Doug

If Fst is larger than Rst, then the most strongly related alleles (i.e., alleles differing by low number of repeats) are more often in different than in the same populations. You can check Pons and Petit (1996) Genetics, for an example with Gst and Nst.

Hope it helps

Pablo

Hi! As Pablo said, you have probably a good mixture of distant alleles in the same groups. Thus, carriers of alleles, that are distant to each other, live side by side happily! This can happen if indeed your nematodes move effectively around your study area (but have a more discrete past). It can also happen if you have alleles that differ much (many bp distance) in a microsatellite where usually mutations are stepwise additions or deletions of one or two nucleotides. This big mutation can have happened due to an unsusal addition or deletion of a bigger fragment. If you have sequences, check these alelles to see if this is true. Good luck! Aristotelis

Just one more thing, Doug. Are you sure your Fst and Rst values are significantly different? It is rather easier to explain Fst=Rst than Fst>>Rst.

Thanks everyone.  Pablo, would testing whether Rst and Fst are significantly different be a simple matter of doing a t test, or something more involved?  Also, for all of my microsat loci, observed heterozygosity is GREATER than expected heterozygosity.  What might this be a sign of?

Hi Doug.

Sorry, not that easy. You would need either an error of your estimates or the 95% confidence intervals. Usually, the confidence intervals would be obtained by simulations, but I do not recall any software doing it for Rst. Perhaps Spagedi? I am not sure.

Regarding your H0>He question, it can have a number of biological reasons (i.e., isolate breaking); but please, check first the differences are statistically significant (use an exact test) and check the frequencies of rare alleles (they usually cause heterozygotes excess).

hope it helps

Pablo

Hi Doug. PermutCpSSR 2.0 (Petit software) does the comparison for haplotypes. I have no idea if you can do the same with allele frequencies and alleles. It is a Utest with permutations. And (as Pablo said) about the Ho>He, see if you have rare alleles in populations that also differ in size much than the rest. This could be an explanation for your results.

Thanks Aristotelis.

As I recall, PermutCpSSR does not estimate true Rst (even if it calls it so), but an analogous based on Nst

Pablo

Indeed, it is an option. But be sure to modify your Rst estimates accordingly and make clear within the Mat&Met what you are estimating.

Pablo,

One thing to consider is that Rst is based on a stepwise mutation model, and the actual processes generating microsatellite alleles are probably a lot messier than that model in most cases.  This has been shown empirically in some cases where folks have actually sequenced their microsat alleles.  The increase in repeat length variance with time since isolation, which was Slatkin's basic assumption with the stepwise model, is probably violated in several respects in most real world situations.  In fact, I don't think I've seen many papers (if any) that got results showing Rst being as large as Fst, let alone larger.

Thank you both very much.

Doug

David, I agree with you about the violations of the stepwise mutation model that can happen in nature. A study on cpDNA haplotypes with Nst > Gst at a significant level was published by Hatziskakis et al. in 2009 (https://www.researchgate.net/publication/26241576_High_chloroplast_haplotype_diversity_in_Greek_populations_of_beech_%28Fagus_sylvatica_L.%29).  I know that this is not the same thing as Rst vs. Fst, but the reason can be the same: haplotypes of different size are found in the same populations, more frequently than haplotypes with similar fragmet length. Furthermore, one fregment used in this study shows differences between haplotypes due to a a 5bp indel, much unlike the SMM for the cp microsatellites where single bp mutations are expected.

Article High chloroplast haplotype diversity in Greek populations of...

Hello Doug,

This is due to the difference between the 2 diversity indices. I would say that Fst is more similar to Gst than to Slatkin's Rst which calculates gene diversity at the inter-population level relative to the intra-population vs the intra-population reduction in heterozygosity relative to the total population heterozygosity for Fst). The level of significance is also very crucial in infirming or confirming your initial hypotheses.