cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.cd546/118
title: Online Appendix 23

description: Analysis of the mitochondrial genome dataset with coding and noncoding regions treated as separate partitions. The outgroup branch is not to scale; otherwise, branches are shown proportional to ML branch lengths; branch coloration follows Fig. 1.
DOI: 10.5061/dryad.cd546/119
title: Online Appendix 24

description: Analysis of the mitochondrial genome dataset with no partitioning scheme. The outgroup branch is not to scale; otherwise, branches are shown proportional to ML branch lengths; branch coloration follows Fig. 1.
DOI: 10.5061/dryad.cd546/120
title: Online Appendix 25

description: Mitochondrial phylogeny including only samples in upper 50th percentile in terms of coverage (unpartitioned). The topology is largely congruent with the tree containing 66 taxa, indicating that the topology is not sensitive to low-coverage samples. The outgroup branch is not to scale; otherwise, branches are shown proportional to ML branch lengths; branch coloration follows Fig. 1.
DOI: 10.5061/dryad.cd546/121
title: Online Appendix 26

description: Cluster network depicting conflict between plastid and nuclear topologies; blue branches represent reticulation, while black branches show tree-like relationships held in common between the two phylogenies. The topological conflict is so extreme and involves such distantly related taxa that almost no clades are held in common between the two datasets. In the two input trees, all clades with &lt; 70% bootstrap support were collapsed.
DOI: 10.5061/dryad.cd546/122
title: Online Appendix 27

description: Tanglegram comparing mitochondrial and concatenated nuclear phylogenies, optimized in Dendroscope to minimize line crossings. Again, the concatenation tree is used to represent the nuclear phylogeny in order to maintain comparability and to show divergent placement of subspecific samples in the mitochondrial tree. In order to minimize spurious disagreement between phylogenies due to estimation error, all clades with &lt; 70% bootstrap support have been collapsed.
DOI: 10.5061/dryad.cd546/123
title: Online Appendix 28

description: Proposed introgression events (from Table 2) mapped onto the ASTRAL topology as a visual representation of hypothesized gene flow. Solid red arrows represent proposed hybridization ancestral to a clade; dotted lines represent hybridization among species or populations only; asterisks mark taxa where there was evidence for introgression but the source of the organellar DNA was unresolved.
DOI: 10.5061/dryad.cd546/124
title: Online Appendix 29

description: The mitochondrial tree (see Fig. 3), pruned to only mitochondrial clade A, and rerooted with Mitella pentandra to match the plastid tree. This figure demonstrates that the mitochondrial tree differs from the plastid tree in ways that cannot be explained simply by subtree misrooting.
DOI: 10.5061/dryad.cs17q.1
title: Data from: Abiotic proxies for predictive mapping of near-shore benthic assemblages: implications for marine spatial planning
DOI: 10.5061/dryad.cs17q.2
title: Data from: Abiotic proxies for predictive mapping of near-shore benthic assemblages: Implications for marine spatial planning
DOI: 10.5061/dryad.cs17q.2/1.2
title: McHenry_etal_2016_Survey_Data

description: The data comes from a remotely operated vehicle (ROV) survey conducted during the summer months of 2010-2013 along the coastal Gulf of Maine shelf. The survey aimed 1) to characterize the distribution and abundance of benthic megafauna with respect to near-shore abiotic conditions, 2) to develop  spatially-explicit maps of ecological attributes of near-shore benthic assemblages, and 3) use such maps to inform the application of ecological principles when engaging in marine spatial planning. This file contains a  data matrix of  species abundances for the most dominantly observed species (i.e., greater than 5 observations), assemblage biomass, economic value, and shannon-weiner species diversity  by site, along with values of associated summertime abiotic conditions (i.e.,mean transect depth, substrate type, water-mass position, bottom temperature, bottom current speed/direction, and bottom salinity). Depth and substrate type values were recorded from the ROV surveys, while the water-mass values were acquired from HYCOM GLBu0.08 4D model output via the Marine Geo-spatial Ecology Toolbox in ArcGIS 10.3. See McHenry et al. 2016 for a full description  the survey design, data processing methods, and analytical approaches used by this study.
DOI: 10.5061/dryad.cs17q.2/2.2
title: McHenry_etal2016_benthic_maps

