RUB126_genotypes

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

CBA28_genotypes

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

Lolium SSR data genepop format

File containing genotype data from 12 microsatellite (SSR) loci for 412 individuals from 14 Lolium perenne ssp. multiflorum populations from California in genepop file format for easy conversion to other file formats

fruticosus

Samples in the "fruticosus" analysis group

Lolium SSR genalex format

File containing genotype data from 12 microsatellite (SSR) loci for 412 individuals from 14 Lolium perenne ssp. multiflorum populations from California formatted for analysis with Genalex package in Excel software

RUB262_distances

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

CBA28_distances

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

Data from: Genetic diversity and structure of Lolium perenne ssp. multiflorum in California vineyards and orchards indicates potential for spread of herbicide resistance via gene flow

Management of agroecosystems with herbicides imposes strong selection pressures on weedy plants leading to the evolution of resistance against those herbicides. Resistance to glyphosate in populations of Lolium perenne L. ssp. multiflorum is increasingly common in California, USA, causing economic losses and the loss of effective management tools. To gain insights into the recent evolution of glyphosate resistance in L. perenne in perennial cropping systems of northwest California and to inform management, we investigated the frequency of glyphosate resistance and the genetic diversity and structure of 14 populations. The sampled populations contained frequencies of resistant plants ranging from 10% to 89%. Analyses of neutral genetic variation using microsatellite markers indicated very high genetic diversity within all populations regardless of resistance frequency. Genetic variation was distributed predominantly among individuals within populations rather than among populations or sampled counties, as would be expected for a wide-ranging outcrossing weed species. Bayesian clustering analysis provided evidence of population structuring with extensive admixture between two genetic clusters or gene pools. High genetic diversity and admixture, and low differentiation between populations, strongly suggests the potential for spread of resistance through gene flow and the need for management that limits seed and pollen dispersal in L. perenne

cultivated

Samples in the "cultivated" analysis group