Gentle Africanized Honeybees

An interesting article from the science magazine Nature Communications. It’s about microevolution in africanized honeybees in Puerto Rico, where gentle behaviour has developed by selection pressure, as it seems.

Africanized bees provide hope in the management of the Varroa mite. Not a problem here yet, but might become any time in the future.

I have left out the scientific details, leaving only the parts readable by non-scientists. The full paper has been just published and is available online.

Enjoy the reading

Nature Communications 2017

A soft selective sweep during rapid evolution of gentle behaviour in an Africanized honeybee

Arian Avalos, Hailin Pan, Cai Li, Jenny P. Acevedo-Gonzalez, Gloria Rendon, Christopher J. Fields, Patrick J. Brown, Tugrul Giray, Gene E. Robinson, Matthew E. Hudson & Guojie Zhang

Highly aggressive Africanized honeybees (AHB) invaded Puerto Rico (PR) in 1994, displacing gentle European honeybees (EHB) in many locations. Gentle AHB (gAHB), unknown anywhere else in the world, subsequently evolved on the island within a few generations. Here we sequence whole genomes from gAHB and EHB populations, as well as a North American AHB population, a likely source of the founder AHB on PR. We show that gAHB retains high levels of genetic diversity after evolution of gentle behaviour, despite selection on standing variation. We observe multiple genomic loci with significant signatures of selection. Rapid evolution during colonization of novel habitats can generate major changes to characteristics such as morphological or colouration traits, usually controlled by one or more major genetic loci. Here we describe a soft selective sweep, acting at multiple loci across the genome, that occurred during, and may have mediated, the rapid evolution of a behavioural trait.

In 1956, the escape of experimental colonies of an African subspecies of honeybee (Apis mellifera scutellata) in Brazil led to broad scale interbreeding with the local European-derived honeybees (EHB)1. This resulted in the infamously aggressive, admixed, invasive, New World hybrid population of Africanized honeybees (AHB). AHB achieved its current intercontinental distribution within 30 years, and is now commonly found in the Neotropic and southern ranges of the Nearctic2, 3. Aggression of AHB towards humans is well documented4 and has caused several deaths and widespread public concern in many geographic locations previously dominated by EHB2, 4. In 1994, highly aggressive, invasive AHB was first detected in the Caribbean Islands, in Puerto Rico5.

A remarkable characteristic of the Puerto Rico invasion is that within ca. 12 honeybee generations 1994–2006, the highly aggressive founder AHBs had undergone a drastic reduction in aggression6, resulting in gentle AHB (gAHB). Current levels of aggression in the Puerto Rico gAHB population resemble those observed in EHB. However, gAHB retains other traits typically associated with AHB, e.g., morphometric dimensions, Varroa parasite removal behaviours, and faster queen development6.

Aggression is generally polygenic7 and its adaptive value dependent on environmental interactions, making it unlikely that a simple selective sweep can explain rapid evolution of this complex behavioural trait. Rapid phenotypic change on similar timescales to the evolution of gentleness in gAHB has been widely documented across a spectrum of organisms, yet the mechanisms mediating these changes differ from classical models of selection8,9,10,11,12. Mounting evidence suggests that admixture13 or selective sweeps at one or more loci14 likely mediate such rapid changes in phenotype. However, few examples are known of rapid evolution in behavioural traits, and without genomic analysis it is not clear how such a complex trait might undergo rapid change outside the context of selective breeding. Because they depend on the combined, possibly epistatic interactions of many gene products7, many of which may have multiple functions, behavioural phenotypes are likely to require more complex models than those where single loci confer clear selective advantages in isolation, and are ultimately swept to fixation when under sustained selection.

