cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.187nt/7
title: ZLB_tests_01-23-13

description: An R script for running and recreating the figures related to zero-length branch simulations described in the Discussion section of the main paper, and was used to create Figure 10. If the attached 'ZLB' workspace file is used, it should be able to recreate Figure 10 exactly.
DOI: 10.5061/dryad.28mb1/1
title: 4-Table S4 GOOD

description: Algae, macroinvertebrate, and fish taxa and numbers of individuals identified at each of 41 sites along a 4100 m elevational–logitudinal gradient in an Andean headwater of the Amazon Basin.
DOI: 10.5061/dryad.32b88/7
title: FinalContigs120611.fa

description: fasta file of RAD contigs
DOI: 10.5061/dryad.35321/10
title: Diplodactylinae nexus file

description: Nexus matrix of ND2 from Diplodactyline species and outgroups.
DOI: 10.5061/dryad.35321/11
title: Lerista nexus file

description: Nexus matrix of 12S, 16S, ATPsB, and ND$ from Lerista species and outgroups.
DOI: 10.5061/dryad.35321/12
title: Pygopodidae nexus file

description: Nexus matrix of 16S, c-mos, and ND2 from Pygopodidae species and outgroups.
DOI: 10.5061/dryad.35321/7
title: Sliding window grids

description: Contains grid files used to sample species distributions in the sliding window analysis.
DOI: 10.5061/dryad.35321/8
title: Ctenophorus nexus file

description: Nexus matrix of ND1 and ND2 from Ctenophorus species and outgroups.
DOI: 10.5061/dryad.35321/9
title: Ctenotus nexus file

description: Nexus matrix of ATPsB, cytb, GAPDH, and ND4 from Ctenotus species and outgroups.
DOI: 10.5061/dryad.35td0/1
title: Data
DOI: 10.5061/dryad.38v59/2
title: Tree

description: Tree file used for phylogenetically independent contrasts and phylogenetic generalized least squares.
DOI: 10.5061/dryad.3p545/10
title: Additional File 1. Total differential gene lists.

description: Total differential gene lists for day 8 migrant compared to resident, pre-release smoltscale 3 compared to smoltscale 2, and resident day 48 compared to resident day 8.
DOI: 10.5061/dryad.3p545/11
title: Figure S1. Correlation between qPCR and microarray.

description: (a) R2 and slope for each gene measured by microarray and qPCR (i.e., log2(qPCR) against log2(microarray)), and two example correlation plots (b) s100a4 and (c) irf1.
DOI: 10.5061/dryad.3p545/13
title: resub_readme2

description: Readme file associated with all files in this package.
DOI: 10.5061/dryad.4291n/1
title: WA_countershading_in_ruminants_comparative_data

description: Column A contains species names. The corresponding phylogenetic tree can be obtained at: (http://purl.org/phylo/treebase/phylows/study/TB2:S12968). Columns B-I are the countershading measures taken from analysis of calibrated images of museum specimens. Columns J-O are ecological and beavioural predictors of countershading variation. Column headings are self-explanatory. Can be saved as a tab-delimited .txt file.
DOI: 10.5061/dryad.4291n/2
title: TreeBASE S12968
DOI: 10.5061/dryad.6h822/15
title: Figure_5_Tank10(A26C)

description: Paternity analysis for Tank 10 (A26C). Study Day indicates the day on which each embryo analysed was spawned. The first 3 rows in the table are the parent fish and below that are the 20 selected offspring. The microsatellite loci used for analysis are listed along the top of the table and corresponding allelles are detailed below.
DOI: 10.5061/dryad.6h822/3
title: Figure_4_2hr Viability

description: Embryo viability assessed at 2 hours post fertilisation, across the 10 day study periods of Experiment I and II (as indicated in table)
DOI: 10.5061/dryad.6h822/6
title: Figure_5_Tank1(A21A)

