cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4v875/17
title: NEWAppendix 6_18S-FINAL3

description: Maximum likelihood tree based on 18S data
DOI: 10.5061/dryad.4v875/2
title: Appendix 2_ATOL Lobsters morpho list

description: Morphological characters and states used in combined Bayesian analysis.
DOI: 10.5061/dryad.4v875/3
title: Appendix 3_morphomatrix

description: Morphomatrix used in combined Bayesian analysis
DOI: 10.5061/dryad.5hh3h/1
title: Buffalo Mortality Table

description: This table contains a description of Buffalo mortalities (Old or fresh). Buffalo mortalities were encountered by field technicians during their daily movements in the field, either accidentally coming across them on foot, by actively pursuing vultures, or because the animal had a VHF or GPS collar.See Readme file
DOI: 10.5061/dryad.5hh3h/2
title: Buffalo Capture Sessions

description: This table contains all the details of capture session. In some cases, multiple individuals were captured simultaneously. This table contains the information about the overall site and event, while data about each captured individual are in Buffalo captures.  These two tables can be linked based on the CapsessionID field. Two main types of techniques were utilized depending on the requirements of the capture. For individual recaptures the animals were darted from a vehicle. While for mass chemical immobilizations the animals were darted from a helicopter.  See Readme file.
DOI: 10.5061/dryad.5hh3h/3
title: Buffalo Captures

description: Table with data on individual buffalo captures. Can be linked to the site data based on the CapSessionID field and the Buffalo Capture Sessions Table. See readme file.
DOI: 10.5061/dryad.5hh3h/4
title: Buffalo Named

description: This is a reference table with one row per known buffalo (either based on visual characteristics or a VHF, GPS, or marker collar). This table contains data on all Identified buffalo. Each row refers to a single buffalo. The name field is a unique identifier. These were buffalo that were thought to be easily identifiable in field and were used to increase sample number for mark recapture analysis.
DOI: 10.5061/dryad.5hh3h/5
title: Buffalo Sightings

description: This is for those identifiable individuals, either radiocollared or previously named.  These data were intended for use in a mark-recapture analysis of survival, resighting, and dispersal rates.
DOI: 10.5061/dryad.5tt4r/1
title: blackwater lake stream morphology

description: Here we provide the data table required to recreate Figure 1 from Bolnick and Otto, "The magnitude of local adaptation under genotype-dependent dispersal," published in Ecology and Evolution. The data table presents clinical data of threespine stickleback across a lake-stream interface, demonstrating remarkably abrupt transition in phenotype between these habitats. The data comes from samples collected and measured as described in Bolnick,D.I. L. Snowberg, C. Patenia, O. L. Lau, W. E. Stutz, and T. Ingram. 2009. Phenotype-dependent native habitat preference facilitates divergence between parapatric lake and stream stickleback. Evolution 63:2004-2016. However, the analyses in the present figure 1 of Bolnick and Otto are a novel reanalysis of that prior data.
DOI: 10.5061/dryad.6h5v1/1
title: fish_polyploidy

description: Phylogenetic and ploidy level data of 4 fish groups examined: Acipenseridae, Botiidae, Cyprininae, and Salmoniformes.
DOI: 10.5061/dryad.7t354/3
title: h3

description: H3 histone sequence alignment
DOI: 10.5061/dryad.7t354/4
title: melanocortin

description: Melanocortin sequence alignment
DOI: 10.5061/dryad.7t354/5
title: nd2

description: ND2 sequence alignment
DOI: 10.5061/dryad.7t354/6
title: prlr

description: PRL- R sequence alignment
DOI: 10.5061/dryad.7t354/7
title: Rag

description: Rag 1 sequence alignment
DOI: 10.5061/dryad.7vj03/10
title: R code to produce Figure 1: Proportion of surviving larvae in absence of settlement cues, and proportion of larvae settled and swimming at the end of the experiment in presence of settlement cues for Cyphastrea japonica, Favites stylifera and Acropora millepora at 27, 29 and 31oC .

