LTP results, 7) GAD65/67 and VGLUT levels and VGLUT/GAD65/67 ratio, 8) Ki67, DCX, CLR and DAPI values, 9) DG volume and SGZ ratio, 10) Body weight and 11) Motor tests data
DOI: 10.5061/dryad.q03g2/10
title: Slope GIS raster layer

description: Slope (in degrees), untransformed (i.e., slope^1); Albers Equal Area projection (Africa)
DOI: 10.5061/dryad.q03g2/11
title: Elephant Genetic Sampling GIS Polygons

description: GIS polygons describing the extent of genetic sample locations for each population, Albers Equal Area (Africa)
DOI: 10.5061/dryad.q9s30/1
title: Vargas-Ramirez et al. 2013 APPENDICES

description: APPENDIX I and APPENDIX II
DOI: 10.5061/dryad.r139p/2
title: Population locations for Leavenworthia stylosa and field and genetic population means

description: Latitude and longitude for 68 extant Leavenworthia stylosa populations. Population means for density, coefficient of variation for plant density, flower number, fruit number, fruit set, and average seed number per flower. All population means were collected in the field by AL Dixon, CR Herlihy, and JW Busch. Expected heterozygosity and allelic diversity were calculated using GENEPOP and HP-RARE, respectively from 12 microsatellite loci scored by AL Dixon at Washington State University.
DOI: 10.5061/dryad.r2n58/1
title: D buzzatii_GENEPOP_data_file

description: Genotypic data for seven allozyme loci for D. buzzatii flies collected at 67 localities, with a total of 195 samples (collections made more than once at 26 localities). File format - GENEPOP
DOI: 10.5061/dryad.r2n58/2
title: Supplementary Table 1

description: Identification of the 67 localities (listed north to south), locality code numbers, geographical coordinates and sample size (number of genes assayed)
DOI: 10.5061/dryad.r8n7c/10
title: Alignment of short historical COI sequences
DOI: 10.5061/dryad.sn1m7/2
title: phylog_syl_input_tess

description: fichier input for TESS analyses
DOI: 10.5061/dryad.v6f4d/10
title: bgc input file for hybrid-parent test population, all 77 markers

description: bgc input file for hybrid-parent test population, all 77 markers
DOI: 10.5061/dryad.v6f4d/11
title: a.out_parental sympatry

description: Output from BGC run on parental sympatry test population: estimates of cline parameter alpha for the 77 loci.
DOI: 10.5061/dryad.v6f4d/4
title: Genotypes for parental sympatry test population

description: Genotypes for the individuals in the admixed test population. 'BGC column' refers to the number given to indivudlas by the bgc output.
DOI: 10.5061/dryad.v6f4d/5
title: Genotypes for the hybrid-parents test population

description: Genotypes for the individuals in the hybrid-parents test population. 'BGC column' refers to the number given to individuals by the bgc output.
DOI: 10.5061/dryad.v6f4d/6
title: File to link locus names with bgc output

description: File showing which loci refers to which 'bgc output number' for all 77 markers, only autosomal markers and only Z-linked markers
DOI: 10.5061/dryad.v6f4d/7
title: File with the code used when running bgc

description: File with the code used when running bgc
DOI: 10.5061/dryad.v6f4d/8
title: bgc input file for house sparrow parental population (reference population), all 77 markers

description: bgc input file for house sparrow parental population (reference population)
DOI: 10.5061/dryad.v6f4d/9
title: bgc input file for Spanish sparrow parental population (reference population), all 77 markers

description: bgc input file for Spanish sparrow parental population (reference population)
DOI: 10.5061/dryad.vg0b5/1
title: BiofilmCheatingData
DOI: 10.7925/drs1.ucdlib_31937
title: Tangier Lane 2

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 & stone structure, 4 levels above ground.
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_31939
title: Tangier Lane 3

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: 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_31941
title: 5 Johnson's Place, 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: Rendered facade structure, 2 levels above ground.
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_31943
title: Tangier Lane 5

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: 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_31945
title: Tangier Lane 6

