TABLE 1

Gene and sample summary statistics

Locus	n_sim^a	n_mau	n_sec	Map^b	E_nc^c	Rec^d	Length^e	Coding	Noncoding
Adh	6	6	2	2 35B2	31.2	0.0020	698	567	131
ase	6	5	6	X 1B4	55.7	0.0000	1067	1067	0
ci	9	6	4	4 101F1	51.8	0	1075	957	118
est6	4	6	2	3 69A1	54.6	0.0027	1520	1470	50
hb	10	9	8	3 85A6	45.2	0.0006	252	0	252
In(2L)t	11	9	3	2 34A8	NA	0.0026	680	0	680
janus	3	3	1	3 99D4	54.6	0.0037	1072	558	514
mt:ND5	9	8	8	mt	25.2	0	277	277	0
per	6	6	6	X 3B2	41.2	0.0029	1870	1677	193
Sxl	13	9	14	X 6F5	51.5	0.0038	236	0	236
w	9	7	6	X 3C2	47.7	0.0034	194	0	194
yp2	6	6	6	X 9A2	33.1	0.0029	1100	1044	56
z	6	6	6	X 3A3	45.9	0.0027	980	799	181
Zw	12	6	2	X 18E	34.5	0.0023	1298	1164	134

↵^a The sample sizes for each locus and species.
↵^b The genomic location of the gene in D. melanogaster. The physical maps of these species are all identical to each other and nearly identical to D. melanogaster with the exception of one inverted segment on the third chromosome (sections 84F-93F; Lemeunier and Ashburner 1976). The chromosome (X, 2, 3, or 4) is shown followed by the polytene chromosome band number (Bridges 1938) as listed in Flybase (http://flybase.bio.indiana.edu:82/). The mt:ND5 gene is located in the mitochondrial (mt) genome.
↵^c The effective number of codons (Wright 1990). Values near the upper limit of 61 have a low codon bias, whereas values near the lower limit of 20 have a high codon bias. Values were taken from Kliman and Hey (1993b) or calculated from the complete coding portion of the gene as reported in the GenBank record. NA, not applicable; In(2L)t was positionally cloned and has no associated protein coding gene.
↵^d The estimated recombination rate per generation as reported for D. melanogaster in the Appendix of Kliman and Hey (1993b). Units are centimorgans per kilobase pair.
↵^e The average number of aligned base positions from all pairwise comparisons. Values are shown for total length, as well as for amino acid coding regions, and noncoding regions.