Table 1. Number of genes identified by the screening methods 1 and 2.

	X	2L	2R	3L	3R	Totals
Screening 1	67	112	106	88	144	517
Screening 2	101	74	89	77	98	439
Common	14	73	76	61	96	320

The genes identified by method 1 have divergences inferior to the average plus standard deviation for the chromosomes in which they are located in sim-sec and higher divergences than the average plus standard deviation in sim-mel and sec-mel. Screening 2 selects genes that retained ancestral features and diverge significantly form D. melanogaster. Note that screening 2 appears more stringent than screening 1. Note also that a large number of common genes that can be found by both screenings in the autosomes, but considerably less on the X. No ancestral alleles could be found on the fourth chromosome (see text).