# Natural Selection Shapes the Mosaic Ancestry of the Drosophila Genetic Reference Panel and the D. melanogaster Reference Genome

## TL;DR

The study shows how natural selection has shaped the genetic ancestry patterns in fruit flies from North America, revealing differences in African and European ancestry across their genomes.

## Contribution

The study provides the first detailed analysis of genomic admixture patterns in Drosophila populations and identifies the role of natural selection in shaping ancestry.

## Key findings

- The DGRP has 20% African ancestry while the reference genome has 9%.
- Ancestry levels differ across genomic regions, with less African ancestry on the X chromosome and in high recombination areas.
- Genome-wide ancestry disequilibrium suggests natural selection against incompatible genetic variants.

## Abstract

North American populations of Drosophila melanogaster are thought to derive from both European and African source populations, but despite their importance for genetic research, patterns of admixture along their genomes are essentially undocumented. Here, I infer geographic ancestry along genomes of the Drosophila Genetic Reference Panel (DGRP) and the D. melanogaster reference genome. Overall, the proportion of African ancestry was estimated to be 20% for the DGRP and 9% for the reference genome. Based on the size of admixture tracts and the approximate timing of admixture, I estimate that the DGRP population underwent roughly 13.9 generations per year. Notably, ancestry levels varied strikingly among genomic regions, with significantly less African introgression on the X chromosome, in regions of high recombination, and at genes involved in specific processes such as circadian rhythm. An important role for natural selection during the admixture process was further supported by a genome-wide signal of ancestry disequilibrium, in that many between-chromosome pairs of loci showed a deficiency of Africa-Europe allele combinations. These results support the hypothesis that admixture between partially genetically isolated Drosophila populations led to natural selection against incompatible genetic variants, and that this process is ongoing. The ancestry blocks inferred here may be relevant for the performance of reference alignment in this species, and may bolster the design and interpretation of many population genetic and association mapping studies.