cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bk78q/3
title: Phylogeny_of_Typhlocharis_BEAST_dated_tree_(Rates_ULN_bd)_Complete

description: Dated phylogenetic tree obtained with BEAST 1.8.1 (Drummond et al. 2012). For the analyses the original concatenated dataset was collapsed to haplotypes and the outgroups were excluded, resulting in a dataset of 330 terminals. We used as calibration prior for each gene an uniform function on the mean substitution rate encompassing the 95% confident interval values obtained for the same DNA fragments (cox1-a, cox1-b, rrnL, LSU and SSU genes) in the confamilial genus Carabus (Andújar et al., 2014, 2012) and the tribe Anillini (Andújar et al., 2016) (Table 1 in original paper). We additionally applied a gamma prior on the root age for the most recent common ancestor (crown group) of Typhlocharina. We used TreeStat 1.6.1 (Rambaut & Drummond 2010) to recover the node age of the ancestor of Typhlocharina from the sample of the MCMC search of the BEAST analysis favoured in Andújar et al. (2016), and we used the “fitdistr” option of the R package MASS to obtain the values of a gamma function adjusting the distribution of sampled ages, thus accounting for the uncertainty associated to the age estimations (Table 1 on the original paper). 
Analyses were conducted under the model of substitution best fitting to each gene and codon partition as above, and were run for 50 million generations sampling one tree in every 5,000 generations. In the molecular clock settings gene partitions were uncorrelated, and two independent analyses were conducted  applying an uncorrelated lognormal (ULN) to all genes. Analyses were conducted under  a Birth-Death model (BD) and with the inclusion of the constraint on the age for the ancestor of Typhlocharina (Table 1 on the original paper)
DOI: 10.5061/dryad.bk78q/4
title: Phylogeny_of_Typhlocharis_BEAST_dated_tree_(Rates_ULN_bd)_Pruned_to_species

description: Time calibrated tree pruned to keep a single tip branch per species.
DOI: 10.5061/dryad.fp001/1
title: Hethke_et_al_2017_S1-14
DOI: 10.5061/dryad.g9k46.2
title: Data from: Evaluating the accuracy of biodiversity changes through geological times: from simulation to solution
DOI: 10.5061/dryad.g9k46.2/1.2
title: Supplementary results S1-S21

description: Supplementary results and figures S1-S21 for Evaluating the accuracy of biodiversity changes through geological times: from simulation to solution
DOI: 10.5061/dryad.g9k46.2/2.2
title: R function. Evaluating the accuracy of biodiversity changes through geological times

description: Based on a presence/absence matrix, the function allows the back-transformation of this discretized dataset into a reconstructed continuous-time dataset. The function generates plots of taxonomic richness and Foote’s taxonomic rates variation through time and a list of the 3 different (richness, origination p rate and extinction q rate) datasets and the associated 95 % confidence interval.
DOI: 10.5061/dryad.g9k46.2/3.2
title: Supplementary Tables S1-S12

description: Pearson correlation coefficient between original, discretized and reconstructed richness and rates time series : Supplementary Tables S1-S12
DOI: 10.5061/dryad.g9k46.2/4.2
title: ContinuousTime.random
DOI: 10.5061/dryad.j4h5c/1
title: Nitrogen experiment data
DOI: 10.5061/dryad.j4n09/10
title: rawspecimens_202_R_1

description: Landmark coordinate data in 3D of the right valve (202 landmarks) for 859 specimens of scallops. Coordinate data are raw coordinates digitised from 3D surface models, first of two replicates. Specimen IDs correspond to file "ID classifier all.csv".
DOI: 10.5061/dryad.j4n09/3
title: ID classifier all

description: Classifier file to relate specimen IDs to species. Corresponds to specimen IDs in the following files: avspecimen_coords_L_ProcLR.tps
avspecimen_coords_L.csv
avspecimen_coords_R_ProcLR.tps
avspecimen_coords_R.csv
rawspecimens_202_L_1.tps
rawspecimens_202_L_2.tps
rawspecimens_202_R_1.tps
rawspecimens_202_R_2.tps
DOI: 10.5061/dryad.j4n09/4
title: 86sp scallop tree

