By the end of our field work, we should have several tubes full of preserved bees, a hard drive full of pictures (about 10 of which will be any good), and plenty of blogworthy/non-blogworthy stories (hopefully none of which involve malaria). This is all well and good, but at the end of the day only one question really matters: what exactly can we learn from a bunch of preserved bees?
As Jeff mentioned yesterday, my background is in genomics, so I’ll be using these techniques to answer that question. Genomics seems to be a term that is thrown around quite a bit, but there are many people (let alone PhD students) who may be confused by what it actually means. As simple as I can put it: the field of genomics is concerned with analyzing the information contained within the genetic material that makes up individuals. Specifically, I’ll be working with other researchers at Penn State and elsewhere to analyze the genetic sequence of the bees we collect and the viruses that live inside them.
Each individual organism has a unique genetic makeup composed of a sequence of millions, billions or even trillions of small molecules known as nucleotides (ever seen the movie GATTACA?). Recent developments in technology allow researchers to quickly retrieve this trove of sequence information. Once the sequence data are in hand, a series of analyses can yield biologically and ecologically relevant results.
This work requires some “heavy-lifting” (as Jeff calls it) with computational and statistical tools to assemble the sequence data into full genomes, correct for errors inherent in the technology, and identify genetic differences between individuals. Once the genomes of individuals are assembled, we can then scan regions for places where there are many differences in the code within the same species, a potential hint at signs of recent selection or adaptation.
In fact, a team of researchers at Penn State and I have recently published a paper describing the development of some user-friendly, web-based stats tools to help researchers apply various methods to find these genomic regions suggestive of adaptive evolution. With potential regions ID’ed, we can then do more sophisticated analyses experimentally to link specific mutations to biological adaptations.
We’ll also take the virus genomes from the bees to identify the pathogens present in different populations across Kenya and use this information to study how these viruses spread across species.
Together, this genomics approach will allow us to study virus spread and genetic adaptations by bees to their spread. Basically we’re tracking an arms race!
Our final day at ICIPE has been busy but fun as we finalize logistics and supplies needed for the collections. Tomorrow we hit the road towards our first field site near Lake Naivasha, about a 90 km drive north west of Nairobi.
We will be joined by our driver and a collaborator from Jomo Kenyatta University of Agriculture and Technology (JKUAT). More to come soon (if we can get our internet stick to work…)
Special thanks to Dartmouth Beekeeping Society and to GoPro for helping us get set up prior to the trip. The video above is some test footage we took outside a Dartmouth hive in New Hampshire.