description: Paternity analysis for Tank 1 (A21A). Study Day indicates the day on which each embryo analysed was spawned. The first 3 rows in the table are the parent fish and below that are the 20 selected offspring. The microsatellite loci used for analysis are listed along the top of the table and corresponding allelles are detailed below.
DOI: 10.5061/dryad.72p7k/1
title: Solidago SSR paired end reads

description: Included is a file detailing the paired-end Illumina reads used to design primers for the 14 SSR loci reported in the manuscript.  Each read begins with the corresponding locus name from Table 1.
DOI: 10.5061/dryad.7gp1f/6
title: DRYAD_BaumsEtAl_2012_StructureParameters

description: Parameters for Structure v 2.3.3.
DOI: 10.5061/dryad.7pg3d/1
title: Supplemental material

description: Supplemental tables 1-5, figures 1-7 and boxes 1-2
DOI: 10.5061/dryad.8nh1q/1
title: Jasmin_Zeyl_JEB_data

description: Data used in "Evolution of pleiotropic costs in experimental populations" by Jean-Nicolas Jasmin and Clifford Zeyl, published in Journal of Evolutionary Biology (2013).
DOI: 10.5061/dryad.8rd4v/1
title: Data From EndlerGaburroKelley

description: Data and some MATLAB files which are the basis of this publication.
DOI: 10.5061/dryad.9c568/7
title: flu H1 Beast Nulldata file for generating the prior
DOI: 10.5061/dryad.9r2h3/1
title: Kelleretal2012MEC_genotypes

description: Genotypic data from 16 nuclear microsatellites and 1 chloroplast indel marker.
DOI: 10.5061/dryad.d24c7/1
title: data

description: This dataset aimed to assess the joint effect of the environment and plant-plant interactions in the phylogenetic pattern of semiarid plant communities. Data were obtained for 11 30 m x 30 m sites across a rainfall gradient in Spain. We assessed species co-occurrence at two different scales, at the site-level, using 80 1.5 m x 1.5 m quadrats, and at the microsite-scale, using 30 0.5 m x 0.5 m quadrats beneath three different microsites (open areas, stipa tenacissima tussocks and quercus coccifera shrubs). From the data at the site-scale we obtained plant species richness, plant co-occurrence metrics (C-score, Species combination indices) and the phylogenetic pattern of the plant community. See associated article for further details. From the data at the patch-scale we obtained similarity indices and the phylogenetic pattern of those species that were more abundant beneath a nurse than in the open. The dataset was complemented with climatic data available in the literature (Ninyerola M, Pons X y Roure JM. 2005. Atlas Climático Digital de la Península Ibérica. Metodología y aplicaciones en bioclimatología y geobotánica. ISBN 932860-8-7. Universidad Autónoma de Barcelona, Bellaterra). More details in the data can be obtained both in the metadata spreadsheet in the Excel file. Empty data is in blank. There is only one empty space (MPDfac in the Camporreal site). Data was taken by S. Soliveres and F.T. Maestre, both authors of the associated paper. Contact for further information: Dr. Santiago Soliveres (e-mail: santiagosoliverescodina@gmail.com)
DOI: 10.5061/dryad.dr283/1
title: Frequencies and compositions of cpSSR

description: This files contains two sheets, one is the chlorotype frequency and the other is the composition of 22 chlorotypes.
DOI: 10.5061/dryad.fv91n/1
title: Environmental data and frequency of AFLP markers

description: A number of files containing information for 6 retained environmental variables as well as AFLP marker frequency. We provide a separate file for each primer combination for both the entire study area as well as for the "Hill" transect.
DOI: 10.5061/dryad.fv91n/2
title: AFLP data set of all populations in AFLPsurv format

description: AFLP allele calls for 1509 retained markers in 10 populations. We provide our data in AFLPsurv format.
DOI: 10.5061/dryad.hb653/10
title: gonorynchZIC

description: alignment of zic1 nuclear gene in nexus format
DOI: 10.5061/dryad.hb653/11
title: gonorynchTOT

