Biology subjects

Kopp, A.

Publications and source records attributed to Kopp, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Interspecific differences in second-site modifiers reshape dominance in a Mendelian trait by altering environmental plasticity

Dominance is an important and evolvable property of the genotype-phenotype map. A longstanding debate in evolutionary genetics concerns whether dominance is determined primarily by intrinsic properties of alleles at the focal locus or by modifiers elsewhere in the genome. Theoretical models show that second-site modifiers of dominance can evolve under some conditions. However, direct empirical tests of these models are rare because they require holding the focal heterozygous genotype constant while changing the rest of the genome. In the Drosophila montium species subgroup, female pigmentation is a Mendelian trait controlled by a single gene, POU domain motif 3 (pdm3), but the dominance relationships between pdm3 alleles differ among species. Using reciprocal introgressions among three closely related species, we compared females carrying the same Light/Dark pdm3 allele combinations in different homozygous or heterozygous genomic backgrounds and across different temperatures. In both species-pair comparisons, changing genomic background significantly altered the phenotype of identical pdm3 heterozygotes, demonstrating the existence of second-site modifiers of dominance. The effects of dominance modifiers depend on the particular pair of pdm3 alleles and on rearing temperature. These results show that dominance in this system is a genotype-by-genotype-by-environment trait, rather than a fixed attribute of individual alleles. The finding that second-site modifiers can alter dominance by reshaping reaction norms provides a developmental mechanism that links the evolution of dominance to phenotypic plasticity.

evolutionary biology↗

bioRxiv2026

RNA-Encoded PGT121-LS Anti-HIV Antibody: Comprehensive Preclinical Characterization and Translational Pharmacokinetics

Human Immunodeficiency Virus (HIV)-1 broadly neutralizing antibodies (bNAbs) have demonstrated clinical efficacy, but face manufacturing challenges associated with recombinant protein production and purification. Here, we present a ribonucleic acid (RNA)-encoded bNAb (RibobNAb) platform that enables in vivo antibody production of the clinically validated bNAb PGT121 via lipid nanoparticle (LNP) delivery, supporting rapid evaluation of Fc variants (LS, del294, LS-del294) in vitro and in vivo. We confirmed expression, sub-nanomolar HIV-1 Env binding, and potent neutralization across all RibobNAb variants in vitro. In mice, single RNA-LNP administrations yielded in vivo expression of all RibobNAb variants, with PGT121-LS exhibiting a prolonged half-life compared with PGT121. In non-human primates (NHPs), a single intravenous administration of PGT121-LS RNA-LNP was well tolerated without anti-drug antibody (ADA) formation over 180 days and resulted in PGT121-LS half-lives comparable to the reference protein. Single intramuscular administration showed RibobNAb expression but resulted in ADA development from Day 14 onwards and lower bioavailability. In vivo-expressed PGT121-LS RibobNAb retained identical antiviral functionality to PGT121-LS reference protein. An NHP pharmacokinetics model integrating RNA transfection and translation dynamics enabled allometric scaling and first-in-human dose prediction. We highlight RibobNAbs as an alternative to conventional purified protein antibodies for rapid development of bNAb-based therapeutic strategies. O_FIG O_LINKSMALLFIG WIDTH=193 HEIGHT=200 SRC="FIGDIR/small/734219v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@141319forg.highwire.dtl.DTLVardef@120caadorg.highwire.dtl.DTLVardef@1da2782org.highwire.dtl.DTLVardef@158064d_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG

immunology↗

bioRxiv2026

A framework for identifying transcript orthologs: the evolution of sex bias in alternative transcript structure in Drosophila

BackgroundRecent advances in long read technologies provide an unprecedented opportunity to study transcript evolution. However, comparative evolutionary studies, even in Drosophila, are limited by inconsistent and incomplete annotation, and the lack of annotated transcript homology. ResultsIn this study of five species spanning 28 million years (D. melanogaster, D. simulans, D. yakuba, D. santomea and D. serrata), we infer transcript homology using reciprocal liftover, and orthology using network analyses, with data validation from long read RNA-seq of male and female head tissue. We build the first genus level annotation, with 15,996 genes and 56,370 transcripts. Expressed transcripts are conserved, 73% of transcript orthologs are detected in all species. Even the improved annotation underestimates the number of genes with alternative transcripts, with 75% of genes expressing multiple structurally diverse transcripts. In a replicated quantitative evaluation of [~]10,000 genes, both male and female-biased transcripts are expressed in 410 (D. melanogaster), 608 (D. simulans), and 493 (D. serrata) genes and in 118 orthologous genes in the D. melanogaster - D. simulans species pair, indicating greater potential for resolution of sexual conflict by alternative transcription than previously appreciated. We identified 605 transcript orthologs conserved for sex bias in the D. melanogaster-D. simulans species pair and of these, 22 male and 19 female-biased transcripts were conserved in sex bias with the outgroup D. serrata, including transcripts of genes involved in brain development, Sxl target Glutamine synthetase 2 and ciboulot. ConclusionsConserved alternative transcripts suggest that transcriptional diversity is a pervasive driver of the evolution of functional diversity.

