cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gs7k6/2
title: SexCloneSummary

description: This file summarizes the sex of each clone from Clonality.Sagittaria.Sexclones.xls. Within each population’s worksheet each line represents a clone for which sex phenotype is known.  Genotypic sex ratio is calculated based on these assignments. The final column “Clone.Size.Area” is the estimate of area covered (m2) by each clone (calculated by GenAlEx, see Clonality.Sagittaria.SexclonesArea.xls).
DOI: 10.5061/dryad.gs7k6/3
title: SexCloneSummary

description: This file summarizes phenotypic and genotypic sex ratio for 11 dioecious populations. It is used for the R analysis of correlation between phenotypic and genotypic sex ratio. Popn – population code. Lat – Latitude in degrees N. Long – Longitude in degrees W.	Ph.Num.f – number of ramets phenotyped as female (in field). Ph.Num.h - number of ramets phenotyped as hermaphrodite (in field). Ph.Num.m - number of ramets phenotyped as male (in field). Ph.Num.hm - number of ramets phenotyped as hermaphrodite or male (in field). Ph.Num.fh - number of ramets phenotyped as female of hermaphrodite (in field). Ph.Total – total number of ramets sex phenotyped (in field). Ph.Freq.f - proportion of ramets phenotyped as female (in field). Ph.Freq.h - proportion of ramets phenotyped as hermaphrodite (in field). Ph.Freq.m - proportion of ramets phenotyped as male (in field). G.Num.f - number of female multilocus genotypes. G.Num.h - number of hermaphrodite multilocus genotypes. G.Num.m - number of male multilocus genotypes.	G.Total – total number of multilocus genotypes with known sex phenotype. G.Freq.f - proportion of multilocus genotypes female. G.Freq.h - proportion of multilocus genotypes hermaphrodite. G.freq.m - proportion of multilocus genotypes male. Gcorr.Num.f.corr - number of female multilocus genotypes (corrected for by scoring error / mutations). G.Num.m.corr	- number of male multilocus genotypes (corrected for by scoring error / mutations). G.Total.corr – total number of multilocus genotypes (corrected for by scoring error / mutations). G.Freq.f.corr - proportion of multilocus genotypes female (corrected for by scoring error / mutations). G.freq.m.corr – proportion of multilocus genotypes male (corrected for by scoring error / mutations).
DOI: 10.5061/dryad.gs7k6/4
title: CloneSize_FvsM

description: Input file for R analysis – comparison of clone size between female and male clones in 11 dioecious populations. Each line contains information on a single multilocus genotype. Popn – population ID. Clone.ID. Clone.Sex. Clone.Size.Num – number of ramets assigned to the multilocus genotype. Clone.Size.NumNot – number of ramets assayed not assigned to this multilocus genotype	. Total.Clone.Num – total number ramets assayed in population. Clone.Size.Ppn – proportion of ramets assigned to multilocus genotype
DOI: 10.5061/dryad.gs7k6/5
title: CloneSize_byClone_GenoDive_flw

description: Input file for R analysis – comparison of clone size between female and male clones in 11 dioecious populations. Each line contains information on a single multilocus genotype. This data file was made following clone assignments corrected for scoring errors / mutations (GenoDive). Popn – population ID. Threshold – threshold genetic distance (GenoDive, see Supplement 3)	. ind. Clones. Clone.Sex. Clone.Size.Num - number of ramets assigned to the multilocus genotype	. Clone.Size.NumNot - number of ramets assayed not assigned to this multilocus genotype. Total.Clone.Num - total number ramets assayed in population. Clone.Size.Ppn - proportion of ramets assigned to multilocus genotype
DOI: 10.5061/dryad.gs7k6/6
title: Clonality.Sagittaria.SexclonesArea
DOI: 10.5061/dryad.gs7k6/7
title: CloneArea_FvsM

