cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fn627/4
title: Camaenidae alignment

description: The concatenated alignment of the 2,648 exons which were sequenced from representatives of the family Camaenidae using exon capture. This alignment was used to produce the camaenidae phylogeny presented in the paper.
DOI: 10.5061/dryad.fn627/5
title: Camaenidae_exon_capture_probe_set

description: This file contains the probes for the Camaenidae exon capture design. These probes target exons from 490 orthologous genes. The probes were designed for use with the Mycroarray Mybaits custom kit which consists of 120 bp RNA probes.
DOI: 10.5061/dryad.g8g20/1
title: Target relative frequency response

description: The frequency response (38-120 kHz) of single targets identified between 900 and 1200 m for each transect type (low, alternate, high Ziphius use).
DOI: 10.5061/dryad.g8g20/2
title: Target strength

description: The target strength distribution of single targets consistent with squid between 900 and 1200 m within three sampling zones (high, alternate, and low Ziphius use).
DOI: 10.5061/dryad.k2p51/1
title: SPTO EPP data all nests

description: Sheet one includes each nest with park data, distance to edge data, and female and male ID, plus the extra-pair status of the nestlings. Sheet two includes all nesting attempts by each female per year, along with the extra-pair paternity data, and male and female morphological data for the "best" nest (the nest used in our analysis w/ the greatest number of nestlings typed).
DOI: 10.5061/dryad.pk20h/2
title: configuration files and admix'em input file for selection simulations

description: admix'em configuration files for simulations with epistatic selection under a hybrid swarm (admixsimul.cfg), bottleneck (admixsimul_bottle.cfg) and continuing migration model (admixsimul_mig.cfg) as well as admix'em input files called by these configuration files
DOI: 10.5061/dryad.pk20h/3
title: simulation shell script

description: shell script to run admix'em simulations for a given configuration file, number of generations, and number of individuals. NOTE: assumes admixem is installed in the same directory and that the executable is called admixemp. Also assumes that perl and sh scripts provided with this submission are available in the same directory. Usage: perl simulated_ld_shell.pl cfg_file out_folder_name num_iterations focal_gen num_indiv_sample
DOI: 10.5061/dryad.pk20h/4
title: generate_msg_data_header_200locisim.pl

description: script to convert admix'em output for the simulation parameters provided to genotype format. This script is called by the simulation shell script: simulated_ld_shell_YB_MS.pl
DOI: 10.5061/dryad.pk20h/5
title: hybrid_index.pl

description: script to calculate hybrid index from the genotype-format admix'em output for the 200 loci simulated. This script is called by the simulation shell script: simulated_ld_shell_YB_MS.pl
DOI: 10.5061/dryad.pk20h/6
title: random_sample.sh

description: script to subsample the simulated individuals from the genotypes file to the desired number of individuals. This script is called by the simulation shell script: simulated_ld_shell_YB_MS.pl
DOI: 10.5061/dryad.pk20h/7
title: compressed neutral simulation files for reproduction of results figure 2

description: "neutral.zip" contains neutral simulation results files and scripts needed to reproduce figure 2 in the main text
DOI: 10.5061/dryad.pk20h/8
title: compressed selection simulation files for reproduction of results figure 3

description: "selection.zip" contains neutral simulation results files and scripts needed to reproduce figure 3 in the main text
DOI: 10.5061/dryad.rf8th/1
title: Mean Data_Cool echidnas survive the fire

description: Individual mean data
DOI: 10.5061/dryad.rf8th/2
title: Data figure 2_Cool echidnas survive the fire

description: Body temperature traces of the same echidna a) 7 days before and b) 7 days after the fire on the 21th of April.
DOI: 10.5061/dryad.rf8th/3
title: Data figure 3_Cool echidnas survive the fire

description: Mean body temperatures  before and after the burn for a) the control echidnas (n=5) and b) fire animals (n=5; individual that died in the fire not shown) in relation to c) ambient conditions (maximum ambient temperature; minimum ambient temperature; precipitation).
DOI: 10.5061/dryad.rf8th/4
title: Data figure 4_Cool echidnas survive the fire

