Markers used and their resulting map order

OrderaGenebGene abbreviationcLocationdSize relationeSourcef
X chromosome
1 Phosphogluconate dehydrogenase Pgd *62D4RsaI cuts simIntron
2 scute sc 1A8sec > sim1
3 period per 3B2–3sim > secRepeat
4 defective chorion dec1 7C1DdeI cuts simX96929, X96931
5 DS01391 (microsatellite) DS01391 9A1–2sec > sim2
6 no-on-or-off-transient A nonA*414B18–C1secsimIntron
7 orked f2 15F7–9Morphological
8 Zwischenferment (G6PD) Zw 18D13sec > simIntron
Second chromosome
1 expanded ex 21C5–6sec > sim3
2 net nt 21A5Morphological
3 anterior open yan 22D1sec > sim2
4 odd skipped odd 24A1sim > sec4
5 Mst26Aa Mst 26A1sec > simX70899, X72630; intron
6 neither inactivation nor afterpotential C ninaC 27F3Hsp92II cuts sim5
7 big brain bib 30F5sec > simRepeat
8 spalt sal 32F1–2sim > secIntron
9 Suppressor of Hairless Su(H) 35B8sim > sec4
10 caudal cad 38E6sec > simRepeat
11 Phosphoglucose isomerase Pgi*144F6TaqI cuts simIntron
12 Gprotein oα 47A Dgα 47A7–9sim > sec1
13 slit sli*352C9–D1sec > sim2
14 grainy head grh 54E1–F1sim > sec4
15 plum pm 59E2–3Morphological
16 twist twi 59C2TaqI cuts simRepeat
Third chromosome
1 Cdc37 Cdc37 62B4Alw26I cuts sim 6
2 veinlet ve 62A1–2sim > sec1
3 temperature-induced-paralytic-E tipE*764A10sim > secIntron
4 Laminin B2 LamB2 67C2MfeI cuts sec 7
5 Superoxide dismutase Sod 68A7HaeIII cuts simIntron
6 Esterase 6 Est6 69A1BsrGI cuts secIntron
7 Accessory gland peptide 70A Acp70A 70A4sim > secX99414, X99417; intron
8 scarlet st 73A3Morphological
9 transformer tra 73A10sec > simIntron
10 Catalase Cat 75E1sim > sec1
11 Glucose dehydrogenase Gld 84D3HaeIII cuts simNoncoding
12 ebony e 93D1Morphological
13 nanos nos*291F7sim > sec3
14 glass gl 91A3RsaI cuts sec 6
15 prospero pros 86E5–6CfoI cuts sim 1
16 Metallothionein A Mtn 85E9DraI cuts secIntron
17 slowpoke slo 96A14–17sec > simIntron
18 Myosin alkali light chain 1 Mlc1 98A14–15Cuts secL49010, L49009; intron
19 janus jan 99D3DdeI cuts sec 5
20 similar sima*599D3–7Hsp92II cuts sec 8
Fourth chromosome
1 eyeless ey 102C2simsecIntron
  • a The order is that on the mapped chromosome (Figure 1).

  • b Candidate genes are identified by underlining.

  • c Significant markers from forward/backward stepwise regression are designated by an asterisk and their rank order (1–7).

  • d Cytological locations were obtained from FlyBase ( and are for D. melanogaster.

  • e Size of PCR products of D. simulans (sim) relative to D. sechellia (sec) or restriction enzyme used to digest PCR products. Five markers are morphological, not molecular, and are designated as such.

  • f Sequences of primers can be found in these references: 1, Schug et al. (1997); 2,; 3, Goldstein and Clark (1995); 4, Michalakis and Veuille (1996); 5, Liu et al. (1996); 6, Schug et al. (1998); 7, Colson and Goldstein (1999); 8, Colson et al. (1999). Of these, numbers in italic designate primers for microsatellite sequences for which we did not find PCR product length differences. Instead, a restriction enzyme was used to resolve the two species. The designations “intron,” “repeat,” and “noncoding” indicate markers new to this study that are PCR products crossing an intron, incorporating a repeat, or in a noncoding sequence, respectively. GenBank accession numbers are given for sequences available from both species. Primer sequences and PCR conditions are available by request from the authors.