cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.85950/1
title: PCA of female zebra finches_table2

description: PCA of 219 female zebra finches based on six traits: fecundity, mass day 8, mass day 100, inbreeding coefficient (Fshort), brood size and beak color (BC).
DOI: 10.5061/dryad.85950/2
title: PCA of male zebra finches_table2

description: PCA of 217 male zebra finches based on 10 traits: siring success, Natal brood size, Mass day 8, Mass day 100, Inbreeding_coefficient (Fshort), Beak color(BC), Cheek patch size, Courtship rate(meanroot11), Repertoire size, Amplitude.
DOI: 10.5061/dryad.85950/3
title: Pearson r of 7 traits_population wide_table3

description: Test for assortative mating for various quality traits of males and females (seven traits) calculated at the population-wide. At the population level, sample size (n) indicates the number of pairs for which a Pearson correlation coefficient was calculated. ‘Fitness’ refers to the number of eggs laid (female fecundity) or fertilized (male siring success). PCA score refers to the estimate of overall quality (Table 2) based on the other breeding round, i.e. when not paired to the focal partner.
DOI: 10.5061/dryad.85950/4
title: Pearson r of 7 traits_within aviary_table3

description: Test for assortative mating for various quality traits of males and females calculated at the within-aviary level. At the aviary level, the sample size indicates the number of aviaries for which a Pearson correlation coefficient was calculated; shown are the mean correlation coefficients for each trait. ‘Fitness’ refers to the number of eggs laid (female fecundity) or fertilized (male siring success). PCA score refers to the estimate of overall quality (Table 2) based on the other breeding round, i.e. when not paired to the focal partner.
DOI: 10.5061/dryad.85950/5
title: Pearson r of Pairing status_table 4

description: Test for assortative mating for male versus female estimates of quality (PCA scores, Table 2) across pairs of various status categories (all pair bonds observed, all exclusively monogamous relationships, the subset of monogamous relationships that lasted until the end of a breeding round, and all polygamous relationships).
DOI: 10.5061/dryad.85950/6
title: model testing the differential-allocation hypothesis_table5

description: Data for the linear mixed-effect model testing the differential-allocation hypothesis based on observations of the proportion of female incubation in 283 out of 292 lasting monogamous pairs that initiated breeding. The dependent variable is the relative count of female versus male nest visit (FIDInc and MIDinc) records (using the ‘cbind’ function in R) within each pair. The random effects male and female identity (ID) reflect the individual repeatability across different partners (variance component V), while the random effect pair ID controls for overdispersion in the binomial counts. The predictor of interest (quality difference) is the difference in estimated quality between the partners (female PCA score minus male PCA score:diff_FM).
DOI: 10.5061/dryad.85950/7
title: Pairing success ~ quality_figure1

description: Data for the Figure1: Pairing success of individuals as a function of their quality (scored as the first principal component reflecting the quality indicators given in Table 2).
DOI: 10.5061/dryad.85950/8
title: data for figure2

description: Data for figure2: Principal component scores reflecting individual quality of males and females that formed a pair bond during the first and second breeding round. Note that PC scores are calculated from data of the other breeding round.
DOI: 10.5061/dryad.85950/9
title: pair status & quality_ FigS1

description: Data for figureS1: PC scores of monogamous, polygamous and unpaired individuals of both sexes. Pairing status during the first breeding round in relation to the PC score from the second breeding round (PC1_other_round); Pairing status from the second round in relation to the PC score from the first round (PC1_other_round).
DOI: 10.5061/dryad.8hv0k/1
title: MrBayes samples and summary topologies using nucleotide alignment

description: MrBayes version 3.2.2
DOI: 10.5061/dryad.8hv0k/2
title: MrBayes samples and summary topologies using amino acid alignment

