Ecology and Management of African Honey Bees (Apis mellifera L.).

In Africa, humans evolved as honey hunters of honey bee subspecies adapted to diverse geographical regions. Beekeeping today is practiced much as it was when Africans moved from honey hunting to beekeeping nearly 5,000 years ago, with beekeepers relying on seasonally available wild bees. Research suggests that populations are resilient, able to resist diseases and novel parasites. Distinct biomes, as well as environmental pressures, shaped the behavior and biology of these bees and in turn influenced how indigenous beekeeping developed. It appears that passive beekeeping practices that enabled free-living populations contributed to the overall resilience and health of the bee. There is clearly a need for research aimed at a deeper understanding of bee biology and the ecosystems from which they benefit and on which humans depend, as well as a growing realization that the management of these bees requires an indigenous approach that reflects a broader knowledge base and the economics of local communities and markets.

Fragmented landscapes affect honey bee colony strength at diverse spatial scales in agroecological landscapes in Kenya.

Landscape fragmentation and habitat loss at multiple scales directly affect species abundance, diversity, and productivity. There is a paucity of information about the effect of the landscape structure and diversity on honey bee colony strength in Africa. Here, we present new insights into the relationship between landscape metrics such as patch size, shape, connectivity, composition, and configuration and honey bee (Apis mellifera) colony strength characteristics. Remote-sensing-based landscape variables were linked to honey bee colony strength variables in a typical highly fragmented smallholder agroecological region in Kenya. We examined colonies in six sites with varying degrees of land degradation during the period from 2017 to 2018. Landscape structure was first mapped using medium resolution bitemporal Sentinel-1 and Sentinel-2 satellite imagery with an optimized random forest model. The influence of the surrounding landscape matrix was then constrained to two buffer distances, i.e., 1 km representing the local foraging scale and 2.5 km representing the wider foraging scale around each investigated apiary and for each of the six sites. The results of zero-inflated negative binomial regression with mixed effects showed that lower complexity of patch geometries represented by fractal dimension and reduced proportions of croplands were most influential at local foraging scales (1 km) from the apiary. In addition, higher proportions of woody vegetation and hedges resulted in higher colony strength at longer distances from the apiary (2.5 km). Honey bees in moderately degraded landscapes demonstrated the most consistently strong colonies throughout the study period. Efforts towards improving beekeeper livelihoods, through higher hive productivity, should target moderately degraded and heterogeneous landscapes, which provide forage from diverse land covers.

Coexistence of honeybees with distinct mitochondrial haplotypes and hybridised nuclear genomes on the Comoros Islands.

The honeybee, Apis mellifera, is a globally distributed species that has spread both naturally and by humans across the globe resulting in many natural and secondary contact zones. The geographic isolation of honeybees is likely to contribute to genetic differentiation. Secondary contact has resulted in hybridization at the nuclear genome, but replacement of mitochondrial. Here, we used a mitochondrial marker and 19 microsatellite markers to test for the variations in the mitochondrial and nuclear genomes of honeybee populations on the Comoros islands. We used samples of 160 workers for mtDNA analysis and 288 workers from 16 colonies spread across the three islands for microsatellite analyses. Our results showed that the wild honeybee populations of the Comoros Islands consist of coexisting mitochondrial haplotypes. One belongs to the typical African A-lineage, and the other, the newly described L-lineage, is closely related to Apis koschevnikovi, a honeybee species native to Southeast Asia. The nuclear genomes show complete hybridization, high genetic diversity, and strong differentiation according to the island of origin. Based on our results, we hypothesise that the Asian honeybee could have been transported from Southeast Asia to Madagascar and Comoros via the human migrations that occurred 6000 years ago, and has hybridised with African honeybees at the nuclear genome, but maternal ancestry still can be traced using the mtDNA markers. We conclude that mtDNA plays a pivotal role in adaptation to the local environment, with both haplotypes of the honeybees of Comoros contributing significantly to the mito-nuclear coadaptation resulting in maintenance at almost equal frequency.

Population abundance of Varroa destructor and its effects on Apis mellifera scutellata colonies in Kenya.

The devastating effects of Varroa destructor Anderson and Trueman on Western honeybee colonies (Apis mellifera L.) have been well documented. Not only do these mites cause physical damage to parasitized individuals when they feed on them, but they also transmit viruses and other pathogens, weaken colonies and ultimately may cause their death. Unlike the subspecies of European origin, the honeybees of African origin suffer less from mite infestations. Absconding is one of the factors contributing to low V. destructor population in honeybee colonies as it creates a brood-free period. For a long time, researchers hypothesized that absconding was the main mechanism to control the parasite. The effects of V. destructor are well documented under temperate climatic conditions with a break during winter. Therefore, our study aimed at investigating the impact of V. destructor population growth on colony size, absconding and productivity under natural infestation levels of a tropical/subtropical climate with continuous brood production. We measured several characteristics related to the mite populations, the bee colonies and the resources of the bee colonies for a period of 8 months. The seven colonies that absconded during the study period were not influenced by densities of V. destructor. Absconding of the colonies occurred as a result of low numbers of capped brood. Mite densities were generally low throughout the study period (ranged between 26.9 and 59.8 mites per month) but were positively associated with adult bee densities. The amount of open and capped brood was positively associated with densities of V. destructor in the brood and negatively associated with denisities of V. destructor on screen boards, which appeared as extremely important factors that should be monitored regularly alongside colony stores and availability of pollen.

Detection of Pesticide Residues in Selected Bee Products of Honeybees (Apis melllifera L.) Colonies in a Preliminary Study from Seychelles Archipelago.

