cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7sb0f/4
title: FASTA_alignments

description: Complete FASTA alignments, one file per genomic regions, for all captured sequences described in the paper. Data are phased using Fastphase as described and provided as two haplotypes per sample (A and B)
DOI: 10.5061/dryad.81840/1
title: Euphorbia nicaeensis AFLP data matrix

description: AFLP genotypes for E. nicaeensis individuals in 40 plots. "Open" refers to plots of non-facilitated individuals, while "Facilit" refers to plots of individuals growing under Juniperus sabina shrubs. Rows correspond to individual plants, while columns are the 112 loci genotyped. This is a tab-delimited text file.
DOI: 10.5061/dryad.82vr1.1
title: Data from: Is diagnosability an indicator of speciation? Response to ‘Why one century of phenetics is enough’
DOI: 10.5061/dryad.82vr1.2
title: Data from: Is diagnosability an indicator of speciation? Response to ‘Why one century of phenetics is enough’
DOI: 10.5061/dryad.82vr1.2/3.1
title: Appendix 1

description: UNSUPPORTED SPLITS IN G&G
DOI: 10.5061/dryad.82vr1.2/4.1
title: Appendix 2

description: EXAMPLES OF INTRASPECIFIC DIAGNOSABILITY BASED ON GENETIC DATA
DOI: 10.5061/dryad.8rg46/1
title: Supplementary Material Cox et al.

description: Latex generated PDF.
DOI: 10.5061/dryad.9c568/8
title: flu H1 MCMCtree in.BV file
DOI: 10.5061/dryad.bm676/2
title: WEATHER_daily_2005_2009

description: WEATHER_daily_2005_2009 contains summarized daily data from automated weather stations, processed with Hobo ware software (Onset Computer Corp., Bourne, MA, USA). Columns are as follows. | site_abbr = abbreviated site weather_id = site index no. | demography_id = index number of the site if it resided at a population where demographic data were collected | easting_UTM_NAD27 - easting in meters UTM NAD 1927, zone 11 North | northing_UTM_NAD27 - northing in meters UTM NAD 1927, zone 11 North | elevation - meters above sea level | date_time | year | month | Precip_mm – daily cumulative precipitation in mm | Tmax_C - daily maximum temperature, in degrees centigrade | Tmin_C – daily minimum temperature, in degrees centigrade | Tmean_C - daily mean temperature, in degrees centigrade
DOI: 10.5061/dryad.c37h8/2
title: Data By Nestling

description: This file contains data for each nestling that was sampled and included in the paper. Columns are self-explanatory. These data can be linked to the males in the 'Data by Male' file using the 'Lookup_Code' column in each file.
DOI: 10.5061/dryad.d71n2/1
title: Parker_et_al_2012

description: Linear (mm) measures of the forearm, and weight (mg) of the body and testes of quacking frogs collected from 10 natural populations in Western Australia
DOI: 10.5061/dryad.dc976/1
title: Poe.supplTable
DOI: 10.5061/dryad.f65bn/1
title: Formica aquilonia - Morphometrics

description: Landmark assignation data from tps morphometry suite.
DOI: 10.5061/dryad.f65bn/2
title: Formica fennica - Morphometrics

description: Landmark assignation data from tps morphometry suite.
DOI: 10.5061/dryad.f65bn/3
title: Formica pratensis - Morphometrics

description: Landmark assignation data from tps morphometry suite.
DOI: 10.5061/dryad.f9j72/1
title: feather melanin composition

description: comma-separated file
DOI: 10.5061/dryad.f9j72/2
title: feather spectophotometry

description: comma-separated data
DOI: 10.5061/dryad.k41qk/3
title: 1_AntSesB_120620
DOI: 10.5061/dryad.rd37p/1
title: Fritz_2014_Pelomedusa_Zootaxa_Supporting Information

