cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8jb83/4
title: resampling_brain.200b.windows

description: Alignments of extensive sequencing of Brain samples (~320 million reads) were split into three different sets of 100 million reads per taxon, such that each set would contain sets of independent observations. Pair-relationships were maintained, so that pairs of the same fragments would be in the same set. Here we report the quantification per window of each of those resampled transcriptome sets. Coverage of the mm10 mouse reference genome. Computed from transcriptome alignments of three populations of Mus musculus domesticus (AH from Iran, CB from Germany, MC from France), two populations of Mus musculus musculus (KH from Kazakhstan, WI from Austria), Mus musculus castaneus (TA), Mus spicilegus (SC), Mus spretus (SP), Mus mattheyi (MA) and Apodemus uralensis (AP). The first six fields correspond to the genomic location and the following each of the transcriptomes of the species mentioned here. Features were generated with bedtools, converted into SAF format, and extracted from BAM alignments using the featureCounts suite.
DOI: 10.5061/dryad.8jb83/5
title: TaxonomicRestrictedExpressionWindows

description: Multiple files corresponding to windows with expression above 50 reads in one taxon and absent in all others. Most regions represent only a single taxon, with the exception of those defined for Mus musculus musculus and Mus musculus domesticus populations, in which windows could be present in at least one population, but could also be present in more than one population, provided they would be absent in any other regions. Taxon codes as indicated in the main body of the manuscript. Tissue samples correspond to brain (B), liver (L), and testis (T), and to additional extensive sequencing of brain samples (UDS). Files are in bigWig format, for visualization together with the mm10 version of the mouse reference genome. We provide two IGV (Integrative Genomics Viewer) sessions XML files, which the user can directly load onto the genome browser. One session uses local files, and files have to be present in the same directory as the session file, another makes use of existing files in our local ftp server and does not require the local files, but does require internet connection. In addition to this we provide the expression values supporting the taxonomically-restricted status (*.dat), and a bed file of the relevant regions.
DOI: 10.5061/dryad.9f1p2/17
title: 24bsdcdeltacytopbs5

description: Raw image for Figure 4
DOI: 10.5061/dryad.9f1p2/18
title: sdcdeltaectoPBS

description: Raw image for Figure 4
DOI: 10.5061/dryad.9f1p2/19
title: sdctmswapPBS

description: Raw image for Figure 4
DOI: 10.5061/dryad.9f1p2/20
title: Normalized Bouton Counts Resubmission

description: This file contains all the bouton counts for this manuscript.
DOI: 10.5061/dryad.g56f4/1
title: Alstonville_Dryad
DOI: 10.5061/dryad.g56f4/2
title: Barcelona_Dryad
DOI: 10.5061/dryad.g56f4/3
title: Brownsville_Dryad
DOI: 10.5061/dryad.kc20m/1
title: JFMA cases and the covariates tested and used in our model

description: This data has all variables used in the statistical model as they entered the generalized linear model and the generalized linear mixed model. The variables included are (in the order they appear): year, kebeleID, JFMA total cases, log expected cases, scaled log ratio of SOND cases to the expected SOND cases, scaled DJF mean temperature in degree Celsius, scaled DJF total rainfall in mm, scaled population density from overlapping circles of 5km radius, scaled population density from overlapping circles of 10km radius, scaled weighted distance to roads, scaled inverse square distance to perennial water bodies, scaled average soil water holding capacity, scaled average slope, scaled average NDVI, scaled SST anomalies from the Nino 3.4 region, and IRS status (0/1).
DOI: 10.5061/dryad.kc20m/2
title: Count of neighboring kebeles

description: This data set contains the count of kebeles neighboring each kebele. This file should be used in combination with the Nieghborhood.csv.  For example the first kebele (ID=1) has 4 neighbors. Thus, the first four numbers in neighborhood.csv are kebele ID's of those kebeles neighboring kebele 1. Similarly, the second kebele has 3 neighbors, and thus the next three number in neighborhood.csv are IDs of its three neighbors. The remaining neighbors are identified by matching them with corresponding kebele IDs in the file neighborhood.csv in this manner.
DOI: 10.5061/dryad.kc20m/3
title: neighborhood

