Here we use genomes from the Drosophila Population Genomics Project (DPGP), downloaded from the Drosophila Genome Nexus (http://www.johnpool.net/genomes.html) in October 2015. From that page:
The D. melanogaster genomes aligned here are from the following sources: Drosophila Population Genomics Project (DPGP) Phase 1 - Malawi extraction lines only (Langley et al. 2012 Genetics) Phase 2 - Most from a variety of African populations (Pool et al. 2012 PLoS Genetics) Phase 3 - Nearly 200 genomes from a single high diversity and low admixture Zambia
population (unpublished, sequenced by the Langley lab) Drosophila Genetic Reference Panel (DGRP) - ~200 genomes from a North American
sample (Mackay et al. 2012 Nature) Drosophila Synthetic Population Resource (DSPR) - parental strain genomes Additional African genomes sequenced by the Pool labInformation regarding the populations of origin is here: POPULATION SPREADSHEET.
A summary of the individual genomes is here: INDIVIDUAL SPREADSHEET. Included are depth, coverage, read characteristics, and chromosomal representation. Each genome's origin from inbred, isofemale, or homozygous chromosome line adults, or else a haploid embryo (Langley et al. 2011 Genetics), is also noted.
Citation: For the DGN alignments, please cite Lack et al. 2015 Genetics. Users of these genomes should also always cite the original publications that described them.