Difference between PhiPT and Fst in pairwise calculations of population differences. Documentation of how and why to use would be appreciated.
Phi-statistics is a modified version of Wright’s F that refers to the relative contributions of between-population separation to the overall genetic variation in the whole sample. The greater the Fst values are, the greater the differences between populations.
Unlike conventional F-statistics, Phi-statistics can take into consideration genealogical information from your data. So when using e.g. sequence data (where this kind of information is available, e.g. in Arlequin you would select the "compute distance matrix" option), Phi-statistics are generally preferable.
Next question - why would Phi-pt be preferable to Phi-st? In most cases, it probably makes little difference, but if you've got data from very different marker types that you would like to compare directly (e.g. codominant intron data vs. haploid mitochondrial data), Phi-pt would be the statistic of choice.
No, only for sequence data. A microsatellite equivalent for the Phi statistics would be Rst, but it's fallen out of fashion. I would recommend using Jost's D, G''st and (for comparison) Fst for microsats.
cool, thanks! :) I'm missing only Jost's D then. I'll try that but so far for my data they all seem to give fairly the same result, even the Phi, which I used incorrectly on microsatellites and I'm taking out, now that I know better. Thanks again!
"ΦST from analysis of molecular variance (AMOVA) is used for haplotype data (for example, nucleotide sequence data or mapped restriction site data) and requires a measure of evolutionary distance among all pairs of haplotypes." - Holsinger, Weir
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