description: This layer package (.lpk) contains raster layers (.tif) and associated metadata (.xml) for spatially explicit maps of average summertime benthic species diversity, assemblage biomass (kg per 100 square meters), and economic value ($ per 100sq meters) along the Gulf of Maine coastal shelf. These maps were derived by McHenry et al. 2016-- a study that aimed 1) to characterize the distribution and abundance of benthic megafauna with respect to near-shore abiotic conditions, 2) to develop spatially-explicit maps of ecological attributes of near-shore benthic assemblages, and 3) to use such maps to inform the application of ecological principles when engaging in marine spatial planning. See McHenry et al. 2016 for a full description the survey assessment design, data processing methods, and modeling approaches used.
DOI: 10.5061/dryad.gs835/1
title: SpermVelocityWater_Lehnert-BE

description: Sperm velocity (VAP, VCL, VSL) of red and white Chinook salmon males at 5 seconds post-activation in water. Each male is represented by replicate velocity measures (if applicable).
DOI: 10.5061/dryad.gs835/2
title: SpermVelocityOF_Lehnert-BE

description: Sperm velocity (VAP, VSL, VCL) and sperm path straightness (STR) of red and white Chinook salmon males when sperm is activated in ovarian fluid of red and white females. Sperm metrics were recorded at 5 seconds post-activation in ovarian fluid.
DOI: 10.5061/dryad.gs835/3
title: PaternityCompetitiveFertilizations_Lehnert-BE

description: Paternity assignment for competitive fertilizations in red and white Chinook salmon. For each competitive fertilization, the number of red sired and white sired eggs are provided Difference between paired males is sperm velocity (VAP) in water and ovarian fluid at 5 seconds post-activation are provided, as well as the sperm density ratio (red:white sperm cells) within each competitive fertilization.
DOI: 10.5061/dryad.h67t6/13
title: Overview_Volume_Sections_205-504
DOI: 10.5061/dryad.h67t6/14
title: File Information

description: Readme file.
DOI: 10.5061/dryad.h67t6/15
title: Zip File Information

description: read me
DOI: 10.5061/dryad.k0218/1
title: Headed apple architecture data year 1 and 2

description: Phenotypic data of 1-year-old and 2-year-old headed trees from a germplasm collection modern cultivars and older local varieties
DOI: 10.5061/dryad.k47b2/1
title: Site-level abundance data

description: Abundance data at site level
DOI: 10.5061/dryad.k47b2/2
title: Trap_level_trapping_data

description: Capture data at trap level for binomial modelling of capture patterns
DOI: 10.5061/dryad.k47b2/3
title: Genotypes

description: Genotype data in Genalex format (http://biology-assets.anu.edu.au/GenAlEx/Welcome.html).
DOI: 10.5061/dryad.k9b6f/4
title: LangoScholey_Test_Sequence_Files

description: This folder contains the test sequences used to validate the assay
DOI: 10.5061/dryad.k9b6f/5
title: ReadMe

description: This file is a description of the contents of the archive
DOI: 10.5061/dryad.n04g0/1
title: Nitrogen_Biogeochemical_Network_Sanjay_Lamba_Chakraborty_ESM

description: This Auxiliary Material includes five supplementary tables (Table S1-S5), fifteensupplementary figures (Figs. S1-S15) and ten supplementary texts(Text S1-S10).Detailed methods and mathematical techniques are described in the supplementary texts;all the simulated model results in the form of tables and figures are presented in theauxiliary figures and tables. This material presents how the nitrogen biochemical systemruns and is regulated over time and how it is responded to external ammonium supply.
DOI: 10.5061/dryad.n0c67/1
title: Evolution during range expansion_dataSheets

