cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.80m5b/3
title: Scripts for empirical application to B. pallida data

description: The R scripts in this file were used to simulate data for the Biorhiza pallida analysis.
DOI: 10.5061/dryad.80m5b/4
title: Lines used to simulate models in msABC

description: This text file gives the basic msABC (Pavlidis et al. 2010) lines used to simulate data under the 7 models considered in our study, using parameter/variable names instead of values in the command line code.
DOI: 10.5061/dryad.8kd16/1
title: Camarasaurus_skull

description: A surface file of the skull and jaw model of Camarasaurus lentus created for this study
DOI: 10.5061/dryad.953hv/4
title: 3 MER R code summary

description: R code
DOI: 10.5061/dryad.b1772/1
title: Effects of fluoxetine on fish - Dataset - Margiotta-Casaluci et al. 2014

description: The file provides the results of a study during which male fathead minnows were exposed for 28 days to the anti-depressant fluoxetine.
DOI: 10.5061/dryad.d2990/1
title: Supplement_selected_phylogenies

description: File describing how phylogenies were selected, and a list of all the papers from which phylogenies were selected.
DOI: 10.5061/dryad.d334b/1
title: Protein sequences of NBS genes in diverse sorghum genotypes

description: Protein sequences of NBS-genes in sorghum for 47 sorghum genotypes
DOI: 10.5061/dryad.d334b/2
title: Multiple sequence alignments of sorghum NBS genes

description: Multiple sequence alignments of NBS genes identified in the sorghum genome
DOI: 10.5061/dryad.d334b/3
title: Phylogenetic tree of NBS genes in sorghum

description: Phylogenetic tree constructed using TreeBest based on the PFAM00931 domain of the NBS genes in the sorghum genome
DOI: 10.5061/dryad.d334b/4
title: Alignments of NBS genes across sorghum, maize and rice

description: Multiple sequence alignment of PFAM00931 domains of NBS genes identified in sorghum, maize and rice genomes
DOI: 10.5061/dryad.d334b/5
title: Phylogenetic tree of NBS genes across sorghum, maize and rice

description: Phylogenetic tree, constructed using TreeBest, based on the PFAM00931 domain of NBS genes identified in sorghum, maize and rice
DOI: 10.5061/dryad.g08c7/3
title: FET_RADs

description: This file contains the results of Fisher exact tests (FET) of allelic differentiation conducted in all pairwise comparisons with the RADtools software. We present the negative logarithm ( -Log10) of the p-value in a FET. SNPs with Bonferroni-corrected p values lower than 5% were considered outliers for that comparison. We provide information on the identity of the SNP, the RAD-tag where it is located and the genomic contig where this tag was mapped.
DOI: 10.5061/dryad.h1n02/1
title: 2007-10-31_140001_HF_Clip1

description: DIDSON data file. See Table 1 in Hightower et al.
DOI: 10.5061/dryad.h1n02/2
title: 2007-10-31_172000_HF_Clip2

description: DIDSON data file. See Table 1 in Hightower et al.
DOI: 10.5061/dryad.h1n02/3
title: 2007-11-01_160549_HF_Clip3

description: DIDSON data file. See Table 1 in Hightower et al.
DOI: 10.5061/dryad.h1n02/4
title: 2007-11-02_082740_HF_Clip4

description: DIDSON data file. See Table 1 in Hightower et al.
DOI: 10.5061/dryad.j015n/6
title: fish-probe-matches-to-genome-enabled.sqlite.gz

description: SQLITE database of LASTZ matches between data from genome-enabled taxa and the UCE probes in fish-500-loci-enrichment-probes.fasta.gz. This database is used to construct data sets containing loci that are shared across taxa and prep data for alignment.
DOI: 10.5061/dryad.kt71r/3
title: Bcanorus_GeographicDistanceMatrix

description: Bufo canorus geographic distance matrix.  Pairwise geographic distances for B. canorus populations (standardized), part of an example dataset for MMRR analysis.
DOI: 10.5061/dryad.m3h18/1
title: TTC Integrated Consensus Map

