Data from: Spontaneous hybrids between native and exotic Rubus in the Western United States produce offspring both by apomixis and by sexual recombination

Clark LV, Jasieniuk M

Date Published: July 10, 2012

DOI: http://dx.doi.org/10.5061/dryad.m466f

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title README
Downloaded 41 times
Description Description of files in the package.
Download README.txt (9.725 Kb)
Details View File Details
Title apomixis_analysis_111211
Downloaded 23 times
Description "apomixis_analysis_111211.R" is a text file of R code for the analysis of reproductive mode. It was created in Emacs Speaks Statistics but can be opened in any text editor. When executed in R, the working directory will need to contain the files in this data archive.
Download apomixis_analysis_111211.R (2.968 Kb)
Details View File Details
Title apomixis_genotypes_110218
Downloaded 25 times
Description This is a tab-delimited text file in the format produced by Applied Biosystems GeneMapper software version 3.7. Each sample*locus genotype is represented in one row. The "Sample Name" column gives names of samples that directly correspond to those used in "apomixis_samples_110218.csv". The "Marker" column indicates the microsatellite marker. The "Panel" column indicates groups of markers that were run simultaneously on the ABI3100 capillary sequencer. The "Dye" column indicates the fluorescent tag used to detect the PCR fragments: Y for NED, G for HEX, and B for FAM. The eight "Allele" columns contain the names of all alleles detected for each genotype. Cells are left blank if fewer than eight alleles were detected. The "Height" columns indicate the height of the peak representing each allele, and the "Size" columns indicate the exact size of the DNA fragment as calculated by GeneMapper. A value of "TRUE" in the "AE" column indicates that the genotype was manually edited in GeneMapper, although all genotypes were visually inspected. The R package "polysat" can read this file directly, and will use the "Sample Name", "Marker", and "Allele" columns, and will ignore all other columns.
Download apomixis_genotypes_110218.txt (177.2 Kb)
Details View File Details
Title apomixis_samples_110218
Downloaded 9 times
Description This file contains four columns of information regarding the parent plants, seeds, and seedlings that were genotyped for the study to determine the reproductive mode of the hybrids. The "Sample Name" column lists the names of the samples as they were used in analysis. The names of the parents correspond to the wells that they were in on the DNA dilution plates from the hybridization study. The formatting of the names of seed and seedling samples vary only because different researchers were working on the project over a long period. The "Parent clone" indicates the species or hybrid type from which seeds were collected, and each unique entry in this column corresponds to one clone. The "Type" column indicates whether the sample was the original parent, a seed embryo, or a seedling. The "DNA extraction" column indicates whether the DNA was extracted with a routine CTAB protocol or with a Zymo ZR Plant/Seed DNA Micro kit.
Download apomixis_samples_110218.csv (5.841 Kb)
Details View File Details
Title CBA6_distances
Downloaded 13 times
Description Pairwise genetic distances at locus CBA6 between the 579 samples that were analyzed. These distances were calculated using the meandistance.matrix function in the R package "polysat" version 0.1, using the Bruvo.distance measure. File contains a square matrix with row names and column names (sample names), as produced by the write.csv function in R version 2.11 under default parameters.
Download CBA6_distances.csv (4.471 Mb)
Details View File Details
Title CBA6_genotypes
Downloaded 27 times
Description Microsatellite genotypes at locus CBA6. This is a tab-delimited text file in the format produced by Applied Biosystems GeneMapper software version 3.7. Each sample*locus genotype is represented in one row. The "Sample Name" column gives names of samples that directly correspond to those used in "species_chloroplast_latlong.csv". The "Well" column indicates the location of the sample on the DNA dilution plates. The "Marker" column indicates the microsatellite marker. The "Panel" column indicates groups of markers that were run simultaneously on the ABI3100 capillary sequencer. The "Dye" column indicates the fluorescent tag used to detect the PCR fragments: Y for NED, G for HEX, and B for FAM. The "Allele" columns contain the names of all alleles detected for each genotype. Cells are left blank if fewer alleles were detected than the number of columns. A value of -9 for Allele 1 indicates missing data. The "Height" columns indicate the height of the peak representing each allele, and the "Size" columns indicate the exact size of the DNA fragment as calculated by GeneMapper. A value of "TRUE" in the "AE" column indicates that the genotype was manually edited in GeneMapper, although all genotypes were visually inspected. The R package "polysat" can read these file directly, and will use the "Sample Name", "Marker", and "Allele" columns, and will ignore all other columns.
