Genomic correlates of recombination rate and its variability across eight recombination maps in the western honey bee (Apis mellifera L.)

Background

Meiotic recombination has traditionally been explained based on the structural requirement to stabilize homologous chromosome pairs to ensure their proper meiotic segregation. Competing hypotheses seek to explain the emerging findings of significant heterogeneity in recombination rates within and between genomes, but intraspecific comparisons of genome-wide recombination patterns are rare. The honey bee (Apis mellifera) exhibits the highest rate of genomic recombination among multicellular animals with about five cross-over events per chromatid.

Results

Here, we present a comparative analysis of recombination rates across eight genetic linkage maps of the honey bee genome to investigate which genomic sequence features are correlated with recombination rate and with its variation across the eight data sets, ranging in average marker spacing ranging from 1 Mbp to 120 kbp. Overall, we found that GC content explained best the variation in local recombination rate along chromosomes at the analyzed 100 kbp scale. In contrast, variation among the different maps was correlated to the abundance of microsatellites and several specific tri- and tetra-nucleotides.

Conclusions

The combined evidence from eight medium-scale recombination maps of the honey bee genome suggests that recombination rate variation in this highly recombining genome might be due to the DNA configuration instead of distinct sequence motifs. However, more fine-scale analyses are needed. The empirical basis of eight differing genetic maps allowed for robust conclusions about the correlates of the local recombination rates and enabled the study of the relation between DNA features and variability in local recombination rates, which is particularly relevant in the honey bee genome with its exceptionally high recombination rate.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1281-2) contains supplementary material, which is available to authorized users.     

Life history strategy of the honey bee,Apis mellifera

Summary The feral honey bee queens (colonies) of central New York State (USA) show a K-type life history strategy. Their demographic characteristics include low early life mortality, low reproductive rate, long lifespan, high population stability and repeated reproductions. Identifying the life history strategy of these bees reveals the general pattern of selection for competitive ability, rather than productivity, which has shaped their societies. Selection for competitive power explains the adaptiveness (compared with alternatives found in many other insect societies) of the large perennial colonies, infrequent but expensive offspring, and efficient foraging which characterize the social organization of these bees.     

Comparative reproduction of <Emphasis Type="Italic">Varroa destructor</Emphasis> in different types of Russian and Italian honey bee combs

Earlier studies showed that Russian honey bees support slow growth of varroa mite population. We studied whether or not comb type influenced varroa reproduction in both Russian and Italian honey bees, and whether Russian bees produced comb which inhibited varroa reproduction. The major differences found in this study concerned honey bee type. Overall, the Russian honey bees had lower (2.44 ± 0.18%) levels of varroa infestation than Italian honey bees (7.20 ± 0.60%). This decreased infestation resulted in part from a reduced number of viable female offspring per foundress in the Russian (0.85 ± 0.04 female) compared to the Italian (1.23 ± 0.04 females) honey bee colonies. In addition, there was an effect by the comb built by the Russian honey bee colonies that reduced varroa reproduction. When comparing combs having Russian or Italian colony origins, Russian honey bee colonies had more non-reproducing foundress mites and fewer viable female offspring in Russian honey bee comb. This difference did not occur in Italian colonies. The age of comb in this study had mixed effects. Older comb produced similar responses for six of the seven varroa infestation parameters measured. In colonies of Italian honey bees, the older comb (2001 dark) had fewer (1.13 ± 0.07 females) viable female offspring per foundress than were found in the 2002 new (1.21 ± 0.06 females) and 1980s new (1.36 ± 0.08 females) combs. This difference did not occur with Russian honey bee colonies where the number of viable female offspring was low in all three types of combs. This study suggests that honey bee type largely influences growth of varroa mite population in a colony.     

Genotypical Variability for the Tasks of Water Collecting and Scenting in a Honey Bee Colony

The polyandrous mating behaviour of the honey bee queen increases the genotypical variability amongst her worker offspring. Microsatellite DNA analyses revealed a total of 16 subfamilies in one colony of honey bees. The subfamilies were represented in significantly different proportions in two subgroups of bees, water collecting bees and scenting bees, indicating a genetic component in task choice.     

Detection of multiple viruses in queens of the honey bee Apis mellifera L

Individual honey bee Apis mellifera L. queens were examined for the presence of six honey bee viruses including acute bee paralysis virus, chronic bee paralysis virus, black queen cell virus, deformed wing virus, Kashmir bee virus, and sacbrood virus. All viruses, except ABPV, were detected in the samples. Among queens examined for virus infections, 93% had multiple virus infections. The detection of viruses in queens raises the possibility of a vertical transmission pathway wherein infected queens can pass virus through their eggs to their offspring.     

