A microRNA is the effector gene of a classic evolutionary hotspot locus.

In Lepidoptera (butterflies and moths), the genomic region around the gene is a "hotspot" locus, repeatedly implicated in generating intraspecific melanic wing color polymorphisms across 100 million years of evolution. However, the identity of the effector gene regulating melanic wing color within this locus remains unknown. We show that none of the four candidate protein-coding genes within this locus, including , serve as major effectors.

Plasticity and environment-specific relationships between gene expression and fitness in Saccharomyces cerevisiae.

The environment influences how an organism's genotype determines its phenotype and how this phenotype affects its fitness. Here, to better understand this dual role of environment in the production and selection of phenotypic variation, we determined genotype-phenotype-fitness relationships for mutant strains of Saccharomyces cerevisiae in four environments. Specifically, we measured how promoter mutations of the metabolic gene TDH3 modified expression level and affected growth for four different carbon sources.

Plasticity and environment-specific relationships between gene expression and fitness in .

Phenotypic evolution is shaped by interactions between organisms and their environments. The environment influences how an organism's genotype determines its phenotype and how this phenotype affects its fitness. To better understand this dual role of the environment in the production and selection of phenotypic variation, we empirically determined and compared the genotype-phenotype-fitness relationship for mutant strains of the budding yeast in four environments.

A micro-RNA is the effector gene of a classic evolutionary hotspot locus.

In Lepidoptera (butterflies and moths), the genomic region around the gene is a 'hotspot' locus, repeatedly used to generate intraspecific melanic wing color polymorphisms across 100-million-years of evolution. However, the identity of the effector gene regulating melanic wing color within this locus remains unknown. Here, we show that none of the four candidate protein-coding genes within this locus, including , serve as major effectors.

Divergence of Grainy head affects chromatin accessibility, gene expression, and embryonic viability in .

Pioneer factors are critical for gene regulation and development because they bind chromatin and make DNA more accessible for binding by other transcription factors. The pioneer factor Grainy head (Grh) is present across metazoans and has been shown to retain a role in epithelium development in fruit flies, nematodes, and mice despite extensive divergence in both amino acid sequence and length. Here, we investigate the evolution of Grh function by comparing the effects of the fly () and worm () Grh orthologs on chromatin accessibility, gene expression, embryonic development, and viability in transgenic .

Active compensation for changes in TDH3 expression mediated by direct regulators of TDH3 in Saccharomyces cerevisiae.

Genetic networks are surprisingly robust to perturbations caused by new mutations. This robustness is conferred in part by compensation for loss of a gene's activity by genes with overlapping functions, such as paralogs. Compensation occurs passively when the normal activity of one paralog can compensate for the loss of the other, or actively when a change in one paralog's expression, localization, or activity is required to compensate for loss of the other.

Emerging questions in transcriptional regulation.

What new questions can we ask about transcriptional regulation given recent developments in large-scale approaches?

Contributions of mutation and selection to regulatory variation: lessons from the gene.

Heritable variation in gene expression is common within and among species and contributes to phenotypic diversity. Mutations affecting either - or -regulatory sequences controlling gene expression give rise to variation in gene expression, and natural selection acting on this variation causes some regulatory variants to persist in a population for longer than others. To understand how mutation and selection interact to produce the patterns of regulatory variation we see within and among species, my colleagues and I have been systematically determining the effects of new mutations on expression of the gene in and comparing them to the effects of polymorphisms segregating within this species.

Active compensation for changes in expression mediated by direct regulators of in .

Genetic networks are surprisingly robust to perturbations caused by new mutations. This robustness is conferred in part by compensation for loss of a gene's activity by genes with overlapping functions, such as paralogs. Compensation occurs passively when the normal activity of one paralog can compensate for the loss of the other, or actively when a change in one paralog's expression, localization, or activity is required to compensate for loss of the other.

Differential Grainy head binding correlates with variation in chromatin structure and gene expression in Drosophila melanogaster.

Phenotypic evolution is often caused by variation in gene expression resulting from altered gene regulatory mechanisms. Genetic variation affecting chromatin remodeling has been identified as a potential source of variable gene expression; however, the roles of specific chromatin remodeling factors remain unclear. Here, we address this knowledge gap by examining the relationship between variation in gene expression, variation in chromatin structure, and variation in binding of the pioneer factor Grainy head between imaginal wing discs of two divergent strains of Drosophila melanogaster and their F hybrid.

Network Topology Can Explain Differences in Pleiotropy Between Cis- and Trans-regulatory Mutations.

A mutation's degree of pleiotropy (i.e., the number of traits it alters) is predicted to impact the probability of the mutation being detrimental to fitness.

Mechanisms of regulatory evolution in yeast.