description: Phylogenetic tree (time calibrated) for 86 species of scallop.
DOI: 10.5061/dryad.j4n09/5
title: Spec classifier_ALL

description: Classifier file to relate species IDs to phylogenetic tree. See Supplementary Materials Table S1 of paper for full list of species.
DOI: 10.5061/dryad.j4n09/6
title: avspecimen_coords_L_ProcLR

description: Landmark coordinate data in 3D of the left valve (202 landmarks) for 699 specimens of scallops. Coordinate data are Procrustes residuals, from a Procrustes fit of both lefts and x-flipped rights. Specimen IDs correspond to file "ID classifier all.csv".
DOI: 10.5061/dryad.j4n09/7
title: avspecimen_coords_R_ProcLR

description: Landmark coordinate data in 3D of the right valve (202 landmarks) for 699 specimens of scallops. Coordinate data are Procrustes residuals, from a Procrustes fit of both lefts and x-flipped rights. Specimen IDs correspond to file "ID classifier all.csv".
DOI: 10.5061/dryad.j4n09/8
title: rawspecimens_202_L_1

description: Landmark coordinate data in 3D of the left valve (202 landmarks) for 933 specimens of scallops. Coordinate data are raw coordinates digitised from 3D surface models, first of two replicates. Specimen IDs correspond to file "ID classifier all.csv".
DOI: 10.5061/dryad.j4n09/9
title: rawspecimens_202_L_2

description: Landmark coordinate data in 3D of the left valve (202 landmarks) for 933 specimens of scallops. Coordinate data are raw coordinates digitised from 3D surface models, second of two replicates. Specimen IDs correspond to file "ID classifier all.csv".
DOI: 10.5061/dryad.mp0df/1
title: Average egg pattern energies

description: Data in this file were used in the egg pattern discriminate function analysis to determine if the Pacific Koel exhibited host-specific egg mimicry in egg pattern. This data includes eggs from the CSIRO museum in Canberra, ACT, Australia and fresh from the field in Sydney, NSW and Canberra, ACT. Specific information about each clutch can be found in the appendix of the manuscript and details about this analysis can be found in the Methods section of the manuscript.
DOI: 10.5061/dryad.mp0df/2
title: Egg size analyses data

description: This workbook contains three sheets all related to the egg size analyses. The first sheet contains average egg volume for all koel and host eggs used in an ANOVA analysis. The second sheet is data that was used in the first linear model mentioned in the manuscript, which was run to determine if koel egg volume was predicted by host species. The third sheet is data that was used in the second linear model, which was run to determine if koel egg volume was predicted by host egg volume. Eggs were from the CSIRO museum in Canberra, ACT, Australia and fresh from the field from Sydney, NSW and Canberra, ACT. For more information about each clutch, please see the supplemental material in the manuscript. For more information about the analyses, please see the Methods and Results sections in the manuscript.
DOI: 10.5061/dryad.p48k7/1
title: Seed sowing experiment

description: Data recording counts from seed sowing experiment of 25 Brassica species in Canterbury NZ. Also includes biotic and abiotic covariate data.
DOI: 10.5061/dryad.p48k7/2
title: buried_germ

description: Seed survival data, after burial for 1 year. Wholed = dead seed, wholea =  alive seed
DOI: 10.5061/dryad.pc830/1
title: Nicrophorus_carcassmicrobiome_analysis

description: This contains files used in the analysis of the Nicrophorus vespilloides microbiome.It contains denoised, quality filtered reads for bacterial (Nvesp_16S_seqs.fna) and fungal (Nvesp_ITS_seqs.fna) datasets, metadata mapping files (16S_metadata.txt and ITS_metadata.txt), representative sequence sets for all OTUs (16S_rep_set.fna and ITS_repset.fasta) and the final OTU tables (16S_otutable.csv and ITS_otutable.csv).
DOI: 10.5061/dryad.q3f2j/1
title: LARNT data

