{
  "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 r2 = 85%, median r2 = 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.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": null,
  "arxiv": null,
  "author_total": 16,
  "authors": [
    {
      "name": "Dylan K. Ryals"
    },
    {
      "name": "Mulusew Fikere"
    },
    {
      "name": "Madeline H. Carpenter"
    },
    {
      "name": "J Krispn Given"
    },
    {
      "name": "James C. Fulton"
    },
    {
      "name": "Matthew R. Moore"
    },
    {
      "name": "Ethel M. Villalobos"
    },
    {
      "name": "Robyn Underwood"
    },
    {
      "name": "Myra Dickey"
    },
    {
      "name": "Andrew D. Sweet"
    },
    {
      "name": "Julie M. Allen"
    },
    {
      "name": "Juliana Rangel"
    },
    {
      "name": "Margarita M. López-Uribe"
    },
    {
      "name": "Luiz F. Brito"
    },
    {
      "name": "Andrew H. Paterson"
    },
    {
      "name": "Brock A. Harpur"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/dtvzy0d6vsa12.bib",
  "cited_by": 0,
  "doi": "10.1007/s13592-026-01311-2",
  "fulltext_url": null,
  "id": "dtvzy0d6vsa12",
  "issns": [
    "0044-8435",
    "1297-9678"
  ],
  "landing_url": "https://hal.science/hal-05793438v1",
  "language": "en",
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "hal",
      "0.sdv"
    ],
    [
      "openalex",
      "1311|Genetic and phenotypic traits in livestock"
    ]
  ],
  "openalex": "W7220465290",
  "pdf_url": "https://hal.science/hal-05793438/document",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-12",
  "publisher": "Springer Verlag",
  "ris": "https://research.draconitic.com/paper/dtvzy0d6vsa12.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:54Z",
      "native_id": "hal-05793438",
      "source": "hal",
      "url": "https://hal.science/hal-05793438v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "openalex:1311|Genetic and phenotypic traits in livestock",
      "subfield": "genetics-genomics"
    }
  ],
  "title": "Evaluating imputation methods for determining North American honey bee (Apis mellifera) ancestry from low-pass whole-genome sequencing data",
  "title_text": "Evaluating imputation methods for determining North American honey bee (Apis mellifera) ancestry from low-pass whole-genome sequencing data",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:17:54Z",
  "url": "https://research.draconitic.com/paper/dtvzy0d6vsa12",
  "venue": "Apidologie",
  "versions": []
}