‘Wake… from your sleep‘ sang Radiohead. If you are working with microsatellites, it is about the time – there is a blow coming on your direction. In a recent issue of Molecular Ecology, Lou Joost lays out the mathematical details as to why Fst/Gst- estimators of genetic differentiation do not actually measure what they are envisioned to measure when genetic diversity is high. Same goes with the heterozygosity. As he points out with crisp clarity, the traditional estimators are often suggesting entirely misleading estimates of diversity and differentiation. For instance, in one particular empirical study, the between population differentiation was indicated be at 5% (Fst), while correct calculation placed the estimate to 100%.
In a way, this has been in the air for a while, but this might be the first paper where the problems are pointed out in a way that they might actually be understood also by less theoretically inclined geneticists. The particularly nice feature of this paper is it’s constructive, non-preaching tone: alternative and better behaving measures are derived and presented.
After taking home the new doctorine, one is naturally left to wonder how should we deal with those mountains of publications where the measures are wrong? Likewise, how long will it take before the new measures are deployed as a standard in empirical studies and implemented in standard software packages? Above all, I was left to wonder what this means from the perspective of Fst/Qst comparisons, and inference drawn out of them?
Oh yes, there was also Déja vu here: is it a coincidence that it seems to be ‘always’ these ratios that lead to hangovers? Namely, there are many examples in the history ecology, systematics and genetics where ratios have – after initial enthusiasm – been found to lead us into ashtray. Looks almost as if our strive towards intuitive measures is bound to backfire.
Jost L (2008) GST and its relatives do not measure differentiation. Molecular Ecology 17:4015-4026.