Data from: High-resolution single-cell analyses reveal evolutionary constraints and evolvability of sexual circuits in Drosophila
Data files
Nov 05, 2025 version files 2.82 GB
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dsx_neurons_melanogaster_female_rawdata.zip
25.16 MB
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dsx_neurons_melanogaster_male_rawdata.zip
153.46 MB
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dsx_neurons_santomea_male_rawdata.zip
38.32 MB
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dsx_neurons_teissieri_male_rawdata.zip
47.50 MB
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dsx_neurons_yakuba_male_rawdata.zip
138.40 MB
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FourSpecies_RdsFiles.zip
1.98 GB
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MaleFemale_RdsFiles.zip
432.84 MB
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README.md
6.47 KB
Abstract
To understand how the cellular and molecular composition of neural circuits evolves to generate species-specific behaviors, we performed single-cell transcriptomic profiling of sexual circuits labeled by the sex determination gene doublesex (dsx) in adult males of four Drosophila species: D. melanogaster, D. yakuba, D. santomea, and D. teissieri. Using this dataset, we compared molecularly defined dsx⁺ cell types across species, quantified transcriptomic divergence within each cell type, and analyzed differences in gene expression. In addition, we characterized sex differences in dsx⁺ neurons by generating a single-cell transcriptomic dataset from adult females of D. melanogaster, enabling us to examine species divergence in the context of sexual dimorphism. These datasets are shared here for public access.
Dataset DOI: 10.5061/dryad.f4qrfj78h
Description of the data and file structure
We generated flies with genetically labeled doublesex+ (dsx) neurons and dissected the brains and ventral nerve cords of ~100 flies per sample, dissociated the tissue into single cells, and used fluorescence-activated cell sorting to collect dsx+ neurons. Next, we followed standard 10X genomics protocols to generate single-cell libraries before using CellRanger to generate expression matrices. We used Seurat for clustering analyses to explore the evolution of dsx+ neurons across Drosophila species and between male and female D. melanogaster. In our clustering analyses, to explore the heterogeneity of cell types, we identified and separated out cells from each dsx+ parental clusters and performed additional clustering analyses. We included three replicates of D. melanogaster males, three replicates of D. yakuba males, one replicate of D. santomea males, one replicate of D. teissieri males, and one replicate of D. melanogaster females. We only included genes with orthologs across all four species for data analyses.
Files and variables
File: FourSpecies_RdsFiles.zip
Description: Rds files including clustering, metadata, and expression data for males from D. melanogaster, D. yakuba, D. santomea, and D. teissieri. File names indicate the specific cell populations included in the clustering analyses. Gene expression also can be directly visualized on UMAP space through a Shiny app (https://apps.yenchungchen.com/dsx_neurons/).
Parameters used for Seurat clustering for the four-species male dataset are as follows:
| Parental cluster | # PCs included in clustering | Clustering resolution |
|---|---|---|
| All | 15 | 0.5 |
| aDN | 3 | 0.05 |
| pC1 | 16 | 0.11 |
| pC2l | 12 | 0.05 |
| pC2m | 8 | 0.05 |
| pCd-1 | 4 | 0.1 |
| pCd-2 | 3 | 0.05 |
| TN1 | 7 | 0.1 |
| TN2 | 7 | 0.05 |
| ANm | 44 | 0.18 |
File: MaleFemale_RdsFiles.zip
Description: Rds files including clustering, metadata, and expression data for D. melanogaster males and females. Male data were downsampled to match the cellular coverage of female data prior to data analyses. File names indicate which cells are included for the clustering. Gene expression also can be directly visualized on UMAP space through a Shiny app (https://apps.yenchungchen.com/dsx_neurons/).
Parameters used for Seurat clustering for D. melanogaster male/female dataset are as follows:
| Parental cluster | # PCs included in clustering | Clustering resolution |
|---|---|---|
| All | 22 | 0.5 |
| aDN | 3 | 0.1 |
| pC1 | 13 | 0.2 |
| pC2l | 12 | 0.12 |
| pC2m | 9 | 0.1 |
| pCd-1 | 3 | 0.15 |
| pCd-2 | 3 | 0.5 |
| TN1 | 5 | 0.15 |
| TN2 | 3 | 0.7 |
| ANm | 46 | 1.7 |
File: dsx_neurons_yakuba_male_rawdata.zip
Description: Barcode, feature, and matrix files for each of the three male D. yakuba replicates. The barcode file includes the cell-associated barcode sequences, the features file contains metadata for each gene (gene ID and name), and the matrix file contains a sparse matrix of UMI counts linking each gene to each barcode.
File: dsx_neurons_melanogaster_male_rawdata.zip
Description: Barcode, feature, and matrix files for each of the three male D. melanogaster replicates. The barcode file includes the cell-associated barcode sequences, the features file contains metadata for each gene (gene ID and name), and the matrix file contains a sparse matrix of UMI counts linking each gene to each barcode.
File: dsx_neurons_teissieri_male_rawdata.zip
Description: Barcode, feature, and matrix files for the male D. teissieri data. The barcode file includes the cell-associated barcode sequences, the features file contains metadata for each gene (gene ID and name), and the matrix file contains a sparse matrix of UMI counts linking each gene to each barcode.
File: dsx_neurons_melanogaster_female_rawdata.zip
Description: Barcode, feature, and matrix files for the female D. melanogaster data. The barcode file includes the cell-associated barcode sequences, the features file contains metadata for each gene (gene ID and name), and the matrix file contains a sparse matrix of UMI counts linking each gene to each barcode.
File: dsx_neurons_santomea_male_rawdata.zip
Description: Barcode, feature, and matrix files for the male D. santomea data. The barcode file includes the cell-associated barcode sequences, the features file contains metadata for each gene (gene ID and name), and the matrix file contains a sparse matrix of UMI counts linking each gene to each barcode.
Access information
Other publicly accessible locations of the data:
- The first D. melanogaster and D. yakuba replicates (MelSample1 and YakSample1) are also available from NCBI's GEO: GSE262732.