Download CBA6_genotypes.txt (139.3 Kb)
Details View File Details
Title CBA14_distances
Downloaded 15 times
Description Pairwise genetic distances at locus CBA14 between the 579 individuals analyzed. These distances were calculated using the meandistance.matrix function in the R package "polysat" version 0.1, using the Bruvo.distance measure. Each file contains a square matrix with row names and column names (sample names), as produced by the write.csv function in R version 2.11 under default parameters.
Download CBA14_distances.csv (4.215 Mb)
Details View File Details
Title CBA14_genotypes
Downloaded 19 times
Description Microsatellite genotypes for locus CBA14. This is a tab-delimited text file in the format produced by Applied Biosystems GeneMapper software version 3.7. Each sample*locus genotype is represented in one row. The "Sample Name" column gives names of samples that directly correspond to those used in "species_chloroplast_latlong.csv". The "Well" column indicates the location of the sample on the DNA dilution plates. The "Marker" column indicates the microsatellite marker. The "Panel" column indicates groups of markers that were run simultaneously on the ABI3100 capillary sequencer. The "Dye" column indicates the fluorescent tag used to detect the PCR fragments: Y for NED, G for HEX, and B for FAM. The "Allele" columns contain the names of all alleles detected for each genotype. Cells are left blank if fewer alleles were detected than the number of columns. A value of -9 for Allele 1 indicates missing data. The "Height" columns indicate the height of the peak representing each allele, and the "Size" columns indicate the exact size of the DNA fragment as calculated by GeneMapper. A value of "TRUE" in the "AE" column indicates that the genotype was manually edited in GeneMapper, although all genotypes were visually inspected. The R package "polysat" can read these file directly, and will use the "Sample Name", "Marker", and "Allele" columns, and will ignore all other columns.
Download CBA14_genotypes.txt (151.5 Kb)
Details View File Details
Title CBA15_distances
Downloaded 15 times
Description Pairwise genetic distances at locus CBA15 for the 579 samples analyzed. These distances were calculated using the meandistance.matrix function in the R package "polysat" version 0.1, using the Bruvo.distance measure. Each file contains a square matrix with row names and column names (sample names), as produced by the write.csv function in R version 2.11 under default parameters.
Download CBA15_distances.csv (3.262 Mb)
Details View File Details
Title CBA15_genotypes
Downloaded 26 times
Description Microsatellite genotypes at locus CBA15. This is a tab-delimited text file in the format produced by Applied Biosystems GeneMapper software version 3.7. Each sample*locus genotype is represented in one row. The "Sample Name" column gives names of samples that directly correspond to those used in "species_chloroplast_latlong.csv". The "Well" column indicates the location of the sample on the DNA dilution plates. The "Marker" column indicates the microsatellite marker. The "Panel" column indicates groups of markers that were run simultaneously on the ABI3100 capillary sequencer. The "Dye" column indicates the fluorescent tag used to detect the PCR fragments: Y for NED, G for HEX, and B for FAM. The "Allele" columns contain the names of all alleles detected for each genotype. Cells are left blank if fewer alleles were detected than the number of columns. A value of -9 for Allele 1 indicates missing data. The "Height" columns indicate the height of the peak representing each allele, and the "Size" columns indicate the exact size of the DNA fragment as calculated by GeneMapper. A value of "TRUE" in the "AE" column indicates that the genotype was manually edited in GeneMapper, although all genotypes were visually inspected. The R package "polysat" can read these file directly, and will use the "Sample Name", "Marker", and "Allele" columns, and will ignore all other columns.
