cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.n3pg1hm/2
title: Patlar2018_RScript_SFPexpression

description: File includes working R codes used in the study to perform all statistical analyses reported.
DOI: 10.5061/dryad.pg28510/1
title: Potter_et_al_2018_JAE

description: Zip file containing all data and R code required to perform the analysis
DOI: 10.5061/dryad.pm71k02/1
title: Development of a PCR-RFLP assay to identify Drosophila melanogaster among field-collected larvae

description: Sanger sequencing of COI PCR fragment from wild Drosophila larvae
DOI: 10.5061/dryad.r34k1/7
title: Data from Figure 4 (part 4 of 4): The E3 ubiquitin ligase MARCH1 regulates glucose-tolerance and lipid storage in a sex-specific manner

description: Data for quantification of immunoblots
DOI: 10.5061/dryad.rd681sp/1
title: Dryad Additional Methods

description: Flowchart describing how the final number of s study participants was arrived at.
DOI: 10.5061/dryad.rd681sp/2
title: Dryad Additional Results

description: 1) Tables reporting concentrations of MRS metabolites in the precuneus/PCC region across the different diagnostic/amyloid groups, at baseline, visit 1 and visit 2. 2) Boxplots presenting serial spectroscopic data groups based on baseline Aβ status.
DOI: 10.5061/dryad.s3p3m0d/1
title: Table e-1. Baseline cardiovascular risk factors

description: Baseline cardiovascular risk factors
DOI: 10.5061/dryad.s3p3m0d/2
title: Table e-2. Treatment-emergent adverse events (TEAEs) after the first dose in patients with ≥2 cardiovascular risk factors

description: Treatment-emergent adverse events (TEAEs) after the first dose in patients with ≥2 cardiovascular risk factors
DOI: 10.5061/dryad.sv74pj2/1
title: Ancient scarlet macaw bam files, revised A. m. macao reference, and consensus files

description: This dataset includes 1) aligned bam files for 17 ancient scarlet macaws, 2) aligned and masked bam files for 17 ancient scarlet macaws, 3) the revised A. m. macao reference sequence, and the consensus sequence fasta files.
DOI: 10.5061/dryad.13sb67b/1
title: Davies et al heat stress data

description: Data includes fresh and dry weight , FvFm measurements and Heat shock protein relative expressions following a heat wave for 6 grass species.  Data includes replicates of control plants, droughted plants, heated plants and heated and droughted plants.
DOI: 10.5061/dryad.14ks803/1
title: erisor_code
DOI: 10.5061/dryad.14ks803/2
title: ERISOR_S2_L002_R1_001.fastq.gz_replace
DOI: 10.5061/dryad.14ks803/3
title: ERISOR_NoIndex_L006_R1_001.fasta.gz_replace
DOI: 10.5061/dryad.20k3fj0/1
title: COI Alignment Echinometra sp.

description: Eight Echinometra COI sequences were included in this alignment; E. sp. C, E. oblonga, E. sp. A, E. mathaei, E. sp. EZ, our sample, the COI sequence extracted from the published E. mathaei mitogenome (denoted with an asterisk), and E. lucunter as an outgroup. We used a MAFFT alignment and an E-INS-i algorithm to align COI sequences (441 column nucleotide alignment) in Geneious v11.1.4. Accession numbers are to the right of the species name.
DOI: 10.5061/dryad.20k3fj0/2
title: Maximum likelihood tree Echinometra species COI