description: Input file for R analysis of clone size by sex. Each line is a multilocus genotype. Popn – population code. Lat – Latitude in degrees N. Long – Longitude in degrees W. Clone.ID. Clone.Sex. Clone.Size.Num – number of ramets assigned to the multilocus genotype. Clone.Size.Area-no1s - area (m2) of each multilocus genotype for which more than 1 ramet was assigned; ramets with unique genotypes are NA. Clone.Size.Area-all - area (m2) of each multilocus genotype; single ramets with unique genotypes were assigned a value of 0.1
DOI: 10.5061/dryad.gv536.2/1.1
title: Normalized small RNA read counts from whole seeds

description: Normalized reads per million (RPM) values in 300 bp windows across the entire A. thaliana genome for 21-24 nucleotide small RNAs from ColxCol, LerxLer, CvixCvi, ColxLer, LerxCol, CvixCol and ColxCvi whole seeds 6 days after pollination.
DOI: 10.5061/dryad.gv536.2/2.1
title: Allele-specific classification of small RNAs from whole seeds

description: Small RNAs overlapping Col-Cvi or Col-Ler SNPs were classified according to strain origin from ColxCol, LerxLer, CvixCvi, ColxLer, LerxCol, ColxCvi and CvixCol whole seeds 6 days after pollination.
DOI: 10.5061/dryad.gv536.2/3.1
title: Mean methylation in Arabidopsis embryo and endosperm

description: Mean methylation in overlapping 300 bp windows for embryo and endosperm from ColxCol, LerxLer, CvixCvi, CvixCol, ColxCvi, LerxCvi, and CvixLer seeds dissected 6 days after pollination. CG, CHG, and CHH methylation are quantified in separate files.
DOI: 10.5061/dryad.gv536.2/4.1
title: Weighted methylation in Arabidopsis embryo and endosperm

description: Weighted methylation values in 300 nt windows for Arabidopsis embryo and endosperm from ColxCol, LerxLer, CvixCvi, ColxCvi, CvixCol, LerxCvi, and CvixLer seeds dissected 6 days after pollination.
DOI: 10.5061/dryad.gv536.2/5.1
title: mRNA-seq read counts for Arabidopsis embryo and endosperm

description: Total and allele-specific mRNA-seq read counts, along with FPKM values, are quantified for genes and TEs from embryo and endosperm tissue from ColxCol, LerxLer, CvixCvi, ColxLer, LerxCol, ColxCvi, CvixCol, LerxCvi and CvixLer seeds dissected 6 days after pollination, along with whole seeds from ColxCvi and CvixCol.
DOI: 10.5061/dryad.gv536.2/6.1
title: Allele-specific mRNA SNP counts for Arabidopsis embryo and endosperm

description: The number of mRNA-seq reads matching each Col-Ler, Col-Cvi, or Ler-Cvi SNP is reported for data from ColxLer, LerxCol, ColxCvi, CvixCol, LerxCvi, and CvixLer embryo and endosperm dissected 6 days after pollination, along with ColxCvi and CvixCol whole seeds.
DOI: 10.5061/dryad.h738s/10
title: Fasta file of adaptive genes
DOI: 10.5061/dryad.qk22t/1
title: RT_Oorc11-VariantFinal.2.4.2-Dryad

description: GATK Unified genotyper results from multisample genotype calling of RAD sequencing of killer whales worldwide
DOI: 10.5061/dryad.s0h82/1
title: Data

description: This is data from: Active foraging for toxic prey during gestation in a snake with maternal provisioning of sequestered chemical defenses, Kojima, Yosuke, Mori, Akira.
DOI: 10.5061/dryad.t3jd5/1
title: Alignment figure S2

description: The alignment of sequences obtained by PCR amplification of putative RPS7 gene with universal primers was used to built the tree reported in Figure S2 of supplementary material.
DOI: 10.5061/dryad.t3jd5/2
title: Alignment Figure S3

description: Alignment of the first intron (locus A) of the gene RPS7 gene obtained from different species. The alignment was used to identify diagnostic polymorphisms which are highlighted in the published version (figure S3 of the supplementaty material).
DOI: 10.5061/dryad.v7d6t/1
title: Microsatellite data and geospatial coordinates for three study species

