cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ff18q9d/6
title: Appendix S6 - Phylogenomic trees

description: Phylogenomic trees of Papilionoidea inferred with both maximum-likelihood and Bayesian inference using 760 orthologous genes (Dataset 1) and 6,621 orthologous genes (Dataset 2).
DOI: 10.5061/dryad.fj02s0j/66
title: Supplementary Figure S2

description: Supplementary Figure S2  Support for alternative hypotheses of the sister group to emu + cassowary from phylogenomic subsampling using MP-EST (a-c), ASTRAL (d-f), and ExaML (g-i).  Plots display the mean bootstrap support for each hypothesis from 10 replicates of randomly sampled loci within each data set size category (e.g. 50–3000 loci, shown on x-axis).
DOI: 10.5061/dryad.fj02s0j/67
title: Supplementary Figure S3

description: Supplementary Figure S3  Heatmap of the number of replicates from phylogenomic subsampling that support each alternative hypothesis for the sister group to emu + cassowary at a minimum bootstrap support of 70% (a-i) and 90% (j-r), with results from each analysis method displayed in separate panels (e.g. MP-EST a-c & j-l, ASTRAL d-f & m-o, ExaML g-I & p-r).  Rows labelled H1-H4 within each panel correspond to the four alternative hypotheses outlined in the legend.  Columns within each panel labelled 50-3000 indicate the number of loci subsampled at random with replacement from all loci for each marker type.  Coloring of cells indicates the number of replicates (of 10 in total for each data set size category) that support each hypothesis at the given bootstrap cut off, corresponding to the colouring scheme outlined in the legend.
DOI: 10.5061/dryad.fj02s0j/68
title: Supplementary Figure S4

description: Supplementary Figure S4  Support for the four most common gene tree topologies for each marker type.  Median bootstrap support (a-c) and the median number of substitutions under a parsimony criterion (d-f) for branches in gene tree topologies that conflict with the species tree are shown for each marker type.  Letters below each group refer to topologies shown in (j), with numbers referring to branches labelled on those topologies.  Reference lines in (a-c) are drawn at 50% bootstrap support. (g-i) Violin plots of ΔAIC for loci belonging to each AGT category for CNEEs (part g), introns (part h), and UCEs (part i).  Values show the difference in AIC for sequence alignments given the majority rule extended consensus gene tree topology, relative to the AIC when sequence alignments are constrained to the species tree topology.  A reference line is drawn at ΔAIC(gene tree–species tree)= -2, with values beneath this cut off indicating substantially stronger support in favor of the gene tree topology (Burnham and Anderson 2002).
DOI: 10.5061/dryad.fj02s0j/69
title: Supplementary Figure S5

description: Supplementary Figure S5  Summary measures of aligned sequence data for each marker type (CNEEs, introns, UCEs), showing the total aligned sequence length per locus (a-c), variable alignment columns as a percent of the total alignment length (d-f), and the percent of parsimony informative alignment columns per locus (g-i).
DOI: 10.5061/dryad.fj02s0j/70
title: Supplementary Figure S6

description: Supplementary Figure S6  Pairs of short successive internal branches are consistent with expectations for the anomaly zone.  Species tree topologies for CNEEs (a), introns (b), and UCEs (c) are shown with internal branch lengths in coalescent units estimated from best maximum likelihood gene trees with ASTRAL.  Terminal branch lengths are uninformative and are drawn as a constant value across taxa.  Coalescent branch lengths for all pairs of branches (x and y) are given in (d), with a(x) calculated following Equation 4 from Degnan and Rosenberg (2006).  Anomalous gene trees are expected when y &lt; a(x).  Clades fulfilling this anomaly zone criterion are shaded in (d), with the corresponding branches indicated in a-c.
DOI: 10.5061/dryad.fj02s0j/71
title: Supplementary Tables
DOI: 10.5061/dryad.fj02s0j/72
title: README
DOI: 10.5061/dryad.g5q6g80/2
title: Demultiplexed_reads_pt_1