description: Supporting InformationTABLE S1. Used samples, GenBank sequences and their accession numbers.TABLE S2. Primer sequences for mtDNA fragments for fresh samples. Nucleotides in brackets represent variable positions.TABLE S3. Primer sequences and lengths of amplified PCR products of mtDNA fragments of the 12S, cyt b and ND4 genes for historical DNA samples. TABLE S4. PCR conditions for historical and fresh samples.TABLE S5. Degree of overlap for individual mtDNA fragments yielding 251–252 bp of the 12S rRNA gene.TABLE S6. Degree of overlap for individual mtDNA fragments yielding 319 bp of the cyt b gene.TABLE S7. Degree of overlap for individual mtDNA fragments yielding 437 bp of the ND4 gene.TABLE S8. Partitioning scheme and models selected by the Akaike Information Criterion in MrMODELTEST 2.3 (Nylander 2004).
DOI: 10.5061/dryad.rh686/1
title: Morphology

description: Geometric morphometric landmarks and linear measurements for experimental F1 threespine stickleback, their parents, wild type adults and young of the year individuals. Wild caught fish derive either from a lake or a stream site whereas experimental families were split and raised either under a benthic or limnetic diet.
DOI: 10.5061/dryad.t85n3/4
title: Input files for ordination analysis

description: The six essential files here relate to the main ordination results and Fig. 3 of the main paper. They are based on the data sets for large trees (stem diameter ≥ 50 cm) in the P- and NW plots, viz. p91lar, p05lar and nw03lar, and applying the two alternative 1-ha grids (‘xa’, origin of plot [offset = 0, in title line]; ‘xb’, origin shifted [=1]: see main paper text for explanation). The format is ‘Cornell condensed’: each set of lines starting with the sample number (here 1-ha subplots) has several pairs of values – one the species’ number and the other its abundance (in this case basal area dm2/ha [‘ba/d’ = 1 in title line]), for those species present in that subplot. At the end of the file are listed the species’ codes (refer to codes.txt) and sample numbers (80 for P-plot, 49 for NW-plot). Rare species were not excluded. Note: the format line may need adjusting slightly to suit different programs; here it is set for PC-ORD; McCune & Grace 2002).
DOI: 10.5061/dryad.t894r/1
title: Flaxman_Feder_Nosil_data
DOI: 10.5061/dryad.t9f2g/1
title: Cattle SNP data

description: Text file "Cattle SNP data_Heredity" involves genotypes from 771 SNPs on BTA27 of the German Holstein-Friesian cattle. First column "id" represents 806 animals with two haplotypes each. Every column represents a SNP with the position at the top. Positions are provided as inter-marker distance to the next SNP.
DOI: 10.5061/dryad.td12f/1
title: AFLPscore

description: AFLP scores for the specimens examined.
DOI: 10.5061/dryad.td12f/2
title: morphology

description: Morphometric characters and body coloration of the specimens examined.
DOI: 10.5061/dryad.tf8rn/1
title: Skua individual collecting sites and genotypes

description: Collecting sites and genotypes for each individual arctic skua and long-tailed skua. Genotypes are given in terms of haplotype numbers which correspond to numbers given in the haplotype alignment file and Genbank Accessions
DOI: 10.5061/dryad.tf8rn/2
title: Skua Haplotype alignments

description: Alignments of arctic skua and long-tailed skua haplotypes.
DOI: 10.5061/dryad.ts2hj/1
title: pyRAD output: c88_d6m4p2_wRE.readloci

description: Locus file from pyRAD, clustering at 0.88 similarity, a minimum of 4 individuals per locus. This file can be read in using the read.pyRAD function of the R package RADami (http://cran.r-project.org/web/packages/RADami/index.html); structure of the data is described in the documentation to pyRAD (code.google.com/p/pyrad/; www.dereneaton.com/software). Briefly, each locus is represented by a sequence alignment of those individuals for which the cluster was found, and loci are delimited by a break line that indicates variable sites.
DOI: 10.5061/dryad.ts2hj/2
title: pyRAD loci output: c88_d6m10p2_wRE.readloci

description: Locus file from pyRAD, clustering at 0.88 similarity, a minimum of 10 individuals per locus. This file can be read in using the read.pyRAD function of the R package RADami (http://cran.r-project.org/web/packages/RADami/index.html); structure of the data is described in the documentation to pyRAD (code.google.com/p/pyrad/; www.dereneaton.com/software). Briefly, each locus is represented by a sequence alignment of those individuals for which the cluster was found, and loci are delimited by a break line that indicates variable sites.
DOI: 10.5061/dryad.ts2hj/3
title: Phylip file: d6m10.phy

