RAD sequences - The worldwide invasion history of a pest ambrosia beetle inferred using population genomics

Xylosandrus crassiusculus, a fungus-farming wood borer native to Southeastern Asia, is the most rapidly spreading invasive ambrosia species worldwide. Previous studies focusing on its genetic structure suggested the existence of cryptic genetic variation in this species. Yet, these studies used different genetic markers, focused on different geographical areas, and did not include Europe.Our first goal was to determine the worldwide genetic structure of this species based on both mitochondrial and genomic markers. Our second goal was to study X. crassiusculus' invasion history on a global level and identify the origins of the invasion in Europe.We used a COI and RAD sequencing design to characterize 188 and 206 specimens worldwide, building the most comprehensive genetic dataset for any ambrosia beetle to date.To remove potential human DNA contaminations in the RAD data (which can occur during whole genome amplification), we aligned the remaining reads on the reference genome GRCh38.p13 of Homo sapiens (accession number: GCA_000001405.28) using the BWA-MEM algorithm (Li and Durbin 2009). We also removed the potential fungal contaminations using Ambrosiella xylebori's reference genome (accession number: ASM277803v1 (Vanderpool et al. 2018)), as it was the closest complete reference genome available to X. crassiusculus' symbiotic fungus.The sequences obtained are available here.