description: MrBayes version 3.2.2
DOI: 10.5061/dryad.8hv0k/3
title: t2_aln_v02_nt.fasta NT alignment of T2/S-RNases
DOI: 10.5061/dryad.8hv0k/4
title: t2_aln_v02_aa.fasta AA alignment of T2/S-RNases
DOI: 10.5061/dryad.8hv0k/5
title: Unrooted best NT/GTR RAxML tree with posterior support values from MrBayes analysis
DOI: 10.5061/dryad.8hv0k/6
title: Rooted best NT/GTR RAxML tree with posterior support values from MrBayes analysis
DOI: 10.5061/dryad.9hn0m/1
title: Satellite tracking data Caretta caretta

description: Date, latitude, longitude and acuracy of location.
DOI: 10.5061/dryad.b464m/1
title: Complete set of aligned UCE loci

description: This file contains the complete set of 2510 aligned, untrimmed ultraconserved element loci in FASTA format
DOI: 10.5061/dryad.b464m/2
title: 10-gene Sanger sequencing dataset

description: This file contains a broad selection of data files for analyses of the 10 gene Sanger sequencing dataset, including constrained and unconstrained analyses, BEAST xml files, and input for BUCKy, MrBayes, IQ-TREE, and RAxML.
DOI: 10.5061/dryad.b464m/3
title: UCE ASTRAL analysis input files

description: This file contains the binned, weighted input files for the ASTRAL species tree analysis of the ultraconserved element dataset.
DOI: 10.5061/dryad.b464m/4
title: UCE analysis input files

description: This file contains the 'min90' and 'coding' ultraconserved elements alignments and their associated partition files.
DOI: 10.5061/dryad.b464m/5
title: BioGeoBEARS

description: This file contains the input files for the BioGeoBEARS analysis of the empirical data, as well as a script for model-averaging BioGeoBEARS output.
DOI: 10.5061/dryad.b464m/6
title: HiSSE scripts

description: This file contains the scripts and input files for the HiSSE analysis of arboreality and parasitism in Temnothorax.
DOI: 10.5061/dryad.gd844/1
title: Genotype Data for Naturalized Rainbow Trout from Lake LLanquihue and Lake Todos Los Santos (Lake District X Region - Chile)

description: This dataset corresponds to multilocus genotypes for naturalized rainbow trout from Lake Llanquihue and Lake Todos Los Santos (Lake District, Chile) screened for 86 single nucleotide polymorphisms (coded A=1, C=2, G=3, T=4, Missing=0). Each allele (A1 or A2) is found in a separate column (two columns per SNP locus). Metadata for sampling location, Lake, Individual ID, Year, Season (austral winter or spring) are provided.
DOI: 10.5061/dryad.gk90t/3
title: ult_mm.tar

description: Min-max data for each aligned protein, one row per position of the alignment. This data went into the co-occurrence analysis
DOI: 10.5061/dryad.gk90t/4
title: minmax_pval_aln.tar

description: Min max data with p-values per position, across the orthologs in alignment position space
DOI: 10.5061/dryad.gk90t/5
title: groupCATH.boundaries

description: aligned position relative to CATH domains; format is: ortholog group, IN/OUT, position in domain, position in alignment. If a given position is not in a domain NA is placed in the domain position
DOI: 10.5061/dryad.gk90t/6
title: groupSCOP.boundaries

description: aligned position relative to SCOP domains; format is: ortholog group, IN/OUT, position in domain, position in alignment. If a given position is not in a domain NA is placed in the domain position
DOI: 10.5061/dryad.gk90t/7
title: sig_pruned_masked_p.05

description: final set of significantly co-occurring codons with a p-value &lt;= 0.05 after pruning as described in the text
DOI: 10.5061/dryad.hb8b5.1
title: Data from: The physical boundaries of public goods cooperation between surface-attached bacterial cells
DOI: 10.5061/dryad.hb8b5.2
title: Data from: The physical boundaries of public goods cooperation between surface-attached bacterial cells
DOI: 10.5061/dryad.hb8b5.2/1.2
title: Data for Weigert et al._Manuscript