description: Excel file with three digit microsatellite data for Hybognathus placitus, Cyrinella lutrensis and Notropis atherinoides. File also contains geospatial coordinates for each sample collection.
DOI: 10.7925/drs1.ucdlib_32218
title: 24 Suffolk Street, Dublin

description: Consists of an orthorectified image of the structure in Adobe PhotoShop (PSD) format. The orthorectified image has been derived from one or more photographic images that are included as layers in the original Adobe PhotoShop (PSD) file. The composite and all other image layers have been extracted and saved in TIFF image files, and JPEG files in various resolutions have been derived from the flattened image layer to facilitate inspection.
description: Brickwork & stone structure, 4 levels above ground, constructed 1919.
description: Funded by an award from the Irish Research Council for Science, Engineering and Technology (IRCSET), Embark Initiative Postgraduate Scholarship, grant identifier RS/2011/435.
DOI: 10.7925/drs1.ucdlib_32221
title: 25 Suffolk Street, Dublin

description: Consists of 2 orthorectified images of the structure. The orthorectified images have been derived from one or more photographic image that are included as layers in the original Adobe PhotoShop (PSD) file. The composite and other image layers have been extracted and saved in TIFF image files, as well as JPEG files in various resolutions to facilitate inspection.
description: Brickwork structure, 4 levels above ground.
description: Funded by an award from the Irish Research Council for Science, Engineering and Technology (IRCSET), Embark Initiative Postgraduate Scholarship, grant identifier RS/2011/435.
DOI: 10.7925/drs1.ucdlib_32225
title: 1 St. Andrew Street, Dublin 2, Ireland

description: Consists of an orthorectified image of the structure in Adobe PhotoShop (PSD) format. The orthorectified image has been derived from one or more photographic images that are included as layers in the original Adobe PhotoShop (PSD) file. The composite and all other image layers have been extracted and saved in TIFF image files, and JPEG files in various resolutions have been derived from the flattened image layer to facilitate inspection.
description: Blockwork structure, 4 levels above ground.
description: Dublin City Council, Record of Protected Structures (2010), no. 7564
description: Funded by an award from the Irish Research Council for Science, Engineering and Technology (IRCSET), Embark Initiative Postgraduate Scholarship, grant identifier RS/2011/435.
DOI: 10.7925/drs1.ucdlib_32228
title: 2 St. Andrew Street, Dublin 2, Ireland

description: Consists of an orthorectified image of the structure in Adobe PhotoShop (PSD) format. The orthorectified image has been derived from one or more photographic images that are included as layers in the original Adobe PhotoShop (PSD) file. The composite and all other image layers have been extracted and saved in TIFF image files, and JPEG files in various resolutions have been derived from the flattened image layer to facilitate inspection.
description: Brickwork structure, 4 levels above ground.
description: Dublin City Council, Record of Protected Structures (2010), no. 7565
description: Funded by an award from the Irish Research Council for Science, Engineering and Technology (IRCSET), Embark Initiative Postgraduate Scholarship, grant identifier RS/2011/435.
DOI: 10.7925/drs1.ucdlib_32231
title: 3-4 Saint Andrew Street, Dublin

description: Consists of an orthorectified image of the structure in Adobe PhotoShop (PSD) format. The orthorectified image has been derived from one or more photographic images that are included as layers in the original Adobe PhotoShop (PSD) file. The composite and all other image layers have been extracted and saved in TIFF image files, and JPEG files in various resolutions have been derived from the flattened image layer to facilitate inspection.
description: Brickwork structure, 4 levels above ground.
description: Funded by an award from the Irish Research Council for Science, Engineering and Technology (IRCSET), Embark Initiative Postgraduate Scholarship, grant identifier RS/2011/435.
DOI: 10.7925/drs1.ucdlib_32234
title: 3-4 Saint Andrew Street, Dublin