The effects of honey bee (Apis mellifera L.) queen reproductive potential on colony growth

Reproduction in species of eusocial insects is monopolized by one or a few individuals, while the remaining colony tasks are performed by the worker caste. This reproductive division of labor is exemplified by honey bees (Apis mellifera L.), in which a single, polyandrous queen is the sole colony member that lays fertilized eggs. Previous work has revealed that the developmental fate of honey bee queens is highly plastic, with queens raised from younger worker larvae exhibiting higher measures in several aspects of reproductive potential compared to queens raised from older worker larvae. Here, we investigated the effects of queen reproductive potential (“quality”) on the growth and winter survival of newly established honey bee colonies. We did so by comparing the growth of colonies headed by “high-quality” queens (i.e., those raised from young worker larvae, which are more queen-like morphologically) to those headed by “low-quality” queens (i.e., those raised from older worker larvae, which are more worker-like morphologically). We confirmed that queens reared from young worker larvae were significantly larger in size than queens reared from old worker larvae. We also found a significant positive effect of queen grafting age on a colony’s production of worker comb, drone comb, and stored food (honey and pollen), although we did not find a statistically significant difference in the production of worker and drone brood, worker population, and colony weight. Our results provide evidence that in honey bees, queen developmental plasticity influences several important measures of colony fitness. Thus, the present study supports the idea that a honey bee colony can be viewed (at least in part) as the expanded phenotype of its queen, and thus selection acting predominantly at the colony level can be congruent with that at the individual level.     

Population structure of honey bees in the Carpathian Basin (Hungary) confirms introgression from surrounding subspecies

Carniolan honey bees (Apis mellifera carnica) are considered as an indigenous subspecies in Hungary adapted to most of the ecological and climatic conditions in this area. However, during the last decades Hungarian beekeepers have recognized morphological signs of the Italian honey bee (Apis mellifera ligustica). As the natural distribution of the honey bee subspecies can be affected by the importation of honey bee queens or by natural gene flow, we aimed at determining the genetic structure and characteristics of the local honey bee population using molecular markers. All together, 48 Hungarian and 84 foreign (Italian, Polish, Spanish, Liberian) pupae and/or workers were used for mitochondrial DNA analysis. Additionally, 53 sequences corresponding to 10 subspecies and the Buckfast hybrid were downloaded from GenBank. For the nuclear analysis, 236 Hungarian and 106 foreign honey bees were genotyped using nine microsatellites. Heterozygosity values, population‐specific alleles, FST values, principal coordinate analysis, assignment tests, structure analysis, and dendrograms were calculated. Haplotype and nucleotide diversity values showed moderate values. We found that one haplotype (H9) was dominant in Hungary. The presence of the black honey bee (Apis mellifera mellifera) was negligible, but a few individuals resembling other subspecies were identified. We proved that the Hungarian honey bee population is nearly homogeneous but also demonstrated introgression from the foreign subspecies. Both mitochondrial DNA and microsatellite analyses corroborated the observations of the beekeepers. Molecular analyses suggested that Carniolan honey bee in Hungary is slightly affected by Italian and black honey bee introgression. Genetic differences were detected between Polish and Hungarian Carniolan honey bee populations, suggesting the existence of at least two different gene pools within A. m. carnica.     

The habitat disruption induces immune-suppression and oxidative stress in honey bees

The honey bee is a major insect used for pollination of many commercial crops worldwide. Although the use of honey bees for pollination can disrupt the habitat, the effects on their physiology have never been determined. Recently, honey bee colonies have often collapsed when introduced in greenhouses for pollination in Japan. Thus, suppressing colony collapses and maintaining the number of worker bees in the colonies is essential for successful long-term pollination in greenhouses and recycling of honey bee colonies. To understand the physiological states of honey bees used for long-term pollination in greenhouses, we characterized their gene expression profiles by microarray. We found that the greenhouse environment changes the gene expression profiles and induces immune-suppression and oxidative stress in honey bees. In fact, the increase of the number of Nosema microsporidia and protein carbonyl content was observed in honey bees during pollination in greenhouses. Thus, honey bee colonies are likely to collapse during pollination in greenhouses when heavily infested with pathogens. Degradation of honey bee habitat by changing the outside environment of the colony, during pollination services for example, imposes negative impacts on honey bees. Thus, worldwide use of honey bees for crop pollination in general could be one of reasons for the decline of managed honey bee colonies.     