description: Includes raw data for all figures (including supplementary figures).
DOI: 10.5061/dryad.hb8b5.2/2.2
title: Code_Weigert_et_al

description: Includes the code for single cell analysis. Please refer to the supplementary protocol for instructions.
DOI: 10.5061/dryad.hb8b5.2/3.2
title: Example_data

description: Contains example images needed for the supplementary protocol.
DOI: 10.5061/dryad.hk30k/1
title: OIK-04536.R1_Data

description: The excel file contains 26 worksheets that correspond to the 26 studied patches. In all 26 sheets, columns are butterfly species and rows are plant species. When there is a trophic interaction between butterfly and plant species, there is a 1, while when there is no interaction between them there is a 0. Butterfly and plant species names are coded. Extended names and codes are included in the Supplementary material.
DOI: 10.5061/dryad.j4n09/1
title: avspecimen_coords_L

description: Landmark coordinate data in 3D of the left valve (202 landmarks) for 933 specimens of scallops. Coordinate data are Procrustes residuals, and the average shape from 2 replicates. Specimen IDs correspond to file "ID classifier all.csv".
DOI: 10.5061/dryad.j4n09/2
title: avspecimen_coords_R

description: Landmark coordinate data in 3D of the right valve (202 landmarks) for 859 specimens of scallops. Coordinate data are Procrustes residuals, and the average shape from 2 replicates. Specimen IDs correspond to file "ID classifier all.csv"
DOI: 10.5061/dryad.jm00k/1
title: Species and soil data from Amazonia
DOI: 10.5061/dryad.q2932/2
title: Linkage Groups

description: Linkage group mapping for the 3 backcross populations.
DOI: 10.5061/dryad.q2932/3
title: Marker Genotypes

description: Marker genotypes for the 3 backcross families.
DOI: 10.5061/dryad.r5d10/2
title: R scripts

description: Zip file contains R scripts for redoing all analyses in the paper.
DOI: 10.5061/dryad.r5d10/3
title: TableS1

description: Table containing detailed information (model output, parameter estimates etc.) for each fossil time series analyzed in the paper. Table also contains sources (references) for all time series.
DOI: 10.5061/dryad.r5nj3/1
title: Data for selection analysis on male black-throated blue warblers

description: The data file includes morphological measurements and reproductive success data for individual males, as well as average morphological measurements for individual males' competitors. We include standardized and unstandardized variables, as well as weighted and unweighted values for the morphology of the competitors. Full details are in the ReadMe file, as is R code to assist with re-creating analyses from the article.
DOI: 10.5061/dryad.s3953/1
title: University of Georgia weather station data

description: Daily mean, minimum, maximum temperature and relative humidity data by calendar month and date
DOI: 10.5061/dryad.s3953/2
title: Aquatic temperature logger data

description: Daily temperature data recorded within experimental pots. Temperature is recorded daily (1-31) at 10 min intervals from the months of June (month 6) through October (month 10). Pot_ID represents a site indicator and the experimental pot (e.g. 6-L1; site 6, larval pot 1)
DOI: 10.5061/dryad.s3953/3
title: Air temperature and relative humidity logger data

description: Air temperatures and relative humidity were recorded at 10 min intervals daily (day 1-31) from June (month 6) to October (month 10).  Pot_ID represents a site indicator and the experimental pot the ambient data logger was paired with (e.g. 1_A5 = Site 1, experimental pot 5).
DOI: 10.5061/dryad.02sk7/12
title: Physconelloides mt concatenated alignment

description: Concatenated alignment of mitochondrial sequence data from ground-dove body lice.
DOI: 10.5061/dryad.02sk7/13
title: Physconelloides gene alignments

description: Sequence alignments of nuclear exons from ground-dove body lice.
DOI: 10.5061/dryad.02sk7/14
title: Physconelloides Jane input

description: Input file used for the Jane4 cophylogenetic analysis of ground-doves and their body lice.
DOI: 10.5061/dryad.02sk7/15
title: Physconelloides association matrix