description: Consists of an orthorectified image of the structure in Adobe PhotoShop (PSD) format. The orthorectified image has been derived from one or more photographic images that are included as layers in the original Adobe PhotoShop (PSD) file. The composite and all other image layers have been extracted and saved in TIFF image files, and JPEG files in various resolutions have been derived from the flattened image layer to facilitate inspection.
description: Brickwork structure, 4 levels above ground.
description: Funded by an award from the Irish Research Council for Science, Engineering and Technology (IRCSET), Embark Initiative Postgraduate Scholarship, grant identifier RS/2011/435.
DOI: 10.7925/drs1.ucdlib_32237
title: 5 St. Andrew Street, Dublin 2, Ireland

description: Consists of an orthorectified image of the structure in Adobe PhotoShop (PSD) format. The orthorectified image has been derived from one or more photographic images that are included as layers in the original Adobe PhotoShop (PSD) file. The composite and all other image layers have been extracted and saved in TIFF image files, and JPEG files in various resolutions have been derived from the flattened image layer to facilitate inspection.
description: Brickwork structure, 4 levels above ground.
description: Dublin City Council, Record of Protected Structures (2010), no. 7568
description: Funded by an award from the Irish Research Council for Science, Engineering and Technology (IRCSET), Embark Initiative Postgraduate Scholarship, grant identifier RS/2011/435.
DOI: 10.7925/drs1.ucdlib_32240
title: 6 St Andrew Street, Dublin

description: Consists of an orthorectified image of the structure in Adobe PhotoShop (PSD) format. The orthorectified image has been derived from one or more photographic images that are included as layers in the original Adobe PhotoShop (PSD) file. The composite and all other image layers have been extracted and saved in TIFF image files, and JPEG files in various resolutions have been derived from the flattened image layer to facilitate inspection.
description: Brickwork structure, 4 levels above ground.
description: Funded by an award from the Irish Research Council for Science, Engineering and Technology (IRCSET), Embark Initiative Postgraduate Scholarship, grant identifier RS/2011/435.
DOI: 10.5061/dryad.289c7/1
title: Data_paper2014

description: Data for paper Biology Letters Schork and Young
DOI: 10.5061/dryad.2b906/1
title: Thermal performance data for 10 Mimulus species

description: This data file includes mean performance, measured as relative growth rate in stem length or leaf number, for each family of each Mimulus species at 15, 20, 25, 30, 35, 40, 45, and 50 degrees Celsius (see publication for further details). Column names are as follows: species: species of Mimulus. family: unique ID corresponding to full-sibling seed family. temperature: daytime temperature of growth chamber. RGR_stem: mean relative growth rate in stem length (in units of cm/cm/day) across individuals of each family. RGR_leaf: mean relative growth rate in leaf number (in units of leaf #/leaf #/day) across individuals of each family.
DOI: 10.5061/dryad.3723p/10
title: Data_Fig4_and_SFig3_Human

description: Raw data used to produce Figure 4 and Figure S3 (Human dataset)
DOI: 10.5061/dryad.3723p/2
title: Code_Fig3_and_SFig2

description: Matlab code used to generate our model based panels.
DOI: 10.5061/dryad.3723p/3
title: Figure 1A

description: Neurolucida reconstructed pair of synaptically connected human pyramidal cells.
DOI: 10.5061/dryad.3723p/4
title: Poisson_Human

description: raw traces used in the average trace displayed in Figure 3B.
DOI: 10.5061/dryad.3723p/5
title: Poisson_Mouse

description: raw traces used in the average trace displayed in Figure 3A.
DOI: 10.5061/dryad.3723p/6
title: Data_Fig5_and_SFig4

description: Raw data used to produce Figure 5 and Figure S4.
DOI: 10.5061/dryad.3723p/7
title: Data S1

description: Excel sheet with numbers displayed in Figures 1C, 1D, 1E and S1A, S1B, S1C and S1D.
DOI: 10.5061/dryad.3723p/8
title: Data S2

