cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2nf1v/1
title: mean genotypes

description: This file contains our point estimate of each individuals genotype for each locus. There are 186,575 rows with one row per locus. The genotype is given as the number of reference alleles (between 0 and 2) and is estimated at SUM_g = {0, 1, 2} g * Pr (g).
DOI: 10.5061/dryad.57vg4/3
title: Long PCR product - all cycles with fusion primers

description: Sequencing of this amplicon was performed on a Pico Titer Plate using a GS FLX platform, according to manufacturer’s instructions (Roche Applied Sciences, Penzberg, Germany). Reads still comprise fusion primer sequences (forward 5'-CGTATCGCCTCCCTCGCGCCATCAGAGACGCACTCCGGTTGGGGTGACCTCGGA-3, reverse 5'-CTATGCGCCTTGCCAGCCCGCTCAGAGACGCACTCAGATAGAAACCGACCTGGAT-3').
DOI: 10.5061/dryad.57vg4/4
title: Long PCR product - last 5 cycles with fusion primers

description: Sequencing of this amplicon was performed on a Pico Titer Plate using a GS FLX platform, according to manufacturer’s instructions (Roche Applied Sciences, Penzberg, Germany). Reads still comprise fusion primer sequences (forward 5'-CGTATCGCCTCCCTCGCGCCATCAGAGACGCACTCCGGTTGGGGTGACCTCGGA-3, reverse 5'-CTATGCGCCTTGCCAGCCCGCTCAGAGACGCACTCAGATAGAAACCGACCTGGAT-3').
DOI: 10.5061/dryad.67f8v/1
title: amyrel sim sech mau mel
DOI: 10.5061/dryad.67f8v/2
title: joc sim sech mau mel
DOI: 10.5061/dryad.67f8v/3
title: notch sim sech mau mel
DOI: 10.5061/dryad.68s5c1r4/1
title: EDOIMa2

description: Full data set for IMa2 analyses of Euphaea decorata and Euphaea ornata.
DOI: 10.5061/dryad.68s5c1r4/2
title: EFYIMa2

description: Full data set for IMa2 analyses of Euphaea formosa and Euphaea yayeyamana.
DOI: 10.5061/dryad.6n9d5/2
title: Data_Spider

description: Spider species abundance frequency counts in two canopy manipulation treatments (Ellison et al. 2010, Sackett et al. 2011).
DOI: 10.5061/dryad.6pt8g/3
title: Audio data of Bengalese finch songs

description: This file contains the sound (wav) files of the Bengalese finch songs we analyzed. Each directory labeled BFXX contains songs from one bird where XX indicates the bird ID.
DOI: 10.5061/dryad.6pt8g/4
title: Audio data of white-rumped munia songs

description: This file contains the sound (wav) files of the white-rumped munia songs we analyzed. Each directory labeled WMXX contains songs from one bird where XX indicates the bird ID.
DOI: 10.5061/dryad.7b185/3
title: Mitopus AFLP genotypes

description: Individual 0/1 genotype matrices in FASTA format
DOI: 10.5061/dryad.8th12/1
title: Experiment1

description: Data from Experiment 1. GroupCondition & Male are binary. Ethnicity: 1=African, 2=East Asian, 3=South Asian, 4=Caucasian, 5=Mixed
DOI: 10.5061/dryad.8th12/2
title: Experiment2

description: Data from Experiment 1. GroupCondition, Male, NativeSpeaker, Exp.Sailing & Exp.Climbing are binary. Ethnicity: 0=African, 1=East Asian, 2=South Asian, 3=Caucasian, 4=Mixed, 5=Other
DOI: 10.5061/dryad.98pt3/1
title: Hydractinia_Trinity

description: Fasta file containing transcriptome assembly described in Plachetzki et al, 2014
DOI: 10.5061/dryad.98pt3/2
title: Hydrac_3500

description: the reduced assembly containing only contigs with greater than 10 counts per library
DOI: 10.5061/dryad.98pt3/3
title: black

description: Fasta file containing transcript sequences from black module
DOI: 10.5061/dryad.98pt3/4
title: blue

