DOI: 10.25338/b89p86
title: Population structure of Drosophila suzukii and signals of multiple invasions in the continental United States

description: Drosophila suzukii, or spotted-wing drosophila, is now an established pest
 in many parts of the world, causing significant damage to numerous fruit
 crop industries. Native to East Asia, D. suzukii infestations started in
 the United States a decade ago, occupying a wide range of climates. To
 better understand invasion ecology of this pest, knowledge of
 past migration events, population structure, and genetic diversity is
 needed. In this study, we sequenced whole genomes of 237 individual flies
 collected across the continental U.S., as well as several representative
 sites in Europe, Brazil, and Asia, to identify hundreds of thousands of
 genetic markers for analysis. We analyzed these markers to detect
 population structure, to reconstruct migration events, and to estimate
 genetic diversity and differentiation within and among the continents. We
 observed strong population structure between West and East Coast
 populations in the U.S., but no evidence of any population structure North
 to South, suggesting there is no broad-scale adaptations occurring in
 response to the large differences in regional weather conditions. We also
 found evidence that repeated migration events from Asia into North America
 have provided increased levels of genetic diversity, which does not appear
 to be the case for Brazil or Europe. This large genomic dataset will spur
 future research into the genomic adaptations underlying D. suzukii pest
 activity and development of novel control methods for this agricultural
 pest.
description: We received either flash-frozen or ethanol-preserved samples of
 <i>Drosophila suzukii</i> for genomic analysis. Japanese
 samples were a lab strain from the Kyoto Japanese Stock Center; Hawaiian
 samples were wild-caught in 2009 and kept as a lab colony until DNA
 extraction in 2017; all other samples were field-collected.
 Ethanol-preserved samples were re-hydrated in 100uL water prior to DNA
 extraction. Flies were individually disrupted using a 3mm diameter steel
 bead in a TissueLyser (Qiagen, Germantown, MD) for 30 seconds at 30Hz in
 100uL of 2mg/mL Proteinase K in PK buffer (MagMAX™, Thermofisher
 Scientific, Pleasanton, CA) before being spun down in a centrifuge for 1
 minute at 10,000rpm and incubated for 2 hours at 56°C. 100uL of MagMAX DNA
 lysis buffer was added to each sample, followed by a 10 minute incubation,
 before proceeding to DNA purification using a BioSprint DNA Blood Kit on a
 BioSprint 96 Workstation (Qiagen), using protocol “BS96 DNA Tissue” as per
 manufacturer’s instructions. Illumina sequencing libraries were prepared
 using either the Kappa HyperPlus Kit (Roche, South San Francisco, CA)
 (lanes 2-4) or Qiaseq FX DNA Library Kit (Qiagen) (lanes 5-8) using 50 ng
 of input DNA. We followed the manufacturer’s instructions for both library
 preparation kits with few exceptions. With the Kappa HyperPlus Kit, we
 fragmented DNA at 30°C for 20 minutes and increased adapter incubation
 time to 1 hour. We also added a 0.6X and 0.7X size selection with AmPure
 XP beads (Beckman Coulter Life Sciences, Indianapolis, IN) following 5
 cycles of PCR amplification with an Eppendorf Master Cycler Pro
 (ThermoFisher Scientific). With the Qiagen FX kit, we fragmented DNA at
 30°C for 15 minutes, and amplified with 7 cycles of PCR. In both cases,
 DNA library concentration and fragment size were quantified on a Qubit
 (ThermoFisher Scientific) and a Bioanalyzer High-Sensitivity DNA chip
 (Agilent, Santa Clara, CA). Paired-end 150 base-pair sequencing was
 performed by Novogene, Inc. (Sacramento, CA) on the Illumina HiSeq 4000
 platform.