cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1pk42/16
title: mechanistic_mods

description: This script defines a suite of useful functions that will be used often adapted from Sarah Orlofske & Brett Melbourne's code by Max Joseph 6/8/14

Biological models for trematode Ribeiroia ondatrae transmission of cercariae to tadpole second intermediate hosts. Each model contains a separate 'biological model' which is then combined with the stochastic component in the negative log likelihood.
DOI: 10.5061/dryad.1pk42/17
title: likelihoods

description: Negative log likelihood functions for evaluating the biological models with data and incorporating stochasticity in the distribution generally, parameters to be estimated are packed into the object p fixed parameters are named and need not be unrolled our expected values (meta) are calculated with the mechanistic model observed numbers of metacercariae are called metacerc.
DOI: 10.5061/dryad.1pk42/18
title: helpers

description: Helper functions for use with the other R code files. Contains the library information and other code needed to generate AICc results, AIC tables, and plots.
DOI: 10.5061/dryad.1pk42/8
title: Time_data

description: Raw data from the experiment varying duration of exposure. Trt is the number of R. ondatrae cercariae added. ID is the unique tadpole number. Stage is Gosner stage of the tadpole. Meta is number of metacercariae recovered. Mass is final wet mass of tadpole. SVL is snout vent length of the tadpole at the end of the experiment. TL is total length of the tadpole at the end of the experiment.
DOI: 10.5061/dryad.1pk42/9
title: Volume

description: Raw data from the experiment varying parasite number (constant parasite density, variable volume). Cerc_Number is the number of R. ondatrae cercariae added. ID is the unique tadpole number. Stage is Gosner stage of the tadpole. Meta is number of metacercariae recovered. Mass is final wet mass of tadpole. SVL is snout vent length of the tadpole at the end of the experiment. TL is total length of the tadpole at the end of the experiment. Volume is the size of the arena in liters.
DOI: 10.5061/dryad.4jn05/1
title: Teets and Hahn Cold Tolerance Data

description: The spreadsheet has two tabs. The first tab includes raw cold tolerance data for the DGRP Core 40. Each line was exposed to temperatures from -1 to -7 deg. C in 1 deg. C increments. For each line, each temperature was replicated a minimum of four times, with each replicate consisting of a vial of ~20 female flies. The second tab contains cold tolerance data and cross information for the RNAi experiment. F1 Females from each cross were tested for cold tolerance at -2, -4, and -6 deg. C. In the table to the right, the lines used for each cross are denoted. The "driver line" is the GAL4 line, while the "effector line" is the line UAS-RNAi (or control) line. The line numbers refer to Bloomington Drosophila Stock Center stock numbers.
DOI: 10.5061/dryad.8153g/1
title: mtDNA_alignment_1_allPartns.nex

description: Mitochondrial genome alignment data set 1. White rhino outgroup. All partitions.
DOI: 10.5061/dryad.8153g/2
title: mtDNA_alignment_1_reducedPartns.nex

description: Mitochondrial genome alignment data set 1. White rhino outgroup. Reduced partitions.
DOI: 10.5061/dryad.8153g/3
title: mtDNA_alignment_2_allPartns.nex

description: Mitochondrial genome alignment data set 2. Malayan tapir outgroup. All partitions.
DOI: 10.5061/dryad.8h439/1
title: supporting data on isotope composition and physiological status in Monoporeia affinis in both experiments

description: supporting data on isotope composition and physiological status in Monoporeia affinis in both experiments. see sheet "read me" for instructions
DOI: 10.5061/dryad.ch0vn/4
title: Supplementary Tables
DOI: 10.5061/dryad.ch0vn/5
title: Phylogenies and biogeographies used in simulations

description: This .zip file contains .RData objects that contain lists of length 100. For the *_tree files, each of these list entries contains a simulated phylogeny. For the *_geo files, each of these list entries contains a geography object specifying sympatry and allopatry through time (see ?CreateGeoObject in the R package RPANDA for a description of the contents of geography objects).  Together, phylogenies and geography objects were used to simulate data under character displacement using sim.divergence.geo or sim.convergence.geo in RPANDA.
DOI: 10.5061/dryad.ch0vn/6
title: Supplementary Material
DOI: 10.5061/dryad.d71b0/1
title: Field.Laboratory.Survival.Comparison.Excel.File