description: Comparison of home ranges for individuals of the fire group before (unfilled polygon) and after the fire (grey polygon). Home ranges were calculated as MCPs; overlap areas are indicated as dashed areas.
DOI: 10.5061/dryad.v28t5/2
title: Female and male life tables for seven wild primate species

description: Table 2A. Female life tables for 7 species of wild primates. Table 2B. Male survival tables for 7 species of wild primates. Table 3. Female summary demographic statistics for 7 species of wild primates. Table 4. How to convert a life table to a Leslie matrix; an example using the female baboon life table.
DOI: 10.5061/dryad.1kr29/1
title: HGDP00222
DOI: 10.5061/dryad.1kr29/2
title: chimp-Y.annotated.kmer

description: Files accompanying "Y-chromosome structural diversity in the bonobo and chimpanzee lineages" by Oetjens et al. 2016chimpY and humanY .kmer files are bed files of k-mers referenced in the manuscript used for calculating depth of Y-amplicons.  Positions refer to panTro4 and hg19 coordinates for chimp and human k-mers respectively.column 1: chromosomecolumn 2: k-mer start column 3: k-mer endcolumn 4: k-mer sequencecolumn 5: annotation
DOI: 10.5061/dryad.1kr29/3
title: humanY.annotated.ddPCR.kmer

description: Files accompanying "Y-chromosome structural diversity in the bonobo and chimpanzee lineages" by Oetjens et al. 2016chimpY and humanY .kmer files are bed files of k-mers referenced in the manuscript used for calculating depth of Y-amplicons.  Positions refer to panTro4 and hg19 coordinates for chimp and human k-mers respectively.column 1: chromosomecolumn 2: k-mer start column 3: k-mer endcolumn 4: k-mer sequencecolumn 5: annotation
DOI: 10.5061/dryad.1v6p1/1
title: Dryad_Data microsat genotypes_Zachos et al_Red deer_J Heredity

description: All 668 13-locus genotypes of European red deer that our study is based on.
DOI: 10.5061/dryad.25qp5/1
title: Pull-in area plot code

description: Matlab code to plot the data from the pull-in analysis. This code utilizes the csv files included. Code written by M. Pankow.
DOI: 10.5061/dryad.25qp5/2
title: Test_data

description: Zip file containing csv datafiles for each of the twenty high-speed puncture experiments run. Each row represents a frame of video. The first column is the lateral area of the pull-in region as measured by the shadow seen in the frame. The second column is the depth of puncture of the arrow in each frame. The third column is the height from the center of the arrow to the top of the pull-in region along the impact surface. The data in this last column is used as the radius of the pull-in area on the impact surface.
DOI: 10.5061/dryad.25qp5/3
title: DataCode1_1

description: Matlab code to calculate the pull-in area of ballistics gel during puncture experiments. Puncture depth and the height of the pull-in region on the impact surface are calculated for every frame of the high-speed video analyzed. The height measure is later used to calculate the pull-in area on the impact surface. The high-speed videos used in this code consist of tiff stacks averaging 1 GB in size. Those video are freely available upon request from the corresponding author, P. Anderson. Code written by M. Pankow
DOI: 10.5061/dryad.25qp5/4
title: format_ticks

description: Matlab code that adds formatting to makes the pull-in area plot look as it does in the paper. Code written by M. Pankow
DOI: 10.5061/dryad.29h6k/15
title: Protoparmelia
DOI: 10.5061/dryad.29h6k/16
title: Punctelia
DOI: 10.5061/dryad.29h6k/17
title: Xanthomendoza
DOI: 10.5061/dryad.29h6k/18
title: Austroparmelina
DOI: 10.5061/dryad.29h6k/19
title: Bulbothrix
DOI: 10.5061/dryad.29h6k/20
title: Fuscopannaria
DOI: 10.5061/dryad.29h6k/21
title: Hypogymnia
DOI: 10.5061/dryad.29h6k/22
title: Pannaria
DOI: 10.5061/dryad.29h6k/23
title: Parmelina
DOI: 10.5061/dryad.37312/1
title: Fox et al_Review data 2004-2014_one line per paper

