I was looking for a tutorial to estimate FST for my microbial (aka haploid) dataset but sadly there was no specific instruction, although other researchers are definitely looking for it (see here). Sadly, one respondent said that “there is no way to estimate Fst for microbial data”. However, ultimately I found a “way” to estimate Fst, and here is a quick R tutorial.
The fixation index, otherwise known as FST, is population differentiation due to genetic structure and is one of the fundamental concepts in population genetics. Essentially, FST is the proportion of the total genetic variance contained in a subpopulation (the S-subscript) compared to the total genetic variance (the T-subscript). Its value can range from 0 to 1. Higher FST indicates a considerable degree of differentiation among populations. The figure below illustrates what it means for two populations to have very different genetic structures.Continue reading “Calculating Fst for haploid data in R”