description: This file contains data on the survival rates (%) of replicate split-brood clutches of Chelymorpha alternans (Coleoptera: Chrysomelidae: Cassidinae) individuals. It was established to compare survival rates between developmental stadia (larvar, pupae, adult) for individuals reared under laboratory and field conditions.
DOI: 10.5061/dryad.d71b0/2
title: C.alternans.field.lab.survival.Rscript

description: This is the r script used to run the T-tests comparing survival of individuals maintained under laboratory and field conditions.
DOI: 10.5061/dryad.d8ts9.1
title: Data from: Environmental variation partitioned into separate heritable components
DOI: 10.5061/dryad.d8ts9.1/1.1
title: Supporting Table S1

description: Line mean, standard error and number of replicates per trait for all DGRP lines
DOI: 10.5061/dryad.d8ts9.1/2.1
title: Supporting Table S4

description: Top SNPs associated with V(plast), V(v.plast), V(WE), and V(AE)
DOI: 10.5061/dryad.d8ts9.2/3.2
title: Original CTmin data

description: CTmin for all five thermal rearing environments (17, 20, 23, 26, and 29 °C), with the grouping of each observation due to experimental factors, and with the indication of five major chromosomal inversions and Wolbachia infection status
DOI: 10.5061/dryad.d8ts9/3
title: Original CTmin data

description: CTmin for all five thermal rearing environments (17, 20, 23, 26, and 29 °C), with the grouping of each observation due to experimental factors, and with the indication of five major chromosomal inversions and Wolbachia infection status
DOI: 10.5061/dryad.ft3ps/1
title: PC movies

description: ZIPped folder containing .mov files showing the shape deformations along principal component axes (PC1-PC8) for our analyses at x1 magnification and x2 magnification of the observed magnitudes of shape change.
DOI: 10.5061/dryad.ft3ps/2
title: 3D labyrinth models

description: ZIPped folder containing 3D virtual models in .ply format of the endosseous labyrinth and semicircular canals. These models, and the parent microCT data are also housed at Morphosource (http://morphosource.org/Detail/ProjectDetail/Show/project_id/377)
DOI: 10.5061/dryad.ft3ps/3
title: Landmarks and semilandmarks

description: Landmark and semi landmark data used in our analyses. Abbreviations: ASC, anterior semicircular canal; PSC, posterior semicircular canal; LSC, lateral semicircular canal.
DOI: 10.5061/dryad.ft3ps/4
title: Quantitative data table

description: Flight mode classification, body mass, brachial index (BI), inter-canal plane angles (in radians), and PC scores (for PC1-PC65) used in our analyses.
DOI: 10.5061/dryad.ft3ps/5
title: Phylogenetic trees

description: Set of 100 phylogenetic trees from Jetz et al (2008; Ericson backbone) used in our analyses)
DOI: 10.5061/dryad.ft3ps/6
title: Supplementary text figures tables

description: Fig. S1. Summary of 2B-PLS results comparing multivariate flight style to PC shape axes for endosseous labyrinth morphology including outliers and including all shape axes.

Fig. S2. Summary of 2B-PLS results comparing multivariate flight style to PC shape axes for endosseous labyrinth morphology including outliers and including all shape axes except PC1.

Fig. S3. Summary of 2B-PLS results comparing multivariate flight style to PC shape axes for endosseous labyrinth morphology including outliers and including all shape axes, excluding four outlier taxa.

Table S1. Results of regressions of labyrinth inter-canal angles on body mass and BI.

Table S2. Results of regressions of positivised deviations of labyrinth inter-canal angles from 90 ° on body mass and BI. Table S3. Results of regressions of summed positivised devia- tions of labyrinth inter-canal angles from 90 ° on body mass and BI.

Table S4. Regression model comparison results for principal component PC4.

Table S5. Regression model comparison results for principal component PC5.

