Table 2.

Model Variables Associated with Site i.

Variable	Type	Description
Oi	Observed	Set of aligned bases from outgroup species
	Observed	Base for major allele in target population
	Observed	Base for minor allele in target population ( for monomorphic sites)
Yi	Observed	MAF class for site i: “M” for monomorphic sites (MAF = 0)
		“L” for polymorphic sites with MAF
		“H” for polymorphic sites with MAF
Si	Hidden	Selection class: “” for neutral sites
		“” for sites under selection
Zi	Hidden	Ancestral allele at the MRCA of the target
		Population and the closest outgroup
Ai	Hidden	Ancestral allele at the MRCA of samples from the target population