The genomic basis of evolutionary differentiation among honey bees.

In contrast to the western honey bee, Apis mellifera, other honey bee species have been largely neglected despite their importance and diversity. The genetic basis of the evolutionary diversification of honey bees remains largely unknown. Here, we provide a genome-wide comparison of three honey bee species, each representing one of the three subgenera of honey bees, namely the dwarf (Apis florea), giant (A. dorsata), and cavity-nesting (A. mellifera) honey bees with bumblebees as an outgroup. Our analyses resolve the phylogeny of honey bees with the dwarf honey bees diverging first. We find that evolution of increased eusocial complexity in Apis proceeds via increases in the complexity of gene regulation, which is in agreement with previous studies. However, this process seems to be related to pathways other than transcriptional control. Positive selection patterns across Apis reveal a trade-off between maintaining genome stability and generating genetic diversity, with a rapidly evolving piRNA pathway leading to genomes depleted of transposable elements, and a rapidly evolving DNA repair pathway associated with high recombination rates in all Apis species. Diversification within Apis is accompanied by positive selection in several genes whose putative functions present candidate mechanisms for lineage-specific adaptations, such as migration, immunity, and nesting behavior.

Comparative linkage mapping suggests a high recombination rate in all honeybees.

Meiotic recombination is required for proper chromosome assortment, and accordingly, 1-2 chiasmata per chromosome are found in most species. However, observed recombination rates deviate in some cases from neutral expectations between and within genomes and may play an important role in adaptive evolution. One potentially important argument for an adaptive evolution of recombination rates is the exceptionally high genome-wide recombination rates of social Hymenoptera, in particular the Western honeybee, Apis mellifera. It has the highest metazoan recombination rate reported so far. Proximate or ultimate causes for this elevated recombination rate have not yet been resolved. In a comparative study, we investigated meiotic recombination in the red dwarf honeybee Apis florea. Microsatellite markers developed for A. mellifera were genotyped in a natural mapping population of A. florea. From these genotypes, we calculated local recombination rates, using the physical distances from A. mellifera. In addition to a few comparisons of intervals across the genome, we particularly focused on chromosomes 3 and 12. Confirming marker synteny, we found that recombination rates in A. florea are as high as or higher than those in A. mellifera. Our results are limited to select genomic regions but suggest that A. florea also exhibits an exceptionally high genome-wide recombination rate. This trait may thus occur genus wide. Although our study cannot identify a single explanation for the high rates of recombination in Apis, it favors hypotheses that apply to the entire genus. Furthermore, we conclude that the genome structure of the 2 species has been largely conserved, at least in the parts we investigated.

Evidence for convergent nucleotide evolution and high allelic turnover rates at the complementary sex determiner gene of Western and Asian honeybees.

Our understanding of the impact of recombination, mutation, genetic drift, and selection on the evolution of a single gene is still limited. Here we investigate the impact of all these evolutionary forces at the complementary sex determiner (csd) gene that evolves under a balancing mode of selection. Females are heterozygous at the csd gene and males are hemizygous; diploid males are lethal and occur when csd is homozygous. Rare alleles thus have a selective advantage, are seldom lost by the effect of genetic drift, and are maintained over extended periods of time when compared with neutral polymorphisms. Here, we report on the analysis of 17, 19, and 15 csd alleles of Apis cerana, Apis dorsata, and Apis mellifera honeybees, respectively. We observed great heterogeneity of synonymous (piS) and nonsynonymous (piN) polymorphisms across the gene, with a consistent peak in exons 6 and 7. We propose that exons 6 and 7 encode the potential specifying domain (csd-PSD) that has accumulated elevated nucleotide polymorphisms over time by balancing selection. We observed no direct evidence that balancing selection favors the accumulation of nonsynonymous changes at csd-PSD (piN/piS ratios are all <1, ranging from 0.6 to 0.95). We observed an excess of shared nonsynonymous changes, which suggest that strong evolutionary constraints are operating at csd-PSD resulting in the independent accumulation of the same nonsynonymous changes in different alleles across species (convergent evolution). Analysis of csd-PSD genealogy revealed relatively short average coalescence times ( approximately 6 Myr), low average synonymous nucleotide diversity (piS < 0.09), and a lack of trans-specific alleles that substantially contrasts with previously analyzed loci under strong balancing selection. We excluded the possibility of a burst of diversification after population bottlenecking and intragenic recombination as explanatory factors, leaving high turnover rates as the explanation for this observation. By comparing observed allele richness and average coalescence times with a simplified model of csd-coalescence, we found that small long-term population sizes (i.e., N(e) < 10(4)), but not high mutation rates, can explain short maintenance times, implicating a strong historical impact of genetic drift on the molecular evolution of highly social honeybees.

Marked interspecific differences in the neuroanatomy of the male olfactory system of honey bees (genus Apis).

All honey bee species (genus Apis) display a striking mating behavior with the formation of male (drone) congregations, in which virgin queens mate with many drones. Bees' mating behavior relies on olfactory communication involving queen-but also drone pheromones. To explore the evolution of olfactory communication in Apis, we analyzed the neuroanatomical organization of the antennal lobe (primary olfactory center) in the drones of five species from the three main lineages (open-air nesting species: dwarf honey bees Apis florea and giant honey bees Apis dorsata; cavity-nesting species: Apis mellifera, Apis kochevnikovi, and Apis cerana) and from three populations of A. cerana (Borneo, Thailand, and Japan). In addition to differences in the overall number of morphological units, the glomeruli, our data reveal marked differences in the number and position of macroglomeruli, enlarged units putatively dedicated to sex pheromone processing. Dwarf and giant honey bee species possess two macroglomeruli while cavity-nesting bees present three or four macroglomeruli, suggesting an increase in the complexity of sex communication during evolution in the genus Apis. The three A. cerana populations showed differing absolute numbers of glomeruli but the same three macroglomeruli. Overall, we identified six different macroglomeruli in the genus Apis. One of these (called MGb), which is dedicated to the detection of the major queen compound 9-ODA in A. mellifera, was conserved in all species. We discuss the implications of these results for our understanding of sex communication in honey bees and propose a putative scenario of antennal lobe evolution in the Apis genus.