description: Integrated consensus map of the Leymus TTC1 and TTC2 mapping populations in MapQTL format.
DOI: 10.5061/dryad.m3h18/4
title: TTC1_Traits9b

description: MapQTL traits file for Leymus TTC1 population.
DOI: 10.5061/dryad.n4mm0/10
title: Single-donor crosses_Briscoe Runquist et al

description: We performed intra- and intersubspecific crosses in sympatric populations (crosses were only within populations) or allopatric populations (crosses were preformed in all combinations of all allopatric populations). There were 4 crosstypes (treatments) (1 = xantiana to xantiana), 2 = xantiana to parviflora; 3 = parviflora to xantiana; 4 = parviflora to parviflora). We counted the number of fully formed seeds, number of fertilized but aborted ovules, and the number of unfertilized ovules for each fruit collected.
DOI: 10.5061/dryad.n4mm0/8
title: Pollinator_transitions-constancy_Briscoe Runquist et al

description: This file contains all of the pollinator bouts that contained intersubspecific transitions in pollinator arrays of greenhouse grown sympatric plants that were placed out into the field. We noted the number of visits to each subspecies. We also noted the different numbers of each transition type. Transition categories are detoed "from_to" (i.e. "x_p" transition was from a xantiana to a parviflora). We also noted that parviflora may have different colors (pp = pink; wp = white; up = unknown) and the should sum to the category with only a "p". We also have separate entries using all flowers or plants only (no geitnogamy). The entries with all flowers used end in "_f".
DOI: 10.5061/dryad.n4mm0/9
title: Pollinator-pref-data_Briscoe Runquist et al

description: In pollinator arrays of greenhouse grown plants in the field, we watched plants in the arrays (position) and at each observation time noted the number of visits to a flower subspecies and the number of each type of flower subspecies. The file also contains information on the date of observation, the observer, and whether the observation took place in the morning or afternoon.
DOI: 10.5061/dryad.n5d15/1
title: Behavioral observations 2011

description: Data collected on spider predator and grasshopper prey locations in behavioral terraria. This data was collected during summer 2011.
DOI: 10.5061/dryad.n5d15/2
title: Behavioral observations 2012

description: Data collected on spider predator and grasshopper prey locations in behavioral terraria. This data was collected during summer 2012.
DOI: 10.5061/dryad.n5d15/4
title: Activity distance moved 2011-2012

description: Data collected on spider predator and grasshopper prey activity as the distance moved per interval during behavioral observations. Includes data from 2011 and 2012 at 3-min and 20-min intervals.
DOI: 10.5061/dryad.nd2mb/4
title: Supplementary Figure 4

description: Extinction and origination rates for our whole-fauna dataset (A and D, respectively), the UW (B and E) and the SQS (C and F) subsampled untrimmed Neptune dataset.
DOI: 10.5061/dryad.nd2mb/5
title: Supplementary Figure 5

description: Shannon H' index for studied samples. A. In the first 2,000 specimens. B. In the total sample.
DOI: 10.5061/dryad.nd2mb/6
title: Supplementary Figure 6

description: Effect of range-trimming on diversity. Black line is without any trimming, dark grey line with a light trimming (3% at the top, 1% at the bottom), grey line with a moderate trimming (5 and 3%) and light grey line with a very strong trimming (12 and 8%).
DOI: 10.5061/dryad.pc14j/1
title: Growth and survival data for Westley et al. Proc. B

description: Recapture histories and growth data from common garden and reciprocal transplant experiments
DOI: 10.5061/dryad.pp0q1/1
title: Microsatellite genotypes of wild populations

description: Microsatellite genotypes used for population genetic analyses
DOI: 10.5061/dryad.pp0q1/2
title: MtDNA sequence alignment

description: mtDNA sequence alignment used to construct haplotype network
DOI: 10.5061/dryad.ps12h/19
title: Beast XML input file for H3 gene tree - preliminary runs