description: Excel sheet with numbers displayed in Figure 2.
DOI: 10.5061/dryad.3723p/9
title: Data S3

description: Excel sheet with numbers displayed in Figures 5 and S4.
DOI: 10.5061/dryad.574s4/3
title: Monogenics vs amphigenics

description: Data used to distinguish the monogenic from amphigenic hermaphrodites.
DOI: 10.5061/dryad.574s4/4
title: Relative male survival

description: Population data used to calculate relative male survival.
DOI: 10.5061/dryad.574s4/5
title: Eggs & Length

description: Size and egg number data by individual shrimp used to calculate inbreeding depression.
DOI: 10.5061/dryad.7kc79/1
title: Westhus&al.2014.DRYAD.AntisepticBehaviourData
DOI: 10.5061/dryad.7kc79/2
title: Westhus&al.2014.DRYAD.SporeRemovalData
DOI: 10.5061/dryad.84t75/1
title: Brusatte et al. 2014 Current Biology Dryad File1

description: Supplementary appendices: list of phylogenetic characters, phylogenetic character-taxon matrix, list of taxon ages, list of supplementary figure captions (relevant to Dryad File 2)
DOI: 10.5061/dryad.84t75/2
title: Brusatte et al. 2014 Current Biology Dryad File2

description: Supplementary figures
DOI: 10.5061/dryad.84t75/3
title: Brusatte et al. 2014 Current Biology Dryad File3

description: R code (Graeme T. Lloyd)
DOI: 10.5061/dryad.8bk20/1
title: Lucek_et_al_JEB-2014-00477.R1_Dryad

description: Microsatellite data for contemporary and linear morphology for historical and contemporary stickleback populations from the Lake Geneva region and Switzerland.
DOI: 10.5061/dryad.9bg43/1
title: Li et al. PLoS ONE Raw Data

description: Raw data for two main studies, and supplementary masculinity discrimination and working memory studies
DOI: 10.5061/dryad.dp0qj/1
title: Ernest-etal-Genotypes_PLosOne2014

description: README file: Ernest et al. California puma (mountain lion) genetics published in PLOS ONE 2014. Title: Fractured genetic connectivity threatens a southern California puma (Puma concolor) population. Authors:  Holly B. Ernest, T. Winston Vickers, Scott A. Morrison, Michael R. Buchalski, Walter M. Boyce.  Corresponding author: Holly B. Ernest  hbernest-at-ucdavis-dot-edu and hernest-at-uwyo-dot-edu. Data file (tab-delim. text):Ernest-etal-Genotypes_PLosOne2014_FracturedConnecPumasCalif_14Aug2014.txt. File contents: Sample ID #; Population identifier; 3-digit nuclear microsatellite genotypic data (diploid, one allele per column, two columns per locus) for 46 loci (42 for the focal populations of this paper).  Locus identifier is listed in the first of the two columns for data of each locus. Data in one row per individual sample.
DOI: 10.5061/dryad.ff1tq/10
title: RAxML_bipartitions.concat_alllegume.fsa.raxml.out

description: RAxML best tree with bootstrap values estimated from concatenation of 101 orthogroups alignments. This is a Newick tree file.
DOI: 10.5061/dryad.ff1tq/11
title: DNA alignments

description: cDNA alignments for all gene families in the project, made using pal2nal. These are multifasta alignment files.
DOI: 10.5061/dryad.ff1tq/3
title: CDS translations

description: Corresponding CDS sequences for the peptide translations. These are multifasta files.
DOI: 10.5061/dryad.ff1tq/4
title: trees - bipartitions

description: The RAxML bipartitions trees for the 3360 orthogroup alignments containing Glycine max. syntelogs. These are Newick tree files.
DOI: 10.5061/dryad.ff1tq/5
title: Legume pairs - ksplots

description: Putative paralog pairs estimated from Ks plots for multiple species from study. These were used to test for other WGD events (other than PWGD). This is a tab delimited file with the first and second columns being Ks plot identified putative paralogs and the third column being a designation for the putative event.
DOI: 10.5061/dryad.ff1tq/6
title: alignments for other WGD tests

