Polymorphism (π) and divergence (Dxy) of MSL-binding regions in D. melanogaster, D. simulans, and D. yakuba (%)

D. melanogasterD. simulansD. yakuba
18D10Sequenced region (1.2 kb)0.898.182.651.497.353.430.5717.1010.55
Binding site (0.6 kb)0.226.441.781.214.592.280.5012.257.56
Nonbinding region (0.6 kb)1.539.853.511.7710.264.650.6321.4013.22
roX1Sequenced region (1.3 kb)1.156.574.271.146.972.740.1512.199.63
Binding site (0.2 kb)
Nonbinding region (1.1 kb)1.356.894.491.367.412.950.1713.7511.02
roX2Sequenced region (1.3 kb)0.245.602.920.965.441.830.4113.6410.49
Binding site (0.1 kb)0.068.595.340.914.873.020.0613.8210.34
Nonbinding region (1.2 kb)
X-linked(6 loci, 4 kb)2.9714.688.712.5114.575.361.5028.5721.76
  • For comparison, synonymous site diversity of 6 X-linked protein-coding genes sequenced in the same populations is given. Binding and nonbinding regions were defined by experimental data derived from DNase protection assays and genetic assays defining minimal fragments necessary for location of the MSL complex in vivo (Kageyama et al. 2001; Park et al. 2003; Oh et al. 2004). The sequenced flanking region (nonbinding region) is part of the transcribed noncoding roX RNA for roX1 and roX2, while it consists of intergenic sequence for 18D10.

  • a Dxy is the weighted average pairwise divergence per site (%) to an outgroup species (D. simulans for the D. melanogaster and D. yakuba populations and D. melanogaster for the D. simulans population), corrected for multiple hits (Jukes–Cantor).

  • b DxyANC is the weighted average pairwise divergence per site (%) to a reconstructed ancestral species, corrected for multiple hits (Jukes–Cantor).