= Solution
The observed <folded site frequency spectrum> has a larger $3:1$ to $2:2$ ratio than either expectation in part (d), and is closer to the <Yule process> expectation than to the constant-size <Kingman's coalescent> expectation. Both models can nevertheless produce deviations in one finite sample, especially because all mitochondrial sites largely share one genealogy; this observation alone is not a formal model-selection result.
For the <Yule process>, one possible violation is a \b[recent reduction in the per-lineage branching rate] rather than a constant $\lambda$. Lengthening the terminal four-branch interval adds one-descendant branch length and therefore preferentially increases the $3:1$ class.
For <Kingman's coalescent>, one possible violation is \b[recent population expansion] rather than a constant <effective population size>. Backward in time, coalescence is slow in the large recent population and faster in the smaller ancestral population. The resulting long external branches tend to increase the $3:1$ class relative to the $2:2$ class.
Back to article page