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Related Experiment Video

Updated: Jun 27, 2026

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When One's Not Enough: Colony Pool-Seq Outperforms Individual-Based Methods for Assessing Introgression in Apis

Victoria G Buswell1,2, Jonathan S Ellis1, J Vanessa Huml1

  • 1School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK.

Insects
|May 26, 2023
PubMed
Summary

Estimating honey bee introgression is complex. This study compared genetic methods, finding that individual bee sampling can underestimate colony-level introgression, especially when using certain statistical models.

Keywords:
ABBA BABAADMIXTUREApis melliferaRAD-seqSNP arraycolonyintrogressionpool-seq

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Area of Science:

  • Population Genetics
  • Evolutionary Biology
  • Apiculture

Background:

  • Human activities have led to the introduction of honey bee (Apis mellifera) subspecies outside their native ranges.
  • The introgression of European dark bees (Apis mellifera mellifera) by C lineage honey bees impacts adaptive potential and long-term viability.
  • Accurately estimating introgression in haplodiploid, colony-living insects like honey bees presents significant challenges.

Purpose of the Study:

  • To compare the accuracy of different genetic and statistical approaches for estimating honey bee introgression.
  • To evaluate the impact of sampling strategy (individual vs. pooled) on introgression estimates.
  • To identify reliable methods for assessing honey bee subspecies introgression.

Main Methods:

  • Comparison of three genetic methods: SNP array, individual RAD-seq, and pooled colony RAD-seq.
  • Evaluation of two statistical approaches: ADMIXTURE (maximum likelihood clustering) and ABBA BABA (incomplete lineage sorting model).
  • Analysis of introgression estimates derived from individual workers, individual drones, and pooled colony samples.

Main Results:

  • Individual sampling approaches generally yielded lower introgression estimates than pooled colony samples when using the ADMIXTURE program.
  • The pooled colony ABBA BABA method produced lower introgression estimates compared to all ADMIXTURE-based estimates.
  • Results indicate that single individuals may not sufficiently represent colony-level introgression.

Conclusions:

  • Estimating honey bee introgression requires careful consideration of both genetic and statistical methodologies.
  • Pooled colony sampling can provide different introgression estimates than individual sampling, necessitating method validation.
  • Future studies using pooled colony data should not rely solely on clustering programs like ADMIXTURE for introgression assessments.