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Population Sequencing Study Highlights Honeybee History, Adaptations

NEW YORK (GenomeWeb) – A population sequencing study published online this weekend in Nature Genetics suggests the honeybee species Apis mellifera is descended from bees that originated in Asia rather than from African bees.

"The evolutionary tree we constructed from genome sequences does not support an origin in Africa," Matthew Webster, a medical biochemistry and microbiology researcher at Uppsala University, said in a statement. He said the analysis "gives us new insight into how honeybees spread and became adapted to habitats across the world."

Webster led an international team that re-sequenced the genomes of 140 honeybees from more than a dozen honeybee populations and sub-species around the world. Using millions of SNPs detected in the bee genomes, the group started untangling relationships between the populations, along with the historical events and adaptive processes that have shaped honeybee genomes at various sites.

For example, the researchers saw signs of honeybee population growth in Africa during glaciation periods that affected other parts of the planet some 20,000 years ago, followed by more recent population dips. Conversely, European honeybees apparently dwindled during those ice ages but experienced population bursts between glacial periods.

"Our analysis indicates that honeybee population sizes have varied greatly in the past, likely owing to climactic changes," the researchers wrote.

In present day honeybee populations, meanwhile, they saw relatively high levels of genetic diversity — especially amongst managed bees — despite domestication and recent population scourges such as colony collapse disorder.

"In contrast to other domestic species, management of honeybees seems to have increased levels of genetic variation by mixing bees from different parts of the world," Webster said. "The findings may also indicate that high levels of inbreeding are not a major cause of global colony losses."

Honeybees pollinate a substantial fraction of food crops, providing an estimated $200 billion or more in agricultural services annually, Webster and his co-authors noted. Given the economic and ecological importance of the insects, which have been used by humans for some 7,000 years, the researchers hoped to get a better sense of honeybee history and the current genetic landscape for A. mellifera.

The team used a Thermo Fisher Scientific Applied Biosystems SOLiD 5500xl instrument to sequence samples of 140 worker bees from unrelated colonies representing 14 populations and several different A. mellifera sub-species. It also assessed 10 A. cerana workers bees from Japan and a drone bee descended from the same line used to develop the first honeybee reference genome.

Together, the re-sequenced honeybees ran the gamut of populations present around the world — from mixed ancestry bees harvested at European or North American apiaries to Africanized honeybees from South America and native sub-species collected at African, western Asian, and European sites during initial honeybee expansions.

By putting these sequences up against the honeybee reference genome, the researchers tracked down 8.3 million SNPs, which they subsequently used to construct a bee tree comprising four main clusters.

African sub-species fell into the so-called A group of honeybees, while sub-species from the Middle East and western Asian made up group O. Group C largely contained honeybee sub-species from eastern and southern Europe, the team noted, with western and northern European bees belonging to the group M cluster.

The "Africanized" bees from South America tended to cluster with honeybee groups found in Africa, though they had a smattering of variants that share closer genetic ties to the group M bees from Europe.

Based on the broader patterns identified in that phylogenetic tree, the researchers argued that honeybees do not appear to have originated in Africa, as previously proposed, but are more likely to have their roots in Asia, where a wide range of Apis species are still found.

The genetic diversity displayed by honeybee populations as a whole was high, they found, but was particularly pronounced among the domestic honeybee strains kept by beekeepers, which tended to be hybrid strains that clustered broadly with the bees in eastern and southern Europe.

Within the native bee sub-species, on the other hand, the African bees had greater genetic variation than their European counterparts, with native Middle Eastern bees falling somewhere between them.

A look at the genetic variants and gene expression profiles that differed in queen bees, drones, and workers, as well as bees from different parts of the world, provided hints about the selective pressures that have influenced the honeybee genome and their functional effects.

When they compared African and European bee populations, for instance, the researchers detected distinct SNP patterns in and around hormone- and odor receptor-related genes. They also saw differences in genes involved in antibacterial activity, innate immunity, and wound healing, consistent with known differences in African bees' ability to survive Varroa mite infections.

By getting a glimpse at the adaptive mechanisms that honeybees have used to deal with pathogens, disease, and environmental changes in the past, the study's authors explained, it may be possible to develop strategies for helping the insects deal with these and other challenges in the future.

"The study provides new insights into evolution and genetic adaptation, and establishes a framework for investigating the biological mechanisms behind disease resistance and adaptation to climate, knowledge that could be vital for protecting honeybees in a rapidly changing world," Webster said.