cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.33k09/8
title: doubleKD_ten1ten2KD_deltaCt_CFU

description: Data on the efficiency of the knock down by qPCR in the double knock down of tenecin 1 and tenecin 2 in relationship to the number of CFU of Staphylococcus aureus recovered from beetls of each treatment.
DOI: 10.5061/dryad.33k09/9
title: doubleKD_ten1ten4KD_deltaCt_CFU

description: Data on the efficiency of the knock down by qPCR in the double knock down of tenecin 1 and tenecin 4 in relationship to the number of CFU of Staphylococcus aureus recovered from beetls of each treatment.
DOI: 10.5061/dryad.348k2/1
title: HxSPhenotypingData

description: Tab delimited raw symbiosis phenotype data
DOI: 10.5061/dryad.349h0/1
title: Pefka_E_census_counts

description: This file contains complete fossil benthic foraminiferal census counts (fraction &gt;150 µm), total foraminiferal numbers, sample split, and (modified) plankton to benthos ratios (of the &gt;125µm fraction) from the Pefka E section. In the first column the adjusted section depth (in cm) is given.
DOI: 10.5061/dryad.349h0/2
title: WMed_census_counts

description: This file contains the complete modern dead benthic foraminiferal census counts (fraction &gt;150 µm), total foraminiferal numbers, sample split, and sample volume from three study areas in the Western Mediterranean Sea (Alboran Platform, Oran Bight and Mallorca Shelf). In the first two columns the station IDs and the water depth (in m) is given.
DOI: 10.5061/dryad.349h0/3
title: Reduced_modern_data

description: This file contains the relative abundance of modern benthic foraminifera in the combined modern data set used for the development of the transfer function in this study. In the first two columns the station IDs and water depth (in m) is given.
DOI: 10.5061/dryad.349h0/4
title: Modern_station_IDs

description: This file contains the station IDs used in the Reduced_modern_data.txt, their original station IDs, water depth (in m) and station location (Adriatic Sea or Western Mediterranean Sea (Alboran Platform, Oran Bight and Mallorca Shelf)). The data from the Adriatic Sea are from Jorissen (1987, 1988):

-Jorissen FJ. The distribution of benthic foraminifera in the Adriatic Sea. Mar Micropaleontol. 1987;12:21-48. 
doi: 10.1016/0377-8398(87)90012-0.
-Jorissen FJ. Benthic foraminifera from the Adriatic Sea: principles of phenotypic variation. Utrecht Micropaleontological Bulletins. 1988;37:1-174.
DOI: 10.5061/dryad.349h0/5
title: Reduced_Pefka_E_data

description: This file contains the relative abundance of fossil benthic foraminifera from the Pefka E section used for the application of the transfer function in this study. In the first column the adjusted section depth (in cm) is given.
DOI: 10.5061/dryad.35j3j/1
title: Supporting Data for  "Synthesis of gypsogenin derivatives with capabilities to arrest cell cycle and induce apoptosis in human cancer cells"

description: This file includes figures, tables, scheme and spectrum of compounds.
DOI: 10.5061/dryad.69bb2/2
title: Appendix

description: Online-only appendix
DOI: 10.5061/dryad.7h3f6/10
title: combined_analyses.tar

description: An archived folder containing the following files for each of the five datasets (g2, g5, g9, i37, and i57; example file names for the g5 dataset are given): concatenated alignment in fasta format (c2p1pgtc2_g5_combined_72inds_163seqs.fa), the RAxML tree from the concatenated alignment (RAxML_bipartitions.c2p1pgtc2_g5_combined_72inds_163seqs), the astral tree (c2p1pgts2_g5_astral.tre), and the list of included loci for each of the five datasets (c2p1gt2_Locus_List_g5.txt).
DOI: 10.5061/dryad.7h3f6/11
title: individual_loci.tar

description: An archived folder containing the following files for each of the individual loci (example file names for ppc2 are given): alignment in fasta format (c2p1pgts2_ppc2.fa), the RAxML tree without bootstrap values (RAxML_bestTree.c2p1pgts2_ppc2), and trees from 100 bootstrap replicates conducted in RAxML (RAxML_bootstrap.c2p1pgts2_ppc2).  (The latter two files are the input for an Astral analysis.)
DOI: 10.5061/dryad.7h3f6/2
title: Supp_Table_1