Heat stress during development affects immunocompetence in workers,queens and drones of Africanized honey bees (Apis mellifera L.) (Hymenoptera: Apidae)

Though social insects generally seem to have a reduced individual immunoresponse compared to solitary species, the impact of heat stress on that response has not been studied. In the honey bee, the effect of heat stress on reproductives (queens and males/drones) may also vary compared to workers, but this is currently unknown. Here, we quantified the activity of an enzyme linked to the immune response in insects and known to be affected by heat stress in solitary species: phenoloxidase (PO), in workers, queens and drones of Africanized honey bees (AHBs) experimentally subjected to elevated temperatures during the pupal stage. Additionally, we evaluated this marker in individuals experimentally infected with the entomopathogenic fungus Metarhizium anisopliae. Differences in PO activity were found between sexes and castes, with PO activity generally higher in workers and lower in reproductives. Such differences are associated with the likelihood of exposure to infection and the role of different individuals in the colony. Contrary to our expectation, heat stress did not cause an increase in PO activity equally in all classes of individual. Heat stress during the pupal stage significantly decreased the PO activity of AHB queens, but not that of workers or drones, which more frequently engage in extranidal activity. Experimental infection with Metarhizium anisopliae reduced PO activity in queens and workers, but increased it in drones. Notably, heat stressed workers lived significantly shorter after infection despite exhibiting greater PO activity than queens or drones. We suggest that this discrepancy may be related to trade-offs among immune response cascades in honey bees such as between heat shock proteins and defensin peptides used in microbial defence. Our results provide evidence for complex relationships among humoral immune responses in AHBs and suggest that heat stress could result in a reduced life expectancy of individuals.     

Differential expression of odorant-binding proteins in the mandibular glands of the honey bee according to caste and age

Odorant-binding proteins (OBPs) and chemosensory proteins (CSPs) mediate both perception and release of chemical stimuli in insects. The genome of the honey bee contains 21 genes encoding OBPs and 6 encoding CSPs. Using a proteomic approach, we have investigated the expression of OBPs and CSPs in the mandibular glands of adult honey bees in relation to caste and age. OBP13 is mostly expressed in young individuals and in virgin queens, while OBP21 is abundant in older bees and is prevalent in mated queens. OBP14, which had been found in larvae, is produced in hive workers' glands. Quite unexpectedly, the mandibular glands of drones also contain OBPs, mainly OBP18 and OBP21. We have expressed three of the most represented OBPs and studied their binding properties. OBP13 binds with good specificity oleic acid and some structurally related compounds, OBP14 is better tuned to monoterpenoid structures, while OBP21 binds the main components of queen mandibular pheromone as well as farnesol, a compound used as a trail pheromone in the honey bee and other hymenopterans. The high expression of different OBPs in the mandibular glands suggests that such proteins could be involved in solubilization and release of semiochemicals.     

Non-destructive sources of DNA used to genotype honey bee (Apis mellifera) queens

We describe a method for genotyping honey bee queens Apis mellifera L. (Hymenoptera: Apidae), using biological materials that are normally cast off during development (larval and pupal exuviae), or can be removed without apparent damage to queen longevity or acceptability to workers (wing clippings). Highly polymorphic microsatellite loci were successfully amplified from DNA from all of these sources, although with differing degrees of success. DNA was extracted using a simple Chelex 100® boiling procedure. Four microsatellite primers were used to amplify the DNA, and the PCR products were visualized on an ALFexpress Automated Sequencer. Genotypes created from these sources were consistent with those originating from tarsal tissue. Successful retrieval and amplification of DNA from the exuviae from immature queens allows potential breeding individuals to be genotyped and selected before they become adults. This procedure may therefore have value as DNA marker‐assisted breeding programs are developed for honey bees.     

Sperm viability and gene expression in honey bee queens (Apis mellifera) following exposure to the neonicotinoid insecticide imidacloprid and the organophosphate acaricide coumaphos

