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Runs of homozygosity derived from pool-seq data reveal fine-scale population structures in Western honey bees (Apis mellifera)
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  • Annik Gmel,
  • Matthieu Guichard,
  • Benjamin Dainat,
  • Geoffrey Williams ,
  • Sonia Eynard,
  • Alain Vignal,
  • bertrans servin,
  • Beestrong Consortium,
  • Markus Neuditschko
Annik Gmel
Agroscope Location Posieux

Corresponding Author:annik.gmel@agroscope.admin.ch

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Matthieu Guichard
Agroscope Location Posieux
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Benjamin Dainat
Agroscope Liebefeld Location
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Geoffrey Williams
Auburn University Department of Entomology and Plant Pathology
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Sonia Eynard
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Alain Vignal
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bertrans servin
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Beestrong Consortium
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Markus Neuditschko
Agroscope Location Posieux
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Runs of homozygosity (ROH) are continuous homozygous segments that arise through the transmission of haplotypes that are identical by descent (IBD). The length and distribution of ROH segments provide insight into the genetic diversity of populations and are useful to detect selection signatures. Here, we analysed pooled whole-genome sequencing data from 265 Western honey bee colonies from the two subspecies Apis mellifera mellifera and Apis mellifera carnica. Integrating individual ROH patterns and admixture levels in a high-resolution population network visualization allowed us to ascertain major differences between the two subspecies. Within A. m. mellifera, we identified well-defined substructures according to the genetic origin of the colonies and a fair amount of admixed colonies, despite the current applied conservation efforts. In contrast, A. m. carnica colonies were more inbred and could not be differentiated according to the geographical origin. We identified 29 coding genes in overlapping ROH segments within the two subspecies. Genes embedded in A. m. carnica specific homozygosity islands suggested a strong selection for production and behavioural traits, whilst the identified cuticula protein-coding genes (CPR3 and CPR4) were associated with their breed-specific stripe pattern. Local adaption of the two subspecies could be confirmed by the identification of two genes involved in the response to ultraviolet (UV) light. We demonstrated that colony genotypes derived from pooled honey bee workers are reliable to unravel the population dynamics in A. mellifera and provide fundamental information to conserve native honey bees.
28 Sep 2021Submitted to Ecology and Evolution
29 Sep 2021Submission Checks Completed
29 Sep 2021Assigned to Editor
07 Oct 2021Reviewer(s) Assigned
28 Oct 2021Review(s) Completed, Editorial Evaluation Pending
05 Nov 2021Editorial Decision: Revise Minor
27 Oct 20221st Revision Received
31 Oct 2022Assigned to Editor
31 Oct 2022Submission Checks Completed
31 Oct 2022Review(s) Completed, Editorial Evaluation Pending
01 Nov 2022Reviewer(s) Assigned
01 Dec 2022Editorial Decision: Revise Minor
15 Dec 20222nd Revision Received
15 Dec 2022Assigned to Editor
15 Dec 2022Submission Checks Completed
15 Dec 2022Review(s) Completed, Editorial Evaluation Pending
19 Dec 2022Editorial Decision: Accept