description: Phylip-style (sequential) multiple alignment file, generated from pyRAD loci d6m10 file.
DOI: 10.5061/dryad.ts2hj/4
title: blast2go results: 2013-04-09.data

description: blast2go results of d6m10 loci against three EST databases.
DOI: 10.5061/dryad.ts2hj/5
title: Phylogenetic analyses.EST.2013-03-28

description: Results of phylogenetic analyses conducted on EST-length subsets of the original RAD dataset.
DOI: 10.5061/dryad.ts2hj/6
title: BLASTN results: blasts.2013-02-21

description: BLASTN results of m10 RAD locus consensus sequences against EST databases in NCBI.
DOI: 10.5061/dryad.v0668/1
title: focal bee data

description: Field observations.  See original manuscript for more information.
DOI: 10.5061/dryad.vq587/12
title: Appendix_A_Intersection_HAO_SPD_TADS

description: List of correspondences found in common between HAO, SPD & TADS.
DOI: 10.5061/dryad.vq587/13
title: Appendix_B_Intersection_HAO_TGMA_FBbt

description: List of correspondences found in common between HAO, TGMA & FBbt.
DOI: 10.5061/dryad.vq587/15
title: Appendix_D_SPD_HAO_Manual_vs_LOOM

description: Comparison of manually identified correspondences and those found by the algorithm LOOM (from Bioportal) between HAO & SPD.
DOI: 10.5061/dryad.vq587/16
title: Appendix_E_TGMA_HAO_Manual_vs_LOOM

description: Comparison of manually identified correspondences and those found by the algorithm LOOM (from Bioportal) between HAO & TGMA.
DOI: 10.5061/dryad.vq587/17
title: Appendix_F_FBbt_HAO_Manual_vs_LOOM

description: Comparison of manually identified correspondences and those found by the algorithm LOOM (from Bioportal) between HAO & FBbt.
DOI: 10.5061/dryad.1012q/2
title: kin vs random group

description: means used to generate graphs of selection response
DOI: 10.5061/dryad.1j6v6/3
title: Fasta S3 Design primers
DOI: 10.5061/dryad.1j6v6/4
title: Fasta S4 Reference Samples

description: Alignment of rodent haplotypes obtained from the 265 reference samples
DOI: 10.5061/dryad.1j6v6/5
title: Fasta S5 Rodentia Haplotypes

description: Alignment of the rodent haplotypes obtained for ethanol preserved samples
DOI: 10.5061/dryad.1j6v6/6
title: Fasta S6 Prey Haplotypes

description: Alignment of the prey haplotypes obtained from faecal and pellet samples
DOI: 10.5061/dryad.1j6v6/7
title: Fasta S7 Museum Murinae True Haplotypes

description: Alignment of the rodent haplotypes obtained from museum samples
DOI: 10.5061/dryad.1j6v6/8
title: Fasta S8 Museum Human DNA contamination Haplotypes

description: Alignment of the human haplotypes retrieved from rodent museum sample analysis
DOI: 10.5061/dryad.1j6v6/9
title: Fasta S9 Museum DNA contamination Haplotypes

description: Alignment of the vertebrate haplotypes corresponding to contaminations detected in rodent museum samples
DOI: 10.5061/dryad.57rr4/1
title: Data from Louis et al. Mol Ecol
DOI: 10.5061/dryad.57vg4/5
title: Supporting Alignment S1

description: All Sanger sequences generated for this study.
DOI: 10.5061/dryad.6h822/9
title: Figure_5_Tank4(A24C)

description: Paternity analysis for Tank 4 (A24C). Study Day indicates the day on which each embryo analysed was spawned. The first 3 rows in the table are the parent fish and below that are the 20 selected offspring. The microsatellite loci used for analysis are listed along the top of the table and corresponding allelles are detailed below.
DOI: 10.5061/dryad.6s241/2
title: raw morphology of random sample of Ejagham Tilapia
DOI: 10.5061/dryad.76r4c/1
title: Posterior lobe coordinates

description: Posterior lobe outline x,y coordinates
DOI: 10.5061/dryad.76r4c/2
title: Wounding data

