cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.c0t6s/8
title: Supplementary Information

description: The file ‘Supplementary Information.pdf’ contains the following subjects:	1) Deriving the maximum accurate time 2) The effect of non-uniform recombination rate 3) Graphical proof analogous to figure 2, but for random markers 4) Simulations of variation in the number of junctions
DOI: 10.5061/dryad.c0t6s/9
title: README_Supplement

description: Overall README of the contents of all files on dryad for 'The breakdown of genomic ancestry bocks in hybrid lineages given a finite number of recombination sites'
DOI: 10.5061/dryad.c4r81/1
title: Haplotype_Dataset_Genotyped_All_Individuals

description: Haplotype data obtained using loci genotyped in all individuals
DOI: 10.5061/dryad.d1240.1/11.1
title: 1914_2012 SaltRiverChangesFlowTiming Apr 2017

description: Changes in timing of peak spring flows in Salt River near Roosevelt, Arizona.
DOI: 10.5061/dryad.d1240.1/9.1
title: 1914_2012 SaltRiverStreamflow Apr 2017

description: Monthly flows and trend estimates from 1914-2012 for the Salt River near Roosevelt in central Arizona.
DOI: 10.5061/dryad.fs728/1
title: DNA_and_tissue_pools

description: Taxonomic composition of DNA and tissue pools and recovered read counts for all taxa.
DOI: 10.5061/dryad.fs728/2
title: DNAPools.tar

description: Illumina read files for the different markers and 16 DNA pools. Reads for the mitochondrial and nuclear markers are merged into each one file.
DOI: 10.5061/dryad.fs728/3
title: PCRCycles.tar

description: Illumina read files for the 23 DNA pools of the PCR cycle experiment. The number of PCR cycles for each sample is indicated in the file name.
DOI: 10.5061/dryad.fs728/4
title: SingleSpecimens.tar

description: Illumina read files of all 8 markers sequenced separately for each of the 43 taxa, which were used to prepare the DNA mock communities. Reads for all 8 markers are merged into single files.
DOI: 10.5061/dryad.fs728/5
title: TissuePools.tar

description: Illumina read files of the tissue pools. Each pool was sequenced twice, once using degraded DNA (L) and once using intact high molecular weight DNA (H).
DOI: 10.5061/dryad.fs728/6
title: gDNA.tar

description: Illumina read files of the sequenced genomic DNA pools. Due to low coverage, we merged the pools into one file, using equal read numbers from each file.
DOI: 10.5061/dryad.hg375/1
title: filtered SNP set used for population structure and clustering analysis

description: These SNPs were called from 109 Metchnikowia sp whole genomes mapped to MR_a10 reference genome using GATK best practices guidelines. Hard filtering of initial SNPs was performed using the GATK variant filtration tool (v3.4) and VCFtools (v1.5) as per best practices (Danecek et al. 2011), using the following parameters: base quality = 20, quality by depth = 2.0, mapping quality = 30, Fisher strand bias = 60, mapping quality rank sum =-12.5, and ReadPosRankSum = -8.0. Post InDel removal, the SNP set consisting 1.27 million SNPs across 109 strains was further filtered to exclude: non-bi-allelic SNPs, a minor allele frequency below 0.05 and polymorphisms with more than 50% missing data. To resolve SNPs in linkage, a window size of 50 SNPs advanced by 5 SNPS at a time and an r2 threshold of 0.5 was used. The final set of high confidence SNPs consisted of 88, 192 polymorphisms. See attached scripts.
DOI: 10.5061/dryad.hg375/2
title: Dhamietal-MEC-duplicate-removal-gvcf-callingRMDUP_and_RAW_GVCF_all_master

description: SNP calling and duplicate removal
DOI: 10.5061/dryad.hg375/3
title: Dhamietal-MEC-Rerefence-mapping

description: Mapping to reference genomes.
DOI: 10.5061/dryad.hg375/4
title: Dhamietal-MEC-hardfiltering

description: SNP filtering
DOI: 10.5061/dryad.hg375/5
title: Dhamietal-MEC-vcftools_filtering

description: SNP filtering 2
DOI: 10.5061/dryad.hg375/6
title: Dhamietal-MEC-fastStructure

