Admixture increases diversity in managed honey bees: reply to De la Rúa et al. (2013)

Genetics of tolerance in honeybees to the neonicotinoid clothianidin

The effects of neonicotinoid insecticides (NNIs) on honeybee health are intensely debated, with numerous studies showing negative effects of exposure, while others report no such effects. We carried out experiments to study the genetic and molecular basis of NNI tolerance in honeybees, which may underlie the discrepancies observed in the literature. We discovered that worker survival post-exposure to an acute oral dose of clothianidin is heritable (H ² = 37.8%). Tolerance to clothianidin was not associated with differences in the expression of detoxification enzymes in our experiments. Instead, mutations in the primary neonicotinoid detoxification genes CYP9Q1 and CYP9Q3 were strongly associated with worker survival post-clothianidin exposure. In some instances, the strong association between CYP9Q haplotypes and worker survival was associated with the protein's predicted binding affinity for clothianidin. Our findings have implications regarding future toxicological studies utilizing honeybees as a model pollinator.

Meta-analysis of genetic diversity and intercolony relatedness among reproductives in commercial honey bee populations

Honey bee colonies are large kin groups, each with a single mother queen and thousands of female workers. Queen bees are highly polyandrous, each mating with an average of approximately 12 drones from other colonies. We used a meta-analysis approach to compare the pedigree relationships of honey bee reproductives (queens and their mates) across five different studies and to quantify the overall genetic diversity of breeding populations. We compared the inferred genotypes of queens and their mates from microsatellite analyses of worker offspring from a feral Africanized honey bee population (which served as a negative control for inbreeding), an experimentally derived population of sister queens (which served as a positive control for inbreeding), and three separate commercially managed populations. We then compared the relatedness of all drones mated to each queen (mate-mate), all queens within each population (queen-queen), each queen with each of her mates (queen-mate), and all drones within each population (drone-drone). We found, as expected, the lowest levels of genetic similarity in the outcrossed population and highest levels of genetic similarity in the inbred population. Levels of genetic similarity among the managed honey bee populations were intermediate but closer to that of the inbred population. Genetic structuring of the entire breeding population resulted in two major subpopulations, likely deriving from breeders on the east and west coast. The effects that these findings have on the overall population genetic diversity of managed honey bees is discussed.

Further Evidence of Population Admixture in the Serbian Honey Bee Population

Simple Summary

The western honey bee is one of the most ecologically and economically important pollinator species. Due to human interference, it faces serious challenges, not only in number decline and habitat loss, but also in natural subspecies diversity and distribution. The conservation of genetic diversity and perseverance of locally adapted populations and subspecies becomes a crucial task in the face of rapid environmental changes. In order to further assess present genetic variability in Serbian honey bee populations, we analyzed 14 microsatellite loci and then compared nine of them with previously published data. Our results suggest that Serbia now harbors a distinct, relatively homogenous honey bee population, although some local differences are still preserved.

Abstract

Socioeconomic interests and beekeeper preferences have often taken precedence over the conservation of locally native honey bee subspecies, leading to the predominance of admixture populations in human-dominated areas. To assess the genetic diversity of contemporary managed Serbian honey bee colonies, we used 14 microsatellite loci and analyzed 237 worker bees from 46 apiaries in eight localities of northern and southern Serbia. Furthermore, we compared data for nine microsatellite loci with 338 individuals from Italy, Hungary, Poland, and Spain. The standard parameters of genetic diversity in Serbian honey bee populations were in line with other analyses, although somewhat smaller. STRUCTURE analysis showed the existence of two equally distributed genetic clusters and Analysis of molecular variances could not confirm the presence of a geographically discrete population but showed local differences. Discriminant analysis of principal components showed overlapping of worker bees from different parts of Serbia. Clear genetic differentiation can be observed when comparing all populations between geographical regions and their corresponding subspecies. The absence of the A. m. macedonica subspecies from its historical distribution range in southern Serbia as well as the lack of distinctive geographical groups suggest that selective breeding, queen import, and migratory beekeeping practices strongly influence the genetic structure and diversity of honey bees, leading to the genetic uniformization and creation of the admixture population.