description: Supp Table 1. Gene families included in the bait design and sequencing project, showing the full name of each gene family, the shortened version of its name that is used in the paper, and whether the gene was classified as related to C4 or CAM photosynthesis.
DOI: 10.5061/dryad.7h3f6/3
title: Supp_Table_2

description: Supp. Table 2. Voucher table for all individuals included in phylogenetic analyses, including statistics on enrichment success and NCBI SRA accession numbers.
DOI: 10.5061/dryad.7h3f6/4
title: Supp_Table_3

description: Supp. Table 3. Sequencing statistics for g2, g5, g9, i37, and i57 datasets.
DOI: 10.5061/dryad.7h3f6/5
title: Supp_Table_4

description: Supp. Table 4. Paralogs per individual per gene family (the same data shown in the heatmap in Supp. Fig. 2).
DOI: 10.5061/dryad.7h3f6/9
title: locusMAPTreePlots

description: The results of the MrBayes analyses for all loci with individuals color-coded according to family and posterior probabilities for major groups shown.
DOI: 10.5061/dryad.81ps2/1
title: PNAS.201710186.vcf
DOI: 10.5061/dryad.8mc44/1
title: Matrix of anatomical characters

description: Matrix of five anatomical characters observed from 32 specimens of Vauquelinia corymbosa complex.
DOI: 10.5061/dryad.8mc44/2
title: Matrix of geographic distances

description: Matrix of geographic distances of data occurrence of 201 specimens of the subspecies of Vauquelinia corymbosa utilized in the Mantel Test.
DOI: 10.5061/dryad.8ph59/1
title: Extract reads from bam file based on presence of specific allele

description: Python script that reads from bam file based on presence of alleles in text file (text file with three columns: 1. Chromsome, 2. Position, 3. alllele [A, T, C, G]). Returns a bam file with extracted reads. See script for more details. 
example: python get_male_spec_reads.py -b bam.file -s snp.file
DOI: 10.5061/dryad.8ph59/2
title: Pipeline for determining Y-linked gene transfers. R script.

description: R script used to determine incipient Y-linked transfers using male/female pairs from two D. melanogaster strains. All data are publicly available. See supplementary materials for full description of pipeline, and description of data used in pipeline.
DOI: 10.5061/dryad.8ph59/3
title: Use polymorphism data to determine age of Y-linked transfer

description: R script for determining the age of a Y-linked transfers and perform statistical tests comparing age distribution of non-genic and genic transfers. See supplementary materials for more details, including description of datasets used.
DOI: 10.5061/dryad.9c50s/10
title: bgc_bie-fum_hybridzone_in

description: BGC bie-fum hybrid zone input file.
DOI: 10.5061/dryad.9c50s/2
title: all_samples

description: Genotypes for all samples in the study Blackburn et al 2017.
DOI: 10.5061/dryad.9c50s/3
title: pcadapt_in

description: PCADAPT input file.
DOI: 10.5061/dryad.9c50s/4
title: hiest_bie&occ&fum_parent_in

description: HIEST parent input file.
DOI: 10.5061/dryad.9c50s/5
title: hiest_bie-occ-fum_hybridzone_in

description: HIEST hybrid zone input file.
DOI: 10.5061/dryad.9c50s/6
title: bgc_bie_parent_in

description: BGC bie parent input file.
DOI: 10.5061/dryad.9c50s/7
title: bgc_occ_parent_in

description: BGC occ parent input file.
DOI: 10.5061/dryad.9c50s/8
title: bgc_fum_parent_in

description: BGC fum parent input file.
DOI: 10.5061/dryad.9c50s/9
title: bgc_bie-occ_hybridzone_in

description: BGC bie-occ hybrid zone input file.
DOI: 10.5061/dryad.c5961/2
title: MeDIP fold-enrichment data from RSC of LO/LO male prairie voles

description: MeDIP fold-enrichment data (bedgraph format) at the avpr1a locus (calculated against INPUT control from a pool of RSC from 4 LO/LO male prairie voles.
DOI: 10.5061/dryad.c5961/3
title: MeDIP enrichment difference between LO and HI

description: A bedgraph track for the difference in avpr1a MeDIP enrichments between LO/LO and HI/HI prairie voles in the RSC.
DOI: 10.5061/dryad.c5961/4
title: Ontogeny-meta data