description: .rar file including 12 Beast XML input files with distinct population/clock models used for defining the best-fit priors for estimating the H3 gene tree for Sicarius from the Brazilian Caatinga
DOI: 10.5061/dryad.ps12h/20
title: COI gene tree

description: Annotated COI gene tree for Sicarius from the Brazilian Caatinga, with divergence time estimates
DOI: 10.5061/dryad.ps12h/21
title: H3 gene tree

description: Annotated gene tree for H3 for Sicarius from the Brazilian Caatinga, including divergence times estimates
DOI: 10.5061/dryad.ps12h/22
title: Alignment of COI sequences from Sicarius from the Brazilian Caatinga

description: 715 base pairs alignment of COI sequences from Sicarius from the Brazilian Caatinga
DOI: 10.5061/dryad.ps12h/23
title: Alignment of H3 sequences from Sicarius from the Brazilian Caatinga

description: 327 base pairs unphased alignment of H3 sequences from Sicarius from the Brazilian Caatinga
DOI: 10.5061/dryad.ps12h/24
title: Geographic and haplotypic information for Sicarius samples from the Brazilian Caatinga

description: Tab-delimited text file with voucher, geographic and haplotypic data for all samples used in this study. Voucher= institution acronym and number for the voucher individual. Pop= population number (check Figure 3 from the manuscript). Code= code used for this study (the same used for the tree/alignment files). Sex= M, male; F, female; J, juvenile. Type= whether the sample was freshly collected or was deposited in 80% ethanol in a museum. Hap-COI and Hap-H3= codes for haplotypes (the same used in table S2 and in the GenBank submission). Locality= name of the locality where the sample was collected, followed by latitude and longitude information.
DOI: 10.5061/dryad.q2n78/1
title: 16S_rRNA_sequences_for_16_soils

description: These sequences were demultiplexed using the 'split_libraries_fastq.py' command in QIIME v1.6.0 with default settings.
DOI: 10.5061/dryad.sj5b6/2
title: Mortality and Land Use

description: Pesticide Mortality and Land Use Data: this file includes mortality estimates for each population-by-pesticide combination and measures of agricultural land use.
DOI: 10.5061/dryad.t1n04/4
title: pooled_data_monkeys

description: Behavioral response data of monkeys, pooled across sessions. This is computed from raw_data_monkey.mat file.
DOI: 10.5061/dryad.v6qj0/5
title: Wing beat frequency

description: Raw data on wing beat frequency, total time rested, mid-point crosses and number of calling bouts
DOI: 10.5061/dryad.v6qj0/6
title: Distance crawled

description: Raw data of total distance walked, resting time and mid-point crosses
DOI: 10.5061/dryad.v6qj0/7
title: Weight loss

description: Raw data on weight of the flies, weight loss. water content and metabolisms
DOI: 10.5061/dryad.v6qj0/8
title: Proportion of success to failure attempts

description: Raw data on proportionate successful mating attempts
DOI: 10.5061/dryad.v6qj0/9
title: RT-PCR

description: Raw data on delta ct values for candidate genes
DOI: 10.5061/dryad.0sd30/1
title: Passerines: Colour variability and associated variables

description: Variable names (see Methods for more details)Data collated from the Handbook of Australian, New Zealand and Antarctic Birds vols. 5-7animal: species code used in the phylogenyav.col.var: average colour variability (sexes pooled)m.col.var: average colour variability (males)f.col.var: average colour variability (females)polymorphic: considered polymorphic in Galeotti et al. (2003)sex.dich: sexual dichromatism scoremove.score: mobility scorerange: number of occupied 1’ cells in The New Atlas of Australian Birdshabitats: habitat heterogeneity scorethreat: threat status, 1=endangered, 0=not endangereddiet.het: dietary heterogeneity
DOI: 10.5061/dryad.14m55/1
title: Abundance data