description: This data set contains the IDs of kebeles neighboring each kebele in the file named "Count of neighboring kebeles". This file should be used in combination with the "Count of neighboring kebeles".  For example the first kebele (ID=1) has 4 neighbors. The first four number in this data set are the kebele ID's of those kebeles neighboring kebele 1. Similarly, the second kebele has 3 neighbors, and the next three number in this data set are IDs of its three neighbors. The remaining neighbors are identified by matching them with corresponding kebele IDs in similar manner.
DOI: 10.5061/dryad.p3hr1/1
title: Fig. 2A data

description: G. mellonella mortality after infection with experimental X. nematophila.
DOI: 10.5061/dryad.p3hr1/2
title: Fig. S1 data

description: G. mellonella mortality after X. nematophila infection. X. nematophila strains were experimentally evolved apart from their nematode host, S. carpocapsae for 10 generations.
DOI: 10.5061/dryad.p3hr1/3
title: Fig. 2B data

description: G. mellonella mortality exposed to experimental S. carpocapsae and X. nematophila populations.
DOI: 10.5061/dryad.p3hr1/5
title: Fig. 3 data

description: G. mellonella mortality after infection with recapitulated mutualisms. S. carpocapsae were derived from the ancestral population, while X. nematophila populations were the experimental populations.
DOI: 10.5061/dryad.pp75d/1
title: Hertzetal16ChinookIsotopes

description: d13C, d15N of dorsal muscle tissue and weights (g) of juvenile Chinook Salmon caught off the west coast of Vancouver Island from 2000-2009. d13C values were corrected for differences in sample preparation following Fig S3, and were lipid-corrected following Post et al. 2007.
DOI: 10.5061/dryad.vv28j/1
title: IRRI MET 2011 2012 phenotype data all files

description: This archive contains the raw multi-environment (MET) phenotype data used for the MET GS experiments reported in this publication. Each .csv file in the archive contains the data for a particular year, season, and site. See ReadMe file for description of columns.
DOI: 10.5061/dryad.06sd9/1
title: Data from Rana muscosa-Bd temperature experiment

description: This data file gives the results from a laboratory experiment conducted at University of California, Santa Barbara where the Mountain yellow-legged frogs Rana muscosa housed at different temperatures were infected with Batrachochytrium dendrobatidis (Bd) and monitored for 120 days.  Every 3 days, the animals were swabbed and the Bd load was calculated using quantitative PCR. The data file has the following columns: size: the Bd load in zoospore equivalents at the current time point; sizeNext: the Bd load in zoospore equivalents at the next time point; time: the time in days between swabs; individual: A unique identifier of individual frogs in the experiment; temp: The temperature in Celsius at which the frog was housed; surv: whether or not a frog survived the time period; stage: the life stage of frog, all adults.
DOI: 10.5061/dryad.0bg04/12
title: TuMV_R2

description: TuMV-aligned reads R2
DOI: 10.5061/dryad.26031/1
title: DataFieldandClimatechamber

description: Phenotype data of A. thaliana plants grown in either a field environment or in a climate chamber environment. In the climate chamber environment plants were grown under control conditions or salt stress.
DOI: 10.5061/dryad.2d7km/1
title: Morphological measurements in labyrinth fishes

description: Morphological measurements for individual specimens from 24 labyrinth fish species. These characters describe dimensions of the body and head as well as the number and shape of individual vertebrae in the precaudal and caudal regions of the axial skeleton. Abbreviations are as follows: SL is standard length, BD is body depth, BW is body width, HL is head length, HD is head depth, HW is head width, PCN is number of precaudal vertebrae, PCL is length of precaudal vertebrae, PCD is depth of precaudal vertebrae, PCW is width of precaudal vertebrae, CN is number of caudal vertebrae, CL is length of caudal vertebrae, CD is depth of caudal vertebrae, and CW is width of caudal vertebrae. All linear measurements are in mm.
DOI: 10.5061/dryad.4d3n1/1
title: genotypes of 132 hoary bats and 87 silver-haired bats from Alberta, Canada

