This is the datasets to produce the main text figures and supplementary figures in the study of Yamashita et al.(2018).<div><br></div><div><div>The evolution of unique organ structures is associated with changes in conserved developmental programs. However, functional conservation and variation of homologous transcription factors (TFs) that dictate species-specific cellular dynamics have remained elusive. Here, we dissect shared and divergent functions of Pax6 during amniote brain development. Comparative functional analyses revealed that neurogenic function of Pax6 is highly conserved in the developing mouse and chick pallium, while stage-specific binary functions of Pax6 in neurogenesis are unique to mouse neuronal progenitors, which are consistent with temporal regulation of Notch signaling. Furthermore, we identified that Pax6-dependent enhancer activity of Dbx1 is extensively conserved between mammals and chick, although Dbx1 expression in the developing pallium are highly divergent in these species. Our results suggest that spatio-temporal changes in Pax6-dependent regulatory programs contributed to species-specific neurogenic patterns in mammalian and avian lineages, which underlie morphological divergence of amniote pallial architectures.<br></div></div
