Table 2.

Explanation of Statistics

Statistic	Samples	Allele Conditions	Pattern
D	1 sample each from $p_1,\hspace{0.17em}{p}_2,\hspace{0.17em}{p}_3$, O	$p_1!=p_2,\hspace{0.17em}{p}_3=B,\hspace{0.17em}O=A$	ABBA or BABA
dcfs	1 sample each from $p_1,p_3,O$	$p_1$=A, $p_2$=B, $p_3$=B, $O=A$	ABBA
	n samples from $p_2$
SFS	1 sample each from $p_3,O$	$O=A$, f($p_2=B$)$>0$	-BBA
	n samples from $p_2$
LD	1 sample each from $p_3,O$	$p_3=B,\hspace{0.17em}O=A$, f($p_{2||3}=B$)$\le 0.1$	-BBA or B-BA
	n samples each from $p_{1}or{p}_2$

SFS is the unconditional spectrum. $p_1,\hspace{0.17em}{p}_2$ are the two present day populations, $p_3$ is the archaic population, O is denoted the outgroup. Alleles “A” and “B” are the ancestral (state at O) and derived alleles, respectively.