description: Excel file containing genotypes of 132 hoary bats (Lasiurus cinereus) and 87 silver-haired bats (Lasionycteris noctivagans) collected at a wind energy facility in south-western Alberta, Canada in 2006 and 2007. Hoary bats were genotyped at 19 loci and silver-haired bats at 18 loci. This data was used to determine relatedness of individuals, so includes the year the individual was killed and their age/sex.
DOI: 10.5061/dryad.4f92n/17
title: SubC_Wake_1
DOI: 10.5061/dryad.4f92n/18
title: SubC_Wake2
DOI: 10.5061/dryad.4f92n/19
title: SubD_Sleep1_part1
DOI: 10.5061/dryad.4f92n/20
title: SubD_Sleep1_part2
DOI: 10.5061/dryad.4f92n/21
title: SubD_Sleep2
DOI: 10.5061/dryad.4f92n/22
title: SubD_Wake1
DOI: 10.5061/dryad.4f92n/23
title: SubD_Wake2
DOI: 10.5061/dryad.4gb62/1
title: PALs

description: PAL files are provided for each species described in the publication in text format.
DOI: 10.5061/dryad.4gb62/2
title: A_gran_reads
DOI: 10.5061/dryad.4gb62/3
title: A_pras_reads
DOI: 10.5061/dryad.4gb62/4
title: C_rhyn_reads
DOI: 10.5061/dryad.4gb62/5
title: G_kuhl_reads
DOI: 10.5061/dryad.4vs36/6
title: Exp_V_maternal_effects

description: Maternal effects data from experiment V.
DOI: 10.5061/dryad.5t5m4/1
title: Figure 1, phylogenetic tree

description: Nexus file executable in MrBayes that was used to generate the tree from aligned and trimmed Amyrel sequences (GenBank accession numbers in the Supporting Information). Tree file created in FigTree from the resulting 50% majority rule consensus phylogeny.
DOI: 10.5061/dryad.5t5m4/2
title: Figure 2, cellular immunity

description: For all replicates of every fly-wasp species combination, number of dissected larvae that were attacked (contained a parasitoid egg), unattacked, or multiply attacked (contained &gt;1 parasitoid egg). Number of surviving larvae that were moved to food vials to measure eclosion success (larvae_moved), which involved four possible outcomes: (i) fly emerges without a melanized capsule (unattacked_fly), (ii) fly emerges with a melanized capsule (fly_survived), (iii) wasp emerges (wasp_survived), or (iv) both insects die (death). Proportional eclosion outcomes (ii)-(iv) (fly_success, wasp_success, and death_rate) were calculated after subtracting unattacked_fly from larvae_moved, such that unattacked fly larvae were ignored in the analyses.
DOI: 10.5061/dryad.5t5m4/3
title: Figure 3, oviposition maintenance

description: Number of eggs laid over 5-day forced co-habitation assays by flies in vials without wasps (ctrl), with L. boulardi (Lb17), and with L. heterotoma (Lh14), where each row represents a vial. For each day (#1-5), f# is the number of female flies alive at the beginning of the day, e# is the number of eggs laid by the end of the day, and c# is the cumulative number of eggs laid per female, i.e. c1 = e1/f1, c2 = c1 + e2/f2, c3 = c2 + e3/f3, etc. Sets of replicates for each fly species are arranged by date; control and wasp vials were run simultaneously in approximately equal numbers and multiple groups were run if &lt;5 vials per treatment. day5_dOR = (c5 for each Lb17 or Lh14 replicate) / (mean c5 across control vials run for the same fly species at the same time). Oviposition maintenance indices in Fig. 3 are mean day5_dOR across all Lb17 or Lh14 replicates for each fly species.
DOI: 10.5061/dryad.5t5m4/4
title: Figure 4, trade-offs

description: Newick tree file (same as Fig. 1) and "infiles" for Lb17 and Lh14, with mean cellular immunity index in column 1 and mean oviposition maintenance index in column 2 for each fly species, used as inputs for the Contrast program in PHYLIP v. 3.69. Phylogenetically independent contrasts from the resulting "outfiles" are compiled into Fig4.csv: cellular immunity index contrasts (CI_Lb17 and CI_Lh14) and oviposition maintenance index contrasts (OMI_Lb17 and OMI_Lh14).
DOI: 10.5061/dryad.5t5m4/5
title: Figure 5a, D. yakuba oviposition

