Qsuber_mssats

Population structure in Quercus suber L. revealed by nuclear microsatellite markers - paper scripts

Scripts

Qsuber_PCA.R

Script used to make the paper's PCA analyses. The data filenames are hard-coded in the file, but everything is quite self-explanatory. In order to run the script, just modify the path to the input files to match that of your filesystem and it's ready to use.

Fst_dendro.R

Script used to create Fst dendrograms. Ended up not being used in the paper, but since it had been written we decided it was a good a idea to leave it here, both as a reference, and in case it might be of use to someone else.

pairwise_test.R

Script used to calculate the t-test for the FIS values. It's so simple it didn't warrant any special documentation.

map_plotter.py

Python script based on the one from pyRona used to draw the plot from figure 1. Requires cartopy, numpy and matplotlib. Takes 3 arguments: sample_coords.csv, output.svg and shapefile.shp It will draw a map, based on the sample coordinates, with the distribution shapefile superimposed.

Datafiles

17_pops_13_loci_DIPLOID.gen

Genepop formatted file containing microssatellite alleles (17 populations and 13 loci)

17_pops_11_loci_DIPLOIDS_NEUTRAL.gen

Genepop formatted file containing 'neutral' microssatellite alleles (17 populations and 11 loci)

fsts-dist.csv

Tab-separated pairwise Fst triangular matrix required for Fst_dendro.R. Like the script that requires it, this file ended up not being used in the paper itself.

FIS_values.csv

Tab-separated file containing FIS values per microssat, each column has values calculated from different population arrangements

Sample_coords.csv

Tab-separated file containing sampling site coordinates. First column is sample name, second is Latitude, third is Longitude.

Citation

Not yet available.