Practical Applications of Genomics in Managing Honey bee Health

The honey bee Apis mellifera is a model organism for sociogenomics and one of the most important managed pollinators. High mortalities experienced by honey bee colonies over the past several decades are expected to have a substantive effect on crop pollination and global food security. These threats and the availability of a growing number of genomic resources for the honey bee have motivated research on how genetics and genomics can be practically applied to manage bee health. The authors review 3 such applications: (1) Certification of bee lineages using single-polymorphism markers; (2) breeding bees using marker-assisted selection; (3) diagnosing honey bee stressors using biomarkers.

MtDNA Analysis Indicates Human-Induced Temporal Changes of Serbian Honey Bees Diversity

Simple Summary

The western honey bee is one of the most economically and ecologically important species currently facing serious challenges in its whole area of distribution. The honey bee is a highly diverse species with about 30 subspecies that are adapted to regional climate factors, vegetation, pests and pathogens. The local populations of honey bees are rapidly changing and their diversity is constantly manipulated by beekeepers through the import of foreign queens, selection and migratory beekeeping. This manipulation may lead to such changes that honey bees lose their ability to thrive in the areas that were previously suitable for their wellbeing. To see how this human interference changed the genetic variability of native honey bee populations from Serbia, we sequenced part of the mitochondrial genome and compared them with published sequences. Our results suggest that human influence significantly changes the natural composition of honey bees in Serbia and that the presence of some previously reported subspecies could not be confirmed.

Abstract

Local populations of Apis mellifera are rapidly changing by modern beekeeping through the introduction of nonnative queens, selection and migratory beekeeping. To assess the genetic diversity of contemporary managed honey bees in Serbia, we sequenced mitochondrial tRNA^leu-cox2 intergenic region of 241 worker bees from 46 apiaries at eight localities. Nine haplotypes were observed in our samples, with C2d being the most common and widespread. To evaluate genetic diversity patterns, we compared our data with 1696 sequences from the NCBI GenBank from neighbouring countries and Serbia. All 32 detected haplotypes belonged to the Southeast Europe lineage C, with two newly described haplotypes from our sample. The most frequent haplotype was C2d, followed by C2c and C1a. To distinguish A. m. carnica from A. m. macedonica, both previously reported in Serbia, PCR-RFLP analysis on the COI gene segment of mtDNA was used, and the result showed only the presence of A.m. carnica subspecies. An MDS plot constructed on pairwise F_ST values showed significant geographical stratification. Our samples are grouped together, but distant from the Serbian dataset from the GenBank. This, with the absence of A. m. macedonica subspecies from its historic range of distribution in southern Serbia, indicates that honey bee populations are changing rapidly due to the anthropogenic influence.

Disentangling Ethiopian Honey Bee (Apis mellifera) Populations Based on Standard Morphometric and Genetic Analyses

Simple Summary

We conducted this population study of Ethiopian honey bees, using morphometric and genetic methods, to decipher their controversial classification. These honey bees are highly diverse and showed differentiation based on size and genetic information according to prevailing agro-ecological conditions, demonstrating morphological and molecular signatures of local adaptation. The results of both morphometric and genetic analyses suggest that Ethiopian honey bees differ from populations in the neighboring geographic regions and are characterized by extensive gene flow within the country, enhanced by honey bee colony trade. Consequently, future research that includes studying traits of vitality, behavior and colony performance of honey bees in remaining pocket areas of highland agro-ecological zones could contribute to the development of appropriate conservation management.

Abstract

The diversity and local differentiation of honey bees are subjects of broad general interest. In particular, the classification of Ethiopian honey bees has been a subject of debate for decades. Here, we conducted an integrated analysis based on classical morphometrics and a putative nuclear marker (denoted r7-frag) for elevational adaptation to classify and characterize these honey bees. Therefore, 660 worker bees were collected out of 66 colonies from highland, midland and lowland agro-ecological zones (AEZs) and were analyzed in reference to populations from neighboring countries. Multivariate morphometric analyses show that our Ethiopian samples are separate from Apis mellifera scutellata, A. m. jemenitica, A. m. litorea and A. m. monticola, but are closely related to A. m. simensis reference. Linear discriminant analysis showed differentiation according to AEZs in the form of highland, midland and lowland ecotypes. Moreover, size was positively correlated with elevation. Similarly, our Ethiopian samples were differentiated from A. m. monticola and A. m. scutellata based on r7-frag. There was a low tendency towards genetic differentiation between the Ethiopian samples, likely impacted by increased gene flow. However, the differentiation slightly increased with increasing elevational differences, demonstrated by the highland bees that showed higher differentiation from the lowland bees (F_ST = 0.024) compared to the midland bees (F_ST = 0.015). An allelic length polymorphism was detected (denoted as d) within r7-frag, showing a patterned distribution strongly associated with AEZ (X² = 11.84, p < 0.01) and found predominantly in highland and midland bees of some pocket areas. In conclusion, the Ethiopian honey bees represented in this study are characterized by high gene flow that suppresses differentiation.