description: Population structure analysis
DOI: 10.5061/dryad.j3tg5/1
title: Magnitude and direction of population trends, ecological and life-history traits of 36 passerine species breeding in Europe between 2001 and 2012

description: Magnitude and direction of population trends (1 = 100%), ecological and life-history traits of 36 passerine species breeding in Europe between 2001 and 2012. Non-breeding niche position varies from 1 (closed forest) to 7 (open country) and non-breeding niche breadth expresses the difference between the values of the two main habitats; non-breeding habitat wetness scores from (1) dry to (3) aquatic habitats. Non-breeding regions: (1) west–central region, (2) west–east region, (3) central–south region, (4) ‘entire’ region. Breeding habitat: forest (F), wetland (W), urban (U) and open habitat (O). PC 1 expresses a gradient from ‘slower strategy’ (K-selected) species to ‘faster strategy’ (r-selected) species. PC 2 depicts a gradient from species allocating most of their energy to just one breeding attempt per season to species spreading their investments across multiple breeding attempts per season.
DOI: 10.5061/dryad.n24q8/10
title: Supplementary_FIGS4

description: FIG. S4. Results from the niche overlap analyses in the space environmental (E) space obtained using the PCA-env method. A. Correlation circle showing the contribution of environmental variables on the first two axes of the PCA-env, and the percentage of inertia explained by the two axes. B ̶ C. Values for the first two principal components obtained in the PCA-env analyses in the studied area. B. Values for the PC1. C. Values for the PC2. Red dots represent specimen records for species included in the clade A (S. imbricatifolia, S. lagunae, S. suffruticosa), while blue dots represent  occurrences for species of clade B (S. lechleri, S. parvifolia, S. chillanensis, S. colchaguensis, S. stenophylla).
DOI: 10.5061/dryad.n24q8/2
title: Appendix2

description: APPENDIX 2. Taxa and GenBank accession numbers for the ITS, trnL-F, and trnH-psbA sequences downloaded from GenBank and used in the phylogenetic analyses. New sequences generated for this study are shown in APPENDIX 1.
DOI: 10.5061/dryad.n24q8/3
title: Supplementary_TableS1

description: TableS1. Species ocurrence data of Stenodraba used in the niche analyses
DOI: 10.5061/dryad.n24q8/4
title: Supplementary_TableS2

description: TABLE S2. Features of the DNA regions included in the phylogenetic analyses within Eudemeae.
DOI: 10.5061/dryad.n24q8/5
title: Supplementary_TableS3

description: TABLE S3. Loadings on the first two components obtained from the principal component analysis (PCA-env) using bioclimatic variables extracted from the study area (50 km-buffered minimum convex polygon enclosing the Stenodraba species distribution).
DOI: 10.5061/dryad.n24q8/6
title: Supplementary_TableS4

description: TABLE S4. Number of ocurrences (n), area under the receiver operating characteristic curve (AUC), variable contribution (%), and permutation importance (%) obtained in the MAXENT modeling for each Stenodraba clade. Variable contributions to overall performance greater than 25% are indicated in bold. BIO3: Isothermality, BIO4: Temperature Seasonality, BIO8: Mean Temperature of Wettest Quarter, BIO12: Annual Precipitation, BIO15: Precipitation Seasonality.
DOI: 10.5061/dryad.n24q8/7
title: Supplementary_FIGS1

description: FIG. S1. Bayesian 50% majority-rule consensus tree from 3,002 trees generated by Bayesian inference with MrBayes for Brassicaceae. A. ITS dataset. B. trnL-F dataset. Tribes are indicated to the right of the boxes. Thick branches indicate &gt;0.90 Bayesian posterior probability. The white arrows indicate phylogenetic position of Stenodraba, while black arrows show the position of Pennellia (tribe Halimolobeae) and Weberbauera (tribe Thelypodieae) .
DOI: 10.5061/dryad.n24q8/8
title: Supplementary_FIGS2

description: FIG. S2. Phylogenetic placement of Stenodraba within tribe Eudemeae, and including indel data in the analyses (nucleotide substitution + indel data). A ̶ C. Bayesian 50% majority-rule consensus trees from 6,002 trees generated by Bayesian inference with MrBayes. A. nrITS dataset. B. cpDNA dataset (trnL-F/trnH-psbA). C. Concatenated cpDNA + nrITS dataset (substitution + indel data). Values on branches correspond to Bayesian posterior probability (%). The start indicates the crown node of tribe Eudemeae.
DOI: 10.5061/dryad.n24q8/9
title: Supplementary_FIGS3