description: Association matrix for ground-doves and their body lice. Used as input for cophylogenetic analyses in ParaFit and PACo.
DOI: 10.5061/dryad.02sk7/16
title: Physconelloides voucher photographs

description: Voucher photographs (TIFFs) of ground-dove body lice specimens used for Illumina full genome sequencing.
DOI: 10.5061/dryad.13bp2/1
title: Wurno zone Sokoto Nigeria_2005

description: This data was part of an all-age blindness prevalence survey conducted in Sokoto state Nigeria in 2005. The data is for persons aged 50 years and over who were examined in Wurno health of Sokoto state. The sample were selected using a stratified sampling strategy. The operational definitions were based on WHO/PBL coding instructions for eye examination record.
DOI: 10.5061/dryad.1gk77/1
title: Oviposition in response to presence of basal fruits

description: This file contains processed data of oviposition events of Tegeticula yuccasella in response to presence or absence of basal fruits in experimental trials. Results from this dataset are reported in the section “Oviposition in response to presence of basal fruits”, Figure 2ab, and Tables S1-S5 of the article. The dataset also includes variables associated with the experiment in addition to those used in the article. See the README file for more details.
DOI: 10.5061/dryad.1gk77/2
title: Larval emergence in response to the presence of basal fruits

description: This file contains processed data of larval emergence from fruits of naturally-pollinated inflorescences. This dataset was used for results reported in the section “Larval emergence in response to the presence of basal fruits”, Figure 3abc, and Table S6. The dataset includes data from fruits/flowers from all positions on the inflorescences. See the README file for more details.
DOI: 10.5061/dryad.1gk77/3
title: Eclosion of lab-reared Tegeticula spp.

description: This file contains data of eclosion of yucca moths from lab-reared larvae. This dataset was used for results reported in the section “Larval emergence in response to the presence of basal fruits”. See the README file for more details.
DOI: 10.5061/dryad.1gk77/4
title: Predictors of moth arrival at onset of flowering

description: This file contains processed data of moth arrival at inflorescences at onset of flowering. This dataset was used for results reported in the section “Predictors of T. yuccasella arrival at onset of flowering”, Figures 4ab-5ab, Tables S7-S12, and Appendix S3. The dataset also includes variables associated with the inflorescences and moth arrival in addition to those used in the article. See the README file for more details.
DOI: 10.5061/dryad.1gk77/5
title: IBM code for moth oviposition in response to basal fruits

description: This R script contains the code for the Individual Based Model in Appendix 2 of the article. The model was developed to support our prediction that with increasing number of basal fruits fewer yucca moth larvae will emerge from distal fruits because of fewer ovipositions in those flowers with increasing number of basal fruits.
DOI: 10.5061/dryad.2538d/1
title: Acute hyperbaric tolerance heart rate and molar oxygen consumption data

description: Acute hyperbaric tolerance mass-normalised heart rate and mass-normalised mass-specific molar oxygen consumption.
DOI: 10.5061/dryad.2538d/2
title: Sustained hyperbaric tolerance heart rate and molar oxygen consumption data

description: Sustained hyperbaric tolerance mass-normalised heart rate and mass-normalised mass-specific molar oxygen consumption.
DOI: 10.5061/dryad.2b8f1/1
title: VCF file

description: VCFv4.0 file for the 673 Lake Trout (Salvelinus namaycush) individuals from 31 populations from Quebec, Canada.
DOI: 10.5061/dryad.2cq2g/1
title: Coalition_mating_data

description: This file contains number of matings appropriated by coalition males. This was used to compute mating indices and compare that between coalition partners.
DOI: 10.5061/dryad.2cq2g/2
title: Singleton_mating_data

description: This file contains mating data on single males
DOI: 10.5061/dryad.2cq2g/3
title: Feeding_data_coalition

description: This file contains data from coalitions on predation incidents. Time spent on kills were used to compute consumption and skew in consumption between partners. Aggressive encounters on kills have been coded for understanding competition.
DOI: 10.5061/dryad.2cq2g/4
title: Male_fitness

