cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.22n3d/1
title: Filtered_RADseq_datasets_crested_porcupine

description: This file contains three datasets of African porcupines (*Hystrix cristata* and *H. africaeaustralis*) samples as presented in the paper "Long live the alien: is high genetic diversity a pivotal aspect of crested porcupine(*Hystrix cristata*) long-lasting and successful invasion?" doi: 10.1111/mec.13698. Data were produced by single-digestion RAD sequencing using SbfI as restriction enzyme and analyzed in Stacks (Catchen et al. 2013) using denovo_map.pl. Catalogs of RAD loci were exported using export_sql.pl script in the Stacks package and further filtered using the custom python script “loci_selector.py” released as Supplementary Material in the above mentioned publication.
DOI: 10.5061/dryad.271k9/3
title: Experiment 1 - male-male aggression

description: Counts of aggressive interactions between dominant and subordinate males in experiment 1
DOI: 10.5061/dryad.271k9/4
title: Experiment 2 - colour change

description: Details of percentage black body colouration before and after each interaction in experiment 2
DOI: 10.5061/dryad.3m8p1/1
title: Absolute Basal Cover by Species

description: Analyses reported in the paper are based on the basal cover data included in this file. A species list is included to link species codes with scientific names.
DOI: 10.5061/dryad.3q111/1
title: JOH2015154R1_RawData_Updated

description: Genotypes, behavior scores and sampling information for all horses used
DOI: 10.5061/dryad.4kj53/1
title: Microsatellite genotyping - field samples

description: The file lists the sample location, coordinates, host plant and microsatellite marker genotypes for each of the 1100 aphids analyzed for this study. Markers used are listed in the paper Materials and Methods.
DOI: 10.5061/dryad.4kj53/2
title: 2011 Pantraps and Sweeps

description: Record of aphids sampled from the Palouse region, from which a subsample was genotyped for the study. There is a separate sheet for those sampled in pan traps and those sampled by sweep net. Geographic coordinates are provided on one of these sheets.
DOI: 10.5061/dryad.4kj53/3
title: 2012 Pantraps and Sweeps

description: Aphids collected in pan traps and sweep nets during 2012 from which a subsample was genotyped for the study. There is a separate sheet for pan and sweep net. One of these sheets has the geographic coordinates.
DOI: 10.5061/dryad.564q7/1
title: Data from: Interactive Influences of Climate Change and Agriculture on Aquatic Habitat in a Pacific Northwestern Watershed.

description: This file contains reach-specific data on aquatic habitat in the Umatilla Subbasin for current conditions, six climate change scenarios, and two agricultural intensification scenarios. Variables examined include summer water temperature, low flow, embeddedness, fine sediment, metals in sediment and soils, turbidity, miscellaneous toxins in the water, dissolved oxygen, riparian function, and large woody debris.
DOI: 10.5061/dryad.5r774/1
title: cluhar_rc6_codingGene_GOonGene.gff
DOI: 10.5061/dryad.5r774/2
title: Individual.GATK.filtered.only.SNPs.vcf
DOI: 10.5061/dryad.5r774/3
title: Pool_20.filtered.vcf
DOI: 10.5061/dryad.66cf7/1
title: Preference trial results

description: Preference for one host plant over the other for two species, Cephalelus uncinatus and C. pickeri. Three host plants were tested Hypodiscus (H), Elegia (E), and Staberoha (S).
DOI: 10.5061/dryad.66cf7/2
title: Survivaldata

description: Survival on two different host plants, Hypodiscus and Elegia. For adults survival per cage was out of 10, and for C. pickeri larvae it was out of 20.
DOI: 10.5061/dryad.6js40/1
title: Trait and environmental data for Salix herbacea in Switzerland

description: Trait and environmental data for Salix herbacea in the eastern Swiss Alps, Davos Switzerland, collected from plants in the field 2011-2013. Data saved in Excel file. See associated metadata in README.xlsx for variable abbreviations.
DOI: 10.5061/dryad.78fm3/1
title: Suspected to have PTB
DOI: 10.5061/dryad.78fm3/2
title: Suspected to have respiratory diseases other than PTB
DOI: 10.5061/dryad.94768/1
title: BDNF

