legend figure 6.8

Chapters/genetic_drift_pop_structure.tex

@@ -355,12 +355,12 @@ \section{Incomplete Lineage Sorting}
 \end{figure}
 %JRI: here and in text you refer to populations ABCD but figure is labelled ``species'' and 1234. I think ABCD for populations and AB for alleles is confusing. I don't know if you need A/B for alleles. Why not use A1A2 or just 1/2 as you have previously? sure you miss the fun mnemonic, but it's clearer for a novice reader
 
-Take a look at Figure \ref{fig:ABBA_BABA}. In both cases the lineages from A and B fail to coalesce in
+Take a look at Figure \ref{fig:ABBA_BABA}. In both cases the lineages from 1 and 2 fail to coalesce in
 their initial shared ancestral population, and one or the other of them
-coalesces with the lineage from C before they coalesce with each other. Each option is equally
+coalesces with the lineage from 3 before they coalesce with each other. Each option is equally
 likely; therefore the mutational patterns ABBA and BABA are equally likely to occur under ILS.  \sidenote{Here we have to assume no structure in the ancestral population.}
 
-However, if gene flow occurs from population C into population B, in addition to ILS the lineage from B can more recently coalesce with the lineage from C, and so we should see more ABBAs than BABAs. To test for this effect of gene flow, we can sample a sequence from each of our 4 populations and count up the number of sites that show the two mutational patterns consistent with the gene-tree discordance $n_{ABBA}$ and
+However, if gene flow occurs from population 3 into population 2, in addition to ILS the lineage from 2 can more recently coalesce with the lineage from 3, and so we should see more ABBAs than BABAs. To test for this effect of gene flow, we can sample a sequence from each of our 4 populations and count up the number of sites that show the two mutational patterns consistent with the gene-tree discordance $n_{ABBA}$ and
 $n_{BABA}$ and calculate
 \begin{equation}
 \frac{n_{ABBA}-n_{BABA}}{n_{ABBA}+n_{BABA}}