description: FIG. S3. Phylogenetic placement of Stenodraba within tribe Eudemeae. A. Maximum clade credibility species tree (MCCT) estimated from nuclear ribosomal ITS and two chloroplast DNA regions (trnL-F, trnH-psbA) using the multispecies coalescent method implemented in *BEAST. Bayesian posterior probability values &gt;50 % are given at each node. B. Filtered supernetwork generated in SplitsTree using 1000 Bayesian posterior trees per each nuclear ITS and plastid (trnL-F/trnH-psbA) dataset, and filtering the splits to show only those present in a minimum of 35% input trees. The start indicate the crown node of tribe Eudemeae.
DOI: 10.5061/dryad.nb3r0/1
title: data revised
DOI: 10.5061/dryad.nm35n/1
title: Debarre-Rode-Ugelvig_2018_20180104

description: Data and analysis scripts; please see README file for more details.
DOI: 10.5061/dryad.p49b1/1
title: WSU Common garden data for 2010 on A. carbonifera

description: Data associated with Am. Nat. publication: Adaptive divergence in a defense symbiosis driven from the top down. Includes the WSU Common Garden data for 2010 on Asteromyia carbonifera selection. See Readme.txt file for variable descriptions.
DOI: 10.5061/dryad.pg4d9/1
title: Data set - Acoustic masking male mosquitoes
DOI: 10.5061/dryad.qj812/1
title: EAG_Asecodes parviclava

description: EAG responses of antennae from Asecodes parviclava females.
DOI: 10.5061/dryad.td3r1/1
title: Survival & developmental time

description: Time from egg to pupation and the proportion of larvae surviving to pupation. The values are means for each replicate bottle. The results are reported in Fig 1B,C in the paper.
DOI: 10.5061/dryad.td3r1/2
title: Weight & Growth Rate

description: Data on dry weight and growth rate reported in Fig. 5A and Fig. S2. Data for germ-free females of Control populations CTL5 and CTL6 are missing due an insufficient number of flies surviving to adulthood.
DOI: 10.5061/dryad.td3r1/3
title: Digestive enzymes RT-qPCR

description: The raw data (expressed as Ct-values) from RT-qPCR on genes for digestive proteases and amylases and maltases, measured in larvae of Control and Selected populations, developing at the poor diet at two stages, (early and late 3rd instar). Actin was used as the reference gene (column "Actin_Ct"). The data underlie the results presented in Fig. 2A,B and Fig. 3B,C in the paper.
DOI: 10.5061/dryad.td3r1/4
title: Protease activity

description: The absorbance data from the protease activity assay (results presented in Fig. 2C). Protease activity was analyzed as log or the ratio of absorbance at 440 nm to 280 nm. Samples were taken at different time points during larval development, expressed as relative time during the 3rd larval instar. There were three technical replicates per sample, processed in three blocks.
DOI: 10.5061/dryad.td3r1/5
title: Amylase activity

description: The raw data from the amylase activity assay (results presented in Fig. 3A). The amylase activity was analyzed as the log-transformed ratio of the rate of reaction k (defined in the Methods of the paper) to absorbance at 280 nm.
DOI: 10.5061/dryad.td3r1/6
title: Microbiota abundance by qPCR after experimental inoculation

description: The raw data from qPCR quantifying the abundance of Acetobarcter 16S ribosomal subunit genomic DNA relative to host genomic Actin DNA in larvae experimentally colonized with the dominant Acetobacter strain and in GF larvae. CT values are averaged over 3 biological replicates. The data underlie results reported in Fig. 4B and S1, orange and blue points.
DOI: 10.5061/dryad.td3r1/7
title: Microbiota abundance in conventionally reared larvae

