cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.d6b23.2/35.2
title: Figure S1

description: Mexican states with and without constitutional amendment to protect the unborn starting at conception between 2008 and 2011. Political maps of Mexican states are shown for 2008 (top panel), 2009 (middle panel), and 2010 (bottom panel), indicating whether they exhibit a constitutional amendment to protect the unborn starting at conception1 in dark green (with amendment) and cyan (without amendment). The state of Chihuahua enacted its political constitution in 1994; Baja California, Morelos, and Sonora in 2008; Campeche, Chiapas, Colima, Durango, Guanajuato, Jalisco, Nayarit, Oaxaca, Puebla, Querétaro, Quintana Roo, San Luis Potosí, and Yucatán in 2009; and Tamaulipas in 2010. Campeche revoked the amendment in 2010. Ag, Aguascalientes; Co, Colima; FD, Federal District; Mo, Morelos; Tl, Tlaxcala.
DOI: 10.5061/dryad.j90q0/1
title: data
DOI: 10.5061/dryad.7kn5k/2
title: Vent barnacle sanger-based dating

description: Input and tree files from bayesian inference phylogenetic/dating analyses using sanger-based markers.
DOI: 10.5061/dryad.7kn5k/3
title: Vent barnacle pyRAD

description: Command, output and statistics files from RAD-seq clustering using pyRAD. Phylogenetic trees and bootstrap consensus from maximum likelihood inferences.
DOI: 10.5061/dryad.f1612/2
title: Cane toad directional movement data with mean vector column added.

description: Cane toad directional movement data with mean vector column added
DOI: 10.5061/dryad.gm627/1
title: vcf_fasta

description: Perl script for creating FASTA file from vcf file.
DOI: 10.5061/dryad.gm627/2
title: R codes for generating graphs
DOI: 10.5061/dryad.hj68b/1
title: Killifish DNA alignment file

description: DNA alignment file. 311 taxa. 10960 bp. Phylip format.
DOI: 10.5061/dryad.hj68b/2
title: Killifish DNA partition file

description: Text file indicating DNA data partitions.
DOI: 10.5061/dryad.qb2jk/1
title: Locality, habitat and species composition matrices

description: Details of the locations, habitats and composition of all samples included in the paper
DOI: 10.5061/dryad.76173/1
title: Site1_WesternSahara1

description: Pollination network from Western Sahara (Site 1). Pollination networks are arranged with pollinators in the rows and plant species in the columns. Values in the matrix represents total number of observed visits between plants and pollinators.
DOI: 10.5061/dryad.76173/2
title: Site2_WesternSahara2

description: Pollination matrix from Western Sahara (Site 2). Pollination networks are arranged with pollinators in the rows and plant species in the columns. Values in the matrix represents total number of observed visits between plants and pollinators.
DOI: 10.5061/dryad.hj68b/10
title: Nothobranchius furzeri long-term embryo survival

description: Data on long-term survival as a function of developmental pathway in Nothobranchius furzeri embryos.
DOI: 10.5061/dryad.hj68b/3
title: RAxML_bipartitions

description: Killifish RAxML tree with bootstrap values.
DOI: 10.5061/dryad.hj68b/4
title: Killifish timetree (Auto, Soft)

description: Killifish timetree generated with MCMCTree program in PAML 4.5. Autocorrelated rates, soft-bounded constraints.
DOI: 10.5061/dryad.hj68b/5
title: Killifish timetree (IR, Soft)

description: Killifish timetree generated with MCMCTree program in PAML 4.5. Independent rates, soft-bounded constraints.
DOI: 10.5061/dryad.hj68b/6
title: Killifish timetree (Auto, Hard)

description: Killifish timetree generated with MCMCTree program in PAML 4.5. Autocorrelated rates, hard-bounded constraints.
DOI: 10.5061/dryad.hj68b/7
title: Killifish timetree (IR, Hard)

description: Killifish timetree generated with MCMCTree program in PAML 4.5. Independent rates, hard-bounded constraints.
DOI: 10.5061/dryad.hj68b/8
title: Embryo developmental pathway data set