description: Eight Echinometra COI sequences were included in our Maximum likelihood tree (ML); E. sp. C, E. oblonga, E. sp. A, E. mathaei, E. sp. EZ, our sample, the COI sequence extracted from the published E. mathaei mitogenome (denoted with an asterisk), and E. lucunter as an outgroup. The published E. mathaei mitogenome COI sequence is most closely grouped with the E. sp. EZ sequences. In order to generate the ML tree, we used a MAFFT alignment and an E-INS-i algorithm to align COI sequences (441 column nucleotide alignment) in Geneious v11.1.4. MEGA v7.0.21 was used to determine that the best fit model for the ML tree construction was K2+G. The ML tree was constructed in the PhyML v.3.0 plugin in Geneious v11.1.4.  The numbers above the branches specify bootstrap percentages (1,000 replicates) and accession numbers are to the right of the species name. The sequence alignment used to generate this tree is also included in this data package submission.
DOI: 10.5061/dryad.20k3fj0/3
title: SNP table

description: Table includes SNPs that differentiate our Echinometra sp. EZ mitogenome from the published Echinometra mathaei mitogenome. Table includes polymorphism type, the base pair found in each respective mitogenome for that SNP position, the numerical position of the SNP in the mitogenome, and mitochondrial region the SNP is found in.
DOI: 10.5061/dryad.20k3fj0/4
title: Figure 1: Complete mitogenome sequence alignment

description: The sequence alignment used to generate the maximum likelihood (ML) tree (figure 1) with six Echinoidea species: Strongylocentrotus purpuratus (accession number: X12631.1), Lytechinus variegatus (NC_037785.1), Heterocentrotus mammillatus (NC_034768.1), Hemicentrotus pulcherrimus (NC_023771.1), Echinometra mathaei (NC_034767.1), Arbacia lixula (NC_001770.1), and one Holothuroidea as an outgroup: Holothuria forskali (FN562582.1). We used a MAFFT alignment (16,520 column alignment) with the E-INS-i algorithm implemented in Geneious v11.1.4.
DOI: 10.5061/dryad.2b6039d/1
title: Figure S1

description: Figure S1. Psittacosaurus lujiatunensis landmark figures showing landmarks (numbered) and semi-landmark curves (red) for the (A) scapula, (B) humerus in cranial view, (C) humerus in medial view, (D) humerus in caudal view, (E) ilium, (F) femur in cranial view, and (G) femur in caudal view. Scale = 25 mm.
DOI: 10.5061/dryad.2b6039d/2
title: Figure S2

description: Figure S2. Red-tailed hawk (Buteo jamaicensis) landmark figures showing landmarks (numbered) and semi-landmark curves (red) for the (A) scapula, (B) humerus in cranial view, (C) humerus in medial view, (D) humerus in caudal view, (E) ilium, (F) femur in cranial view, and (G) femur in caudal view. Scale = 25 mm.
DOI: 10.5061/dryad.2b6039d/3
title: Figure S3

description: Figure S3. American alligator (Alligator mississippiensis) landmark figures showing landmarks (numbered) and semi-landmark curves (red) for the (A) scapula, (B) humerus in cranial view, (C) humerus in medial view, (D) humerus in caudal view, (E) ilium, (F) femur in cranial view, and (G) femur in caudal view. Scale = 50 mm.
DOI: 10.5061/dryad.2b6039d/4
title: Figure S4

description: Figure S4. White-tailed deer (Odocoileus virginianus) landmark figures showing landmarks (numbered) and semi-landmark curves (red) for the (A) scapula, (B) humerus in cranial view, (C) humerus in medial view, (D) humerus in caudal view, (E) ilium, (F) femur in cranial view, and (G) femur in caudal view. Scale = 50 mm.
DOI: 10.5061/dryad.2b6039d/5
title: Figure S5

description: Figure S5. Principal component analysis of humeri (cranial view) showing the relative divergence between left and right humeri (cranial view) in morphospace for P. lujiatunensis (A), Alligator (C), and Buteo (D). Each individual is colored with a line connecting the right and left humeri (cranial view) for P. lujiatunensis and the first five specimens are given for the extant taxa, which were randomly selected. Bones were measured three times each for inclusion in the error analysis so one animal is made up of six individual points, three for the right humerus and three for the left. To identify how shape trends were affected by removing the asymmetric component of variation, we plotted thin plate splines of the symmetric component of variation for P. lujiatunesis next to thin plate splines for the total variation (B).
DOI: 10.5061/dryad.2b6039d/6
title: Figure S6

