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. 2024 Feb 23;15:1670. doi: 10.1038/s41467-024-46052-x

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© The Author(s) 2024, corrected publication 2024

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Fig. 2 — a Hi-C contact map of the neo-Z and neo-W of the crested ibis presenting territories homologous to chicken chr22. b IGV screenshot of the results of raw reads mapping to the neo-Z. The dashed line indicates the fusion site of the neo-Z, which is crossed by consecutive reads. The three panels display the distributions of genes, TEs, and repeats within 100 kb upstream and downstream of the fusion loci. c FISH images for the probes of chicken chr22 hybridized in crested ibis chrZ. The total length of probes is approximately 9 kb. The dashed boxes show the chrZ of crested ibis, and the arrows point towards the enlarged area within the dashed box. The Red dots are hybrid signals. The FISH experiments were repeated for twice with similar results. d Schematic diagram of the evolutionary process for the neo-sex chromosomes. After a part of chr22 underwent inversion, a new SDR (blue rectangle) formed, and the remaining part (yellow semicircle) formed a new-PAR. e Sequence divergence of the Z and W reveals the pattern of evolutionary strata. Different color shows each of the evolutionary strata. Size of circles is scaled to the length of sequence alignments. f dS values for the Z–W gametologs of each stratum. The numbers of genes for S0, S1, S2, S3, and S4 are 14, 29, 79, 21, and 32, respectively. The number on the horizontal line above each two boxes represents p-values (two-sided Wilcoxon signed rank test). NS indicates no significant difference between two data groups. The line in the middle of the box represents the median, the upper and lower boundaries of the box represent the upper and lower quartiles, respectively. The boundaries of the upper and lower whiskers represent the maxima and minima, respectively. g Phylogeny of the Z–W gametologs for S4. EGG represents egret (Egretta garzetta, belongs to Ardeidae family). Threskiornithidae genes are clustered by sex chromosome rather than species, suggesting this autosomal-sexual chromosome fusion event happened after the divergence of Threskiornithidae and Ardeidae. Additional gene trees are given in Supplementary Fig. 11. Source data are provided as a Source Data file.