Chapter 29 Topics in pop gen
This is just a bunch of ideas. But basically, I want to have some topics here that everyone should know about. Slanted toward things that are relevant for inference or simulation.
29.1 Coalescent
Gotta have a lecture on the coalescent. It would be nice to try to motivate all the topics from this backward in time perspective.
Get far enough to discuss \(\pi\) and the expected site frequency spectrum.
29.2 Measures of genetic diversity and such
It would really be good for me to write a chapter / give a few lectures on different measures like dxy and fst
From Ash’s paper: However, population genomic analyses (outlined below) use FST only, as dxy was highly correlated to nucleotide diversity (for early stage diverging populations the correlation between dxy and \(\pi\) is > 0.91, Pearson correlation). As such variation in dxy across the genome reflects variation in diversity, not differentiation (Riesch et al., 2017).
Tajima’s \(D\) and such. The influence of selection on such measures.
29.4 Balls in Boxes
Would be worthwhile to have a review of all these sorts of variants of population assignment, structure, admixture, etc.
Population structure and PCAs.
finestructure and fineRADstructure.
Might want to insert Bradburd, Coop, and Ralph (2018).
Might also want to discuss Pickrell and Pritchard (2012).
Also: Pritchard, Stephens, and Donnelly (2000)
What if we go and try to put the same one in? Like Pritch 2000 again: (Pritchard, Stephens, and Donnelly 2000)
29.5 Some landscape genetics
After talking with Amanda about her dissertation I realized it would be good to talk about some landscape genetics stuff. For sure I want to talk about EEMS and maybe CircuitScape, just so I know well what is going on with the latter.
29.7 Tests for Selection
A look at a selection of the methods that are out there. FST outliers, Bayescan, Lositan, PCAdapt, and friends. It would be good to get a nice succinct explanation/understanding of all of these.