description: The abundance of the limpet Cellana toreuma in the study site from July 2012 to April 2013. The total numbers of limpets in the two transects were recorded from 1.0m to 5.0 m above chart datum.
DOI: 10.5061/dryad.14m55/2
title: Precipitation data

description: The “relevant precipitation” data recorded from September 2011 to April 2013.
DOI: 10.5061/dryad.14m55/3
title: Raw data of operative body temperature

description: Daily maximum, mean and minimum operative body temperatures in limpets from a mid-intertidal south-facing rocky slope (2.5-3.0 m above CD) measured using Robolimpets, as described by Lima and Wethey (2009). Data were collected every 30 min between August 2011 and May 2013.
DOI: 10.5061/dryad.14m55/4
title: Raw gene expression and body temperature data

description: Levels of hsp70, hsp90, hsp90, ampkα, ampkβ and sirt1 mRNA in Cellana toreuma and the body temperature. Samples were collected on different dates from September 2011 to April 2013. When the sample was sampled, a thermocouple was inserted into the shells and the body temperature of each individual was recorded using a thermometer (Fluke 54II, Fluke, WA, USA).
DOI: 10.5061/dryad.16v7n/6
title: Pollen

description: Pollen produced by H. virgata flowerheads in the 1 x 1 m plots also used for nectar measurements. Flowerheads were collected in the morning before insects became active. See ReadMe file associated with Visitation.csv for further information.
DOI: 10.5061/dryad.1pb77/1
title: whole dataset
DOI: 10.5061/dryad.31vb0/1
title: Hook measurements from female Echinorhynchus salmonis (Acanthocephala) from Bothnian Bay, Baltic Sea.

description: Hook measurements from 36 female specimens of Echinorhynchus salmonis Müller, 1784 (Acanthocephala: Echinorhynchidae) from the Bothnian Bay, Baltic Sea.
DOI: 10.5061/dryad.3pf37/1
title: cytb

description: Nexus file containing haplotype sequences obtained for the mitochondrial cytochrome b gene from Delphinus delphis, Delphinus capensis and Delphinus tropicalis. Samples were collected from stranded or live animals using biopsies in the Atlantic, Pacific and Indian Oceans.
DOI: 10.5061/dryad.3pf37/4
title: del15

description: Nexus file containing sequences obtained for the anonymous locus Del_15 from Delphinus delphis, Delphinus capensis and Delphinus tropicalis. Samples were collected from stranded or live animals using biopsies in the Atlantic, Pacific and Indian Oceans.
DOI: 10.5061/dryad.3pf37/5
title: del17

description: Nexus file containing sequences obtained for the anonymous locus Del_17 from Delphinus delphis, Delphinus capensis and Delphinus tropicalis. Samples were collected from stranded or live animals using biopsies in the Atlantic, Pacific and Indian Oceans.
DOI: 10.5061/dryad.3pf37/6
title: plp

description: Nexus file containing sequences obtained for PLP (proteolipid protein 1) from Delphinus delphis, Delphinus capensis and Delphinus tropicalis. Samples were collected from stranded or live animals using biopsies in the Atlantic, Pacific and Indian Oceans.
DOI: 10.5061/dryad.3pf37/7
title: GenBank Accession Numbers

description: GenBank Accession Numbers for the sequences used in this study and their respective codes used in the nexus files.
DOI: 10.5061/dryad.3q5k0/2
title: LaDigue_tmvp_input

description: TMVP input file (.prn) for La Digue historical and contemporary Ne.
DOI: 10.5061/dryad.3q5k0/3
title: Praslin_tmvp_input

description: Praslin TMVP input file. Format is .prn file. For calculation of historical (age of the oldest sample) and contemporary Ne from genotype data
DOI: 10.5061/dryad.3q5k0/4
title: Input file for calculating the proportion of alleles captured

description: Input file for calculating the proportion of alleles present in the La Digue source population that could be  captured by translocating differing numbers of individuals
DOI: 10.5061/dryad.50v83/1
title: Longitudinal Lung Cancer Data