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, 3 levels above ground.
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_31947
title: 34-39 Nassau Street, Dublin

description: Consists of 2 orthorectified images of the structure. The orthorectified images have been derived from one or more photographic image that are included as layers in the original Adobe PhotoShop (PSD) file. The composite and other image layers have been extracted and saved in TIFF image files, as well as JPEG files in various resolutions to facilitate inspection.
description: Frame structure, 5 levels above ground.
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_31949
title: 6-9 Trinity 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: Frame structure, 5 levels above ground.
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_31951
title: 44 Nassau 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.
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_31953
title: 9B Trinity 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, 5 levels above ground.
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.16737/3
title: Acuclavella_EF1a_Richart&Hedin

description: 30 Acuclavella ingroup sequences with intron.
DOI: 10.5061/dryad.25696/3
title: Table2_matchedprobes_bothComp
DOI: 10.5061/dryad.25696/4
title: Table2_LRvsPS_Neoprobes
DOI: 10.5061/dryad.2k462/2
title: Data for Figure 2 (part 2)

description: Data for figure 2 (part 2), see README.Rmd
DOI: 10.5061/dryad.331f7/1
title: Data extraction

description: Audited table of extracted and derived variables. Data were extracted on MS Word extraction tables. These tables were then brought into Microsoft Excel. Subsequently selected variables were audited (double-checked) and are presented in this Excel file. The Excel file contains multiple "sheets" (worksheets). Their contents are described in the readme file.
DOI: 10.5061/dryad.3qd54/5
title: Neobatrachia_mt_nucleotide

description: Mitochondrial nucleotide data set, including all codon positions of protein-coding genes.
DOI: 10.5061/dryad.5j2h4/1
title: HabronattusChromosomes2013-MaddisonLeducRobert

description: DNA sequences from Maddison & Hedin (2003), realigned, plus original observations on sex chromosomes and chiasma localization.  Phylogenies from BEAST analysis and Maddison & Hedin 2003.
DOI: 10.5061/dryad.6c44q/4
title: Macro_Spatial_Dispersion

description: Given a set of isotropic, equidimensional binary stacks of squared images, this ImageJ macro calculates the number of 
cycles of rhombicubocthedric dilation necessary to fill 90%, 95% and 99% of each volume 
on the basis of the distribution of the black pixels. The macro asks for a source folder containing
a set of subfolders (mandatory) containing binary image stacks (.tif files) with equal dimensions.
The procedure  is iterated over the nested folders for all the images present in every folder. 
The results are saved in a target location, choosed by the operator, as a number of .txt result files 
- one for each subfolder - named after the source subfolders.
Results are expressed as raw values (Hv) which are normalized, subfolder after subfolder,
according to the highest percentual volume observed in each subfolder to give nHv results. To 
normalize all subfolders in a single run, the image presenting the highest percentual volume 
should be present in all subfolders.

This macro has been validated against simple images manually dilated. This version analyzes all .tif stacks
present in nested folders. It behaves alike the accompanying ImageJ plugin but it is at least an order of magnitude slower. Its function was essentially that of validating the results obtained with the plugin.
DOI: 10.5061/dryad.7535k/10
title: raref_nG6XN_nchl_filtered_sorted_host_L2

description: This phylum table was built in QIIME from raref_nG6XN_nchl_filtered_sorted_host_L7.txt. Chloroplast sequences and the most shallowly sequenced sample (G6CXN) are removed, and all samples have been rarefied to the next most shallowly sequenced sample (202 sequences). Columns are sorted by host. This table was used for ANOVAs conducted on individual taxa.
DOI: 10.5061/dryad.7535k/3
title: nG6XN_nchl_filtered_sorted_host

description: OTU table built in QIIME from NiwotB_all_denoised.fna. This table has had chloroplast sequences removed. Also the most shallowly sequenced sample (G6CXN) has been removed. Columns sorted by host and treatment. Unrarefied. This table was used for dbRDA. 100 rarefactions tables (in which each sample was rarefied to the most shallowly sequenced sample = 202 sequences) were also built from this table, and alpha diversity measures were conducted on each of those 100 rarefaction tables.
DOI: 10.5061/dryad.7535k/4
title: raref_nG6XN_nchl_filtered_sorted_host_L7

description: This OTU table was built in QIIME from NiwotB_all_denoised.fna. Chloroplast sequences and the most shallowly sequenced sample (G6CXN) are removed, and all samples have been rarefied to the next most shallowly sequenced sample (202 sequences). Columns are sorted by host. This table was used for ANOVAs conducted on individual taxa.
DOI: 10.5061/dryad.7535k/5
title: read.qiime.table

description: This script is used to read any qiime table into R. It was run prior to the other R scripts, so that the files would be uploaded correctly.
DOI: 10.5061/dryad.7535k/6
title: raref_nG6XN_nchl_filtered_sorted_host_L6

