Population Genetics Primer

Check out this nice primer of population genetics by Anya Plutynski and Warren Ewens from the Philosophy of Science Encyclopedia. A lot of it deals with classical population genetics (Wright, Fisher, et al), and I especially like their description of Hardy-Weinberg equilibrium:

Weinberg and Hardy independently established the "law of panmictic equilibrium" -- today known as the Hardy-Weinberg "law" or "principle". The law might be better described as a neutral or equilibrium model -- a mathematical derivation starting from assumptions (some known to be false) for the purposes of evaluating the "baseline" state of a Mendelian system absent perturbing forces.

Much of population genetics theory is devoted to null models, which we then test using data from natural populations. If we reject the null model, we conclude that at least one of the assumptions has been violated. This is a real popular way to detect natural selection or identify interesting demographic histories. Hardy-Weinberg equilibrium is one of the most basic models, although it is quite robust to violations of the unrealistic assumptions. That means it ain't a very good null because it's difficult to reject.

Plutynski's and Ewens's review also provides a good treatment of the influence of molecular data population genetics theory. They describe the influence of the neutral theory and the coalescent. The neutral theory revolutionized how we think about evolution at the molecular level. It also provides an excellent null hypothesis for detecting natural selection on DNA and protein sequences. It is not, however, an anti-selectionist model, something that Plutynski and Ewens point out:

Kimura's theory was met with a great deal of controversy, as many interpreted it to run counter to the neo-Darwinian view that selection was the main agent of evolutionary change. This false impression was exacerbated by a paper published immediately afterward by King and Jukes (1969), defending roughly the same thesis. Many were led to the mistaken view that the neutral theory denies the fact of adaptive evolution. However, the neutral theory simply states that a large quantity of the overturn of molecular variation within populations has nothing to do with adaptation -- it is simply neutral with respect to selection, that is, it has no effect on an organism's survival.

There is room for adaptive evolution within the neutral theory (and the nearly neutral theory). One of the ways we can test the neutral theory is through coalescent simulations. The coalescent allows us to generate null models for sequence polymorphism generated from natural populations. Their review of coalescent theory is terse, but this is a primer to population genetics not a comprehensive guide. Their take home message is that coalescent theory allows us to estimate the most recent common ancestor of a sample of DNA sequences, which, in turn, allows us to estimate certain population parameters.

I would recommend this review to a reader who has some familiarity with evolutionary genetics -- it would be a difficult read for someone who does not know how to calculate allele frequencies. It's definitely not a true primer because it's not the first thing you would read if you want to learn about the field. But it provides a good summary of the history of population genetics and introduces some important concepts that are relevant to current research. It's especially valuable because of the focus on null models and how models make simplifying assumptions.

(Via Gene Expression.)