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150 Publications

Showing 1-10 of 150 results
03/12/24 | Analysis of meiotic recombination in Drosophila simulans shows heterozygous inversions do not cause an interchromosomal effect
Bowen Man , Elizabeth Kim , Alekhya Vadlakonda , David L Stern , Nicole Crown
bioRxiv. 2024 Mar 12:. doi: 10.1101/2024.03.09.584235

Chromosome inversions are of unique importance in the evolution of genomes and species because when heterozygous with a standard arrangement chromosome, they suppress meiotic crossovers within the inversion. In Drosophila species, heterozygous inversions also cause the interchromosomal effect, whereby the presence of a heterozygous inversion induces a dramatic increase in crossover frequencies in the remainder of the genome within a single meiosis. To date, the interchromosomal effect has been studied exclusively in species that also have high frequencies of inversions in wild populations. We took advantage of a recently developed approach for generating inversions in Drosophila simulans, a species that does not have inversions in wild populations, to ask if there is an interchromosomal effect. We used the existing chromosome 3R balancer and generated a new chromosome 2L balancer to assay for the interchromosomal effect genetically and cytologically. We found no evidence of an interchromosomal effect in D. simulans. To gain insight into the underlying mechanistic reasons, we qualitatively analyzed the relationship between meiotic double-strand break formation and synaptonemal complex assembly. We find that the synaptonemal complex is assembled prior to double-strand break formation as in D. melanogaster; however, we show that the synaptonemal complex is assembled prior to localization of the oocyte determination factor Orb, whereas in D. melanogaster, synaptonemal complex formation does not begin until Orb is localized. Together, our data show heterozygous inversions in D. simulans do not induce an interchromosomal effect and that there are differences in the developmental programming of the early stages of meiosis.

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02/28/24 | Sensory neuron population expansion enhances odor tracking without sensitizing projection neurons
Suguru Takagi , Gizem Sancer , Liliane Abuin , S. David Stupski , J. Roman Arguello , Lucia L. Prieto-Godino , David L. Stern , Steeve Cruchet , Raquel Álvarez-Ocaña , Carl F. R. Wienecke , Floris van Breugel , James M. Jeanne , Thomas O. Auer , Richard Benton
bioRxiv. 2024 Feb 28:. doi: 10.1101/2023.09.15.556782

The evolutionary expansion of sensory neuron populations detecting important environmental cues is widespread, but functionally enigmatic. We investigated this phenomenon through comparison of homologous neural pathways of Drosophila melanogaster and its close relative Drosophila sechellia, an extreme specialist for Morinda citrifolia noni fruit. D. sechellia has evolved species-specific expansions in select, noni-detecting olfactory sensory neuron (OSN) populations, through multigenic changes. Activation and inhibition of defined proportions of neurons demonstrate that OSN population increases contribute to stronger, more persistent, noni-odor tracking behavior. These sensory neuron expansions result in increased synaptic connections with their projection neuron (PN) partners, which are conserved in number between species. Surprisingly, having more OSNs does not lead to greater odor-evoked PN sensitivity or reliability. Rather, pathways with increased sensory pooling exhibit reduced PN adaptation, likely through weakened lateral inhibition. Our work reveals an unexpected functional impact of sensory neuron expansions to explain ecologically-relevant, species-specific behavior.

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02/26/24 | Nested neural circuits generate distinct acoustic signals during Drosophila courtship
Joshua L. Lillvis , Kaiyu Wang , Hiroshi M. Shiozaki , Min Xu , David L. Stern , Barry J. Dickson
Current Biology. 2024 Feb 26;34(4):808-24. doi: 10.1016/j.cub.2024.01.015

Many motor control systems generate multiple movements using a common set of muscles. How are premotor circuits able to flexibly generate diverse movement patterns? Here, we characterize the neuronal circuits that drive the distinct courtship songs of Drosophila melanogaster. Male flies vibrate their wings towards females to produce two different song modes – pulse and sine song – which signal species identity and male quality. Using cell-type specific genetic reagents and the connectome, we provide a cellular and synaptic map of the circuits in the male ventral nerve cord that generate these songs and examine how activating or inhibiting each cell type within these circuits affects the song. Our data reveal that the song circuit is organized into two nested feed-forward pathways, with extensive reciprocal and feed-back connections. The larger network produces pulse song, the more complex and ancestral song form. A subset of this network produces sine song, the simpler and more recent form. Such nested organization may be a common feature of motor control circuits in which evolution has layered increasing flexibility on to a basic movement pattern.