description: This genus table was built in QIIME from raref_nG6XN_nchl_filtered_sorted_host_L7.txt. Chloroplast sequences and the most shallowly sequenced sample (G6CXN) are removed, and all samples have been rarefied to the next most shallowly sequenced sample (202 sequences). Columns are sorted by host. This table was used for ANOVAs conducted on individual taxa.
DOI: 10.5061/dryad.7535k/7
title: raref_nG6XN_nchl_filtered_sorted_host_L5

description: This family table was built in QIIME from raref_nG6XN_nchl_filtered_sorted_host_L7.txt. Chloroplast sequences and the most shallowly sequenced sample (G6CXN) are removed, and all samples have been rarefied to the next most shallowly sequenced sample (202 sequences). Columns are sorted by host. This table was used for ANOVAs conducted on individual taxa.
DOI: 10.5061/dryad.7535k/8
title: raref_nG6XN_nchl_filtered_sorted_host_L4

description: This order table was built in QIIME from raref_nG6XN_nchl_filtered_sorted_host_L7.txt. Chloroplast sequences and the most shallowly sequenced sample (G6CXN) are removed, and all samples have been rarefied to the next most shallowly sequenced sample (202 sequences). Columns are sorted by host. This table was used for ANOVAs conducted on individual taxa.
DOI: 10.5061/dryad.7535k/9
title: raref_nG6XN_nchl_filtered_sorted_host_L3

description: This class table was built in QIIME from raref_nG6XN_nchl_filtered_sorted_host_L7.txt. Chloroplast sequences and the most shallowly sequenced sample (G6CXN) are removed, and all samples have been rarefied to the next most shallowly sequenced sample (202 sequences). Columns are sorted by host. This table was used for ANOVAs conducted on individual taxa.
DOI: 10.5061/dryad.7k66b/1
title: Genotypes for Cronin et al JOH bison genetics
DOI: 10.5061/dryad.7m6kg/73
title: Additional Chinese material of Nectocaris ?pteryx (large morph)

description: ZIP file containing images of two specimens, with scales
DOI: 10.5061/dryad.926nd/1
title: Seedlingtraitdataexperiment2

description: Experiment 2Morphological traits were assessed independently of Experiment 1. We grew tree seedlings under optimal conditions by planting pre-grown 4 weeks old tree seedlings ( see plant material)  into the center of a (10 cm wide) pot, using a density of one seedling per pot. The pots were filled with sterilized organic soil, watered daily and kept under the same glasshouse light and humidity conditions as Experiment 1. Pots were arranged in five replicated blocks. Both the blocks and the pots within a block were randomly moved once a week. For more information on columnheadings see Table 1 in the associated MS
DOI: 10.5061/dryad.926nd/2
title: Traitsandsurvival

description: Traits assessed in Experiment 2 were used to relate to seedling survival in Experiment 1. This file contains trait data from experiment 2 and seedling survival of seven conifer species in experiment 1 kept under contrasting moisture conditions (Dry, Wet)
DOI: 10.5061/dryad.926nd/3
title: Traitplasticityseedlingsmosssoil

description: To assess the plasticity of the morphological traits, we compared the morphological traits based on seedlings from Experiment 2 (grown on soil) with values measured on seedlings in Experiment 1 under contrasting moisture conditions
DOI: 10.5061/dryad.926nd/4
title: germination

description: To assess germination, we introduced seeds to Experiment 1 in the third week, corresponding to the time when pot water contents had stabilized. Three seeds were placed around the seedling of the same species, on the capitulum of a moss individual, using 3 x 140 = 420 seeds in total. Germination was checked twice a week until harvest, 5 weeks later. We considered a seed germinated when the integument had broken and a ‘shoot’ of at least 1 mm had emerged from the seed.
DOI: 10.5061/dryad.926nd/5
title: Mossgrowth and seedling performance

description: The file contains growth and survival of seedlings grown on moss in experiment 1 as well as the moss growth itself
DOI: 10.5061/dryad.9q1n4/2
title: ordered_transcriptome_trinity.txt

description: This is the genetic map used to position genes and SNPs. Column 1 refers to the contig name, column 2 to the chromosome number and column 3 to the position in centimorgans
DOI: 10.5061/dryad.9q1n4/4
title: ann_pet_fst_map

