DOI: 10.5061/dryad.wwpzgmsp5
title: Range-wide population genomics of the spongy moth, Lymantria dispar (Erebidae): Implications for biosurveillance, subspecies classification and phylogeography of a destructive moth

description: The spongy moth, Lymantria dispar, is an irruptive forest pest native to
 Eurasia where its range extends from coast to coast and overspills into
 northern Africa. Accidentally introduced from Europe in Massachusetts in
 1868–69, it is now established in North America where it is considered a
 highly destructive invasive pest. A fine-scale characterization of its
 population genetic structure would facilitate identification of source
 populations for specimens intercepted during ship inspections in North
 America and would enable mapping of introduction pathways to help prevent
 future incursions into novel environments. In addition, detailed knowledge
 of L. dispar’s global population structure would provide new insight into
 the adequacy of its current subspecies classification system and its
 phylogeographic history. To address these issues, we generated
 &gt;2,000 genotyping-by-sequencing-derived SNPs from 1,445
 contemporary specimens sampled at 65 locations in 25 countries/3
 continents. Using multiple analytical approaches, we identified eight
 subpopulations that could be further partitioned into 28 groups, achieving
 unprecedented resolution for this species’ population structure. Although
 reconciliation between these groupings and the three currently recognized
 subspecies proved to be challenging, our genetic data confirmed
 circumscription of the japonica subspecies to Japan. However, the genetic
 cline observed across continental Eurasia, from L. dispar asiatica in East
 Asia to L. d. dispar in Western Europe, points to the absence of a sharp
 geographical boundary (e.g., the Ural Mountains) between these two
 subspecies, as suggested earlier. Importantly, moths from North America
 and the Caucasus/Middle East displayed high enough genetic distances from
 other populations to warrant their consideration as separate subspecies of
 L. dispar. Finally, in contrast with earlier mtDNA-based investigations
 that identified the Caucasus as L. dispar’s place of origin, our analyses
 suggest continental East Asia as its evolutionary cradle, from where it
 spread to Central Asia and Europe, and to Japan through Korea.
description: <strong><em>Moth
 sampling</em></strong> The
 bulk of spongy moth specimens were collected during the summers of 2017
 and 2018, using milk-carton type pheromone-baited traps. Additional
 samples (whole moths or parts thereof) from regions not fully covered by
 our network of traps were provided by colleagues who had collected them in
 the context of independent studies; with the exception of a few samples,
 collection dates for these were recent (overall, 93% of the moths used
 were collected between 2013 and 2018, and most specimens were males [only
 0.8% of females]) <strong><em>DNA extraction and
 sequencing</em></strong>
 For DNA extraction, we sampled one antenna and three legs from each moth. These were frozen in liquid nitrogen and ground using
 a Retsch MM 200 mixer mill (Retsch technology, Haan, Germany). Then,
 DNA was extracted with the
 DNeasy 96 Blood & Tissue Kit (Qiagen, Carlsbad, CA, USA) following
 the manufacturer's instructions, with the exception of an additional
 RNase A treatment before the addition of buffer AL/ethanol (4 µL of 100
 mg/mL Rnase A; 5 min digestion at room temperature). DNA concentration and
 purity of the extracts were assessed using a NanoDrop 8000
 spectrophotometer (Thermo scientific, Waltham, MA, USA). Samples were
 diluted to 10 ng/μL prior to library construction. Libraries were prepared
 based on a genotyping-by-sequencing (GBS) protocol using the restriction
 enzymes PstI and MspI (Poland et al., 2012). Individuals were barcoded with unique
 sequences and pooled in multiplexes of 96 individuals per library.
 Moths from the same
 sampling site were randomized in the different libraries to reduce the
 chances of artifactual library effects being interpreted as a biological
 pattern. Library preparation and sequencing on Ion Torrent Proton P1v2
 chips were carried out at the Genomic Analysis Platform of Université
 Laval, Quebec City, Canada (for a detailed description of the
 method, see Abed et al. 2019).
 <strong><em>GBS
 data</em></strong> The data consists of 1445 sequence individuals
 from 65 populations and sampled in 25 different counrties, The files
 <em>Picq_EvolApp_SpongyMothBiosafe_Table_1_20221107.xlsx</em> 
 and <em>Picq_EvolApp_SpongyMothBiosafe_Figure_population_localisation_20221018.docx</em> give the details for each studied populations (localisation, effective etc.). Raw data 12 plates of 96 individuals; sequencing in 2018; sequencer ouput filename  <em>Cusson_p*_c01.fastq.txt.gz</em> 4 plates of 96 individuals; sequencing in 2019; sequencer ouput filename <em>Cusson_AGM_p*_c01.fastq.gz</em> 1 plate de 96 individuals but only 10 individusals considered in the present project (popultion from Georgia); sequencing in 2020; sequencer ouput filename <em>I.Giguere_BioSAFE_AGM_c01.fastq.gz</em> The file providing the barcodes is named <em>Picq_EvolApp_SpongyMothBiosafe_SampleBarcodes_20221221.xls</em>. Filtered data <em>Picq_EvoApp_SpongyMothBiosafe_datafiltered.vcf</em> For filtering details, please see section 2.4 in the article related to this dataset.
description: The different filtering procedures were carried out using
 VCFtools v0.1.16 (Danecek et al., 2011), and the resulting VCF file was
 converted to file formats suitable for each subsequent analysis using
 <em>PGDSpider</em> <em>v2.1.1.5</em> (Lischer
 & Excoffier, 2012). Danecek, P.,
 Auton, A., Abecasis, G., Albers, C.A., Banks, E., DePristo, M.A.,
 Handsaker, R.E., Lunter, G., Marth, G.T., Sherry, S.T., McVean, G.,
 Durbin, R., & 1000 Genomes Project Analysis Group. (2011). The
 variant call format and VCFtools. <em>Bioinformatics</em>,
 27(15), 2156‑2158. DOI: 10.1093/bioinformatics/btr330
 Lischer, H.E.L., & Excoffier, L. (2012). PGDSpider : An
 automated data conversion tool for connecting population genetics and
 genomics programs. <em>Bioinformatics</em>, 28(2), 298‑299.
 DOI: 10.1093/bioinformatics/btr642