cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.855pg/7
title: Concatenated alignment of RADseq data: sub_c85d6m20p3.phy

description: Concatenated alignments of RADseq data for seven Virentes taxa and eight outgroup taxa (25 samples total) used to infer phylogenetic trees. The sub_c85d6m20p3.phy alignment is 817673 bp in length. Filtered reads were clustered at an 85% threshold for within-sample clustering. The number of samples for which data needed to be recovered to include a RAD locus in the data set was 20.
DOI: 10.5061/dryad.855pg/8
title: Concatenated alignment of RADseq data: virentes_ME_c85d6m20p3.phy

description: Concatenated alignments of RADseq data for seven Virentes taxa and eight outgroup taxa (35 samples total) used to infer phylogenetic trees. The c85d6m20p3.phy alignment is 1,703,783 bp in length. Filtered reads were clustered at an 85% threshold for within-sample clustering. The number of samples for which data needed to be recovered to include a RAD locus in the data set was 20.
DOI: 10.5061/dryad.855pg/9
title: Concatenated alignment of RADseq data: virentes_ME_c85d6m4p3

description: Concatenated alignments of RADseq data for seven Virentes taxa and eight outgroup taxa (35 samples total) used to infer phylogenetic trees. The virentes_ME_c85d6m4p3.phy alignment is 6,252,421 bp in length. Filtered reads were clustered at an 85% threshold for within-sample clustering. The number of samples for which data needed to be recovered to include a RAD locus in the data set was 4.
DOI: 10.5061/dryad.8sc5p/10
title: S6-1
DOI: 10.5061/dryad.8sc5p/11
title: S7-1
DOI: 10.5061/dryad.8sc5p/12
title: S8-1
DOI: 10.5061/dryad.8sc5p/13
title: S9-1
DOI: 10.5061/dryad.8sc5p/14
title: S10-1-1
DOI: 10.5061/dryad.8sc5p/5
title: S3-1
DOI: 10.5061/dryad.8sc5p/6
title: S4-1-1
DOI: 10.5061/dryad.8sc5p/7
title: S4-1-2
DOI: 10.5061/dryad.8sc5p/8
title: S4-1-3
DOI: 10.5061/dryad.8sc5p/9
title: S5-1
DOI: 10.5061/dryad.f8j12/1
title: Additional file Table S1

description: Alignment data for Phalaenopsis amabilis species complex rDNA ITS
DOI: 10.5061/dryad.g7641/7
title: Fig 5 (extinction threshold) Matlab code

description: Matlab code to run the simulations necessary to determine the relationship between the speed of climate change (avshift) and probability of extinction.
DOI: 10.5061/dryad.p3ks4/2
title: Perl scripts used in designing and evaluating ITS primers of plants.

description: These perl scripts were designed by Tao Cheng in 2014 for designing and evaluating ITS primers of plants. The related article has been submitted to Molecular Ecology Resources. The descriptions of each script are as follow: Classifier_Fungi.plFunction: Divide the total Fungi sequences into lower classification level.Classifier_Viridiplantae.plFunction: Divide the total sequences into lower classification level.N_Degenerate_Filter_New.plFunction: Get rid of the sequences with 'n' or degenerate character.contaminantsFilter.plFunction: Remove the potential contaminated sequences from GenBank based on mega-blast.GenBanktoFastawithClassName.plFunction: Convert a GB file to fasta format in following style:# &gt;Class_Genus_Species_TaxonID_GI_ACC_length description# &gt;Nelumbonaceae_Nelumbo_lutea_4431_1479989_L75835_1713 Nelumbo lutea 18S ribosomal RNA (18S rDNA) gene# nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnncc atgcatgtgt# aagtatgaac taattcagac tgtgaaactg cgaatggctc attaaatcag ttatagtttg# tttgatggta tctactactc ggataaccgt agtaattcta gagctaatac gtgcaccaaa# .................................................................# ttgcaattgt tggtcttcaa cgaggaattc ctagtaagcg cgagtcatca gctcgcgttg# actacgtccc tgccctttgt acacaccgcc cgtcgctcct accgattgaa tggtccggtg# aagtgttcgg atcgcggcga cgtgggcggt tcgFind_Conserved_DNA_Segments.plFunction: This script is used to extract conserved DNA segments from an alignment file.MismatchDetect-Batch.plFunction: Calculate the species coverage between the primer and every target sequence.User set the mismatch allowed and the threshold of nucleotides constrained in the 3'-end.getPCRProductLengthByPrimerBlast.plFunction: This script is used to get the PCR product length of a certain primer-pair based on PrimerBlast.
DOI: 10.5061/dryad.pj620/1
title: Centroid sizes of the mapping family

