Biology subjects

Hopkins, B. R.

Publications and source records attributed to Hopkins, B. R..

10 recordsLinked to original sources

bioRxiv2026

Morphological innovation without gene co-option: the Drosophila sex comb evolved via changes in developmental tempo and energy metabolism

The individualization of serially repeated homologs is one route through which novel traits are thought to evolve. Under this model, a repeated character--like a limb, digit, or sensory bristle--is individualized from its homologs by changes in the regulatory apparatus ( character identity network, ChIN) that specifies its development. Individualization then enables downstream gene networks that build the repeated character to diverge from one another in different parts of the body, ultimately allowing new phenotypic endpoints to be reached. Despite this models intuitive appeal, the genetic mechanisms through which new ChINs rewire trait-building gene networks remain largely uncharacterized. A promising system in which to study this process is the Drosophila sex comb. Found in a sublineage of Drosophila species, the sex comb is a recently evolved, male-specific innovation that evolved from a more evolutionarily ancient precursor--the mechanosensory (MS) bristle--following the gain of a novel ChIN centered on the sex determination gene dsx and HOX gene Scr. Here, we use time-series single-cell RNA-seq to show that rather than co-opting new genes, this new ChIN orchestrates quantitative and heterochronic changes in the ancestral MS bristle transcriptome. These changes affect gene modules that control energy metabolism, endoreplication, and actin dynamics. The net effect of these changes is an organ-specific shift in developmental rate, leading to accelerated growth in sex comb teeth. Collectively, our work suggests that morphological innovation can proceed without the co-option of new genes into downstream trait-building networks and instead through metabolically driven differences in developmental rate between serial homologs.

evolutionary biology↗

bioRxiv2025

Molecular evolution of octopamine receptors in Drosophila

Octopamine (OA), the insect analog of noradrenaline, plays important roles in diverse behavioral and physiological processes, from modulating fight-or-flight behavior to regulating post-mating ovulation. In Drosophila, six OA receptors have been identified: Oamb, Oct2R, Oct{beta}1R, Oct{beta}2R, Oct{beta}3R, and Oct-TyrR, and they have been linked to different behavioral and physiological processes. Here, we investigated the evolutionary characteristics of these receptors across Drosophila species. We found that OA receptors are generally found as single-copy genes. Notably, Oct{beta}2R and Oct{beta}3R exhibit positive selection within the melanogaster group, though in different structural regions from one another. The positively selected sites in Oct{beta}2R are exclusively located in regions important for ligand binding, whereas those in Oct{beta}3R are predominantly found in regions crucial for signal transduction. Interestingly, Oct{beta}2R remains highly conserved outside the melanogaster group, so the detection of positive selection in its ligand-binding related domains within this clade raises the possibility that it has evolved an additional, melanogaster-specific ligand interaction(s), among other potential reasons. These findings highlight the evolutionary flexibility of aminergic signaling and suggest lineage-specific adaptations of OA receptor function in Drosophila, likely shaped by lineage-specific selective pressures. Article summaryOctopamine is a chemical messenger in insects, analogous to noradrenaline in vertebrates, and influences many processes such as fight-or-flight responses, locomotion, and reproduction. In fruit flies and other insects, multiple octopamine receptors detect and respond to this signal. We explored how these receptors have changed over millions of years across various fly species. We found that while some receptors remain similar, others have evolved more rapidly, possibly due to changes in the insects lifestyles, environments, or other biological demands. Understanding these differences can help reveal how insects fine-tune their behaviors and adapt to diverse challenges.

evolutionary biology↗

bioRxiv2025

Mosquito Cell Atlas: A single-nucleus transcriptomic atlas of the adult Aedes aegypti mosquito

The female Aedes aegypti mosquitos remarkable ability to hunt humans and transmit pathogens relies on her unique biology. Here, we present the Aedes aegypti Mosquito Cell Atlas, a comprehensive single-nucleus RNA sequencing dataset of more than 367,000 nuclei from 19 dissected tissues of adult female and male Aedes aegypti, providing cellular-level resolution of mosquito biology. We identify novel cell types and expand our understanding of sensory neuron organization of chemoreceptors to all sensory tissues. Our analysis uncovers male-specific cells and sexually dimorphic gene expression in the antenna and brain. In female mosquitoes, we find that glial cells in the brain, rather than neurons, undergo the most extensive transcriptional changes following blood feeding. Our findings provide insights into the cellular basis of mosquito behavior and sexual dimorphism. The Aedes aegypti Mosquito Cell Atlas resource enables systematic investigation of cell type-specific expression across all mosquito tissues.

genomics↗

bioRxiv2024

Regulatory Changes in the Fatty Acid Elongase eloF Underlie the Evolution of Sex-specific Pheromone Profiles in Drosophila prolongata