description: Alignment of the nuclear locus BDNF
DOI: 10.5061/dryad.94768/2
title: BMP2

description: Alignment of the nuclear locus BMP2
DOI: 10.5061/dryad.94768/3
title: CMOS

description: Alignment of the nuclear locus CMOS
DOI: 10.5061/dryad.94768/4
title: NTF3

description: Alignment of the nuclear locus NTF3
DOI: 10.5061/dryad.bq70c/12
title: Table 2
DOI: 10.5061/dryad.bq70c/13
title: Table S1
DOI: 10.5061/dryad.bq70c/9
title: Dataset S2, nDNA Phylogeny

description: Data used to generate Figure S2
DOI: 10.5061/dryad.cr1m5/4
title: Vega et al BJLS Sorex minutus skulls

description: Photographs of skulls of Sorex minutus (ventral side)
DOI: 10.5061/dryad.cr1m5/5
title: Sorex minutus Eurasia mandibles Left

description: TPS file with landmark configurations for Sorex minutus mandibles
DOI: 10.5061/dryad.cr1m5/6
title: Sorex minutus Eurasia Skulls Left

description: TPS file with landmark configurations for Sorex minutus skulls
DOI: 10.5061/dryad.jc00c/1
title: Data from: The pace of plant community change is accelerating in remnant prairies

description: Data for colonizations (Col) and extinctions (Extinc) were calculated from three surveys of remnant prairies in 1950, 1987 and 2012.  Data for drivers were obtained from records of previous surveys and from land managers.  Numerical suffix 1 corresponds to the period between the 1950 and 1987 (first and second) surveys, while 2 corresponds to the period between the 1987 and 2012 (second and third) surveys.  The second tab contains functional trait data.  Functional trait values for each species were obtained from Leach and Givnish 1996.
DOI: 10.5061/dryad.k0n77/1
title: Dimond_Zufall_data_dryad3

description: Raw measurements and categorical data used for all analyses in manuscript# JEB12868.
DOI: 10.5061/dryad.m03vf/30
title: mimulus_chain1

description: Log file for chain 1 for Mimulus phylogeny
DOI: 10.5061/dryad.m03vf/31
title: mimulus_chain2

description: Log file for chain 2 for Mimulus phylogeny
DOI: 10.5061/dryad.m03vf/32
title: mimulus_chain3

description: Log file for chain 3 for Mimulus phylogeny
DOI: 10.5061/dryad.mp10n/1
title: DNA sequences of species of the Daucus guttatus complex , and others

description: DNA sequences and trees obtained using Maximum Parsimony
DOI: 10.5061/dryad.mp10n/3
title: Supplementary Figure 1

description: SUPPL. FIG. 1. Maximum parsimony phylogenetic reconstruction of the Daucus guttatus complex including species that belong to Clades A and B using 10 nuclear orthologs. Numbers above branches represent bootstrap values. Clades 1, 2, and 3 were identified in Arbizu et al. (2014a). Clade 4 is a new finding in the present study.
DOI: 10.5061/dryad.mp10n/4
title: Supplementary Figure 2

description: SUPPL. FIG. 2. Box plot (histogram) analyses of the 41 morphological characters examined for all taxa in this study. The box plot displays individual plant values for median, 25% and 75% percentile, range, and outliers.
DOI: 10.5061/dryad.mp10n/5
title: Supplementary Figure 3

description: SUPPL. FIG. 3. Hierarchical cluster analysis of the Daucus guttatus complex, D. involucratus, and D. littoralis.
DOI: 10.5061/dryad.mp10n/6
title: Supplementary Figure 4

description: SUPPL. FIG. 4. Mericarp measurements. A. Commissural face (Daucus setulosus Ames 25608) showing mericarp length (1), mericarp width (2), length of spines (3), crest width (4) and spine width (5). B. Cross section of mericarp (D. conchitae Ames 25878) showing elliptical vittae. C. Cross section of mericarp (D. setulosus PI 652329) showing triangular vitae length (1) and width (2) (photos: F. Martínez-Flores).
DOI: 10.5061/dryad.mp10n/7
title: Supplementary Data 1