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02/01/24 | The density of regulatory information is a major determinant of evolutionary constraint on non-coding DNA in Drosophila
Gonzalo Sabarís , Daniela M. Ortíz , Ian Laiker , Ignacio Mayansky , Sujay Naik , Giacomo Cavalli , David L. Stern , Ella Preger-Ben Noon , Nicolás Frankel
Molecular Biology and Evolution. 2024 Feb 01;41(2):msae004. doi: 10.1093/molbev/msae004

The density and distribution of regulatory information in non-coding DNA of eukaryotic genomes is largely unknown. Evolutionary analyses have estimated that ∼60% of nucleotides in intergenic regions of the D. melanogaster genome is functionally relevant. This estimate is difficult to reconcile with the commonly accepted idea that enhancers are compact regulatory elements that generally encompass less than 1 kilobase of DNA. Here, we approached this issue through a functional dissection of the regulatory region of the gene shavenbaby (svb). Most of the ∼90 kilobases of this large regulatory region is highly conserved in the genus Drosophila, though characterized enhancers occupy a small fraction of this region. By analyzing the regulation of svb in different contexts of Drosophila development, we found that the regulatory architecture that drives svb expression in the abdominal pupal epidermis is organized in a dramatically different way than the information that drives svb expression in the embryonic epidermis. While in the embryonic epidermis svb is activated by compact and dispersed enhancers, svb expression in the pupal epidermis is driven by large regions with enhancer activity, which occupy a great portion of the svb cis-regulatory DNA. We observed that other developmental genes also display a dense distribution of putative regulatory elements in their regulatory regions. Furthermore, we found that a large percentage of conserved non-coding DNA of the Drosophila genome is contained within putative regulatory DNA. These results suggest that part of the evolutionary constraint on non-coding DNA of Drosophila is explained by the density of regulatory information.

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01/10/24 | Song Torrent: A modular, open-source 96-chamber audio and video recording apparatus with optogenetic activation and inactivation capabilities for Drosophila
Steve Sawtelle , Lakshmi Narayan , Yun Ding , Elizabeth Kim , Emily L. Behrman , Joshua L. Lillvis , Takashi Kawase , David L. Stern
bioRxiv. 2024 Jan 10:. doi: 10.1101/2024.01.09.574712


  • Many Drosophila species use acoustic communication during courtship and studies of these communication systems have provided insight into neurobiology, behavioral ecology, ethology, and evolution.

  • Recording Drosophila courtship sounds and associated behavior is challenging, especially at high throughput, and previously designed devices are relatively expensive and complex to assemble.


  • We present construction plans for a modular system utilizing mostly off-the-shelf, relatively inexpensive components that provides simultaneous high-resolution audio and video recording of 96 isolated or paired Drosophila individuals.

  • We provide open-source control software to record audio and video.

  • We designed high intensity LED arrays that can be used to perform optogenetic activation and inactivation of labelled neurons.

  • The basic design can be modified to facilitate novel study designs or to record insects larger than Drosophila.

  • Fewer than 96 microphones can be used in the system if the full array is not required or to reduce costs.


  • Our hardware design and software provide an improved platform for reliable and comparatively inexpensive high-throughput recording of Drosophila courtship acoustic and visual behavior and perhaps for recording acoustic signals of other small animals.

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09/15/23 | Sensory neuron population expansion enhances odour tracking through relaxed projection neuron adaptation
Suguru Takagi , Liliane Abuin , S. David Stupski , J. Roman Arguello , Lucia Prieto-Godino , David L. Stern , Steeve Cruchet , Raquel Álvarez-Ocaña , Carl F. R. Wienecke , Floris van Breugel , Thomas O. Auer , Richard Benton
bioRxiv. 2023 Sep 15:. doi: 10.1101/2023.09.15.556782

From the star-nosed mole’s eponymous mechanosensory organ to the platypus’ electroreceptive bill, the expansion of sensory neuron populations detecting important environmental cues is a widespread evolutionary phenomenon in animals16. How such neuron increases contribute to improved sensory detection and behaviour remain largely unexplained. Here we address this question through comparative analysis of olfactory pathways in Drosophila melanogaster and its close relative Drosophila sechellia, which feeds and breeds exclusively on Morinda citrifolia noni fruit79. We show that D. sechellia displays selective, large expansions of noni-detecting olfactory sensory neuron (OSN) populations, and that this trait has a multigenic basis. These expansions are accompanied by an increase in synaptic connections between OSNs and their projection neuron (PN) partners that transmit information to higher brain centres. Quantification of odour-evoked responses of partner OSNs and PNs reveals that OSN population expansions do not lead to heightened PN sensitivity, beyond that due to sensory receptor tuning differences. Rather, these pathways – but not those with conserved OSN numbers – exhibit non-adapting PN activity upon odour stimulation. In noni odour plume-tracking assays, D. sechellia exhibits enhanced performance compared to D. melanogaster. Through activation and inhibition of defined proportions of a noni-sensing OSN population, we establish that increased neuron numbers contribute to this behavioural persistence. Our work reveals an unexpected functional impact of sensory neuron expansions that can synergise with peripheral receptor tuning changes to explain ecologically-relevant, species-specific behaviour.