description: Figure S6. Principal component analysis of humeri (medial view) showing the relative divergence between left and right humeri (medial view) in morphospace for P. lujiatunensis (A), Alligator (C), and Buteo (D). Each individual is colored with a line connecting the right and left humeri (medial view) for P. lujiatunensis and the first five specimens are given for the extant taxa, which were randomly selected. Bones were measured three times each for inclusion in the error analysis so one animal is made up of six individual points, three for the right humerus and three for the left. To identify how shape trends were affected by removing the asymmetric component of variation, we plotted thin plate splines of the symmetric component of variation for P. lujiatunesis next to thin plate splines for the total variation (B).
DOI: 10.5061/dryad.3qq5bm7/7
title: Extended Data Figure - Imaging

description: This folder contains raw imaging dataset supporting Extended Data Figures of this study.
DOI: 10.5061/dryad.413tm83/17
title: Figure 6C
DOI: 10.5061/dryad.413tm83/18
title: Figure 6–figure supp1
DOI: 10.5061/dryad.413tm83/19
title: Figure 6–figure supp2.
DOI: 10.5061/dryad.413tm83/21
title: FIgure 7 and supp
DOI: 10.5061/dryad.42075m1/1
title: GenAIEx data_working file_Kuwi, S.O

description: The leaf samples were originally collected from natural population in Tanzania
DOI: 10.5061/dryad.53m6f5n/1
title: Rubin et al. - behavioral data sheets

description: Behavioral data files: Bat-moth interactions, kinematics and echolocation
DOI: 10.5061/dryad.5c38fv8/2
title: SCFM project - Phenotypes and morphology of evolved and clinical isolates

description: See description for SCFM project - Phenotypes of all evolved isolates. This file contains the same data along with the colony morphology of each isolate. Below the evolved isolates are traits of 24 clinical isolates (described in Schick and Kassen 2018).
DOI: 10.5061/dryad.5c38fv8/3
title: R scripts for data analysis

description: This folder contains 5 R scripts for analysis of data in this publication. At the top of each script is a description of what the script is for and the data file used.
DOI: 10.5061/dryad.63s8h/1
title: Otter_tg_code

description: Main code for analyses. Run this file in R. Note: May require installation of additional R package dependencies.
DOI: 10.5061/dryad.63s8h/2
title: Otter_tg_Functions

description: Custom functions used by Otter_tg_code. Keep this file in the same working directory
DOI: 10.5061/dryad.63s8h/3
title: Data Prep

description: Data preparation and variable creation code needed for Otter_tg_code. Keep in the same working directory
DOI: 10.5061/dryad.63s8h/4
title: otter_tg_dataset

description: Primary dataset
DOI: 10.5061/dryad.7b423q5/1
title: Couzens&Prideaux_dryad_pack

description: Compressed directory containing data files (.csv,.txt) and R script files.
DOI: 10.5061/dryad.b8m8g7s.2
title: Data from: Feeding ecology underlies the evolution of cichlid jaw mobility
DOI: 10.5061/dryad.b8m8g7s.2/1.2
title: Landmark data for cichlid motion shapes

description: Landmark data for cichlid motion shapes. File is in .tps format, which can be opened in the tps series of morphometric programs as well as the package geomorph in R (with the readland.tps function). Note that scale is not provided in this file and must be implemented separately, with the "scale" factor in the accompanying "strike info.txt" file.
DOI: 10.5061/dryad.b8m8g7s.2/2.2
title: Sliding semilandmarks

description: File designating which cranial landmarks will be treated as "sliding semilandmarks" during shape alignment.
DOI: 10.5061/dryad.b8m8g7s.2/3.2
title: Feeding Strike Information