description: A complete metadata set of all ontogeny data, including animal IDs, genotype, sex, RSC-V1aR, etc. See each tab for study names.
DOI: 10.5061/dryad.c5961/5
title: MeDIP and INPUT alignments for HI/HI RSC

description: bwa generated alignments, quality filtered and sorted bam format
DOI: 10.5061/dryad.c5961/6
title: MeDIP and INPUT alignments for LO/LO RSC

description: bwa generated alignments, quality filtered and sorted bam format
DOI: 10.5061/dryad.c5961/7
title: MeDIP and INPUT raw reads for HI/HI RSC
DOI: 10.5061/dryad.c5961/8
title: MeDIP and INPUT raw reads for HI/HI RSC
DOI: 10.5061/dryad.df564/32
title: gaqu_bbs_a

description: Raster file of Gambel's quail abundance estimates derived from Breeding Bird Survey (BBS) data.
DOI: 10.5061/dryad.df564/33
title: mouq_bbs_a

description: Raster file of mountain quail abundance estimates derived from Breeding Bird Survey (BBS) data.
DOI: 10.5061/dryad.df564/34
title: nobo_bbs_a

description: Raster file of northern bobwhite abundance estimates derived from Breeding Bird Survey (BBS) data.
DOI: 10.5061/dryad.df564/35
title: scqu_bbs_a

description: Raster file of scaled quail abundance estimates derived from Breeding Bird Survey (BBS) data.
DOI: 10.5061/dryad.df564/36
title: gaqumaxenteapnatureserve

description: Collated and spatially rarefied occurrence locations of Gambel's quail used to create ecological niche models through Maxent. Data were collated from both Breeding Bird Survey and eBird databases.
DOI: 10.5061/dryad.df564/37
title: monq_maxentEAP

description: Collated and spatially rarefied occurrence locations of Montezuma quail used to create ecological niche models through Maxent. Data were collated from both Breeding Bird Survey and eBird databases.
DOI: 10.5061/dryad.df564/38
title: caqumaxenteapnatureserve

description: Collated and spatially rarefied occurrence locations of California quail used to create ecological niche models through Maxent. Data were collated from both Breeding Bird Survey and eBird databases.
DOI: 10.5061/dryad.df564/39
title: mouq_maxentfileEAP

description: Collated and spatially rarefied occurrence locations of mountain quail used to create ecological niche models through Maxent. Data were collated from both Breeding Bird Survey and eBird databases.
DOI: 10.5061/dryad.g36qr/1
title: Marion Island mouse SECR

description: Zip file contains capture-mark-recapture file formatted for SECR analysis, trapping grid files, and session covariates for Marion Island mice 1991-2011
DOI: 10.5061/dryad.g36qr/2
title: Marion_invertebrate_biomass

description: Invertebrate biomass 1976-77, 1996-97, and 2006-07
DOI: 10.5061/dryad.g36qr/3
title: Marion_mouse_diet_2008-11

description: Stomach contents of mice collected on Marion Island 2008-11
DOI: 10.5061/dryad.g36qr/4
title: Marion_mouse_density_climate

description: Data for Bayesian meta-analysis exploring role of weather variables on changing mouse densities
DOI: 10.5061/dryad.m1b34/1
title: Supporting Information
DOI: 10.5061/dryad.mb14c/1
title: Appendix 1

description: The coded characters and their different states of turritelline species and some mathildidoid species.
DOI: 10.5061/dryad.p8k18/1
title: DCVC_Tag4_microarray_cel files

description: cel (Cell intensity file) -Raw Tag4 affy data files for each biological replicate at each dose (3 biological replicates, 3 doses). Contains a single intensity value for each probe cell delineated by the grid (calculated by the Cell Analysis algorithm). These files should be used for other programs to analyze the data.
DOI: 10.5061/dryad.pn397/1
title: Lai et al., 2017_DataSets_Biology letter

description: Cp values and priming efficiencies were calculated using the second derivative maximum method (Roche Lightcycler 480; Rasmussen, 2001) and the LinRegPCR software (Ruijter et al., 2009), respectively. Subsequently, relative mRNA expression levels were calculated using the following formula: 

Expression of target gene = (Ega^Cpga/Etar^Cptar)

Where ga is the geometric average of the two reference genes; tar is the target gene of interest, E is priming efficiency and Cp is the crossing point. 