description: Number of eggs laid over a 6-day forced co-habitation assay by D. yakuba in vials without wasps (control), with L. boulardi (exp_Lb17), and with L. heterotoma (exp_Lh14). Number of females in each vial at the start of the experiment (none of them died during the experiment), eggs# = eggs laid on days #1-6, total_eggs = sum from eggs1:eggs6, eggs_per_female = total_eggs / females.
DOI: 10.5061/dryad.5t5m4/6
title: Figure 5b, D. yakuba offspring survival

description: Eggs laid by D. yakuba in the three parental treatments (control, exp_Lb17, and exp_Lh14) were transferred to Petri dishes, grown to second instar, then exposed to female L. boulardi. The larvae were moved to food vials to eclose and egg-to-adult survival was measured. capsule = adult flies that had melanized capsules and thus survived parasitism; no_capsule = adult flies that did not have capsules and thus were not attacked as larvae; total = capsule + no_capsule.
DOI: 10.5061/dryad.5t5m4/7
title: Figure 6, sight and smell mutants

description: Number of eggs laid over 5-day forced co-habitation assays by flies in vials without wasps (ctrl), with L. boulardi (LB17), and with L. heterotoma (LH14), where each row represents a vial. Four D. melanogaster strains are represented: Orco2 = smell-deficient mutant, GMRhidII = sight-deficient mutant, w1118 = white-eyed mutant, OregonR = wild-type. For each day (#1-5), e# is the number of eggs laid by the end of the day, f# is the number of female flies alive at the beginning of the day, and cu# is the cumulative number of eggs laid per female, i.e. cu1 = e1/f1, cu2 = cu1 + e2/f2, cu3 = cu2 + e3/f3, etc.
DOI: 10.5061/dryad.5t5m4/8
title: Figure S1, melanogaster / simulans adaptive significance

description: D. melanogaster and D. simulans offspring produced in embryo collection chambers without wasps (control) and with Lb17 or Lh14 (wasp) were grown to second instar, then exposed to wasps. fly_win = number of flies that survived with melanized capsules; wasp_win = number of wasps that survived; death = number of larvae that did not eclose.
DOI: 10.5061/dryad.66vb3/1
title: Brachiopod genus local ranges

description: csv file with the local stratigraphic ranges of brachiopod taxa (species where resolved, otherwise genera).  Please contact authors with specific questions about the structure of the database and the meaning of column headings.  R code for analysis of this dataset is included as Supplemental Material in the publication.
DOI: 10.5061/dryad.7qk36/1
title: IMR90 overexpressing MyoD in growth medium

description: Human fibroblasts IMR90 transfected with doxycycline inducible mouse MYOD were cultured in growth media (DMEM high glucose, 10% FBS). MYOD was induced with doxycycline treatment 24 hrs prior collection.
DOI: 10.5061/dryad.7qk36/2
title: IMR90 overexpressing MyoD in growth medium, replicate

description: Human fibroblasts IMR90 transfected with doxycycline inducible mouse MYOD were cultured in growth media (DMEM high glucose, 10% FBS). MYOD was induced with doxycycline treatment 24 hrs prior collection.
DOI: 10.5061/dryad.7qk36/3
title: IMR90 overexpressing MyoD in differentiation medium

description: Human fibroblasts IMR90 transfected with doxycycline inducible mouse MYOD were cultured in growth media (GM, DMEM high glucose, 10% FBS). MYOD was induced with doxycycline treatment 24 hrs in GM and 72-96 hrs in differentiation media (DM, DMEM high glucose, 2% HS, ITS) prior collection.
DOI: 10.5061/dryad.7qk36/4
title: IMR90 overexpressing MyoD in differentiation medium, replicate

description: Human fibroblasts IMR90 transfected with doxycycline inducible mouse MYOD were cultured in growth media (GM, DMEM high glucose, 10% FBS). MYOD was induced with doxycycline treatment 24 hrs in GM and 72-96 hrs in differentiation media (DM, DMEM high glucose, 2% HS, ITS) prior collection.
DOI: 10.5061/dryad.7v5p3/6
title: 28ConpleteGeneTrees

description: Subset of 28 UCE loci from complete data matrix.
DOI: 10.5061/dryad.7v5p3/8
title: 157kUCEs

description: BEAST xml file for 362 UCE loci dataset.
DOI: 10.5061/dryad.7v5p3/9
title: 157k_38subsets