description: interleaved alignment of all 9 nuclear genes and morphological data in nexus format
DOI: 10.5061/dryad.hb653/12
title: gonorynchTIPa

description: BEAST input file for divergence time estimation
DOI: 10.5061/dryad.hb653/4
title: gonorynchMYH

description: alignment of myh6 nuclear gene in nexus format
DOI: 10.5061/dryad.hb653/5
title: gonorynchPLAG

description: alignment of plagl2 nuclear gene in nexus format
DOI: 10.5061/dryad.hb653/6
title: gonorynchPTR

description: alignment of Ptr nuclear gene in nexus format
DOI: 10.5061/dryad.hb653/7
title: gonorynchRAG

description: alignment of rag1 nuclear gene in nexus format
DOI: 10.5061/dryad.hb653/8
title: gonorynchSH3

description: alignment of SH3PX3 nuclear gene in nexus format
DOI: 10.5061/dryad.hb653/9
title: gonorynchTBR

description: alignment of tbr1 nuclear gene in nexus format
DOI: 10.5061/dryad.jt85h/1
title: DRYAD_MEC-12-1092
DOI: 10.5061/dryad.k41qk/4
title: 2_RpL37_120620
DOI: 10.5061/dryad.kp5cn/1
title: matrixes used for analysis

description: This contains 105 matrixes including intra-individual allele heterozygotes (IIAHs) and 82 matrixes excluding IIAHs.
DOI: 10.5061/dryad.kp5cn/2
title: GenBank accessions

description: This contains the GenBank accession numbers of all the sequences used in ths study.
DOI: 10.5061/dryad.t12v8/1
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.t12v8/2
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.t12v8/3
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.t12v8/4
title: Simulated_data

description: Simulated data created using the QMSim software. Three genetic architecture types were simulated each with ten replicates (see manuscript), giving ten of each file type within each of the three folders. Folders contain phenotypic, genotypic, QTL, marker and linkage data.
DOI: 10.5061/dryad.t3jp4/1
title: Data from: Impact of host nutritional status on infection dynamics and parasite virulence in a bird-malaria system

description: Repeated measurements of body mass, haematocrit and blood parasitaemia (RQ) taken over a -15/17 day-period in birds infected by Plasmodium relictum and fed with control or supplemented diets (experiment 1). Parasites originating from control/supplemented hosts were inoculated to new birds that were also fed either control or supplemented diet (experiment 2). For more details, refer to the Materials and Methods section of the manuscript.
DOI: 10.5061/dryad.t7t54/1
title: Figure 2a and b Area Dispersed

description: Data shows the colony area of Pseudomonas aeruginosa after 48 hours growth and dispersal under different phage treatments (no phage, local phage and global phage), and different agar types (hard and soft). Data was collected in vitro and excel was used to create data file.
DOI: 10.5061/dryad.t7t54/2
title: Figure 3 Relative fitness

description: Data shows the relative fitness of dispersers to non-dispersers (i.e. CFU disperser/ CFU non-disperser) in Pseudomonas aeruginosa after 48 hours growth and dispersal. Motility variants were tested across three treatment groups: No Phage, Local Phage and Global Phage. Excel was used to create the data file.
DOI: 10.5061/dryad.t85n3/2
title: Tree stem growth data

description: Sixteen small files provide the stem diameters (‘Diamp’, cm) at the start of intervals (p), absolute growth rates, agr (‘Agrp-q’, cm/yr), and – as appropriate – species’ codes (‘Code’). The format is ANSI text (space-delimited). Fourteen files concern one or more of the three main caesalp species (Microberlinia bisulcata, Tetraberlinia bifoliolata and T. korupensis), for different time intervals and different size classes as uniquely indicated in their file names. Mean (± SE) of the agr-values are those given in Table 8 of the main paper. The two remaining files concern ‘other’ (Az) species measured in the P-plot and at the Isangele Road (IR) site for all large and some medium trees respectively. The former has species’ codes; the latter not because identifications were not certain. The Az mean (± SE) agr-values appear in the main paper text. A small script in R (agr_in) allows all of these files to be easily read into data-frames. To find relative growth rates, rgr, the time intervals will need to be applied to agr-values, and the resulting increments used to find final diameters and hence the rgr-values. The interval lengths are given in Table 8 ibid.
DOI: 10.5061/dryad.t85n3/3
title: Data files for spatial statistics analysis

