Continued the analysis I started the other day. Still following Katherine Silliman’s notebook for guidance.
Quick summary of this analysis:

Mean Fst comparing all populations = 0.139539326187024

Mean Fst HL vs NF = 0.143075552548742

Mean Fst HL vs SN = 0.155234939276722

Mean Fst NF vs SN = 0.117889300124951
NOTE: Mean Fst values were calculated after replacing negative Fst values with 0. Thus, the means are higher than they would be had the raw data been used. I followed Katherine’s notebook and she doesn’t explicitly explain why she does this, nor what the potential implications are for interpreting the data. Will have to discus her rationale behind this with her.
Jupyter notebook: 20161201_docker_oly_vcf_analysis_R.ipynb