description: This file contains data on reproductive fitness of males. Tenure holding probabilities and mating events were used to parameterize fitness quotients.
DOI: 10.5061/dryad.5415m/1
title: Franciscana dolphin diet

description: Samples of franciscana dolphins (n = 58) incidentally caught by artisanal gillnet fisheries from the Northern (n = 11, municipalities of Ubatuba, Ilhabela, Caraguatatuba, and São Sebastião), Central (n = 40, municipalities of Bertioga, Guarujá, Santos, São Vicente, Praia Grande, Mongaguá, Itanhaém, and Peruíbe), and Southern regions (n = 7, Iguape, Ilha Comprida and Cananéia) of the São Paulo State coast in Brazil.  Franciscana dolphins were classified into juveniles (n = 8), subadults (n = 18) or adults (n = 32) according to total length.  For females (n = 34), juveniles were &lt; 90 cm, subadults were &gt; 90 cm and &lt; 119 cm, and adults were &gt; 119 cm.  For males (n = 24), juveniles were &lt; 90 cm, subadults were &gt; 90 cm and &lt; 107 cm, and adults were &gt; 107 cm. The detailed distribution of specimens of franciscana dolphin bycaught according to region, season, sex, and age is shown in the table.
DOI: 10.5061/dryad.5q1q6/3
title: Seagrass Census - Arkle 2017

description: Average seagrass and macroalgal abundances from seven localities around St. Croix, USVI. First two letters in row names (sites) indicate locality (SC=Smuggler's Cove, CH=Christiansted Harbor, PP=Power Plant, SR=Salt River Bay, MP=Molasses Pier, HP=Ha'Penny Bay, DS=Dump Site). First set of numbers in sample labels indicate position on the transect (in meters), and numbers 11 and 12 indicate sampling years (2011 and 2012, respectively). Columns are species names.
DOI: 10.5061/dryad.63474/1
title: 16S-[UPARSE_otu_table.txt]

description: the OTU table of prokaryotes generated by UPARSE
DOI: 10.5061/dryad.63474/2
title: ITS-[UPARSE_otu_table.txt]

description: the OTU table of fungi generated by PUARSE
DOI: 10.5061/dryad.63m81/1
title: Morphological data on basal Acariformes formatted for phylogenetic analysis in PAUP

description: Includes representatives of all families of Endeostigmata. Data also includes many representatives of basal Trombidiformes. This dataset was generated to test hypotheses on the phylogenetic location of Eriophyoidea. It includes 6 species of Nematalycidae and 8 species of Eriophyoidea (including 3 Triassic species). Character coding is explained in detail in the text of the associated publication.
DOI: 10.5061/dryad.68hv7/1
title: Russian cattle breed genotypes from Yurchenko et al. 2017

description: A set of 26,740 high quality SNPs genotyped on 322 samples from 19 cattle breeds used to reveal origins and diversity within the Russian native cattle breeds when combined with world breed genotypes from Decker et al., 2014 and Iso-Touru et al., 2016.
DOI: 10.5061/dryad.7j4t8/10
title: X-Ray Powder Diffraction raw data for G4M
DOI: 10.5061/dryad.7j4t8/6
title: X-Ray Powder Diffraction raw data for G4M-(Pt3/Pd7)
DOI: 10.5061/dryad.7j4t8/7
title: X-Ray Powder Diffraction raw data for G4M-(Pt5/Pd5)
DOI: 10.5061/dryad.7j4t8/8
title: X-Ray Powder Diffraction raw data for G4M-(Pt7/Pd3)
DOI: 10.5061/dryad.7j4t8/9
title: X-Ray Powder Diffraction raw data for GnM-(Pt)
DOI: 10.5061/dryad.83h1h/1
title: Data - Seasonal and geographic temperature effects on D. lineata

