TABLE 3

Contrasting levels of synonymous and replacement variation

LocusSyn polyRep polySyn fixedRep fixedGaP
Adh90311.5760.2093
ase32210.0290.8628
ci02422.7160.0994
est-6681816124.7920.0286*
    (sim vs. mau)6818134.2370.0396*
    (sim vs. sec)53111295.1360.0234*
    (mau vs. sec)24914111.7050.1916
janus141445.0400.0248*
    (sim vs. mau)14100NANA
    (sim vs. sec)91443.3060.0690
    (mau vs. sec)91443.3060.0690
mt:ND5201310.1170.7323
per7171620.0680.7943
yp242220.2370.6264
Zw140846.2400.0125*
    (sim vs. mau)140237.9530.0048**
    (sim vs. sec)70843.7380.0532
    (mau vs. sec)70610.9740.3237
  • McDonald-Kreitman tests of amino acid replacement and synonymous polymorphisms, within and between species (McDonald and Kreitman 1991): Syn poly, synonymous polymorphisms; Rep poly, replacement polymorphisms; Syn fixed, synonymous fixed differences; Rep fixed, replacement fixed differences. Tests include all three species. A site is counted as polymorphic if it is variable in any of the species. For those tests that were statistically significant (* P < 0.05; ** P < 0.01), tests on individual species pairs are also shown (sim, D. simulans; mau, D. mauritiana; sec, D. sechellia).

  • a Williams’ correction is applied to G-tests (Sokal and Rohlf 1981).