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

Animal coloration is one of the most conspicuous phenotypic traits in natural populations and has important implications for adaptation and speciation. Changes in coloration can occur over surprisingly short evolutionary timescales, 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 2 × 2 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 prepatterning 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 result from an interaction between divergence in upstream elements of the melanogenesis pathway and genes that provide an underlying prepattern across the body through positional information. A model of evolutionary stable prepatterns 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.

动物体色（animal coloration）是自然种群中最显著的表型性状之一，对物种适应与形成具有重要意义。体色变化可在出人意料的短进化时间尺度内发生，而在较远的系统发育距离下重复出现相似的颜色模式也较为常见。尽管色素生成的遗传基础已被充分阐明，但调控体色模式形成的机制仍鲜为人知。本研究针对两个遗传上近乎一致的鸦类类群展开解析，二者基于真黑色素（eumelanin）的表型存在显著差异：分别为通体黑色的食腐鸦与灰羽头巾鸦。我们构建了高质量的基因组注释，并对2×2实验设计的活跃黑色素生成毛囊转录组（transcriptome）数据进行分析，采样部位包括头部（两个类群的头部均为黑色）与躯干（食腐鸦躯干为黑色，头巾鸦躯干为灰色）。两个类群中躯干与头部的表达差异广泛且平行，且显著富集了黑色素生成（melanogenesis）相关基因（如ASIP、CORIN与ALDH6），这表明通体黑色的食腐鸦体内也存在隐蔽的预模式。与此同时，体色特异性表达（灰色vs黑色）仅局限于少数与核心转录因子MITF紧密关联的黑色素生成基因，其中最为突出的包括HPGDS、NDP与RASGRF1。本研究得出结论，两个类群间的体色模式差异，可能源于黑色素生成通路上游元件的分化，与通过位置信息在全身构建基础预模式的基因之间的互作。这种可通过简单调控变化暴露或隐藏的进化稳定预模式模型，或可解释鸦科（corvids）及其他众多脊椎动物类群中观察到的系统发育独立重复出现的体色模式。