Since duplicate cDNA syntheses were performed, and each of these were analysed in duplicates in the qPCR analyses, four data points were present for each original sample for each primer pair used, and their means were used in the mRNA expression calculations.
DOI: 10.5061/dryad.qg1p0/1
title: Morphological_Data

description: Morphological data for putative Iris hybrids from Lake Martin, LA. 346 individuals x 14 traits.
DOI: 10.5061/dryad.qg1p0/2
title: irisLakeMartin_reads.tar

description: The file contains all of the parsed reads for the Lake Martin Iris hybrid zone project. Please note: the uncompressed file size is ~55GB.
DOI: 10.5061/dryad.qp667/1
title: 539.nex

description: The 539-locus concatenated data set in interleaved nexus alignment format from "Phylogenomic analyses of 539 highly informative loci dates a fully resolved time tree for the major clades of living turtles (Testudines)." The alignment contains 605,087 bp for each of 26 in-group turtle species and two outgroup species (Alligator mississippiensis and Gallus gallus).
DOI: 10.5061/dryad.v1c28/1
title: Ferlian et al. 2017-Soil fauna density data

description: This data file contains the data on soil invertebrate density response to invasive earthworms. Data in this file are extracted from the literature.
DOI: 10.5061/dryad.vv469/33
title: imputed-seq-genotypes-12k-Chr1.153640000-154640000.vcf

description: Imputed genotypes for variants within 1Mbp of the Chr1:154.14 LC QTL, for 12,000 animals.
DOI: 10.5061/dryad.vv469/34
title: imputed-seq-genotypes-12k-Chr2.127140000-128140000.vcf

description: Imputed genotypes for variants within 1Mbp of the Chr2:127.64 LC QTL, for 12,000 animals.
DOI: 10.5061/dryad.vv469/35
title: imputed-seq-genotypes-12k-Chr3.15020000-16020000.vcf

description: Imputed genotypes for variants within 1Mbp of the Chr3:15.52 LC QTL, for 12,000 animals.
DOI: 10.5061/dryad.vv469/36
title: imputed-seq-genotypes-12k-Chr3.53340000-54340000.vcf

description: Imputed genotypes for variants within 1Mbp of the Chr3:53.84 LC QTL, for 12,000 animals.
DOI: 10.5061/dryad.vv469/37
title: imputed-seq-genotypes-12k-Chr5.20640000-21640000.vcf

description: Imputed genotypes for variants within 1Mbp of the Chr5:21.14 LC QTL, for 12,000 animals.
DOI: 10.5061/dryad.vv469/38
title: imputed-seq-genotypes-12k-Chr5.31060000-32060000.vcf

description: Imputed genotypes for variants within 1Mbp of the Chr5:31.56 LC QTL, for 12,000 animals.
DOI: 10.5061/dryad.vv469/39
title: imputed-seq-genotypes-12k-Chr5.43660000-44660000.vcf

description: Imputed genotypes for variants within 1Mbp of the Chr5:44.16 LC QTL, for 12,000 animals.
DOI: 10.5061/dryad.vv469/40
title: imputed-seq-genotypes-12k-Chr5.93440000-94440000.vcf

description: Imputed genotypes for variants within 1Mbp of the Chr5:93.94 LY QTL, for 12,000 animals.
DOI: 10.5061/dryad.vv469/41
title: imputed-seq-genotypes-12k-Chr6.37260000-38260000.vcf

description: Imputed genotypes for variants within 1Mbp of the Chr6:37.76 LC QTL, for 12,000 animals.
DOI: 10.5061/dryad.1t3r4/1
title: Appendix S1

description: Methods and results for dinosaur body mass estimates, including Tables S1–S12.
DOI: 10.5061/dryad.1t3r4/2
title: Appendix S2.