description: Fasta file containing transcript sequences from blue module
DOI: 10.5061/dryad.98pt3/5
title: brown

description: Fasta file containing transcript sequences from  brown module
DOI: 10.5061/dryad.98pt3/6
title: green

description: Fasta file containing transcript sequences from green module
DOI: 10.5061/dryad.98pt3/7
title: magenta

description: Fasta file containing transcript sequences from magenta module
DOI: 10.5061/dryad.9h91m/3
title: Table S1 Genbank accession numbers

description: Genbank accession numbers of Mesobuthus scorpion and outgroup sequences
DOI: 10.5061/dryad.c857r/1
title: Richardson and Urban 2013_Evol_AMMA 13 pop genotypes_2

description: Genepop formated genotype file for all 13 populations in the analyses, including the two outlying populations (Saltonstall and Trimountain).
DOI: 10.5061/dryad.c857r/2
title: Richardson and Urban 2013_Evol_AMMA genotypes_3 risk classes

description: Genepop formated genotype file for the 11 Northford Ridge populations in the analyses. This dataset divides populations and individuals based on the three A. opacum predation risk categories described in the text.
DOI: 10.5061/dryad.c8c58/1
title: Standardized Trait Data
DOI: 10.5061/dryad.cd233/1
title: Life history characteristics of penguin species
DOI: 10.5061/dryad.cj56q/1
title: Crossin et al Biology Letters 2012
DOI: 10.5061/dryad.ck1rq/1
title: 2497_indiv_5591_markers

description: The 2497_indiv_5591_markers.map file is a file of marker names and positions, slightly amended from the plink format with column headings: chromosome, marker_name, marker_order, genetic_distance_(cM). For more information see the ReadMe.txt file.
DOI: 10.5061/dryad.ck1rq/2
title: 2497_indiv_5591_markers

description: The .ped file is a file of genotypes in plink style (see http://pngu.mgh.harvard.edu/~purcell/plink/). The column headings are: Family ID, Individual ID, Paternal ID, Maternal ID, Sex (1=male; 2=female; other=unknown), Phenotype (followed by the genotypes). For more information see the ReadMe.txt file
DOI: 10.5061/dryad.ck1rq/3
title: 2497_indiv_phenotype

description: 2497_indiv_phenotype.txt file. This file contains the phenotypes used in the analysis. Note that phenotypes are not available for all genotyped individuals. For more information please see the ReadMe.txt file
DOI: 10.5061/dryad.gt0p4/1
title: Baryconus measurements ImageJ (17.vii.2012)
DOI: 10.5061/dryad.jr40f/1
title: valide_responses_original_file

description: This excel file has the 372 valid responses as its original format.
DOI: 10.5061/dryad.jr40f/2
title: questionnaire

description: This Word file (questionnaire.doc) has the questionnaire consisted of 24 questions.
DOI: 10.5061/dryad.km6ph/1
title: Table 1_withMOTU

description: Taxonomic assignment of MOTUs through the BOLD online identification engine using two different methods: the neighbour-joining hierarchical tree-based ‘strict’ (S) and the sequence similarity ‘best match’ (BM) approach (Ross et al. 2008). Only sequences with &gt;98% similarity were considered as a possible match: &gt;98% for a “genus” match and &gt;99% for a “species” match. For the BM approach, only matches with sampling sites in Australia were considered; * indicates sampling sites in south-western WA while ** indicates sampling sites in WA but outside of the south-west. Species highlighted in grey are thought to use hearing based defences against the echolocation calls of bats. This table is a modified version of Table 1 and includes each associated MOTU.
DOI: 10.5061/dryad.km6ph/2
title: TableS1_Bat_Species_Traits

description: Table listing bat species traits.
DOI: 10.5061/dryad.km6ph/3
title: TableS2_Bdiversity

description: β-diversity results for all MOTUs and subset of MOTUs.
DOI: 10.5061/dryad.km6ph/4
title: TableS3_Sites

description: Table with geographic coordinates of data collection locations.
DOI: 10.5061/dryad.km6ph/5
title: TableS4_CNV_unweighted_unifrac

description: Input table used for analyses within R – unweighted unifrac distance matrix.
DOI: 10.5061/dryad.km6ph/6
title: TableS5_Species_Accumulation