description: Supplementary data 1. The 83 accessions of Daucus, and one accession of related genus examined in this study, the new identification and the locality information. (a) These names correspond to those in the Germplasm Resources Information Network (GRIN) database. The 14 accessions designated with an asterisk sign were not analyzed using morphological characters, but DNA sequences only. The 38 accessions designated with a plus sign were only analyzed using 11 morphological mericarp characters (results not shown in this study). DNA sequences of the 31 accessions designated with a pound sign were obtained from Arbizu et al. (2014a). The 25 accessions designated with a square sign were used in Bayesian concordance analysis. The 2n chromosome numbers are those known for the species, not the individual accessions, according to Grzebelus et al. (2011) and IPCN Chromosome Reports (http://www.tropicos.org/Project/IPCN). (b) Plant Introduction (PI) numbers are permanent numbers designated to germplasm accessions maintained at the National Plant Germplasm System (NPGS) in Ames, Iowa, USA. Ames numbers are assigned for carrots and other Apiaceae in the NPGS temporarily to newly acquired germplasm until passport data of an accession and taxonomy is verified. Also, accessions with Ames numbers have to be determined they are not duplicate accession, and that they can be successfully maintained. These accessions may or may not be assigned a PI number after the assessment period. (c) Location refers to where the germplasm was collected in the wild, while source refers to germplasm obtained through another entity such as a market vendor or genebank.
DOI: 10.5061/dryad.mp10n/9
title: Supplementary Data 2

description: Supplementary data 2. GenBank accession numbers for new sequence data, and model of evolution of the ten nuclear orthologs used for ML, BCA, and coalescent approach for the study of the phylogeny of Daucus. (a) Models of evolution were obtained in jModelTest. The second model, in parentheses, was the next lower AIC value accepted in MrBayes and BEAST analysis. Models for the concatenated data are just for reference. They were not used for any analyses.
DOI: 10.5061/dryad.n6k49/1
title: Bark traits of 11 temperate tree species

description: Bark traits of 11 temperate tree species after 15 months incubation in a common forest site in the LOGLIFE experiment.
DOI: 10.5061/dryad.n6k49/2
title: Fauna data at Major clade level

description: Fauna data at major clades level. Fauna were collected from the logs of 11 temperate tree species after 15 months incubation in a common forest site in the LOGLIFE experiment.
DOI: 10.5061/dryad.n6k49/3
title: Fauna data at Family level

description: Fauna data at family level. Fauna were collected from the logs of 11 temperate tree species after 15 months incubation in a common forest site in the LOGLIFE experiment.
DOI: 10.5061/dryad.n6k49/4
title: Fauna data of Diplopoda and Isopoda species

description: Fauna data of Diplopoda and Isopoda species. Fauna were collected from the logs of 11 temperate tree species after 15 months incubation in a common forest site in the LOGLIFE experiment.
DOI: 10.5061/dryad.q2764/1
title: Flat stimulus

description: Flat calls (F) in which the frequency among notes did not vary. This data if for Fig.1
DOI: 10.5061/dryad.q2764/2
title: Natural stimulus

description: Natural calls (N) in which the fundamental frequency (F0) increases in the species-typical manner (i.e. naturally) from note to note: 441 Hz, 551 Hz, 589 Hz, 606 Hz, 618 Hz, 628 Hz, 628 Hz and 628 Hz, respectively.This data if for Fig.1
DOI: 10.5061/dryad.q2764/3
title: Extra increase stimulus

description: Exaggerated frequency increase calls (E) in which the increase in frequency among notes was exaggerated artificially using Avisoft SAS-Lab Pro.This data if for Fig.1
DOI: 10.5061/dryad.q2764/4
title: Phonotaxis data of the three group with different frequency increase

description: Phonotaxis data of the three group with different frequency increase(before combine the data of ratio 0.6 and 0.625)
DOI: 10.5061/dryad.q2764/5
title: Phonotaxis data of the three group with different frequency increase (after combine the ratios of 0.6 and 0.625)