description: Zipped folder containing each of the 38 data partitions selected from the k-means algorithm.
DOI: 10.5061/dryad.85nf3/1
title: ASSIP Data file

description: Data file from the ASSIP 24-months follow-up randomized controlled study.
DOI: 10.5061/dryad.85nf3/2
title: Analysis script for ASSIP

description: We provide a short analysis script (survival.R) to replicate the main findings of our study using the original data (assip.RData).
DOI: 10.5061/dryad.dn60n/1
title: PGM1 PRRS histopathological grading data

description: Excel File contains histopathological grading data for distribution, and severity of vasculitis, endometrial inflammation score in the uterine tissues associated with 679 fetuses, qRT-PCR PRRS virus RNA concentration values in the uterine tissues and fetal thymuses, number of fetal and umbilical histopathological lesions and fetal preservation status of 679 fetuses. Also file contains explanation of histological grading schemes used for assessment in this study.
DOI: 10.5061/dryad.g56f4/11
title: Oregon_Dryad
DOI: 10.5061/dryad.g56f4/12
title: Puerto Montt_Dryad
DOI: 10.5061/dryad.g56f4/13
title: Sweden_Dryad
DOI: 10.5061/dryad.g56f4/4
title: Dahomey_Dryad
DOI: 10.5061/dryad.g56f4/5
title: Hawaii_Dryad
DOI: 10.5061/dryad.g56f4/6
title: Israel_Dryad
DOI: 10.5061/dryad.g56f4/7
title: Japan_Dryad
DOI: 10.5061/dryad.g56f4/8
title: Madang_Dryad
DOI: 10.5061/dryad.g56f4/9
title: Mysore_Dryad
DOI: 10.5061/dryad.k2qc4/1
title: Anaspid matrix
DOI: 10.5061/dryad.p3hr1/4
title: Fig. 2C data

description: G. mellonella survival and S. carpocapsae emergence from recapitulated mutualisms generated with experimental populations of X. nematophila.
DOI: 10.5061/dryad.qp50f/2
title: Fig 1

description: Type specimens of Piper species; (A) Piper argyrites Ridl. ex. C.DC, Ridley 8176 (K), (B) Piper baccatum Blume, Blume 624 (L), (C) Piper leptostachyum Wall. ex Miq., Wallich 6649 (K-W), (D) Piper majusculum Blume, Blume s.n. (L).
DOI: 10.5061/dryad.qp50f/3
title: Fig 2

description: Figure 2. Type specimens of Piper species (A) Piper peepuloides Roxb., Wallich 6650A (U), (B-1) Chavica neesiana Miq., (B-2) Chavica sphaerostachya Miq., Wallich 6656 (U), (C) Piper quinqueangulatum Miq. Zollinger 1233 (P), (D) Piper sulcatum Blume, Blume s.n. (L).
DOI: 10.5061/dryad.qp50f/4
title: Fig 3 P. argyrites

description: Figure 3. Piper argyrites Ridl. ex C.DC. (A) branch with an infructescence, (B) male inflorescence, (C) female inflorescence, (D) a portion of male inflorescence, (E) stamen, (F) floral bract (top view), (G) a portion of female inflorescence, (H) ovary (C. Suwanphakdee 246♂ & C. Suwanphakdee 247♀ (BK, BKF, KKU and QBG)). — Drawn by O. Kerdkaew.
DOI: 10.5061/dryad.qp50f/5
title: Fig 4 P. baccatum

description: Figure 4.  Piper baccatum Blume (A) branch with infructescences, (B) male inflorescence, (C) female inflorescence, (D) a portion of male inflorescence, (E) male flower, (F) stamen, (G) a portion of female inflorescence, (H) ovary (C. Suwanphakdee 211♀ (BK, BKF and QBG), C. Suwanphakdee 285♂ (BKF)). — Drawn by O. Kerdkaew.
DOI: 10.5061/dryad.qp50f/6
title: Fig 5 P. leptostachy

description: Figure 5. Piper leptostachyum Wall. ex Miq. (A) branch with a female inflorescence, (B) a portion of male inflorescence, (C) floral bracts (front and back views), (D) stamen, (E) infructescence (C. Suwanphakdee  464♀ (BK, BKF, KKU & QBG), C. Suwanphakdee 465♂ (BKF, KKU and QBG)). — Drawn by L. Loe-Khachon.
DOI: 10.5061/dryad.v16ns/1
title: CoMET data archive