description: Centroid sizes of the samples from the mapping family and the populations of the founder's origin in NTS format. The numbers and the population codes (see supplementary Table S1) of the analysed populations are: 1 granddam, 8 E2H, 1 grandsire, 12 CN, 40 F1, and 195 F2, in this order.
DOI: 10.5061/dryad.pj620/2
title: Shape variables of the mapping family

description: Partial warps and uniform components of the samples from the mapping family and the populations of the founder's origin in NTS format. The numbers and the population codes (see supplementary Table S1) of the analysed populations are: 1 granddam, 8 E2H, 1 grandsire, 12 CN, 40 F1, and 195 F2, in this order.
DOI: 10.5061/dryad.pj620/3
title: Centroid sizes of the samples from natural populations

description: Centroid sizes of the samples from the natural populations in NTS format. The numbers and the population codes (see supplementary Table S1) of the analysed populations are: 11 E1T, 20 E1S, 34 E1D, 32 E1M, 8 E2H, 18 E2R, 10 E2K, 6 E2I, 14 E3K, 10 E3I, 3 S, 28 CM, and 12 CN, in this order.
DOI: 10.5061/dryad.pj620/4
title: Shape variables of the samples from the natural populations

description: Partial warps and uniform components of the samples from the natural populations in NTS format. The numbers and the population codes (see supplementary Table S1) of the analysed populations are: 11 E1T, 20 E1S, 34 E1D, 32 E1M, 8 E2H, 18 E2R, 10 E2K, 6 E2I, 14 E3K, 10 E3I, 3 S, 28 CM, and 12 CN, in this order.
DOI: 10.5061/dryad.pj620/5
title: Input file for QTL analysis

description: Phenotypic and genotypic data of the F2 offsprings for QTL analysis in R/qtl format. Missing values are coded as "-".
DOI: 10.5061/dryad.pj620/6
title: Vertebral numbers

description: Vertebral numbers and standard lengths of the samples from the natural populations and the mapping family. Individual IDs, names and the codes (see supplementary Table S1) of the populations are also included. Missing values are coded as "-".
DOI: 10.5061/dryad.q9690/1
title: adult_pollen_beetle

description: This file contains the counts of adult pollen beetles on the main raceme of oilseed rape plants at the field edge and the field centre.
DOI: 10.5061/dryad.q9690/2
title: pollen_beetle_larvae_and_parasitism

description: This file contains the counts of pollen beetle larvae on oilseed rape plants at the field centre and at the field edge as well as the parasitism rates of pollen beetle larvae by Tersilochus heterocerus.
DOI: 10.5061/dryad.q9690/3
title: yield_landscape

description: This file contains the seed weight per plant and the yield data received from the farmers as well as the proportion of oilseed rape, the inter-annual change in the proportion of oilseed rape and the proportion of semi-natural habitats in the 1-km landscape radius around the study sites.
DOI: 10.5061/dryad.r17k4/1
title: TransplantExperiment_2012

description: Collected in the field.
DOI: 10.5061/dryad.r17k4/2
title: TransplantExperiment_2011

description: Collected in the field
DOI: 10.5061/dryad.rs5g0/1
title: Short adenovirus (hexon sequences) derived from great ape and human fecal samples

description: This FASTA file comprises 582 sequences
DOI: 10.5061/dryad.1d49q/1
title: ortholog clusters

description: Ortholog gene clusters of four Radix species created with HaMStR. These clusters were used to infer selected loci with PAML and TreeSAAP.
DOI: 10.5061/dryad.1d49q/2
title: Phylogeny clusters

description: orthologos gene clusters used for phylogenetic reconstruction of four Radix species plus Biomphalaria glabrata as outgroup
DOI: 10.5061/dryad.3c3r3/1
title: RY mtDNA tree (K-Pg constraint)