description: This is an anonymized version of the dataset used for most of the analyses in the associated paper. Manuscript ID numbers are random and the sort order within years is random; manuscript ID numbers can be used to link the three files uploaded for this paper. Editor ID is also randomized. Columns that could allow the dataset to be de-anonymized, such as editor seniority and editor years on the editorial board, have been deleted. The dataset includes one line per manuscript. This file (combined with the others uploaded for this manuscript) allows recreation of most but not all analyses in the published manuscript.
DOI: 10.5061/dryad.3sm6t/1
title: Peredo and Uhen Matrix

description: A nexus file containing the matrix used for the phylogenetic analysis
DOI: 10.5061/dryad.53n6n/1
title: Paleobiology Database Mammalian Occurrence Data

description: Occurrence data obtained from the Paleobiology Database (https://www.paleobiodb.org) on May 21, 2015 (data were primarily derived from the North American Fossil Mammal Systematics Database; https://paleobiodb.org/cgi-bin/bridge.pl?page=OSA_3_North_American_mammals).
DOI: 10.5061/dryad.53n6n/2
title: R file of results of 10,000 pseudoreplicate analyses

description: These are the the results of our 10,000 pseudoreplicate analyses described in the paper.  They can be loaded into the R environment by placing them into the working directory and using the command: load("ldg_rez_2My_10000_20151023.R")
DOI: 10.5061/dryad.53n6n/3
title: Stable Isotope Data from Zachos et al. 2001

description: These include the stable isotope data and dates used to calculate correlation between d18O and fossil slopes. All data are from Zachos J, Pagani M, Sloan L, Thomas E, Billups K (2001) Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292(5517):686–693.
DOI: 10.5061/dryad.6qq65/1
title: Cricket measurements and microsatellite data

description: Sheet 1 contains morphometric and fitness data on all wild-caught crickets used in selection analyses. Sheet 2 contains the results of genotyping lab-reared crickets after mating them to a known number of males.
DOI: 10.5061/dryad.6r9q6.1
title: Data from: Measuring fecal testosterone in females and fecal estrogens in males: comparison of RIA and LC/MS/MS methods for wild baboons (Papio cynocephalus).
DOI: 10.5061/dryad.6r9q6.2/4.2
title: Dryad Males

description: This data file contains the estrogens (E) and testosterone (T) concentrations (in ng/g feces) and their logarithm transformed values for immature males (3-5 years old) and adult males (8-10 years old).
DOI: 10.5061/dryad.6s0s8/4
title: Tai_var

description: Features of vocal responses from Tai
DOI: 10.5061/dryad.6s0s8/5
title: Tiwai_var

description: Features of vocal responses from Tiwai
DOI: 10.5061/dryad.7rm62.1
title: Data from: Egg morphology fails to identify nests parasitized by conspecifics in common pochard: a test based on protein fingerprinting and including female relatedness
DOI: 10.5061/dryad.7rm62.2
title: Data from: Egg morphology fails to identify nests parasitized by conspecifics in common pochard: a test based on protein fingerprinting and including female relatedness
DOI: 10.5061/dryad.7rm62.2/1.2
title: Aythya ferina characteristics of eggs

description: The file contains information about eggs of Common pochard (Aythya ferina). Data were collected during 2004 - 2006 in the Třeboň Biosphere Reserve, South Bohemia, Czech Republic.
DOI: 10.5061/dryad.b3d76/1
title: Andersonetal2016_Evo&Dev_data

description: Zip file containing the raw tps and centroid size files used for morphometric analyses in the paper.
DOI: 10.5061/dryad.cc03n/1
title: Sedlacek_etal_MarkerData

description: This data file provides the data on the SSR markers. An explanation of the variables is provided in the ReadMe file.
DOI: 10.5061/dryad.cc03n/2
title: Sedlacek_etal_PhenotypicData