"Up" or "down" that makes the difference. How giant honeybees (Apis dorsata) see the world.

A. dorsata builds its large exposed comb high in trees or under ledges of high rocks. The "open" nest of A. dorsata, shielded (only!) by multiple layers of bees, is highly vulnerable to any kind of direct contact or close range attacks from predators. Therefore, guard bees of the outer layer of A. dorsata's nest monitor the vicinity for possible hazards and an effective risk assessment is required. Guard bees, however, are frequently exposed to different objects like leaves, twigs and other tree litter passing the nest from above and falling to the ground. Thus, downward movement of objects past the nest might be used by A. dorsata to classify these visual stimuli near the nest as "harmless". To test the effect of movement direction on defensive responses, we used circular black discs that were moved down or up in front of colonies and recorded the number of guard bees flying towards the disc. The size of the disc (diameter from 8 cm to 50 cm) had an effect on the number of guard bees responding, the bigger the plate the more bees started from the nest. The direction of a disc's movement had a dramatic effect on the attraction. We found a significantly higher number of attacks, when discs were moved upwards compared to downward movements (GLMM (estimate ± s.e.) 1.872 ± 0.149, P < 0.001). Our results demonstrate for the first time that the vertical direction of movement of an object can be important for releasing defensive behaviour. Upward movement of dark objects near the colony might be an innate releaser of attack flights. At the same time, downward movement is perceived as a "harmless" stimulus.

A New Metazoan Recombination Rate Record and Consistently High Recombination Rates in the Honey Bee Genus Apis Accompanied by Frequent Inversions but Not Translocations.

Western honey bees (Apis mellifera) far exceed the commonly observed 1­2 meiotic recombination events per chromosome and exhibit the highest Metazoan recombination rate (20 cM/Mb) described thus far. However, the reasons for this exceptional rate of recombination are not sufficiently understood. In a comparative study, we report on the newly constructed genomic linkage maps of Apis florea and Apis dorsata that represent the two honey bee lineages without recombination rate estimates so far. Each linkage map was generated de novo, based on SNP genotypes of haploid male offspring of a single female. The A. florea map spans 4,782 cM with 1,279 markers in 16 linkage groups. The A. dorsata map is 5,762 cM long and contains 1,189 markers in 16 linkage groups. Respectively, these map sizes result in average recombination rate estimates of 20.8 and 25.1 cM/Mb. Synteny analyses indicate that frequent intra-chromosomal rearrangements but no translocations among chromosomes accompany the high rates of recombination during the independent evolution of the three major honey bee lineages. Our results imply a common cause for the evolution of very high recombination rates in Apis. Our findings also suggest that frequent homologous recombination during meiosis might increase ectopic recombination and rearrangements within but not between chromosomes. It remains to be investigated whether the resulting inversions may have been important in the evolutionary differentiation between honey bee species.

Whole-genome scan in thelytokous-laying workers of the Cape honeybee (Apis mellifera capensis): central fusion, reduced recombination rates and centromere mapping using half-tetrad analysis.

While workers of almost all subspecies of honeybee are able to lay only haploid male eggs, Apis mellifera capensis workers are able to produce diploid female eggs by thelytokous parthenogenesis. Cytological analyses have shown that during parthenogenesis, egg diploidy is restored by fusion of the two central meiotic products. This peculiarity of the Cape bee preserves two products of a single meiosis in the daughters and can be used to map centromere positions using half-tetrad analysis. In this study, we use the thelytokous progenies of A. m. capensis workers and a sample of individuals from a naturally occurring A. m. capensis thelytokous clone to map centromere position for most of the linkage groups of the honeybee. We also show that the recombination rate is reduced by >10-fold during the meiosis of A. m. capensis workers. This reduction is restricted to thelytokous parthenogenesis of capensis workers and is not observed in the meiosis of queen within the same subspecies or in arrhenotokous workers of another subspecies. The reduced rate of recombination seems to be associated with negative crossover interference. These results are discussed in relation to evolution of thelytokous parthenogenesis and maintenance of heterozygosity and female sex after thelytoky.

Extensive population admixture on drone congregation areas of the giant honeybee, Apis dorsata (Fabricius, 1793).

The giant honeybee Apis dorsata often forms dense colony aggregations which can include up to 200 often closely related nests in the same location, setting the stage for inbred matings. Yet, like in all other Apis species, A. dorsata queens mate in mid-air on lek like drone congregation areas (DCAs) where large numbers of males gather in flight. We here report how the drone composition of A. dorsata DCAs facilitates outbreeding, taking into the account both spatial (three DCAs) and temporal (subsequent sampling days) dynamics. We compared the drones' genotypes at ten microsatellite DNA markers with those of the queen genotypes of six drone-producing colonies located close to the DCAs (Tenom, Sabah, Malaysia). None of 430 sampled drones originated from any of these nearby colonies. Moreover, we estimated that 141 unidentified colonies were contributing to the three DCAs. Most of these colonies were participating multiple times in the different locations and/or during the consecutive days of sampling. The drones sampled in the DCAs could be attributed to six subpopulations. These were all admixed in all DCA samples, increasing the effective population size an order of magnitude and preventing matings between potentially related queens and drones.