description: The raw data from qPCR quantifying the abundance of Acetobarcter 16S ribosomal subunit genomic DNA relative to host genomic Actin DNA in larvae experimentally conventionally reared under the same conditions as in the experimental evolution regimes (i.e., Selected larvae are raised on the poor diet but the Controls are raised on the standard diet). The data underlie results reported in Fig. 4B and S1, green points.
DOI: 10.5061/dryad.vc7ss.1
title: Data from: Intra-ejaculate sperm selection in female zebra finches
DOI: 10.5061/dryad.vc7ss.1/2.1
title: Sperm morphology data for faecal and seminal glomerus samples

description: Head length, midpiece length, tail length, and total length of sperm from faecal samples (i.e. obtained non-invasively) and seminal glomerus samples (obtained by dissection) from 13 male zebra finches. These were used to validate the assumption that faecal sample sperm are representative of the population of sperm that are stored in the male tract prior to ejaculation.
DOI: 10.5061/dryad.13p0s/1
title: Input data
DOI: 10.5061/dryad.17rh3/1
title: DIYABC sequence datafile for Synergus umbraculus

description: Sequence data for seven loci for Synergus umbraculus populations from four putative refugial populations, in a format allowing analysis in DIYABC v1.0.4.46beta 2
DOI: 10.5061/dryad.1c990.2
title: Data from: Host-pathogen metapopulation dynamics suggest high elevation refugia for boreal toads
DOI: 10.5061/dryad.1d7n9/1
title: Smith et al SNP data set

description: SNP data set for the PLOS ONE submitted manuscript "SNP markers tightly linked to root knot nematode resistance in grapevine (Vitis cinerea) identified by a genotyping-by-sequencing approach followed by Sequenom MassARRAY validation".
DOI: 10.5061/dryad.1j81k/1
title: RTAT_data

description: Excel sheet containing the song, color, and morphological data from male red-throated ant-tanagers (RTAT). The excel sheet also contains the territory ids, song, color, and morphology principal components, and the playback ID used to elicit male songs.
DOI: 10.5061/dryad.3p5r6/1
title: Finnerty_et_al_Data

description: Collected data in separate labeled tabs
DOI: 10.5061/dryad.4k40j/14
title: Lib5_Run2_Index2_S2_L001_R1_001.fastq

description: gzipped tar file containing Illumina sequencing data from: Library 5 (second run); Index 2; Read 1
DOI: 10.5061/dryad.4k40j/15
title: Lib5_Run2_Index1_S1_L001_R2_001.fastq

description: gzipped tar file containing Illumina sequencing data from: Library 5 (second run); Index 1; Read 2
DOI: 10.5061/dryad.4k40j/16
title: Lib8_Index12_S4_L001_R2_001.fastq

description: gzipped file containing Illumina sequencing data from: Library 8; Index 12; Read 2
DOI: 10.5061/dryad.4k40j/17
title: Lib8_Index12_S4_L001_R1_001.fastq

description: gzipped file containing Illumina sequencing data from: Library 8; Index 12; Read 1
DOI: 10.5061/dryad.4k40j/18
title: Lib8_Index6_S3_L001_R2_001.fastq

description: gzipped file containing Illumina sequence data from: Library 8; Index 6; Read 2
DOI: 10.5061/dryad.4k40j/19
title: Lib8_Index6_S3_L001_R1_001.fastq

description: gzipped file containing Illumina sequence data from: Library 8; Index 6; Read 1.
DOI: 10.5061/dryad.4k40j/20
title: Lib8_Index1_S1_L001_R2_001.fastq

description: gzipped file containing Illumina sequence data from: Library 8; Index 1; Read 2
DOI: 10.5061/dryad.4k40j/21
title: Lib8_Index1_S1_L001_R1_001.fastq

description: gzipped file containing Illumina sequence data from: Library 8; Index 1; Read 1
DOI: 10.5061/dryad.4k40j/22
title: Lib8_Index2_S2_L001_R2_001.fastq

description: gzipped file containing Illumina sequencing data from: Library 8; Index 2; Read 2
DOI: 10.5061/dryad.642p1/1
title: Data_the consequences of sexual selection in well adapted and maladapted populations

description: The file contains lifetime reproductive success data of the seed beetle acanthoscelides obtectus."offspring" is the absolute number of offspring per individual, "relfit" is relative fitness, standardized by mean fitness within subsets of the data as indicated in the titles (for example, relfit_sex,or,tr is relative fitness standardized by the mean within each sex, environment of origin and assay environment combination, which was the main response variable used in the analysis).
DOI: 10.5061/dryad.65286/1
title: Bukowski_Data

