" Every decade or so, starting with Jaccard in the 1950s, good population geneticists have told us not to confuse:
Hardy-Weinberg expected heterozygosity He (also called gene diversity). Eg for a 2-allele SNP, where p and q are proportions of the two alleles, A1 and A2, Gene diversity/Heterozygosity: He=2pq
With
Inbreeding coefficient (FIS, also measures effect of other things such as selection for or against heterozygotes). Inbreeding coefficient: FIS=1-(Ho/He) where Ho is the observed proportion of heterozygotes.
You can see from the equations that there will not be a simple linear relationship between FIS and He. Or you can see the same thing from these two examples of different populations, both with p=q=0.5:
EG1: if there is total inbreeding, with 50% of families having only A1 homozygotes, and the other families only having A2 homozygotes, so that He=0.5, Ho=1 then FIS =0.5.
EG2: Alternatively if all individuals are heterozygotes, He=0.5, Ho=0 then FIS=1.
Those are extreme examples, but they show that with the same He, you can get a very wide range of FIS values. So, it is not reasonable to expect any tight relationship between the two measures – they measure different things, so they behave independently.
MORAL: NEVER say that a population with low He is ‘inbred’ – there may be zero consanguineous matings occurring in this population; there is just low gene diversity – most of the A1 or A2 alleles have been lost by drift (which is NOT inbreeding)."
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Hi Manuela,Based on the data you sent me, I found that FIS is actual positive (see attached).- What method did use to estimate FIS?- You have a small sample size, heterozygosity estimates are not accurate with such a small sample sizes, There should be at least ten individuals per population.- In dartR, heterozygosity estimates have a correction for sample size.Cheers,Luis
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Hi Manuela,
Based on the data you sent me, two of your populations (Mount_Solitary and Waterfall_Creek) are very different from the other populations. They might be different subspecies.
That’s one of the reasons you have a lot of missing data in your dataset. This missing data is due to null alleles arising from a mutation at one or both restriction enzyme recognition sites. The species has a low genetic variation that, together with the filtering you are using (MAF, call rate, and reproducibility), amplifies the effect you observe in FIS.
One usually filters by call rate, reproducibility, and MAF to remove potential sequencing artefacts; however, what is driving missing data and allele frequencies in your dataset is the large genetic differentiation between populations.
Some ideas about what you could do:
TechNote_fixed_difference_analysis_25-Feb-22.pdf (biomatix.org)
Cheers,
Luis
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