Table 3.

Numbers of unpreferred and preferred polymorphisms in D. simulans

Outgroup	Chromosome	Unpreferred	Preferred
D. melanogaster	X (n = 21)	112	42
	3R (n = 19)	221	85
	G-test, P = 0.91
D. melanogaster/D. yakuba	X (n = 8)	66	13
	3R (n = 12)	131	26
	G-test, P = 0.98

Unpreferred and preferred polymorphisms (51, 52) within D. simulans were assigned by using D. melanogaster as the outgroup for the entire data set of 40 genes, or by using D. melanogaster and D. yakuba for a subset of the data set constituting 20 genes (Rh3, ry, Rel, hyd, Tcp-1, AP50, Osbp, boss, Tpi, mir, CP190, Hsc70, G6pd, sog, v, sn, dec-1, X, per, z). Only codons for which the outgroup codon(s) was identical to one of the segregating D. simulans codons were used. Because sequence evolution in these species approximates the infinite sites model, few errors are made in determining ancestral state by this method; errors in assignment of ancestral state should be random with respect to chromosome arm. n is the number of loci surveyed on each arm.