description: Table with information associated with each shape from feeding motions included in the "cichlid feeding LM.TPS" file.
DOI: 10.5061/dryad.b8m8g7s.2/4.2
title: Sample GM motion code

description: A sample of the code used to measure the magnitude of strike kinesis and kinematic efficiency. Files utilized in code: "cichlid feeding LM.TPS", "sliding_semi.txt", and "strike info.txt".
DOI: 10.5061/dryad.cm736/1
title: Fusani et al - Manacus vitellinus microsatellite allele frequencies

description: Allele frequencies at 8 microsatellite loci in adult male, females and juvenile male Manacus vitellinus
DOI: 10.5061/dryad.d9r3321/1
title: Morphology data from 9 populations

description: Body and genital sizes of males and females in 9 study populations of Carabus insulicola. MBL, male body length; CPL, copulatory piece length; FBL, female body length; VAL, vaginal appendix length.
DOI: 10.5061/dryad.d9r3321/2
title: Genetic data from 9 populations

description: Microsatellite genotypes of individuals in 9 study populations of Carabus insulicola. Analyzed 6 loci are based on Takami and Katada (2001) Mol Ecol Notes. Data are arranged in GenAlEx format.
DOI: 10.5061/dryad.d9r3321/3
title: Experimental data from 2 populations

description: Morphological and behavioral data of individuals from 2 study populations (Aobayama and Ohshima) of Carabus insulicola.
DOI: 10.5061/dryad.f78fc08/1
title: Spider resting interaction networks

description: Edge list of spider resting interactions. 24 groups of 10 adult female spiders, from 3 source colonies. Groups had one of three boldness compositions: all bold spiders, all shy spiders, and 9 shy individuals with one bold individual. Overall, these groups contained more initially shy individuals than bold individuals because this represents the spiders’ natural boldness distribution. We manually recorded the physical contacts among spiders three times a week, during the day, while spiders are inactive for long periods of time. Therefore, we refer to these interactions as ‘resting interactions’ and define an interaction as a physical contact between any body parts of two spiders, when the colony is not active. Colony activity is minimal in the lab (initial web construction and collective predation when fed) and most of the time spiders are resting. Therefore, observing their interactions every 2-3 days samples most social interactions. We used the interactions to construct unweighted (binary), undirected (symmetrical), networks for each spider group during each observation. Spiders were collected from roadside Acacia trees in the Northern Cape of South Africa in March 2016. Groups were housed in large round containers (11cm diameter, 10cm depth) with a vertical wire mesh (a 5x5cm sheet) to allow the spiders to build both a retreat and a capture web. Experimental observations were made during June-August, 2016.
DOI: 10.5061/dryad.f78fc08/2
title: Spider boldness measurements

description: Each spider’s boldness was measured once a week a total of 7 times, using an assay that recorded the recovery of a spider from exposure to air puffs, which mimic the approach of an avian predator. After placing spiders individually in a plastic container (15x15cm) we waited for 30sec until the spiders were acclimated and stopped moving around the arena. We then administered two puffs of air to the anterior prosoma using an infant nose-cleaning bulb. Spiders react to the air puffs by huddling, i.e. pulling their legs under their body, and remaining motionless. Boldness was measured as the latency to resume movement and move one body length. Because bolder individuals resume movement faster, the latency to resume movement was subtracted from the maximum duration of the procedure (600s) to create a metric that increases with boldness. We designated as ‘shy’ those individuals with a latency to resume movement of 400-600s (boldness of 0-200), while ‘bold’ individuals were those with a latency to resume movement of 0-200s (boldness of 400-600).
DOI: 10.5061/dryad.fm9284v/4
title: Atrazine Transport to Epikarst_Daily Flow-weighted Concentrations

description: Computed daily flow-weighted concentrations for six herbicides and two metabolites at the WF-1 site.
DOI: 10.5061/dryad.fm9284v/5
title: Atrazine Transport to Epikarst_Daily Loads

