Sarah Signor

Genetic Convergence in the Evolution of Male-Specific Color Patterns in Drosophila

Convergent evolution provides a type of natural replication that can be exploited to understand the roles of contingency and constraint in the evolution of phenotypes and the gene networks that control their development. For sex-specific traits, convergence offers the additional opportunity for testing whether the same gene networks follow different evolutionary trends in males versus females. Here, we use an unbiased, systematic mapping approach to compare the genetic basis of evolutionary changes in male-limited pigmentation in several pairs of Drosophila species that represent independent evolutionary transitions. We find strong evidence for repeated recruitment of the same genes to specify similar pigmentation in different species. At one of these genes, ebony, we observe convergent evolution of sexually dimorphic and monomorphic expression through cis-regulatory changes. However, this functional convergence has a different molecular basis in different species, reflecting both parallel fixation of ancestral alleles and independent origin of distinct mutations with similar functional consequences. Our results show that a strong evolutionary constraint at the gene level is compatible with a dominant role of chance at the molecular level.

Genomic resources for multiple species in the Drosophila ananassae species group

The development of genomic resources in non-model taxa is essential for understanding the genetic basis of biological diversity. Although the genomes of many Drosophila species have been sequenced, most of the phenotypic diversity in this genus remains to be explored. To facilitate the genetic analysis of interspecific and intraspecific variation, we have generated new genomic resources for seven species and subspecies in the D. ananassae species subgroup. We have generated large amounts of transcriptome sequence data for D. ercepeae, D. merina, D. bipectinata, D. malerkotliana malerkotliana, D. m. pallens, D. pseudoananassae pseudoananassae, and D. p. nigrens. de novo assembly resulted in contigs covering more than half of the predicted transcriptome and matching an average of 59% of annotated genes in the complete genome of D. ananassae. Most contigs, corresponding to an average of 49% of D. ananassae genes, contain sequence polymorphisms that can be used as genetic markers. Subsets of these markers were validated by genotyping the progeny of inter- and intraspecific crosses. The ananassae subgroup is an excellent model system for examining the molecular basis of speciation and phenotypic evolution. The new genomic resources will facilitate the genetic analysis of inter- and intraspecific differences in this lineage. Transcriptome sequencing provides a simple and cost-effective way to identify molecular markers at nearly single-gene density, and is equally applicable to any non-model taxa.

Social effects for locomotion vary between environments in Drosophila melanogaster females

Despite strong purifying or directional selection, variation is ubiquitous in populations. One mechanism for the maintenance of variation is indirect genetic effects (IGEs), as the fitness of a given genotype will depend somewhat on the genes of its social partners. IGEs describe the effect of genes in social partners on the expression of the phenotype of a focal individual. Here, we ask what effect IGEs, and variation in IGEs between abiotic environments, has on locomotion in Drosophila. This trait is known to be subject to intralocus sexually antagonistic selection. We estimate the coefficient of interaction, Ψ, using six inbred lines of Drosophila. We found that Ψ varied between abiotic environments, and that it may vary across among male genotypes in an abiotic environment specific manner. We also found evidence that social effects of males alter the value of a sexually dimorphic trait in females, highlighting an interesting avenue for future research into sexual antagonism. We conclude that IGEs are an important component of social and sexual interactions and that they vary between individuals and abiotic environments in complex ways, with the potential to promote the maintenance of phenotypic variation.

The Evolution of Gene Expression in cis and trans

There is abundant variation in gene expression between individuals, populations, and species. The evolution of gene regulation and expression within and between species is thought to frequently contribute to adaptation. Yet considerable evidence suggests that the primary evolutionary force acting on variation in gene expression is stabilizing selection. We review here the results of recent studies characterizing the evolution of gene expression occurring in cis (via linked polymorphisms) or in trans (through diffusible products of other genes) and their contribution to adaptation and response to the environment. We review the evidence for buffering of variation in gene expression at the level of both transcription and translation, and the possible mechanisms for this buffering. Lastly, we summarize unresolved questions about the evolution of gene regulation.