description: Raw data (traits, biomass) and calculated feedback for biomass.
DOI: 10.5061/dryad.656k6/1
title: reTURBT

description: This dataset comprises a total of 198 patients who underwent transurethral resection bladder tumor surgery.
DOI: 10.5061/dryad.74v01/1
title: Immune function versus antioxidant defense

description: This file holds data collected in the field on sedentary and migratory common blackbirds (Turdus merula). It gives values of the birds' baseline innate immune function (microbial killing capacity) and oxidative state (total non-enzymatic antioxidant capacity and malondialdehyde level, indicate of oxidative damage to lipids).
DOI: 10.5061/dryad.7p090/1
title: Colony Survival_11_1_2017

description: colony survival data, data on chimeric colonies, follower data, and supplementary data on methods
DOI: 10.5061/dryad.9jj84/1
title: Goat characteristics and FAMACHA/anemia data

description: Data used for logistic regression evaluating associations with high FAMACHA score (indicating anemia) before and after the rainy season. Reported in paper section "Spatial and seasonal variability in parasite burden in goats".
DOI: 10.5061/dryad.c0t6s/10
title: Figure_6_data

description: Files and data used to create figure 6 and figure S3.
DOI: 10.5061/dryad.c0t6s/2
title: Figure_4_data

description: Files and data used to create figure 4
DOI: 10.5061/dryad.c0t6s/3
title: Figure_3

description: R code to reproduce figure 3
DOI: 10.5061/dryad.c0t6s/4
title: Figure_5_data

description: Files and data used to create figure 5
DOI: 10.5061/dryad.c0t6s/5
title: Figure_S2_data

description: Files and data used to create figure S2
DOI: 10.5061/dryad.c0t6s/6
title: Figure_S4_data

description: Files and data used to create figure S4
DOI: 10.5061/dryad.c0t6s/7
title: Standalone Code

description: For those not willing or able to install the R package ‘junctions’ from CRAN, we provide stand-alone code. The code is accompanied by a walkthrough vignette.
DOI: 10.5061/dryad.c4r81/2
title: Haplotype_Dataset_Genotyped_66%Individuals

description: Haplotype data obtained using loci genotyped in &gt;66.67% of the individuals
DOI: 10.5061/dryad.f4m18/1
title: Data

description: This data file contains 19 worksheets. Worksheet "Data" contains the raw data for all individuals showing their identity, patriline, fertility status (0 = ovaries non-activated, 1 = ovaries activated), drifting status (0 = collected in natal nest, 1 = collected in foreign nest), natal colony identity, social context of the natal colony, host colony identity (if applicable), social context of the host colony (if applicable), distance of drifting in metres (if applicable), and replicate number. Worksheets "QR1" to "HQL6" contain the genotypes of all workers for all microsatellite loci, respectively for each colony (n = 18). The queens' deduced genotypes are also reported for each colony.
DOI: 10.5061/dryad.fq7h2/1
title: Supplementary Table 1

description: Diversity and evolutionary rates in Ordovician-Silurian graptoloids
DOI: 10.5061/dryad.fq7h2/2
title: Supplementary R Code

description: R code used for simulations and analyses
DOI: 10.5061/dryad.g0t42/1
title: Scripts and analyses for polygyny in ant-plants

description: This zipped folder contains scripts and analyses for Boyle et al., Polygyny does not explain the superior competitive ability of dominant ant associates in the African ant plant, Acacia (Vachellia) drepanolobium.
DOI: 10.5061/dryad.ht617/1
title: DATA  for Peng et al.

