Adaptive evolution in a conifer hybrid zone is driven by a mosaic of recently introgressed and background genetic variants

Associated scripts for: "Adaptive evolution in a conifer hybrid zone is driven by a mosaic of recently introgressed and background genetic variants" (COMMSBIO-20-0007-A)

This directory lists all the custom scripts that were used in the analyses conducted in COMMSBIO-20-0007-A.
For some of them, the input files are also provided at figshare doi: 10.6084/m9.figshare.c.5130104
The bash scripts usually used to submit the jobs are not provided. But often times the output from those is provided in the figshare collections
Instances where the program or software name is listed in the manuscript and the setting used are mentioned or the default settings were used are also not provided.

#############If you use these script:##################
            Modify the path to fit yours
            Install all the needed libraries (for R)
            Lastly, remember to cite us if you use the scripts as is.

##########################################################            
************** structure********************

SNPfiltering_AdaptIntro.ipynb: Script for conducting custom filtering of SNPs identified through dDocent. 

    
   ##Basic analyses:

BasicPopGen.R : contains scripts to estimate heterozygosity and format data to run hierfstat. 
    
##Bayenv:
contains scripts used to combine the output from multiple chains of Bayenv (the GEA part of it), to get a stringent set of outlier SNPs.
Figure 2 provides a representation of this. 
It assumes that you already have the output from Bayenv runs. Have to make sure that the file naming is similar.

    Bayenv_forGit.R
    
    
    
    
    
##RDA:
Conduct the RDA variance partioning.

    RDA.R: Script for performing RDA as used in this paper.
    
    
    
    
##LD: 

Contains scripts for conducting LD based analyses represented in various panels of Figure 3. 
Some of the steps here are very time consuming due to the estimation of pwLD and hence were performed on a GridEngine. I mention this specifically within the script. 

    LDnr_archive.Rmd: Script for conducting LD based network analyses. 
    OhtaD_pwEst.Rmd: Script for conducting PW estimation of Ohta's D using SNPs identified as outliers via. Bayenv. 
    
    
    
    
    
##AdapIntro:

A series of scripts that were used to assess adaptive introgression. 
These include the script (AdapIntro_FE.Rmd) used for the FE analyses represented in Figure 4 and the analyses presented in Appendix S2.

    
    AF_LP_EnvDiff.R : Simple correlation based env association approach detailed in the supplemental Info. 
    AdapIntro_FE.Rmd :Basic introgress based outlier identification and FE approach implemented in the main document.