Gene networks and developmental context: the importance of understanding complex gene expression patterns in evolution

Animal development is the product of distinct components and interactions—genes, regulatory networks, and cells—and it exhibits emergent properties that cannot be inferred from the components in isolation. Often the focus is on the genotype‐to‐phenotype map, overlooking the process of development that turns one into the other. We propose a move toward micro‐evolutionary analysis of development, incorporating new tools that enable cell type resolution and single‐cell microscopy. Using the sex determination pathway in Drosophila to illustrate potential avenues of research, we highlight some of the questions that these emerging technologies can address. For example, they provide an unprecedented opportunity to study heterogeneity within cell populations, and the potential to add the dimension of time to gene regulatory network analysis. Challenges still remain in developing methods to analyze this data and to increase the throughput. However this line of research has the potential to bridge the gaps between previously more disparate fields, such as population genetics and development, opening up new avenues of research.

Population genomics of Wolbachia and mtDNA in Drosophila simulans from California

Wolbachia pipientis is an intracellular endosymbiont infecting many arthropods and filarial nematodes. Little is known about the short-term evolution of Wolbachia or its interaction with its host. Wolbachia is maternally inherited, resulting in co-inheritance of mitochondrial organelles such as mtDNA. Here I explore the evolution of Wolbachia, and the relationship between Wolbachia and mtDNA, using a large inbred panel of Drosophila simulans. I compare this to the only other large population genomic Wolbachia dataset from D. melanogaster. I find reduced diversity relative to expectation in both Wolbachia and mtDNA, but only mtDNA shows evidence of a recent selective sweep or population bottleneck. I estimate Wolbachia and mtDNA titre in each genotype, and I find considerable variation in both phenotypes, despite low genetic diversity in Wolbachia and mtDNA. A phylogeny of Wolbachia and of mtDNA suggest a recent origin of the infection derived from a single origin. Using Wolbachia and mtDNA titre as a phenotype, I perform the first association analysis using this phenotype with the nuclear genome and find several implicated regions, including one which contains four CAAX-box protein processing genes. CAAX-box protein processing can be an important part of host-pathogen interactions in other systems, suggesting interesting directions for future research.

Conservation of social effects (Ψ) between two species of Drosophila despite reversal of sexual dimorphism

Abstract Indirect genetic effects (IGEs) describe the effect of the genes of social partners on the phenotype of a focal individual. Here, we measure indirect genetic effects using the “coefficient of interaction” (Ψ) to test whether Ψ evolved between Drosophila melanogaster and D. simulans. We compare Ψ for locomotion between ethanol and nonethanol environments in both species, but only D. melanogaster utilizes ethanol ecologically. We find that while sexual dimorphism for locomotion has been reversed in D. simulans, there has been no evolution of social effects between these two species. What did evolve was the interaction between genotype‐specific Ψ and the environment, as D. melanogaster varies unpredictably between environments and D. simulans does not. In this system, this suggests evolutionary lability of sexual dimorphism but a conservation of social effects, which brings forth interesting questions about the role of the social environment in sexual selection.

Evolution of phenotypic plasticity in response to ethanol between sister species with different ecological histories (Drosophila melanogaster and D. simulans)

The role of phenotypic plasticity in evolution is contentious, in part because different types of plasticity – adaptive, neutral, or non-adaptive, are often not distinguished. Adaptive plasticity is expected to facilitate expansion into new environments, while non-adaptive plasticity will result in a mean phenotype further from the adaptive optimum and/or an increase in variance due to the expression of variation that was neutral and shielded from selection in the prior environment. We explore these patterns here by exposing Drosophila melanogaster and D. simulans to high ethanol concentrations, with the knowledge that D. melanogaster associates with high concentrations of ethanol in nature while D. simulans does not. Using changes in gene expression and splicing we find that in D. simulans there is a large genotype-specific response to ethanol, orders of magnitude larger than any effect that is not genotype-specific. In D. melanogaster the response to ethanol is limited, and it is concordant among different genotypes. This response to ethanol in D. simulans is enriched for non-protein coding nested genes that do not have orthologs in D. melanogaster, suggesting rapid evolution of transcription. Sequence variation in ethanol-implicated genes is consistent with balancing selection or selection relaxation in D. simulans, and they are more divergent from D. melanogaster than the genome average. Overall, these patterns are consistent with a maladaptive passive response to ethanol-induced stress in D. simulans, while in D. melanogaster the reduced response and lack of genotype-specific variation suggests selection for an optimal response.