description: SNP table for H. annuus - H. petiolaris comparison. This table also contain Fst ("Fst" column) values for each SNP and the position ("map_centiMorgan") and chromosome number ("LG") were SNPs are found.
DOI: 10.5061/dryad.9q1n4/6
title: pet_arg_fst_map

description: SNP table for H. petiolaris -H. argophyllus comparison. This table also contain Fst ("Fst" column) values for each SNP and the position ("map_centiMorgan") and chromosome number ("LG") were SNPs are found.
DOI: 10.5061/dryad.d9p7h/3
title: bw3ldne

description: Effective population size estimates from LDNE and population genetic summary values for all Sample Window Sizes and Breeding Window 3.
DOI: 10.5061/dryad.dj828/1
title: Bretman et al 2013 Evolution Dryad

description: Original data file including metadata.
DOI: 10.5061/dryad.g08c7/1
title: Contigs_RADs

description: Genomic divergence according to RADs genotyping. In this file we present the results of genomic analyses as evaluated by RADs genotyping. For each genomic contig we provide annotation data, including the best BLAST hit as well as the results of a gene set enrichment analysis (enriched biological process in the Gene Ontology, GO). We also present genetic differentiation data obtained with RADtools and Popoolation and summarize results of GxE associations conducted with the Bayenv software. Finally we show the nodal distances (calculated with Topd) between contig-specific trees and two other trees, one showing the parallel evolution of the ecotypes (PE) and one showing a single origin of them (SO). Note that some contigs were not sampled (NS) in all analyses.
DOI: 10.5061/dryad.hm796/2
title: Nuni12

description: XL spreadsheet in GenAlEx format with the scores of 12 microsatellite loci. Four of these were found not to conform with Hardy-Weinberg equilibrium but this is somewhat questionable because they were only tested on a single adult population. This data set is arranged as year-class recruitment cohorts and adult fishes.
DOI: 10.5061/dryad.jf361/10
title: counts

description: a Perl script for counting the number loci at different tolerance levels (output a txt file)
DOI: 10.5061/dryad.jf361/11
title: phyliprand

description: a Perl script for generating phylip formatted sequence files with two tolerance levels (as the number of minimal individuals)--one for specifying the number of loci, and one for specifying the mutation-rate spectrum
DOI: 10.5061/dryad.jf361/2
title: ms

description: Perl script to simulate coalescent genealogies for given species tree
DOI: 10.5061/dryad.jf361/3
title: seqgene_paramter

description: short R script to generate random mutation rates (as  the theta for simulating dna sequences ) from a log normal distribution
DOI: 10.5061/dryad.jf361/4
title: seqgen parameters

description: the result from seqgene_paramter.R-- the mutation rates used in simulating sequences
DOI: 10.5061/dryad.jf361/5
title: seq-gen

description: Perl script to simulate sequences given genealogies and mutation rate (as theta)
DOI: 10.5061/dryad.jf361/6
title: infomissing

description: a Perl script to filter out sequences with mutations at enzyme cutting sites
DOI: 10.5061/dryad.jf361/7
title: coverage

description: a Perl script for filtering out sequences with no read (coverage draw from a poisson distribution)
DOI: 10.5061/dryad.jf361/8
title: cluster

description: a Perl script for generating post-sequencing missing data
DOI: 10.5061/dryad.jf361/9
title: lociind

description: a perl script for summarizing the number of individuals for each locus (output in a txt file)
DOI: 10.5061/dryad.jr583/1
title: Alcaide_etal_PeerJ_MHC_classI_alignment

description: This alignment was used in the analysis of the paper in PeerJ by M. Alcaide, M. Liu and S. Edwards entitled "Major Histocompatibility Complex class I evolution in songbirds: universal primers, rapid evolution and base compositional shifts in exon 3". The alignment begins on the first position of the codon and was made according to methods described in the paper. Taxa without Genbank numbers are original data; Genbank nubmers for these sequences can be found on Genbank. Taxa with Genbank numbers were taken from Genbank.
DOI: 10.5061/dryad.rr65n/1
title: Neighbor-joining trees of H. erato and H. melpomene combined using aligned fragments from the region of highest association

description: Trees output from a neighbor-joining distance analysis run in PAUP*4b10 of the aligned fragments in melperato_alignedfrags_D454to742KB_DATA.nex.  NJ trees were constructed to test monophyly of fragments across the peak region of association (from 454 -742KB in H. erato) in the red color pattern interval. The format is a nexus tree file format with extra notes from PAUP* output.