description: Computed daily loads for six herbicides and two metabolites at the WF-1 site.
DOI: 10.5061/dryad.g59r413/1
title: Interspecific competition between larvae of two newt species

description: The influence of heterospecific interactions on initial total length (mean per tank), final total length, somatic growth rate, final developmental stage, proportion of injured individuals (damaged tail fins or missing limbs), and proportion survived in larvae of two newt species, Ichthyosaura alpestris and Lissotriton vulgaris.
DOI: 10.5061/dryad.g59r413/2
title: Susceptibility to predation in larvae of two newt species

description: Proportion of injured and killed individuals after 24 h exposure to a predator (dragonfly larva) in two newt species.
DOI: 10.5061/dryad.g5f7v1j/1
title: Behavioral data for learning and memory scores, subjective ratings for the main learning condition

description: This file contains the mean learning and memory scores (percentage of words learned on Day 1, Total number of words remembered on Day 2, Recognition rate on Day 2) and subjective ratings (Pleasantness, Arousal, Confidence) for the main learning condition (M+; the condition in which participants could actually learn the meaning of a word using the congruent context provided by two sentences). The file also contains demographic data (age, sex, weight) and the results of the Physical Anhedonia Scale (PAS)
DOI: 10.5061/dryad.kc835.5
title: Data from: Genome sequence of M6, a diploid inbred clone of the high glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity.
DOI: 10.5061/dryad.kc835.5/14.5
title: Readme.txt
DOI: 10.5061/dryad.kc835.5/2.5
title: 523_3_assembly_ALLPATHS_v4.1.fasta

description: Genome assembly of S. chacoense M6, containing 8,260 scaffold sequences
DOI: 10.5061/dryad.m7d9414/1
title: Fine-root production, mortality and standing crop

description: The worksheet titled "ProdMortCrop" includes average species fine-root production, mortality and standing crop by date. The worksheet titled "Info" includes data column descriptions.
DOI: 10.5061/dryad.m7d9414/2
title: fine-root lifespan

description: The worksheet titled "Survival" includes lifespan for individual roots appearing in a specific frame of  minirhizotron tubes. 
 Each root includes appearance date, disappearance date (except censored), depth, appearance length and appearance diameter information. The worksheet titled "Info" includes data column descriptions.
DOI: 10.5061/dryad.m7d9414/3
title: MSU ROOTS output

description: Individual root observations including root depth, length and diameter over more than two years.  The  "Tristis0996" worksheet includes data for hybrid poplar (Populus tristis X P. balsamifera cv. ‘Tristis no. 1’). The "PINE1196" worksheet includes  data for pine (Pinus resinosa).  The "Info" worksheet  includes data column descriptions.
DOI: 10.5061/dryad.m7d9414/4
title: Soil respiration

description: The data in the "RS.wk1" worksheet includes soil respiration collected at each minirhizotron tube during root observation sessions.  The "mean" worksheet includes averages and standard errors of the four measurement locations presented in "RS.wk1".
DOI: 10.5061/dryad.mk968sm/1
title: Microsatellite data, Rhinanthus angustifolius
DOI: 10.5061/dryad.r765jb8/1
title: conduits3

description: Conduit diameters for gymnosperm and Angiosperm species in Chile. For species and sampling details please refer to the manuscript.
DOI: 10.5061/dryad.r765jb8/2
title: WD and stem NSC G vs A

description: Density and concentration of non-structural carbohydrates of heartwood and sapwood in angiosperms and gymnosperms species of southern South América
DOI: 10.5061/dryad.r765jb8/3
title: NSC different organs

description: Concentrations of total non-structural carbohydrates, starch, and soluble sugars in fine and coarse roots, twigs, branches, stem sapwood, and leaves, in angiosperms and gymnosperm species of southern South América. For species details please refer to the manuscript.
DOI: 10.5061/dryad.rp257gt/1
title: microsatellite genotypes table