Mitochondrial genomes illuminate the evolutionary history of the Western honey bee (Apis mellifera)

Western honey bees (Apis mellifera) are one of the most important pollinators of agricultural crops and wild plants. Despite the growth in the availability of sequence data for honey bees, the phylogeny of the species remains a subject of controversy. Most notably, the geographic origin of honey bees is uncertain, as are the relationships among its constituent lineages and subspecies. We aim to infer the evolutionary and biogeographical history of the honey bee from mitochondrial genomes. Here we analyse the full mitochondrial genomes of 18 A. mellifera subspecies, belonging to all major lineages, using a range of gene sampling strategies and inference models to identify factors that may have contributed to the recovery of incongruent results in previous studies. Our analyses support a northern African or Middle Eastern origin of A. mellifera. We show that the previously suggested European and Afrotropical cradles of honey bees are the result of phylogenetic error. Monophyly of the M, C, and O lineages is strongly supported, but the A lineage appears paraphyletic. A. mellifera colonised Europe through at least two pathways, across the Strait of Gibraltar and via Asia Minor.

Digging into the Genomic Past of Swiss Honey Bees by Whole-Genome Sequencing Museum Specimens

Historical specimens in museum collections provide opportunities to gain insights into the genomic past. For the Western honey bee, Apis mellifera L., this is particularly important because its populations are currently under threat worldwide and have experienced many changes in management and environment over the last century. Using Swiss Apis mellifera mellifera as a case study, our research provides important insights into the genetic diversity of native honey bees prior to the industrial-scale introductions and trade of non-native stocks during the 20th century—the onset of intensive commercial breeding and the decline of wild honey bees following the arrival of Varroa destructor. We sequenced whole-genomes of 22 honey bees from the Natural History Museum in Bern collected in Switzerland, including the oldest A. mellifera sample ever sequenced. We identify both, a historic and a recent migrant, natural or human-mediated, which corroborates with the population history of honey bees in Switzerland. Contrary to what we expected, we find no evidence for a significant genetic bottleneck in Swiss honey bees, and find that genetic diversity is not only maintained, but even slightly increased, most probably due to modern apicultural practices. Finally, we identify signals of selection between historic and modern honey bee populations associated with genes enriched in functions linked to xenobiotics, suggesting a possible selective pressure from the increasing use and diversity of chemicals used in agriculture and apiculture over the last century.

Eusociality influences the strength of negative selection on insect genomes

While much of the focus of sociobiology concerns identifying genomic changes that influence social behaviour, we know little about the consequences of social behaviour on genome evolution. It has been hypothesized that social evolution can influence the strength of negative selection via two mechanisms. First, division of labour can influence the efficiency of negative selection in a caste-specific manner; indirect negative selection on worker traits is theoretically expected to be weaker than direct selection on queen traits. Second, increasing social complexity is expected to lead to relaxed negative selection because of its influence on effective population size. We tested these two hypotheses by estimating the strength of negative selection in honeybees, bumblebees, paper wasps, fire ants and six other insects that span the range of social complexity. We found no consistent evidence that negative selection was significantly stronger on queen-biased genes relative to worker-biased genes. However, we found strong evidence that increased social complexity reduced the efficiency of negative selection. Our study clearly illustrates how changes in behaviour can influence patterns of genome evolution by modulating the strength of natural selection.

Population genomics of honey bees reveals a selection signature indispensable for royal jelly production

In order to interpret the molecular mechanisms that modulating the organism variations and selection signatures to drive adaptive evolutionary changes are indispensable goals in the new evolutionary ecological genetics. Here, we identified the gene locus associated to royal jelly production through whole-genome sequencing of the DNA from eight populations of honeybees. The analysis of the samples was composed of 120 individuals and each pointed extremely opposite trait values for a given phenotype. We identified functional single nucleotide polymorphisms (SNPs) candidate that might be essential in regulating the phenotypic traits of honeybee populations. Moreover, selection signatures were investigated using pooling sequencing of eight distinct honeybee populations, and the results provided the evidence of signatures of recent selection among populations under different selection objectives. Furthermore, gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that selected genes were potentially involved in several biological processes and molecular functioning, which could directly or indirectly influence the production of royal jelly. Our findings can be used to understand the genomic signatures, as well as implicate a profound glance on genomic regions that control the production trait of royal jelly in honey bees.

