Fig. 3

The zebra finch germline-restricted chromosome is ancient and highly dynamic. a Phylogeny of the intergenic 27L4 locus previously sequenced by Itoh et al.⁸ suggests stable inheritance of the GRC paralog (alternative or ‘alt’ in red; cf. reference or ‘ref’) among the sampled zebra finches. b–f Phylogenies of GRC-linked genes (‘alt’, in red; most selected from expressed genes) diverging from their A-chromosomal paralogs (‘ref’) before/during early songbird evolution (b; bicc1, stratum 1; cf. Supplementary Fig. 9), during songbird evolution (c; ugdh, stratum 2), during estrildid finch evolution (d; psip1, stratum 3), in the ancestor of the zebra finch species (e; rnf17, stratum 4), and in the Australian zebra finch subspecies (f; secisbp2l; stratum 5). The maximum likelihood phylogenies in panels a–f (only bootstrap values ≥50% shown) include available somatic genome data from estrildid finches and other songbirds. g Species tree of selected songbirds showing the chronological emergence of evolutionary strata (S1–S5) on the GRC (red gene names). Molecular dates are based on previous phylogenies^28,73. Bird illustrations were used with permission from Lynx Edicions. h Circos plot indicating A-chromosomal origin of high-confidence GRC-linked genes from 18 autosomes and the Z chromosome. Due to the lack of chromosome-level scaffolding information for the GRC, we were unable to attribute the relative order between most of the genes in the GRC (see details in Supplementary Fig. 1c). Therefore, the represented genes are indicated in the same spot in the GRC placeholder (red box; not to scale). Note that A-chromosomal paralogs of 37 genes remain unplaced on chromosomes in the current zebra finch reference genome taeGut2.