Nine high-quality Anas genomes provide insights into Anas evolution and domestication.

Evolutionary studies of wild and domestic organisms have yielded fascinating discoveries, while the species diversity and the domestication of ducks remain unclear. Here, we assembled eight chromosome-level Anas genomes, combined with the Pekin duck genome, to investigate Anas evolution and domestication. We found that, compared to autosomes, the Z chromosome was less affected by introgression and exhibited relatively stable local phylogenies. From the Z chromosome perspective, we proposed that the speciation of Anas platyrhynchos and Anas zonorhyncha was accompanied by continuous female-biased gene flow and remodeled duck domestication history. Moreover, we constructed an Anas pan-genome and identified several differentiated structural variations (SVs) between domestic and wild ducks. These SVs likely regulate their neighboring genes (i.e., GHR and FER), which represented the promising "domestication genes." Furthermore, a long terminal repeat (LTR) retrotransposon burst was found to have accelerated duck domestication, specifically contributing to functional shifts of the notable MITF and IGF2BP1 genes. These findings presented a live example for understanding animal evolutionary processes.