description: Data set documenting morphological and physiological divergence along alternative developmental pathways in annual killifish.
DOI: 10.5061/dryad.hj68b/9
title: Nothobranchius furzeri embryo metabolic rate

description: Rate of oxygen consumption (metabolic rate) in Nothobranchius furzeri embryos over the course of development.
DOI: 10.5061/dryad.76173/10
title: Site10_TenerifeTeno2

description: Pollination matrix from Tenerife Teno (Site 10). Pollination networks are arranged with pollinators in the rows and plant species in the columns. Values in the matrix represents total number of observed visits between plants and pollinators.
DOI: 10.5061/dryad.76173/11
title: Site11_Gomera1

description: Pollination matrix from La Gomera (Site 11). Pollination networks are arranged with pollinators in the rows and plant species in the columns. Values in the matrix represents total number of observed visits between plants and pollinators.
DOI: 10.5061/dryad.76173/3
title: Site3_Fuerteventura1

description: Pollination matrix from Fuerteventura (Site 3). Pollination networks are arranged with pollinators in the rows and plant species in the columns. Values in the matrix represents total number of observed visits between plants and pollinators.
DOI: 10.5061/dryad.76173/4
title: Site4_Fuerteventura2

description: Pollination matrix from Fuerteventura (Site 4). Pollination networks are arranged with pollinators in the rows and plant species in the columns. Values in the matrix represents total number of observed visits between plants and pollinators.
DOI: 10.5061/dryad.76173/5
title: Site5_GranCanaria1

description: Pollination matrix from Gran Canaria (Site 5). Pollination networks are arranged with pollinators in the rows and plant species in the columns. Values in the matrix represents total number of observed visits between plants and pollinators.
DOI: 10.5061/dryad.76173/6
title: Site6_GranCanaria2

description: Pollination matrix from Gran Canaria (Site 6). Pollination networks are arranged with pollinators in the rows and plant species in the columns. Values in the matrix represents total number of observed visits between plants and pollinators.
DOI: 10.5061/dryad.76173/7
title: Site7_TenerifeSouth1

description: Pollination matrix from Tenerife South (Site 7). Pollination networks are arranged with pollinators in the rows and plant species in the columns. Values in the matrix represents total number of observed visits between plants and pollinators.
DOI: 10.5061/dryad.76173/8
title: Site8_TenerifeSouth2

description: Pollination matrix from Tenerife South (Site 8). Pollination networks are arranged with pollinators in the rows and plant species in the columns. Values in the matrix represents total number of observed visits between plants and pollinators.
DOI: 10.5061/dryad.76173/9
title: Site9_TenerifeTeno1

description: Pollination matrix from Tenerife Teno (Site 9). Pollination networks are arranged with pollinators in the rows and plant species in the columns. Values in the matrix represents total number of observed visits between plants and pollinators.
DOI: 10.5061/dryad.76173/12
title: Site12_Gomera2

description: Pollination matrix from La Gomera (Site 12). Pollination networks are arranged with pollinators in the rows and plant species in the columns. Values in the matrix represents total number of observed visits between plants and pollinators.
DOI: 10.5061/dryad.76173/13
title: Site13_Hierro1

description: Pollination matrix from El Hierro (Site 12). Pollination networks are arranged with pollinators in the rows and plant species in the columns. Values in the matrix represents total number of observed visits between plants and pollinators.
DOI: 10.5061/dryad.76173/14
title: Site14_Hierro2

description: Pollination matrix from El Hierro (Site 12). Pollination networks are arranged with pollinators in the rows and plant species in the columns. Values in the matrix represents total number of observed visits between plants and pollinators.
DOI: 10.5061/dryad.76173/15
title: Distance_between_sites_Dryad

description: Pairwise geographical distance between all 14 sites. Measured in meters.
DOI: 10.5061/dryad.b42h2/1
title: assembled transcripts

description: Total assembled transcripts
DOI: 10.5061/dryad.b42h2/2
title: SSRs from giant panda transcriptome

description: microsatellites identified in giant panda blood transcriptome
DOI: 10.5061/dryad.b42h2/3
title: novel gene id

description: the ids of novel gene
DOI: 10.5061/dryad.b42h2/4
title: transcript expression value FPKM and TPM

