Table 1.

Fixed nucleotidic differences between Mayotte D. yakuba (D. y. mayottensis) and 3 populations of mainland D. yakuba (D. y. yakuba) with their ancestral states from D. santomea genome shown. The three populations of D. y. yakuba represent 21 lines from Côte d'Ivoire, Cameroon and Kenya. Gene names are given according to D. melanogaster ortholog. Sites shared between D. y. mayottensis and D. santomea are underlined.

Site	Gene	D. y. yakuba	D. y. mayottensis	D. santomea
2L:2216873	CG4267 (intron)	A	G	A
2L:2217239	CG4267 (exon)	C	T	C
2L:2220466	CG4267 (downstream)	A	G	A
2L:2236992	CG17243 (downstream)	C	A	C
2L:2237074	CG17243 (downstream)	G	A	G
2L:2237075	CG17243 (downstream)	G	A	G
2R:11743017	Egfr (intron)	T	A/C	T
2R:13045177	CG8908 (exon)	C	G	G
2R:15111406	CG33958 (intron)	G	A	A
2R:15776372	Patronin (intron)	T	G	G
2R:19611509	egl (intron)	C	A	G
2R:19612352	egl (exon)	A	G	A
2R:19612407	egl (exon)	T	C	C
2R:19612428	egl (exon)	A	G	G
2R:19615823	CG34105/CG12491 (intergenic)	T	C	T
X:8980250	CG9518 (upstream)	G	A	G
X:8989321	CG9514 (downstream)	A	C	A
X:8997990	CG9514 (intron)	C	T	C
X:9003564	CG9514 (upstream)	A	T	T
X:9004874	CG9514/CG9512(intergenic)	A	T	A
X:9019266	CG12398 (exon)	G	A	G
X:9019413	CG12398 (upstream)	C	A	C
X:9023586	CG9503 (exon)	T	A	T
X:9024569	CG9503 (exon)	C	A	C
X:9034448	Flo2 (upstream)	T	A	T
X:9040907	pdgy (intron)	C	G	C
X:9060210	eag (intron)	A	C	A
X:9061187	eag (intron)	C	T	C
X:9068430	eag (intron)	A	G	A
X:9069386	eag (intron)	G	A	G
X:9383509	CG5877 (upstream)	T	C	T
X:9387538	CG5877 (upstream)	T	C	C
X:9398249	gce (intron)	C	G	C
X:9407136	gce (intron)	A	T	A
X:9410040	gce (exon)	A	G	A
X:21717401	stnB (intron)	A	C	A