Population Genomics Provide Insights into the Evolution and Adaptation of the Eastern Honey Bee (Apis cerana)

The mechanisms by which organisms adapt to variable environments are a fundamental question in evolutionary biology and are important to protect important species in response to a changing climate. An interesting candidate to study this question is the honey bee Apis cerana, a keystone pollinator with a wide distribution throughout a large variety of climates, that exhibits rapid dispersal. Here, we resequenced the genome of 180 A. cerana individuals from 18 populations throughout China. Using a population genomics approach, we observed considerable genetic variation in A. cerana. Patterns of genetic differentiation indicate high divergence at the subspecies level, and physical barriers rather than distance are the driving force for population divergence. Estimations of divergence time suggested that the main branches diverged between 300 and 500 Ka. Analyses of the population history revealed a substantial influence of the Earth's climate on the effective population size of A. cerana, as increased population sizes were observed during warmer periods. Further analyses identified candidate genes under natural selection that are potentially related to honey bee cognition, temperature adaptation, and olfactory. Based on our results, A. cerana may have great potential in response to climate change. Our study provides fundamental knowledge of the evolution and adaptation of A. cerana.

Population genomics and morphological features underlying the adaptive evolution of the eastern honey bee (Apis cerana)

Background

The adaptation of organisms to changing environments is self-evident, with the adaptive evolution of organisms to environmental changes being a fundamental problem in evolutionary biology. Bees can pollinate in various environments and climates and play important roles in maintaining the ecological balance of the earth.

Results

We performed an analysis of 462 Apis cerana (A. cerana) specimens from 31 populations in 11 regions and obtained 39 representative morphological features. We selected 8 A. cerana samples from each population and performed 2b-RAD simplified genome sequencing. A total of 11,506 high-quality single nucleotide polymorphism (SNP) loci were obtained. For these SNPs, the minor allele frequency (MAF) was > 1%, the average number of unique labels for each sample was 49,055, and the average depth was 72.61x. The ratios of the unique labels of all samples were 64.27–86.33%.

Conclusions

Using 39 morphological characteristics as the data set, we proposed a method for the rapid classification of A. cerana. Using genomics to assess population structure and genetic diversity, we found that A. cerana has a large genetic difference at the ecotype level. A comparison of A. cerana in North China revealed that some physical obstacles, especially the overurbanization of the plains, have isolated the populations of this species. We identified several migration events in North China and Central China. By comparing the differences in the environmental changes in different regions, we found that A. cerana has strong potential for climate change and provides a theoretical basis for investigating and protecting A. cerana.

Recent advances in population and quantitative genomics of honey bees

The increase in the availability of individual Apis mellifera genomes has resulted in significant progress toward understanding the evolution and adaptation of the honey bee. These efforts have identified new subspecies, evolutionary lineages, and a significant number of genes involved with adaptations and colony-level quantitative traits. Many studies have also developed genetic assays that are being used to monitor the movement and admixture of honey bee populations. These resources are valuable for conservation and breeding programs that seek to improve the economic value of colonies or preserve locally adapted populations and subspecies. This review provides a brief discussion on how population and quantitative genomic studies has improved our understanding of the honey bee.

Effects of group size on learning and memory in the honey bee, Apis mellifera

In animals that experience interactions with conspecifics while young, social interactions appear to be a necessary prerequisite for typical behaviour. Eusocial insects have large colonies where individuals experience a great deal of social interactions with nest mates during all life stages, making them excellent candidates for understanding the effects of social isolation on brain development and behaviour. Here we used the honey bee Apis mellifera to study the effect of social isolation and group size on reward perception and discrimination learning and memory. We confined day old adult workers into three different size groups (1 bee, 8 or 32 bees) for six days during a critical period associated with adult behavioural maturation. We quantified their sucrose responsiveness, their ability to use and remember olfactory cues to discriminate between sucrose and salt (i.e. discrimination learning), and four biogenic amines in the brain. We found that the smaller the group size, the more responsive a worker was to the sucrose reward. Honey bees raised in groups of 32 performed the best in the learning trials and had the highest levels of dopamine. We found no effect of group size on memory. The observed group size effect on learning but not memory supports the hypothesis that social interactions modulate learning through the dopaminergic system.