description: all transcripts expression value FPKM and TPM
DOI: 10.5061/dryad.b42h2/5
title: SNP sites
DOI: 10.5061/dryad.r69g1/1
title: Oxalis_pes-caprae_SSR

description: Range, population, individual code, morph and ploidy level, together with microsatellite data for Oxalis pes-caprae individuals. Columns are separated by TABs. Due to the polyploid constitution of these taxa, multiple alleles per individual and locus were scored.
DOI: 10.5061/dryad.r69g1/2
title: Oxalis_pes-caprae_FCM

description: Ploidy level of Oxalis pes-caprae populations investigated in this study. The sample size, genome size estimates (in pg) using flow cytometry and minimum (Min) and maximum (Max) genome size estimates are provided for each population and ploidy level (2x, diploid; 4x, tetraploid; 5x, pentaploid).
DOI: 10.5061/dryad.r69g1/3
title: Oxalis pes-caprae neighbor-joining tree

description: Tree output from a neighbor-joining distance analysis based on dissimilarity matrix of 380 individuals of Oxalis pes-caprae and seven SSR markers. The format is a nexus tree file format and the analyses were carried in the package 'ape' (Paradis et al. 2004) in R.
DOI: 10.5061/dryad.sk6d5/1
title: Gene Expression Relative to Average Housekeeping

description: This file is a cvs that has the level of expression of each of the 9 opsins, 1 rhodopsin and 3 housekeeping genes measured relative to the average of the 3 housekeeping genes (Bactin, COI, and MyosinHC). These numbers are for each individual along with information on the sex, standard length (SL), population (AHP- Aripo High Predation, ALP- Aripo Low Predation, MHP- Marianne High Predation, MLP- Marianne Low Predation), Watershed, Predation regime, Day of collection and Time of day collected (1- 07:30, 2- 10:30, 3- 13:30, 4- 16:30).
DOI: 10.5061/dryad.sk6d5/2
title: Opsin Gene Expression As Proportion of Total Opsin Expression

description: This file is a csv that has the level of expression of each of the 9 opsins measured as a proportion of total opsin expression. These numbers are for each individual along with information on the sex, standard length (SL), population (AHP- Aripo High Predation, ALP- Aripo Low Predation, MHP- Marianne High Predation, MLP- Marianne Low Predation), Watershed, Predation regime, Day of collection and Time of day collected (1- 07:30, 2- 10:30, 3- 13:30, 4- 16:30).
DOI: 10.5061/dryad.sk6d5/3
title: Stats in R

description: This file has all stats run on this project and utilizes the data sets also available in Dryad.
DOI: 10.5061/dryad.sk6d5/4
title: Trinidad Environmental Parameters

description: This is a csv file that has the raw environmental parameters measured for each of the populations on each of the 3 days. These include: Temperature (C), Conductivity, Dissolved Oxygen (DO), pH, Total Dissolved Oxygen (TDS), Salinity, and Resistivity
DOI: 10.5061/dryad.sk6d5/6
title: Ala Ser 180 Frequency of LWS1

description: This file has the genotype data for LWS-1 for individuals sequenced as well as the population information.
DOI: 10.5061/dryad.4g42q.2
title: Data from: Phylogeny, palaeontology, and primates: do incomplete fossils bias the tree of life?
DOI: 10.5061/dryad.8ff2v.1
title: Data from: Uterine gene expression in the live-bearing lizard, Chalcides ocellatus, reveals convergence of squamate reptile and mammalian pregnancy mechanisms
DOI: 10.5061/dryad.8ff2v.2
title: Data from: Uterine gene expression in the live-bearing lizard, Chalcides ocellatus, reveals convergence of squamate reptile and mammalian pregnancy mechanisms
DOI: 10.5061/dryad.8ff2v.2/1.2
title: Identified cDNAs from combined pregnant and non-pregnant uteri of Chalcides ocellatus.