description: This file contains the first part of the microfluidic PRC reads from the Access Array System
DOI: 10.5061/dryad.g5q6g80/3
title: Demultiplexed_reads_pt_2

description: This file contains the first part of the microfluidic PRC reads from the Juno System
DOI: 10.5061/dryad.g5q6g80/4
title: Chloroplast_alignment_with_annotations_and_primers

description: This is a Geneious file with the chloroplast alignment used to primer design with primer and gene annotations.
DOI: 10.5061/dryad.jk17vk0/1
title: Epoched Pupil Data

description: This is epoched pupil data from the fMRI session, as detailed in the paper, and can be used to reproduce the pupil results.
DOI: 10.5061/dryad.r837vv7/1
title: Supplementary Tables S1-S32 (Tran 2019, Journal of Cell Science, doi:10.1242/jcs.231662

description: This archive contains the following: 1) Lists of yeast proteins and their associated P2-residues and localizations based on a global GFP-localization study; 2) P2-residue frequencies in the Saccharomyces cerevisiae proteome based on sub-cellular localization and/or compatibility with Ubr1; 3) Protein abundance levels based on a global GFP-localization study; 4) Topological analyses and P2-residue frequency analyses of a signal-sequence bearing protein set; 5) Raw statistical calculations; 6) Yeast strains, plasmids, and primers used in the study
DOI: 10.5061/dryad.rg576jq/8
title: Whole genome alignment between Eurasian skylark and zebra finch

description: Whole genome alignment .delta file from the nucmer tool of MUMmer. Only scaffolds larger than 1 Mb and alignments longer than 5 kb are included.
DOI: 10.5061/dryad.rg576jq/9
title: Genotypes from RAD-seq data

description: Genotype calls from RAD-seq data for 78 individuals against the Skylark reference genome. Only genotypes with in individual depth of coverage of at least 5X are included. This file was used to compute individual heterozygosity in sliding windows across the genome.
DOI: 10.5061/dryad.s0k808d/1
title: Dryad_Dimension, mechanical properties and force-displacement curves of triceps surae aponeuroses

description: This file contains dimension (thickness, width, length), mechanical properties (Stiffness, Young's modulus, hysteresis) and force-displacement curve data of each specimen of triceps surae aponeuroses.
DOI: 10.5061/dryad.s6s9p58/2
title: Presence of Babesia spp. in rodents from 3 countries of mainland Southeast Asia

description: Rodents were screened for Babesia infection using molecular methods. Original data and methods are given in:
Karnchanabanthoeng A., Morand S., Jittapalapong S., Carcy B. (2017) Babesia occurrence in rodents in relation to landscapes of mainland Southeast Asia. Vector-Borne and Zoonotic Diseases 18:121-130. https://doi.org/10.1089/vbz.2017.2196.

If you use the data in this file, please cite the original publication.
DOI: 10.5061/dryad.s6s9p58/3
title: Presence of Bartonella queenslandensis in rodents from 3 countries of mainland Southeast Asia

description: Rodents were screened for Bartonella infection using molecular methods. Original data and methods are given in:
Jiyipong T., Jittapalapong S., Morand S., Raoult D., Rolain J.-M. (2012) Prevalence and genetic diversity of Bartonella spp. in small mammals from southeastern Asia. Applied and Environmental Microbiology 78: 8463-8466. https://doi.org/10.1128/AEM.02008-12.

If you use the data in this file, please cite the original publication.
DOI: 10.5061/dryad.s6s9p58/4
title: Seroprevalance of Hantavirus in rodents from 3 countries of mainland Southeast Asia

description: Rodents were screened for hantavirus infection using serological method. Original data and methods are given in:
Blasdell K., Cosson J.-F., Chaval Y., Herbreteau V., Douangboupha B., Jittapalapong S., Lundqvist A., Hugot J.-P., Morand S., Buchy, P. (2012) Rodent-borne Hantaviruses in Cambodia, Laos PDR and Thailand. EcoHealth 8(4): 432-443. https://doi.org/10.1007/s10393-011-0725-7.