description: Data for LARNT paper
DOI: 10.5061/dryad.s156b/1
title: GavishEtAl2017Dryad
DOI: 10.5061/dryad.s3953/4
title: Mosquito wing size data

description: Wing sizes of individual male (M) and female (F) mosquitoes emerging from experimental pots (1-6) per day (1-31) during a given month (June = 6, July = 7, Sep = 9, October = 10) on sites (1-9) of different land uses (urban, suburban, and rural) and across different seasons (block 1 = summer; block 2 = fall).
DOI: 10.5061/dryad.s3953/5
title: Daily adult emergence data

description: The number (Num_Em) and the cumulative number (Cum_Em) of adult mosquitoes emerging per day (1-31) across four months (June = 6, July = 7, September = 9, October = 10) and two seasons (Block 1 = summer, Block 2 = fall) from experimental pots (1-6) located on 9 different sites of different land uses (urban, suburban, and rural).
DOI: 10.5061/dryad.s3953/6
title: Intrinsic population growth rate (r) data

description: We estimated the instrinsic population growth rate for each experimental pot (1-6) across 9 sites (1-9) of varying land uses (urban, suburban, and rural) and across two seasons (block 1 = summer; block 2 = fall). Intrinsic growth rates were estimated from using methods outlined in Livdahl TP, Willey MS. Prospects for an invasion: competition between Aedes albopictus and native Aedes triseriatus. Science. 1991;253(5016):189-91.
DOI: 10.5061/dryad.s3953/7
title: Digitized data from Lounibos et al. 2002

description: This file includes wing length and egg production in the first gonotrophic cycle digitized from Lounibos LP, Suarez S, Menendez Z, Nishimura N, Escher RL, O'Connell SM, et al. Does temperature affect the outcome of larval competition between Aedes aegypti and Aedes albopictus? J Vector Ecol. 2002;27(1):86-95.
DOI: 10.5061/dryad.s3953/8
title: Uncertainty Analysis Code html

description: This is a html file describing the code we used in R for our uncertainty analysis and vectorial capacity estimations.
DOI: 10.5061/dryad.s3953/9
title: Uncertainty Analysis Code Rmd

description: This is the actual code in R markdown of our uncertainty analysis and vectorial capacity estimations.
DOI: 10.5061/dryad.tj1ss/1
title: Eucalyptus microcarpa SNP dataset

description: VCF file containing 4218 SNPs for 580 Eucalyptus microcarpa samples used in climate adaptation and associated analyses
DOI: 10.5061/dryad.v475g/1
title: Trait-CWMs From Guisane Valley in the French Alps

description: The file  contains the necessary data to repeat the analyses presented in the article "Integrating correlation between traits improves spatial predictions of plant functional composition". The first column "plotID" contains an identifier for each plot. The following four columns list the centered values of community weighted means of the four analyzed traits, where "height" stands for vegetation height, "seedm" stands for seed mass, "ldmc" stands for leaf dry matter content, and "sla" stands for specific leaf area. The remaining four columns contain the environmental data that characterizes the plots, where "precip" stands for precipitation, "relh" stands for relative humidity, "mintemp" stands for minimal temperature, and "topo" stands for topography. Be aware that all data are centered and scaled such that each column's mean is zero, their standard deviation is one.
DOI: 10.5061/dryad.1411n/1
title: Lake location, zooplankton species abundance and body size data

description: This file contains the raw data used in all analyses. Within the file is the zooplankton species composition from 2011 (relative abundance) and historical samples (relative abundance and presence/absence). In addition, body length data (micrometers) for a subset of the lakes is present. Finally, geographic coordinates for each lake (latitude/longitude) are in the data file.
DOI: 10.5061/dryad.28524/1
title: lizard nest environment and its influence on hatchling fitness
DOI: 10.5061/dryad.29710/1
title: Ankutowicz_and_Laird_data

