Many paleognaths (ratites and tinamous) have a pair of homomorphic ZW sex chromosomes in contrast to the highly differentiated sex chromosomes of most other birds. To understand the evolutionary causes for the different tempos of sex chromosome evolution, we produced female genomes of 12 paleognathous species and reconstructed the phylogeny and the evolutionary history of paleognathous sex chromosomes. We uncovered that Palaeognathae sex chromosomes had undergone stepwise recombination suppression and formed a pattern of “evolutionary strata”. Nine of the 15 studied species' sex chromosomes have maintained homologous recombination in their long pseudoautosomal regions extending more than half of the entire chromosome length. We found that in the older strata, the W chromosome suffered more serious functional gene loss. Their homologous Z-linked regions, compared with other genomic regions, have produced an excess of species-specific autosomal duplicated genes that evolved female-specific expression, in contrast to their broadly expressed progenitors. We speculate such “defeminization” of Z chromosome with underrepresentation of female-biased genes and slow divergence of sex chromosomes of paleognaths might be related to their distinctive mode of sexual selection targeting females rather than males, which evolved in their common ancestors.

与大多数其他鸟类的高度分化性染色体相比，许多古颚类（平胸类和 tinamous）具有一对同态的 ZW 性染色体。为了解性染色体进化速度不同的进化原因，我们制作了 12 个古颚类物种的雌性基因组，并重建了古颚类性染色体的系统发育和进化史。我们发现，古颚类的性染色体经历了逐步的重组抑制，形成了“进化层”的格局。15 个被研究物种的性染色体中有 9 个在其较长的假常染色体区域中保持同源重组，延伸了整个染色体的一半以上染色体长度。我们发现，在较老的地层中，W 染色体的功能基因丢失更为严重。与其他基因组区域相比，它们的同源 Z 连锁区域产生了过量的物种特异性常染色体重复基因，这些基因进化出雌性特异性表达，与其广泛表达的祖细胞相反。我们推测 Z 染色体的这种“女性化”，女性偏向基因的代表性不足和古颌骨性染色体的缓慢分化可能与它们针对女性而不是男性的独特性选择模式有关，这种模式是在它们的共同祖先中进化而来的。