Transcriptomics of colour patterning and coloration shifts in crows

Abstract

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.

Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex

“…More generally, pigmentation candidate genes from across all contact zones contained at least one gene associated with the Wnt signalling component of the melanogenesis pathway ( AXIN2 , LEF1 , LRP5/6 ), a central modulator of the microphthalmia-associated transcription factor ( MITF ) that has been functionally implicated in the phenotypic differences between European crows26.…”

“…The KEGGREST package72 was used to extract KEGG pathway annotations for zebra finch genes (other annotations were natively supported by the goseq package). We also tested for enrichment of melanogenesis-related genes specifically using a manually curated list of melanogensis genes2673.…”

“…1b). Recent genomic and transcriptomic work across the European hybrid zone ( corone – cornix ) has shown that only a small number of narrow genomic regions, associated with the striking difference in pigmentation pattern, exhibited resistance to gene flow and suggests a simple, yet multi-locus genetic architecture for the trait1726. Here, we analysed whole-genome re-sequencing data of 124 individuals from 10 populations, including 11 phenotypic hybrids, and 6 individuals from the recently diverged American sister species C. brachyrhynchos (mean coverage: 12.5 × ; range: 6.6–26.6; Supplementary Table 2).…”

Diversidad Genética de Palomas Domésticas (Columba livia) en Lorica, Colombia, Utilizando Genes que Codifican la Coloración del Plumaje

“…Los cambios en la coloración se producen en escalas de tiempo evolutivas sorprendentemente cortos, mientras que la repetición de patrones de colores similares a través de grandes distancias filogenéticas es común (Poelstra et al, 2015).…”

Regulatory architecture of gene expression variation in the threespine stickleback, Gasterosteus aculeatus

“…Variation in gene expression has been shown to underlie several well-documented cases of phenotypic and/or adaptive divergence. These include plumage coloration and beak shape in birds (Mallarino et al 2011;Poelstra et al 2015), mimetic wing patterns in butterflies (Reed et al 2011;Hines et al 2012), and flower color (Durbin et al 2003). Further, differences in gene expression patterns have been found to correlate with adaptive divergence in multiple species (e.g., Bernatchez et al 2010;Barreto et al 2011).…”