genomics↗

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

Evolution of dominance in a Mendelian trait is linked to the evolution of environmental plasticity.

Allelic dominance and phenotypic plasticity both influence how genetic variation is expressed in phenotypes, shaping evolutionary responses to selection. In both cases, changes in genotype or environment can cause sharp, nonlinear phenotypic shifts, hinting at shared underlying features of development that may link dominance and plasticity. Here, we investigate these links using a Mendelian, female-limited color dimorphism found in many species of the Drosophila montium lineage. In most species, the Dark allele is dominant, but two species--D. jambulina and D. cf. bocqueti--have been reported to have dominant Light alleles. We show that in both Dark-dominant and Light-dominant species, the color dimorphism is linked to the same locus: the POU domain motif 3 (pdm3) transcription factor. We then demonstrate that the interspecific differences in dominance relationships between pdm3 alleles are due to changes in phenotypic plasticity. In the Dark-dominant species D. rufa and D. burlai, the Dark allele is dominant across all developmental temperatures. In contrast, in both Light-dominant species, dominance is temperature-dependent, with the Light allele becoming increasingly dominant at higher temperatures. These results suggest a mechanistic connection between the evolution of dominance and phenotypic plasticity. We propose this connection may emerge from threshold-like properties of developmental systems. Teaser textThis study reveals a direct relationship between the evolution of dominance and phenotypic plasticity in a Mendelian, female-limited color dimorphism. This trait is linked to the same transcription factor gene, pdm3, in multiple species of the Drosophila montium lineage. However in some species, the Light pdm3 allele becomes increasingly dominant at higher temperature, while in others the Dark allele is fully dominant under all conditions. Based on these results, we propose that the evolution of dominance and plasticity may be connected by threshold-like properties of developmental systems.

evolutionary biology↗

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↗

bioRxiv2024

Quantifying transcriptome turnover on phylogenies bymodeling gene expression as a binary trait

Changes in gene expression are a key driver of phenotypic evolution, leading to a persistent interest in the evolution of transcriptomes. Traditionally, gene expression is modeled as a continuous trait, leaving qualitative transitions largely unexplored. In this paper, we detail the development of new Bayesian inference techniques to study the evolutionary turnover of organ-specific transcriptomes, which we define as instances where orthologous genes gain or lose expression in a particular organ. To test these techniques, we analyze the transcriptomes of two male reproductive organs, testes and accessory glands, across 11 species of the Drosophila melanogaster species group. We first discretize gene expression states by estimating the probability that each gene is expressed in each organ and species. We then define a phylogenetic model of correlated transcriptome evolution in two or more organs and fit it to the expression state data. Inferences under this model show that many genes have gained and lost expression in each organ, and that the two organs experienced accelerated transcriptome turnover on different branches of the Drosophila phylogeny.

evolutionary biology↗

bioRxiv2024

In vivo Auto-tuning of Antibody-Drug Conjugate Delivery for Effective Immunotherapy using High-Avidity, Low-Affinity Antibodies

Antibody-drug conjugates (ADCs) have experienced a surge in clinical approvals in the past five years. Despite this success, a major limitation to ADC efficacy in solid tumors is poor tumor penetration, which leaves many cancer cells untargeted. Increasing antibody doses or co-administering ADC with an unconjugated antibody can improve tumor penetration and increase efficacy when target receptor expression is high. However, it can also reduce efficacy in low-expression tumors where ADC delivery is limited by cellular uptake. This creates an intrinsic problem because many patients express different levels of target between tumors and even within the same tumor. Here, we generated High-Avidity, Low-Affinity (HALA) antibodies that can automatically tune the cellular ADC delivery to match the local expression level. Using HER2 ADCs as a model, HALA antibodies were identified with the desired HER2 expression-dependent competitive binding with ADCs in vitro. Multi-scale distribution of trastuzumab emtansine and trastuzumab deruxtecan co-administered with the HALA antibody were analyzed in vivo, revealing that the HALA antibody increased ADC tumor penetration in high-expression systems with minimal reduction in ADC uptake in low-expression tumors. This translated to greater ADC efficacy in immunodeficient mouse models across a range of HER2 expression levels. Furthermore, Fc-enhanced HALA antibodies showed improved Fc-effector function at both high and low expression levels and elicited a strong response in an immunocompetent mouse model. These results demonstrate that HALA antibodies can expand treatment ranges beyond high expression targets and leverage strong immune responses.