description: This data file provides all raw phenotypic data collected on the Salix herbacea plants in the field. Note that some of these variables were not used for the publication. An explanation of the variables is given in the ReadMe file.
DOI: 10.5061/dryad.dm57j/2
title: Copes et al. Dryad submission

description: The zipped folder contains the original Excel spreadsheet with 3D digitized points from ~400 non-human primate skulls.  It also contains "cleaned up" versions of the points split into separate files by infraorder (strepsirrhines, catarrhines, platyrrines) and R code for importing the files.  Many thanks to Randi Griffin for her assistance in reformatting the original data to make it more useful/accessible for analysis.
DOI: 10.5061/dryad.fn627/6
title: Manual_curation_500_genes_seperated_into_exons

description: This file contains the alignments for the 500 manually curated genes seperated out into alignments per exon based on the exon boundaries from the Lottia gigantea genome. These alignments contain the regions which are masked out in the gene alignments but the mask is not presented.
DOI: 10.5061/dryad.fn627/7
title: Trinity_assemblies

description: Transcriptome assemblies for 21 eupulmonate species. The transcriptomes were assembled using the program Trinity.
DOI: 10.5061/dryad.k37q7/1
title: VRS-chlorophyll-a data from 23 sediment cores from study lakes in the Athabasca Oil Sands Region, Alberta, Canada
DOI: 10.5061/dryad.k37q7/2
title: Nutrient (TN, DIN, TP, TDP, SRP) data from snowpack samples in the Athabasca Oil Sands Region, Alberta, Canada
DOI: 10.5061/dryad.n4m62/1
title: A domesticus bite force

description: These data describe the effects of two rounds of combat and their outcomes on bite forces of A. domesticus males, as well as a control group that did not experience combat.
DOI: 10.5061/dryad.p0q25/1
title: Latitudinal range limits of birds at global scales

description: Latitudinal range limits of bird genera and species at global scales defined on the basis of 2,785,600 occurrences from published literature, sightings, and from museum specimens (Rahbek and Graves 2001; Rahbek et al. 2012). Ranges were compiled at a resolution of 1° x 1°. References: Rahbek, C. & Graves, G. R. 2001 Multiscale assessment of patterns of avian species richness. Proc. Natl. Acad. Sci. USA 98, 4534-4539. Rahbek, C., Hansen, L. A. & Fjelds, J. 2012. One degree resolution database of the global distribution of birds. Natural History Museum of Denmark, University of Copenhagen, Denmark.
DOI: 10.5061/dryad.p0q25/2
title: Latitudinal range limits of birds in the New World

description: Latitudinal range limits of bird genera and species in the New World defined on the basis of occurrences from published literature, sightings, and from museum specimens (Rahbek and Graves 2001; Rahbek et al. 2012). Ranges were compiled at a resolution of 1° x 1°. References: Rahbek, C. & Graves, G. R. 2001 Multiscale assessment of patterns of avian species richness. Proc. Natl. Acad. Sci. USA 98, 4534-4539. Rahbek, C., Hansen, L. A. & Fjelds, J. 2012. One degree resolution database of the global distribution of birds. Natural History Museum of Denmark, University of Copenhagen, Denmark.
DOI: 10.5061/dryad.p0q25/3
title: Latitudinal range limits of bivalves at global scales

description: Latitudinal range limits of bivalve genera and species at global scales, occurring at depths &lt; 200 m. They were compiled from both the literature and museum collections. Reference: Jablonski, D., Belanger, C. L., Berke, S. K., Huang, S., Krug, A. Z., Roy, K., Tomasovych, A. & Valentine, J. W. 2013 Out of the tropics, but how? Fossils, bridge species, and thermal ranges in the dynamics of the marine latitudinal diversity gradient. Proc. Natl. Acad. Sci. USA 110, 10487-10494.
DOI: 10.5061/dryad.p0q25/4
title: Latitudinal range limits of bivalves in the Eastern Pacific