description: R code to produce Figure 1 where observations and model predictions are compared. This code includes the estimate of survival and competence parameters for all species.
DOI: 10.5061/dryad.7vj03/11
title: R code to produce Figure 2: Relative increase in the proportion of larvae that attain competence while retained on the natal reef over a realistic range of mean residence times around a reef with a 2 and 4°C increase

description: R code to produce Figure 2, including estimating of all parameters for all species, local retention and relative increase in local retention.
DOI: 10.5061/dryad.7vj03/12
title: R code to produce Figure 3: Schematic of the proportion of potential settlers for reefs with short, intermediate and long mean residence times

description: Proportion of potential settlers (live larvae not yet flushed from the reef) for reefs with short (1 day, light blue), intermediate (2.5 days, dark blue) and long (10 days, green) mean residence times, using estimates for A. millepora (Table S2).  In A&B, mortality rate is equal for all reefs (λ27), and the vertical distance between the dashed lines represents the increased proportion of potential settlers due to the reduction in the minimum time to competence from tc27 to tc31. In C&D, minimum competence time is fixed at tc27, and mortality rate is low on the top (λ27) and higher on the bottom (λ31) of each shaded band; thus, the vertical distance between the dashed lines shows the reduction in the proportion of potential settlers due to the increased mortality rate.
DOI: 10.5061/dryad.7vj03/9
title: Larval survival of Acropora millepora at different temperatures

description: "temp" is the temperature the larvae were raised in; "age" is the larval age (h), "surv" is the number of larvae alive (swimming as no settlement cue was provided), "larvae" is the  number of embryo/larvae in the beginning of the experiment; "propsurv" is the proportion of larvae alive, calculated as "surv"/"larvae"
DOI: 10.5061/dryad.89v53/1
title: RAST_Annotations

description: RAST-generated annotations for all genomes included in the analyses in this manuscript.
DOI: 10.5061/dryad.89v53/2
title: Raw_sequence_reads

description: Fragment libraries were constructed for eight species of the family Halobacteriacea, three from the genus Haloarcula (Har. californiae, Har. sinaiiensis, Har. vallismortis) and five from the genus Haloferax (Hfx. denitrificans, Hfx. mediterranei, Hfx. mucosum, Hfx. sulfurifontis, and Hfx. volcanii), and sequenced on a single GS FLX Titanium run following standard protocols (454 Life Sciences - http://454.com/). Hfx. volcanii was included as a sequencing control, as its genome had been completed previously [19]. Additionally, for Har. sinaiiensis and Hfx. mediterranei, 8 Kb pair-end libraries were constructed and the terminal 100 bp of each end was sequenced, according to standard protocols. The paired-end information and any trimming information are specified using annotation strings on the description line of the reads. Reads were assembled using the Genome Sequencer De Novo assembler (454 Life Sciences - http://www.my454.com/).
DOI: 10.5061/dryad.8gj1c/1
title: AlbrechtEtAl_DataTable1
DOI: 10.5061/dryad.8gj1c/2
title: AlbrechtEtAl_DataTable2
DOI: 10.5061/dryad.8gj1c/3
title: AlbrechtEtAl_DataTable3
DOI: 10.5061/dryad.9g6q2/1
title: Summary of sites

description: Two replicates at each of 18 sites, with the starting time, date, number of discoveries, treatment, and replicate number.
DOI: 10.5061/dryad.9mg16/4
title: Data from 6 turtles exposed to vibrtion during temperature change

description: Data consists of wav files containing recorded data from 6 turtles exposed to vibration during cooling from 25 C to 3 C, and reheating from 5 C to 25 C.
DOI: 10.5061/dryad.9mg16/5
title: Movement data for hibernating turtles

description: The data consists of MatLab files containing the differentiated brightness scores from turtle movement during hibernation, before and after stimulus (heat, light, oxygen and vibration.) Further information is available in the ReadMe file.
DOI: 10.5061/dryad.b7f53/1
title: chengsupp2_datasets 1-4 for the meta-analysis study

description: The data sets 1-4 for the meta-analysis study.
DOI: 10.5061/dryad.c221m/1
title: mec13390_genotypes

