Cédric Finet, Victoria A Kassner, Antonio B Carvalho, Henry Chung, Jonathan P Day, Stephanie Day, Emily K Delaney, Francine C De Ré, Héloïse D Dufour, Eduardo Dupim, Hiroyuki F Izumitani, Thaísa B Gautério, Jessa Justen, Toru Katoh, Artyom Kopp, Shigeyuki Koshikawa, Ben Longdon, Elgion L Loreto, Maria D S Nunes, Komal K B Raja, Mark Rebeiz, Michael G Ritchie, Gayane Saakyan, Tanya Sneddon, Machiko Teramoto, Venera Tyukmaeva, Thyago Vanderlinde, Emily E Wey, Thomas Werner, Thomas M Williams, Lizandra J Robe, Masanori J Toda, Ferdinand Marlétaz

https://doi.org/10.1093/gbe/evab179

Abstract

The vinegar fly Drosophila melanogaster is a pivotal model for invertebrate development, genetics, physiology, neuroscience, and disease. The whole family Drosophilidae, which contains over 4,400 species, offers a plethora of cases for comparative and evolutionary studies. Despite a long history of phylogenetic inference, many relationships remain unresolved among the genera, subgenera, and species groups in the Drosophilidae. To clarify these relationships, we first developed a set of new genomic markers and assembled a multilocus data set of 17 genes from 704 species of Drosophilidae. We then inferred a species tree with highly supported groups for this family. Additionally, we were able to determine the phylogenetic position of some previously unplaced species. These results establish a new framework for investigating the evolution of traits in fruit flies, as well as valuable resources for systematics.

Jesse T. Hughes, Melissa E. Williams, Mark Rebeiz, Thomas M. Williams

https://doi.org/10.1002/jez.b.23068

Abstract

Changes in gene expression are a prominent feature of morphological evolution. These changes occur to hierarchical gene regulatory networks (GRNs) of transcription factor genes that regulate the expression of trait-building differentiation genes. While changes in the expression of differentiation genes are essential to phenotypic evolution, they can be caused by mutations within cis-regulatory elements (CREs) that drive their expression (cis-evolution) or within genes for CRE-interacting transcription factors (trans-evolution). Locating these mutations remains a challenge, especially when experiments are limited to one species that possesses the ancestral or derived phenotype. We investigated CREs that control the expression of the differentiation genes tan and yellow, the expression of which evolved during the gain, modification, and loss of dimorphic pigmentation among Sophophora fruit flies. We show these CREs to be necessary components of a pigmentation GRN, as deletion from Drosophila melanogaster (derived dimorphic phenotype) resulted in lost expression and lost male-specific pigmentation. We evaluated the ability of orthologous CRE sequences to drive reporter gene expression in species with modified (Drosophila auraria), secondarily lost (Drosophila ananassae), and ancestrally absent (Drosophila willistoni) pigmentation. We show that the transgene host frequently determines CRE activity, implicating trans-evolution as a significant factor for this trait’s diversity. We validated the gain of dimorphic Bab transcription factor expression as a trans-change contributing to the dimorphic trait. Our findings suggest an amenability to change for the landscape of trans-regulators and begs for an explanation as to why this is so common compared to the evolution of differentiation gene CREs.

Original Research ARTICLE

Front. Ecol. Evol., 26 March 2020 | https://doi.org/10.3389/fevo.2020.00080

Gene Regulatory Network Homoplasy Underlies Recurrent Sexually Dimorphic Fruit Fly Pigmentation

Jesse T. Hughes¹, Melissa E. Williams¹, Rachel Johnson¹, Sumant Grover¹, Mark Rebeiz^2* and Thomas M. Williams^1,3*

1. ¹Department of Biology, University of Dayton, Dayton, OH, United States
2. ²Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States
3. ³The Integrative Science and Engineering Center, University of Dayton, Dayton, OH, United States

