Abstract
BackgroundWith numerous endemic subspecies representing four of its five evolutionary lineages, Europe holds a large fraction of Apis mellifera genetic diversity. This diversity and the natural distribution range have been altered by anthropogenic factors. The conservation of this natural heritage relies on the availability of accurate tools for subspecies diagnosis. Based on pool-sequence data from 2145 worker bees representing 22 populations sampled across Europe, we employed two highly discriminative approaches (PCA and FST) to select the most informative SNPs for ancestry inference.ResultsUsing a supervised machine learning (ML) approach and a set of 3896 genotyped individuals, we could show that the 4094 selected single nucleotide polymorphisms (SNPs) provide an accurate prediction of ancestry inference in European honey bees. The best ML model was Linear Support Vector Classifier (Linear SVC) which correctly assigned most individuals to one of the 14 subspecies or different genetic origins with a mean accuracy of 96.2% ± 0.8 SD. A total of 3.8% of test individuals were misclassified, most probably due to limited differentiation between the subspecies caused by close geographical proximity, or human interference of genetic integrity of reference subspecies, or a combination thereof.ConclusionsThe diagnostic tool presented here will contribute to a sustainable conservation and support breeding activities in order to preserve the genetic heritage of European honey bees.
Highlights
With numerous endemic subspecies representing four of its five evolutionary lineages, Europe holds a large fraction of Apis mellifera genetic diversity
The diagnostic tool presented here will contribute to a sustainable conservation and support breeding activities in order to preserve the genetic heritage of European honey bees
Selected Singlenucleotide polymorphism (SNP) While main evolutionary lineages were differentiated with only few SNPs (Figure S1A), it was more challenging to differentiate closely related subspecies with a reduced number of genetic markers
Summary
With numerous endemic subspecies representing four of its five evolutionary lineages, Europe holds a large fraction of Apis mellifera genetic diversity This diversity and the natural distribution range have been altered by anthropogenic factors. Europe holds a large fraction of this honey bee diversity with numerous endemic subspecies representing four evolutionary lineages, namely the African lineage (A), Central and Eastern European lineage (C), Western and Northern European lineage (M), and Near East and Central Asian lineage (O) [7, 8] This diversity and the natural distribution range of European honey bees have been influenced by anthropogenic factors to an extent that several locally adapted populations are at risk due to introgression and crossbreeding [9,10,11]. To conserve the honey bees’ natural heritage and thereby its adaptive potential to future global change, there is a need to promote the sustainable breeding of certified local subspecies
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