Studies of regulatory variation in yeast - at the level of new mutations, polymorphisms within a species, and divergence between species - have provided great insight into the molecular and evolutionary processes responsible for the evolution of gene expression in eukaryotes. The increasing ease with which yeast genomes can be manipulated and expression quantified in a high-throughput manner has recently accelerated mechanistic studies of cis- and trans-regulatory variation at multiple evolutionary timescales. These studies have, for example, identified differences in the properties of cis- and trans-acting mutations that affect their evolutionary fate, experimentally characterized the molecular mechanisms through which cis- and trans-regulatory variants act, and illustrated how regulatory networks can diverge between species with or without changes in gene expression.

Pleiotropic effects of trans-regulatory mutations on fitness and gene expression.

Variation in gene expression arises from cis- and trans-regulatory mutations, which contribute differentially to expression divergence. We compare the impacts on gene expression and fitness resulting from cis- and trans-regulatory mutations in , with a focus on the gene. We use the effects of cis-regulatory mutations to infer effects of trans-regulatory mutations attributable to impacts beyond the focal gene, revealing a distribution of pleiotropic effects.

Evolution of transcription factor binding through sequence variations and turnover of binding sites.

Variations in noncoding regulatory sequences play a central role in evolution. Interpreting such variations, however, remains difficult even in the context of defined attributes such as transcription factor (TF) binding sites. Here, we systematically link variations in -regulatory sequences to TF binding by profiling the allele-specific binding of 27 TFs expressed in a yeast hybrid, in which two related genomes are present within the same nucleus.

Distinct genetic architectures underlie divergent thorax, leg, and wing pigmentation between Drosophila elegans and D. gunungcola.

Pigmentation divergence between Drosophila species has emerged as a model trait for studying the genetic basis of phenotypic evolution, with genetic changes contributing to pigmentation differences often mapping to genes in the pigment synthesis pathway and their regulators. These studies of Drosophila pigmentation have tended to focus on pigmentation changes in one body part for a particular pair of species, but changes in pigmentation are often observed in multiple body parts between the same pair of species. The similarities and differences of genetic changes responsible for divergent pigmentation in different body parts of the same species thus remain largely unknown.

Mutational sources of -regulatory variation affecting gene expression in .

Heritable variation in a gene's expression arises from mutations impacting - and -acting components of its regulatory network. Here, we investigate how -regulatory mutations are distributed within the genome and within a gene regulatory network by identifying and characterizing 69 mutations with -regulatory effects on expression of the same focal gene in . Relative to 1766 mutations without effects on expression of this focal gene, we found that these -regulatory mutations were enriched in coding sequences of transcription factors previously predicted to regulate expression of the focal gene.

Leadership.

We asked group leaders how they foster mutually reinforcing research productivity and psychological safety in their teams.

Molecular and evolutionary processes generating variation in gene expression.

Heritable variation in gene expression is common within and between species. This variation arises from mutations that alter the form or function of molecular gene regulatory networks that are then filtered by natural selection. High-throughput methods for introducing mutations and characterizing their cis- and trans-regulatory effects on gene expression (particularly, transcription) are revealing how different molecular mechanisms generate regulatory variation, and studies comparing these mutational effects with variation seen in the wild are teasing apart the role of neutral and non-neutral evolutionary processes.

Genetic architecture of a body colour cline in Drosophila americana.

Phenotypic variation within a species is often structured geographically in clines. In Drosophila americana, a longitudinal cline for body colour exists within North America that appears to be due to local adaptation. The tan and ebony genes have been hypothesized to contribute to this cline, with alleles of both genes that lighten body colour found in D.

affects pigmentation divergence and cuticular hydrocarbons in and .

pigmentation has been a fruitful model system for understanding the genetic and developmental mechanisms underlying phenotypic evolution. For example, prior work has shown that divergence of the gene contributes to pigmentation differences between two members of the virilis group: , which has a light yellow body color, and , which has a dark brown body color. Quantitative trait locus (QTL) mapping and expression analysis has suggested that divergence of the gene might also contribute to pigmentation differences between these two species.

Co-evolving wing spots and mating displays are genetically separable traits in Drosophila.

The evolution of sexual traits often involves correlated changes in morphology and behavior. For example, in Drosophila, divergent mating displays are often accompanied by divergent pigment patterns. To better understand how such traits co-evolve, we investigated the genetic basis of correlated divergence in wing pigmentation and mating display between the sibling species Drosophila elegans and Drosophila gunungcola.

Compensatory -regulatory alleles minimizing variation in expression are common within .

Heritable variation in gene expression is common within species. Much of this variation is due to genetic differences outside of the gene with altered expression and is -acting. This -regulatory variation is often polygenic, with individual variants typically having small effects, making the genetic architecture and evolution of -regulatory variation challenging to study.