DOI: 10.5683/sp3/jsfbfn
title: Genome-scale phylogeography resolves the native population structure of the Asian longhorned beetle, Anoplophora glabripennis (Motschulsky)

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;&lt;span lang="EN-US"&gt;Human assisted movement has allowed the Asian longhorned beetle (ALB, &lt;em&gt;Anoplophora glabripennis&lt;/em&gt; (Motschulsky)) to spread beyond its native range and become a globally regulated invasive pest. Within its native range of China and the Korean peninsula, human-mediated dispersal has also caused cryptic translocation of insects, resulting in population structure complexity. Previous studies used genetic methods to detangle this complexity but were unable to clearly delimit native populations which is needed to develop downstream biosurveillance tools. We used genome-wide markers to define historical population structure in native ALB populations and contemporary movement between regions. We used genotyping-by-sequencing to generate 6,102 single nucleotide polymorphisms (SNPs) and amplicon sequencing to genotype 53 microsatellites. In total, we genotyped&lt;/span&gt; &lt;span lang="EN-US"&gt;712 individuals from&lt;/span&gt; &lt;span lang="EN-US"&gt;ALB’s native distribution. We observed six distinct population clusters among native ALB populations, with a clear delineation between northern and southern groups. Most of the individuals from South Korea were distinct from populations in China. Our results also indicate historical divergence among populations and suggest limited large-scale admixture, but we did identify a restricted number of cases of contemporary movement between regions. We identified SNPs under selection and describe a clinal allele frequency pattern in a missense variant associated with glycerol kinase, an important enzyme in the utilization of an insect cryoprotectant. We further demonstrate that small numbers of SNPs can assign individuals to geographic regions with high probability, paving the way for novel ALB biosurveillance tools.&lt;/span&gt;&lt;/p&gt;
description: &lt;b&gt;Methods&lt;/b&gt;&lt;br /&gt;&lt;p&gt;&lt;span lang="EN-US"&gt;The dataset was obtained from &lt;/span&gt;samples of &lt;span lang="EN-US"&gt;Anoplophora Glabripennis&lt;/span&gt;&lt;span lang="EN-US"&gt; across its native range in China and South Korea. &lt;/span&gt;DNA was extracted using the DNeasy 96 Blood &amp;Tissue Kit (Qiagen) following the manufacturer's instructions. GBS libraries were prepared and sequenced at the Institut de Biologie Intégrative et des Systèmes (IBIS; Université Laval, Quebec City, Canada) with the Ion Proton sequencer. &lt;span lang="EN-US"&gt;The Fast-GBS pipeline v1&lt;/span&gt;.0 &lt;span lang="EN-US"&gt;was adopted to process raw sequencing reads&lt;/span&gt;&lt;span lang="EN-US"&gt;. &lt;/span&gt;Basic filters were applied to retain only biallelic SNPs, remove indels and variants with a FILTER flag other than PASS, and remove loci with more than 50% missing data. Samples with &gt; 60% missing data were removed. Finally, only loci with read depth &gt; 5, minor allele frequency (MAF) &gt; 0.05, minor allele count (MAC) &gt; 3, and missing data per site &lt; 10%.&lt;/p&gt;
description: <b>Dryad version number:</b> 5
<b>Version status:</b> submitted
<b>Dryad curation status:</b> Published
<b>Sharing link:</b> https://datadryad.org/stash/share/8SrWzGjS5qMAb3A5RjSD_iKhZIcRj5dSHKLYv5I-omU
<b>Storage size:</b> 75243442
<b>Visibility:</b> public