Pheromones play a key role in regulating sexual behavior throughout the animal kingdom. In Drosophila and other insects, many cuticular hydrocarbons (CHCs) are sexually dimorphic, and some are known to perform pheromonal functions. However, the genetic control of sex-specific CHC production is not understood outside of the model species D. melanogaster. A recent evolutionary change is found in D. prolongata, which, compared to its closest relatives, shows greatly increased sexual dimorphism in both CHCs and the chemosensory system responsible for their perception. A key transition involves a male-specific increase in the proportion of long-chain CHCs. Perfuming D. prolongata females with the male-biased CHCs reduces copulation success, suggesting that these compounds function as sex pheromones. The evolutionary change in CHC profiles correlates with a male-specific increase in the expression of multiple genes involved in CHC biosynthesis, including fatty acid elongases and reductases and other key enzymes. In particular, elongase F, which is responsible for producing female-specific pheromones in D. melanogaster, is strongly upregulated in D. prolongata males compared both to females and to males of the sibling species. Induced mutations in eloF reduce the amount of long-chain CHCs, resulting in a partial feminization of pheromone profiles in D. prolongata males while having minimal effect in females. Transgenic experiments show that sex-biased expression of eloF is caused in part by a putative transposable element insertion in its regulatory region. These results reveal one of the genetic mechanisms responsible for a recent evolutionary change in sexual communication.

evolutionary biology↗

bioRxiv2023

Decoupled evolution of the Sex Peptide gene family and Sex Peptide Receptor in Drosophilidae

Across internally fertilising species, males transfer ejaculate proteins that trigger wide-ranging changes in female behaviour and physiology. Much theory has been developed to explore the drivers of ejaculate protein evolution. The accelerating availability of high-quality genomes now allows us to test how these proteins are evolving at fine taxonomic scales. Here, we use genomes from 264 species to chart the evolutionary history of Sex Peptide (SP), a potent regulator of female post-mating responses in Drosophila melanogaster. We infer that SP first evolved in the Drosophilinae subfamily and has followed markedly different evolutionary trajectories in different lineages. Outside of the Sophophora-Lordiphosa, SP exists largely as a single-copy gene with independent losses in several lineages. Within the Sophophora-Lordiphosa, the SP gene family has repeatedly and independently expanded. Up to seven copies, collectively displaying extensive sequence variation, are present in some species. Despite these changes, SP expression remains restricted to the male reproductive tract. Alongside, we document considerable interspecific variation in the presence and morphology of seminal microcarriers that, despite the critical role SP plays in microcarrier assembly in D. melanogaster, appear to be independent of changes in the presence/absence or sequence of SP. We end by providing evidence that SPs evolution is decoupled from that of its receptor, SPR, in which we detect no evidence of correlated diversifying selection. Collectively, our work describes the divergent evolutionary trajectories that a novel gene has taken following its origin and finds a surprisingly weak coevolutionary signal between a supposedly sexually antagonistic protein and its receptor. SignificanceIn insects, seminal fluid proteins (SFPs) induce dramatic changes in female behaviour and physiology. How this degree of male influence evolves remains a central question in sexual selection research. Here, we map the origin and diversification of the posterchild insect SFP, the Drosophila Sex Peptide (SP), across 264 Diptera species. We show that SP first evolved at the base of the subfamily Drosophilinae and followed markedly different evolutionary trajectories in different lineages, including accelerated change in sequence, copy number, and genomic position in the lineage leading to D. melanogaster. By contrast, we find only limited, uncorrelated change in the sequence of its receptor, SPR, arguing against a sexually antagonistic coevolutionary arms race between these loci on macroevolutionary time scales.

evolutionary biology↗

bioRxiv2022

Charting the development of Drosophila leg sensory organs at single-cell resolution

To respond to the world around them, animals rely on the input of a network of sensory organs distributed throughout the body. Distinct classes of sensory organ are specialized for the detection of specific stimuli such as strain, pressure, or taste. The features that underlie this specialization relate both to the neurons that innervate sensory organs and the accessory cells that comprise them. This diversity of cell types, both within and between sensory organs, raises two fundamental questions: what makes these cell types distinct from one another, and how is this diversity generated during development? To address these questions, we performed single-cell RNA sequencing on a developing tissue that displays a wide variety of functionally and structurally distinct sensory organs: the first tarsal segment of the pupal male Drosophila melanogaster foreleg. We characterize the cellular landscape in which the sensory organs reside, identify a novel cell type that contributes to the construction of the neural lamella, and characterize the transcriptomic differences among support cells within and between sensory organs. We identify the genes that distinguish between mechanosensory and chemosensory neurons, resolve a combinatorial transcription factor code that defines four distinct classes of gustatory neuron and several types of mechanosensory neuron, and match the expression of sensory receptors to specific neuron classes. Collectively, our work identifies core genetic features of a variety of sensory organs and provides a rich, annotated resource for studying their development and function.

developmental biology↗

bioRxiv2019

Structural variation in Drosophila melanogaster spermathecal ducts and its association with sperm competition dynamics