description: This datafile containes all the life-history data that were used in Van Petegem et al._Evolution during range expansion. They were assessed for two-spotted spider mites collected in the field in 2011-2012 (Belgium, the Netherlands, Germany and Denmark) -after at least two generations of common garden breeding.
DOI: 10.5061/dryad.n0c67/2
title: Evolution during range expansion_scripts

description: This file contains the scripts that were used for the analyses of the life-history data in Van Petegem et al._Evolution during range expansion. The text in this file can be copy-pasted into SAS. You then only need to copy-paste the data (available in the data file in Dryad) into the indicated place.
DOI: 10.5061/dryad.pf550.2
title: Data from: Population genomic analyses reveal a history of range expansion and trait evolution across the native and invaded range of yellow starthistle (Centaurea solstitialis)
DOI: 10.5061/dryad.pf550.2/1.2
title: YST_Core_N550_1013loc

description: SNP data file for STRUCTURE and DAPC analysis of "CORE" data set
DOI: 10.5061/dryad.pf550.2/2.2
title: YST_Full_N591_747loc

description: SNP data file for STRUCTURE and DAPC analysis of "FULL" data set
DOI: 10.5061/dryad.pf550.2/3.2
title: YST_Outgroups_N392_440loc

description: SNP data file for STRUCTURE and DAPC analysis of "OUTGROUPS" data set
DOI: 10.5061/dryad.pf550.2/4.2
title: YST_Core_N550_1013loc_BAPS

description: SNP data file for BAPS analysis of "CORE" data set
DOI: 10.5061/dryad.pf550.2/5.2
title: YST_Full_N591_747loc_BAPS

description: SNP data file for BAPS analysis of "FULL" data set
DOI: 10.5061/dryad.q8150/1
title: Raw Data

description: This file contains the raw data supporting all figures in the manuscript. Flow cytometry data is in FCS file format, and can be read with programs such as flowjo. JEX data is in arff format and can be read with the R application as described in the manuscript.
DOI: 10.5061/dryad.qm344/2
title: Data, Figures, Tables

description: Data for analyses, figures, and tables (including supplemental)
DOI: 10.5061/dryad.rt201.1
title: Data from: A fresh approach reveals how dispersal shapes metacommunity structure in a human-altered landscape
DOI: 10.5061/dryad.rt201.2/6.2
title: Water & Air Temperatures

description: Air and water temperatures recorded at two sites on each of Hughes Creek and Seven Creeks during summer and spring in 2008 and 2009.
DOI: 10.5061/dryad.s5700/1
title: Data for 31 Valeriana-Uromyces populations over 28 years

description: File contains three work sheets giving all epidemiological, spatial and environmental data
DOI: 10.5061/dryad.v54jq/2
title: DataLochyEtAl_PNAS2016

description: complete data set for the two experiments (see ReadMe).
DOI: 10.5061/dryad.v82g6/1
title: Lichen Diameters

description: Raw Rhizocarpon sp. lichen diameters from soil deflation patches in West Greenland. We measured all yellow-green Rhizocarpon sp. without identifying to the species level. Lichen diameter measurements were collected along transects perpendicular to the active margin of the erosional landform. We measured the long axis of the lichens using digital calipers.
DOI: 10.5061/dryad.v82g6/2
title: Deflation Patch Characteristics

description: Landscape position data for soil deflation landforms in West Greenland. Field measurements include scarp length, scarp height, and patch size. Elevation, aspect, slope, and distance to the Greenland Ice Sheet were calculated with imagery acquired from the Polar Geospatial Center. We calculated the patch expansion rate using the lichenometry dataset also available in this data package.
DOI: 10.5061/dryad.089cr/1
title: grasshopperData

