10.5 The \(D\) statistic

Introgression creates an imbalance in the number of ABBA or BABA trees if only one of the human populations has admixed with Neanderthals. The \(\textbf{D}\) statistic quantifies this imbalance:

\[ D = \frac{\textrm{# BABA sites} - \textrm{# ABBA sites}}{\textrm{# BABA sites} + \textrm{# ABBA sites}} \]

\(D > 0\) is evidence for Neanderthal gene flow into the H2 population, while \(D < 0\) is evidence for gene flow into H1.

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Choice of populations for the \(D\) statistic

The choice of populations is very important when calculating the \(D\) statistic.

When assessing archaic introgression, H2 is typicaly set as a human population without archaic admixture (e.g., a population from Africa). If H2 instead were a European population that did possess introgressed sequence, we would not expect a significant \(D\) statistic.

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