This repo contains the code/data used to test for the signature of selection on maintaining locally adapted variants in the face of gene flow in Trinidadian guppies.
These analyses are associated with the manuscript: Fitzpatrick et al. (2019) Genetic rescue without genomic swamping in wild populations.
The data and individual R scripts used for the analyses in the paper
are divided into the different steps in the pipeline.
You can examine each (and the output they produce) within
the relevant subfolder, or you can run all steps at once using
the exe.master.R script.
The current contents of each folder contain the output
expected after successfully running the exe.master.R script.
- 1_data
- R script for formatting raw data
- raw vcf data files for each stream
- plink binary files for running ADMIXTURE
- 2_admixture
- R script for running ADMIXTURE
- estimated admixture proportions for each drainage
- estimated allele frequencies in each ancestral population
- 3_reconcile_alleles
- R script for ensuring the same alleles are being counted in each dataset
- allele frequencies in each population
- 4_silico_sims
- R script for simulating admixed headwater populations
- R object with saved simulations
- 5_test_ancestry_bias
- R script for testing for selection on putatively locally adapted alleles
- 6_figs
- PDF output figures for different stages in the analysis
Please direct all queries to bradburd (at) msu.edu, or post as issues on the git repo.