Table S6. Regression model comparison results for principal component PC6.

Table S7. Regression model comparison results for principal component PC7.

Table S8. Regression model comparison results for principal component PC8.

Appendix S1. Discussion of flight categories.
DOI: 10.5061/dryad.gk117/1
title: Western Blots
DOI: 10.5061/dryad.gk117/2
title: Barnes Maze
DOI: 10.5061/dryad.gk117/3
title: Buried Marbles
DOI: 10.5061/dryad.gk117/4
title: Buried Marbles
DOI: 10.5061/dryad.gk117/5
title: Cell Counts
DOI: 10.5061/dryad.gk117/6
title: Conduction Velocity
DOI: 10.5061/dryad.gk117/7
title: EZM
DOI: 10.5061/dryad.jf7np/3
title: diversification information

description: - BS_summ_div.tre = bootstrap results for medusa diversification
- ML_summ_div.tre = ML results for medusa diversification
DOI: 10.5061/dryad.kd1d4/62
title: CHELSA_bio10_13_land
DOI: 10.5061/dryad.kd1d4/63
title: CHELSA_bio10_14_land
DOI: 10.5061/dryad.kd1d4/64
title: CHELSA_bio10_15_land
DOI: 10.5061/dryad.kd1d4/65
title: CHELSA_bio10_16_land
DOI: 10.5061/dryad.kd1d4/66
title: CHELSA_bio10_17_land
DOI: 10.5061/dryad.kd1d4/67
title: CHELSA_bio10_18_land
DOI: 10.5061/dryad.kd1d4/68
title: CHELSA_bio10_19_land
DOI: 10.5061/dryad.ps534/1
title: Cod_lipid_protein

description: lipids, fatty acids, proteins in cod
DOI: 10.5061/dryad.ps534/4
title: Liver_index

description: Liver index of cod
DOI: 10.5061/dryad.q7p5j/1
title: Data tables

description: The excel file includes the data underlying the analysis of the importance of the flower form in mediating pollination effectiveness in a sexually deceptive orchid. All data is based on manipulation experiments performed in the field on Ophrys leochroma and its pollinator Eucera kullenbergi. Each sheet contains a separate dataset, abbreviations for the manipulations and the behavioral response of males are listed within each sheet. Other abbreviations: "Approach freq", refers to data regarding the frequency with which males approached flowers; "without", refers to the fact that experiments were conducted with flowers where the removed flower tissue was discarded; "with", refers to the fact that experiments were conducted with flowers where the removed flower tissue was re-attached;"Length_PS_", refers to data regarding the length of each pseudocopulation.
DOI: 10.5061/dryad.r58q7/1
title: Phylogenetic characters and taxon codings

description: List of phylogenetic characters, data matrix
DOI: 10.5061/dryad.s14m0/3
title: SNP segregation files and the custom R scripts
DOI: 10.5061/dryad.s14m0/4
title: Data_S1
DOI: 10.5061/dryad.sf211.1
title: Data from: Induced parental care in a poison frog: a tadpole cross-fostering experiment
DOI: 10.5061/dryad.sf211.1/1.1
title: Spreadsheet: Tracking data of tadpole group frogs

description: Tracking points spreadsheet of tadpole group frogs
DOI: 10.5061/dryad.sf211.1/2.1
title: Spreadsheet: Tracking data of jelly group frogs

description: Tracking points spreadsheet of tadpole group frogs
DOI: 10.5061/dryad.sf211.2/10.2
title: Photograph of A. femoralis tadpoles inside egg-jelly

description: Photograph showing A. femoralis tadpoles hatched inside egg-jelly before the tadpole adding procedure.
DOI: 10.5061/dryad.sf211.2/11.2
title: Supplementary movie 1: natural transport

description: Movie showing the cascade of behaviors involved in natural tadpole transport.
DOI: 10.5061/dryad.sf211.2/12.2
title: Supplementary movie 2: induced transport

description: Movie showing the induced tadpole transport.
DOI: 10.5061/dryad.sf211.2/7.2
title: GIS shapefile: jelly group lines