description: Although these data could be found from the main plot data sets with a little light programming, the coordinates of the large and medium trees of the three principal species (Mb, Microberlinia bisulcata; Tb, Tetraberlinia bifoliolata; and Tk, T. korupensis) are given more simply here in six files, one for each species in each of the P- and NW-plots. Each file has the same format (ANSI text, tab-delimited), with coordinates (‘x’ and ‘y’, m), stem diameter (‘diam’, cm), the size class (‘dcl’; 1 = medium [10 – &lt; 50 cm], 2 = large [≥ 50 cm]) and species code (as immediately above). This allows spatial analysis of each species individually, or for large and medium trees separately, as well as same-species large/medium bivariate analyses. However, to run (a) analyses on the large trees divided into two more size classes (see main paper text), the median must be first found, and then trees labelled ‘diam’ &lt; or ≥ the median; or (b) different-species large/medium bivariate analyses, the medium trees of one species needs be recombined with large trees of either of the other two (six possible combinations).
DOI: 10.5061/dryad.vq587/10
title: HAO vs FBbt (Drosophila)

description: Excel aligment between Hymenoptera (HAO) and Drosophila melanogaster (FBbt).
DOI: 10.5061/dryad.vq587/11
title: Arthropod_Alignment_Cytoscape_Network

description: Arthropod alignment Cytoscape network file.
DOI: 10.5061/dryad.vq587/8
title: HAO vs TADS (tick)

description: Excel aligment between Hymenoptera (HAO) and Ixodidae(TADS).
DOI: 10.5061/dryad.vq587/9
title: HAO vs SPD (spider)

description: Excel aligment between Hymenoptera (HAO) and Araneae (SPD).
DOI: 10.5061/dryad.1077n/9
title: Nuclear_520_sequence_alignment

description: Aligned nuclear marker 520 sequences for all locations.
DOI: 10.5061/dryad.1683s/1
title: wilson et al_12-0024

description: Body size measurements of South American Cinnamon Teal (Anas cyanoptera) taken from recently collected individuals before museum skin preparation (Table 1) and from museum specimens (Table 2).
DOI: 10.5061/dryad.187nt/8
title: ZLB_test_01-23-13

description: The saved R workspace (as an .Rdata file) from the zero length branch simulations described in the Discussion of the paper, and produced using the ZLB_test R script. Can be used with the same script to recreate Figure 10 from the main paper.
DOI: 10.5061/dryad.20r9k/18
title: nyctimene_reads

description: reads used to assemble Common tube-nosed fruit bat
DOI: 10.5061/dryad.20r9k/5
title: remove_primers

description: Script to remove primers
DOI: 10.5061/dryad.256qh/1
title: isophya_dochia_morphological_characters

description: Studied morphological characters: body length (BL), head width (HW), head length (HL), pronotum maximum width (PW), pronotum length (PL), left tegmen maximum width (TW), tegmina length (TL), cercus length (CL), femur length (FL), ovipositor (O).
DOI: 10.5061/dryad.2dh5n/1
title: Ventura-Microsats-Pyrenees

description: Microsatellite genotyping results. Twenty five populations distributed at regional scale in the Eastern Pyrenees (Catalonia) were used for this analysis. Individual ID and sample location are shown.
DOI: 10.5061/dryad.2dh5n/2
title: Ventura et al - Pyrenees- New Haplotypes

description: fasta file showing the alignment of the partial sequence of the 12S mtDNA gene. Individual ID and correspondent GenBank accession number are shown
DOI: 10.5061/dryad.2k55t/2
title: Antibodies