description: Identified cDNAs from combined pregnant and non-pregnant uteri of Chalcides ocellatus.  Identifications by blastx search against multiple vertebrate genomes.
DOI: 10.5061/dryad.8ff2v.2/2.2
title: Chalcides Illumina read files
DOI: 10.5061/dryad.fb436/1
title: Nuclear microsatellite data

description: Nuclear microsatellite data for 772 maritime pine trees.
DOI: 10.5061/dryad.fb436/2
title: Candidate gene SNP data

description: Data for 266 SNPs obtained from candidate genes and genotyped on 772 trees.
DOI: 10.5061/dryad.fb436/3
title: Control SNP data

description: Data for 1745 control SNPs genotyped on 495 trees.
DOI: 10.5061/dryad.sk6d5/5
title: Light Measures

description: This is a csv file of the measures of lambda p50 for each population measured on each of the 3 days.
DOI: 10.5061/dryad.sk6d5/7
title: LWS1 Alignment

description: Alignment of LWS-1 sequences in FASTA format. Individuals correspond with other data sets in this Dryad file and can be correlated with environmental data presented there.
DOI: 10.5061/dryad.4g42q.1
title: Data from: Phylogeny, palaeontology, and primates: do incomplete fossils bias the tree of life?
DOI: 10.5061/dryad.4g42q.2/1.2
title: Dataset S1. Combined morphology-DNA data matrix in nexus format

description: We compiled a dataset of morphological and molecular characters, sampled at genus level for 24 extant primates and two outgroups. Genera represented in previous studies (Seiffert et al. 2009; Springer et al. 2012) by multiple species were condensed into single terminals in order to minimize missing data. In cases where different species within a genus exhibited different character states, we coded the genus as polymorphic for that character. Condensing taxa to genus-level also has the advantage of improving the tractability of both MP and Bayesian phylogenetic analysis by slightly reducing the number of terminals. 	We used the alignment of Springer et al. (2012; Treebase accession #S13451) as our molecular dataset, consisting of 61199 nucleotide characters distributed across 69 nuclear and 10 mitochondrial genes. This alignment comprises part of our morphology-DNA data matrix in our supplementary data file S1.
DOI: 10.5061/dryad.4g42q.2/2.2
title: Dataset S2. Morphological data matrix in nexus format

description: Our morphological dataset was derived primarily from Seiffert et al. (2009), updated by Gladman et al. (2013) and Boyer and Seiffert (2013), and enabled us to sample 85 fossil taxa. In order to improve overlap with the available DNA sequences, several extant taxa were added: Callicebus sp., Cebus sp., Chlorocebus aethiops, Colobus sp., Daubentonia madagascariensis, Hylobates sp., Macaca sp., and a composite Dermoptera consisting of Cynocephalus volans and Galeopithecus variegatus, treated as a single taxon. Characters were coded from direct observations of museum specimens housed at the University Museum of Zoology, Cambridge, based on the descriptions in the matrix of Seiffert et al. (2009), supplemented with images available from www.digimorph.org, and data from Luckett (1976), Wible and Covert (1987), Beard et al. (1988), Dagosto (1990), Yoder (1994), Ross et al. (1998), Gebo (2001), and Pilbeam (2004). Our morphology matrix is available in nexus format as supplementary data (S2) and from http://www.datadryad.org. Postcranial data for Callicebus moloch and Chlorocebus aethiops were derived primarily from Ross et al. (1998) and Yoder (1994), respectively. Alouatta seniculus and Pan troglodytes were added to the matrix using data from Boyer and Seiffert (2013) and Seiffert (pers. comm.). Facial vibrissae (Yoder 1994: character 61) were coded for new taxa according to the presence of vibrissae musculature as reported in Muchlinski et al. (2013). Not all characters have been treated consistently by previous investigators, or were sufficiently described and illustrated so as to enable coding new taxa. Where the anatomical basis for making a particular coding decision was not clear to us, we have left previous codings as-is and added only "?" to our new taxa.
DOI: 10.5061/dryad.4g42q.2/4.2
title: Table S1.

description: Table S1: Key linking X-axis of Fig. 8 to taxon names.
DOI: 10.5061/dryad.4g42q.2/5.2
title: Figure S1.