description: Microsatellite data set (n=692) follows the Structure input file format (Unix format txt) with individual information on a single line (two columns per marker). The file contains loci names (1st row), individual names (1st column), codes for sampling localities (2nd col.) and 3 additional columns (GenBank Acc. n., haplogroup and haplotype for cyt-b mtDNA sequence).
DOI: 10.5061/dryad.c221m/2
title: mec13390_SimDataset6000inds

description: Microsatellite data set (n=6,000) simulated with HYBRIDLAB 1.0 (Nielsen et al. 2001). The file is in Genepop format, with 6 populations representing B. plebejus purebreds, B. barbus purebreds, F1, F2, Backcross F1 X B. plebejus and Backcross F1 X B. barbus.
DOI: 10.5061/dryad.c45f0/1
title: Sites and physical measurements 2003

description: GPS coordinates and measurements of dissolved oxygen, temperature, and salinity taken during field surveys in the York and Rappahannock Rivers, VA, in 2003.
DOI: 10.5061/dryad.c45f0/2
title: Sites and physical measurements 2004

description: GPS coordinates and measurements of dissolved oxygen, temperature, and salinity taken during field surveys in the York and Rappahannock Rivers, VA, in 2003.
DOI: 10.5061/dryad.c45f0/3
title: Field predation and non-predatory mortality rates

description: Calculated predation rates from a caging study on Macoma balthica in the York River in 2006.  Rates were calculated based on the number of marked clams recovered after approximately 4 weeks exposure time.  Non-predatory mortality rates were based on the recovery of marked dead clams (i.e. undamaged shells).  The major predator on M. balthica in this system is the blue crab Callinectes sapidus.
DOI: 10.5061/dryad.c45f0/4
title: Field predation experiment DO Datasond

description: This file contains the measurements of dissolved oxygen (DO) in mg O2/L recorded by a Hydrolab DS5X with a luminescent DO probe (Hach Environmental, Loveland, CO) at a single deep site during the predation experiment in the York River in 2006.  Date/time represents the data and time (EST) of each measurement.
DOI: 10.5061/dryad.c45f0/5
title: Field predation sites and physical measurements

description: This file contains the measurements of dissolved oxygen (DO) in mg O2/L at each site during the predation experiment using an YSI 85.  Date represents the date of each measurement.  Latitude and longitude are in decimal degrees.  Temperatures are in degrees Celsius, salinity in practical salinity units (psu) and dissolved oxygen (DO) in mg O2/L.
DOI: 10.5061/dryad.c45f0/6
title: Lab experiment DO and temp

description: This file contains the measurements of dissolved oxygen (DO) and temperature in tanks during a laboratory experiment examining the effects of low DO on the clam Macoma balthica.   Treatment represents the nominal dissolved oxygen (mg O2/L) treatment group.  Replicate represents the replicate tank number.  DO is in mg O2/L) and temperature is in degrees Celsius.  The date is the date of each measurement and time is approximate time in EST.
DOI: 10.5061/dryad.c45f0/7
title: Macoma balthica densities

description: This file contains the average Macoma balthica densities at each site sampled in box cores during the field surveys in 2003-2004.  The minimum summer DO represents the minimum dissolved oxygen concentration (mg O2/L) observed at each site during that year. River is represent the river the sample was taken in, Date the day the sample was taken, and Site the nominal site at which the sample was taken.  Note that sites changed location between years, (i.e. site M2 in 2003 in the York was at a different location than site M2 in 2004).  Site location and raw DO measurements are available in the Sites and physical measurements files.
DOI: 10.5061/dryad.c45f0/8
title: Macoma balthica lengths and masses

description: This file contains the average Macoma balthica shell lengths in mm and ash free dry masses (AFDM) in mg at each site sampled during the field surveys 2004.  River represents the river the sample was taken in, Site represents the site name, Date represents the date the sample was taken.  The average summer DO represents the average dissolved oxygen concentration (mg O2/L) observed at each site during that summer.  Site locations and raw DO measurements are available in the Sites and physical measurements 2004 file.
DOI: 10.5061/dryad.d48hq/1
title: Data from: Looking at Cerebellar Malformations through Text-Mined Interactomes of Mice and Humans