description: GIS shapefile of jelly group frog trajectory lines
DOI: 10.5061/dryad.sf211.2/8.2
title: GIS shapefile: deposition sites

description: GIS shapefile of tadpole deposition sites in the study area
DOI: 10.5061/dryad.sf211.2/9.2
title: Supplementary Table 1: induced transport per individual

description: Spatio-temporal variables of induced tadpole transport per individual.
DOI: 10.5061/dryad.t2ch6/1
title: Parenting Heritability Data and Analysis Files

description: 4 data files, a metadata file describing the columns in these files, and an analysis script file that can be used to recreate all analyses and figures.
DOI: 10.5061/dryad.t39g3/5
title: exp_2b_13C_15N_part2_harvest_macroinvertebrates
DOI: 10.5061/dryad.t39g3/6
title: exp_2b_survival_and_biomass_harvest_macroinvertebrates

description: See first tab for information
DOI: 10.5061/dryad.t39g3/7
title: exp_2b_biomass_t0_macroinvertebrates

description: See first tab for information
DOI: 10.5061/dryad.tq71j/1
title: Genotypes of microsatellites and InDels markers for Calanus spp.

description: Sheet 1: Genotypes of 10 microsatellites used for population differentiation study of Calanus finmarchicus and Calanus glacialis. Sheets 2-3: Genotypes of 6 InDels markers used for species identification of Calanus species in the North Atlantic and the Arctic Oceans.
DOI: 10.5061/dryad.ts608/1
title: Fig 3 data

description: See Readme file
DOI: 10.5061/dryad.v8dk1/1
title: Geographical location of tracked barn swallows

description: The file contains position of barn swallows Hirundo rustica (n=19). For position determination during migration cycle, we used light-level locators (type Intigeo-P55B1). Fieldwork was carried out in the period 2013-2015 in South Bohemia (48°59'6.619"N, 14°46'48.355"E), Czech Republic. For position determination we used R statistical package GeoLight 2.0.0, when we excluded the period ± 15-21 days around each equinox.
DOI: 10.17632/92vsw5bwr3.1
title: Data for: The Interaction of QRS Duration with Cardiac Magnetic Resonance Derived Scar and Mechanical Dyssynchrony in Systolic Heart Failure: Implications for Cardiac Resynchronization Therapy.
DOI: 10.5061/dryad.1pk42/19
title: fit_model

description: R code file for taking the data from each experiment and fitting them across the different transmission functions.
DOI: 10.5061/dryad.1pk42/20
title: fig2

description: R code file for creating figure 2 (Figure 1 in the final manuscript).
DOI: 10.5061/dryad.1pk42/21
title: fig3

description: R code file for creating figure 3 (Figure 2 in the final manuscript).
DOI: 10.5061/dryad.1pk42/22
title: fig4

description: R code file for creating figure 4 (Figure 3 in the final manuscript).
DOI: 10.5061/dryad.1pk42/23
title: behavior_volume2

description: R code that takes the data from the Host Behavior experiment and integrates with the other R code files to fit the models, make the AIC table, and make the parameter table.
DOI: 10.5061/dryad.1pk42/24
title: density

description: R code that takes the data from the varying parasite density experiment and integrates with the other R code files to fit the models, make the AIC table, and make the parameter table.
DOI: 10.5061/dryad.1pk42/25
title: host_number

description: R code that takes the data from the varying host density (constant volume, variable host number) experiment and integrates with the other R code files to fit the models, make the AIC table, and make the parameter table.
DOI: 10.5061/dryad.1pk42/26
title: karvonen1

description: R code that takes the data from Karvonen et al. 2003 using rainbow trout Oncorhynchus mykiss and Diplostomum spathaceum varying parasite density experiment and integrates with the other R code files to fit the models, make the AIC table, and make the parameter table.
DOI: 10.5061/dryad.1pk42/27
title: karvonen2