description: The zip-File includes all longitudinal MR data files for each patient separately which were used to determine treatment monitoring in non-small cell lung cancer patients using diffusion-weighted imaging and functional diffusion maps. The detailed scan parameters and acquisition time points can be found in the manuscript.
DOI: 10.5061/dryad.60659/1
title: dryad

description: Genotypes in genepop 3-digit format, from microsatellites described in Peichel et al. 2001 (The genetic architecture of divergence between threespine stickleback species. Nature,414, 901-905) and Shimada et al. (A high incidence of selection on physiologically important genes in the three-spined stickleback, Gasterosteus aculeatus. Molecular Biology and Evolution, 28, 181-193). Population codes are as follows in Table 1.
DOI: 10.5061/dryad.62gj0/1
title: Gene expression changes upon inactivation of TFIID subunit TAF4 in neontal mouse liver
DOI: 10.5061/dryad.6d8g5/1
title: SPAGeDi_Reef19_completegenospace

description: Input file for the program, Spatial Pattern Analysis of Genetic Diversity (SPAGeDi; Hardy and Vekemans 2002) giving spatial and multi-locus genetic data for Reef 19, the focal reef of our study where Pocillopora damicornis was near-exhaustively surveyed. From left to right, columns represent Sample ID Number, x coordinate, y coordinate, and genotypes at each of 6 microsatellite loci.
DOI: 10.5061/dryad.6hc0f/7
title: Contig sequences for P. leucopus transcriptome (fasta file)

description: A second transcriptome is included named, “Pleucopus_Transcriptome_Contigs_Annotated.fasta”.  This file includes unique contigs that mapped to the Mus musculus transcriptome.  Gene annotations are included in the header for each sequence.
DOI: 10.5061/dryad.6hc0f/8
title: Alternative splice events identified in Peromyscus leucopus transcriptome

description: This FASTA file contains two sequences for each alternative splicing sequence, labeled as upper and lower splice, that was identified in the Peromyscus leucopus transcriptome.
DOI: 10.5061/dryad.6hc0f/9
title: Contigs from Peromyscus leucopus transcriptome that represent splice variants
DOI: 10.5061/dryad.6s241/1
title: raw diet morphology color and lightness of pairs
DOI: 10.5061/dryad.8mc3s/1
title: Terebratulide body size measurements from museum specimens

description: Data on the maximum body size of terebratulide genera collected via measurements of museum specimens. More than 2000 intact specimens of Paleozoic terebratulides were measured in the collections at the Natural History Museum (London), the National Museum of Natural History (Washington, D.C.), and the Yale Peabody Museum (New Haven, Conn.). Each specimen was aligned and photographed from two orthogonal angles, one angle representing the commissure margin and the other representing the “profile,” or the side view. 101 equally spaced coordinates were sampled around the commissure margin, using the software program tpsDig v. 1.4 written by James Rohlf and then scaled to millimeters. Centroid size for was then calculated each individual, using the coordinates sampled from the commissure view. Each genus is represented by the individual specimen with the largest measured centroid size. Centroid sizes were gathered for 28 Devonian genera, with the median number of specimens measured per genus equal to 5.5 (interquartile range was 2 to 18.25 specimens).
DOI: 10.5061/dryad.8mc3s/2
title: Terebratulide body size measurements from figured specimens

description: Data on the maximum body size of terebratulide genera collected from figured specimens in the Treatise on Invertebrate Paleontology (Kaesler 2000). Linear measurements of shell width and length were gathered, as well as shell height wherever possible. For genera comprising two or more species, genus body size was calculated as the geometric mean of the holotype specimen for each species. If the holotype was not figured for a species, the paratype, neotype, or best-resolution illustration was used, in that order. Length: shell length (in mm) - beak to commissure; Width: shell width (in mm) - parallel to hinge; Height: shell height (in mm) - perpendicular to the other two axes; Area: product of shell length and width, in log10 mm^2; Volume: product of shell length, width, and height, in log10 mm^3; Figure: figure number of the measured illustration in the Treatise on Invertebrate Paleontology; Figure_part: figure part in the Treatise (required to get the exact specimen measured); Founder: this is the authority for the species as reported in the Treatise; Year: this is the year in which the measured species was described.
DOI: 10.5061/dryad.8mc3s/3
title: Terebratulide occurrences