description: Data from Ankutowicz and Laird, "Offspring of older parents are smaller—but no less bilaterally symmetrical—than offspring of younger parents in the aquatic plant Lemna turionifera"; see associated README file for column-header details.
DOI: 10.5061/dryad.29710/2
title: Ankutowicz_and_Laird_R_scripts

description: R scripts accompanying Ankutowicz and Laird, "Offspring of older parents are smaller—but no less bilaterally symmetrical—than offspring of younger parents in the aquatic plant Lemna turionifera"
DOI: 10.5061/dryad.29710/3
title: otsu

description: Matlab function for image thresholding.
DOI: 10.5061/dryad.29710/4
title: seg

description: Matlab function for image segmentation.
DOI: 10.5061/dryad.29710/5
title: filt

description: Matlab function for image filtering.
DOI: 10.5061/dryad.29710/6
title: floodfill

description: Matlab function for flood-filling an image.
DOI: 10.5061/dryad.29710/7
title: bound

description: Matlab function for boundary detection of an image.
DOI: 10.5061/dryad.29710/8
title: csm_mirror

description: Matlab function for finding the continuous symmetry measure (CSM) associated with bilateral (/mirror) symmetry in an image.
DOI: 10.5061/dryad.2k80f/1
title: JoE Data for Dryad

description: Turf and Sediment average heights over time
DOI: 10.5061/dryad.2tv2s/1
title: Data and analysis script for GAL screen
DOI: 10.5061/dryad.2tv2s/2
title: Data and analysis script for PHO screen
DOI: 10.5061/dryad.2tv2s/3
title: Data and analysis script to measure cycloheximide effect
DOI: 10.5061/dryad.541q2/1
title: Zokan 2015 Savannah River Site Zooplankton Data

description: The data associated with Marcus Zokan's dissertation (2015) on zooplankton communities of ephemeral wetlands (Carolina Bays) at the Savannah River Site.
DOI: 10.5061/dryad.5k67r/1
title: network_model_NEURON

description: Package containing Python and NEURON code used for simulations. Remember to compile .mod file . The code requires a community detection module available at https://bitbucket.org/taynaud/python-louvain. Up to date versions can be found at https://github.com/dlonardoni/Cell-Culture-Model.
DOI: 10.5061/dryad.5k67r/2
title: Spontaneous spiking activity recordings

description: The data consist of the spiking activity of hippocampal cell cultures recorded with the high density 4096 electrodes MEA device. File format: Each file contains a matrix made two rows and N columns (N is the number of spikes). The second row corresponds to the time stamps of the spiking activity and the first one to the corresponding electrode ID (numbered from 1 - top left of the recording matrix - to 4096 - bottom right of the recording matrix).
DOI: 10.5061/dryad.5k67r/3
title: BIC_recordings

description: The data consist of the spiking activity of hippocampal cell cultures recorded with the high density 4096 electrodes MEA device. The following protocol was repeated for each chip 1. control: spontaneous activity is recorded 4. APV: spontaneous activity is recorded under APV. File format: Each file contains a matrix made two rows and N columns (N is the number of spikes). The second row corresponds to the time stamps of the spiking activity and the first one to the corresponding electrode ID (numbered from 1 - top left of the recording matrix - to 4096 - bottom right of the recording matrix).
DOI: 10.5061/dryad.5k67r/4
title: APV recordings

description: The data consist of the spiking activity of hippocampal cell cultures recorded with the high density 4096 electrodes MEA device. The following protocol was repeated for each chip 1. control: spontaneous activity is recorded 4. bicuculline: spontaneous activity is recorded under bicuculline. File format: Each file contains a matrix made two rows and N columns (N is the number of spikes). The second row corresponds to the time stamps of the spiking activity and the first one to the corresponding electrode ID (numbered from 1 - top left of the recording matrix - to 4096 - bottom right of the recording matrix).
DOI: 10.5061/dryad.5q7k4/1
title: Replicate number, time and X-Y coordinates of attacks

