Introduction
The Western honey bee (Apis mellifera , hereafter honey
bee), is a key pollinator of agricultural crops (Klein et al.,
2007). To date, more than 27 subpopulations have been reported globally,
which can be grouped into four distinct lineages, namely M (Western and
Northern Europe), C (Eastern Europe), O (Near East and Central Asia) and
A (Africa) (Cridland, Tsutsui, & Ramírez, 2017; Friedrich Ruttner,
1988). These lineages are characterized by differences in morphology,
physiology and behaviour (Friedrich Ruttner, 1988). Within their native
range, honey bees are commonly kept in hives for honey production and
pollination purposes. In Europe, several selection programmes have been
initiated to increase the productivity of honey bees (Adam, 1983;
Büchler, Berg, & Le Conte, 2010; Chauzat et al., 2013; Guichard et al.,
2020; H. Ruttner, 1972; Uzunov, Brascamp, & Büchler, 2017), while in
Africa the majority of honey bees essentially evolved under natural
selection (Dietemann, Pirk, & Crewe, 2009).
In some countries, honey bees are considered as a domesticated livestock
species (Geldmann & González-Varo, 2018), due to the strong impact of
human-mediated selection. In the beginning of the 19thcentury, importation of foreign honey bees among European regions began
to increase, which profoundly reshaped the genetic structure of this
species (Parejo, Wragg, Henriques, Charrière, & Estonba, 2020).
Historically, native honey bees of Europe mainly belong to M and C
evolutionary lineages. They are locally adapted to different climatic
and geographical regions, resulting in several subspecies (Momeni et
al., 2021; Friedrich Ruttner, 1988). Nevertheless, beekeepers in
Northern Europe continue to replace native honey bees (A. m.
mellifera ) with South-European honey bees (e.g. A. m. carnicaand A. m. ligustica ), as these subspecies are known to be more
productive, gentle and calm (Bouga et al., 2011; Guichard et al., 2021).
This practice has led to multiple admixture events between subspecies
and the extinction of locally adapted honey bees (Bieńkowska, Splitt,
Węgrzynowicz, & Maciorowski, 2021; F Ruttner, 1995). Furthermore,
native honey bees are threatened by the widespread use of stabilised
hybrid strains such as Buckfast (Adam, 1983; Bieńkowska et al., 2021).
The relocation of subspecies accompanied by admixture is a major risk
factor of losing local adaptation and genetic diversity of honey bees
(De la Rúa, Jaffé, Dall’Olio, Muñoz, & Serrano, 2009). Therefore,
several conservation programmes have been initiated to maintain the
genetic diversity of native honey bees. In Switzerland, the first
conservation area for A. m. mellifera was established in 1977 in
canton Glarus (Soland-Reckeweg, Heckel, Neumann, Fluri, & Excoffier,
2009 ). Nowadays, an additional conservation area exists in canton
Obwalden. The two conservatories encompass a total area of 830
km2 and ~1050 colonies (Parejo et al.,
2016). To limit admixture events with other foreign subspecies (e.g.A. m. carnica and Buckfast) these areas are typically located in
remote alpine valleys. Besides the maintenance of the conservation
areas, the breeding association of A. m. mellifera (mellifera.ch)
established a selection programme including several mating stations.
These stations are also located at geographically isolated areas and
consist of 10 up to 20 selected drone-producing colonies. Currently, an
ancestry-informative (microsatellites or single nucleotide
polymorphisms; SNPs) marker panel is applied to determine the admixture
level of conserved and selected A. m. mellifera colonies, and
highly admixed colonies (>10%) are replaced with purebredA. m. mellifera (Parejo, Henriques, Pinto, Soland-Reckeweg, &
Neuditschko, 2018). However, the replacement of admixed queens is
expected to lead to an increase in inbreeding that could be detrimental
to the small conserved A. m. mellifera population. Given that the
survival of honey bees is strongly dependent on the genetic diversity
(Jones, Myerscough, Graham, & Oldroyd, 2004; Kryger, 1990; Mattila,
Rios, Walker-Sperling, Roeselers, & Newton, 2012; Mattila & Seeley,
2014; Oldroyd, Rinderer, Harbo, & Buco, 1992), monitoring of inbreeding
in small conserved populations, such as A. m. mellifera in
Switzerland, is crucial.
Inbreeding level indicates the probability that an animal receives the
same allele from both parents. Genetic marker information allows to
determine that alleles are identical-by-descent (IBD), while
pedigree-based estimations require prior knowledge of individual
ancestry (Kardos, Luikart, & Allendorf, 2015), which in case of the
honey bee is often not available. Runs of homozygosity (ROH), IBD
transmitted haplotypes, are one of the tools to estimate inbreeding
levels without ancestry information (McQuillan et al., 2008). In fact,
the length of ROH segments can be used to ascertain historical changes
in population size and structure including admixture (few and short ROH
segments), current inbreeding (multiple and long ROH segments) and a
recent bottleneck (multiple and short ROH segments); see Ceballos (2018)
for a complete review. Furthermore, it is possible to derive the genomic
inbreeding coefficient (FROH) for an animal by dividing
the sum of all homozygous segments (SROH) by the length
of the analysed genome (McQuillan et al., 2008). Numerous studies have
demonstrated that overlapping ROH segments, so-called homozygosity
islands, can be successfully used to identify selection signatures in
cattle (Purfield, Berry, McParland, & Bradley, 2012; Zhang,
Guldbrandtsen, Bosse, Lund, & Sahana, 2015), sheep (Mastrangelo et al.,
2017; Purfield, McParland, Wall, & Berry, 2017; Signer‐Hasler, Burren,
Ammann, Drögemüller, & Flury, 2019), and horses (Druml et al., 2018;
Grilz-Seger, Druml, et al., 2019; Grilz-Seger et al., 2018; Metzger et
al., 2015), as well as in cultivated plants such as avocados (Rubinstein
et al., 2019), almonds (Pavan et al., 2021) and pears (Kumar et al.,
2020).
In this study we investigated the utility of colony genotypes derived
from pooled workers to identify ROH segments in honey bees. Furthermore,
we integrated individual admixture and FROH in a
high-resolution population structure analysis to enhance the genetic
monitoring of conserved A. m. mellifera. Finally, we screened the
genome for homozygosity islands to detect selection signatures betweenA. m. mellifera and A. m. carnica honey bee colonies,
related to geographic adaptations and human mediated selection.