description: Summary figures from SURFACE analyses for Triassic–Jurassic Dinosauria, Sauropodomorpha, Ornithischia and Triassic–Aptian Theropoda, ordered by AICc or pBIC score.
DOI: 10.5061/dryad.1t3r4/3
title: Appendix S3

description: Diagrams comparing the pBIC scores of SURFACE regime configurations from analysis of timescaled phylogenies mapped to the same phylogenies timescaled using other methods.
DOI: 10.5061/dryad.1v4t5/1
title: Data_FE-2017-00030.R1
DOI: 10.5061/dryad.348k2/10
title: PairwiseResults.101.034

description: Tab delimited file with pairwise test results and log fold changes in expression between HM101 and HM034 nodules containing E. medicae and E. meliloti
DOI: 10.5061/dryad.348k2/11
title: PairwiseResults.056.340

description: Tab delimited file with pairwise test results and log fold changes in expression between HM056 and HM340 nodules containing E. medicae and E. meliloti
DOI: 10.5061/dryad.348k2/2
title: HxSPhenotypeAnalysis

description: R code to analyze the raw symbiosis phenotypes
DOI: 10.5061/dryad.348k2/3
title: ExpressedNodGenesTable

description: Tab delimited file that summarizes expression category results and cluster membership for all the genes found to be expressed in nodules
DOI: 10.5061/dryad.348k2/4
title: RNAseqcounts_allconditions_head

description: A tab delimited file containing raw gene counts of all RNAseq samples and for all Mtv4 genes
DOI: 10.5061/dryad.348k2/5
title: DESeq2code

description: R source code for the differential expression analysis
DOI: 10.5061/dryad.348k2/6
title: FullModelHostSymResults

description: Tab delimited file with DEseq2 output summarizing full model results for all genes expressed in nodules. Tabulated and compiled versions of the significance category results are  in the ExpressedNodGenesTable.txt file which should be sufficient for most interested parties.
DOI: 10.5061/dryad.348k2/7
title: FullModelRootResults

description: Tab delimited file testing if host genotypes different in gene expression in roots. This is not emphasized in the paper but I included it in case anyone was interested.
DOI: 10.5061/dryad.348k2/8
title: PairwiseResults.101.340

description: Tab delimited file with pairwise test results and log fold changes in expression between HM101 and HM340 nodules containing E. medicae and E. meliloti
DOI: 10.5061/dryad.348k2/9
title: PairwiseResults.101.056

description: Tab delimited file with pairwise test results and log fold changes in expression between HM101 and HM056 nodules containing E. medicae and E. meliloti
DOI: 10.5061/dryad.349h0/6
title: Readme

description: Readme file
DOI: 10.5061/dryad.3qs54/1
title: StabilizingSelectionNemoInitFiles

description: Init files for running with Nemo v2.3.4 (with variable modularity). For 10,000 generations of stabilizing selection to reach mutation-selection balance. G-matrix eigen decomposition and evolutionary metric analyses performed on 10,000th generation for each simulation averaged over 50 replicates.
DOI: 10.5061/dryad.3qs54/2
title: DirectionalSelectionNemo_Init_Files

description: Init files for running with Nemo v2.3.4 (with variable modularity). For 2,000 generations of directional selection performed on 10,000th generation of Stabilizing Selection population simulation output. Number of generations to a fitness cut-off for each simulation averaged over 50 replicates.
DOI: 10.5061/dryad.5kc61/1
title: Ecosystem variables at the end of Phase I

description: Abundance and size of planktonic and benthic prey, and abundance of primary producers, surveyed in 50 mesocosms at the end of Phase I (occupation by adult stickleback from 2 lineages and at 2 densities).
DOI: 10.5061/dryad.5kc61/2
title: Benthic invertebrate stable isotope values

description: SI values are for individual invertebrates sampled at the end of Phase I except for Zebra mussels and prosobranch snails, for which each sample is an assay of 3 pooled individuals.
DOI: 10.5061/dryad.5kc61/3
title: Juvenile fish stable isotope values

description: Stable isotope values for individual juvenile fish sampled at the end of Phase II (muscle tissue).
DOI: 10.5061/dryad.5kc61/4
title: Juvenile fish survival for each mesocosm

description: Total surviving juveniles of each type (Constance, Geneva, and F1 Hybrids).
DOI: 10.5061/dryad.5kc61/5
title: Juvenile fish condition from mesocosms

description: Body condition for all mesocosm juveniles, calculated as residuals from a length-weight regression and standardized to weight of a fish of average length.
DOI: 10.5061/dryad.681q5/1
title: Migrant_and_Resident_Dark-eyed_Junco_Telomere_Lengths