description: Fig S1: Asymmetric means of calculating topological similarity. AFT-ECT represents number of splits in extant combined topology shared with artificial fossil topologies (also given in Fig. 1).  ECT-AFT represents splits in artificial fossil topologies shared with extant combined topology. Number of morphological characters (X-axis) corresponds to 0-100% complete (out of 360 total) in 10% intervals.
DOI: 10.5061/dryad.4g42q.2/6.2
title: Figure S2. Q accuracy

description: Fig. S2: Relationship between Q and topological accuracy. Q quantifies the extent to which a dataset is evenly sampled across partitions; as Q approaches 1 all partitions are evenly sampled; as Q approaches 0 only one partition contains data. Topological accuracy is quantified as the number of splits (i.e., unrooted clades) in the well corroborated, extant combined topology (or ECT, Fig. 1) present in the artificialfossil topology (or AFT).  For the 85 fossil templates, there is astatistically significant correlation (Pearson’s R = 0.694, p &lt;&lt;0.01, Rohlf & Sokal 1995: table R) between Q values (X-axis) and ECT splits present in AFTs (Y-axis). “All fossils” (black circles) represent our 85 real fossil templates, with a select few identified with polygons. “Random templates” (open circles) indicate artificial fossils generated using real character state data with missing entries inserted at randomacross partitions (see Fig. 2a and Methods).
DOI: 10.5061/dryad.f20v3/1
title: Capture Matrix

description: Annual capture histories for porcupines at Sandhill Wildlife Area, WI from 1996 to 2013.
DOI: 10.5061/dryad.17m5q/1
title: Data from: Ebola cases and health system demand in Liberia

description: This zip directory contains the data, R code, and simulation results required to reproduce analyses reported in the associated paper.
DOI: 10.5061/dryad.2n6p6/1
title: gorilladata
DOI: 10.5061/dryad.7613f/1
title: The combined COI and 28S rRNA Bayesian tree and DNA sequences

description: The combined COI and 28S rRNA Bayesian tree and DNA sequences
DOI: 10.5061/dryad.9s3k6/1
title: TgenBeetlesWildLab
DOI: 10.5061/dryad.dh2vr/1
title: Scavenger Activity at Puma Kills and Experimental Carcasses
DOI: 10.5061/dryad.f20v3/2
title: Spring_fall_KM_datafile

description: Weekly monitoring record radio-collared juvenile and adult porcupines at Sandhill Wildlife Area from 23 April through 15 October 2012.
DOI: 10.5061/dryad.mc5m6/1
title: Guppy Data
DOI: 10.5061/dryad.mc5m6/2
title: All Ecosystem Data
DOI: 10.5061/dryad.nf2h5/1
title: DRYAD_Luza_et_al.

description: Data is organized in dynamic spreadsheets. Basic trapping unity was a sampling point composed by two traps (See Sampling of non-volant small mammals on Material and methods). Sampling unities used in data analysis were transects composed by eight trapping points. The file “Data_bank_Luza_et_al.” is composed by two spreadsheets: Occurrence_data and Individual_traits. Species traits and information about phylogenetic reconstruction will be available with the manuscript and appendices.
DOI: 10.5061/dryad.rj370/1
title: Schrader_Jarrett_Kilner_2015_dataset

description: Data for the analyses described in Schrader, Jarrett, and Kilner 2015.  Columns are as follows: line (the experimental line, F = Full Care, N = No Care), treatment (the breeding environment, F = Full Care, N = No Care), rep (replicate), block (the experimental block, A or B), carcass_mass (the mass of the breeding carcass in grams), no_larvae (the number of larvae at dispersal), brood_mass (the mass of the entire brood at dispersal in grams), mean_larval_mass (the average mass of larvae at dispersal in grams), success (whether the breeding attempt produced at least one larva, 0 = no dispersing larvae, 1 = at least 1 dispersing larva), carcass_consumption (whether the brood consumed the breeding carcass, 0 = carcass not completely consumed, 1 = carcass completely consumed).
DOI: 10.5061/dryad.4r5b8/1
title: Materials and methods

description: Detailed description of the required to reproduce the analysis presented in Figure 1 of the letter.
DOI: 10.5061/dryad.4r5b8/2
title: Raw data of empirical phylogenetic analyses

description: Alignment and trees associated with empirical results.
DOI: 10.5061/dryad.4r5b8/3
title: Raw data of simulation analyses

