Table 1. Signs of the QTL effects in the case of four taxa, for each possible cross and each possible partition.

	Partition of taxa
Cross	$\text{A}|\text{BCD}$	$\text{B}|\text{ACD}$	$\text{C}|\text{ABD}$	$\text{D}|\text{ABC}$	$\text{AB}|\text{CD}$	$\text{AC}|\text{BD}$	$\text{AD}|\text{BC}$
A × B	+	−	0	0	0	+	+
A × C	+	0	−	0	+	0	+
A × D	+	0	0	−	+	+	0
B × C	0	+	−	0	+	−	0
B × D	0	+	0	−	+	0	−
C × D	0	0	+	−	0	+	−

For each partition, the taxa to the right of the vertical bar have the high allele. For each cross, the sign of the effect is for the right vs. the left taxon.