Honey bee population declines are of global concern. Numerous factors appear to cause these declines including parasites, pathogens, malnutrition and pesticides. Residues of the organophosphate acaricide coumaphos and the neonicotinoid insecticide imidacloprid, widely used to combat Varroa mites and for crop protection in agriculture, respectively, have been detected in wax, pollen and comb samples. Here, we assess the effects of these compounds at different doses on the viability of sperm stored in the honey bee queens’ spermatheca. Our results demonstrate that sub-lethal doses of imidacloprid (0.02 ppm) decreased sperm viability by 50%, 7 days after treatment. Sperm viability was a downward trend (about 33%) in queens treated with high doses of coumaphos (100 ppm), but there was not significant difference. The expression of genes that are involved in development, immune responses and detoxification in honey bee queens and workers exposed to chemicals was measured by qPCR analysis. The data showed that expression levels of specific genes were triggered 1 day after treatment. The expression levels of P450 subfamily genes, CYP306A1, CYP4G11 and CYP6AS14 were decreased in honey bee queens treated with low doses of coumaphos (5 ppm) and imidacloprid (0.02 ppm). Moreover, these two compounds suppressed the expression of genes related to antioxidation, immunity and development in queens at day 1. Up-regulation of antioxidants by these compounds in worker bees was observed at day 1. Coumaphos also caused a repression of CYP306A1 and CYP4G11 in workers. Antioxidants appear to prevent chemical damage to honey bees. We also found that DWV replication increased in workers treated with imidacloprid. This research clearly demonstrates that chemical exposure can affect sperm viability in queen honey bees.     

Egg‐size plasticity in Apis mellifera: Honey bee queens alter egg size in response to both genetic and environmental factors

Social evolution has led to distinct life‐history patterns in social insects, but many colony‐level and individual traits, such as egg size, are not sufficiently understood. Thus, a series of experiments was performed to study the effects of genotypes, colony size and colony nutrition on variation in egg size produced by honey bee (Apis mellifera) queens. Queens from different genetic stocks produced significantly different egg sizes under similar environmental conditions, indicating standing genetic variation for egg size that allows for adaptive evolutionary change. Further investigations revealed that eggs produced by queens in large colonies were consistently smaller than eggs produced in small colonies, and queens dynamically adjusted egg size in relation to colony size. Similarly, queens increased egg size in response to food deprivation. These results could not be solely explained by different numbers of eggs produced in the different circumstances but instead seem to reflect an active adjustment of resource allocation by the queen in response to colony conditions. As a result, larger eggs experienced higher subsequent survival than smaller eggs, suggesting that honey bee queens might increase egg size under unfavourable conditions to enhance brood survival and to minimize costly brood care of eggs that fail to successfully develop, and thus conserve energy at the colony level. The extensive plasticity and genetic variation of egg size in honey bees has important implications for understanding life‐history evolution in a social context and implies this neglected life‐history stage in honey bees may have trans‐generational effects.     

Characterization of the active microbiotas associated with honey bees reveals healthier and broader communities when colonies are genetically diverse

Recent losses of honey bee colonies have led to increased interest in the microbial communities that are associated with these important pollinators. A critical function that bacteria perform for their honey bee hosts, but one that is poorly understood, is the transformation of worker-collected pollen into bee bread, a nutritious food product that can be stored for long periods in colonies. We used 16S rRNA pyrosequencing to comprehensively characterize in genetically diverse and genetically uniform colonies the active bacterial communities that are found on honey bees, in their digestive tracts, and in bee bread. This method provided insights that have not been revealed by past studies into the content and benefits of honey bee-associated microbial communities. Colony microbiotas differed substantially between sampling environments and were dominated by several anaerobic bacterial genera never before associated with honey bees, but renowned for their use by humans to ferment food. Colonies with genetically diverse populations of workers, a result of the highly promiscuous mating behavior of queens, benefited from greater microbial diversity, reduced pathogen loads, and increased abundance of putatively helpful bacteria, particularly species from the potentially probiotic genus Bifidobacterium. Across all colonies, Bifidobacterium activity was negatively correlated with the activity of genera that include pathogenic microbes; this relationship suggests a possible target for understanding whether microbes provide protective benefits to honey bees. Within-colony diversity shapes microbiotas associated with honey bees in ways that may have important repercussions for colony function and health. Our findings illuminate the importance of honey bee-bacteria symbioses and examine their intersection with nutrition, pathogen load, and genetic diversity, factors that are considered key to understanding honey bee decline.     

Polyandry in Honey Bees (APIS MELLIFERA L.): Sperm Utilization and Intracolony Genetic Relationships

Sperm usage by queen honey bees was examined by progeny analyses using six phenotypically distinct genetic markers. No evidence was found for sperm displacement or precedence. All queens used the sperm of all males that inseminated them during all sampling periods. Sperm usage, as measured by phenotypic frequencies, did fluctuate nonrandomly but did not result in abnormally high representation of a single phenotype or the elimination of other phenotypes as has often been suggested. The genetic relationships of workers within honey bee colonies are estimated from the data presented. Average genetic relatedness is shown to be low among colony nestmates and probably approaches 0.25 in colonies with naturally mated queens. There is no evidence for elevated relatedness among colony subfamilies due to nonrandom fluctuations in sperm usage by queens or for numerical dominance of any subfamilies.     

