Work

Evaluating imputation methods for determining North American honey bee (Apis mellifera) ancestry from low-pass whole-genome sequencing data

Year: 2026

Type: article

Abstract: Honey bee ( Apis mellifera ) movement is tightly regulated throughout North America to prevent disease spread and the introduction of unwanted subspecies, such as the ‘scutellatized’ bee (also known as “Africanized,” a mix of A. m. scutellata and managed European bees). In this study, we evaluated the effectiveness of low-coverage whole-genome sequencing (3X) with genotype imputation for ancestry estimation and phenotypic prediction in 289 honey bee samples from the USA and Caribbean. Imputation showed high accuracy (mean r 2 = 85%, median r 2 = 90%) and concordance (r > 95%) with full-depth sequencing, indicating this approach can reliably detect common genetic variation in North American populations. We tested this method’s utility in a key regulatory application: detecting scutellatized ancestry. Low-pass sequence data allowed both genome-wide ancestry estimation and mitochondrial haplotype reconstruction, the latter showing near-perfect agreement with a widely used PCR test. We found that mitochondrial haplotypes were poor predictors of genomic ancestry, and genomic ancestry a better predictor of colony phenotypes. This questions the reliability of mitochondrial-DNA-based detection methods alone in the face of complicated systems of hybridization. Our findings demonstrate that low-coverage sequencing with imputation is a powerful tool for enabling whole genome analyses in honey bees—including ancestry assignment and variant detection—despite a small loss in accuracy. It will likely find application in regulatory screening, design breeding schemes, and population studies.

Source: Apidologie

DOI: 10.1007/s13592-026-01311-2