description: Tab-delimited text file with wounding measures and associated data.
DOI: 10.5061/dryad.80q86/1
title: datos_encuesta_estudiantes_6medicina_2011

description: Stata.v11 datafile containing survey responses. Identifiers (such as date of graduation, postal code, nationality, university, and parents who are physicians) have been removed to protect confidentiality. Age is recoded to intervals.
DOI: 10.5061/dryad.9g3cm/1
title: UCE_concat_annotated

description: Concatenated nucleotide alignment for 854 ultraconserved genomic elements (UCEs) in nine avian species and green anole reptilian outgroup
DOI: 10.5061/dryad.9g3cm/2
title: exons_concat_annotated

description: Concatenated nucleotide alignment for 594 protein-coding gene sequences in seven avian species and green anole reptilian outgroup
DOI: 10.5061/dryad.9g3cm/3
title: retroelements.tar

description: Aligned palaeognath sequences for eight retroelement insertions and surrounding flanking sequence shared by moa and tinamous, and for one retroelement insertion shared by ratites (including moa) to the exclusion of tinamous (locus 7292)
DOI: 10.5061/dryad.bm676/10
title: GIS_Slope_aspect

description: Ascii file for species distribution modeling, locations in UTM NAD 1927, Zone 11 North, cellsize = 100 m. This file contains slope aspect, in degrees, estimated from a re-scaled 30 m digital elevation model (USGS).
DOI: 10.5061/dryad.bm676/11
title: GIS_Slope_inclination

description: Ascii file for species distribution modeling, locations in UTM NAD 1927, Zone 11 North, cellsize = 100 m. This file contains slope inclination, in degrees, estimated from a re-scaled 30 m digital elevation model (USGS).
DOI: 10.5061/dryad.bm676/5
title: SPECIES_LOCATIONS_forty_one

description: Locations of Clarkia xantiana ssp. xantiana populations. Easting is eastward position (longitude) in meters, UTM NAD 27 zone 11 North, and northing is northward position (latitude) in meters, UTM NAD 27 zone 11 North.
DOI: 10.5061/dryad.bm676/6
title: SPECIES_LOCATIONS_lambda_1_or_greater

description: Locations of Clarkia xantiana ssp. xantiana populations confirmed to have long-term stochastic lambda estimates greater than 1.Easting is eastward position (longitude) in meters, UTM NAD 27 zone 11 North, and northing is northward position (latitude) in meters, UTM NAD 27 zone 11 North.
DOI: 10.5061/dryad.bm676/8
title: GIS_Elevation_mask

description: Ascii file for species distribution modeling, locations in UTM NAD 1927, Zone 11 North, cellsize = 100 m. This file is a "mask" for excluding areas &gt; 1500 m in elevation.
DOI: 10.5061/dryad.bm676/9
title: GIS_Sampling_mask

description: Ascii file for species distribution modeling, locations in UTM NAD 1927, Zone 11 North, cellsize = 100 m. This file is a "mask" for excluding areas that were searched less thoroughly for natural populations.
DOI: 10.5061/dryad.d1013/1
title: Oxytricha trifallax macronuclear PE-Assembler/SSAKE assembly

description: Contigs in gzipped fasta format.
DOI: 10.5061/dryad.dp7b8/1
title: readme

description: Description of each data file.
DOI: 10.5061/dryad.dp7b8/2
title: survival.development

description: Survival and development in Burkholderia-positive and -negative Alydus tomentosus. Includes separate .csv files with survival and time to development data and the R script used to analyze these data.
DOI: 10.5061/dryad.dp7b8/3
title: 16Sphylogeny

description: Nexus file with Greengenes-aligned sequences presented inthe 16S phylogeny.
DOI: 10.5061/dryad.dp7b8/4
title: mlst

description: Separate .fasta files  for each mlst gene and nexus file used to make mlst phylogeny.
DOI: 10.5061/dryad.dp7b8/5
title: PERMANOVA

description: Sample x OTU matrix and R script used to perform PERMANOVA analysis.
DOI: 10.5061/dryad.dp7b8/6
title: AMOVA