Checking your breaks: surveillance mechanisms of meiotic recombination

Numerous DNA double-strand breaks (DSBs) are introduced into the genome in the course of meiotic recombination. This poses a significant hazard to the genomic integrity of the cell. Studies in a number of organisms have unveiled the existence of surveillance mechanisms or checkpoints that couple the formation and repair of DSBs to cell cycle progression. Through these mechanisms, aberrant meiocytes are delayed in their meiotic progression, thereby facilitating repair of meiotic DSBs, or are culled through programmed cell death, thereby protecting the germline from aneuploidies that could lead to spontaneous abortions, birth defects and cancer predisposition in the offspring. Here we summarize recent progress in our understanding of these checkpoints. This review focuses on the surveillance mechanisms of the budding yeast S. cerevisiae, where the molecular details are best understood, but will frequently compare and contrast these mechanisms with observations in other organisms.     

The genomic basis of adaptation to high‐altitude habitats in the eastern honey bee (Apis cerana)

The eastern honey bee (Apis cerana) is of central importance for agriculture in Asia. It has adapted to a wide variety of environmental conditions across its native range in southern and eastern Asia, which includes high‐altitude regions. eastern honey bees inhabiting mountains differ morphologically from neighbouring lowland populations and may also exhibit differences in physiology and behaviour. We compared the genomes of 60 eastern honey bees collected from high and low altitudes in Yunnan and Gansu provinces, China, to infer their evolutionary history and to identify candidate genes that may underlie adaptation to high altitude. Using a combination of F_ST‐based statistics, long‐range haplotype tests and population branch statistics, we identified several regions of the genome that appear to have been under positive selection. These candidate regions were strongly enriched for coding sequences and had high haplotype homozygosity and increased divergence specifically in highland bee populations, suggesting they have been subjected to recent selection in high‐altitude habitats. Candidate loci in these genomic regions included genes related to reproduction and feeding behaviour in honey bees. Functional investigation of these candidate loci is necessary to fully understand the mechanisms of adaptation to high‐altitude habitats in the eastern honey bee.     

Age and Behavior of Honey Bees,Apis mellifera (Hymenoptera: Apidae), that Perform Vibration Signals on Queens and Queen Cells

The vibration signal of the honey bee (Apis mellifera) may play a central role in the regulation of queen behavior during reproductive swarming and supersedure. We examined honey bee workers that performed vibration signals on queens and developing queen cells in three observation hives, each containing a population of marked bees of known age. In all three colonies, workers of all ages greater than 2 d old could perform vibration signals on queens and queen cells. However, most signals were performed by a small proportion of the bees of greater than 10 d of age. Relatively few workers less than 10 d old vibrated queens and queen cells, even though this age-group is typically associated with queen care. Thus, the regulation of queen behavior by the vibration signal may occur primarily through a relatively small subset of older workers that, under most circumstances, have only limited involvement with queens. It is unclear what triggers the vibrating of queens. Workers producing vibration signals did not differ from same-age non-vibrating controls in rate of locomotion in the hive or in task performance, and they rarely engaged in foraging, even though the majority of observed bees were of foraging age; vibrators also did not spend more time with queens and queen cells compared with controls. Vibration signals performed on queens and queen cells therefore do not appear to be influenced by task performance or increased contact with queens.     

Mating Frequencies of Honey Bee Queens (Apis mellifera L.) in a Population of Feral Colonies in the Northeastern United States

Across their introduced range in North America, populations of feral honey bee (Apis mellifera L.) colonies have supposedly declined in recent decades as a result of exotic parasites, most notably the ectoparasitic mite Varroa destructor. Nonetheless, recent studies have documented several wild populations of colonies that have persisted. The extreme polyandry of honey bee queens—and the increased intracolony genetic diversity it confers—has been attributed, in part, to improved disease resistance and may be a factor in the survival of these populations of feral colonies. We estimated the mating frequencies of queens in feral colonies in the Arnot Forest in New York State to determine if the level of polyandry of these queens is especially high and so might contribute to their survival success. We genotyped the worker offspring from 10 feral colonies in the Arnot Forest of upstate New York, as well as those from 20 managed colonies closest to this forest. We found no significant differences in mean mating frequency between the feral and managed queens, suggesting that queens in the remote, low-density population of colonies in the Arnot Forest are neither mate-limited nor adapted to mate at an especially high frequency. These findings support the hypothesis that the hyperpolyandry of honey bees has been shaped on an evolutionary timescale rather than on an ecological one.