description: Time (hours since experiment beginning) and X-Y coordinates (in centimeters) of Ips typographus attacks collected on 8 fallen trees (Picea abies) on the field (Libin, Belgium). Each tree is separated into a bottom (odd replicate number) and a top replicate (even replicate number); successive each pair of odd and even number are part of the same tree.
DOI: 10.5061/dryad.6h5p0/1
title: Data from: Two-thirds of global cropland area impacted by climate oscillations

description: Zip-file contains crop production and harvested areas data used in the study titled 'Two-thirds of global cropland area impacted by climate oscillations'. Detailed information of the data can be found in the related 'README.docx' file.
DOI: 10.5061/dryad.82nt3/1
title: Mecistops mtDNA

description: The file is a concatenated alignment of cyt-b (bp 1 - 927) and COI (bp 928 - 1849).
DOI: 10.5061/dryad.82nt3/2
title: Osteolaemus mtDNA

description: The file is a concatenated alignment of cyt-b (bp 1 - 621) and COI (bp 622 - 1354).
DOI: 10.5061/dryad.82nt3/3
title: Mecistops mtDNA Sample Localities

description: Geographic coordinates for each sample used in the mtDNA analysis and for sequences available in the associated fasta file.
DOI: 10.5061/dryad.84655.1
title: Data from: A whole-transcriptome approach to evaluating reference genes for quantitative gene expression studies: a case study in Mimulus
DOI: 10.5061/dryad.84655.2/10.2
title: Mg_T1

description: Mimulus guttatus inbred line CG - transcriptome T1 - complete annotated transcriptome
DOI: 10.5061/dryad.84655.2/11.2
title: Ml_T1

description: Mimulus luteus var. luteus inbred line EY7 - transcriptome T1 - complete annotated transcriptome
DOI: 10.5061/dryad.84655.2/12.2
title: Mg_T1_RPKM

description: M. guttatus inbred line CG - transcriptome T1 - RPKM expression report plus raw counts
DOI: 10.5061/dryad.84655.2/13.2
title: Ml_T1_RPKM

description: M. l. luteus inbred line EY7 - transcriptome T1 - RPKM expression report plus raw counts
DOI: 10.5061/dryad.84655.2/14.2
title: Mimulus luteus transcript IDs and sequences
DOI: 10.5061/dryad.84655.2/15.2
title: Mimulus guttatus transcript IDs and sequences
DOI: 10.5061/dryad.8pv03/1
title: light availability datafile

description: The research was conducted across 53 plots (30 m x 30 m) located in mature forests in the region of Ghent, Belgium (the ‘TREEWEB’ platform) Light transmittance was measured with hemispherical images before and after leaf expansion at four locations in each of the 53 plots. We calculated the gap light index (GLI), which is the total transmitted PAR to the forest floor as a percentage of total incident PAR above the canopy.
DOI: 10.5061/dryad.97bt8/1
title: Stroke_PoP_Data
DOI: 10.5061/dryad.c520h/1
title: Supplementary Material for RSC Open Science 23.6.2017
DOI: 10.5061/dryad.c520h/2
title: XRD data of raw lotus fibers and lotus fibers after being treated with hydrogen peroxide
DOI: 10.5061/dryad.c8f7r/1
title: Appendix 1
DOI: 10.5061/dryad.c8f7r/2
title: Appendix 2
DOI: 10.5061/dryad.c8f7r/3
title: Appendix 3
DOI: 10.5061/dryad.c8f7r/4
title: Appendix 4
DOI: 10.5061/dryad.c8f7r/5
title: Appendix 5
DOI: 10.5061/dryad.c8f7r/6
title: Appendix 6
DOI: 10.5061/dryad.c8f7r/7
title: Appendix 7
DOI: 10.5061/dryad.d24pj/1
title: Nunes and Kotanen Ecol Evol 2017
DOI: 10.5061/dryad.d3b3t/1
title: Field and flight performance data

description: Excel tables containing: a) Field and oxidative stress data, b) Flight performance data, c) A brief explanation about each column.
DOI: 10.5061/dryad.dd0b1/1
title: Cole et al. Supplemental Data