Download CBA15_genotypes.txt (134.1 Kb)
Details View File Details
Title CBA23_distances
Downloaded 12 times
Description Pairwise distances at locus CBA23 between the 579 individuals that were analyzed. These distances were calculated using the meandistance.matrix function in the R package "polysat" version 0.1, using the Bruvo.distance measure. Each file contains a square matrix with row names and column names (sample names), as produced by the write.csv function in R version 2.11 under default parameters.
Download CBA23_distances.csv (4.596 Mb)
Details View File Details
Title CBA23_genotypes
Downloaded 15 times
Description Microsatellite genotypes at locus CBA23. This is a tab-delimited text file in the format produced by Applied Biosystems GeneMapper software version 3.7. Each sample*locus genotype is represented in one row. The "Sample Name" column gives names of samples that directly correspond to those used in "species_chloroplast_latlong.csv". The "Well" column indicates the location of the sample on the DNA dilution plates. The "Marker" column indicates the microsatellite marker. The "Panel" column indicates groups of markers that were run simultaneously on the ABI3100 capillary sequencer. The "Dye" column indicates the fluorescent tag used to detect the PCR fragments: Y for NED, G for HEX, and B for FAM. The "Allele" columns contain the names of all alleles detected for each genotype. Cells are left blank if fewer alleles were detected than the number of columns. A value of -9 for Allele 1 indicates missing data. The "Height" columns indicate the height of the peak representing each allele, and the "Size" columns indicate the exact size of the DNA fragment as calculated by GeneMapper. A value of "TRUE" in the "AE" column indicates that the genotype was manually edited in GeneMapper, although all genotypes were visually inspected. The R package "polysat" can read these file directly, and will use the "Sample Name", "Marker", and "Allele" columns, and will ignore all other columns.
Download CBA23_genotypes.txt (150.4 Kb)
Details View File Details
Title CBA28_distances
Downloaded 13 times
Description Pairwise genetic distances at locus CBA28 for the 579 samples that were analyzed. These distances were calculated using the meandistance.matrix function in the R package "polysat" version 0.1, using the Bruvo.distance measure. Each file contains a square matrix with row names and column names (sample names), as produced by the write.csv function in R version 2.11 under default parameters. For pairs of individuals that both had nine or more alleles at locus RhCBA28, distances were calculated manually in Microsoft Excel and then inserted into the CBA28 matrix.
Download CBA28_distances.csv (5.147 Mb)
Details View File Details
Title CBA28_genotypes
Downloaded 19 times
Description Microsatellite genotypes at locus CBA28. This is a tab-delimited text files in the format produced by Applied Biosystems GeneMapper software version 3.7. Each sample*locus genotype is represented in one row. The "Sample Name" column gives names of samples that directly correspond to those used in "species_chloroplast_latlong.csv". The "Well" column indicates the location of the sample on the DNA dilution plates. The "Marker" column indicates the microsatellite marker. The "Panel" column indicates groups of markers that were run simultaneously on the ABI3100 capillary sequencer. The "Dye" column indicates the fluorescent tag used to detect the PCR fragments: Y for NED, G for HEX, and B for FAM. The "Allele" columns contain the names of all alleles detected for each genotype. Cells are left blank if fewer alleles were detected than the number of columns. A value of -9 for Allele 1 indicates missing data. The "Height" columns indicate the height of the peak representing each allele, and the "Size" columns indicate the exact size of the DNA fragment as calculated by GeneMapper. A value of "TRUE" in the "AE" column indicates that the genotype was manually edited in GeneMapper, although all genotypes were visually inspected. The R package "polysat" can read these file directly, and will use the "Sample Name", "Marker", and "Allele" columns, and will ignore all other columns.
Download CBA28_genotypes.txt (168.0 Kb)
Details View File Details
Title cultivated
Downloaded 10 times
Description Samples in the "cultivated" analysis group.
Download cultivated.txt (219 bytes)
Details View File Details
Title cutcultivated
Downloaded 11 times
Description Individuals in the "cultivated" group with the "cut" trnK allele.
