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SNP Study Finds Invasive Honey Bees Nab Good Genes During Hybridization

NEW YORK (GenomeWeb News) – Honey bees repeatedly invading a new territory gain a genetic advantage by mixing with the native honey bees, new research suggests.
Two University of Illinois researchers used SNP analysis to compare subspecies of honey bees from sub-Saharan Africa with distantly related populations in other regions. Their results, published in the early, online edition of the Proceedings of the National Academy of Sciences yesterday, suggest invasive honey bees acquire some positive genetic attributes from native bees — even though they maintain most of their own characteristics.
There are about two dozen honey bee (Apis mellifera) sub-species, belonging to four geographically and genetically distinct groups in Africa, Asia, Eastern Europe, and Northern and Western Europe. Evidence suggests these bees originated in Africa and then expanded to other parts of the world in two or more distinct waves, giving rise to Western European honey bees in one event and Asian and Eastern European honey bees in another.
In 1956, African honey bees were intentionally introduced to Brazil — with catastrophic consequences. The bees hybridized with European bees to create aggressive, so-called “Africanized” or “killer” bees, which spread invasively into North and South America, displacing other, more docile, honey bee populations.
In an effort to understand how these hybrids were so successful, as well as bee evolution in general, entomologists Charles Whitfield and Amro Zayed used SNP analysis to look for genetic variation in bee populations around the world — from the Americas to Europe, Africa, and Asia. Specifically, they compared four native sub-Saharan honey bee groups with four groups derived from bees in the same region but now living in other places.
In a 2006 paper in Science, Whitfield’s team reported identifying more than 1,500 potential SNPs in the honey bee genome. For this study, though, Zayed and Whitfield honed in on 444 validated SNPs randomly distributed between coding and non-coding regions. Using BLASTN, along with information from the honey bee gene set OGSv1, they classified SNPs based on their position in exons, introns, or intergenic regions.
Because increased SNPs within the coding region are more likely to represent positive selection than those in the non-coding region, they were able to gauge the effects of adaptation and selection on the genome. Using this approach, they found evidence for positive selection on a tenth of the bees’ genome — between 852 and 1,371 genes — in the transition between African honey bees and West European honey bees.
In addition, such positive selection seemed to be associated with Africanized bees that had expanded into other regions. The researchers also detected signature regions within genes that were more likely to undergo positive selection. Areas that were GC-poor but AT-rich tended to undergo more changes under positive selection, a particularly interesting observation given that the honey bee genome overall tends to be AT-rich. 
They also found new evidence of invasive populations using exploitative hybridization, taking on positive traits from the population they displaced. “[W]hat we found was there was a preference for picking up functional parts of the western European genome over the nonfunctional parts,” Zayed said in a statement. “Those African bees are doing better because there were western European bees there for them to mix with. Now we can say we have a signature for evolution in the genome.”
Taken together, the results suggest that adaptive evolution played a key role both in the ancient expansion and modern invasions of African honey bees. And, since the invasive, Africanized, bees tend to preferentially incorporate coding regions from Western European bees into their genomes, the authors speculated that “multiple introductions can provide functional genetic diversity that facilitates adaptive evolution in economically damaging invasive species.”

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