description: Please see README file for description of all data files.
DOI: 10.5061/dryad.2n545/11
title: M1809
DOI: 10.5061/dryad.2n545/14
title: rodents
DOI: 10.5061/dryad.30dn3/1
title: Multiyear selection estimates in Dactylorhiza lapponica and Gymnadenia conopsea

description: Pollen limitation, variance in relative fitness, and estimates of linear selection gradients in open-pollinated and hand-pollinated plants of Dactylorhiza lapponica and Gymnadenia conopsea
DOI: 10.5061/dryad.35321/13
title: Sminthopsinae nexus file

description: Nexus matrix of 12S, 16S, B-fib, cyt b, IRBP, and P1 from Sminthopsinae marsupial species and dasyurid outgroups.
DOI: 10.5061/dryad.35321/17
title: Lerista phylogenetic tree

description: Lerista phylogenetic tree used in community phylogenetic analyses
DOI: 10.5061/dryad.35321/18
title: Pygopodidae phylogenetic tree

description: Pygopodidae phylogenetic tree used in community phylogenetic analyses
DOI: 10.5061/dryad.35321/19
title: Sminthopsinae phylogenetic tree

description: Sminthopsinae phylogenetic tree used in community phylogenetic analyses
DOI: 10.5061/dryad.489s0/1
title: Microsatellites genotype from 406 whale sharks

description: 14 microsatellites genotype from 406 whale sharks collected in 7 different location worldwide. 0 represents missing values. Description of each microsatellites with multiplex detail is included in the supplementary material of the publication. Genemapper was used to read the lenght of each allele.
DOI: 10.5061/dryad.489s0/2
title: Whale Sharks Control region raw 506 individuals

description: This excel dataset can be saved in .fasta - Locations and year of collection are described when available. 'N' means unknown, while '-' indicates gap. Additional sequences can be found on genebank from Castro et al. 2007, but seems to be reversed. Analysis performed in Vignaud et al. 2014 used modified dataset to remove N and large gaps as described in the methods.
DOI: 10.5061/dryad.5h6n5/1
title: PHOXOCEPHALIDAE ALIGNMENT

description: Original source: samples collected in field. Created in BoLD. Sequence names refer to species. replicate number then station. Bar | separates species from collection data.
DOI: 10.5061/dryad.6d250/1
title: data and scripts

description: Complete data and R script.
DOI: 10.5061/dryad.6h822/11
title: Figure_5_Tank6(A25B)

description: Paternity analysis for Tank 6 (A25B). Study Day indicates the day on which each embryo analysed was spawned. The first 3 rows in the table are the parent fish and below that are the 20 selected offspring. The microsatellite loci used for analysis are listed along the top of the table and corresponding allelles are detailed below.
DOI: 10.5061/dryad.6h822/12
title: Figure_5_Tank7(A25C)

description: Paternity analysis for Tank 7 (A25C). Study Day indicates the day on which each embryo analysed was spawned. The first 3 rows in the table are the parent fish and below that are the 20 selected offspring. The microsatellite loci used for analysis are listed along the top of the table and corresponding allelles are detailed below.
DOI: 10.5061/dryad.6h822/14
title: Figure_5_Tank9(A26B)

description: Paternity analysis for Tank 9 (A26B). Study Day indicates the day on which each embryo analysed was spawned. The first 3 rows in the table are the parent fish and below that are the 20 selected offspring. The microsatellite loci used for analysis are listed along the top of the table and corresponding allelles are detailed below.
DOI: 10.5061/dryad.6h822/8
title: Figure_5_Tank3(A23C)

description: Paternity analysis for Tank 3 (A23C). Study Day indicates the day on which each embryo analysed was spawned. The first 3 rows in the table are the parent fish and below that are the 20 selected offspring. The microsatellite loci used for analysis are listed along the top of the table and corresponding allelles are detailed below.
DOI: 10.5061/dryad.78mt2/1
title: data set Trotta et al., 2014