description: Input table used for analyses within R – prey (species) accumulation data.
DOI: 10.5061/dryad.km6ph/7
title: TableS6_Chao1_PD_Rarefaction

description: Input table used for analyses within R – Chao1 and PD rarefaction.
DOI: 10.5061/dryad.km6ph/8
title: AppendixS1_Molecular methods

description: Detailed molecular methods for DNA extraction and amplification and HTS sequencing.
DOI: 10.5061/dryad.km6ph/9
title: AppendixS2_Aligned_sequences

description: Alignment of representative sequences generated for this study.
DOI: 10.5061/dryad.m172g/1
title: for Dryad

description: This data file contains three tabs, each described in the ReadMe file
DOI: 10.5061/dryad.mj3v6/3
title: Bayesian Consensus Topology

description: The maximum clade credibility tree resulting from Bayesian analyses.
DOI: 10.5061/dryad.mj3v6/4
title: RAxML Bootstrap Topology

description: Maximum Likelihood Bootstrap topology resulting from ML analyses in the program RAxML
DOI: 10.5061/dryad.mj3v6/6
title: Morphological Data File

description: This is the morphological data used in the study with georeferenced coordinate information.
DOI: 10.5061/dryad.mk68f/3
title: TRβ alignment sequences

description: TRβ alignment sequences in .fas format used in the phenotype-genotype analyses.
DOI: 10.5061/dryad.nh3d2/5
title: Individual_patch_size_He

description: Patch size and level of heterozygosity per individual. Please read the discussion in the manuscript which deals with some of the reasons to why analyzing inbreeding effects with such microsatellite markers WITHIN populations may not be ideal, which is why this paper is based on between population comparisons.
DOI: 10.5061/dryad.qp367/2
title: Key for taxon identifiers used in concatenation
DOI: 10.5061/dryad.r139p/1
title: Microsatellite alleles for Leavenworthia stylosa in genepop format

description: Alleles for 12 microsatellite loci scored at Washington State University by AL Dixon. Data file is in GENEPOP format.
DOI: 10.5061/dryad.rt01f/3
title: Control: Multicells cannot evolve pseudo-somatic cells
DOI: 10.5061/dryad.rt01f/4
title: Introduction of Defectors
DOI: 10.5061/dryad.rt01f/5
title: Ramped FML Environment
DOI: 10.5061/dryad.rt01f/6
title: Aging of Multicells
DOI: 10.5061/dryad.s5c8k/1
title: Needle Gas Exchange

description: Measurements of light-saturated net photosynthesis, dark respiration and stomatal conductance made on approximately one-week intervals during the 2010 and 2011 growing seasons in three habitat types.
DOI: 10.5061/dryad.sm01b/1
title: TableS1
DOI: 10.5061/dryad.t91gr/1
title: Functional Ecology data file 1

description: Embryo mortality and hatching time
DOI: 10.5061/dryad.t91gr/2
title: Functional Ecology data file 2

description: Hatchling lenght and yolk sac dimensions
DOI: 10.5061/dryad.vj3gm/1
title: sexinfo
DOI: 10.5061/dryad.2f1k3/12
title: Anas crecca LAMARC.menu

description: Menu file for performing LAMARC analyses using the 8 nuclear introns sampled from Eurasian Common Teal.
DOI: 10.5061/dryad.2f1k3/14
title: Anas crecca CRYAB.arp

description: Resolved alleles for Anas crecca crecca (n = 50)and Anas crecca carolinensis (n = 50) for intron 1 of the CRYAB gene. This file is formatted for analyses in Arlequin and sequences are sorted between OW (A. c. crecca) and NW (A. c. carolinensis) samples.
DOI: 10.5061/dryad.2f1k3/15
title: TEAL-CHD1Z

description: Resolved alleles for Anas crecca crecca (n = 42)and Anas crecca carolinensis (n = 36) for intron 19 of the CHD1Z gene. This file is formatted for analyses in Arlequin and sequences are sorted between OW (A. c. crecca) and NW (A. c. carolinensis) samples.
DOI: 10.5061/dryad.2f1k3/20
title: Anas crecca ODC1.arp