bioengineering↗

bioRxiv2024

Highly Contiguous Genome Assembly of Drosophila prolongata - a Model for Evolution of Sexual Dimorphism and Male-specific Innovations

Drosophila prolongata is a member of the melanogaster species group and rhopaloa subgroup native to the subtropical highlands of southeast Asia. This species exhibits an array of recently evolved male-specific morphological, physiological, and behavioral traits that distinguish it from its closest relatives, making it an attractive model for studying the evolution of sexual dimorphism and testing theories of sexual selection. The lack of genomic resources has impeded the dissection of the molecular basis of sex-specific development and behavior in this species. To address this, we assembled the genome of D. prolongata using long-read sequencing and Hi-C scaffolding, resulting in a highly complete and contiguous (scaffold N50 2.2Mb) genome assembly of 220Mb. The repetitive content of the genome is 24.6%, the plurality of which are LTR retrotransposons (33.2%). Annotations based on RNA-seq data and homology to related species revealed a total of 19,330 genes, of which 16,170 are protein-coding. The assembly includes 98.5% of Diptera BUSCO genes, including 93.8% present as a single copy. Despite some likely regional duplications, the completeness of this genome suggests that it can be readily used for gene expression, GWAS, and other genomic analyses.

genomics↗

bioRxiv2023

New insights into the dynamics of de novo gene origin

The evolution of genes de novo from ancestrally nongenic sequences is a significant mechanism of gene origin. Many studies have focused on distant evolutionary comparisons, which bias the sample of de novo genes towards older genes that have acquired important functions and have been refined by selection. In this report, we focus on the earliest steps in de novo gene origin by identifying young, polymorphic transcripts that may be missed by other study designs. To accomplish this, we sequenced tissue-specific transcriptomes from a much larger sample of genotypes than have been used in previous analyses of de novo genes in Drosophila melanogaster. We identified 90 potential species-specific de novo genes expressed in the male accessory glands of 29 D melanogaster lines derived from the same natural population. We find that most young, unannotated transcripts are both rare in the population and transcribed at low abundance. Improved sampling of both ingroup and outgroup genotypes reveals that many young genes are polymorphic in more than one species, resulting in substantial uncertainty about the age and phylogenetic distribution of de novo genes. Among the genes expressed in the same tissue, gene age correlates with proximity to other tissue-specific genes, with the youngest genes being least likely to occur near established tissue-specific genes. This and other lines of evidence suggest that de novo genes do not commonly evolve by simply reutilizing pre-existing regulatory elements. Together, these results provide new insights into the origin and early evolution of de novo genes. Author SummaryGenes may be born and lost without any lasting evidence of their existence. The typical longevity may be especially limited for de novo genes - that is, genes that originate from ancestrally non-genic, untranscribed sequences, since most genomic regions are not expected to be beneficial when transcribed. To better capture the population biology of nascent de novo genes at points close to their origin, we sequenced tissue-specific transcriptomes from a large number of Drosophila melanogaster genotypes. Most de novo genes were expressed in very few genotypes, consistent with the expectation of transience and rapid turnover. However, many young genes showed polymorphic transcription in multiple species, suggesting that the combination of low frequency with limited sampling can lead us to underestimate how long de novo genes persist in populations. We identified several features that de novo genes come to share with established tissue-specific genes the longer they persist. This study highlights important challenges in reconstructing de novo gene origin and helps elucidate why some transcripts may survive long enough to acquire selectable functions.

evolutionary biology↗

bioRxiv2023

Discovery of high affinity and specificity stapled peptide Bcl-xL inhibitors using bacterial surface display