description: See original publication and documentation files included in this archive. Archive format is POSIX 'tar' archive compressed using GNU zip (gzip). The included data files are tab-separated ASCII. Some Matlab scripts are provided.
DOI: 10.5061/dryad.f6p6n/1
title: Data and scripts for the paper

description: Scripts and all data necessary to run the analyses and redo the figures. A detailed script "main.R" describes data processing.
DOI: 10.5061/dryad.gg6qk/1
title: Glazier et al Supplementary tables 1 & 2

description: Two supplementary tables give the raw data used for scaling analyses of eye-facet size and number in relation to total eye size in Eldredgeops rana (original data) and other benthic and pelagic trilobites (literature data).
DOI: 10.5061/dryad.jq470/1
title: DRYAD data archive

description: Raw data for encoding failure experiment and retention interval experiment.
DOI: 10.5061/dryad.mp4vb/1
title: Table S1 WWD Primaries

description: Microsoft Excel file containing data on primary feather replacement for 19 captive-raised juvenile eastern white-winged doves (Zenaida asiatica asiatica) during 2008 at the Duane Leach Research Aviary, Texas A&M University-Kingsville.
DOI: 10.5061/dryad.ph8s5/17
title: Reference database EMBL (ITSPoa)

description: Fasta file of the EMBL reference database (ITSPoa)
DOI: 10.5061/dryad.rv524/1
title: Grindelia_allele_frequencies

description: This is a tab-delimited text file with the information on which alleles were present in each individual.  In total, there are data from six microsatellite loci (columns) and 439 individuals (rows).  Loci and individuals are identified in a header row or column, respectively.  Data were gathered from wild-collected leaf material and scored using PeakScanner v. 1.0.
DOI: 10.5061/dryad.tk400/2
title: Matching Model Simulation Alpha = 2.0

description: Simulation data for generation 1000 derived from the phenotype matching model with Alpha set to 2.0
DOI: 10.5061/dryad.tk400/3
title: Simulation Data for Differences Model Alpha = 0.02

description: Simulation data for the phenotype differences model in generation 2000 with alpha set to 0.02.
DOI: 10.5061/dryad.tk400/4
title: Simulation Data for Differences Model Alpha = 2.0

description: Simulation data for generation 1000 of the phenotype differences model with Alpha set to 2.0.
DOI: 10.5061/dryad.v55p5/12
title: Part of image archive
DOI: 10.5061/dryad.v55p5/13
title: Part of image archive
DOI: 10.5061/dryad.v55p5/14
title: Part of image archive
DOI: 10.5061/dryad.v55p5/15
title: Part of image archive
DOI: 10.5061/dryad.v55p5/16
title: Part of image archive
DOI: 10.5061/dryad.v55p5/17
title: Part of image archive
DOI: 10.5061/dryad.v55p5/18
title: Part of image archive
DOI: 10.5061/dryad.v55p5/19
title: Part of image archive
DOI: 10.5061/dryad.v55p5/20
title: Part of image archive
DOI: 10.5061/dryad.v55p5/21
title: Part of image archive
DOI: 10.5061/dryad.v74b8/1
title: DRYAD SNP data for Limborg et al. 2012

description: This file contains the SNP genotype data used for the associated publication. Genotypes are presented in a 3 digit genepop format with alternate alleles scored as 100 and 200 respectively.
DOI: 10.5061/dryad.18j3d/25
title: c53_SierraMadreOccidental-CentralPlateauProvince

description: Shapefile for SIG
DOI: 10.5061/dryad.18j3d/27
title: c56_TransmexicanVolcanicBelt

description: Shapefile for SIG
DOI: 10.5061/dryad.18j3d/28
title: c60__Chiapas-CentralAmericaProvince

description: Shapefile for SIG
DOI: 10.5061/dryad.18j3d/29
title: c63_MesoamericanProvince

description: Shapefile for SIG
DOI: 10.5061/dryad.18j3d/3
title: c2_TalamancanCordilleraProvince

description: Shapefile for SIG
DOI: 10.5061/dryad.18j3d/30
title: c65_MexicanTransitionZone