If you use the data in this file, please cite the original publication.
DOI: 10.5061/dryad.s6s9p58/5
title: Presence of Leptospira spp in rodents from 3 countries of mainland Southeast Asia

description: Rodents were screened for Leptospira infection using molecular methods. Original data and methods are given in:
Cosson J.-F., Picardeau M., Mielcarek M., Tatard C., Chaval Y., Suputtamongkol Y., Buchy P., Jittapalapong S., Herbreteau V., Morand S. (2014). Epidemiology of Leptospira transmitted by rodents in Southeast Asia. PLoS Neglected Tropical Diseases 8(6): e2902. https://doi.org/10.1371/journal.pntd.0002902.

If you use the data in this file, please cite the original publication.
DOI: 10.5061/dryad.s6s9p58/6
title: Presence of Trypanosoma lewisi in rodents from 3 countries of mainland Southeast Asia

description: Rodents were screened for Trypanosoma infection using molecular methods. Original data and methods are given in:
Pumhom P., Morand S., Tran A., Jittapalapong S., Desquesnes M. (2015) Trypanosoma from rodents as potential source of infection in human-shaped landscapes of South-East Asia. Veterinary Parasitology 208 (3-4): 174–180. https://doi.org/10.1016/j.vetpar.2014.12.027.

If you use the data in this file, please cite the original publication.
DOI: 10.5061/dryad.sr182r0.2
title: Data from: Virulence-driven trade-offs in disease transmission: a meta-analysis
DOI: 10.5061/dryad.sr182r0.2/1.2
title: replication_transmission_extracted_data

description: Raw data extracted from studies that met our inclusion criteria for the replication--transmission relationship.
DOI: 10.5061/dryad.sr182r0.2/2.2
title: replication_transmission_studies_info

description: Information on studies that met our inclusion criteria for the replication--transmission relationship.
DOI: 10.5061/dryad.sr182r0.2/3.2
title: replication_virulence_extracted_data

description: Raw data from studies that met our inclusion criteria for the replication--virulence relationship.
DOI: 10.17632/2zts2pgs65.1
title: Data for: Ammonoid biostratigraphy and paleobiogeography of Lower Jurassic sections from Sonora (northwest Mexico) and their tectonic implications

description: The assessment of paleobiogeographic affinity utilizes a literature-based compilation of ammonoid occurrence data from the North American Cordillera. In order to contribute to debates of controversial large scale terrane movements before or after deposition of fossiliferous Early Jurassic strata, we assembled ammonoid distribution data as a presence-absence matrix at a substage resolution in three time slices (latest Hettangian–Early Sinemurian, Late Sinemurian, Early Pliensbachian) from the Walker Lake terrane in Nevada (Taylor, 1998, 2000; Taylor et al., 2001; Hou, 2014; Porter et al., 2014; Caruthers et al., 2018), the Cadwallader terrane in the Taseko Lakes map area, British Columbia (Smith and Tipper, 2000; Macchioni et al., 2006; Longridge et al., 2006, 2008a, b; Hou, 2014), from the Stikine terrane in northwest British Columbia (Thomson and Smith, 1992; Pálfy and Schmidt, 1994; Johannson et al., 1997), and from Wrangellia terrane in Haida Gwaii (formerly Queen Charlotte Islands), British Columbia (Pálfy, 1991; Pálfy et al., 1994; Smith and Tipper, 1996; Longridge et al., 2008c). Our selection was guided by the aim of including the most complete fossiliferous sections from where recent taxonomic studies are available and obtaining representative coverage for meaningful comparison between the Antimonio terrane, outboard terranes of the Canadian Cordillera and an onboard terrane from Nevada.Dendrograms expressing similarity of Early Jurassic ammonoid faunal assemblages from Sonora with other areas in North American Cordillera: Nevada (Walker Lake terrane), the Intermontane superterrane (including Cadwallader and Stikine terranes in British Columbia) and Wrangellia terrane. Presence-absence matrix given for all the time slices and data also compiled into one summary sheet. The number of species given in the diversity sheet. Assemblages compiled at substage level, cluster analysis performed using UPGMA method and Dice, Simpson, Jaccard, Raup-Crick indices, where these indices also compiled into a separate sheet.
DOI: 10.5061/dryad.1740n0h/1
title: Supplemental Figure 1