description: Simulation results from the grasshopper simulations.
DOI: 10.5061/dryad.1r1j4/1
title: Rhebergen_BMC_2016

description: The folder contains movies of /Drosophila pachea/ copulations, image exports from those movies and scanning electron microscopy images of /D. pachea/ copulation complexes. In addition, we provide three data files, with the measurements that were used to describe mating behavior, mating positions and SEM copulation complexes. The md5sum of Rhebergen_BMC_2016.tar.gz is: d0daef793b2bce7863a482f11bee92b6
DOI: 10.5061/dryad.3f069/1
title: The date for the ascending and descending type of NPC

description: This file lists and describes the sources of all the variables used in the final analysis.
DOI: 10.5061/dryad.3td28/1
title: Allele scores

description: Allele scores for all fish included in study
DOI: 10.5061/dryad.3td28/2
title: Individual fish data

description: Metadata for each fish including individual id, year caught, and habitat
DOI: 10.5061/dryad.3td28/3
title: Landmark data

description: Landmark data for all fish included in geometric morphometric analysis
DOI: 10.5061/dryad.45kf5/1
title: Afro-alpine_taxonomic_ref_library_v2

description: Sequences of the taxonomic reference library version 2.0 for the African alpine flora. Sequences cover the P6 loop of the trnL. Header lines contain the species names followed by identity numbers (O-DP numbers) that correspond to specimen numbers in the herbarium of the Natural History Museum, University of Oslo, Norway.
DOI: 10.5061/dryad.46r48/1
title: Stress study and hormones

description: Main data set
DOI: 10.5061/dryad.46r48/2
title: population FID

description: additional data set
DOI: 10.5061/dryad.4m67g/1
title: Plectropomus leopardus - Microsatellite data

description: Microsatellite data for Plectropomus leopardus in the southern Great Barrier Reef
DOI: 10.5061/dryad.524mc/3
title: sample 2 vertical cross sections

description: Complete series of vertical cross sections through Sample 2 of Parahaentzschelinia.
DOI: 10.5061/dryad.524mc/4
title: bedding parallel cross sections

description: Complete series of bedding parallel cross sections through aff. Parahaentzschelinia showing the endogenic radial mud-lined burrows.
DOI: 10.5061/dryad.5dc12/1
title: Muskipper_Aquatic_feeding

description: A zip containing High speed vid recording of both lateral and ventral views. Four individuals, two recordings per individual. Mudskippers. Periophthalmus barbarus, feeding underwater.
DOI: 10.5061/dryad.5n7f6/1
title: Salisbury et al. 2016 Data Accession

description: "Catostomus catostomus scores for Salisbury et al. 2016.xlsx" contains scores for 869 Catostomus catostomus samples at 17 microsatellite markers. Samples were collected in the Kogaluk River, Labrador, Newfoundland. Row 1 indicates markers, column A indicates individuals, column B indicates lake. Missing scores are denoted by "0". "Pairwise Genetic, Geographic, Elevation Distances for Catostomus catostomus samples from Salisbury et al. 2016.xlsx" contains pairwise Fsts, geographic, and elevation distances among Catostomus catostomus samples collected within 8 lakes in the Kogaluk River, Labrador, Newfoundland.
DOI: 10.5061/dryad.6hj2p/1
title: settlement of wood warbler in 2013-14

description: this file was used for the analysis of settlement of wood warblers on experimental plots in 2013 and 2014 as well as for the MANOVA of plot type in relation to number of trees, number of grass tussocks and number of rodent tracks (column descriptions are given as comments in the first cell of each column where relevant)
DOI: 10.5061/dryad.6hj2p/2
title: daily nest survival rate data 2013-14 during experiment

description: this file was used for the analysis of daily nest survival rate of wood warblers settling in response to experimental treatment (description of variables are given as comments in each column header if necessary)
DOI: 10.5061/dryad.6hj2p/3
title: clutch size and nr of hatchlings during experiment in 2013-14