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09/07/23 | Combinatorial circuit dynamics orchestrate flexible motor patterns in Drosophila.
Hiroshi M. Shiozaki , Kaiyu Wang , Joshua L. Lillvis , Min Xu , Barry J. Dickson , David L. Stern
bioRxiv. 2023 Sep 07:. doi: 10.1101/2022.12.14.520499

Motor systems flexibly implement diverse motor programs to pattern behavioral sequences, yet their neural underpinnings remain unclear. Here, we investigated the neural circuit mechanisms of flexible courtship behavior in Drosophila. Courting males alternately produce two types of courtship song. By recording calcium signals in the ventral nerve cord (VNC) in behaving flies, we found that different songs are produced by activating overlapping neural populations with distinct motor functions in a combinatorial manner. Recordings from the brain suggest that song is driven by two descending pathways – one defines when to sing and the other specifies what song to sing. Connectomic analysis reveals that these “when” and “what” descending pathways provide structured input to VNC neurons with different motor functions. These results suggest that dynamic changes in the activation patterns of descending pathways drive different combinations of motor modules, thereby flexibly switching between different motor actions.

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06/17/23 | The Janelia Atalanta plasmids provide a simple and efficient CRISPR/Cas9-mediated homology directed repair platform for Drosophila
David L. Stern , Elizabeth Kim , Emily L. Behrman
bioRxiv. 2023 Jun 17:. doi: 10.1101/2023.06.17.545412

Homology-directed repair (HDR) is a powerful tool for modifying genomes in precise ways to address many biological questions. Use of Clustered Regularly Interspersed Short Palindromic Repeats (CRISPR)-Cas9 induced targeted DNA double-strand breakage has substantially simplified use of homology-directed repair to introduce specific perturbations in Drosophila, but existing platforms for CRISPR-Cas9-mediated HDR in Drosophila involve multiple cloning steps and have low efficiency. To simplify cloning of HDR plasmids, we designed a new plasmid platform, the Janelia Atalanta (pJAT) series, that exploits recent advances in dsDNA synthesis to facilitate Gateway cloning of gRNA sequences and homology arms in one step. Surprisingly, the pJAT plasmids yielded considerably higher HDR efficiency (approximately 25%) than we have observed with other approaches. pJAT plasmids work in multiple Drosophila species and exhibited such high efficiency that previously impossible experiments in Drosophila, such as driving targeted chromosomal inversions, were made possible. We provide pJAT plasmids for a range of commonly performed experiments including targeted insertional mutagenesis, insertion of phiC31-mediated attP landing sites, generation of strains carrying a germ-line source of Cas9, and induction of chromosomal rearrangements. We also provide “empty” pJAT plasmids with multiple cloning sites to simplify construction of plasmids with new functionality. The pJAT platform is generic and may facilitate improved efficiency CRISPR-Cas9 HDR in a wide range of model and non-model organisms.

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06/01/23 | Single-cell type analysis of wing premotor circuits in the ventral nerve cord of Drosophila melanogaster
Erica Ehrhardt , Samuel C Whitehead , Shigehiro Namiki , Ryo Minegishi , Igor Siwanowicz , Kai Feng , Hideo Otsuna , FlyLight Project Team , Geoffrey W Meissner , David Stern , Jim Truman , David Shepherd , Michael H. Dickinson , Kei Ito , Barry J Dickson , Itai Cohen , Gwyneth M Card , Wyatt Korff
bioRxiv. 2023 Jun 01:. doi: 10.1101/2023.05.31.542897

To perform most behaviors, animals must send commands from higher-order processing centers in the brain to premotor circuits that reside in ganglia distinct from the brain, such as the mammalian spinal cord or insect ventral nerve cord. How these circuits are functionally organized to generate the great diversity of animal behavior remains unclear. An important first step in unraveling the organization of premotor circuits is to identify their constituent cell types and create tools to monitor and manipulate these with high specificity to assess their function. This is possible in the tractable ventral nerve cord of the fly. To generate such a toolkit, we used a combinatorial genetic technique (split-GAL4) to create 195 sparse driver lines targeting 198 individual cell types in the ventral nerve cord. These included wing and haltere motoneurons, modulatory neurons, and interneurons. Using a combination of behavioral, developmental, and anatomical analyses, we systematically characterized the cell types targeted in our collection. Taken together, the resources and results presented here form a powerful toolkit for future investigations of neural circuits and connectivity of premotor circuits while linking them to behavioral outputs.

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12/15/22 | Neural coding of distinct motor patterns during Drosophila courtship song
Hiroshi M. Shiozaki , Kaiyu Wang , Joshua L. Lillvis , Min Xu , Barry J. Dickson , David L. Stern
bioRxiv. 2022 Dec 15:. doi: 10.1101/2022.12.14.520499

Animals flexibly switch between different actions by changing neural activity patterns for motor control. Courting Drosophila melanogaster males produce two different acoustic signals, pulse and sine song, each of which can be promoted by artificial activation of distinct neurons. However, how the activity of these neurons implements flexible song production is unknown. Here, we developed an assay to record neuronal calcium signals in the ventral nerve cord, which contains the song motor circuit, in singing flies. We found that sine-promoting neurons, but not pulse-promoting neurons, show strong activation during sine song. In contrast, both pulse- and sine-promoting neurons are active during pulse song. Furthermore, population calcium imaging in the song circuit suggests that sine song involves activation of a subset of neurons that are also active during pulse song. Thus, differential activation of overlapping, rather than distinct, neural populations underlies flexible motor actions during acoustic communication in D. melanogaster.

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