Adaptive genomic signatures of globally invasive populations of the yellow fever mosquito Aedes aegypti

* These authors contributed equally: Alejandro N. Lozada-Chávez, Irma Lozada-Chávez. Supplementary Dataset This repository contains the Supplementary Data (from 1 to 12) cited in our paper "Adaptive genomic signatures of globally invasive populations of the yellow fever mosquito Aedes aegypti" in Nature Ecology and Evolution: https://doi.org/10.1038/s41559-025-02643-5 These datasets are available in the section "Supplementary Information" of our paper, but with the absence of the SD-9 due its large big size (~3Gb after decompressed). Here you can find the complete set of datasets in a single ZIP file: 41559_2025_2643_MOESM5_ESM_Supplementary_Data.zip LIST OF DATASETS: 1) Supplementary Data 1. SNP statistics for populations through genomic regions (TXT). 2) Supplementary Data 2. Sequences of new detected nrEVEs (FASTA). 3) Supplementary Data 3. Phylogenetic trees for populations and individuals (NEWICK). 4) Supplementary Data 4. Information for 8,120 hard selective sweeps detected with RAiSD in out-of-Africa populations (TXT). 5) Supplementary Data 5. Information for 1,030 SNP outliers detected with PCAdapt within 2,266 genes (VCF format). 6) Supplementary Data 6. Matrix with DoS scores for 11,651 orthologous protein-coding genes in AaegL5 and each Ae. aegypti population (TXT). 7) Supplementary Data 7. Matrix with MKT scores for 11,651 orthologous protein-coding genes in AaegL5 and each Ae. aegypti population (TXT). 8) Supplementary Data 8. Matrix with DoS scores used to estimate relaxed selection (TXT). 9) Supplementary Data 9. Matrix with SNPs and genomic coordinates within adaptive protein-coding genes and ncRNAs that are shared or private for out-of-Africa populations against African populations (TXT). 10) Supplementary Data 10. Matrix with 483 nonsynonymous SNPs and their allele frequencies for our 40 populations Florida and Colombia (TXT).11) Supplementary Data 11. Genomic coordinates of SNPs in AaegL5 obtained from the literature and VectorBase (TXT). 12) Supplementary Data 12. Source data of metrics used to plot Figure 4b (TXT). UPDATES NOTE: Repository version 3. Final version of datasets for the accepted manuscript. Repository version 2. Incomplete datasets: Files as prelimary versions and their content may vary. The SD-10 is not present (matrix with 483 SNPs) was added. The SD-7 is a broken file (cannot be opened). Repository version 1. Incomplete datasets: Files as prelimary versions and their content may vary. Two final SD files are not present. CITATION OF THIS REPOSITORY: Lozada-Chávez, A. N., Lozada-Chávez, I., Alfano, N., Palatini, U., Sogliani, D., Elfekih, S., Degefa, T., Sharakhova, M. V., Badolo, A., Patchara, S., Casas-Martinez, M., Carlos, B. C., Carballar-Lejarazú, R., Lambrechts, L., Souza-Neto, J. A., & Bonizzoni, M. (2024). Adaptive genomic signatures of globally invasive populations of the yellow fever mosquito Aedes aegypti [Data set]. Zenodo. https://doi.org/10.5281/zenodo.14948092