Gene flow in admixed populations and implications for the conservation of the Western honeybee, Apis mellifera

Anthropogenic activity, especially modern apiculture, has considerable impact on the natural distribution of the Western honeybee, Apismellifera, leading to the spread, replacement and fragmentation of many subspecies. This creates demand for the conservation of some subspecies, in particular, Apismelliferamellifera, which once was widely distributed in Western Europe and nowadays is endangered through habitat loss and fragmentation. Moreover, A.m.mellifera may be further endangered by hybridisation in populations that now occur in artificial sympatry with other subspecies. Here, we quantify and compare individual hybridisation between sympatric and allopatric honeybee populations of A.m.mellifera and A.m.carnica using microsatellite markers and a Bayesian model-based approach. We had a special focus on pure breeding populations, which are a major tool in honeybee conservation. Our results demonstrate that subspecies are still highly differentiated, but gene flow is not prevented by the current management strategies, creating urgent demand for an improved conservation management of A.m.mellifera. However, the occurrence of a high number of pure individuals might suggest that some sort of hybrid barrier acts against the complete admixture of the two subspecie

Empirical comparison of microsatellite and SNP markers to estimate introgression in Apis mellifera mellifera

The genetic identity of the dark European honey bee, Apis mellifera mellifera is currently under pressure throughout most of its native range due to large scale commercial trade and replacement with honey bees of mainly Eastern European ancestry (C-lineage: Apis mellifera carnica and Apis mellifera ligustica). To counteract this process, numerous conservation efforts for the protection of native honey bees are sprouting across Europe. For the management of such protected areas and conservation breeding purposes, honey bee subspecies have been routinely identified through wing morphology and through DNA-hybrid tests using microsatellite markers. Currently, new methods are evolving including rapid innovations in single-nucleotide polymorphism (SNP) array technology and high-throughput sequencing. Here, we aim to quantify potential marker-specific biases of hybrid tests and give recommendations for applications in honey bee conservation management. Using an empirical dataset, we first assessed the accuracy of a recently developed reduced SNP panel to estimate C-lineage introgression in A. m. mellifera compared to whole-genome sequence (WGS) data. Using another independent data set, we estimated the differences in admixture proportions between the currently applied hybrid test based on microsatellites and the novel SNP test. We demonstrate that the SNP-based test which contains highly ancestry-informative markers is very efficient to estimate genome-wide ancestry. Furthermore, we report discrepancies between microsatellite and SNP-based admixture proportions. For conservation management, we, therefore, recommend the implementation of SNP-based hybrid tests to maintain high genetic variation within the breeding population, while minimizing influence of introduced honey bees.This work was supported by the Swiss Federal Office for Agriculture FOAG, the Fondation Sur-la-Croix, Basel, and by the 2013–2014 BiodivERsA/FACCE-JPI joint call for research proposals, with the national funders “Fundac¸ão para a Ciência e Tecnologia” (Portugal), “Agence Nationale de la Recherche” (France), and “Ministerio de Economía y Competividad” (Spain).info:eu-repo/semantics/publishedVersio

Genetic integrity of the Dark European honey bee (Apis mellifera mellifera) from protected populations: a genome-wide assessment using SNPs and mtDNA sequence data

The recognition that the Dark European honey bee, Apis mellifera mellifera, is increasingly threatened in its native range has led to the establishment of conservation programmes and protected areas throughout western Europe. Previous molecular surveys showed that, despite management strategies to preserve the genetic integrity of A. m. mellifera, protected populations had a measurable component of their gene pool derived from commercial C-lineage honey bees. Here we used both sequence data from the tRNAleu-cox2 intergenic mtDNA region and a genome-wide scan, with over 1183 single nucleotide polymorphisms (SNPs), to assess genetic diversity and introgression levels in several protected populations of A. m. mellifera, which were then compared with samples collected from unprotected populations. MtDNA analysis of the protected populations revealed a single colony bearing a foreign haplotype, whereas SNPs showed varying levels of introgression ranging from virtually zero in Norway to about 14% in Denmark. Introgression overall was higher in unprotected (30%) than in protected populations (8%), and is reflected in larger SNP diversity levels of the former, although opposite diversity levels were observed for mtDNA. These results suggest that, despite controlled breeding, some protected populations still require adjustments to the management strategies to further purge foreign alleles, which can be identified by SNPs.Pint

Investigation of free-living honey bee colonies in Ireland

Apis mellifera mellifera (Linnaeus), the Western European honey bee, is considered extinct in the wild over most of its range due largely to hybridisation and replacement by other subspecies, parasitism by Varroa destructor, habitat loss, and effects from agricultural pesticides. The purity of the subspecies within the managed cohort is also at risk over much of its range. Here, we investigated if honey bee colonies inhabited locations outside of the apiaries. In those we located, we explored how long the colony persisted and we investigated the genotypes of the bees using multiple markers. We show here that unmanaged free-living honey bee colonies are present and widespread in Ireland, inhabiting a mixture of nesting habitats with some colonies persisting naturally and unaided over multiple years. Molecular data including mitochondrial, microsatellite, and SNPs evidence indicate that the free-living population sampled is largely comprised of pure A. m. mellifera. Finally, we discuss the implications of conserving free-living A. m. mellifera in Ireland and its possible role in improving the fitness of the managed population both in Ireland and the rest of its European range.We particularly thank the custodians of the free-living honey bee colonies and the Native Irish Honey Bee Society (NIHBS) for their assistance. KAB is a recipient of an Irish Research Council postgraduate fellowship (GOIPG/2015/2767) and a Tony Ryan Postgraduate fellowship. Additional funding was gratefully received from the Department of Agriculture, Food and the Marine [grant number GRGAS 16/GR/09], the Federation of Irish Beekeeping Associations, the Eva Crane Trust [grant number ECTA20160303] and The Native Irish Honey Bee Society. Financial support for DH was provided through the program COMPETE 2020 – POCI (Programa Operacional para a Competividade e Internacionalizac¸~ao) and by Portuguese funds through FCT (Fundac¸~ao para a Ci^encia e a Tecnologia) in the framework of the project BeeHappy (POCI-01-0145-FEDER-029871).info:eu-repo/semantics/publishedVersio