Download cutcultivated.txt (81 bytes)
Details View File Details
Title fruticosus
Downloaded 10 times
Description Samples in the "fruticosus" analysis group.
Download fruticosus.txt (2.083 Kb)
Details View File Details
Title hybridization_analysis
Downloaded 20 times
Description "hybridization_analysis.R" is a text file containing R code for replicating the analysis to detect hybridization based on inter-individual distances. It was created in Emacs Speaks Statistics but can be opened in any text editor. When executed in R, the working directory will need to contain the files in this data archive.
Download hybridization_analysis.R (18.11 Kb)
Details View File Details
Title leucodermis
Downloaded 11 times
Description Samples in the "leucodermis" analysis group.
Download leucodermis.txt (67 bytes)
Details View File Details
Title mean_distances
Downloaded 17 times
Description Mean pairwise genetic distances between the 579 samples analyzed. These distances were calculated using the meandistance.matrix function in the R package "polysat" version 0.1, using the Bruvo.distance measure. Each file contains a square matrix with row names and column names (sample names), as produced by the write.csv function in R version 2.11 under default parameters.
Download mean_distances.csv (5.936 Mb)
Details View File Details
Title parviflorus
Downloaded 8 times
Description Samples in the "parviflorus" analysis group.
Download parviflorus.txt (96 bytes)
Details View File Details
Title pensilvanicus
Downloaded 12 times
Description Samples in the "pensilvanicus" analysis group.
Download pensilvanicus.txt (79 bytes)
Details View File Details
Title RUB26_distances
Downloaded 15 times
Description Pairwise genetic distances at locus RUB26 between the 579 samples that were analyzed. These distances were calculated using the meandistance.matrix function in the R package "polysat" version 0.1, using the Bruvo.distance measure. Each file contains a square matrix with row names and column names (sample names), as produced by the write.csv function in R version 2.11 under default parameters.
Download RUB26_distances.csv (5.032 Mb)
Details View File Details
Title RUB26_genotypes
Downloaded 12 times
Description Microsatellite genotypes at locus RUB26. This is a tab-delimited text file in the format produced by Applied Biosystems GeneMapper software version 3.7. Each sample*locus genotype is represented in one row. The "Sample Name" column gives names of samples that directly correspond to those used in "species_chloroplast_latlong.csv". The "Well" column indicates the location of the sample on the DNA dilution plates. The "Marker" column indicates the microsatellite marker. The "Panel" column indicates groups of markers that were run simultaneously on the ABI3100 capillary sequencer. The "Dye" column indicates the fluorescent tag used to detect the PCR fragments: Y for NED, G for HEX, and B for FAM. The "Allele" columns contain the names of all alleles detected for each genotype. Cells are left blank if fewer alleles were detected than the number of columns. A value of -9 for Allele 1 indicates missing data. The "Height" columns indicate the height of the peak representing each allele, and the "Size" columns indicate the exact size of the DNA fragment as calculated by GeneMapper. A value of "TRUE" in the "AE" column indicates that the genotype was manually edited in GeneMapper, although all genotypes were visually inspected. The R package "polysat" can read these file directly, and will use the "Sample Name", "Marker", and "Allele" columns, and will ignore all other columns.
Download RUB26_genotypes.txt (145.4 Kb)
Details View File Details
Title RUB126_distances
Downloaded 16 times
Description Pairwise genetic distances at locus RUB126 between the 579 samples analyzed. These distances were calculated using the meandistance.matrix function in the R package "polysat" version 0.1, using the Bruvo.distance measure. Each file contains a square matrix with row names and column names (sample names), as produced by the write.csv function in R version 2.11 under default parameters.