description: Alignment and trees associated with simulation-based analyses
DOI: 10.5061/dryad.7613f/2
title: The COI Bayesian tree and DNA sequences

description: The COI Bayesian tree of fig pollinating wasps and DNA sequences
DOI: 10.5061/dryad.7613f/3
title: The 28S rRNA Bayesian tree and DNA sequences

description: The 28S rRNA Bayesian tree of fig pollinating wasps and DNA sequences
DOI: 10.5061/dryad.7613f/4
title: The COI Bayesian tree of the genus Ceratosolen and DNA sequences

description: The COI Bayesian tree of the genus Ceratosolen and DNA sequences
DOI: 10.5061/dryad.7613f/5
title: The COI Bayesian tree of the genus Eupristina and DNA sequences

description: The COI Bayesian tree of the genus Eupristina and DNA sequences
DOI: 10.5061/dryad.7613f/6
title: The COI Bayesian tree of Ceratosolen gravelyi and Ceratosolen emarginatus and DNA sequences

description: The COI Bayesian tree of Ceratosolen gravelyi and Ceratosolen emarginatus and DNA sequences
DOI: 10.5061/dryad.d143r/1
title: SingleGeneAlignments

description: Contains four species single gene alignments used for the M-K tests in the manuscript.
DOI: 10.5061/dryad.d143r/3
title: PAMLInputFiles

description: Contains the codeml.ctl text files and tree files used to run the PAML analyses.
DOI: 10.5061/dryad.d143r/4
title: PAMLOutputFiles

description: Contains the output text files for the PAML analyses.
DOI: 10.5061/dryad.d143r/5
title: PAMLAlignments
DOI: 10.5061/dryad.d143r/6
title: clpP full and partial duplication

description: Phylip alignment of the full clpP coding sequence for Campanulastrum americanum as well as the partial duplication of the first exon.
DOI: 10.5061/dryad.t120k/1
title: hemagglutinin trees global

description: Hemagglutinin trees generated by BEAST for global analysis in NEXUS format
DOI: 10.5061/dryad.t120k/2
title: neuraminidase trees global

description: Neuraminidase trees generated by BEAST for global analysis in NEXUS format
DOI: 10.5061/dryad.t120k/3
title: hemagglutinin trees NA/OT

description: Hemagglutinin trees generated by BEAST for NA/OT analysis in NEXUS format
DOI: 10.5061/dryad.t120k/4
title: neuraminidase trees NA/OT

description: Neuraminidase trees generated by BEAST for NA/OT analysis in NEXUS format
DOI: 10.5061/dryad.t120k/10
title: neuraminidase trees global log file

description: Combined log files for neuraminidase trees generated by BEAST for global analysis
DOI: 10.5061/dryad.t120k/11
title: hemagglutinin trees global xml

description: BEAST xml file used to generate hemagglutinin trees for global analysis (a single chain)
DOI: 10.5061/dryad.t120k/12
title: neuraminidase trees global xml

description: BEAST xml file used to generate neuraminidase trees for global analysis (a single chain)
DOI: 10.5061/dryad.t120k/13
title: neuraminidase trees NC/SC/OT log file

description: Combined log files for neuraminidase trees generated by BEAST for NC/SC/OT analysis
DOI: 10.5061/dryad.t120k/14
title: neuraminidase trees NC/SC/OT xml file
DOI: 10.5061/dryad.t120k/5
title: hemagglutinin trees NC/SC/OT log files

description: Combined log files for hemagglutinin trees generated by BEAST for NC/SC/OT analysis
DOI: 10.5061/dryad.t120k/6
title: hemagglutinin trees NC/SC/OT xml
DOI: 10.5061/dryad.t120k/7
title: hemagglutinin trees NC/SC/OT

description: Hemagglutinin trees generated by BEAST for NC/SC/OT analysis in NEXUS format
DOI: 10.5061/dryad.t120k/8
title: neuraminidase trees NC/SC/OT

description: Neuraminidase trees generated by BEAST for NC/SC/OT analysis in NEXUS format
DOI: 10.5061/dryad.t120k/9
title: hemagglutinin trees global log file

description: Combined log files for hemagglutinin trees generated by BEAST for global analysis