10 Archaic admixture

In this lab, we’ll discuss three common statistics, \(D\), \(f_{4}\), and the \(f_{4}\)-ratio, which are used for quantifying and testing hypotheses related to admixture (or “introgression”).

10.0.0.1 Learning objectives

After completing this chapter, you’ll be able to:

1. Explain how incomplete lineage sorting can create patterns of allele sharing that are discordant with species relationships.
2. Describe how introgression is expected to affect patterns of allele sharing.
3. Interpret the \(D\) and \(f_4\) statistics and their associated p-values.
4. Interpret the \(f_{4}\)-ratio ratio statistic and whether it implies differences in archaic admixture between populations.

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