A Thousand Fly Genomes: An ExpandedDrosophilaGenome Nexus

Abstract

The Drosophila Genome Nexus is a population genomic resource that provides D. melanogaster genomes from multiple sources. To facilitate comparisons across data sets, genomes are aligned using a common reference alignment pipeline which involves two rounds of mapping. Regions of residual heterozygosity, identity-by-descent, and recent population admixture are annotated to enable data filtering based on the user's needs. Here, we present a significant expansion of the Drosophila Genome Nexus, which brings the current data object to a total of 1,121 wild-derived genomes. New additions include 305 previously unpublished genomes from inbred lines representing six population samples in Egypt, Ethiopia, France, and South Africa, along with another 193 genomes added from recently-published data sets. We also provide an aligned D. simulans genome to facilitate divergence comparisons. This improved resource will broaden the range of population genomic questions that can addressed from multi-population allele frequencies and haplotypes in this model species. The larger set of genomes will also enhance the discovery of functionally relevant natural variation that exists within and between populations.

Parallel Evolution of Cold Tolerance Within Drosophila melanogaster

“…Additional genomes used here (from a subset of previously studied populations) were sequenced, aligned, and filtered (for heterozygosity, identity by descent, and population admixture) using identical methods to those described previously (Lack et al 2015). Raw data and aligned sequences for these genomes are published in an accompanying article that expands the Drosophila Genome Nexus (Lack, Lange, et al 2016). Recent gene flow into Africa, which may reflect urban adaptation, was masked from this data set (Pool et al 2012; Lack et al 2015; Lack, Lange, et al, 2016).…”

“…Raw data and aligned sequences for these genomes are published in an accompanying article that expands the Drosophila Genome Nexus (Lack, Lange, et al 2016). Recent gene flow into Africa, which may reflect urban adaptation, was masked from this data set (Pool et al 2012; Lack et al 2015; Lack, Lange, et al, 2016). …”

Discovery ofDrosophila melanogasterfrom Wild African Environments and Genomic Insights into Species History

“…Based on sequence comparisons [13,14] against town-sampled genomes with previouslyinferred karyotypes [15], the Kafue population displayed some of the highest chromosomal inversion frequencies ever observed in D. melanogaster. The overall proportion of inverted chromosome arms was 2.3 times higher in Kafue than in the Siavonga, Zambia town population (Table S2; z = 6.49; P < 0.0001), and higher than the previous D. melanogaster collections scored by cytological [16] or genomic [15,17] methods depicted in Figure 2.…”

The spread of resistance to imidacloprid is restricted by thermotolerance in natural populations ofDrosophila melanogaster

“…D. melanogaster is a cosmopolitan and synanthropic species that has a broad range and bears abundant diversity within natural populations 44 , ideal for testing complex evolutionary questions. Wild populations vary in their responses to temperature 45 and insecticide 30 with potential parallels across continents 46 so it is now timely to investigate interactions between multiple genetic and environmental factors with population genomic resolution.…”