description: Figure S1. A species tree of Hyperoliidae inferred from 1,047 gene trees with ASTRAL-III. Node support is shown for quartet support values and multi-locus bootstraps, with branch lengths depicted in coalescent units (except for tree tips, represented by dotted lines).
DOI: 10.5061/dryad.1740n0h/2
title: Supplemental Figure 2

description: Figure S2. A chronogram of Afrobatrachia inferred from the multilocus BEAST analysis of 283 species. Taxa labeled with blue color denote the 153 species included in the hyperoliid species tree that was used as a partial constraint tree in this analysis. Node support values are not shown because the tree topology was fixed, but error bars representing the 95% HPD for dating estimates are provided.
DOI: 10.5061/dryad.1740n0h/3
title: Supplemental Figure 3

description: Figure S3. A comparison of Bayesian ancestral character reconstructions inferred using the stochastic Mk model of character evolution with symmetrical (Mk1) or asymmetrical (Mk2) transition rates in combination with a strict clock or random local clock model. All analyses enforced a monochromatic root prior. The marginal likelihoods and average number of state changes are shown for each analysis. Node sizes reflect the posterior probability for the inferred character state, and tips and nodes are colored with monochromatism in yellow and dichromatism in blue.
DOI: 10.5061/dryad.1740n0h/4
title: Supplemental Figure 4

description: Figure S4. An illustration of transitions to secondary monochromatism inferred using Bayesian ancestral character reconstruction with the Mk2 and strict clock models. Large nodes outlined with red represent inferred transitions to monochromatism from a dichromatic ancestor. States at nodes and tips are colored with monochromatism in yellow and dichromatism in blue.
DOI: 10.5061/dryad.1740n0h/5
title: Supplemental Figure 5

description: Figure S5. Ancestral state reconstruction of the observed and hidden state combinations in Afrobatrachian frogs from the best-fit HiSSE model (HiSSE 19; Table 1). Squares at tips are colored by the observed character states (yellow: monochromatic, blue: sexually dichromatic), whereas node pie charts represent the probability of a state assignment to: 1) monochromatism + hidden state absent (yellow), 2) monochromatism + hidden state present (orange), 3) dichromatism + hidden state absent (blue), or 4) dichromatism + hidden state present (purple). No instance of the monochromatism + hidden state present is reconstructed on the phylogeny, whereas a transition to the dichromatism + hidden state present combination is inferred once in the MRCA of two monotypic genera (Cryptothylax, Morerella), indicating a near absence of the hidden state across the entire tree.
DOI: 10.5061/dryad.1nh544n/10
title: Sim_1000BQs_200Loci_075_Rep7-10

description: We store output data from stochastic simulation studies on honeybee breeding schemes relying on different genetic models. In particular, the infinitesimal model and the finite locus models are taken into consideration. Output files contain data on true and estimated breeding values, performance tests, inbreeding coefficients and pedigree data. For more information please also consult the README file
DOI: 10.5061/dryad.1nh544n/11
title: Sim_1000BQs_400Loci_025_Rep1-3

description: We store output data from stochastic simulation studies on honeybee breeding schemes relying on different genetic models. In particular, the infinitesimal model and the finite locus models are taken into consideration. Output files contain data on true and estimated breeding values, performance tests, inbreeding coefficients and pedigree data. For more information please also consult the README file
DOI: 10.5061/dryad.1nh544n/12
title: Sim_1000BQs_400Loci_025_Rep4-6