Download RUB126_distances.csv (5.431 Mb)
Details View File Details
Title RUB126_genotypes
Downloaded 18 times
Description Microsatellite genotypes at locus RUB126. This is a tab-delimited text file in the format produced by Applied Biosystems GeneMapper software version 3.7. Each sample*locus genotype is represented in one row. The "Sample Name" column gives names of samples that directly correspond to those used in "species_chloroplast_latlong.csv". The "Well" column indicates the location of the sample on the DNA dilution plates. The "Marker" column indicates the microsatellite marker. The "Panel" column indicates groups of markers that were run simultaneously on the ABI3100 capillary sequencer. The "Dye" column indicates the fluorescent tag used to detect the PCR fragments: Y for NED, G for HEX, and B for FAM. The "Allele" columns contain the names of all alleles detected for each genotype. Cells are left blank if fewer alleles were detected than the number of columns. A value of -9 for Allele 1 indicates missing data. The "Height" columns indicate the height of the peak representing each allele, and the "Size" columns indicate the exact size of the DNA fragment as calculated by GeneMapper. A value of "TRUE" in the "AE" column indicates that the genotype was manually edited in GeneMapper, although all genotypes were visually inspected. The R package "polysat" can read these file directly, and will use the "Sample Name", "Marker", and "Allele" columns, and will ignore all other columns.
Download RUB126_genotypes.txt (160.5 Kb)
Details View File Details
Title RUB262_distances
Downloaded 17 times
Description Pairwise genetic distances at locus RUB262 between the 579 samples analyzed. These distances were calculated using the meandistance.matrix function in the R package "polysat" version 0.1, using the Bruvo.distance measure. Each file contains a square matrix with row names and column names (sample names), as produced by the write.csv function in R version 2.11 under default parameters.
Download RUB262_distances.csv (4.123 Mb)
Details View File Details
Title RUB262_genotypes
Downloaded 20 times
Description Microsatellite genotypes at locus RUB262. This is a tab-delimited text file in the format produced by Applied Biosystems GeneMapper software version 3.7. Each sample*locus genotype is represented in one row. The "Sample Name" column gives names of samples that directly correspond to those used in "species_chloroplast_latlong.csv". The "Well" column indicates the location of the sample on the DNA dilution plates. The "Marker" column indicates the microsatellite marker. The "Panel" column indicates groups of markers that were run simultaneously on the ABI3100 capillary sequencer. The "Dye" column indicates the fluorescent tag used to detect the PCR fragments: Y for NED, G for HEX, and B for FAM. The "Allele" columns contain the names of all alleles detected for each genotype. Cells are left blank if fewer alleles were detected than the number of columns. A value of -9 for Allele 1 indicates missing data. The "Height" columns indicate the height of the peak representing each allele, and the "Size" columns indicate the exact size of the DNA fragment as calculated by GeneMapper. A value of "TRUE" in the "AE" column indicates that the genotype was manually edited in GeneMapper, although all genotypes were visually inspected. The R package "polysat" can read these file directly, and will use the "Sample Name", "Marker", and "Allele" columns, and will ignore all other columns.
Download RUB262_genotypes.txt (139.0 Kb)
Details View File Details
Title species_chloroplast_latlong
Downloaded 29 times
Description "species_chloroplast_latlong.csv" contains collection data and chloroplast genotypes for each sample in the hybridization study. **The "Well" column indicates the plate number and well where the sample was located on the DNA dilution plates. **The "Site" column contains a three-letter code for the collection site, which corresponds to a collection site description that can be found in the Supplementary Material fo the paper. **The "Individual" column contains the site code plus number used to uniquely identify each individual. **The "Initial Species Determination" column lists the species as it was determined either during collection or after preliminary analysis. **The "Species based on genetic data" column lists the final species determination. Identification of R. vestitus and R. anglocandicans individuals is described in a manuscript that is in revision for the journal Biological Invasions. **The "ndh Allele" column gives the size of the PCR fragment produced by amplifying the ndhF chloroplast region (using primers and PCR conditions are described in the paper), while the "Peak Height" column gives the height of the peak detected on an ABI3100 capillary sequencer for this allele, and "Run" lists the identity of the run as produced by the data collection software. **The "trnK allele" column gives the result of a CAPS marker in the trnK region of the chloroplast genome: the "cut" allele has a HindIII site while the "uncut" allele does not. **"pch for R" contains the number of the symbol used to represent each individual in Principal Coordinate Analysis in R, based on the ndhF allele. **"color for R" contains the colors initially used to represent each individual in Principal Coordinates Analysis in R, based on the trnK allele and whether the individual is a member of the R. fruticosus agg. or not. All "magenta" individuals were later changed to "red" so that the color would only represent the genetic results. **"LatOrder" contains a number for each population, in order of increasing latitude. **"Latitude" and "Longitude" contain decimal coordinates where the sample was collected, obtained using a Garmin GPSMAP 60CS in the WGS84 datum. **"Collection date" contains the date that leaf tissue was collected in the field, in YYYYMMDD format. **"Comment" contains any additional information, such as whether a pressed voucher was collected, whether the sample was excluded from analysis, or information about morphology or location.
