The Evolutionary Origination and Diversification of a Dimorphic Gene Regulatory Network through Parallel Innovations in cis and trans

Abstract

The origination and diversification of morphological characteristics represents a key problem in understanding the evolution of development. Morphological traits result from gene regulatory networks (GRNs) that form a web of transcription factors, which regulate multiple cis-regulatory element (CRE) sequences to control the coordinated expression of differentiation genes. The formation and modification of GRNs must ultimately be understood at the level of individual regulatory linkages (i.e., transcription factor binding sites within CREs) that constitute the network. Here, we investigate how elements within a network originated and diversified to generate a broad range of abdominal pigmentation phenotypes among Sophophora fruit flies. Our data indicates that the coordinated expression of two melanin synthesis enzymes, Yellow and Tan, recently evolved through novel CRE activities that respond to the spatial patterning inputs of Hox proteins and the sex-specific input of Bric-à-brac transcription factors. Once established, it seems that these newly evolved activities were repeatedly modified by evolutionary changes in the network’s trans-regulators to generate large-scale changes in pigment pattern. By elucidating how yellow and tan are connected to the web of abdominal trans-regulators, we discovered that the yellow and tan abdominal CREs are composed of distinct regulatory inputs that exhibit contrasting responses to the same Hox proteins and Hox cofactors. These results provide an example in which CRE origination underlies a recently evolved novel trait, and highlights how coordinated expression patterns can evolve in parallel through the generation of unique regulatory linkages.

A Pathway Analysis of Melanin Patterning in a Hemimetabolous Insect

“…These observations suggest that the roles in wing melanization are distinct between different melanin-promoting factors: yellow is required for the proper intensity of black melanin in the wings, especially the hindwing, whereas tan may not be involved at all in wing pigmentation in Oncopeltus. Camino et al 2015), indicating that these correlations are functionally meaningful. Thus, we hypothesized that the difference in mechanisms regulating nonblack patterns between forewing (NBAD branch) and hindwing (NADA branch) comprise differential expressions of the relevant core genes.…”

“…In particular, such correlations have been seen in the D. melanogaster abdomen (Rebeiz et al 2009;Camino et al 2015) and forewing (Gompel et al 2005) and occur in diverse Drosophila species with divergent patterns of melanic pigmentation (Werner et al 2010;Arnoult et al 2013;Ordway et al 2014;Camino et al 2015), indicating that these correlations are functionally meaningful. Thus, we hypothesized that the difference in mechanisms regulating nonblack patterns between forewing (NBAD branch) and hindwing (NADA branch) comprise differential expressions of the relevant core genes.…”

Using Drosophila pigmentation traits to study the mechanisms of cis-regulatory evolution

“…The gene yellow is expressed in zones where dark melanic pigmentation occurs on the cuticle [19–21]. While several hypotheses exist about the molecular function of yellow [22], its expression appears to be a general requirement for black melanin formation.…”

“…While other pigmentation enzymes contribute to cuticle coloration, only ebony and yellow have thus far been associated with strong expression patterns that predict the wing phenotypes. For male-specific abdomen pigmentation, an additional gene, tan, is expressed in a pattern which closely matches that of yellow [21]. tan encodes an enzyme with NBAD hydrolase activity which converts NBAD into Dopamine, promoting the formation of darker cuticle pigments [25].…”

“…In the abdomen, the Hox gene Abd-B is expressed in the epidermis underlying the pigmented A5 and A6 tergites and is required for the activation of yellow and tan [21,26]. The expression of yellow and tan in the unpigmented female abdomen is prevented by the Bab1 and Bab2 transcriptional repressors [27].…”