description: We store output data from stochastic simulation studies on honeybee breeding schemes relying on different genetic models. In particular, the infinitesimal model and the finite locus models are taken into consideration. Output files contain data on true and estimated breeding values, performance tests, inbreeding coefficients and pedigree data. For more information please also consult the README file
DOI: 10.5061/dryad.1nh544n/13
title: Sim_1000BQs_400Loci_025_Rep7-10

description: We store output data from stochastic simulation studies on honeybee breeding schemes relying on different genetic models. In particular, the infinitesimal model and the finite locus models are taken into consideration. Output files contain data on true and estimated breeding values, performance tests, inbreeding coefficients and pedigree data. For more information please also consult the README file
DOI: 10.5061/dryad.1nh544n/14
title: Sim_1000BQs_400Loci_075_Rep1-3

description: We store output data from stochastic simulation studies on honeybee breeding schemes relying on different genetic models. In particular, the infinitesimal model and the finite locus models are taken into consideration. Output files contain data on true and estimated breeding values, performance tests, inbreeding coefficients and pedigree data. For more information please also consult the README file
DOI: 10.5061/dryad.1nh544n/15
title: Sim_1000BQs_400Loci_075_Rep4-6

description: We store output data from stochastic simulation studies on honeybee breeding schemes relying on different genetic models. In particular, the infinitesimal model and the finite locus models are taken into consideration. Output files contain data on true and estimated breeding values, performance tests, inbreeding coefficients and pedigree data. For more information please also consult the README file
DOI: 10.5061/dryad.1nh544n/16
title: Sim_1000BQs_400Loci_075_Rep7-10

description: We store output data from stochastic simulation studies on honeybee breeding schemes relying on different genetic models. In particular, the infinitesimal model and the finite locus models are taken into consideration. Output files contain data on true and estimated breeding values, performance tests, inbreeding coefficients and pedigree data. For more information please also consult the README file
DOI: 10.5061/dryad.1nh544n/17
title: Sim_Inf

description: We store output data from stochastic simulation studies on honeybee breeding schemes relying on different genetic models. In particular, the infinitesimal model and the finite locus models are taken into consideration. Output files contain data on true and estimated breeding values, performance tests, inbreeding coefficients and pedigree data. For more information please also consult the README file
DOI: 10.5061/dryad.1nh544n/19
title: BeeSim Program

description: Source code of the Program BeeSim that was used for the simulations. The zipped folder contains a manual that explains the usage of the program.
DOI: 10.5061/dryad.1nh544n/9
title: Sim_1000BQs_200Loci_075_Rep4-6

description: We store output data from stochastic simulation studies on honeybee breeding schemes relying on different genetic models. In particular, the infinitesimal model and the finite locus models are taken into consideration. Output files contain data on true and estimated breeding values, performance tests, inbreeding coefficients and pedigree data. For more information please also consult the README file
DOI: 10.5061/dryad.22k10nd/1
title: Bitcoin price information for part 3

description: Bitcoin information from the Bitstamp exchange, used within part 3 of the paper.
DOI: 10.5061/dryad.22k10nd/2
title: bitcoin information for part 2

description: Bitcoin information used within the second section of the paper, by column: date, market cap, number of active users, average value of transaction, number of transactions per day, median value of transaction, daily volume. All openly available from bitinfocharts.com
DOI: 10.5061/dryad.33jn722/4
title: Alignments

description: 755 final gene alignments in .phy format
DOI: 10.5061/dryad.33jn722/5
title: Transcriptomes

description: Final Cleaned de novo assembled transcriptomes for each species
DOI: 10.5061/dryad.3kf3gg2/1
title: Supplementary Table 1

description: Microwear data of late Pleistocene equid and bison samples studied.
DOI: 10.5061/dryad.3kf3gg2/10
title: Supplementary File 2_Proportion_test

description: MATLAB code
DOI: 10.5061/dryad.3kf3gg2/2
title: Supplementary Table 2

