Science & Technology - Posted by Jim Barlow-Oregon on Friday, February 26, 2010 11:38 - 4 Comments
Genomes tell ‘fishy’ story of adaptation

A six-member research team compared the genomes of threespine stickleback fish from lakes and saltwater sites in Alaska. Researchers found that all of the fish were closely related in most of their genomes, but with differences in very specific regions. Each fish contains 500 million base pairs of DNA. (Courtesy: U. Oregon)
U. OREGON (US)—Twenty billion pieces of DNA in 100 small fish have led biologists to an eye-opening discovery about evolution.
After combining new technologies, researchers now know many of the genomic regions that allowed an ocean-dwelling fish to adapt to fresh water in several independently evolved populations.
The discovery involved threespine stickleback fish taken from three land-locked freshwater Alaskan lakes and two ocean populations. The work appears in the Feb. 26 issue of PLoS Genetics.
Researchers from the University of Oregon were surprised to find that across the independently derived populations very similar regions were identified, indicating that the same genes may be evolving when stickleback adaptation is repeated in different lakes. Researchers now are focusing efforts to understand which specific genes are involved in such adaptation.
The approach taken in the study, says William Cresko, professor of biology and member of Oregon’s Center for Ecology and Evolutionary Biology, could be applied to other organisms. “It would be fascinating to determine whether similar results would be found in studies of ocean-dwelling sockeye salmon and their freshwater counterparts the Kokanee, for example.”
The findings, presented at professional conferences, he added, already are fueling research efforts in a variety of other organisms around the world.
The six-member research team combined Illumina massively parallel sequencing with a specialized technology that they developed. They then compared the genomes of 20 fish each from Alaska’s Bear Paw, Boot, and Mud lakes, and 20 each from saltwater populations in Rabbit Slough and Resurrection Bay.
All sites are located along Alaska’s south-central coast. Researchers found that all of the fish were closely related in most of their genomes, but with differences in very specific regions. Each fish contains 500 million base pairs of DNA.
Sticklebacks are a small silver-colored fish, barely two inches in length; they are found throughout the Northern Hemisphere in both oceans and freshwater.
“Populations of freshwater stickleback arise when new habitats open up and are colonized,” Cresko says. “Alaska has a lot of lakes that have been around only about 10,000 years, formed after glaciers receded. Instead of dying out when they were cut off from saltwater, they evolved very rapidly and in a lot of ways, such as in their bones and armor, the shapes of their jaws, as well as coloration and behavior. When one population no longer recognizes and won’t mate with another population, they effectively become a new species, so some of the regions we are identifying may be important for speciation, too.”
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. Until recently, efforts focused on small numbers of traits, tracking just a few genes at a time. In a 2006 talk, 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 Oregon’s Institute of Molecular Biology.
For the next three years, Cresko and Johnson worked to develop a technique they called Restriction-site Associated DNA 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 says. “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 says, “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 explains. “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 says.
The project was supported by the National Science Foundation and National Institutes of Health.
University of Oregon news: http://uonews.uoregon.edu/
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4 Comments
Elise Villemaire
With all due respect to the previous poster, everyone chooses to read science writings for the interesting studies and often, conclusions. I like not always being able to completely understand what I read. I get the vast majority and am left with some unanswered questions. On the other hand, a scientist or amateur in that subject might prefer having the higher level of technical detail.
This is good for everyone. A minimal amount of added explanation of terminology perhaps would lessen the unanswered questions, but only in certain areas. Don’t “dumb down” your articles! We need to be comfortable in our confusing world and with the idea that we don’t “get” everything. We are surrounded by unanswered questions and science is only a process in which we can attempt to find answers.
P.S.? I think it’s fascinating that with what sounds like a relatively simple tecnical test, humans have discovered that this particular mutation has been repeated over and over again. And it has been relatively quick, but what chance for quick enough to withstand this climate craziness our fossil fuel dependence has caused?
sido islwyn
I agree wholeheartedly with the previous post of Elise Villemaire, much more polite than mine will be. And would invite anyone who finds a term they do not understand to use a dictionary and the occasion to learn, instead of asking that a clearly high level educational site ” dumb down”. This is a site tailored to universirty graduates, where ways and hows of learning is the point of the exercise If this person, or any other, prefers brainpap, there are mahy other sites available that cater to that. If they are here, then one can safely assume that it is to open their learning banks and deposit into their accounts, certainly not to ask that the institution bankrupt itself.
Sharply impatient, yes, as this mewling is inappropriate and widespread and the results of concentrating on NOT challenging one’s capacities to learn correctly anything has led to some of the lowest levels of general ability in educated societies in centuries. Universities, and this site, are not there to teach people to handicap themselves, but how to escape any handicaps imposed and open their and others’ worlds to clarity, joy and creation.
And, as all artists know, that takes work and that work IS the interest and creating passion as well.
I have seen levels of basic English at my own Ivy League University that have left me sad, angry (as you see here) and very concerned for a society taught to be manipulatable and incapacitated, especially in its ability to judge and make an individual decision based on real knowledge and depth. If the English Graduate students at the Top Universities of the world cannot write correcly in their own language, who pulled one over on them and why would there be any reason, ever, to accept such dishonesty? So, T Colman, I would suggest that you honour yourself and other people of this world and of this particular readership more. Get a dictionary and start living, Learn, and give full support to others around you to do the same so that you are capable of making true judgements, and that your life is rich. Asking a Univeristy site to diminish the level of appropriate vocabulary and knowledge presented for YOU to learn with and from is entirely inappropriate judgement. Move your brain, and be happier for it. Life is very short…
Jim
As the writer of the news release in question, I appreciate the feedback. I agree with the comment that science stories should encourage people to consult their dictionaries or additional information as part of the learning and understanding process.
In this release, I attempted to provide definitions for terms could be new or tough, and also I assumed that some terms should be by now acceptable for general consumption, such as the word genome. In this decade of the sequencing and mapping of the human genome, I would assume the majority of readers would be familiar with the word and implications.
However, as a university science writer I am glad to be reminded that some people, such as the first writer, can be turned off by scientific terminology. I try to weave in definitions as part of my releases rather than bog them down with a glossary of terms. We university science writers need to be gently nudged to remove as much jargon as possible so that more people understand the science we describe.
In this case, the science is basic rather than applied. To say too much about the findings’ potential importance in the big picture of genetics could be dangerous. These findings are exciting and important to other scientists who may choose to adopt the technology for their own gene research and for the quest to understand how and which genes trigger adaptation. Application comes much later. For the public, the story provides a glimpse of basic science at work. Cures and advances don’t arise without basic understanding.
























This story needs to be re written so laypersons can understand what you are excited abou.
Whatever it is– genomic sequences are not something I run into every day.
I think you need a summary paragraph at the beginning saying what is happening and why it is so important. Then have someone speak in non RAD talk about how this might affect us, other research, and change our view of the wrold.
Thanks.
Timothy