description: This excel file contains data from all laboratory and field activities reported in this publication. A metadata tab is included with descriptions of all column heads and variables used.
DOI: 10.5061/dryad.84655.2
title: Data from: A whole-transcriptome approach to evaluating reference genes for quantitative gene expression studies: a case study in Mimulus
DOI: 10.5061/dryad.84655.2/1.2
title: JS1

description: M. luteus var. luteus inbred line EY7 - petal transcriptome "T2" - sample JS1
DOI: 10.5061/dryad.84655.2/2.2
title: JS2

description: M. guttatus inbred line IM767 - petal transcriptome "T2" - sample JS2
DOI: 10.5061/dryad.84655.2/3.2
title: JS3

description: M. guttatus inbred line  IM767 - leaf transcriptome "T2" - sample JS3
DOI: 10.5061/dryad.84655.2/4.2
title: JS4

description: M. luteus var. luteus inbred line EY7 - calyx transcriptome "T2" - sample JS4
DOI: 10.5061/dryad.84655.2/5.2
title: JS5

description: M. guttatus inbred line IM767 - stem transcriptome "T2" - sample JS5
DOI: 10.5061/dryad.84655.2/6.2
title: JS6

description: M. luteus var. luteus inbred line EY7 - leaf transcriptome "T2" - sample JS6
DOI: 10.5061/dryad.84655.2/7.2
title: JS7

description: M. guttatus inbred line IM767 - calyx transcriptome "T2" - sample JS7
DOI: 10.5061/dryad.84655.2/8.2
title: JS8

description: M. luteus var. luteus inbred line EY7 - leaf transcriptome "T2" - sample JS8
DOI: 10.5061/dryad.84655.2/9.2
title: JS9

description: M. luteus var. luteus inbred line EY7 - stem transcriptome "T2" - sample JS9
DOI: 10.5061/dryad.85950/10
title: pair status and quality_ FigS2

description: Data for FigS2: Principal component scores of mated pairs of different pairing status (as in Fig. 2, but both breeding rounds combined).
DOI: 10.5061/dryad.85950/11
title: dynamic assortment in aviary_FigS3

description: Data for FigS3: Male and female quality (PC scores from the other breeding round) and level of assortative mating for PC scores (Pearson correlation coefficient r) in relation to the order of pairing within aviaries (AV). All pair bonds that were formed within an aviary were ranked by the order of pair formation (Pairing order within aviary).
DOI: 10.5061/dryad.8s544/1
title: Data for manuscript and supplementary information
DOI: 10.5061/dryad.bk78q/1
title: Phylogeny_of_Typhlocharina_RAxML_BestTree

description: ML trees were obtained using RAxML 7.2.7 (Stamatakis 2006). Data sets were partitioned by gene and the protein-coding genes (cox1-a and cox1-b fragments) were additionally partitioned by separating the third codon positions (Andújar et al. 2012). An independent GTR + G model was applied to each data partition. The best scoring ML tree was selected among 200 searches on the original alignment with different randomized parsimony starting trees. Support values were obtained with 1000 bootstrap replicates (Felsenstein 1985). BI was run in MrBayes 3.2.3 (Huelsenbeck et al. 2001) on the concatenated data, partitioned by gene and codon as before, and for each partition the optimal substitution model was selected using the Akaike information criterion (AIC) in jModelTest 2.1.7 (Darriba et al. 2012).
DOI: 10.5061/dryad.bk78q/2
title: Phylogeny_of_Typhlocharina_MrBayes_MajorityRuleConsensus

description: 50% majority rule consensus tree obtained in MrBayes. Bayesian inference consisted of two independent runs, each with three hot and one cold chain, for 10 million generations, whereby trees were sampled every 1000 generations. The standard deviation of split frequencies was checked to assess the convergence of results, as well as the mean and effective sampled size (ESS) of likelihood values computed with TRACER 1.6 (Rambaut et al. 2013). The 50% majority rule  trees were calculated excluding 50% of the initial trees as a conservative burn-in, ensuring that the plateau in tree likelihood values had been reached.