Other scientists out there! Hi. Can we agree that Fst, as wonderful as it's been, has run its course? It was a good idea - a great first crack at population genetics. When Wright came up with it, it was a wonderful idea. And for some applications - those where heterozygosity is generally low (I'm looking at you allozymes) - it works quite nicely. But once you're outside the Hs of .4 to .6, your Fst value starts becoming highly constrained. Fst = (Ht - Hs)/Ht. If Hs is large, it doesn't matter how much skewed your heterozygostity partitioning is, Fst will be small. There may be a way around this in Jost's D. I'm not a math biologist, so I'm not qualified to review his equations. But Fst is deader than a door nail. It's been a good run
Not convinced? Fair enough. Consider this figure from Gerlach et al 2010.
Why should diversity have any effect on population sub-structure? This makes no sense. Imagine two herds of caribou, one in Alaska, and the other in Quebec. All the herds between them are wiped out by Caribou flu (and you thought pig flu was bad!), so there's no gene flow. They both diversify, generating new genotypes - Alaska generates Alleles A, B, [...] L, M. Quebec generates alleles N, O, L [...] Y, Z. Both populations lose their ancestral form. All alleles are represented at equal frequencies. Neither population has a single allele in common. Divergence is total. And Fst is only 0.04* for this population pair. Fst will only get lower as you add more unique alleles to each population. This is absurd. Adding alleles does nothing to alter the fact that there is no gene flow from Quebec to Alaska in my example.
Jost's D would calculate differentiation as 1.0, which I think is a more accurate reflection of the fact that they have no diversity in common. But, IANAMB**.
Two reasons I bring this up. First, because I'm reading Gerlach et al 2010, which took the approach of using a variety of datasets to show that Fst*** does not reflect true levels of differentiation. It's a heap of data that show that when corrected, Jost's D neatly tracks true population divergence while Fst... well, it's flogging a dead horse at this point. The second reason will become clear in a moment.
I propose the following. You're allowed to use Fst in your publications for one more year. But at the end of 2011, that's it. Either move to other metrics, or take up under-water basket weaving. I've got two manuscripts I've got in prep. that I really hate having to report both Fst and Jost's D within. And in my case, Fst is awful because my species have high heterozygosity all around. I'm to be told that subspecies on different continents have an Fst of ≥0.05. If I were to take the most simpleminded, naïve interpretation of this, I would be to believe that I have around 4 migrants successfully swimming the arctic ocean to Eurasia each generation.
How about not?
*If I got my exact math wrong, you have permission to beat me with a stick. My point stands, though.**I am not a math biologist, so I'm not sure if Jost D's derivation is completely correct.
***Technically Gst, but Fst and Gst are used interchangeably, so 'nuff said.
GERLACH, G., JUETERBOCK, A., KRAEMER, P., DEPPERMANN, J., & HARMAND, P. (2010). Calculations of population differentiation based on GST and D: forget GST but not all of statistics! Molecular Ecology, 19 (18), 3845-3852 DOI: 10.1111/j.1365-294X.2010.04784.x