description: Timetree from divergence dating analysis in BEAST using RY coded mtDNA dataset, with topology constrained and additional maximum constraints applied so that all divergences except those for the Palaeognathae, Neognathae, and Galloanserae are constrained to occur after the K-Pg boundary.
DOI: 10.5061/dryad.3c3r3/2
title: Intron nDNA tree (K-Pg constraint)

description: Timetree from divergence dating analysis in BEAST using intron nDNA dataset, with topology constrained and additional maximum constraints applied so that all divergences except those for the Palaeognathae, Neognathae, and Galloanserae are constrained to occur after the K-Pg boundary.
DOI: 10.5061/dryad.3c3r3/3
title: Exon nDNA tree (K-Pg constraint)

description: Timetree from divergence dating analysis in BEAST using exon nDNA dataset, with topology constrained and additional maximum constraints applied so that all divergences except those for the Palaeognathae, Neognathae, and Galloanserae are constrained to occur after the K-Pg boundary.
DOI: 10.5061/dryad.3c3r3/4
title: NT mtDNA tree (K-Pg constraint)

description: Timetree from divergence dating analysis in BEAST using NT coded mtDNA dataset, with topology constrained and additional maximum constraints applied so that all divergences except those for the Palaeognathae, Neognathae, and Galloanserae are constrained to occur after the K-Pg boundary.
DOI: 10.5061/dryad.3c3r3/5
title: Exon nDNA tree (fully calibrated)

description: Timetree from divergence dating analysis in BEAST using exon nDNA dataset, with topology constrained and 15 fossil calibrations plus one root calibration applied.
DOI: 10.5061/dryad.3c3r3/6
title: Intron nDNA tree (fully calibrated)

description: Timetree from divergence dating analysis in BEAST using intron nDNA dataset, with topology constrained and 15 fossil calibrations plus one root calibration applied.
DOI: 10.5061/dryad.6nt0d/10
title: Pema7

description: fasta file for anonymous nuclear locus Pema7
DOI: 10.5061/dryad.6nt0d/11
title: Pema8

description: fasta file for anonymous nuclear locus Pema8
DOI: 10.5061/dryad.6nt0d/12
title: Pema9

description: fasta file for anonymous nuclear locus Pema9
DOI: 10.5061/dryad.6nt0d/13
title: Pema11

description: fasta file for anonymous nuclear locus Pema11
DOI: 10.5061/dryad.6nt0d/14
title: Pema12

description: fasta file for anonymous nuclear locus Pema12
DOI: 10.5061/dryad.6nt0d/15
title: Pema13

description: fasta file for anonymous nuclear locus Pema13
DOI: 10.5061/dryad.6nt0d/16
title: Pema14

description: fasta file for anonymous nuclear locus Pema14
DOI: 10.5061/dryad.6nt0d/6
title: Pema1

description: fasta file for anonymous nuclear locus Pema1
DOI: 10.5061/dryad.6nt0d/8
title: Pema5

description: fasta file for anonymous locus Pema5
DOI: 10.5061/dryad.6nt0d/9
title: Pema6

description: fasta file for anonymous nuclear locus Pema6
DOI: 10.5061/dryad.855pg/11
title: IMa input file

description: Input file (including chloroplast sequence data, NIA-i3 sequence data, and nuclear SSR data) and command line strings for IMa analyses
DOI: 10.5061/dryad.855pg/12
title: Concatenated chloroplast sequence data: Virentes

description: Concatenated chloroplast DNA sequences from trnD-trnT and rpl32–trnL(UAG) regions or seven Virentes species, 215 individuals. Source information and geographic coordinates are in the ReadMe file.
DOI: 10.5061/dryad.855pg/13
title: Chloroplast trnD-trnT: all Virentes sequences

description: Chloroplast trnD-trnT region for 391 individuals from seven Virentes species. Sequence length is 615 bp.
DOI: 10.5061/dryad.855pg/14
title: Chloroplast rp132 trnL region: all Virentes sequences