description: The Excel file includes 10 datasets associated with the manuscript.
DOI: 10.5061/dryad.j313j/1
title: files-paper-2.zip

description: A zip file that contains the six R scripts used in the paper (see ref [44]] and a pdf file with brief instructions for their use (Notes-on-use-of-R-scripts.pdf)
DOI: 10.5061/dryad.j75g369/1
title: Invasion response data

description: Data used to determine population, invasion experience, and treatment differences in traits and relative interaction index (RII), as well as relationship between suppression and tolerance, for bluebunch wheatgrass populations around the Missoula valley, MT, USA.
DOI: 10.5061/dryad.jj110/1
title: Raw dataset

description: There are seven excel files in this dataset. The spreadsheets "OTU table (bacteria; Anhui)”, “OTU table (fungi; Jiangxi)”, “OTU table(bacteria; Jiangxi)”,“OTU table(fungi; Anhui)”,“Enzyme activity”,“Phylogenetic diversity”and “Physicochemical properties” contain the raw data used in this paper, where a description of all the variables and units can be found.
DOI: 10.5061/dryad.jr74d/1
title: Data C. gouldii HR, MR, Tb
DOI: 10.5061/dryad.k3rv4/1
title: Moatt et al Data_S1

description: Data file for body composition and testes mass
DOI: 10.5061/dryad.k3rv4/2
title: Moatt et al Data_S2

description: Data file for growth data
DOI: 10.5061/dryad.n24q8/11
title: Supplementary_FIGS5

description: FIG. S5. Climatic niches of Stenodraba species in the environmental space produced by the two main axes of the PCA-env. For each species, the gray to black shading represents the grid cell density of the clade occurrence (black being the highest density). The first dashed line represents the 50% of the available environment and the solid line represents the 100 %. A. S. lechleri. B. S. parvifolia. C. S. chillanensis. D. S. colchaguensis. E. S. imbricatifolia. F. S. lagunae. G. S. stenophylla. H. S. suffruticosa.
DOI: 10.5061/dryad.n24q8/12
title: Supplementary_FIGS6

description: FIG. S6. Values of variables that most contribute in the MaxEnt models for clades A and B of Stenodraba along the distribution area. A. BIO3 (Isothermality). B. BIO4 (Temperature Seasonality). C. BIO8 (Mean Temperature of Wettest Quarter). D. BIO12 (Annual Precipitation). E. BIO15 (Precipitation Seasonality). Red and blue dots represent specimen occurrences of clades A and B, respectively, used for the SDM analyses. F. Response curves for variables used in the MaxEnt models of clades A and B. Response curves show the ranges in environmental conditions that are more favorable for the distribution of the species of each clade. The x-axis of the variables represents their ranges for the complete study area, while the y-axis represents the predicted suitability of the focus variable when all of the other variables are set to their average. Red line represents the mean response while blue shaded area represents ± 1 standard deviation.
DOI: 10.5061/dryad.n24q8/13
title: Supplementary_FIGS7

description: FIG. S7. Stenodraba species. A. Stenodraba chillanensis (Zuloaga 15235, SI), habit. B. Stenodraba colchaguensis (Zuloaga 12539, SI), habit. C-D. Stenodraba parvifolia (Zuloaga 15583, SI). C. Habit. D. flowers. Photographs by: A, C, D, D. Salariato; B, C. Zannotii.
DOI: 10.5061/dryad.n24q8/14
title: ITS alignment BRASSICACEAE

description: ITS alignment of Brassicaceae dataset for family-level analyses.
DOI: 10.5061/dryad.n24q8/15
title: trnL-F alignment BRASSICACEAE

description: trnL-F alignment of Brassicaceae dataset for family-level analyses.
DOI: 10.5061/dryad.n24q8/16
title: Maximum likelihood tree ITS BRASSICACEAE

description: Maximum likelihood tree for Brassicaceae generated with RAxML using the ITS dataset.
DOI: 10.5061/dryad.n24q8/17
title: Maximum likelihood tree trnL-F BRASSICACEAE

description: Maximum likelihood tree for Brassicaceae generated with RAxML using the trnL-F dataset
DOI: 10.5061/dryad.n24q8/18
title: Bayesian 50% majority-rule consensus tree ITS BRASS

description: Bayesian 50%  majority-rule consensus tree from 3002 trees generated by Bayesian inference with MrBayes and using the ITS dataset for Brassicaceae
DOI: 10.5061/dryad.n24q8/19
title: Bayesian 50%  majority-rule consensus trees trnL-F BRASS

description: Bayesian 50%  majority-rule consensus trees from 3002 trees generated by Bayesian inference with MrBayes and using the trnL-F dataset for Brassicaceae
DOI: 10.5061/dryad.n8v4m/1
title: Data for Conti et al. 2017 JofEcol