description: Phonotaxis data of the three group with different frequency increase (after combine the ratios of 0.6 and 0.625),this data is for Fig.2
DOI: 10.5061/dryad.qt743/2
title: PROLOGUE_raw data for submission 20160506
DOI: 10.5061/dryad.sn62j/1
title: Microsatellite data_Ceratitis rosa

description: Individual multilocus genotypes (11 microsatellite markers) for Ceratitis rosa.
DOI: 10.5061/dryad.t5145/4
title: Deguines et al 2016_Hymdata

description: This table provide the data of the 1159 Hymenoptera communities analysed as described in Appendix 1.
Field “collection_id” is a unique ID number for each Hymenoptera community; field “long” and “lat” provide longitude and latitude of the site sampled. Field “volunteer_id” gives a unique ID number for each volunteer observing data. Field “prop_Hym_withCSI” gives, for each Hymenoptera community, the proportion of insect that were available for the calculation of the CSI (i.e. for each collection, the proportion of insects with a defined specialisation index). Field “prop_urban_1km” is the proportion of urban areas within 1km of the sampling sites. Fields “richness_Hym” and “CSI_Hym” are respectively the richness and the Community Specialisation Index of the Hymenoptera communities.
DOI: 10.5061/dryad.t5145/5
title: Deguines et al 2016_Lepdata

description: This table provide the data of the 337 Lepidoptera communities analysed as described in Appendix 1.
Field “collection_id” is a unique ID number for each Lepidoptera community; field “long” and “lat” provide longitude and latitude of the site sampled. Field “volunteer_id” gives a unique ID number for each volunteer observing data. Field “prop_Lep_withCSI” gives, for each Lepidoptera community, the proportion of insect that were available for the calculation of the CSI (i.e. for each collection, the proportion of insects with a defined specialisation index). Field “prop_urban_1km” is the proportion of urban areas within 1km of the sampling sites. Fields “richness_Lep” and “CSI_Lep” are respectively the richness and the Community Specialisation Index of the Lepidoptera communities.
DOI: 10.5061/dryad.th7kj/1
title: atratum_primary_data

description: This file contains Genepop and TESS formats of 11 micro satellite loci genotype on 13 Vincetoxicum atratum populations.
DOI: 10.5061/dryad.1v5d3/1
title: all_extractedseq_renamed

description: All transcripts categorized as venom from all species. The headers are sequence ID, species, gene superfamily, and coverage.
DOI: 10.5061/dryad.1v5d3/2
title: conus_phylogeny

description: nexus file used for phylogenetic analysis
DOI: 10.5061/dryad.1v5d3/3
title: scripts

description: scripts and readme files used in processing of all data. Same directory structure kept.
DOI: 10.5061/dryad.1v5d3/4
title: expression_results

description: Expression result output from RSEM for all species.
DOI: 10.5061/dryad.389mt/1
title: Foliar fungal pathogen data for FunDivEUROPE
DOI: 10.5061/dryad.3b56d/1
title: R scripts for figures in Snyder, Ellner, Am. Nat. 2016

description: Snyder, Ellner, Am. Nat. 2016 presents methods for analyzing structured population models (integral projections models or matrix models) to determine what makes an individual more likely to become of the few who dominate reproductive output.  It assumes that all individuals are identical: some are lucky, most are not.  These files contain all that is necessary to generate the figures in that paper.  They include both the functions and data that define the models and the analysis scripts.  Each figure caption references the R script which generated it.
DOI: 10.5061/dryad.486c0/1
title: Summary files for testing sims

description: This includes the summary files from the simulations used to test faMUSSE.
DOI: 10.5061/dryad.486c0/2
title: Scripts

description: These are the R scripts for doing all the analyses in the paper. Note that we include a copy of diversitree with slight modifications (look for BCO in the code).
DOI: 10.5061/dryad.486c0/3
title: Performance check results

description: These files are the result of simulations followed by pruning and analyses to test the new approach. The only modification was to remove (for space concerns) the files associated with batching each of the many jobs.
DOI: 10.5061/dryad.486c0/4
title: Forward in time simulations

description: These are the output of doing simulations forward in time to predict floral evolution.
DOI: 10.5061/dryad.503nd/1
title: Effects of extreme weather and community composition on mothers and their offspring