description: This data archive contains the scripts used to generate and analyze all the data in the accompanying manuscript (May et al., MEE), as well as the simulated data that were analyzed for that work. The archive is broken into five subdirectores, each corresponding to one set of simulations/analyses performed in the manuscript. The descriptions of each subdirectory are provided in the README.txt file.
DOI: 10.5061/dryad.4gb62/6
title: T_grac_reads
DOI: 10.5061/dryad.4gb62/7
title: T_saba_reads
DOI: 10.5061/dryad.4gb62/8
title: U_geyr_reads
DOI: 10.5061/dryad.4gb62/9
title: V_exan_reads
DOI: 10.5061/dryad.66ft5.2
title: Data from: Can the Fisher-Lande process account for birds of paradise and other sexual radiations?
DOI: 10.5061/dryad.66ft5.2/1.2
title: LeCroy data

description: Measurements of wing, tail, and tarsus lengths in 14 populations of birds of paradise in the genus Paradisaea (from LeCroy, M. 1981. The genus Paradisaea - display and evolution. American Museum Novitates 2714:1-52.).  Measurements for each population (mm) are standardized (divided by average within population standard deviation for that trait and sex*).
DOI: 10.5061/dryad.66ft5.2/2.2
title: male_wing4

description: Male wing length data in OUwie format
DOI: 10.5061/dryad.6n4fm/1
title: data_fig3A_suppfig1

description: Raw data from the paper
DOI: 10.5061/dryad.7fg32/1
title: ensembler_dataset-datafiles

description: tar archive containing target and template data files for tyrosine kinase Ensembler project, plus README and script for generating the same data. Extract using 'tar xvf ensembler_dataset-datafiles.tar'. The ensembler_dataset-models* tar archives contain model data and should be extracted at the same location as this archive.
DOI: 10.5061/dryad.7fg32/2
title: ensembler_dataset-models-ABL1-EPHA2
DOI: 10.5061/dryad.847vk/1
title: epics-dist
DOI: 10.5061/dryad.847vk/3
title: Supplementary Material
DOI: 10.5061/dryad.8568n/1
title: Florida Sand Skink Genotypes and Fire Data

description: genotype data with site data on fire history, labels match manuscript burn unit designation
DOI: 10.5061/dryad.8856h/1
title: Tolerance

description: Tolerance data
DOI: 10.5061/dryad.8856h/2
title: Browsing measures and secondary compounds

description: Browsing and secondary compounds
DOI: 10.5061/dryad.8856h/3
title: Mineral Analyses

description: Mineral analyses
DOI: 10.5061/dryad.8dt7r/1
title: F1 Productivity and Juvenile survival
DOI: 10.5061/dryad.8dt7r/2
title: F2 Lifetime Reproductive Success
DOI: 10.5061/dryad.8j65p/1
title: Genetic Distance Matrices

description: One .csv file per study site including the genetic distances among individual pika samples. Genetic distances were calculated from individual genotypes as a principal conponents distance calculated using the ecodist package in R.
DOI: 10.5061/dryad.8j65p/2
title: Pika Habitat Patch Centroids

description: One .csv file per study site including the xy coordinates (UTM, NAD83) for each pika habitat patch used in network analyses. Patch IDs correspond to Patch IDs in Patch Distance Matrices files. Centroids calculated in ArcGIS10.0.
DOI: 10.5061/dryad.8j65p/3
title: Pika Habitat Patch Distances

description: One .csv file per study site as a 3-column matrix including resistance distances and Euclidean distances among pika habitat patches. Resistance distance was calculated from the perimeter of each patch (polygon) using an overlapping tile approach with the program Circuitscape. Patch IDs correspond to Patch IDs in the Habitat Patch Centroid files. Resistance distance was not calculated between habitat patches separated by &gt;10km.
DOI: 10.5061/dryad.8j65p/4
title: Pika Genetic Sample Localities

description: One .csv file including the xy coordinates (UTM, NAD83) for each pika genetic sample used in analyses. Data was collected in the field on handheld GPS units.