Fst, Heterozygosity, and Subspecies

Meirmans and Hendrick (2011), among others, have noted that common measures of population differentiation such as Fst can be misleading (especially when it comes to making cross species comparisons concerning population structure) because Fst/Gst values are dependent on and constrained by the intra populational Heterogeneity (genetic diversity) within species. Simply:


(where Ht is the total genetic diversity and Hs is the within population genetic diversity (or expected genetic diversity)


Fst< 1-Expected Heterozygosity (Hs)

The result is that the magnitudes of the Fst values between subspecific populations are inversely related to the amount of genetic diversity within these populations. Here were, for example, F/Gst values (between subspecies) and Hs values (within subspecies and averaged across), based on autosomal microsatellite data, for 24 species with recognized subspecies (r = -0.57):


(Notice that three quarters don’t pass Alan Templeton’s made up subspecies = Fst > 0.25 – 0.30 criteria.)

Plotting F/Gst against Hs we get:


The relation above is very similar to that reported by Heller and Siegismund (2009). They looked at the association between Gst and Hs in 43 species, though it wasn’t clear if they limited consideration to diversity within and between recognized subspecies:


(Red line added at Fst ~ 0.05, Hs ~ 0.70)

Now, for comparison, the following between continental human race autosomal microsatellite Fst values have been reported:


(The number of loci used, the sample sizes, and the number of Human continental races compared are noted for reference.) The values range from 0.040 to 0.14; the n-weighted (by loci and sample size) average is 0.055.

And, based on Pemberton et al. (2013)’s list of microsatellite Hs values for 267 populations, we can compute the following Human continental race expected Heterozygosity values and the average of them:


We see then that the very low Fst value between Human continental races (Fst (micro) ~ 0.055) is about what one would expect to find were one dealing with subspecies in a species which had as much intra populational diversity as the Human species does (Hs (micro) ~ 0.72).

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