@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 {65363, title = {Characterization of the Genetic Architecture Underlying Eye Size Variation Within Drosophila melanogaster and Drosophila simulans.}, journal = {Genes|Genomes|Genetics}, volume = {10}, year = {2020}, month = {2020 Mar 01}, pages = {1005-18}, doi = {10.1534/g3.119.400877}, url = {http://g3journal.org/lookup/doi/10.1534/g3.119.400877https://syndication.highwire.org/content/doi/10.1534/g3.119.400877}, author = {Gaspar, Pedro and Arif, Saad and Sumner-Rooney, Lauren and Kittelmann, Maike and Bodey, Andrew J. and Stern, David L. and Nunes, Maria D. S. and McGregor, Alistair P.} } @article {65042, title = {Changes throughout a genetic network mask the contribution of Hox gene evolution.}, journal = {Current Biology}, volume = {29}, year = {2019}, month = {2019 Jul 08}, pages = {2157-66}, abstract = {

Hox genes pattern the anterior-posterior axis of animals and are posited to drive animal body plan evolution, yet their precise role in evolution has been difficult to determine. Here, we identified evolutionary modifications in the Hox gene\ Abd-Bthat dramatically altered its expression along the body plan of\ Drosophila santomea.\ Abd-B\ is required for pigmentation in\ Drosophila yakuba, the sister species of\ D.\ santomea, and changes to Abd-B expression would be predicted to make large contributions to the loss of body pigmentation in\ D.\ santomea. However, manipulating\ Abd-B\ expression in current-day\ D.\ santomea\ does not affect pigmentation. We attribute this epistatic interaction to four other genes within the\ D.\ santomea\ pigmentation network, three of which have evolved expression patterns that do not respond to Abd-B. Our results demonstrate how body plans may evolve through small evolutionary steps distributed throughout Hox-regulated networks. Polygenicity and epistasis may hinder efforts to identify genes and mechanisms underlying macroevolutionary traits.

}, issn = {09609822}, doi = {10.1016/j.cub.2019.05.074}, author = {Liu, Yang and Ramos-Womack, Margarita and Han, Clair and Reilly, Patrick and Brackett, Kelly LaRue and Rogers, William and Williams, Thomas M. and Andolfatto, Peter and Stern, David L. and Rebeiz, Mark} }