description: The geographic occurrences of Devonian terebratulide genera. These occurrence data were compiled previously in an exhaustive search of the published literature for a study of Paleozoic terebratulide latitudinal diversity gradients (Fitzgerald and Carlson 2006). The data set consists of 476 occurrences, resolved to 5 degree paleolatitudinal bins, ranging from 85 degrees S to 45 degrees N.
DOI: 10.5061/dryad.8mc3s/4
title: Terebratulide data for extinction selectivity analyses

description: File contains data used in Devonian terebratulide extinction selectivity analyses. "Duration" is the stratigraphic range of each terebratulide genus in millions of years. "Singleton" identifies genera known from only a single geological stage. "Raw_Cumulative_Latitudinal_Range_Size" is the cumulative latitudinal range size of each genus over its duration. "Standardized_Cumulative_Latitudinal_Range_Size" is the cumulative latitudinal range size of each genus scaled to the maximum range size possible over its duration. "Raw_Max_Latitudinal_Range_in_a_Stage" is the maximum latitudinal range of each genus in a given geological stage. "Standardized_Max_Latitudinal_Range_in_a_Stage" is the maximum latitudinal range of each genus in a geological stage scaled to the maximum possible in that stage. "Body_Size_Area" is the product of shell length and width, in log10 mm^2. "Body_Size_Volume" is the product of shell length, width, and height, in log10 mm^3.
DOI: 10.5061/dryad.8mc3s/5
title: Terebratulide stratigrapihc ranges

description: Genus durations calculated from the observed first and last occurrence data from the revised brachiopod Treatise on Invertebrate Paleontology (Curry and Brunton 2007), with genera assumed to range from the base of the stage in which they first occurred to the top of the stage in which they last occurred. Ages of stage boundaries are from the revised Devonian timescale of Ogg et al. (2009).
DOI: 10.5061/dryad.8mc3s/6
title: Terebratulide temporally-calibrated phylogeny

description: Temporally-calibrated phylogenetic hypothesis for Devonian terebratulide genera using the strict consensus of 71 phylogenetic trees reported by Carlson and Fitzgerald (2008). Note that tips in this phylogeny correspond to the first occurrences of terebratulide genera, not last occurrences, so as to reduce any circularity when the tree was used for comparative analyses that included genus duration. Please refer to the article for additional details regarding the phylogeny and temporal calibration.
DOI: 10.5061/dryad.c37h8/1
title: Data By Male

description: This file contains data on reproductive success, ornamentation, and breeding density for each adult male included in the paper. Column headers are mostly self-explanatory and are described in further detail in the associated paper.
DOI: 10.5061/dryad.f7mb0/1
title: LakeSoundscapes_LakexTime_Data

description: Data used in univariate and multivariate statistical analysis of lake soundscapes; data is summarized at the level of lake (sampling site) and time period to reflect the analyses using the manuscript.  Includes site (lake)-level factors and characteristics as well as the acoustic data which was collected in the field. Acoustic data metrics were calculated using Raven Pro 1.4; refer to ReadMe file for detailed descriptions of metrics, calculation methods, and sources.
DOI: 10.5061/dryad.f7mb0/2
title: LakeSoundscapes_AboveBelowWater_Data

description: Acoustic data collected at sites (lakes) for comparison of hydro (below water) and air (above water) sound characteristics. Data is summarized by site (field=Lake_Name) and includes total average power of all sound samples over all time periods (field=Power) as well as for each 1 kHz frequency interval (e.g. 3to4kHz_Power). All power is in decibels (db) calculated in Raven Pro 1.4