description: this file was used to analyze clutch size and number of hatchlings of wood warblers settling on experimental plots in 2013 and 2014 (variable descriptions are given as comments in column headers where necessary)
DOI: 10.5061/dryad.6hj2p/4
title: nr of fledglings during experiment 2013-14

description: this file was used to analyze number of fledglings of wood warblers settling on experimental plots in 2013 and 2014 (variable descriptions are given as comments in column headers where necessary)
DOI: 10.5061/dryad.6hj2p/5
title: pairing rates

description: this file was used to analyze pairing rates of wood warblers settling on experimental plots in 2013 and 2014 (variable descriptions are given as comments in column headers where necessary)
DOI: 10.5061/dryad.6hj2p/6
title: area_year comparisons

description: this file was used to compare reproductive performance of wood warblers during the years of the experiement and during the three years preceding the experiement (variable descriptions are given as comments in column headers where necessary)
DOI: 10.5061/dryad.779rd/1
title: Gachohi et al RVF Model code

description: This code, implemented in R, is about simulating population dynamics of two species of mosquitoes namely Aedes and Culex and two livestock species namely cattle and sheep. Hosts are classified into four age groups (young, weaner, yearling and adult groups) while vectors are classified into eggs, larvae, pupae and adults. Transition rates govern the population dynamics. Further, the code simulates transmission dynamics of Rift Valley fever virus between the mosquitoes and the livestock. Mosquito growth is regulated by amounts of rainfall implicitly through probability functions - suitability function for Aedes and logistic distribution function for Culex. The code is used to simulate diverse policy-relevant interventions on the effectiveness of reactive and periodic Rift Valley fever vaccination strategies.
DOI: 10.5061/dryad.779rd/2
title: Modelling vaccination strategies against Rift Valley fever in livestock in Kenya: Precipitation data

description: This data contains precipitation data used to drive mosquito population growth. In the code, the rain is sourced as follows: Rain
DOI: 10.5061/dryad.78cc8/1
title: metabolomics of a range expanding arthropod_results of GC-MS analysis

description: This file contains the outcomes of the GC-MS analysis described in Van Petegem et al. 2016_Metabolomics of a range expanding arthropod. The analysis was performed for two-spotted spider mites collected in nine localities along this species' latitudinal expansion gradient. For each of the 43 metabolites that were detected in the mite samples (5 samples per locality), nmol/sample is given.
DOI: 10.5061/dryad.9rp2b/1
title: Three_varieties_of_arowana_gene_annotation_gff

description: This '.zip' file contains the three "gff" format annotation files of the genome assemblies of golden, red and green arowana varieties, respectively.
DOI: 10.5061/dryad.9rp2b/2
title: Three_varieties_of_arowana_gene_annotation_protein

description: This ".zip" file contains the three "fasta" format protein files of the genome assemblies of golden, red and green arowana varieties, respectively.
DOI: 10.5061/dryad.9rp2b/3
title: Golden_arowana_chromosomes_gene_annotation

description: This "gff" format file contains the gene annotation of golden arowana chromosomes.
DOI: 10.5061/dryad.c1483/1
title: Buechel & Schmid-Hempel 2015

description: data for Proceedings B: Buechel & Schmid-Hempel 2015
DOI: 10.5061/dryad.cd546/125
title: Online Appendix 30

description: Four mitochondrial regions that were conserved, easily aligned among taxa, and generally were represented by complete sequences in the main alignment (of which were used, respectively: positions 103,060-129,653; 132,480-142,279; 416; 224-428,828; 452,332-467,783).
DOI: 10.5061/dryad.cd546/126
title: Online Appendix 31

description: ASTRAL-II tree, including only those loci for which ϕ-tests could not detect recombination. Methods were otherwise identical to the main ASTRAL-II analysis.
DOI: 10.5061/dryad.ds8j3/1
title: Habitat variables associated with survival and dispersal of translocated juvenile desert tortoises