description: Sequences and corresponding variables for amova in mothur.
DOI: 10.5061/dryad.dp7b8/7
title: heatmap

description: Aligned sequence file and sequence identifiers for the heatmap command in mothur.
DOI: 10.5061/dryad.dp7b8/8
title: ZOIassays

description: Clearance zone data for zone of inhibition experiments.
DOI: 10.5061/dryad.f65bn/10
title: F. pratensis - Aggression Results

description: Aggression bioassay.
DOI: 10.5061/dryad.f65bn/11
title: F. pressilabris - Aggression Results

description: Aggression bioassay.
DOI: 10.5061/dryad.f65bn/12
title: F. truncorum (non-supercolonial) - Aggression Results

description: Aggression bioassay.
DOI: 10.5061/dryad.f65bn/4
title: Formica pressilabris - Morphometrics

description: Landmark assignation data from tps morphometry suite.
DOI: 10.5061/dryad.f65bn/5
title: Formica truncorum (non-supercolonial) - Morphometrics

description: Landmark assignation data from tps morphometry suite.
DOI: 10.5061/dryad.f65bn/6
title: Formica truncorum (supercolonial) - Morphometrics

description: Landmark assignation data from tps morphometry suite.
DOI: 10.5061/dryad.f65bn/7
title: All species - Foraging Results

description: Protein/carbohydrate foraging experiment
DOI: 10.5061/dryad.f65bn/8
title: F. aquilonia - Aggression Results

description: Aggression bioassay.
DOI: 10.5061/dryad.f65bn/9
title: F. fennica - Aggression Results

description: Aggression bioassay.
DOI: 10.5061/dryad.jn16g/1
title: microarraydata_vanholme_etal_2012_tpc102574

description: Microarray data of infloresence stems of twenty arabidopsis mutants in the lignin pathway and four wild type developmental stages.
DOI: 10.5061/dryad.k41qk/5
title: 3_RpS18_120620
DOI: 10.5061/dryad.m06s2/1
title: Fitness data

description: Gives the lLife Time Reproductive success (LRS = number of offspring) of males and females of 73 isofemale lines belonging to two populations (Lome and Ofuya). LRS was measured at 29C and 36C, in 5 different temporal blocks. LRS is given in raw format (number of offspring) and in relative terms (number offspring/mean) per sex:temperature:population.
DOI: 10.5061/dryad.p534s/1
title: dryad_jeb

description: Response of male bluefooted boobies to immune challenge num: bird numberTRAT: experimental treatment (C: control, E: Experimental)Date_initial: date of initial captureDate_first_recapture: date of first recaptureDate_second_recapture: date of second recaptureinitial_body_mass: body mass at initial capture1recap_bodymass: body mass at the first recapture2recap_bodymass: body mass at the second recaptureinitial_gchroma: green chroma at initial capture1recap_gchroma: green chroma at first recapture2recap_gchroma: green chroma at second recaptureprob_laying : probability to estabish a clutchlaying_date: julian laying dateclutchvolume: clutch volume in cm3
DOI: 10.5061/dryad.qt3j5/3
title: R package "resamplediversity" containing genotypes of brown bears from Dinaric Mountains and all functions required to use the reference population approach.

description: This is an R package containing all data and functions for running analyses presented in the manuscript. You will need R (www.r-project.org). You will need to install adegenet package (command: install.packages("adegenet")), and then this downloaded file (command: install.packages(file.choose(),repos=NULL)). Select resamplediversity_1.0.zip when the "File" dialog pops up. When the package is installed, invoke it from within R with library(resamplediversity). There is a user-friendly vignette: vignette("resamplediversity").
DOI: 10.5061/dryad.rh0mv/2
title: Experiment1

description: Phenotypic values measured in experiment 1
DOI: 10.5061/dryad.rh0mv/3
title: Experiment2

description: Phenotypic values measured in experiment 2
DOI: 10.5061/dryad.rh0mv/4
title: Experiment3

description: Phenotypic values measured in experiment 3
DOI: 10.5061/dryad.t788c/1
title: mpb_outbreak_maps