description: Genotypes for 374 crocodile individuals obtained in the study based on 12 polymorphic microsatellites loci
DOI: 10.5061/dryad.t6q1k5v/1
title: Tamburini et al. 2018 Dataset

description: Plant biomass and individual survival.
DOI: 10.5061/dryad.v046c7g/1
title: Simulation output data

description: Simulation data using benchmark parameters and from all three scenarios as described in the paper. Contains data for generations 15001-20000 of 20 simulations for each scenario.
DOI: 10.5061/dryad.v046c7g/2
title: Simulation code

description: Python code (Python 3) used to run all simulations discussed in the paper. The code is fully commented and can be executed as is.
DOI: 10.5061/dryad.v056r5h/1
title: Raw data on species population size and breeding success per colony per year
DOI: 10.5061/dryad.v056r5h/2
title: Cleaned data for analysing population trends
DOI: 10.5061/dryad.v056r5h/3
title: Cleaned data for analysing productivity trends
DOI: 10.5061/dryad.v056r5h/4
title: Dataset for analysing associations with Arctic skua population trends
DOI: 10.5061/dryad.v056r5h/5
title: Dataset for analysing associations with Arctic skua productivity
DOI: 10.5061/dryad.v056r5h/6
title: SAS code for analysing population trends
DOI: 10.17632/5fck5k7j4x.1
title: Data for: Robust Model Predictive Control for Optimal Energy Management of Island Microgrids with Uncertainties

description: the primary data used in the simulation
DOI: 10.17632/jys6ps289p.1
title: Data for: The effect of low stress triaxialities and load paths on ductile fracture simulations of large shell structures

description: This contains all input files needed to run MK-analysis presented in the paper. This example applies for alfa=0.5 and fii=90 degrees, see paper for details. For different stress states or principal stress direction respective values in the *.for file need to be changed. MASTER.inp - Abaqus input file that is runned. Equation.inp - Called by MASTER.inp. Contains linear constraint equations that constrain each boundary node based on the nodal displacement on the opposite edge and phantom node displacement. NODES.inp - Called by MASTER.inp. Gives the nodal coordinates of the unit cell model. vdisp-NODES-imp.for - Example user defined loading file called by Abaqus along with MASTER.inp.
DOI: 10.5061/dryad.2b6039d/10
title: Figure S10

description: Figure S10. Principal component analysis of femora (caudal view) showing the relative divergence between left and right femora (caudal view) in morphospace for P. lujiatunensis (A), Alligator (C), and Buteo (D). Each individual is colored with a line connecting the right and left femora (caudal view) for P. lujiatunensis and the first five specimens are given for the extant taxa, which were randomly selected. Bones were measured three times each for inclusion in the error analysis so one animal is made up of six individual points, three for the right humerus and three for the left. To identify how shape trends were affected by removing the asymmetric component of variation, we plotted thin plate splines of the symmetric component of variation for P. lujiatunesis next to thin plate splines for the total variation (B).
DOI: 10.5061/dryad.2b6039d/11
title: Supplemental Tables 1–9

description: See Main Text For Table Descriptions
DOI: 10.5061/dryad.2b6039d/7
title: Figure S7

description: Figure S7. Principal component analysis of humeri (caudal view) showing the relative divergence between left and right humeri (caudal view) in morphospace for P. lujiatunensis (A), Alligator (C), and Buteo (D). Each individual is colored with a line connecting the right and left humeri (caudal view) for P. lujiatunensis and the first five specimens are given for the extant taxa, which were randomly selected. Bones were measured three times each for inclusion in the error analysis so one animal is made up of six individual points, three for the right humerus and three for the left. To identify how shape trends were affected by removing the asymmetric component of variation, we plotted thin plate splines of the symmetric component of variation for P. lujiatunesis next to thin plate splines for the total variation (B).