Traits that appear discontinuously along phylogenies may be explained by independent origins (homoplasy) or repeated loss (homology). While discriminating between these models is difficult, the dissection of gene regulatory networks (GRNs) which drive the development of such repeatedly occurring traits can offer a mechanistic window on this fundamental problem. The GRN responsible for the male-specific pattern of Drosophila (D.) melanogaster melanic tergite pigmentation has received considerable attention. In this system, a metabolic pathway of pigmentation enzyme genes is expressed in spatial and sex-specific (i.e., dimorphic) patterns. The dimorphic expression of several genes is regulated by the Bab transcription factors, which suppress pigmentation enzyme expression in females, by virtue of their high expression in this sex. Here, we analyzed the phylogenetic distribution of species with male-specific pigmentation and show that this dimorphism is phylogenetically widespread among fruit flies. The analysis of pigmentation enzyme gene expression in distantly related dimorphic and monomorphic species shows that dimorphism is driven by the similar deployment of a conserved metabolic pathway. However, sexually dimorphic Bab expression was found only in D. melanogaster and its close relatives. These results suggest that dimorphism evolved by parallel deployment of differentiation genes, but was derived through distinct architectures at the level of regulatory genes. This work demonstrates the interplay of constraint and flexibility within evolving GRNs, findings that may foretell the mechanisms of homoplasy more broadly.

Changes throughout a Genetic Network Mask the Contribution of Hox Gene Evolution.

Dev Biol. 2018 Sep 1;441(1):159-175. doi: 10.1016/j.ydbio.2018.07.001. Epub 2018 Jul 4.

Augmentation of a wound response element accompanies the origin of a Hox-regulated Drosophila abdominal pigmentation trait.

One primary agenda of the developmental evolution field is to elucidate molecular mechanisms governing differences in animal form. While mounting evidence has established an important role for mutations in transcription controlling cis-regulatory elements (CREs), the underlying mechanisms that translate these alterations into differences in gene expression are poorly understood. Emerging studies focused on pigmentation differences among closely related Drosophila species have provided many examples of phenotypically relevant CRE changes, and have begun to illuminate how this process works at the level of regulatory sequence function and transcription factor binding. We review recent work in this field and highlight the conceptual and technical challenges that currently await experimental attention.

Mark Rebeiz and Thomas M. Williams

Volume 19, February 2017, Pages 1–7

http://www.sciencedirect.com/science/article/pii/S2214574516301456

Drosophilaphilia #2: Silencing silencers to evolve new patterns.

Nice thoughtful overview on my collaborator’s new publication!

Genetic Changes to a Transcriptional Silencer Element Confers Phenotypic Diversity within and between Drosophila Species

Winslow C. Johnson , Alison J. Ordway , Masayoshi Watada, Jonathan N. Pruitt, Thomas M. Williams, Mark Rebeiz

Author Summary

One of the greatest challenges in understanding the relationship between genotype and phenotype is to discern how changes in DNA affect the normal functioning of genes. Mutations may generate a new function for a gene, yet it is frequently observed that they inactivate some aspect of a gene’s normal capacity. Investigations focused on understanding the developmental basis for the evolution of anatomical structures has found a prevalent role for mutations that alter developmental gene regulation. In animals, genes are transcriptionally activated in specific tissues during development by regulatory sequences distributed across their expansive non-protein coding regions. Regulatory elements known as silencers act to prevent genes from being expressed in certain tissues, providing a mechanism for precise control. Here, we show how a silencer that prevents expression of a pigment-producing enzyme in certain Drosophila species has repeatedly been subject to inactivating mutations that increased this gene’s expression. This example illustrates how such negative-acting regulatory sequences can represent a convenient target for increasing gene expression through the loss of a genetic element.

http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005279

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

• Eric M. Camino,
• John C. Butts,
• Alison Ordway,
• Jordan E. Vellky,
• Mark Rebeiz,
• Thomas M. Williams

“Author Summary

The genomic content of regulatory genes such as transcription factors is surprisingly conserved between diverse animal species, raising the paradox of how new traits emerge, and are subsequently modified and lost. In this study we make a connection between the developmental basis for the formation of a fruit fly trait and the evolutionary basis for that trait’s origin, diversification, and loss. We show how the origin of a novel pigmentation trait is associated with the evolution of two regulatory sequences that control the co-expression of two key pigmentation genes. These sequences interact in unique ways with evolutionarily conserved Hox transcription factors to drive gene co-expression. Once these unique connections evolved, the alteration of this trait appears to have proceeded through changes to regulatory genes rather than regulatory sequences of the pigmentation genes. Thus, our findings support a scenario where regulatory sequence evolution provided new functions to old transcription factors, how co-expression can emerge from different utilizations of the same transcription factors, and that trait diversity was surprisingly shaped by changes in some manner to the deeply conserved regulatory genes.”

http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005136