description: Shapefile for SIG
DOI: 10.5061/dryad.18j3d/31
title: c70_CentralAmericaProvince

description: Shapefile for SIG
DOI: 10.5061/dryad.18j3d/32
title: c72_NeotropicalRegion

description: Shapefile for SIG
DOI: 10.5061/dryad.18j3d/33
title: c74_Pacific-CentralAmericaSubregion

description: Shapefile for SIG
DOI: 10.5061/dryad.18j3d/4
title: c4_MexicanTransitionZone

description: Shapefile for SIG
DOI: 10.5061/dryad.25j6h/1
title: 129 taxa

description: Zip file of full datasets. Included are 8 files corresponding to 4 datasets 1)NUCL (nucleotide) based dataset and partition file (partitioned by codon n12 and n3), 2) N12 (excluding 3rd codon) dataset and partition file (by gene), 3) AA (amino acid) dataset and partition file (by gene), 4) DEGEN1 (nucleotide-based accounting for codon degeneracy) based dataset with partition file. Note, no taxa are excluded, although in final analyses rogue taxa are removed.
DOI: 10.5061/dryad.25j6h/2
title: 16 taxa

description: Zip file of reduced taxon datasets (16 exemplar taxa). Included are 8 files corresponding to 4 datasets 1)NUCL (nucleotide) based dataset and partition file (partitioned by codon n12 and n3), 2) N12 (excluding 3rd codon) dataset and partition file (by gene), 3) AA (amino acid) dataset and partition file (by gene), 4) DEGEN1 (nucleotide-based accounting for codon degeneracy) based dataset with partition file.
DOI: 10.5061/dryad.25j6h/3
title: Individual Genes

description: 75 individual gene datasets. All datasets start with the first codon position.
DOI: 10.5061/dryad.25j6h/4
title: 31 genes

description: Zip file of reduced gene datasets (corresponding to turtle question). Included are 8 files corresponding to 4 datasets 1)NUCL (nucleotide) based dataset and partition file (partitioned by codon n12 and n3), 2) N12 (excluding 3rd codon) dataset and partition file (by gene), 3) AA (amino acid) dataset and partition file (by gene), 4) DEGEN1 (nucleotide-based accounting for codon degeneracy) based dataset with partition file. Note, taxon sampling has been reduced by removing rogue taxa.
DOI: 10.5061/dryad.25j6h/5
title: 26 genes

description: Zip file of reduced gene datasets (corresponding to Lissamphibia question). Included are 8 files corresponding to 4 datasets 1)NUCL (nucleotide) based dataset and partition file (partitioned by codon n12 and n3), 2) N12 (excluding 3rd codon) dataset and partition file (by gene), 3) AA (amino acid) dataset and partition file (by gene), 4) DEGEN1 (nucleotide-based accounting for codon degeneracy) based dataset with partition file. Note, taxon sampling has been reduced by removing rogue taxa.
DOI: 10.5061/dryad.25j6h/6
title: 16taxa 31genes

description: Zip file of reduced gene and 16 taxa datasets (corresponding to turtle question). Included are 8 files corresponding to 4 datasets 1)NUCL (nucleotide) based dataset and partition file (partitioned by codon n12 and n3), 2) N12 (excluding 3rd codon) dataset and partition file (by gene), 3) AA (amino acid) dataset and partition file (by gene), 4) DEGEN1 (nucleotide-based accounting for codon degeneracy) based dataset with partition file.
DOI: 10.5061/dryad.25j6h/7
title: 16taxa 26genes

description: Zip file of reduced gene and 16 taxa datasets (corresponding to Lissamphibia question). Included are 8 files corresponding to 4 datasets 1)NUCL (nucleotide) based dataset and partition file (partitioned by codon n12 and n3), 2) N12 (excluding 3rd codon) dataset and partition file (by gene), 3) AA (amino acid) dataset and partition file (by gene), 4) DEGEN1 (nucleotide-based accounting for codon degeneracy) based dataset with partition file.
DOI: 10.5061/dryad.456f3.1
title: Data from: Selection from parasites favors immunogenetic diversity but not divergence among locally adapted host populations
DOI: 10.5061/dryad.456f3.2
title: Data from: Selection from parasites favors immunogenetic diversity but not divergence among locally adapted host populations
DOI: 10.5061/dryad.456f3.2/1.1
title: 1 Parasite communities