description: R code that takes the data from Karvonen et al. 2003 using rainbow trout Oncorhynchus mykiss and Diplostomum spathaceum varying parasite number experiment and integrates with the other R code files to fit the models, make the AIC table, and make the parameter table.
DOI: 10.5061/dryad.24s5j/1
title: VCF file for SNPs used in GEMMA analysis

description: Variant Call Format file (GZipped) for individuals used for genotype-phenotype associations. Sample ID information can be found in the electronic supplementary information on the publisher's website.
DOI: 10.5061/dryad.24s5j/2
title: Plumage association data

description: Phenotype data used for the GEMMA analysis. Columns indicate: Record#, a unique identifier, Site, with nearest city / notable location, whether this site was located in the hybrid zone or in allopatry (myrtle versus Audubon's), Lat, Long, and five plumage characters: throat, spot, line, wing, and auricular.
DOI: 10.5061/dryad.429t4/1
title: Data from tethering experiment to measure in-situ blue crab mortality as a function of structure

description: Data collected from field experiment on blue crab tethers in Wassaw Sound, Georgia.  Abbreviations of variables are as follows, Site (representing general deployment area): TC= Tybee Creek; SK= Skidaway River; RM = Romerly Marsh);  Position: on = on reef; off= off reef;  Date: deployment date in field (treated as blocking factor in analysis);  CW: Carapace width;  CL: Carapace length;  Crab Status: A=alive, D=dead;  Shark Involved?: P=predation by shark; N=no predation by shark (based on forensics evidence and best guess. All alive crabs were automatically coded as N).    To examine the mortality of blue crabs as a function of position (or habitat) , we used a generalized linear mixed effects model to analyze individual crab survival with a binary distribution and a logit link function as influenced by the fixed effect of position (i.e., on reef or off reef).  Because the response of crabs within a given deployment batch may not be fully independent, deployment replicate (i.e., date) was used as a random effect.
DOI: 10.5061/dryad.51256/2
title: SXRD data

description: The file includes the data from the SXRD experiments
DOI: 10.5061/dryad.51256/3
title: TSA data

description: The file includes the data from the TSA experiments
DOI: 10.5061/dryad.51256/4
title: CT plastic zone code

description: Matlab code for determining crack tip plastic zone
DOI: 10.5061/dryad.5t55d/1
title: HackIyengar2017 - Data Tables

description: This document contains tables of the raw numbers for cohabitation among the different trials.
DOI: 10.5061/dryad.5t55d/2
title: HackIyengar2017 - Data File

description: This Excel file contains the raw data for cohabitation among the different trials.
DOI: 10.5061/dryad.5t55d/3
title: HackIyengar2017 - Full GLM

description: This text file contains the results of the Full GLM analyses based on the data.
DOI: 10.5061/dryad.5t55d/4
title: HackIyengar2017 - Final GLM

description: This text file contains the results of the Final GLM analyses, with non-significant interactions removed, based on the data.
DOI: 10.5061/dryad.5t55d/5
title: HackIyengar2017 - Posthoc Tests

description: This text file contains the results of the Posthoc (Tukey) tests based on the GLM analyses.
DOI: 10.5061/dryad.7g1tb/1
title: Mass spectrometry data files

description: Pyrolysis GC-MS and GC-MS wax ester analysis raw datafiles for fossils and modern gland specimens
DOI: 10.5061/dryad.8153g/10
title: mtDNA_alignment_5_reducedPartns.nex

description: Mitochondrial genome alignment data set 5. Reduced equid data set for BEAST analyses. Reduced partitions.
DOI: 10.5061/dryad.8153g/12
title: mtDNA_alignment_6_reducedPartns.nex

description: Mitochondrial genome alignment data set 6. Full equid data set for synapomorphy analyses. Reduced partitions.
DOI: 10.5061/dryad.8153g/4
title: mtDNA_alignment_2_reducedPartns.nex

description: Mitochondrial genome alignment data set 2. Malayan tapir outgroup. Reduced partitions.
DOI: 10.5061/dryad.8153g/5
title: mtDNA_alignment_3_allPartns.nex

description: Mitochondrial genome alignment data set 3. Dog and ceratomorph outgroups. All partitions.
DOI: 10.5061/dryad.8153g/6
title: mtDNA_alignment_3_reducedPartns.nex

