CTRS

Code for research paper in Genetics: "Cultural transmission of reproductive success impacts genomic diversity, coalescent tree topologies and demographic inferences"

Files

CalcIPrimeV2_linux64.exe is used to compute the Ib index from Brandenburg et al., 2012 (input: newick trees, output: imbalance data). File obtained from J.-T. Brandenburg.

format_newick.py is a script written by J.-T. Brandenburg to convert tree sequences to newick format for the .exe input (used in Brandenburg et al., 2012).

sumstats.py contains functions for computing sumstats (using tskit, Kelleher et al., 2016) and for dadi inference (Gutenkunst et al., 2009).

simupop.slim contains the SLiM code for CTRS and demographic modelisation.

Pipeline summary

• The needed parameters for the SLiM simulation were written in a JSON file and loaded in a python script that automatically wrote them into the SLiM code. The python script then launched the SLiM code using the method os.popen().

• The outputs from the SLiM simulations are tree sequences. Those were loaded in a python script. Recapitation and sampling were done, and mutations added to the trees (using tskit, Kelleher et al., 2016).

• Several summary statistics and dadi inferences were computed and the data written as .csv files.

• An R script loaded the final data, and ggplot2 was used to plot the papers' figures.