Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses


Kapun M., Barron M. G. , Staubach F., Obbard D. J. , Wiberg R. A. W. , Vieira J., ...More

MOLECULAR BIOLOGY AND EVOLUTION, vol.37, no.9, pp.2661-2678, 2020 (Peer-Reviewed Journal) identifier identifier identifier

  • Publication Type: Article / Article
  • Volume: 37 Issue: 9
  • Publication Date: 2020
  • Doi Number: 10.1093/molbev/msaa120
  • Journal Name: MOLECULAR BIOLOGY AND EVOLUTION
  • Journal Indexes: Science Citation Index Expanded, Scopus, Agricultural & Environmental Science Database, Aquatic Science & Fisheries Abstracts (ASFA), BIOSIS, CAB Abstracts, Chemical Abstracts Core, EMBASE, MEDLINE, Veterinary Science Database
  • Page Numbers: pp.2661-2678
  • Keywords: population genomics, adaptation, demography, selection, clines, SNPs, structural variants, INCIPIENT SEXUAL ISOLATION, AMINO-ACID POLYMORPHISM, TRANSPOSABLE ELEMENTS, INVERSION IN(3R)PAYNE, LATITUDINAL CLINE, NEXT-GENERATION, NORTH-AMERICAN, LIFE-HISTORY, NUCLEOTIDE POLYMORPHISM, NATURAL-POPULATIONS

Abstract

Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatiotemporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations costly. Here, we address these issues using a collaborative approach, sequencing 48 pooled population samples from 32 locations, and perform the first continent-wide genomic analysis of genetic variation in European Drosophila melanogaster. Our analyses uncover longitudinal population structure, provide evidence for continent-wide selective sweeps, identify candidate genes for local climate adaptation, and document clines in chromosomal inversion and transposable element frequencies. We also characterize variation among populations in the composition of the fly microbiome, and identify five new DNA viruses in our samples.