description: Resolved alleles for Anas crecca crecca (n = 50)and Anas crecca carolinensis (n = 50) for intron 5 of the ODC1 gene. This file is formatted for analyses in Arlequin, and sequences are sorted between OW (A. c. crecca) and NW (A. c. carolinensis) samples.
DOI: 10.5061/dryad.2kt68/1
title: Data_FE-2013-00236-R2

description: These data were collected from Chorthippus biguttulus grasshoppers which were caught from their natural habitats as nymphs (second instar) in North Western Germany in June and July 2012. "Location" describes the broader geographic area (ideally including one roadside habitat and one non-roadside habitat) from which the animals were collected. "Population" is the more specific location (the habitat) where the grasshoppers were caught. "Populations" are either roadside or non-roadside populations from a geographic "Location". "Individuals" are individual male grasshoppers which were mostly recorded more than once. The "Origin" of grasshoppers describes whether they originated from a roadside or a non-roadside population without detailed reference to the geographic locations (as opposed to the "Population" column). Grasshoppers were sorted into two different "Treatments", a noisy and a quiet treatment. In the noisy treatment, grasshoppers were exposed to road noise 24 hours a day, whereas in the quiet treatment, they were kept under normal room noise levels (no sound proof room). Adult males were recorded under constant temperature and under quiet conditions. The respective units for the collected data set are given in the headers, except for syllable to pause ratio of male signals, which is a ratio (length of song syllables in relation to length of the pauses in between).
DOI: 10.5061/dryad.2nf1v/2
title: read counts

description: This compressed direcotry contains one file for each experimental population labeled by the block number and host plant treatment (A = Adenostoma, C = Ceanothus) that includes the sequence read data. The data for each SNP begins with a line that gives the locus (GBS contig number) and position (position within the contig). This is followed by one line (row) per individual with the count or number of sequences with the non-reference and reference allele.
DOI: 10.5061/dryad.2nf1v/3
title: source code for null models

description: This compressed directory includes the C++ source code we used to simulate expected allele frequency change via genetic drift. This software requires GSL. If the appropriate libraries are in standard locations the software should compile with, g++ -O3 -o simdrift main.C func.C -lgsl -lm -lgslcblas. Type the program name (e.g., simdrift) after compiling for usage instructions.
DOI: 10.5061/dryad.2nf1v/4
title: soource code to estimate selection coefficients

description: This source code implements a Bayesian model to estimate selection coefficients. The software was written in C++ and requires GSL to compile. The software takes a genotype and a phenotype file (the phenotypes are just 0 or 1 and indicate whether an individual died = 0 or lived = 1).  The input files contain the following,genotype file:line 1: number of loci, number of populationsline 2: pop1 sample size, pop2 sample size, ...line 3: block for pop1, block for pop2, ....line 4:  treatment for pop1, treatment for pop2, ....line 5-N: population number, locus number, individual number, Pr(AA), Pr(Aa), Pr(aa)phenotype file:line 1: phenotypes for pop1 (in the same order as in the genotype file)line 2: phenotypes for pop2Here are the command line options,./wigs version 0.1 -- 21 August 2012Usage: wigs -g genotypefile -s survivalfile  [options]-g     Infile with genotype posterior probabilities-s     Infile with suvival data for each individual-x     Number of Markov chain Monte Carlo steps-b     Number of MCMC steps to discard as a burnin -t     Specify chain thinning, write samples every nth step-d     Prior probability a SNP experienced selection [0.5]-f     Outfile prefix
DOI: 10.5061/dryad.2nf1v/5
title: reference sequence

description: This FASTA file contains the GBS-based reference sequence that we assembled GBS reads to. The consensus sequence of each GBS contig is separated by a string of 30 N's.
DOI: 10.5061/dryad.2rg92p5v/6
title: 43 most parsimonious trees from parsimony analysis in nexus format European Agabini
DOI: 10.5061/dryad.32b88/3
title: lowhay.tar.gz

description: Raw RAD sequencing data in fastq format for Lower Hay population.
DOI: 10.5061/dryad.34621/1
title: BEAST XML file used for dating