description: Alignments of orthogroups used to look at putative WGD events in data set.  These are multifasta files.
DOI: 10.5061/dryad.ff1tq/7
title: trees for other WGD tests

description: RAxML best trees with bootstrap values added (bipartitions) for orthogroups used to test for putative WGD events in data set identified through Ks plots that are not PWGD. These are Newick tree files.
DOI: 10.5061/dryad.ff1tq/8
title: single copy trees

description: Low-copy trees used to estimate a species phylogeny using MP-EST methods.
DOI: 10.5061/dryad.ff1tq/9
title: concat_alllegume.fsa

description: Concatenated nucleotide alignments for 101 orthogroups used to estimate a species tree in RAxML. This is a multifasta file.
DOI: 10.5061/dryad.gs7k6/10
title: Clonality.Sagittaria.IDclones

description: Raw clone assignments for fine-scale sampling of 10 monoecious and 11 dioecious populations. The raw data for each population is formatted for GenAlEx; dioecious populations are labeled ‘d popname’ and monoecious populations are labeled ‘m popname’.  To the right of each raw data worksheet is the GenAlEx output ‘MS’ file. From the raw output calculations of clone size are shown in columns to the right; mean for the population appears at the bottom.
DOI: 10.5061/dryad.gs7k6/11
title: ClonalDiversity

description: Popn – population ID. Sex.System. Location – south (s) or north (n). Lat – latitude in degrees N. Long – longitude in degrees W. G – number of multilocus genotypes per population (raw clone assignments). G_corr - number of multilocus genotypes per population (corrected for scoring error/mutations). G_1_corr – (G_corr) minus one. N – number of ramets genotyped. G_N – G divided by N. G_1 – G minus one. N_1 – N minus one. N_1_G_1 – (N minus 1) minus (G minus 1). N_1_G_1_corr – (N_corr minus 1) minus (G_corr minus 1). R_corr - genotypic diversity corrected for scoring error / mutations, R - genotypic diversity (calculated from raw data)
DOI: 10.5061/dryad.gs7k6/12
title: Psex-correction

description: Modified output from GenClone. Column “Psex(Fis)” shows Psex for each clone, corrected by Fis.  Column L “Num.ramets” shows the number of ramets associated with the multilocus genotype. Column O “Corr.num.ramets.w1s.Int” shows the number of ramets associated with the multilocus genotype, corrected by Psex.  Rows highlighted in this column show a decrease from column L of at least 1.   Only 4 rows (clones) show this: (CTP-ON) row 4, row 14, (TRL-ON) row 130, row 136.  Only the relevant populations showing any Psex values &lt;0.05 are shown in this file.
DOI: 10.5061/dryad.gs7k6/13
title: CloneArea_MvsD

description: Input file (for R) for analysis of clone area between monoecious and dioecious populations. Popn – populations ID	. Sex.System – M for monoecious, D for dioecious	. Lat – latitude in degrees N. Long – latitude in degrees W. Clone.Genotype – genotype ID. Area – area of genotype in metres-squared.
DOI: 10.5061/dryad.gs7k6/14
title: Spatial_MvsD

description: Popn – population ID. Sex.System = M for monoecious, D for dioecious. Lat – latitude in degrees N. Long – longitude in degrees W. Clonal.subrange – mean clonal subrange calculated by GenClone. Ac – Aggregation index (GenClone). P.Ac – P value associated with Ac. Total.Locations – total number of spatial locations surveyed in field. Num.Occupied – number of spatial locations occupied by a ramet. Num.Not.Occupied – number of spatial location not occupied by a ramet. Ppn.Occupied – proportion of spatial positions surveyed occupied by a ramet
DOI: 10.5061/dryad.gs7k6/15
title: InputFiles

description: Self extracting Stuffin folder of input files (.txt) for each monoecious and dioecious population for GenClone analysis.  Data consists of SSR genotype data and spatial positions of each sample.