description: In each sheet, one response variable (marked in yellow) is presented. Maternal treatments means the weather extremes the mothers were exposed to (drought event, heavy rain spell or ambient conditions (control)). Calluna vulgaris mothers were also growing in two- vs. four species communities. Block means the weather manipulations blocks in which the two different community compositions were nested. The first four sheets refer to maternal data in the years 2005-2010, the other sheets to offspring data, assessed from 2011-2012.
DOI: 10.5061/dryad.5ff80/15
title: Figure 1. Source data 1

description: Figure 1. Source data 1 - Input and output text files containing all H1 and H3 virus data used in Figure 1, Figure1 Supplemental 1,2,3, files
DOI: 10.5061/dryad.5ff80/16
title: Figure 2. Source data 2

description: Figure 2. Source data 2 - Input and output text files used to calculate H1 and H3 comparative rates of antigenic evolution and diversity shown in Figure 2 and Supplementary File 3_ Table 3
DOI: 10.5061/dryad.5ff80/18
title: Supplemental Table 2. Source data

description: Supplemental Table 2.Source data Text infiles, phylogenetic trees and source script for antigenic distance analyses
DOI: 10.5061/dryad.5ff80/19
title: Supplemental Table 1. Source Data

description: Supplemental Table 1. Source Data - Text files and plots of summary statistics of testing in 1, 2, 3, 4 and 5 dimensions
DOI: 10.5061/dryad.5ff80/20
title: Figure 1A

description: gif files for rotational views of 3D antigenic maps in Figure 1
DOI: 10.5061/dryad.5ff80/21
title: Figure 1B

description: gif files for rotational views of 3D antigenic maps in Figure 1
DOI: 10.5061/dryad.5ff80/22
title: Figure 1C

description: gif files for rotational views of 3D antigenic maps in Figure 1
DOI: 10.5061/dryad.5rc70/1
title: DawrinCode records - Symphyta

description: This dataset includes records for "Symphyta" collected near Steel Creek campground along the Buffalo Nation River in Newton County, Arkansas. The dataset uses DarwinCore standard column headings, which are explained in the ReadMe file.
DOI: 10.5061/dryad.6rn80/1
title: Appendix 2 - List of data sources used in analyses

description: Reference list for sources of data used in the analyses.
DOI: 10.5061/dryad.6rn80/2
title: Appendix 1 - Standardized mean effect sizes used in analyses

description: Data that was used in all analyses. See appendix 2 for list of references from which data were collected.
DOI: 10.5061/dryad.94768/10
title: ND4

description: Alignment of the mtDNA locus ND4
DOI: 10.5061/dryad.94768/5
title: ODC

description: Alignment of the nuclear locus ODC
DOI: 10.5061/dryad.94768/6
title: PTGER

description: Alignment of the nuclear locus PTGER
DOI: 10.5061/dryad.94768/7
title: PTPN

description: Alignment of the nuclear locus PTPN
DOI: 10.5061/dryad.94768/8
title: RAG1

description: Alignment of the nuclear locus RAG1
DOI: 10.5061/dryad.94768/9
title: CYTB

description: Alignment of the mtDNA locus CYTB
DOI: 10.5061/dryad.9ht4g/1
title: Flick MetaAnalysis Data

description: Data from manuscripts associated with our meta-analysis. These data include longevity, fecundity, survival, and choice of predators that consume pathogen-infected prey. The pathogen does not infect the predator species. All prey items are insect pests.
DOI: 10.5061/dryad.cf426/3
title: AceranaSSDataFinalPLOSBio

description: Each tab in this excel sheet corresponds to a figure in the paper.
DOI: 10.5061/dryad.cp1cc/1
title: Alpine marmot survival rates
DOI: 10.5061/dryad.cp1cc/2
title: Standardized covariates
DOI: 10.5061/dryad.d18mc/1
title: geosmithia.morbida.transcripts

description: The file contains in silico generated transcripts for Geosmithia morbida.
DOI: 10.5061/dryad.d18mc/2
title: geosmithia.morbida.proteins

description: This file contains in silico generated protein sequences for Geosmithia morbida.
DOI: 10.5061/dryad.dn433/1
title: Code and Data Supplement

