Table 1.

SNP haplotypes (15)

Younger SNP1		Older SNP2
		Allele 1	Allele 2	Total
Allele 1	Number	a	b	a + b
	Frequency	Qρ + QR(1 − ρ)	(1 − ρ)Q(1 − R)	Q
Allele 2	Number	c	d	c + d
	Frequency	(R − Q)ρ + R(1 − Q)(1 − ρ)	(1 − R)[ρ + (1 − Q)(1 − ρ)]	1 − Q
Total	Number	a + c	b + d	N
	Frequency	R	1 − R	1

Covariance: D = ρQ(1 − R). Correlation: Δ = ρ√Q(1 − R)/R(1 − Q). Gene frequency difference: d = ρ(1 − R)/ (1 − Q) or ρQ/R.