Download species_chloroplast_latlong.csv (80.89 Kb)
Details View File Details
Title spectabilis
Downloaded 13 times
Description Samples in the "spectabilis" analysis group.
Download spectabilis.txt (60 bytes)
Details View File Details
Title uncutcultivated
Downloaded 10 times
Description Samples in the "cultivated" analysis group with the "uncut" trnK allele (maternally derived from R. ursinus).
Download uncutcultivated.txt (138 bytes)
Details View File Details
Title uncut_Structure
Downloaded 11 times
Description "uncut_Structure.txt" is a tab-delimited file containing genotypes for all individuals in the hybridization study with the "uncut" trnK chloroplast allele, formatted for the software Structure 2.3.3. The file contains a row of marker names and a row of recessive allele symbols (all of them -9, the missing data symbol, to indicate allele copy number ambiguity), followed by the rows containing the genotypes. The ploidy of the file is 8, so each individual is represented by eight rows. The first column contains labels (sample names for each individual) and the second column contains numbers indicating population identity, corresponding to "LatOrder" in "species_chloroplast_latlong.csv". This file was generated using the R package "polysat" version 0.1.
Download uncut_Structure.txt (92.44 Kb)
Details View File Details
Title ursinus
Downloaded 13 times
Description Samples in the "ursinus" analysis group.
Download ursinus.txt (2.366 Kb)
Details View File Details
Title rubus_photos1
Downloaded 39 times
Description Photographs of plants sampled at sites ARC, ARP, BBG, and BWP. Sample IDs can be seen within the images. Image format is .jpg.
Download rubus_photos1.zip (108.4 Mb)
Details View File Details
Title rubus_photos2
Downloaded 28 times
Description Photographs of plants at sites CMB, CSR, CSP, and CFX. Sample IDs are shown within the images. Images are in .jpg format.
Download rubus_photos2.zip (131.0 Mb)
Details View File Details
Title rubus_photos3
Downloaded 46 times
Description Photographs of plants at sites CMW, CTF, MGH, DVS, DNV, and DMU. Sample IDs are found in the images. Images are in .jpg format.
Download rubus_photos3.zip (87.85 Mb)
Details View File Details
Title rubus_photos4
Downloaded 42 times
Description Photographs of plants at sites FCR, GTN, KLS, KVY, KRC, KNL, MCD, and PSG. Sample IDs can be seen within the images. Images are in .jpg format.
Download rubus_photos4.zip (101.5 Mb)
Details View File Details
Title rubus_photos5
Downloaded 43 times
Description Photographs of plants at sites PLV, RSB, SDW, SFD, SRP, TCM, WIN, and WSH. Sample IDs can be seen in the images. Images are in .jpg format.
Download rubus_photos5.zip (125.6 Mb)
Details View File Details

When using this data, please cite the original publication:

Clark LV, Jasieniuk M (2012) Spontaneous hybrids between native and exotic Rubus in the Western United States produce offspring both by apomixis and by sexual recombination. Heredity 109: 320–328. http://dx.doi.org/10.1038/hdy.2012.45

Additionally, please cite the Dryad data package:

Clark LV, Jasieniuk M (2012) Data from: Spontaneous hybrids between native and exotic Rubus in the Western United States produce offspring both by apomixis and by sexual recombination. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.m466f
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: