Fig 1. Cis- and/or trans-regulatory changes during species differentiation.

(A) During evolution, cis- and/or trans-regulatory elements change gene expression levels between closely related species. (B) Schematic showing selected song-control regions and connections in the songbird brain. The posterior motor pathway and the anterior cortico-basal ganglia-thalamic circuit (anterior forebrain pathway [AFP]) are represented as red and gray lines, respectively. (C) Genome composition of reciprocal F₁ hybrids between zebra finch (ZF) and owl finch (OF). ZO represents F₁ hybrid offspring between ZF♀ and OF♂. OZ hybrids are the opposite. Male F₁ hybrids share identical sets of auto- and sex chromosomes. (D) Classification of species differences in cis- and/or trans-regulations based on the comparison of the relative gene expression ratio between parental species and the allelic expression ratio in their F₁ hybrids. For each gene, “A” and “B” represent gene expression levels in ZF and OF, respectively. “a” and “b” represent gene expression levels from ZF and OF alleles, respectively, in F₁ hybrids. “A/B” and “a/b” are the expression ratio between parental species and the allelic expression ratio in F₁ hybrids, respectively. Area X, Area X of the striatum; DLM, dorsal lateral nucleus of the medial thalamus; F₁, first-generation; HVC, used as a proper name; LMAN, lateral magnocellular nucleus of the anterior nidopallium; nXIIts, tracheosyringeal part of the hypoglossal nucleus; RA, the robust nucleus of the arcopallium.