description: Latitudinal range limits of bivalve genera and species in the Eastern Pacific, occurring at depths &lt; 200 m. They were compiled from both the literature and museum collections. Reference: Jablonski, D., Belanger, C. L., Berke, S. K., Huang, S., Krug, A. Z., Roy, K., Tomasovych, A. & Valentine, J. W. 2013 Out of the tropics, but how? Fossils, bridge species, and thermal ranges in the dynamics of the marine latitudinal diversity gradient. Proc. Natl. Acad. Sci. USA 110, 10487-10494.
DOI: 10.5061/dryad.p0q25/5
title: Latitudinal range limits of bivalves in the Western Atlantic

description: Latitudinal range limits of bivalve genera and species in the Western Atlantic, occurring at depths &lt; 200 m. They were compiled from both the literature and museum collections. Reference: Jablonski, D., Belanger, C. L., Berke, S. K., Huang, S., Krug, A. Z., Roy, K., Tomasovych, A. & Valentine, J. W. 2013 Out of the tropics, but how? Fossils, bridge species, and thermal ranges in the dynamics of the marine latitudinal diversity gradient. Proc. Natl. Acad. Sci. USA 110, 10487-10494.
DOI: 10.5061/dryad.sh2mb/1
title: TableS1

description: Phenotypic, climatic, and geographic data for the Arabidopsis thaliana accessions used in this study.
DOI: 10.5061/dryad.sh2mb/2
title: TableS2

description: Seed oil melting points and box-cox transformed melting points for all replicates of the 391 Arabidopsis thaliana accessions.
DOI: 10.5061/dryad.sh2mb/3
title: TableS3

description: P-values and FDR-corrected values for the a priori candidate gene analysis.
DOI: 10.5061/dryad.sh2mb/4
title: TableS4

description: P-values and FDR-corrected values from GWAS based on analysis of boxcox-transformed melting points.
DOI: 10.5061/dryad.sh2mb/5
title: TableS5

description: Linkage disequilibrium between the two highly significant SNPs and all other SNPs within 1Mb up or downstream.
DOI: 10.5061/dryad.sh2mb/6
title: TableS6

description: P-values from GWAS with highly significant SNP on chromosome 3 (position=3860685 bp) as a covariate in the model.
DOI: 10.5061/dryad.t49h6/1
title: Ornelas et al_ITS

description: 1. ITS_File: Psittacanthus schiedeanus sequences of the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA (nrDNA)  sequences.
DOI: 10.5061/dryad.t49h6/2
title: Ornelas et al_trnL-F

description: 2. trnL-F_File: Psittacanthus schiedeanus sequences of the trnL-F intergenic spacer region from the chloroplast genome (cpDNA).
DOI: 10.5061/dryad.t49h6/3
title: Ornelas et al_IMa_CALYvsSCHI_cp_nr

description: 1. Ornelas_et al_IMa_CALYvsSCHI_nuclear (ITS) and chloroplast (trnL-F): CALY (xeric vegetation in central Oaxaca and tropical deciduous forests in Chiapas) versus SCHI (cloud forests from San Luis Potosí to Oaxaca and Chiapas) populations of Psittacanthus schiedeanus for the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA (nrDNA)  and the trnL-F intergenic spacer region from the chloroplast genome (cpDNA).
DOI: 10.5061/dryad.t49h6/4
title: Ornelas et al_MAXENT_Psittacanthus_schiedeanus

description: 1. Psittacanthus_schiedeanus_MAXENT_File: coordinates longitude and latitude of Psittacanthus schiedeanus.
DOI: 10.5061/dryad.t89hc/1
title: Gibson2016_AmNat_InfectionPrevalence

description: Individual-based data for analysis of infection prevalence. Each row gives collection and dissection data for an individual female snail. Columns: 1) “year” gives year of collection (2006-2015); 2) “sites” gives site of collection (13 sites); 3) length” gives the shell length of the female in millimeters, a proxy for age; and 4) “mic” gives the infection status of the female (0 = healthy, 1 = Microphallus infection).
DOI: 10.5061/dryad.t89hc/2
title: Gibson2016_AmNat_ArtificialInoculations

