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Comparing modern identification methods for wild bees: Metabarcoding and image-based morphological taxonomic assignment

April 2, 2024

With the decline of bee populations worldwide, studies determining current wild bee distributions and diversity are increasingly important. Wild bee identification is often completed by experienced taxonomists or by genetic analysis. The current study was designed to compare two methods of identification including: (1) morphological identification by experienced taxonomists using images of field-collected wild bees and (2) genetic analysis of composite bee legs (multiple taxa) using metabarcoding. Bees were collected from conservation grasslands in eastern Iowa in summer 2019 and identified to the lowest taxonomic unit using both methods. Sanger sequencing of individual wild bee legs was used as a positive control for metabarcoding. Morphological identification of bees using images resulted in 36 unique taxa among 22 genera, and >80% of Bombus specimens were identified to species. Metabarcoding was limited to genus-level assignments among 18 genera but resolved some morphologically similar genera. Metabarcoding did not consistently detect all genera in the composite samples, including kleptoparasitic bees. Sanger sequencing showed similar presence or absence detection results as metabarcoding but provided species-level identifications for cryptic species (i.e., Lasioglossum). Genus-specific detections were more frequent with morphological identification than metabarcoding, but certain genera such as Ceratina and Halictus were identified equally well with metabarcoding and morphology. Genera with proportionately less tissue in a composite sample were less likely to be detected using metabarcoding. Image-based methods were limited by image quality and visible morphological features, while genetic methods were limited by databases, primers, and amplification at target loci. This study shows how an image-based identification method compares with genetic techniques, and how in combination, the methods provide valuable genus- and species-level information for wild bees while preserving tissue for other analyses. These methods could be improved and transferred to a field setting to advance our understanding of wild bee distributions and to expedite conservation research.

Publication Year 2024
Title Comparing modern identification methods for wild bees: Metabarcoding and image-based morphological taxonomic assignment
DOI 10.1371/journal.pone.0301474
Authors Cassandra Smith, Robert S. Cornman, Jennifer A. Fike, Johanna M. Kraus, Sara J. Oyler-McCance, Carrie E Givens, Michelle Hladik, Mark W. Vandever, Dana W. Kolpin, Kelly Smalling
Publication Type Article
Publication Subtype Journal Article
Series Title PLoS ONE
Index ID 70252698
Record Source USGS Publications Warehouse
USGS Organization California Water Science Center; Fort Collins Science Center; Iowa Water Science Center; New Jersey Water Science Center; Oregon Water Science Center; Upper Midwest Water Science Center