At first glance, the three-spined stickleback seems like an unassuming little fish.  But now that scientists have unspooled its DNA and opened up its entire genetic library for inspection, the stickleback has proven to be a powerful tool for studying the genetic roots of evolution.

The cool thing about these fish is that they've not just evolved once -- they've evolved over and over again, says Howard Hughes Medical Institute and Stanford University researcher David Kingsley, the senior author of a new paper appearing in Nature on Wednesday that details the genetic traces of the stickleback's evolutionary path.

Most sticklebacks have a life cycle similar to salmon -- they live in the ocean, but swim into freshwater to spawn.

As the last Ice Age ended tens of thousands of years ago, marine sticklebacks have chased melting glaciers from the sea into new freshwater environments, where they adapted to a more stripped-down appearance: a sleeker shape with less bony body armor. The marine sticklebacks also had to make changes to their color, salt tolerance, and mating preferences to adapt to their new environment, and the process repeated throughout the globe as different populations moved upstream.

We've got many independent cases of adaptation to freshwater, says Michael Bell, a Stony Brook University stickleback researcher who has collaborated with Kingsley but is unaffiliated with the current study.

By looking and seeing which versions of genes are shared amongst far-flung populations of sticklebacks, we can see what's really important for adaption to freshwater, Bell says.

Kingsley and his colleagues sequenced not just one, but 21 stickleback genomes -- the entire library of DNA. They compared sequences from freshwater and seawater sticklebacks that lived near each other to see how their genetic code differed. By examining differences between the linked pairs of marine and freshwater fish, the researchers were able to see how the genome changed as the fish evolved.

The idea wasn't so much to look for specific genes for armor plating or color, but rather to look at the larger picture of what areas of the genome changed in the freshwater sticklebacks.

What we're seeing in this study is a whole suite of genetic variance that's involved in adapting to new environments, said Kingsley.

Still, now researchers can zero in on specific genes that may play a role in various  adaptations to freshwater, according to Bell.
What's more, we can find out which part of the gene is the functionally important part, Bell says.

The scientists found 147 regions in the fish's genome - constituting about .2 percent of all of the stickleback's DNA - that looked very similar in freshwater fish across the globe, but which differed from the same regions in marine fish. This consistent difference between the two kinds of sticklebacks suggests that each time the fish left the sea, they reused this group of genes in order to remodel themselves into forms better suited to freshwater, according to Kingsley.

What's more, those key regions of the genome involved in adaptation weren't randomly scattered; they were clustered in certain sections on certain chromosomes.

We're real curious about those mechanisms that hold those regions into a block, Kingsley said.

The paper also addressed a longstanding debate within evolutionary genetics: whether evolutionary adaptations are primarily driven by new mutations in the coding sequence of DNA, or by mutations in the regulatory sections of genes that determine how existing variations in genes are expressed in the organism.

In the stickleback, the answer isn't necessarily one or the other, as Kingsley and his team found both kinds of mechanisms at work. But one mechanism seems to dominate: in the genetic regions they suspect are involved in adaptation to freshwater, the ratio of regulatory mutations to coding mutations was around 4 to 1.

Dolph Schluter, another researcher unaffiliated with the Nature paper who studies sticklebacks at the University of British Columbia, was especially enthusiastic about the study. He said that all matter of future work will build from these findings.

The paper is a bloody marvel! Schluter said in an email. Beautiful, clever, and with results that will last and last.