To understand how this remarkable decrease in aggression evolved so rapidly, we sequenced whole genomes of gAHB from Puerto Rico, AHB from Mexico, and EHB from the U.S. (n = 30 from each of the three populations) at an average of ×20 coverage. This resulted in 2,808,570 SNP variants, which were characterized within and between populations. We took advantage of the honeybee’s haplodiploid sex determination system and sequenced only haploid (male) genomes, to eliminate ambiguity in the haplotype phase. We hypothesized that the genomic regions under selection unique to the evolution of gAHB would be those that differ from AHB, exhibit a more EHB-like allelic profile, and are under positive selection unique to the island population. To simplify our analysis, we investigated whether the decrease in aggression in gAHB was accompanied by altered frequency of the same alleles as those under selection during the evolution of EHB, which also originated from aggressive populations in Africa in the Pleistocene15, 16 This assumption allowed us to develop a statistically powerful, triangulated analysis.

Our approach identified genomic regions under selection in gAHB that also show EHB-like allelic profiles. These are candidate loci for the EHB-like aggression of gAHB. Haplotype block analysis of these regions showed many haplotypes not found in either of our EHB or AHB populations rapidly became common in gAHB, but that few haplotypes in any regions under selection were fixed in the gAHB population. We conclude that a soft selective sweep across many loci in the genome accompanied, and may be responsible for, the reduction in aggression experienced by the founding AHB as it evolved towards gAHB.

Here we show that gAHB evolved via selective pressure on standing variation within an admixed North American AHB founder population that arrived on Puerto Rico. Genomic regions showing signatures of selection in gAHB (Fig. 1) contain multiple haplotypes at approximately equivalent frequencies (Fig. 2b). This is consistent with the F ST results, which showed that while signatures of selection are present, few alleles are truly fixed in any of the three populations (Fig. 1, Supplementary Fig. 6). Multiple haplotypes with similar frequencies and low degrees of fixation are characteristics of soft selective sweeps9, 30, 31. We therefore conclude that a soft selective sweep occurred in gAHB, and that this accompanied and perhaps mediated a rapid change in behaviour across the population.

Our results contrast with the evolution of decreased aggression by artificial selection during vertebrate domestication32. In domestication, extreme selection pressure and control of pedigree generally leads to hard selective sweeps, and decreased aggression is often associated with retention of juvenile characteristics together with color and morphology changes in a domestication syndrome33. In gAHB, aggressive behaviour in colony defense showed rapid evolutionary change but other characteristics such as morphology, queen pupation rate, and aggression against parasites remained unchanged6. Although predecessors of the EHB population also evolved from an African precursor most similar to the current A genetic group15, the distinct population genetics of gAHB relative to all domesticated bees (Fig. 3b) shows that gAHB and EHB arose by separate events. Gentle honeybees have thus arisen multiple times, from different founder populations, by related but distinct population genetic mechanisms, and with at least some similarities in genetic architecture.

The selection pressure that led to gentleness in gAHB maintained both genetic diversity and other AHB characteristics. Our csd analysis suggests that this occurred despite a genetic bottleneck. We did not observe the evidence of balancing selection in csd expected if sex determination was a driver of gAHB evolution. Also, the high likelihood of diploid male production in gAHB suggests that the cost of the genetic bottleneck is outweighed by the selective advantages of gAHB.

The forces driving the evolution of gAHB are challenging to determine conclusively. We propose that a combination of three factors, negative human–honeybee interactions, geographic isolation, and low levels of predation on honeybee colonies, may have driven selection against honeybee aggression in Puerto Rico, which is presently the only place in the New World where gentle Africanized honeybees have evolved. First, the human population density in Puerto Rico is the highest within the range of any AHB population in the New World34. Destruction of highly aggressive colonies in the expanding AHB population by humans early in the invasion period was likely more frequent than in other New World ecosystems, acting as one key selective force. Second, geographical isolation of Puerto Rico would have increased the selective potency of these negative human–honeybee interactions. The island is remote enough to present serious barriers to natural insect dispersal, particularly to a swarm-founding species such as the honeybee, limiting escape. Third, Puerto Rico does not have major vertebrate35 or invertebrate36 colony-level predators common elsewhere in the range of AHB, likely relaxing selection favouring aggression in feral colonies. Thus, selection likely eliminated the most aggressive of the invasive AHB colonies. With reduced competition for floral resources, gentler colonies would have increased reproductive success. In addition, reduced aggression may also have served as an exaptation, enabling exploitation of nesting sites and resources in urban landscapes inaccessible to the more aggressive AHB colonies. These factors would effectively increase the frequency of certain AHB haplotypes at the expense of most others (Fig. 2). Some of these haplotypes, in combination, presumably confer gentle behaviour.