Intracellular protein-protein interactions are involved in many different diseases, making them prime targets for therapeutic intervention. Several diseases are characterized by their overexpression of Bcl-xL, an anti-apoptotic B cell lymphoma 2 (Bcl-2) protein expressed on mitochondrial membranes. Bcl-xL overexpression inhibits apoptosis, and selective inhibition of Bcl-xL has the potential to increase cancer cell death while leaving healthy cells comparatively less affected. However, high homology between Bcl-xL and other Bcl-2 proteins has made it difficult to selectively inhibit this interaction by small molecule drugs. We engineered stapled peptides, a chemical modification that can improve cell penetration, protease stability, and conformational stability, towards the selective inhibition of Bcl-xL. To accomplish this task, we built a focused combinatorial mutagenesis library of peptide variants on the bacterial cell surface, used copper catalyzed click chemistry to form stapled peptides, and sorted the library for high binding to Bcl-xL and minimal binding towards other Bcl-2 proteins. We characterized the sequence and staple placement trends that governed specificity and identified molecules with [~]10 nM affinity to Bcl-xL and greater than 100-fold selectivity versus other Bcl-2 family members on and off the cell surface. We confirmed the mechanism of action of these peptides is consistent with apoptosis biology through mitochondrial outer membrane depolarization assays (MOMP). Overall, high affinity (10 nM Kd) and high specificity (100-fold selectivity) peptides were developed to target the Bcl-xL protein. These results demonstrate that stapled alpha helical peptides are promising candidates for the specific treatment of cancers driven by Bcl-2 dysregulation.

synthetic biology↗

bioRxiv2023

Single-fly assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life

Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed a cost-effective hybrid Oxford Nanopore (ONT) long-read and Illumina short-read sequencing approach and used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing the number of genome assemblies for this taxonomic group. The next major challenge is to address the laboratory culture bias in taxon sampling by sequencing genomes of species that cannot easily be reared in the lab. Here, we build upon our previous methods to perform amplification-free ONT sequencing of single wild flies obtained either directly from the field or from ethanol-preserved specimens in museum collections, greatly improving the representation of lesser studied drosophilid taxa in whole-genome data. Using Illumina Novaseq X Plus and ONT P2 sequencers with R10.4.1 chemistry, we set a new benchmark for inexpensive hybrid genome assembly at US $150 per genome while assembling genomes from as little as 35 ng of genomic DNA from a single fly. We present 183 new genome assemblies for 179 species as a resource for drosophilid systematics, phylogenetics, and comparative genomics. Of these genomes, 62 are from pooled lab strains and 121 from single adult flies. Despite the sample limitations of working with small insects, most single-fly diploid assemblies are comparable in contiguity (>1Mb contig N50), completeness (>98% complete dipteran BUSCOs), and accuracy (>QV40 genome-wide with ONT R10.4.1) to assemblies from inbred lines. We present a well-resolved multi-locus phylogeny for 360 drosophilid and 4 outgroup species encompassing all publicly available (as of August 2023) genomes for this group. Finally, we present a Progressive Cactus whole-genome, reference-free alignment built from a subset of 298 suitably high-quality drosophilid genomes. The new assemblies and alignment, along with updated laboratory protocols and computational pipelines, are released as an open resource and as a tool for studying evolution at the scale of an entire insect family.

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↗

bioRxiv2023

Antagonistic nanobodies reveal mechanism of GSDMD pore formation and unexpected therapeutic potential

Activation of various inflammasomes converges on the cleavage of gasdermin D (GSDMD) by pro-inflammatory caspases, followed by oligomerization of the N-terminal domain (GSDMDNT) and the assembly of pores penetrating target membranes. Yet, it remained unclear what triggers the conformational changes that allow membrane insertion, as methods to study pore formation in living cells were limited. We raised nanobodies specific for human GSDMD and found two nanobodies that prevent pyroptosis and IL-1{beta} release when expressed in the cytosol of human macrophages. Nanobody binding to GSDMDNT blocked its oligomerization, while inflammasome assembly and GSDMD processing itself were not affected. The nanobody-stabilized monomers of GSDMDNT partitioned into the plasma membrane, suggesting that pore formation is initiated by insertion of monomers, followed by oligomerization in the target membrane. When GSDMD pore formation was inhibited, cells still underwent caspase-1-dependent apoptosis, likely due to the substantially augmented caspase-1 activity. This hints at a novel layer of regulation of caspase-1 activity by GSDMD pores. Moreover, we revealed the unexpected therapeutic potential of antagonistic GSDMD nanobodies, as recombinant nanobodies added to the medium prevented cell death by pyroptosis, likely by entering through GSDMD pores and curtailing the assembly of additional pores. GSDMD nanobodies may thus be suitable to treat the ever-growing list of diseases caused by activation of the (non-) canonical inflammasomes.

