Constrained sequence analyses. Frequency histograms of inter-gap segment lengths are compared against the neutral expectation (solid line) (a,b). The shaded orange area represents the total amount of indel-purified sequence shared by the species pair. Histograms are derived from (a) chicken - G. magnirostris and (b) chicken - zebra finch whole genome alignments. Results are shown for a representative G+C-fraction from the 11th of 20 equal size G+C-bins, with the corresponding histograms from all G+C-fractions presented in Additional file 9, Additional file 10 and Additional file 11. Predicted amounts of constrained sequence estimated between three avian species pairs plotted against (c) the synonymous substitution divergence (d
) and (d) GC content of equally populated GC bins, with data inferred from the T. guttata – G. magnirostris and G. gallus – G. magnirostris alignments, respectively. The larger amount of constrained sequence inferred for the G. magnirostris and T. guttata comparison compared to the two chicken – finch comparisons implies that there is functional sequence that is passerine-specific and thus not present in chicken.