Data from: Transcriptomics of colour patterning and colouration shifts in crows

Animal colouration is one of the most conspicuous phenotypic traits in natural populations, and has important implications for adaptation and speciation. Changes in colouration can occur over surprisingly short evolutionary time scales while recurrence of similar colour patterns across large phylogenetic distances is also common. Even though the genetic basis of pigment production is well understood, little is known about the mechanisms regulating colour patterning. In this study, we shed light on the molecular elements regulating regional pigment production in two genetically near-identical crow taxa with striking differences in a eumelanin-based phenotype: black carrion and grey-coated hooded crows. We produced a high-quality genome annotation and analysed transcriptome data from a 2x2 design of active melanogenic feather follicles from head (black in both taxa) and torso (black in carrion and grey in hooded crow). Extensive, parallel expression differences between body regions in both taxa, enriched for melanogenesis genes (e.g. ASIP, CORIN, and ALDH6), indicated the presence of cryptic pre-patterning also in all-black carrion crows. Meanwhile, colour-specific expression (grey vs. black) was limited to a small number of melanogenesis genes in close association with the central transcription factor MITF (most notably HPGDS, NDP, and RASGRF1). We conclude that colour pattern differences between the taxa likely results from an interaction between divergence in upstream elements of melanogenesis and genes that provide an underlying pre-pattern across the body through positional information. A model of evolutionary stable pre-patterns that can be exposed and masked through simple regulatory changes may explain the phylogenetically independent recurrence of colour patterns that is observed across corvids and many other vertebrate groups.