description: This file contains the executable XML file that generates the chronogram used in the paper as described in the methods. Output from running this file in BEAST 1.6.2 was used to generate the Maximum Clade Credibility chronogram and the set of 1000 randomly sampled posterior chronograms used in all analyses performed in the paper.
DOI: 10.5061/dryad.40sj6/1
title: Gray treefrog advertisement call properties

description: Advertisement call properties recorded from two generations of gray treefrogs (Hyla versicolor). Data are described in the accompanying ReadMe file.
DOI: 10.5061/dryad.52565/3
title: FigS1.concatenation

description: Concatenated data tree from analysis of complete character data set
DOI: 10.5061/dryad.67f8v/10
title: vermilion sim sech mau mel
DOI: 10.5061/dryad.67f8v/11
title: white sim sech mau mel
DOI: 10.5061/dryad.67f8v/4
title: obp sim sech mau mel
DOI: 10.5061/dryad.67f8v/5
title: odysseus sim sech mau mel
DOI: 10.5061/dryad.67f8v/6
title: otu sim sech mau mel
DOI: 10.5061/dryad.67f8v/7
title: period sim sech mau mel
DOI: 10.5061/dryad.67f8v/8
title: PGD sim sech mau mel
DOI: 10.5061/dryad.67f8v/9
title: sqh sim sech mau mel
DOI: 10.5061/dryad.6gd87/1
title: Kotrschaletal.DataforDRYAD

description: this file contains spreadsheets covering the original data used to analyze OPEN FIELD, FOOD TRIALS, and CORTISOL data
DOI: 10.5061/dryad.6gd87/2
title: Kotrschaletal.DataforDRYAD_burstspeed
DOI: 10.5061/dryad.6gd87/3
title: Kotrschaletal.DataforDRYAD_criticalspeed
DOI: 10.5061/dryad.7b579/1
title: Scharf_et_al_Data_File

description: The file contains the main data used for the analyses presented in the manuscript. The first sheet contains information on the behavioral and position observations of the ants, the second one on their morphology and the third sheet contains data on life history and investment patterns differences between parasitized and healthy ant colonies.
DOI: 10.5061/dryad.98pt3/10
title: red

description: Fasta file containing transcript sequences from red module
DOI: 10.5061/dryad.98pt3/11
title: turquoise

description: Fasta file containing transcript sequences from turquoise module
DOI: 10.5061/dryad.98pt3/12
title: yellow

description: Fasta file containing transcript sequences from yellow module
DOI: 10.5061/dryad.98pt3/13
title: README
DOI: 10.5061/dryad.98pt3/14
title: gA_gO_matrix

description: total un-normalized counts matrix derived from bowtie and RSEM
DOI: 10.5061/dryad.98pt3/8
title: pink

description: Fasta file containing transcript sequences from pink module
DOI: 10.5061/dryad.98pt3/9
title: purple

description: Fasta file containing transcript sequences from purple module
DOI: 10.5061/dryad.9ct2f/7
title: Hyrax Femur 3D Geometry

description: Procavia capensis (NMS.Z.2009.76). Body mass = 3.14kg. Created in GeoMagic Studio v12.
DOI: 10.5061/dryad.b922k/10
title: termite16S_distribution

description: The termite16S_distribution.csv is a spreadsheet showing the occurrence of each read in each sample, so that one can easily find out what sequence belongs to what sample. The order of the read names is exactly the same as the sequence file. The output of ESPRIT provides a list of read indices belong to the same OTU (be aware that the indices are zero-based). By summing up the corresponding rows in termite16S_distribution.csv, one will easily get the breakdown of the OTU among samples. The S7 to S18 represent 16S data collected from three different colonies (S7-S10; S11-S14; and S15-S18) fed paper and wood (S7,S11,S15) and paper (S8, S12, S16), wood (S9,S13, S17). Termites sampled directly from lab colonies are represented by S10, S14, and S18.
DOI: 10.5061/dryad.bk272/1
title: Annual matrices for Alliaria petiolata and Trillium erectum and spatial weighting