description: Mesowear data of late Pleistocene equid and bison samples studied.
DOI: 10.5061/dryad.3kf3gg2/3
title: Supplementary Table 3

description: Enamel hypoplasia data of late Pleistocene equid and bison samples studied.
DOI: 10.5061/dryad.3kf3gg2/4
title: RAM DhPg-8_69-1_anterior-dicoms

description: CT-scan data_RAM DhPg-8 69.1_anterior dicoms
DOI: 10.5061/dryad.3kf3gg2/5
title: RAM DhPg-8_69-1_posterior-dicoms

description: CT-scan data_RAM DhPg-8 69.1_posterior dicoms
DOI: 10.5061/dryad.3kf3gg2/6
title: RAM DhPg-8_864

description: CT-scan data_RAM DhPg-8 864_dicoms
DOI: 10.5061/dryad.3kf3gg2/7
title: RAM DhPg-8_876-1_anterior-dicoms

description: CT-scan data_RAM DhPg-8 876.1_anterior dicoms
DOI: 10.5061/dryad.3kf3gg2/8
title: RAM DhPg-8_876-1_posterior dicoms

description: CT-scan data_RAM DhPg-8 876.1_posterior dicoms
DOI: 10.5061/dryad.3kf3gg2/9
title: Supplementary File 1_Var_test

description: MATLAB code
DOI: 10.5061/dryad.4nb96c1/1
title: Supplementary Data

description: The supplementary data file contains 1) A more detailed description of the applied T2water fitting approach to quantify putative oedema in the lower extremity muscles, 2) MRI outcome measures depicted for the 20 individual lower extremity muscles, 3) Detailed outcomes of the multivariate linear regression model used to assess the effect of age and CTG repeat length on lower extremity muscle fat fraction, 4) Effect of AciI-sensitive variant repeats in the expanded allele on lower extremity muscle fat fraction. 5) Detailed overview of the correlation between the 6MWT and the fat fraction in four functional muscle groups (quadriceps, hamstrings, anterior compartment of the lower leg, and triceps surae).
DOI: 10.5061/dryad.57vg809.1
title: Data from: Extended phenotypes and foraging restrictions: ant nest entrances and resource ingress in leaf-cutting ants
DOI: 10.5061/dryad.57vg809.1/1.1
title: Data base ms-repository

description: Data file that includes ant nest dimensions, nest entrances dimensions, ant speed, ant flux
DOI: 10.5061/dryad.57vg809.2
title: Data from: Extended phenotypes and foraging restrictions: ant nest entrances and resource ingress in leaf-cutting ants
DOI: 10.5061/dryad.57vg809.2/1.2
title: Data base ms-repository

description: Data file that includes ant nest dimensions, nest entrances dimensions, ant speed, ant flux
DOI: 10.5061/dryad.5t165h5/1
title: Molt ending date of mountain goats of Caw Ridge, AB, Canada, 1989-2016 and variables of interest

description: Data needed to perform the same analyses that are in the publication associated. This data has been collected during summers from 1989 to 2016. Please read the "read_me" file. E-mail at Steeve.Cote@bio.ulaval.ca if you'd like to use this data, to ensure it is correctly used or to have more information on study system and other data available.
DOI: 10.5061/dryad.60008mj/1
title: 16S amplicon sequencing and qPCR data

description: This archive contains 1) raw Illumina MiSeq reads (300bp, PE, Reagent Kit v3) for all bacterial 16S V3/V4 amplicons used in our study, 2) metadata for each sample/individual, formatted as a QIIME 1.9 mapping file, 3) preprocessed data and .biom tables used to generate our results using phyloseq 1.22.3, and 4) raw data from qPCR analyses used to generate our results. We used two databases, greengenes 13_8 and SILVA NR Small Subunit v128 to assign taxonomy in our study; the filenames of preprocessed data include the database used to generate each file.
DOI: 10.5061/dryad.6vr5888/1
title: Data

description: data csv for GAM