@article {69458, title = {Courtship song differs between African and European populations of Drosophila melanogaster and involves a strong effect locus}, journal = {G3 Genes|Genomes|Genetics}, year = {2025}, month = {2025 Mar 07}, abstract = {

The courtship song of\ Drosophila melanogaster\ has long served as an excellent model system for studies of animal communication and differences in courtship song have been demonstrated among populations and between species. Here, we report that flies of African and European origin, which diverged approximately 13,000 years ago, show significant genetic differentiation in the use of slow versus fast pulse song. Using a combination of quantitative trait mapping and population genetic analysis we detected a single strong QTL underlying this trait and we identified candidate genes that may contribute to the evolution of this trait. Song trait variation between parental strains of our recombinant inbred panel enabled detection of genomic intervals associated with six additional song traits, some of which include known courtship-related genes. These findings improve the prospects for further genetic insights into the evolution of reproductive behavior and the biology underlying courtship song.

bioRxiv Preprint:\ https://www.biorxiv.org/content/early/2024/05/17/2024.05.14.594231

}, doi = {10.1093/g3journal/jkaf050}, url = {https://doi.org/10.1093/g3journal/jkaf050}, author = {Lollar, Matthew J. and Kim, Elizabeth and Stern, David L. and Pool, John E.} } @article {67229, title = {SongExplorer: A deep learning workflow for discovery and segmentation of animal acoustic communication signals}, journal = {bioRxiv}, year = {2021}, month = {03/2021}, abstract = {

Many animals produce distinct sounds or substrate-borne vibrations, but these signals have proved challenging to segment with automated algorithms. We have developed SongExplorer, a web-browser based interface wrapped around a deep-learning algorithm that supports an interactive workflow for (1) discovery of animal sounds, (2) manual annotation, (3) supervised training of a deep convolutional neural network, and (4) automated segmentation of recordings. Raw data can be explored by simultaneously examining song events, both individually and in the context of the entire recording, watching synced video, and listening to song. We provide a simple way to visualize many song events from large datasets within an interactive low-dimensional visualization, which facilitates detection and correction of incorrectly labelled song events. The machine learning model we implemented displays higher accuracy than existing heuristic algorithms and similar accuracy as two expert human annotators. We show that SongExplorer allows rapid detection of all song types from new species and of novel song types in previously well-studied species.Competing Interest StatementThe authors have declared no competing interest.

}, doi = {10.1101/2021.03.26.437280}, url = {https://www.biorxiv.org/content/early/2021/03/26/2021.03.26.437280}, author = {Arthur, Benjamin J. and Ding, Yun and Sosale, Medhini and Khalif, Faduma and Kim, Elizabeth and Waddell, Peter and Turaga, Srinivas C. and Stern, David L.} } @article {48319, title = {Genetic and transgenic reagents for Drosophila simulans, D. mauritiana, D. yakuba, D. santomea and D. virilis.}, journal = {G3 (Bethesda, Md.)}, volume = {7}, year = {2017}, month = {2017 Mar 09}, pages = {1339-47}, abstract = {

Species of the Drosophila melanogaster species subgroup, including the species D. simulans, D. mauritiana, D. yakuba, and D. santomea, have long served as model systems for studying evolution. Studies in these species have been limited, however, by a paucity of genetic and transgenic reagents. Here we describe a collection of transgenic and genetic strains generated to facilitate genetic studies within and between these species. We have generated many strains of each species containing mapped piggyBac transposons including an enhanced yellow fluorescent protein gene expressed in the eyes and a phiC31 attP site-specific integration site. We have tested a subset of these lines for integration efficiency and reporter gene expression levels. We have also generated a smaller collection of other lines expressing other genetically encoded fluorescent molecules in the eyes and a number of other transgenic reagents that will be useful for functional studies in these species. In addition, we have mapped the insertion locations of 58 transposable elements in D. virilis that will be useful for genetic mapping studies.

}, issn = {2160-1836}, doi = {10.1534/g3.116.038885}, author = {Stern, David L and Crocker, Justin and Ding, Yun and Frankel, Nicol{\'a}s and Kappes, Gretchen and Kim, Elizabeth and Kuzmickas, Ryan and Lemire, Andrew and Mast, Joshua D and Picard, Serge} }