Selfing-rate

R functions used to perform the analysis of MLTR, COLONY and RMES output, and COLONY simulation.

Links to software:

• MLTR: http://genetics.forestry.ubc.ca/ritland/programs.html
• COLONY2: https://www.zsl.org/science/software/colony
• RMES: http://www.cefe.cnrs.fr/index.php/fr/recherche/accueil-dpt-ecologie-evolutive/genetique-et-ecologie-evolutive/800-gge/gge-chercheurs/196-patrice-david

Examples:

Parsing results produced with MLTR v.3.4

Single population - run MLTR_extract_single-pop.R Example files: MLTR_sample1a.out, MLTR_sample1b.out, MLTR_sample1c.out)

Multiple populations (MLTR grouping was enabled) - run MLTR_extract_mult-pop.R Example file: MLTR_sample2.out

Parsing results produced with RMES

Copy results from the RMES output window and save them to file, run RMES_extract.R Example file: RMES_default_output.txt

Extraction of selfers from the COLONY simulation

To determine which individuals are the results of selfing in the COLONY simulation - run Colony_Selfer.R Example file: COLONY_simulation_Selfer.Selfer

Preparation of selfing matrix for COLONY simulation

Colony_PrepareRandomMatingMatrix.R - these are internal functions which are used in COLONY_PrepareInputFiles.R Input parameters for the mating.matrix function:

• n = dimensions of mating matrix (for monoecious plants number of males = number of females)
• s = desired selfing rate (diagonal elements)
• cs = vector of known offspring numbers from female (sum of columns)

Batch preparation of input files for COLONY simulation

Directory with input data should contain:

• Design matrix ("COLONY_simulation_Descr.txt")
• Genetic markers information for each population ("Markers_.txt")
• Allele frequency data for each population ("_AlleleFreq.txt")

NB: Population names should be the same as in design matrix ('Meadow' column)

Run COLONY_PrepareInputFiles.R

Several folders (5 replicates by default) will be created for each population.

Copy COLONY files (impi.dll, libguide40.dll, libiomp5md.dll, colony2s.exe, simu2.exe) to each folder with input data, run simu2.exe (from batch file).

NB. Some of the parameters (path to the COLONY folder, etc.) are hard-coded in COLONY_PrepareInputFiles.R and should be tuned for your current project.

Accuracy estimation of COLONY simulation

Run Colony_AccuracyEstimation.R Example file: COLONY_simulation_Accuracy.Accuracy

Prerequisites:

Packages plyr and xlsx

install.packages(c("plyr", "xlsx"))

Citation:

Dulya O.V., Mikryukov V.S. Genetic variation and selfing rate in Lychnis flos-cuculi along an industrial pollution gradient // New Phytologist. 2016. V. 209. № 3. P. 1083-1095. DOI: 10.1111/nph.13636