Novel approach to quantitative spatial gene expression uncovers genetic stochasticity in the developing Drosophila eye

Robustness in development allows for the accumulation of neutral genetically based variation in expression, and here will be termed ‘genetic stochasticity‘. This largely neutral variation is potentially important for both evolution and complex disease phenotypes. However, it has generally only been investigated as variation exhibited in the response to large genetic perturbations. In addition, work on variation in gene expression has similarly generally been limited to being spatial, or quantitative, but because of technical restrictions not both. Here we bridge these gaps by investigating replicated quantitative spatial gene expression using rigorous statistical models, in different genotypes, sexes, and species (Drosophila melanogaster and D. simulans). Using this type of quantitative approach with developmental data allows for effective comparison among conditions, including health versus disease. We apply this approach to the morphogenetic furrow, a wave of differentiation that sweeps across the developing eye disc. Within the morphogenetic furrow, we focus on four conserved morphogens, hairy, atonal, hedgehog, and Delta. Hybridization chain reaction quantitatively measures spatial gene expression, co-staining for all four genes simultaneously and with minimal effort. We find considerable variation in the spatial expression pattern of these genes in the eye between species, genotypes, and sexes. We also find that there has been evolution of the regulatory relationship between these genes. Lastly, we show that the spatial interrelationships of these genes evolved between species in the morphogenetic furrow. This is essentially the first ‘population genetics of development’ as we are able to evaluate wild type differences in spatial and quantitative gene expression at the level of genotype, species and sex.Robustness in development allows for the accumulation of cryptic variation, and this largely neutral variation is potentially important for both evolution and complex disease phenotypes. However, it has generally only been investigated as variation in the response to large genetic perturbations. Here we use newly developed methods to quantify spatial gene expression patterns during development of the Drosophila eye disc, and uncover cryptic variation in wildtype developmental systems. We focus on four conserved morphogens, hairy, atonal, hedgehog, and Delta, that are involved in specifying ommatidia in the developing eye. We find abundant cryptic variation within and between species, genotypes, and sexes, as well as cryptic variation in the regulatory logic between atonal and hairy and their regulators, Delta and hedgehog. This work paves the way for a synthesis between population and quantitative genetic approaches with that of developmental biology.Developmental gene networks are deployed in complex temporal and spatial patterns. Methods for studying gene networks and expression typically only capture variation along one axis, i.e. spatial but not quantitative variation or vice versa. Here we use hybridization chain reaction (HCR) to quantitatively measure spatial gene expression in multiple genotypes from two sexes of two species (Drosophila melanogaster and D. simulans). We do this in the eye imaginal disc, which is initially patterned by a wave of differentiation marked by a visible indentation of the tissue, termed the morphogenetic furrow (MF), that passes from the posterior to the anterior of the disc, giving each disc an element of both time and space in development (Fig 1). The furrow is initiated by hedgehog, which both represses (short range) and activates (long range) hairy (Fig 1) [1,2]. hedgehog also activates the expression of atonal, driving the furrow anteriorly [3-5]. Delta/Notch is under the control of hedgehog and represses atonal [6,7]. We analyze the spatial quantitative expression of hedgehog, hairy, atonal, and Delta to understand the evolving regulatory logic of the gene network and changes in spatial dynamics between sexes and species. We find that gene expression varies among genotypes and sexes, but remains stable between species, with the exception of Delta and hairy. Surprisingly, this apparent stability is accomplished through changes in the interrelations between genes within a network, and is exhibited at both quantitative and spatial levels.

Dynamic changes in gene expression and alternative splicing mediate the response to acute alcohol exposure in Drosophila melanogaster

Environmental changes typically cause rapid gene expression responses in the exposed organisms, including changes in the representation of gene isoforms with different functions or properties. Identifying the genes that respond to environmental change, including in genotype-specific ways, is an important step in treating the undesirable physiological effects of stress, such as exposure to toxins or ethanol. Ethanol is a unique environmental stress in that chronic exposure results in permanent physiological changes and the development of alcohol use disorders. Drosophila is a classic model for deciphering the mechanisms of the response to alcohol exposure, as it meets the criteria for the development of alcohol use disorders, and has similar physiological underpinnings with vertebrates. Because many studies on the response to ethanol have relied on a priori candidate genes, broad surveys of gene expression and splicing are required and have been investigated here. Further, we expose Drosophila to ethanol in an environment that is genetically, socially, and ecologically relevant. Both expression and splicing differences, inasmuch as they can be decomposed, contribute to the response to ethanol in Drosophila melanogaster. However, we find that while D. melanogaster responds to ethanol, there is very little genetic variation in how it responds to ethanol. In addition, the response to alcohol over time is dynamic, suggesting that incorporating time into studies on the response to the environment is important.