... polymorphic.¹

They were discovered as a result of investigations into rejection of transplanted organs and tissues. They are the loci governing acceptance/rejection of transplants in vertebrates.

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... site.²

Of course, we know this isn't true. Multiple substitutions can occur at any site. That's why the percent difference between two sequences isn't equal to the number of substitutions that have happened at any particular site. We're simply assuming that the sequences we're comparing are closely enough related that nearly all mutations have occurred at different positions.

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... sequence.³

I lied. This isn't quite the way you estimate it. To get an unbiased estimate of pi, you have to multiply this equation by $n/(n-1)$, where $n$ is the number of haplotypes in your sample.

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... time.⁴

This is not the same $\theta$ we encountered when discussing $F$-statistics. Weir and Cockerham's $\theta$ is a different beast. I know it's confusing, but that's the way it is. When reading a paper, the context should make it clear which conception of $\theta$ is being used.

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... severe.⁵

Why? Because most of the heterozygosity is due to alleles of moderate to high frequency, and those are not the ones likely to be lost in a bottleneck. See the Appendix for more details.

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