According to this scenario, the founder AHB population would have experienced an initial strong selective pressure towards reduced aggression, which would stabilize as gentle colonies became predominant and instances of negative interactions with humans decreased. High recombination rates in honeybees make selection for multiple loci extremely efficient and may facilitate the speed of evolution in honeybees.

Although we favor initial pressure from unsupervised human-driven selection as a primary driver in the evolution of gAHB, alternatives exist. One possibility is that the founding AHB colony happened to be biased towards haplotypes conferring gentle behaviour, which are now over-represented in gAHB as a result of drift in the founder population followed by a genetic bottleneck. It could be the case that, by chance, the founding AHB colony contained a relatively high proportion of alleles conducive to gentleness. All available reports6 indicate that the founding AHB population in PR was aggressive, and that the reduction in aggression characteristic of gAHB arose after the invasion. Aggression in all other AHB invasion events has been shown to be adaptive and dominant1, 4, hence the expectation in PR was a retention of aggressiveness even if associated haplotypes were initially present in low frequencies. This has not been the case, suggesting a countering factor. We conclude that selection for gentle behaviour, or associated traits, is this factor. Further, the signatures of selection identified here via allele frequency are corroborated by Rsb (i.e., linkage disequilibrium) measures. As linkage disequilibrium is rapidly lost in honey bee populations due to their extreme recombination rates, retention of linkage is a strong indicator of recent selective pressure. Finally, we observe haplotypes at loci under selection in gAHB that are rare or absent in the presumed AHB source population.

Another factor that could be related to the evolution of gAHB is the constraint presented by resource cycles in tropical oceanic islands6, 37. According to this scenario, selection towards a more EHB-like resource acquisition strategy may have led to the current gAHB. This could only occur if either the same underlying traits and loci are involved in resource acquisition and aggression, if these loci are linked genetically, or by epistatic interactions. This speculative explanation would also be consistent with the observed soft selective sweep, retaining AHB haplotypes that likely confer aggressive traits in the population.

Our findings have implications for understanding both rapid evolution and the genetics of biological invasions in colonial organisms. We show that haplotypes not found in our EHB or AHB samples rapidly became common in gAHB. These haplotypes were either present but rare in the founder population, or emerged after the invasion event. Rapid emergence of new haplotypes in honeybees is likely, due to their following genetic characteristics: high within-colony genetic diversity38, extremely high recombination rates23, and extensive outcrossing and thus gene flow between colonies39. Some newly emerged haplotypes may be the key to the separation of aggression at the colony level from other traits that was observed for the first time in gAHB. The future events in this selective process are uncertain. One possibility, consistent with classical evolutionary theory, is that the observed soft selective sweep would harden as the evolutionary process continued, fixing the less aggressive behaviour in the population. However, colony-level selection and haplodiploid outbreeding likely affect the population dynamics even of highly favorable alleles in honeybees in ways that may promote soft over hard selection over longer timescales. We suggest that these factors provide a selective advantage to the species as a whole by enabling multiple, sequential adaptive radiations. Such an advantage in invasive situations could explain the overall success of the haplodiploid system despite its very high biological cost25.

It is also noteworthy that gentle honeybees that are genetically distinct from the extant EHB populations can evolve rapidly from a small founder population of AHB. This is an important result as EHB in particular are principal pollinators of many domesticated plant species, but they are under threat from multiple sources, endangering production of many important agricultural and horticultural crops. Genetically diverse gentle honeybees could help secure agricultural production by providing pollinators more resistant to threats such as parasites and diseases. The evolution of gAHB also provides a paradigm for the adaptation of social organisms to new environments. The ability of eusocial insects to generate and maintain diversity within a colony at loci mechanistically involved with complex traits such as behaviour may be a key to their evolutionary success.