description: Mitochondrial genome alignment data set 3. Dog and ceratomorph outgroups. Reduced partitions.
DOI: 10.5061/dryad.8153g/7
title: mtDNA_alignment_4_allPartns.nex

description: Mitochondrial genome alignment data set 4. Evolutionary Placement algorithm analysis. All partitions.
DOI: 10.5061/dryad.8153g/8
title: mtDNA_alignment_4_reducedPartns.nex

description: Mitochondrial genome alignment data set 4. Evolutionary Placement algorithm analysis. Reduced partitions.
DOI: 10.5061/dryad.8153g/9
title: mtDNA_alignment_5_allPartns.nex

description: Mitochondrial genome alignment data set 5. Reduced equid data set for BEAST analyses. All partitions.
DOI: 10.5061/dryad.8v739/1
title: Longevity experiment

description: We examined the relative longevity of parental species vs. hybrid progeny. We isolated 20 female pupae of EG, iES, cES and hybrids (produced by mating EG and cES wasps in both directions) in 1.2 ml vials, and at emergence we fed the adults with a small drop of honey, and kept them at a constant temperature of 27°C. Vials were checked daily, honey was added when necessary, and the date of female death was recorded.
DOI: 10.5061/dryad.8v739/2
title: Fecundity experiment

description: We compared fecundity of 3 longstanding laboratory colonies (1st exp) and of 2 longstanding lab colonies and colonies recently established from field collected individuals (2nd exp). Female wasps were individually paired for 24 h in small vials with a conspecific male. Females were then placed individually in arenas with leaf disks bearing about 80 whitefly nymphs. The leaf disks rested on a layer of agar in ventilated 35 mm agar Petri dishes. Females were transferred to new whitefly-infested arenas every other day until day eight. At day 4, we provided females with the opportunity to mate again to avoid the risk of sperm depletion by introducing a male into the arena for 24h. Arenas were kept at 27°C, 16L:8D, and 65% RH. After females were removed on day 8, arenas were incubated for approximately 10 more days. At the end of this period, we recorded the number of progeny pupae, a proxy for adult emergence, as a measure of fecundity.
DOI: 10.5061/dryad.8v739/3
title: High Resolution Melting data

description: For each cage of each generation, we randomly selected 24 females among those stored in ethanol at the end of each generation by pipetting without observation. The number of parental species and hybrid progeny per cage per generation as identified by the High Resolution Melting assay is presented here.
DOI: 10.5061/dryad.c014p/1
title: SNP calls for all samples in VCF format (before filtering)

description: SNP call data for all samples across all Hawaiian islands, produced by Stacks in VCF format, before final filtering steps.
DOI: 10.5061/dryad.c014p/2
title: SNP calls for island of Hawaii in VCF format (before filtering)

description: SNP call data for samples from the island of Hawaii, produced by Stacks in VCF format, before final filtering steps.
DOI: 10.5061/dryad.c014p/3
title: SNP calls for island of Hawaii, final in table format

description: SNP calls in tab-separated format with rows as individual samples and columns as loci as inferred from Stacks. These are the final data that were filtered such that the minor allele frequency is greater than 0.05 and there is no more than 30% missing data at a locus. This file contains both Acacia koa and A. koaia samples; the latter were removed prior to environmental association analyses.
DOI: 10.5061/dryad.c014p/4
title: SNP calls for all samples, final in table format

description: SNP calls in tab-separated format with rows as individual samples and columns as loci as inferred from Stacks. These are the final data that were filtered such that the minor allele frequency is greater than 0.05 and there is no more than 30% missing data at a locus. This file contains both Acacia koa and A. koaia samples.
DOI: 10.5061/dryad.fb7r5/1
title: Manuscript_Supplementary Information_Dryad
DOI: 10.5061/dryad.gk117/10
title: Rictor CKO Western
DOI: 10.5061/dryad.gk117/11
title: Rictor Olig2 Open Field
DOI: 10.5061/dryad.gk117/12
title: Rotarod