Figure 1.

Dynamics of recombination suppression on the avian sex chromosomes. The distribution of synonymous (d_S) divergence estimates between G. gallus (black), M. gallopavo (yellow, panel A) and A. platyrhynchos (green, panel B) gametologs, mapped against physical position of the G. gallus Z-linked ortholog. The 95% confidence intervals were calculated using standard errors. Bootstrap values were calculated using 1000 permutations. AZ, GZ, MZ, TZ corresponds to A. platyrhynchos, G. gallus, M. gallopavo, and T. guttata Z-linked genes. The physical Z-linked position of the loci for which gene trees are shown are indicated (*). Meleagris gallopavo d_S estimates map closely onto the G. gallus strata boundaries, and maximum-likelihood gene trees for all gametologs cluster by sex chromosome, not species, indicating that four strata are conserved across the Galliformes (Fig. S2). Anas platyrhynchos d_S estimates map closely onto the two oldest G. gallus strata boundaries, and maximum-likelihood gene trees for gametologs within these regions cluster by sex chromosome indicating that these strata are conserved across the Galloanserae. For the remaining gametologs, maximum-likelihood gene trees reveal that recombination was suppressed independently in the A. platyrhynchos lineage (Fig. S3). The d_S estimates are highly heterogeneous and locus specific, indicating gradual divergence of gametologs with residual recombination across large tracts of the sex chromosomes.