immunology↗

bioRxiv2023

Pyroptosis inhibiting nanobodies block Gasdermin D pore formation

Gasdermin D (GSDMD) is a key mediator of pyroptosis, a pro-inflammatory form of cell death occurring downstream of inflammasome activation as part of the innate immune defence. Upon cleavage by inflammatory caspases, the N-terminal domain of GSDMD forms pores in the plasma membrane resulting in cytokine release and eventually cell death. Targeting GSDMD is an attractive way to dampen inflammation. In this study, six GSDMD targeting nanobodies were characterized in terms of their binding affinity, stability, and effect on GSDMD pore formation. Three of the nanobodies inhibited GSDMD pore formation in a liposome leakage assay, although caspase cleavage was not perturbed. We determined the crystal structure of human GSDMD in complex with two nanobodies at 1.9 [A] resolution, providing detailed insights into the GSDMD-nanobody interactions and epitope binding. The pore formation is sterically blocked by one of the nanobodies that binds to the oligomerization interface of the N-terminal domain in the multi-subunit assembly. Our biochemical and structural findings provide new tools for studying inflammasome biology and build a framework for the design of novel GSDMD targeting drugs.

biochemistry↗

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↗

bioRxiv2022

Secondary reversion to sexual monomorphism associated with tissue-specific loss of doublesex expression

Animal evolution is characterized by frequent turnover of sexually dimorphic traits - new sex- specific characters are gained, and some ancestral sex-specific characters are lost, in many lineages. In insects, sexual differentiation is predominantly cell-autonomous and depends on the expression of the doublesex (dsx) transcription factor. In most cases, cells that transcribe dsx have the potential to undergo sex-specific differentiation, while those that lack dsx expression do not. Consistent with this mode of development, comparative research has shown that the origin of new sex-specific traits can be associated with the origin of new spatial domains of dsx expression. In this report, we examine the opposite situation - a secondary loss of the sex comb, a male-specific grasping structure that develops on the front legs of some drosophilid species. We show that, while the origin of the sex comb is linked to an evolutionary gain of dsx expression in the leg, sex comb loss in a newly identified species of Lordiphosa (Drosophilidae) is associated with a secondary loss of dsx expression. We discuss how the developmental control of sexual dimorphism affects the mechanisms by which sex-specific traits can evolve.

evolutionary biology↗

bioRxiv2022

Sex-specific evolution of a Drosophila sensory system via interacting cis- and trans-regulatory changes

The evolution of gene expression via cis-regulatory changes is well established as a major driver of phenotypic evolution. However, relatively little is known about the influence of enhancer architecture and intergenic interactions on regulatory evolution. We address this question by examining chemosensory system evolution in Drosophila. D. prolongata males show a massively increased number of chemosensory bristles compared to females and males of sibling species. This increase is driven by sex-specific transformation of ancestrally mechanosensory organs. Consistent with this phenotype, the Pox neuro transcription factor (Poxn), which specifies chemosensory bristle identity, shows expanded expression in D. prolongata males. Poxn expression is controlled by non-additive interactions among widely dispersed enhancers. Although some D. prolongata Poxn enhancers show increased activity, the additive component of this increase is slight, suggesting most changes in Poxn expression are due to epistatic interactions between Poxn enhancers and trans-regulatory factors. Indeed, the expansion of D. prolongata Poxn enhancer activity is only observed in cells that express doublesex (dsx), the gene that controls sexual differentiation in Drosophila and also shows increased expression in D. prolongata males due to cis-regulatory changes. Although expanded dsx expression may contribute to increased activity of D. prolongata Poxn enhancers, this interaction is not sufficient to explain the full expansion of Poxn expression, suggesting that cis-trans interactions between Poxn, dsx, and additional unknown genes are necessary to produce the derived D. prolongata phenotype. Overall, our results demonstrate the importance of epistatic gene interactions for evolution, particularly when pivotal genes have complex regulatory architecture. Research HighlightsIn Drosophila prolongata males, many mechanosensory organs are transformed into chemosensory. This is due in part to interacting regulatory changes in Poxn, which controls chemosensory organ development, and dsx, which controls sexual differentiation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=194 HEIGHT=200 SRC="FIGDIR/small/475924v1_ufig1.gif" ALT="Figure 1"> View larger version (65K): org.highwire.dtl.DTLVardef@1b5b5borg.highwire.dtl.DTLVardef@ac2ceorg.highwire.dtl.DTLVardef@7b6db0org.highwire.dtl.DTLVardef@15e4c6b_HPS_FORMAT_FIGEXP M_FIG C_FIG

evolutionary biology↗