description: Chloroplast sequence data for rp132 trnL for seven Virentes species and 327 individuals. Sequence length is 835 bp.
DOI: 10.5061/dryad.8sc5p/15
title: S10-1-2
DOI: 10.5061/dryad.8sc5p/16
title: S10-1-3
DOI: 10.5061/dryad.8sc5p/17
title: S1-2
DOI: 10.5061/dryad.8sc5p/18
title: S2-2
DOI: 10.5061/dryad.8sc5p/19
title: S3-2
DOI: 10.5061/dryad.8sc5p/20
title: S4-2
DOI: 10.5061/dryad.8sc5p/21
title: S5-2
DOI: 10.5061/dryad.8sc5p/22
title: S9-2
DOI: 10.5061/dryad.8sc5p/23
title: S10-2
DOI: 10.5061/dryad.9c698/1
title: Pardon the Interruption: Goal Proximity, Perception of Spare Time, and Impatience.

description: 7 SPSS files (5 experiments) reported in the article
DOI: 10.5061/dryad.f587b/1
title: alignments_for_phylogeny

description: This fasta format file contains an alignment with a length of 9175 base pair. The alignment is constructed by concatenating the four-fold degenerate sites of the 206 high-confidence single-copy genes among 11 species, wich including Anolis carolinensis, Chamaeleo chamaeleon, Chalcides ocellatus, Phrynocephalus erythrurus, Phrynocephalus putjatia, Pogona vitticeps, Rana chensinensis, Rana kukunoris, Sphenodon punctatus, Xenopus tropicalis and Danio rerio.
DOI: 10.5061/dryad.f8j12/2
title: Additional file Table S2

description: Alignment data for Phalaenopsis amabilis species complex trnH-psbA spacer
DOI: 10.5061/dryad.f8vs9/1
title: Scheper et al_J Appl Ecol_bee, flower & landscape data

description: Data on bee abundance and richness, and flower cover and richness, in wildflower strips and control field boundaries. Data was collected in agricultural landscapes in Germany, The Netherlands, Sweden and the UK, in 2011-2013. Data on N input, percentage semi-natural habitat and early(May)- and late(July-August) floral resource availability is provided for each study landscape (1-km radius around wildflower strip or field boundary).
DOI: 10.5061/dryad.f8vs9/2
title: Scheper et al_J Appl Ecol_red listed bees

description: Species richness and abundance of red listed bee species in wildflower strips and control field boundaries in 2011 and 2012-2013 in Germany, The Netherlands, Sweden and the UK.
DOI: 10.5061/dryad.fv6fn/1
title: Weeks Bay Water Level Data

description: The data file includes water levels (m) collected in the field from three restored marshes at Weeks Bay National Estuarine Research Reserve in Baldwin County, Alabama, USA. Data were collected for low, intermediate, and high flooding scenarios using water level recorders (Levelogger & Barologger Model 3001 Edge F15/M5, Solinist Canada Ltd., Ontario, Canada) from which data were exported to MS Excel. A total of 10 water level recorders were deployed, including a control and two weirs for all three flooding scenarios and a weir control from the high flooding scenario. Water levels are relative to the soil surface (0m); NAVD88 elevations (m) for the position of the water level recorders are provided when available (NA = Not Available).
DOI: 10.5061/dryad.mk4f8/1
title: MacLeod & Steart Supplementary Files

description: Images, datafiles, results files, and software code listings for MacLeod, N., and Steart, D., 2015, Automated leaf physiognomic character identification from digital images: Paleobiology, vol. 41, No. 4.
DOI: 10.5061/dryad.nj5h5/1
title: Populus-aligned plastome sequence alignments

description: WGS short reads were aligned to the Nisqually-1 chloroplast reference genome (GenBank: EF489041.1) using BWA version 0.6.2. For each position in the reference plastome, bases were called only if the coverage was greater than 1000 reads, as the average read depth for each base pair was 7000 or greater. To improve accuracy, bases were only called if the 1000+ calls agreed for either the reference or alternate base for at least 80% of the reads. Any position not meeting these criteria was called as missing data. Indels were excluded for all analyses.
DOI: 10.5061/dryad.nj5h5/2
title: Manihot-aligned plastome sequence alignments