Pesticide residues in honey and pollen from Seychelles against a target of 108 pesticides using LC-MS/MS were analyzed. Fifteen pesticides were detected, at trace levels (< 15 ppb) and below the acceptable maximum residue limits (MRLs) as per EU regulations. In honey, six insecticide and three fungicide residues were detected. Eight insecticide and four fungicide residues were detected in the pollen matrix. The least contaminated honey and pollen samples had three and nine chemical residues respectively while the most contaminated honey and pollen samples had eight and eleven chemical residues respectively. Contact and oral LD50 values were used to calculate Pollen Hazard Quotients (PHQ) = concentration in ppb ÷ LD50 as µg/bee. The pollen hazard quotients (PHQ) obtained are way below those reported in literature. Residues were detected in low quantities, however, their high frequency and diversity and possible synergistic interactions may lead to negative impact on honeybees' health in Seychelles.

Genome-wide analysis of signatures of selection in populations of African honey bees (Apis mellifera) using new web-based tools.

BACKGROUND: With the development of inexpensive, high-throughput sequencing technologies, it has become feasible to examine questions related to population genetics and molecular evolution of non-model species in their ecological contexts on a genome-wide scale. Here, we employed a newly developed suite of integrated, web-based programs to examine population dynamics and signatures of selection across the genome using several well-established tests, including F ST, pN/pS, and McDonald-Kreitman. We applied these techniques to study populations of honey bees (Apis mellifera) in East Africa. In Kenya, there are several described A. mellifera subspecies, which are thought to be localized to distinct ecological regions. RESULTS: We performed whole genome sequencing of 11 worker honey bees from apiaries distributed throughout Kenya and identified 3.6 million putative single-nucleotide polymorphisms. The dense coverage allowed us to apply several computational procedures to study population structure and the evolutionary relationships among the populations, and to detect signs of adaptive evolution across the genome. While there is considerable gene flow among the sampled populations, there are clear distinctions between populations from the northern desert region and those from the temperate, savannah region. We identified several genes showing population genetic patterns consistent with positive selection within African bee populations, and between these populations and European A. mellifera or Asian Apis florea. CONCLUSIONS: These results lay the groundwork for future studies of adaptive ecological evolution in honey bees, and demonstrate the use of new, freely available web-based tools and workflows ( http://usegalaxy.org/r/kenyanbee ) that can be applied to any model system with genomic information.

Thrice out of Asia and the adaptive radiation of the western honey bee.

The origin of the western honey bee Apis mellifera has been intensely debated. Addressing this knowledge gap is essential for understanding the evolution and genetics of one of the world's most important pollinators. By analyzing 251 genomes from 18 native subspecies, we found support for an Asian origin of honey bees with at least three expansions leading to African and European lineages. The adaptive radiation of honey bees involved selection on a few genomic "hotspots." We found 145 genes with independent signatures of selection across all bee lineages, and these genes were highly associated with worker traits. Our results indicate that a core set of genes associated with worker and colony traits facilitated the adaptive radiation of honey bees across their vast distribution.

Investigating the viral ecology of global bee communities with high-throughput metagenomics.

Bee viral ecology is a fascinating emerging area of research: viruses exert a range of effects on their hosts, exacerbate impacts of other environmental stressors, and, importantly, are readily shared across multiple bee species in a community. However, our understanding of bee viral communities is limited, as it is primarily derived from studies of North American and European Apis mellifera populations. Here, we examined viruses in populations of A. mellifera and 11 other bee species from 9 countries, across 4 continents and Oceania. We developed a novel pipeline to rapidly and inexpensively screen for bee viruses. This pipeline includes purification of encapsulated RNA/DNA viruses, sequence-independent amplification, high throughput sequencing, integrated assembly of contigs, and filtering to identify contigs specifically corresponding to viral sequences. We identified sequences for (+)ssRNA, (-)ssRNA, dsRNA, and ssDNA viruses. Overall, we found 127 contigs corresponding to novel viruses (i.e. previously not observed in bees), with 27 represented by >0.1% of the reads in a given sample, and 7 contained an RdRp or replicase sequence which could be used for robust phylogenetic analysis. This study provides a sequence-independent pipeline for viral metagenomics analysis, and greatly expands our understanding of the diversity of viruses found in bee communities.

Evaluation of the distribution and impacts of parasites, pathogens, and pesticides on honey bee (Apis mellifera) populations in East Africa.

In East Africa, honey bees (Apis mellifera) provide critical pollination services and income for small-holder farmers and rural families. While honey bee populations in North America and Europe are in decline, little is known about the status of honey bee populations in Africa. We initiated a nationwide survey encompassing 24 locations across Kenya in 2010 to evaluate the numbers and sizes of honey bee colonies, assess the presence of parasites (Varroa mites and Nosema microsporidia) and viruses, identify and quantify pesticide contaminants in hives, and assay for levels of hygienic behavior. Varroa mites were present throughout Kenya, except in the remote north. Levels of Varroa were positively correlated with elevation, suggesting that environmental factors may play a role in honey bee host-parasite interactions. Levels of Varroa were negatively correlated with levels of hygienic behavior: however, while Varroa infestation dramatically reduces honey bee colony survival in the US and Europe, in Kenya Varroa presence alone does not appear to impact colony size. Nosema apis was found at three sites along the coast and one interior site. Only a small number of pesticides at low concentrations were found. Of the seven common US/European honey bee viruses, only three were identified but, like Varroa, were absent from northern Kenya. The number of viruses present was positively correlated with Varroa levels, but was not correlated with colony size or hygienic behavior. Our results suggest that Varroa, the three viruses, and Nosema have been relatively recently introduced into Kenya, but these factors do not yet appear to be impacting Kenyan bee populations. Thus chemical control for Varroa and Nosema are not necessary for Kenyan bees at this time. This study provides baseline data for future analyses of the possible mechanisms underlying resistance to and the long-term impacts of these factors on African bee populations.