description: •	Recipient site (column B): describes four geographic locations in which tortoises were released: Boulder City Conservation Easement (BCCE), Eldorado Valley (EV), Hidden Valley (HV), and Trout Canyon (TC) with their associated elevations (Column D) and the "release zone" (Column C). •	Longevity (column E): describes the number of days that the tortoise survived (if died or went missing) or the number of days the tortoise was monitored (if survived to close of study). •	Status at close of study is 0 if animal died, 1 if animal lived, and a - if the animal was lost. Cause of death (column F) is 0 if the animal was found with signs of depredation (e.g. tooth marks, partially consumed carcass) and 1 if the animal was living or dead with no signs of consumption at close of study. •	MCL: midline carapace length in mm. •	Max Distance (Column J): maximum linear straight line distance a tortoise moved away from its release point before settling into an area reminiscent of a home range. For those tortoises that did not appear to establish a home range before mortality occurred a dash is present. •	Wash present (Release):  indicates whether the animal was released in a wash (ephemeral river bed) by a 1 or over 2 m from one by a 0. •	Proportion wash encounters: frequency with which an animal was found in or within 2 m of a wash across all tracking events during the study period.•	Burrow Number (release): total number of usable rodent burrows (entire body of tortoise fits inside with minimal excavation) within a 2 m radius of the release point.•	Mean Burrow Number (across year): total number of usable rodent burrows or burrows constructed by the tortoise within 2 m averaged across all tracking events during the monitoring period. •	Substrate (release): substrate category ranked between 0 – 5 measuring the prevalence of rocks on the surface as well as the size of the largest rocks present (e.g. small pebbles, or large pebbles and cobble) in the 2 m area surrounding the release point for each individual. In all instances in which larger rocks were present, smaller rocks were also present. •	Mean substrate (year): Substrate category within 2 m of the tortoises averaged across all tracing events during the monitoring period.
DOI: 10.5061/dryad.k28j0/1
title: Primary data used in Mathot, Dekinga and Piersma, Functional Ecology

description: The attached file includes three worksheets: 1) gizzard mass data, 2) ad libitum foraging trial data, and 3) diet choice trials. Complete descriptions of all column headings are provided on the first tab of the excel file. For details of the methodology, please refer to the original publication in Functional Ecology.
DOI: 10.5061/dryad.kf415/1
title: Simulating and estimating Ne

description: This zipped file contains the computer programs (source code and executables for Windows), parameter setting file, user's guide for simulating and analysing genotype data for estimating Ne.
DOI: 10.5061/dryad.kv898/1
title: Pseudamara and Miquihuana sequence data matrix with ML and bootstrap trees

description: This file contains all trimmed and aligned DNA sequence data analyzed for the paper as well as maximum likelihood bootstrap trees and maximum likelihood trees. It is formatted as a NEXUS file, and is compatible with Mesquite version 3.10
DOI: 10.5061/dryad.nq189/1
title: 8_Iran_Cattle_Breeds_geno

description: The file contains genotypes of 8 Iranian cattle breeds (75 animals). The file is in a compressed rds format and can be used and modified in R.
DOI: 10.5061/dryad.p86t5/1
title: NSW dataset and code for prioritization

description: Code and database for New South Wales prioritization. See ReadMe file for additional details, and see NZ dataset and code ReadMe (http://datadryad.org/resource/doi:10.5061/dryad.3qn55) for details on code design.
DOI: 10.5061/dryad.pf550.2/10.2
title: YST_Full_N591_752loc_BayeScan

description: SNP data file for BayeScan analysis of "FULL" data set
DOI: 10.5061/dryad.pf550.2/11.2
title: YST_Outgroups_N392_441loc_BayeScan

description: SNP data file for BayeScan analysis of "OUTGROUPS" data set