The genomic basis of evolutionary differentiation among honey bees

Bertrand Fouks, Philipp Brand, Hung N. Nguyen, Jacob Herman, Francisco Camara, Daniel Ence, Darren E. Hagen, Katharina J. Hoff, Stefanie Nachweide, Lars Romoth, Kimberly K.O. Walden, Roderic Guigo, Mario Stanke, Giuseppe Narzisi, Mark Yandell, Hugh M. Robertson, Nikolaus Koeniger, Panuwan Chantawannakul, Michael C. Schatz, Kim C. WorleyGene E. Robinson, Christine G. Elsik, Olav Rueppell

Research output: Contribution to journalArticlepeer-review


In contrast to the western honey bee, Apis mellifera, other honey bee species have been largely neglected despite their importance and diversity. The genetic basis of the evolutionary diversification of honey bees remains largely unknown. Here, we provide a genome-wide comparison of three honey bee species, each representing one of the three subgenera of honey bees, namely the dwarf (Apis florea), giant (A. dorsata), and cavity-nesting (A. mellifera) honey bees with bumblebees as an outgroup. Our analyses resolve the phylogeny of honey bees with the dwarf honey bees diverging first. We find that evolution of increased eusocial complexity in Apis proceeds via increases in the complexity of gene regulation, which is in agreement with previous studies. However, this process seems to be related to pathways other than transcriptional control. Positive selection patterns across Apis reveal a trade-off between maintaining genome stability and generating genetic diversity, with a rapidly evolving piRNA pathway leading to genomes depleted of transposable elements, and a rapidly evolving DNA repair pathway associated with high recombination rates in all Apis species. Diversification within Apis is accompanied by positive selection in several genes whose putative functions present candidate mechanisms for lineage-specific adaptations, such as migration, immunity, and nesting behavior.

Original languageEnglish (US)
Pages (from-to)1203-1215
Number of pages13
JournalGenome Research
Issue number7
StatePublished - Jul 2021

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)


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