description: Infection data for exposed and control replicates in 2013, 2014, and 2015 artificial inoculations. Each row gives identifying information and infection data for an experimental replicate. Columns: 1) “year” gives the year of the artificial inoculation experiment (2013-2015); 2) “site” gives the site from which experimental juveniles were collected (13 sites); 3) “treatment” gives experimental treatment. Control replicates did not receive parasites and are marked as 0. Infections in control replicates were acquired prior to collection of juvenile snails from the field and reflect early-life exposure to parasites. Exposed replicates received field-collected parasites and are marked as 1. Infections in exposed replicates are the sum of infections acquired in the field and after exposure to high doses of parasites. Susceptibility is defined as the infection rate in exposed replicates; 4) “source” applies to the 2014 artificial inoculation experiment in which two distinct sources of parasites were used for inoculations. Replicates exposed to source 1 (southern end of lake) are marked as 1, replicates exposed to source 2 (northeastern site, JMS) are marked as 2, and control replicates are marked as 0; 5) “replicate” indicates the experimental replicate, nested with year*site; 6) “uninfected” gives the number of female snails that were healthy in the experimental replicate; and 7) “infected” gives the number of female snails infected with Microphallus in the experimental replicate.
DOI: 10.5061/dryad.t89hc/3
title: Gibson2016_AmNat_GPSCoordinates

description: GPS coordinates used in spatial analyses of infection prevalence and susceptibility. Latitude and longitude given in decimal degrees. Coordinates obtained in Google Earth.
DOI: 10.5061/dryad.t89hc/4
title: Gibson2016_AmNat_GeographicDistance

description: Geographic distances used in Mantel tests for infection prevalence and susceptibility. Straight line distances given in meters. Distances obtained in Google Earth.
DOI: 10.5061/dryad.t89hc/5
title: Gibson2016_AmNat_Mortality

description: Mortality data for 2013, 2014, and 2015 artificial inoculations. Each row gives identifying information and infection data for an experimental replicate. Columns: 1) “year” gives the year of the artificial inoculation experiment (2013-2015); 2) “site” gives the site from which experimental juveniles were collected (13 sites); 3) “treatment” gives experimental treatment. Control replicates did not receive parasites and are marked as 0. Infections in control replicates were acquired prior to collection of juvenile snails from the field and reflect early-life exposure to parasites. Exposed replicates received field-collected parasites and are marked as 1; 4) “source” applies to the 2014 artificial inoculation experiment in which two distinct sources of parasites were used for inoculations. Replicates exposed to source 1 (southern end of lake) are marked as 1, replicates exposed to source 2 (northeastern site, JMS) are marked as 2, and control replicates are marked as 0; 5) “replicate” indicates the experimental replicate, nested with year*site; 5) “total” gives the total number of female snails in the experimental replicate at initiation of the experiment; 6) “present” gives the number of female snails that were present (i.e. alive) at the time of dissection of the experimental replicate; and 7) “absent” is “total” minus “present” – the number of female snails missing (i.e. presumed dead) at the time of dissection of the replicate.
DOI: 10.5061/dryad.vq275/2
title: Lohman et al Evaluation of TagSeq

description: All necessary raw data and code (raw sequences deposited on Corral)
DOI: 10.5061/dryad.16n63/1
title: Rosati et al Gaze Development (Study 1)

description: Trial data for gaze development study (variable key in file).
DOI: 10.5061/dryad.16n63/2
title: Rosati et al Gaze Control (Study 2)

description: Trial data for gaze directional control (variable key in file).
DOI: 10.5061/dryad.1b2k5/1
title: Cophyline microhylids supplementary files

description: The file Madagascar_microhylid_matrix.xls contains information on the species, sampling localities of the individuals sequenced for the 16S rRNA mitochondrial fragment, voucher information of each amplified fragment, GenBank accession numbers and all the analysed fragments. The file MrCophylinae_100Mfinal.nex contains the alignment used for the performed molecular analyses.