description: data experimentally collected in lab on Aphidius ervi developed in the host Acyrthosiphon pisum
DOI: 10.5061/dryad.7b185/2
title: 16Scomplete

description: ClustalX alignment of 16S mtDNA
DOI: 10.5061/dryad.7gc7k/1
title: Soil Moisture Datalogger records

description: This database contains data from soil moisture sensors, soil temperature sensors and raingauges near the summit of Cerro Lloque, Comuna Campesina de las lomas de Atiquipa y Taimara, Provincia de Caravelí, Región de Arequipa, Perú. Further detail is contained in the ReadMe file.
DOI: 10.5061/dryad.7gc7k/2
title: Handheld Soil moisture below Caesalpinia spinosa trees

description: This data file (AtiquipaCS620soilmoisture.csv) contains data on spatial patterns of volumetric soil moisture recorded below Caesalpinia spinosa trees on Cerro Lloque, Comuna Campesina de las lomas de Atiquipa y Taimara, Provincia de Caravelí, Región de Arequipa, Perú. All data was recorded using a CS620 handheld TDR soil moisture probe (Cambell Scientfic Inc., Utah, USA). Soilmoisture readings were taken at varying distances from the base of trees (0 to 500cm in 50cm intervals) with 5 replicate measurements at each distance, for transects extending in each cardinal driection from the base of trees. Of this data, only that from a distance of 150cm from the base (below the canopy but unaffected by stemflow) of experimental tree pairs (1 and 2), pooled for all cardinal directions, was used in Stanton, Huallpa et al. 2014. For more any additional information about the data or the study please contact Dr. Daniel Stanton (stan0477@umn.edu). The columns are as follows: Date: Date of sampling as Year-month-day. Number: Number of the experimental tree (1 through 7). Direction: Cardinal direction from tree base of sampling transect (E-East, S-South, W-West, N-North). Distance: Distance in cm from base of tree of sampling location. Soilmoisture: Volumetric soil moisture (%)
DOI: 10.5061/dryad.7gc7k/3
title: GravimetricSoilMoisturePandeAzucar

description: This dataset contains soil masses (wet and dry) below Eulychnia saint-pieana cacti following rainfall in the Lomitas sector, Pan de Azucar National Park, Region de Atacama, Chile. Soil samples were taken from the surface or at a depth of 5cm during the week following a once in a decade rainfall event on May 16th 2010. Samples were taken from open ground or from below cacti with epiphytes untouched (control), epiphytes removed from the south facing side or epiphytes removed from the north-facing half. Cacti for each treatment were chosen to be of comparable size and exposure to fog. For more any additional information about the data or the study please contact Dr. Daniel Stanton (stan0477@umn.edu).
DOI: 10.5061/dryad.7gc7k/4
title: Epiphyte_Microclimate

description: This spreadsheet (Epiphyte_Microclimate.csv) contains microclimate measurements recorded by iButtons (Embedded Datasystems, Texas, USA) on the surface of plants with or without epiphytes. Data was collected in 2009 and 2010 at both the Comuna Campesina de las lomas de Atiquipa y Taimara, Arequipa, Perú and the Parque Nacional Pan de Azúcar, Región de Atacama, Chile. All dataloggers were paired (with and without epiphytes) and attached to the surface of the host plant. For any additional information about the data or the study please contact Dr. Daniel Stanton (stan0477@umn.edu). Column headers are described in the ReadMe file.
DOI: 10.5061/dryad.7sb0f/1
title: migrate_input_file

description: Input file for intergenic regions Migrate analysis described in the paper.
DOI: 10.5061/dryad.7sb0f/2
title: SRA058855

description: Raw Illumina HiSeq data used for all empirical analyses described in the paper.
DOI: 10.5061/dryad.7sb0f/3
title: bayescan_out_with_annotations

description: Output of BayeScan analyses described in the paper. One tab for each site type. Poplar gene model and best Arabidopsis hit are given for each site. In the case of promoter regions, these annotations refer to the nearest gene downstream of the site.