description: This file contains breeding, female junco banding data, year of collection, date of first clutch initiation (the number of days after the first clutch of the year), age (in years), T/S ratio (note: this is a comparative metric- these values can only be compared to other T/S ratios that were run on the same plates), tarsus length (mm), and body weight (in grams).
DOI: 10.5061/dryad.7h3f6/12
title: ppc1E1_alignment.fa

description: The alignment of the ppc1E1 gene family in fasta format (used in the analysis shown in Fig. 5).
DOI: 10.5061/dryad.7h3f6/13
title: ppc1E1_tree.tre

description: The gene family tree for the ppc1E1 gene family created in RAxML (used in the analysis shown in Fig. 5).
DOI: 10.5061/dryad.7h3f6/14
title: contigs.tar.gz

description: An archived folder containing separate folders for each of the nine families in the portullugo (the groups used for the pipeline).  Each folder contains two files for each gene family an sc_*.fa file with the contigs for that gene family and an sb3_*.out file that has the results of BLASTing that fasta file against the database of exons.  These two files are the input for part II of the pipeline.
DOI: 10.5061/dryad.7h3f6/15
title: Supp_Table_5a.csv

description: Supp. Table 5a. Results from the validation analyses after the transcript fragments were run through part II of the pipeline only.
DOI: 10.5061/dryad.7h3f6/16
title: Supp_Table_5b.csv

description: Supp. Table 5b. Results from the validation analyses after the transcript fragments were run through both parts II and III of the pipeline.
DOI: 10.5061/dryad.7h3f6/17
title: Supp_Table_5c.csv

description: Supp. Table 5c. Summary statistics from the validation analyses.
DOI: 10.5061/dryad.7h3f6/18
title: Supp_Table_6.csv

description: Supp. Table 6. Node support for all nodes that conflict or have less than 95% bootstrap support in any of the concatenated or Astral trees (the trees shown in Fig. 3).
DOI: 10.5061/dryad.7h3f6/19
title: Supp_Table_7.pdf

description: Supp. Table 7: Concordance factors from BUCKy analysis for all putative clades with at least 10% genome-wide support.
DOI: 10.5061/dryad.7p5s7/1
title: Exudate production and Growth rates for Dothistroma septosporum

description: This excel file has four pages. The first page lists the 45 isolates from the three races used in the experiment. The isolates come from three races - LPR green, SR orange and NPR blue - and within each race 5 isolates are sampled from each of three populations. The second, third and fourth pages give the exudate (here referred to as toxin) production scores for each isolate (no toxin, l=low, m=medium, h=high) together with the growth in mm after 8 weeks at temperatures 10, 17.5 and 22.5 degrees centigrade respectively. For each isolate the values in replicates I and II for a particular temperature are given.
DOI: 10.5061/dryad.7p5s7/2
title: SSR no missing data points- used for analysis

description: This excel file contains microsatellite allele sizes and mating types for each of 338 Dothistroma septosporum isolates scored at 11 microsatellite loci. The first column gives the individual isolate number, the second gives the code ascribed to each individual, and the third the code for the tree from which the isolate was derived. The fourth column gives the race to which the isolate was assigned (1 = SR, 2 = LPR, 3 = NPR). Columns 5 to 15 give the allele size for each individual at each of 11 microsatellite loci (E, F, G, I, J, K, L, M, O, DS1, DS2). Column 16 gives the mating type of the isolate (1 or 2).
DOI: 10.5061/dryad.88bq8/1
title: Site data

description: Data on six sites used in the analysis, including vertebrate numbers used to calculate the defaunation index.
DOI: 10.5061/dryad.88bq8/2
title: Dispersal syndrome data

description: Data on the means of dispersal for 274 tree species.
DOI: 10.5061/dryad.8d638/1
title: Tree files

description: .tre files from various phylogenetic analyses (RaxML concat, RaxML concat partitioned, MrBayes, ASTRAL, SVD)
DOI: 10.5061/dryad.8d638/2
title: 70% occupancy matrix

description: 70% occupancy (381 loci, 78103 basepairs) UCE matrix
DOI: 10.5061/dryad.8d638/3
title: 50% occupancy matrix

description: 50% occupancy (514 loci, 101652 basepairs) UCE matrix