Genome-scale phylogeography resolves the native population structure of the Asian longhorned beetle, Anoplophora glabripennis (Motschulsky)

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 712 individuals from 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.

Methods

The dataset was obtained from samples of Anoplophora Glabripennis across its native range in China and South Korea. DNA was extracted using the DNeasy 96 Blood &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.

The Fast-GBS pipeline v1.0 was adopted to process raw sequencing reads. 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 > 60% missing data were removed.

Finally, only loci with read depth > 5, minor allele frequency (MAF) > 0.05, minor allele count (MAC) > 3, and missing data per site < 10%.