Sticklebacks have long been a focus for behavioral biologists because of their complex courtship rituals. Only recently have they come under genetic and genomic scrutiny, and the UO has been at the forefront of such studies. Until recently, efforts focused on small numbers of traits, tracking just a few genes at a time. In a 2006 talk on campus, Cresko outlined the challenges of the research, saying that faster, cheaper DNA-analyzing tools were needed to scan entire genomes. In the audience was Eric Johnson of the UO's Institute of Molecular Biology.
For the next three years, Cresko and Johnson worked to develop a technique they called Restriction-site Associated DNA -- the development of which helped spawned Floragenex, a UO technology spinoff company -- and subsequently combined it with a genomic revolution called Next Generation Sequencing using a genome-analyzer tool known as Illumina's GA2 sequencer.
"We combined two technologies to develop sequence RAD (restricted-site associated DNA) tags," Cresko said. "With this, we can quickly look across entire genomes and ask new questions: Can we find genomic regions that were altered due to natural selection? And then compare this with a completely evolved population? How many regions are the same, how many are different?"
Previous research using RAD markers had focused on finding differences between samples grown in labs, Johnson said, "but many interesting biological questions can't be assayed in a lab, and many species of animals cannot be reared in a lab."
"Bill's lab showed that RAD markers can detect differences between natural populations, and his lab developed new analytical tools to understand the data," Johnson said. "It is a great fit for RAD markers, because they sample a genome at a higher density than other marker systems and provide DNA sequence data at a low error rate -- two crucial aspects for this kind of study."
Once the technology was ready, it took Cresko's team about six months to run the DNA analyses. Now that the technique is operating smoothly, the same experiments might be done in several weeks, he said.
Under a new NSF-funded project under the American Recovery and Reinvestment Act, Cresko and Frank von Hippel, a University of Alaska biologist, are looking closely at another set of stickleback populations. They are working on lakes formed when the 1964 Alaska earthquake lifted several offshore islands 10 meters (32.8 feet) in four minutes. "We hope to learn something about these fish while they are still evolving, literally, from an ocean population to a freshwater one," Cresko said.