Whole-genome resequencing of honeybee drones to detect genomic selection in a population managed for royal jelly

Four main evolutionary lineages of A. mellifera have been described including eastern Europe (C) and western and northern Europe (M). Many apiculturists prefer bees from the C lineage due to their docility and high productivity. In France, the routine importation of bees from the C lineage has resulted in the widespread admixture of bees from the M lineage. The haplodiploid nature of the honeybee Apis mellifera, and its small genome size, permits affordable and extensive genomics studies. As a pilot study of a larger project to characterise French honeybee populations, we sequenced 60 drones sampled from two commercial populations managed for the production of honey and royal jelly. Results indicate a C lineage origin, whilst mitochondrial analysis suggests two drones originated from the O lineage. Analysis of heterozygous SNPs identified potential copy number variants near to genes encoding odorant binding proteins and several cytochrome P450 genes. Signatures of selection were detected using the hapFLK haplotype-based method, revealing several regions under putative selection for royal jelly production. The framework developed during this study will be applied to a broader sampling regime, allowing the genetic diversity of French honeybees to be characterised in detail.

Reduced SNP panels for genetic identification and introgression analysis in the dark honey bee (Apis mellifera mellifera)

Beekeeping activities, especially queen trading, have shaped the distribution of honey bee (Apis mellifera) subspecies in Europe, and have resulted in extensive introductions of two eastern European C-lineage subspecies (A. m. ligustica and A. m. carnica) into the native range of the M-lineage A. m. mellifera subspecies in Western Europe. As a consequence, replacement and gene flow between native and commercial populations have occurred at varying levels across western European populations. Genetic identification and introgression analysis using molecular markers is an important tool for management and conservation of honey bee subspecies. Previous studies have monitored introgression by using microsatellite, PCR-RFLP markers and most recently, high density assays using single nucleotide polymorphism (SNP) markers. While the latter are almost prohibitively expensive, the information gained to date can be exploited to create a reduced panel containing the most ancestry-informative markers (AIMs) for those purposes with very little loss of information. The objective of this study was to design reduced panels of AIMs to verify the origin of A. m. mellifera individuals and to provide accurate estimates of the level of C-lineage introgression into their genome. The discriminant power of the SNPs using a variety of metrics and approaches including the Weir & Cockerham’s F_ST, an F_ST-based outlier test, Delta, informativeness (I_n), and PCA was evaluated. This study shows that reduced AIMs panels assign individuals to the correct origin and calculates the admixture level with a high degree of accuracy. These panels provide an essential tool in Europe for genetic stock identification and estimation of admixture levels which can assist management strategies and monitor honey bee conservation programs.

No genetic tradeoffs between hygienic behaviour and individual innate immunity in the honey bee, Apis mellifera

Many animals have individual and social mechanisms for combating pathogens. Animals may exhibit short-term physiological tradeoffs between social and individual immunity because the latter is often energetically costly. Genetic tradeoffs between these two traits can also occur if mutations that enhance social immunity diminish individual immunity, or vice versa. Physiological tradeoffs between individual and social immunity have been previously documented in insects, but there has been no study of genetic tradeoffs involving these traits. There is strong evidence that some genes influence both innate immunity and behaviour in social insects – a prerequisite for genetic tradeoffs. Quantifying genetic tradeoffs is critical for understanding the evolution of immunity in social insects and for devising effective strategies for breeding disease-resistant pollinator populations. We conducted two experiments to test the hypothesis of a genetic tradeoff between social and individual immunity in the honey bee, Apis mellifera. First, we estimated the relative contribution of genetics to individual variation in innate immunity of honey bee workers, as only heritable traits can experience genetic tradeoffs. Second, we examined if worker bees with hygienic sisters have reduced individual innate immune response. We genotyped several hundred workers from two colonies and found that patriline genotype does not significantly influence the antimicrobial activity of a worker’s hemolymph. Further, we did not find a negative correlation between hygienic behaviour and the average antimicrobial activity of a worker’s hemolymph across 30 honey bee colonies. Taken together, our work indicates no genetic tradeoffs between hygienic behaviour and innate immunity in honey bees. Our work suggests that using artificial selection to increase hygienic behaviour of honey bee colonies is not expected to concurrently compromise individual innate immunity of worker bees.