description: This supplement  contains all the code and data necessary to reproduce the full results and figures from the paper. Users will need to install R version 1.1.3 and follow the instructions in the README file. -Jeff Evans
DOI: 10.5061/dryad.f180j/1
title: Maps from Pontal do Paranapanema

description: This file contains maps in shapefile format from Pontal do Paranapanema from years 1956, 1965, 1978, 1984, 1993 and 2003.
DOI: 10.5061/dryad.f180j/2
title: Bird data and Landscape metrics

description: This file contains the dependent and independent data from the manuscript. The independent data correspond to the landscape metrics (Area and degree of Proximity) from the years 1978, 1984 and 2003 for each studied patch. And the dependent data are the richness of bird groups observed in each patch.
DOI: 10.5061/dryad.j4d25/1
title: uploaded data for JAV-00786.R3

description: data package for JAV-00786.R3
DOI: 10.5061/dryad.k3h89/1
title: Data_Dryad

description: .mat files with coord data, matlab scripts and excel work sheets
DOI: 10.5061/dryad.m8k24/1
title: Additional file 1_1dpf_FMRF_aTub_DAPI_lateral

description: Confocal z-stack showing FMRFamide-LIR (purple), aTub-LIR (cyan) and DAPI staining (dark blue) of the 1 dpf stage. Lateral view. Note that the staining of peripheral nerves is scarce.
DOI: 10.5061/dryad.m8k24/2
title: Additional file 2_7dpf_5HT_aTub_DAPI_apical view

description: Confocal z-stack showing 5-HT-LIR (purple), aTub-LIR (cyan) and DAPI staining (dark blue) of the 7 dpf stage. Apical view. Note that the staining of peripheral nerves is scarce.
DOI: 10.5061/dryad.m8k24/3
title: Additional file 3_7dpf_FMRF_aTub_DAPI_apical organ

description: Confocal z-stack showing FMRFamide-LIR (purple), aTub-LIR (cyan) and DAPI staining (dark blue) of the 7 dpf stage. Apical view of the apical organ.
DOI: 10.5061/dryad.m8k24/4
title: Additional file 4_14dpf_aTub_DAPI_lateral

description: Confocal z-stack showing aTub-LIR (cyan) and DAPI staining (dark blue) of the 14 dpf stage. Lateral view.
DOI: 10.5061/dryad.mr076/1
title: subg. Nothoperanema ndhF-trnN+rps16-matK+trnL-L-F+chlL modi

description: The alignment for phylogenetic analyses. The region partition is noted within the nex file.
DOI: 10.5061/dryad.mr076/2
title: subg. Nothoperanema best ML tree

description: The best ML tree in this study.
DOI: 10.5061/dryad.n9j60/1
title: Gonzalez_et_al_Brain_Size

description: This file lists the centroid size of the brain for specimens at 18.5DPC
DOI: 10.5061/dryad.n9j60/2
title: Gonzalez_et_al_Dam

description: This file contains the weight of the dams at each DPC before and after dissection.
DOI: 10.5061/dryad.n9j60/3
title: Gonzalez_et_al_Embryo_Placenta

description: This file contains the weight of embryos and placentas at the three DPC sampled
DOI: 10.5061/dryad.n9j60/4
title: Gonzalez_et_al_genes

description: This file contains the gene expression in the placentas of the low protein groups in relation to control placentas. Data are expresses as fold changes.
DOI: 10.5061/dryad.n9j60/5
title: Gonzalez_et_al_Morphometric_skull

description: This file conains the raw coordinates of landmarks of the skull and the centroid size for specimens at 17.5 and 18.5DPC
DOI: 10.5061/dryad.n9j60/6
title: Pcdh12 area E10 E17 E18 data

description: This file contains the area of Pchd12 expression at the three age stages analyzed.
DOI: 10.5061/dryad.n9j60/7
title: Placenta layers areas E10 E17 E18 data

description: This file contains the area of the three layers of the placenta at the three age stages analyzed.
DOI: 10.5061/dryad.q2764/6
title: Phonotaxis data of the relative attractiveness

description: Phonotaxis data of the relative attractiveness,this data is for Fig.3