description: Using the same protocol as the Populus-aligned dataset, but aligned to the Manihot esculenta reference plastome (NCBI Reference Sequence: NC_010433.1).
DOI: 10.5061/dryad.nj5h5/3
title: pop_to_manihot_beauti.xml

description: XML file generated by BEAUTi for use by BEAST for dating analyses.
DOI: 10.5061/dryad.nj5h5/4
title: pop_to_manihot.log

description: BEAST log file
DOI: 10.5061/dryad.nj5h5/5
title: pop_to_manihot.trees

description: NEXUS tree file containing trees generated by BEAST.
DOI: 10.5061/dryad.nj5h5/6
title: ns_vs_s

description: Divergence statistics for the four species that were de novo assembled (P. trichocarpa, P. balsamifera, P. fremontii, Salix interior). These were calculated using scripts "parse_fasta_to_genes.pl" and "diffs.pl" from https://github.com/daisieh/phylogenomics/releases/tag/v1.01-nph
DOI: 10.5061/dryad.p352h/1
title: Data_Description_ECOG-01477_Comparison of approaches to combine species distribution models based on different sets of predictors

description: Human activities were described using different variables: water bodies (WR, LK, IMAR), population (HPd), distance to highways (Dhi) and land-cover. Land cover layers were processed so that the surface area of each class (PAST, SV, OAKM, CM, OAKW, CW, OLG, DHER, FT, IHER, LW, RW, HE, NM, VIN). Latitude and longitude were used as the spatial variables. Topography was represented by three variables: slope (S), degree of southward exposure (SE), and degree of westward exposure (WE), which were derived from digital elevation models. Climate variables (temperature and precipitation) were obtained from the datasets supplied by the Spanish Institute of Meteorology (Agencia Estatal de Meteorología).
DOI: 10.5061/dryad.r17k4/3
title: MicrosatMarkers_PlantagoLanceolata

description: Data from microsatellite markers for P. lanceolata.
DOI: 10.5061/dryad.r17k4/4
title: MicrosatMarkers_PlantagoMajor

description: Data from microsatellite markers for P. major.
DOI: 10.5061/dryad.rg0v3/1
title: GPS locations_roe deer_Germany

description: GPS locations of individual roe deer in the Bavarian Forest National Park and surrounding areas. The analysis showed in the paper (migration occurrence and related metrics) are based on this dataset, and others related to other population/species.The fields include: sex (sex of the individual animal), acquisition time (timestamp of GPS relocations), UTMx and UTMy coordinates (GPS relocations expressed as UTM easting/northing coordinates), gps_positions_animals_id (unique identifier of the locations), original_animal_id (animal name assigned at captures), animal_year_id (unique individual identifier in the population, and sample unit- i.e. data from one animal in one year).
DOI: 10.5061/dryad.rg0v3/2
title: GPS locations_roedeer_Norway

description: GPS locations of individual roe deer in Norway. The analysis showed in the paper (migration occurrence and related metrics) are based on this dataset, and others related to other population/species.The fields include: sex (sex of the individual animal), acquisition time (timestamp of GPS relocations), UTMx and UTMy coordinates (GPS relocations expressed as UTM easting/northing coordinates), gps_positions_animals_id (unique identifier of the locations), original_animal_id (animal name assigned at captures), animal_year_id (unique individual identifier in the population, and sample unit- i.e. data from one animal in one year).
DOI: 10.5061/dryad.rg0v3/3
title: GPS locations_red deer_Germany

description: GPS locations of individual red deer in the Bavarian Forest National Park and surrounding areas. The analysis showed in the paper (migration occurrence and related metrics) are based on this dataset, and others related to other population/species.The fields include: sex (sex of the individual animal), acquisition time (timestamp of GPS relocations), UTMx and UTMy coordinates (GPS relocations expressed as UTM easting/northing coordinates), gps_positions_animals_id (unique identifier of the locations), original_animal_id (animal name assigned at captures), animal_year_id (unique individual identifier in the population, and sample unit- i.e. data from one animal in one year).
DOI: 10.5061/dryad.rg0v3/4
title: GPS locations_red deer_Norway

