Public DNA archives reveal pervasive cryptic structure and taxonomic confusion in bark and ambrosia beetles (Curculionidae: Platypodinae and Scolytinae)

Public DNA archives support large-scale biodiversity assessment, yet are constrained by taxonomic misidentifications and unrecognized cryptic structure. The challenge is especially acute in hyperdiverse, economically important groups like bark and ambrosia beetles, where morphological conservatism can conceal deep genetic divergence. We applied an investigative data-mining framework to full publicly available GenBank COI sequences for this clade at the time of download, initially retrieving 8,899 sequences from more than 1,000 species. After quality filtering and replication criteria, 3,650 sequences representing 75 species were retained for analysis. Under assemble species by automatic partitioning (ASAP), all 75 species − 100% - contained multiple barcode partitions. However, divergence depth and pattern varied widely. Under a conservative criterion of p-distance, 26 species were flagged as candidate species complexes, and all the remaining ones exhibited continuous structure or fine-scale partitioning of shallow divergences between populations. Concordance delimitation indicated that these patterns are not method artefacts. While cryptic divergence is ubiquitous among scolytines, it has arisen via at least four evolutionary mechanisms, which we demonstrate using case studies. Deeply divergent geographical COI lineages suggesting cryptic complexes are demonstrated with Xyleborus ferrugineus (Fabricius). By contrast, shallow population structure rather than distinct lineages is shown with Tomicus piniperda (Linnaeus) which exhibited high haplotype diversity but minimal inter-MOTU divergence. A taxonomic name–sequence mismatch is exemplified with Ambrosiodmus rubricollis (Eichhoff) which comprised several deeply divergent Asian COI lineages, one of which has spread across Europe and North America. Lastly, a sharp split between European and North American lineages whose taxonomy remains unresolved is shown with Dryocoetes autographus (Ratzeburg). Our findings show that critically analyzed public barcodes can flag cryptic complexes (not formal species delimitation) from shallow structure and clarify the identities of globally significant invasive species. This approach – starting with all available sequences rather than hand-picked groups – provides a scalable framework to use large, uncurated genetic repositories and highlights the need for integrative taxonomy.