The ability of female insects to retain and use sperm for days, months, or even years after mating requires specialised storage organs in the reproductive tract. In most orders these organs include a pair of sclerotised capsules known as spermathecae. Here, we report that some Drosophila melanogaster females exhibit previously uncharacterised structures within the distal portion of the muscular duct that links a spermatheca to the uterus. We find that these spermathecal duct presences (SDPs) may form in either or both ducts and can extend from the duct into the sperm-storing capsule itself. We further find that the incidence of SDPs varies significantly between genotypes, but does not change significantly with the age or mating status of females, the latter indicating that SDPs are not composed of or stimulated by sperm or male seminal proteins. We show that SDPs affect neither the number of first male sperm held in a spermatheca nor the number of offspring produced after a single mating. However, we find evidence that SDPs are associated with a lack of second male sperm in the spermathecae after females remate. This raises the possibility that SDPs provide a mechanism for variation in sperm competition outcome among females.

evolutionary biology↗

bioRxiv2019

BMP-signalling inhibition in Drosophila secondary cells remodels the seminal proteome, and self and rival ejaculate functions

Seminal fluid proteins (SFPs) exert potent effects on male and female fitness. Rapidly evolving and molecularly diverse, they derive from multiple male secretory cells and tissues. In Drosophila melanogaster, most SFPs are produced in the accessory glands, which are composed of [~]1000 fertility-enhancing main cells and [~]40, more functionally cryptic, secondary cells. Inhibition of BMP-signalling in secondary cells suppresses secretion, leading to a unique uncoupling of normal female post-mating responses to the ejaculate: refractoriness stimulation is impaired, but offspring production is not. Secondary cell secretions might therefore make a highly specific contribution to the seminal proteome and ejaculate function; alternatively, they might regulate more global - but hitherto-undiscovered - SFP functions and proteome composition. Here, we present data that supports the latter model. We show that in addition to previously reported phenotypes, secondary cell-specific BMP-signalling inhibition compromises sperm storage and increases female sperm use efficiency. It also impacts second male sperm, tending to slow entry into storage and delay ejection. First male paternity is enhanced, which suggests a novel constraint on ejaculate evolution whereby high female refractoriness and sperm competitiveness are mutually exclusive. Using quantitative proteomics, we reveal a mix of specific and widespread changes to the seminal proteome that surprisingly encompass alterations to main cell-derived proteins, indicating important cross-talk between classes of SFP-secreting cells. Our results demonstrate that ejaculate composition and function emerge from the integrated action of multiple secretory cell-types suggesting that modification to the cellular make-up of seminal fluid-producing tissues is an important factor in ejaculate evolution.

evolutionary biology↗

bioRxiv2019

An exposition of ejaculate senescence and its inhibition in Drosophila

Declining ejaculate performance with male age is taxonomically widespread and has broad ramifications for fertility and fitness. However, we have a poor understanding of age-related changes to specific ejaculate components, how they cause reduced performance, and whether the decline is ameliorable. Here, we show that, in Drosophila, sperm production chronologically declines with age, invariant to mating activity, while repeated mating causes infertility via reduced sperm stores and viability. However, changes to sperm do not fully explain ejaculate deterioration: impacts on seminal fluid contribute to aspects of reduced ejaculate performance, associated with shifts in proteome abundance and quality. We show that ablation of insulin-like peptide-producing cells in males ameliorates aspects of ejaculate performance loss, suggesting that anti-ageing interventions can be coopted to benefit male reproductive health.\n\nOne Sentence SummaryEjaculate performance declines with male age via mating-dependent sperm and seminal protein deterioration, but it can be ameliorated.

evolutionary biology↗

bioRxiv2018

Quantitative proteomics identification of seminal fluid proteins in male Drosophila melanogaster

Seminal fluid contains some of the fastest evolving proteins currently known. These seminal fluid proteins (Sfps) play crucial roles in reproduction, such as supporting sperm function, and - particularly in insects - modifying female physiology and behaviour. Identification of Sfps in small animals is challenging, and often relies on samples taken from the female reproductive tract after mating. A key pitfall of this method is that it might miss Sfps that are of low abundance due to dilution in the female-derived sample or rapid processing in females. Here we present a new and complimentary method, which provides added sensitivity to Sfp identification. We applied label-free quantitative proteomics to Drosophila melanogaster male reproductive tissue - where Sfps are unprocessed, and highly abundant - and quantified Sfps before and immediately after mating, to infer those transferred during copulation. We also analysed female reproductive tracts immediately before and after copulation to confirm the presence and abundance of known and candidate Sfps, where possible. Results were cross-referenced with transcriptomic and sequence databases to improve confidence in Sfp detection. Our data was consistent with 124 previously reported Sfps. We found 8 high-confidence novel candidate Sfps, which were both depleted in mated versus unmated males and identified within the reproductive tract of mated but not virgin females. We also identified 31 more candidates that are likely Sfps based on their abundance, known expression and predicted characteristics, and revealed that four proteins previously identified as Sfps are at best minor contributors to the ejaculate. The estimated copy numbers for our candidate Sfps were lower than for previously identified Sfps, supporting the idea that our technique provides a deeper analysis of the Sfp proteome than previous studies. Our results demonstrate a novel, high-sensitivity approach to the analysis of seminal fluid proteomes, whose application will further our understanding of reproductive biology.

genomics↗