description: These files represent maps of mountain pine beetle infestation in Arapaho and Roosevelt National Forests, Colorado, for the years 2003, 2005, 2006, 2009, and 2010.  They are identical in their format and methods of preparation, with the exception that they represent different time periods.  They were developed from Landsat5 (2005, 2006, 2009, 2010) ora combination of Landsat5 and Landsat7 (pre-scan line corrector failure) imagery (2003) (path 32 row 34).All images were atmospherically corrected and converted to reflectance.  Cloud cover was manually removed,with areas obscured by cloud cover in one year removed from all images. The study area was masked to include only forested areas in Arapaho and Roosevelt National Forests. The images were classified using a supervised maximum-likelihood algorithm in ENVI  v.4.8 with training classes selected based on initial NDVI and change in NDMI between images. The training classes were hand selected so that Red Attack wasrepresented by pixels having high initial NDVI and declining NDMI between image pairs. The classificationwas validated by comparison with high-resolution orthoimagery.  In each file, 2 represents the binaryclass "Red Attack," and 1 represents "Non-Red Attack."  Files use the UTM Zone 13 N projection based on the WGS 1984 geographic coordinate system.
DOI: 10.5061/dryad.t788c/2
title: point_data

description: This is a spreadsheet data set containing data on infestation status (from outbreak maps) forest compositionand structure, topography, and outbreak spatial relationships for 2000 randomly-generated points.  These data were used to create conditional inference tree models analyzing how predictors of MPB spread change during outbreak cycles
DOI: 10.5061/dryad.t8q3k/2
title: Martin and Husband Survival Data

description: This data represents information on the survival of Chamerion angustifolium seedlings (2004) and juveniles (2005) transplanted in to 9 plots in the Canadian Rocky Mountains. See paper for details. Read mes included in workbook.
DOI: 10.5061/dryad.t8q3k/3
title: Martin and Husband Vegetation Survey

description: Data collected during vegetation survey conducted in 2005 at the 9 plots involved in the experiment in the Canadian Rocky Mountains. (Read me included.)
DOI: 10.5061/dryad.tk043/1
title: Adams_etal_Syst_Biol_Supplemental_Table_2_allozyme_raw_data

description: Individual allozyme genotypes for n=838 mountain galaxias at 54 allozyme loci. Gel# = individual allozyme code; Taxon/DD/RB/site no = as per Supplemental Table 1; Locus abbreviations as outlined in main text.
DOI: 10.5061/dryad.tk043/2
title: Adams_etal_Syst_Biol_unique_cytb_haplotypes

description: MEGA file of n=277 unique cytb haplotypes (271 ingroup and 6 outgroup sequences for 602bp),
DOI: 10.5061/dryad.tk043/3
title: Adams_etal_Syst_Biol_Supplemental_Table_1

description: TABLE 1. Locality, collection and sample size information for mountain galaxias specimens used in the molecular studies or prepared and assessed for the morphological studies. Sites arranged according to species, Drainage Division (DD) and River Basin (RB) (AWRC 1976). Alloz = Allozymes; Cytb = Cytochrome-b sequenced; Morph – Morphometrics; Meris – Meristics. Sample sizes for each morphological assessment include the individuals used in the final analyses, plus outliers, plus those subsequently used to assess the geographic range of each species. Taxon codes follow Table 1 and Figure 5. Where provided, sites codes match those of Raadik (2011). Sites were assigned to three regions for some of the allozyme PCoAs, namely ‘northern’ (all sites within DD 2, RB 3–17 or DD 4, RB 10–22), ‘central’ (all sites within DD 2, RB 18–35 or DD 4, RB 1–12), or ‘western’ (all sites within DD 4, RB 26 or DD 5).
DOI: 10.5061/dryad.tk043/4
title: Adams_etal_Syst_Biol_Supplemental_Table_3

description: TABLE 3. Allozyme frequencies for the 15 diagnosable candidate species, as identified using stepwise PCoA. Alleles with a frequency of less than 0.5 % in any taxon are not shown. For polymorphic loci, the frequencies of all but the rarer/rarest alleles are expressed as percentages and shown as superscripts (allowing the frequency of each rare allele to be calculated by subtraction from 100 %). Alleles not separated by a comma all shared the frequency indicated.  Taxon codes follow Table 1 and Figure 3.  A dash indicates no genotype was assignable at this locus.