description: Data for the demographic matrices were collected on individually tagged plants growing in paired plots located in Trillium Trail. Paired plot locations were chosen in Spring 2002 spanning the range of habitats in this forest where our focal species were found to co-occur. In Fall 2002, we established paired plots (n = 6 pairs of 14 x 14-m plots). One plot per pair was randomly assigned to a fenced treatment that excluded deer, eliminating only deer while allowing all other animals free access. Fenced plots were enclosed with 3-m-high, 15 x 15-cm steel mesh. Fences were maintained continuously, creating two treatments: deer access and deer exclusion. Each plot contained 36, 4-m-square subplots, with footpaths every 4 m to ensure minimal disturbance by data collectors.

For Alliaria, which was abundant in all plots, we created separate annual matrices for each plot, six matrices for fenced plots (not accessible to deer) and six matrices for unfenced plots (accessible to deer), for each of the four transition years. Within the range of areas where our focal species were present in Trillium Trail, we chose plots to span the gradient in topography from level to sloped, locating matched pairs along this gradient. We then determined the proportion of the total area of Trillium Trail that was similar to each matched pair. Thus, we were able to apply a weighted average to the data that was representative of the habitats where our focal species were found at the study site. Each plot pair (1–6) was weighted 10%, 10%, 20%, 20%, 20%, and 20%, respectively. To scale up to the level of the entire study site, we created a spatial average by weighting our single plot results accordingly. This resulted in a site-wide spatial average for each transition year and treatment, where the weighting for Alliaria was by abundance of the habitat at the site.

For Trillium, which varied in abundance among the pairs of plots (and was absent from the habitat represented by one of the pairs), we created a single matrix for each treatment and transition year, pooling data across all plots of a given treatment (fenced vs. unfenced, abbreviated NO_DEER and DEER) for each of the transition years (2003–2004, 2004–2005, 2005–2006, 2006–2007, abbreviated 2003, 2004, 2005, and 2006). This resulted in a site-wide spatial average, where the weighting for Trillium was by abundance of individuals in each plot.
DOI: 10.5061/dryad.c0g2t/1
title: Sound files and results for the Carite Forest site

description: The zip file contains 2 folders: 1) Carite_Forest_ACI_values with 3 files: readme.txt, heard.txt - ACI values for the site when the recordings were listened to only, filtered.txt - ACI values for the site when the recordings were analyzed with computer software and analyzed. 2) Carite_Forest_wav with 16 files: readme.htm, 15 one-minute recordings in wav format (mono, 16-bit, 48 kHz).
DOI: 10.5061/dryad.ck461/1
title: MerseyGenotypes

description: Mersey salmon genotypes: text document in Genepop format, 14 microsatellite loci.
DOI: 10.5061/dryad.cq70k/1
title: Operational Taxonomic Units

description: This is  Fasta file with all the OTU characterized from the microbial community associated with the Scleractinian coral Porites astreoides from this study
DOI: 10.5061/dryad.cq70k/2
title: Relative Abundance of Taxonomic Operational Unit

description: This file shows the relative Abundance of all Taxonomic Operational Units reported in this study. The samples are grouped within the following populations sites: Pop1 (Samples A1, A2, A3, A4, A5), Pop2 (Samples A6, A7, A8, A9), Pop 3 (Samples A10, A11, A12, B1, B2), Pop 4 (Samples B3, B4, B5, B6) and Pop 5 (Samples B7, B8, B9, B10, B11)
DOI: 10.5061/dryad.cv003/1
title: JQO GRTI rawdata

description: Hormone samples (raw) collected in the field during March and May, 2009-2011
DOI: 10.5061/dryad.cv86385c/1
title: UC_survey_data_raw_final
DOI: 10.5061/dryad.cv86385c/2
title: PrivateInst_survey_data_raw_final
DOI: 10.5061/dryad.cv86385c/3
title: CSU_survey_data_raw_final
DOI: 10.5061/dryad.cv86385c/4
title: eEcology_Survey_questions

description: This file contains the survey questions used in our study. This is a documentation file associated with our data files, it is not a data file itself.
DOI: 10.5061/dryad.d1n31/1
title: anemone_IMA2_input

description: Input files for IMa2 analysis