Using Whole-Genome Sequence Information to Foster Conservation Efforts for the European Dark Honey Bee, Apis mellifera mellifera

Abstract

Pollination is a key ecosystem service for agricultural systems and Western honey bees, Apis mellifera, are the most important managed pollinators. Major losses of managed honey bee colonies reinforced the need to take advantage of locally adapted subspecies and ecotypes to buffer populations against various stressors. However, introductions of non-native honey bees from distant lineages are likely to undermine respective conservation efforts unless reliable and cost effective tools can be used to identify hybridization. The purpose of this study is to characterize current population structure and genetic diversity, and to assess the degree of admixture between native and introduced honey bees. Moreover, we aim to select a reduced number of genetic markers to improve conservation management strategies. We take advantage of recent developments in next-generation sequencing and network-based clustering to investigate conservation efforts for the native European Dark honey bee, A. m. mellifera, which is threatened by introgression in most of its range. We collected whole-genome sequence information from haploid drones of A. m. mellifera, A. m. carnica, and Buckfast sampled throughout Switzerland (N = 81), as well as from four Swiss A. m. mellifera conservation areas (N = 39) and from one conservatory in the French Alps (N = 31). Population structure analyses based upon 3.375 M genome-wide SNPs discerned samples by subspecies and geographic origin (Switzerland or France). Ancestry inference indicated admixed individuals in all of the protected areas, calling for improved management efforts. After testing different subsets of ancestry informative SNPs using three different selection strategies (F ST , PCA-based or at random), as few as 50 SNPs are found to be sufficient to differentiate native from introduced honey bees. Therefore, our data suggests that a low-density SNP panel can be a precise and cost-effective tool to support conservation management efforts for managed pollinators.

Developing reduced SNP assays from whole‐genome sequence data to estimate introgression in an organism with complex genetic patterns, the Iberian honeybee (Apis mellifera iberiensis)

“…Developing cost‐effective molecular tools for accurate estimation of introgression in A. mellifera is increasingly important as commercial strains (mostly of C‐lineage ancestry) are threatening native genetic diversity in many regions throughout Europe (Bertrand et al., 2015; De la Rúa et al., 2009; Jensen et al., 2005; Parejo et al., 2016; Pinto et al., 2014; Soland‐Reckeweg et al., 2009). In the postgenomics era, rapid innovations in high‐throughput sequencing technologies make it possible to construct extensive whole‐genome data sets, especially in model organisms with small genomes like the honeybee (Weinstock et al., 2006).…”

“…The whole‐genome sequences used in this study were obtained from 176 pure haploid males, representing 117 A. m. iberiensis , 28 A. m. carnica and 31 A. m. ligustica (DH and MAP, unpublished data; Parejo et al., 2016) sampled across a wide geographical range (Figure 1). All samples were sequenced on an Illumina HiSeq 2500 with an aimed sequencing depth of 10× per individual.…”

“…To foster and monitor such conservation efforts, reliable, cost‐ and time‐effective tools are needed to accurately assess admixture levels between introduced and native honeybees. For the endangered A. m. mellifera , reduced assays of highly informative SNPs have already been developed to estimate C‐lineage introgression (Muñoz et al., 2015; Parejo et al., 2016). However, equivalent tools for application in conservation and breeding efforts are still required for its sister subspecies, A. m. iberiensis .…”

“…A diverse array of molecular tools has been employed to monitor C‐lineage introgression including PCR‐RFLP of the intergenic tRNA leu ‐cox2 mtDNA region (Bertrand et al., 2015), microsatellites (Jensen et al., 2005; Soland‐Reckeweg et al., 2009) and, more recently, SNPs (Parejo et al., 2016; Pinto et al., 2014). Among these, SNPs are becoming the tool of choice for many applications because they are easily transferred between laboratories, have low genotyping error, provide high‐quality data, are suitable for automation in high‐throughput technologies (Vignal, Milan, SanCristobal, & Eggen, 2002), and are more powerful for estimating introgression in honeybees (Muñoz et al., 2017).…”

Whole‐genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations

“…Parejo et al, () used huWGR data of 151 haploid drones to assess the degree of admixture between native European dark honey bee ( Apis mellifera mellifera ) and two introduced honey bee subspecies ( A. m. carnica and buckfast) in four conservation areas of A. millifera millifera in Switzerland and one in France. They found genetic differentiation between subspecies that coincided with geography and admixed individuals in protected areas.…”