description: Character matrix and constraint for phylogenetic analysis of Priscillacrinus and other Ordovician camerates.
DOI: 10.5061/dryad.dn58p/1
title: Environmental data at sampling localities

description: [primary data file] This file contains information on five environmental variables documented at the studied sample localities
DOI: 10.5061/dryad.dn58p/2
title: Results of BayeScan

description: [output file] This file contains the results of the BayeScan analysis. This output file has been used to identify loci that are putatively under selection.
DOI: 10.5061/dryad.dn58p/3
title: Raw amplified fragment length polymorphism dataset (NA = 9)

description: [primary data file] This file contains the raw AFLP dataset with NA’s coded as '9'.
DOI: 10.5061/dryad.f4k4t/1
title: BaligaMehtaAmNat_OntoData

description: Full raw dataset used in the study. See README file for further details.
DOI: 10.5061/dryad.f81c5/1
title: Red fox immune-gene sequences

description: Red fox immune-gene sequences (2,229,152 bp) used to design the sequence capture assay.
DOI: 10.5061/dryad.f81c5/2
title: Red fox immune-gene SNPs

description: Red fox SNP variant call information.
DOI: 10.5061/dryad.f81c5/3
title: Red fox NimbleGen SeqCap EZ_probes

description: Coordinates used to design the overlapping NimbleGen SeqCap EZ probes.
DOI: 10.5061/dryad.g9k46.1
title: Data from: Evaluating the accuracy of biodiversity changes through geological times: from simulation to solution
DOI: 10.5061/dryad.g9k46.1/1.1
title: Supplementary results S1-S21

description: Supplementary results and figures S1-S21 for Evaluating the accuracy of biodiversity changes through geological times: from simulation to solution
DOI: 10.5061/dryad.g9k46.1/2.1
title: R function. Evaluating the accuracy of biodiversity changes through geological times

description: Based on a presence/absence matrix, the function allows the back-transformation of this discretized dataset into a reconstructed continuous-time dataset. The function generates plots of taxonomic richness and Foote’s taxonomic rates variation through time and a list of the 3 different (richness, origination p rate and extinction q rate) datasets and the associated 95 % confidence interval.
DOI: 10.5061/dryad.g9k46.1/3.1
title: Supplementary Tables S1-S12

description: Pearson correlation coefficient between original, discretized and reconstructed richness and rates time series : Supplementary Tables S1-S12
DOI: 10.5061/dryad.g9k46/4
title: Reconstruction algorithm : the R function
DOI: 10.5061/dryad.j4n09/11
title: rawspecimens_202_R_2

description: Landmark coordinate data in 3D of the right valve (202 landmarks) for 859 specimens of scallops. Coordinate data are raw coordinates digitised from 3D surface models, second of two replicates. Specimen IDs correspond to file "ID classifier all.csv".
DOI: 10.5061/dryad.j4n09/12
title: Sherratt et al BMC Evo Bio Asymmetry Rate MS

description: R script for the analyses of the paper.
DOI: 10.5061/dryad.jb7m1/1
title: data_bovet_2017_dryad

description: Results of the attractiveness test. Each row of the table corresponds to one judgment (one pair). 
For each pair, the rater was instructed to click on the photograph depicting the woman he found the most attractive. The position of the photograph on the screen (left or right) was randomly ascribed. Each rater had 30 distinct pairs of photographs to assess, corresponding to 60 different women. 
The outcome variable is named “Score”: this binary variable corresponds to being chosen or not for the focal woman (arbitrarily the woman presented at the left position) during the presentation of each pair.
DOI: 10.5061/dryad.k8m4v/1
title: Clinostomus elongatus ATPase6+8 sequence alignment

description: sequence alignment file of mitochondrial ATPase 6 and 8 sequences from redside dace (Clinostomus elongatus), aligned using MEGA 6
DOI: 10.5061/dryad.k9f51/1
title: Data_Puy_et_al_2017

description: Data used for the comparative analysis of two methylation experiments. DNA methylation levels and other phenotypic measurements.