description: GPS locations of individual red deer in Norway. The analysis showed in the paper (migration occurrence and related metrics) are based on this dataset, and others related to other population/species.The fields include: sex (sex of the individual animal), acquisition time (timestamp of GPS relocations), UTMx and UTMy coordinates (GPS relocations expressed as UTM easting/northing coordinates), gps_positions_animals_id (unique identifier of the locations), original_animal_id (animal name assigned at captures), animal_year_id (unique individual identifier in the population, and sample unit- i.e. data from one animal in one year).
DOI: 10.5061/dryad.rg0v3/5
title: GPS locations_reindeer_Norway

description: GPS locations of individual reindeer in Norway. The analysis showed in the paper (migration occurrence and related metrics) are based on this dataset, and others related to other population/species.The fields include: sex (sex of the individual animal), acquisition time (timestamp of GPS relocations), UTMx and UTMy coordinates (GPS relocations expressed as UTM easting/northing coordinates), gps_positions_animals_id (unique identifier of the locations), original_animal_id (animal name assigned at captures), animal_year_id (unique individual identifier in the population, and sample unit- i.e. data from one animal in one year).
DOI: 10.5061/dryad.s355k/1
title: DNA sequence alignment for phylogeny inference

description: DNA sequence alignments used for RAxML phylogeny inference
DOI: 10.5061/dryad.s355k/2
title: Divergence time estimate

description: BEAST input file for divergence time analyses
DOI: 10.5061/dryad.s355k/3
title: RAxML bootstrap phylogeny
DOI: 10.5061/dryad.060tg/1
title: Adams_etal_2015_DNA_extraction_method_qPCR

description: The file contains all data used in the statistical analyses described in the materials and methods section of the paper. The dataset includes: “ZE” (number of zoospore equivalents detected for each treatment or swab event), “mass” (weight in grams of individual animals prior to formalin fixation), “frogid” (unique identifiers for each individual frog), and “SF” (success or failure of Batrachochytrium dendrobatidis detection for each swab or treatment type; 1= success, 0 = fail).
DOI: 10.5061/dryad.181qq/1
title: Hobbs_et_al_Ecological_Monograph

description: These data were collected by Yellowstone National Park.  Details of data collection are given in the paper.Data files were created using R.  Details on the data files are given in the text file Description of Data files.text
DOI: 10.5061/dryad.2ps14/1
title: Flow meter ASL tests

description: Complete variable set from ASL5000 simulations (identical in xlsx and SPSS data format). A guide to calculated variables and labels is included.
DOI: 10.5061/dryad.2ps14/2
title: Flow recordings

description: Flow recordings (xlsx) for flow meters in experiments with bias flow and with Infant Flow. An example graph is provided for each recording to allow identification of variables.
DOI: 10.5061/dryad.3530j/3
title: qPCR data for β-glucosidases in females
DOI: 10.5061/dryad.3530j/4
title: qPCR data for β-glucosidases in males
DOI: 10.5061/dryad.3530j/5
title: qPCR data for peptidoglycan recognition protein in females
DOI: 10.5061/dryad.3c3r3/10
title: Intron nDNA tree (strict clock)

description: Timetree from strict clock divergence dating analysis in BEAST using intron nDNA dataset.
DOI: 10.5061/dryad.3c3r3/11
title: NT mtDNA tree (strict clock)

description: Timetree from strict clock divergence dating analysis in BEAST using NT coded mtDNA dataset.
DOI: 10.5061/dryad.3c3r3/12
title: RY mtDNA tree (strict clock)

description: Timetree from strict clock divergence dating analysis in BEAST using RY coded mtDNA dataset.
DOI: 10.5061/dryad.3c3r3/13
title: NT mtDNA tree (nominally calibrated)

description: Timetree from nominally calibrated divergence dating analysis in BEAST using NT coded mtDNA dataset and only a single root calibration.
DOI: 10.5061/dryad.3c3r3/14
title: RY mtDNA tree (nominally calibrated)

description: Timetree from nominally calibrated divergence dating analysis in BEAST using RY coded mtDNA dataset and only a single root calibration.
DOI: 10.5061/dryad.3c3r3/16
title: Intron nDNA tree (nominally calibrated)

description: Timetree from nominally calibrated divergence dating analysis in BEAST using intron nDNA dataset and only a single root calibration.