description: This file includes the raw data about the occurrence of parasites across 6 sites investigated in the study. Included are data for individual hosts and counts of specific parasites as outlined in the paper. Variables include an individual identification number (which is also used for the MHC and microsatellite data), population of origin for each host individual, sex, standard length (in millimeter), as well as the number of Oodinium, Ambiphyra, Trichodina, Dactylogyrus, Gyrodactylus, Diplostomum cf. spathaceum, Echinochasmus cf. donaldsoni, Uvulifer, Trematode 1, Trematode 2, Trematode 3, Nematode, Cestode, and Lernea recorded per host.
DOI: 10.5061/dryad.4v875/18
title: NEWAppendix 7_28S_FINAL2

description: Maximum likelihood tree based on 28S data
DOI: 10.5061/dryad.4v875/19
title: NewAppendix_8_H3_FINAL2

description: Maximum Likelihood tree based on H3 data
DOI: 10.5061/dryad.4v875/20
title: NEWAppendix_9_IGTP_FINAL2

description: IGTP Species Tree Analysis for all taxa in this study
DOI: 10.5061/dryad.4v875/21
title: NewAppendix 10 Molecular_FINAL

description: Maximum likelihood tree based on molecular data (6 genes)
DOI: 10.5061/dryad.4v875/22
title: NEWAppendix 11_PhyloBayes_species_FINAL

description: Phylobayes analysis of all taxa in this study
DOI: 10.5061/dryad.4v875/23
title: NewAppendix 12_fossil justification

description: Justification for each fossil included in the 28 fossil divergence time analysis.
DOI: 10.5061/dryad.4v875/24
title: NEWAppendix 1_Jan_2014

description: Taxonomy, voucher catalog numbers, and GenBank accession numbers for gene sequences used in study. An “N/A” (not available) indicates missing sequence data.
DOI: 10.5061/dryad.4v875/25
title: NEWAppendix 5mito_FINAL2

description: Mitochondrial (12S, 16S, COI) gene tree for species included in combined analysis.
DOI: 10.5061/dryad.5hh3h/6
title: Buffalo Disease Tests

description: Table contains the data on all disease testing (Bovine TB, Brucellosis, and Rift Valley Fever) done on the captured buffalo.
DOI: 10.5061/dryad.5hh3h/7
title: Herd Sightings
DOI: 10.5061/dryad.5hh3h/8
title: Herd Sightings Freq

description: his table contains the VHF frequencies of those individuals “seen” in each herd at a specific sighting. This table should be used in conjunction with the herd sighting table by linking on HerdName and Date. Note that individuals were often not visually observed but were deduced to be in the herd based upon radio-telemetry.
DOI: 10.5061/dryad.7f4m96c3/1
title: Dryad ecological data
DOI: 10.5061/dryad.8837q/1
title: Sampling and Ecological Data

description: This file includes data on geographical sampling and measured environmental variables.
DOI: 10.5061/dryad.8837q/2
title: Genetic Data

description: This file contains the genotypic data at all AFLP markers, for each individual Pieris rapae.
DOI: 10.5061/dryad.8837q/3
title: Morphological Data

description: This file contains the morphological wing measurements for Pieris rapae.
DOI: 10.5061/dryad.8b35s/1
title: Confocal Images

description: Confocal images of grids at 0 to 10 % strain increments. Each sample is identified by a number. Please see the ReadMe file for a description of the abbreviations
DOI: 10.5061/dryad.8b35s/2
title: Fatigue test raw data

description: Raw data from fatigue loading experiments. Samples are denoted by horse number followed by fascicle number. See ReadMe file for details of horse ages and naming conventions.
DOI: 10.5061/dryad.9c7bq/1
title: Data from: Within-group male relatedness reduces harm to females in Drosophila

description: Details are given in the readme.doc file