Not far from milepost 200 on a stretch of the Pacific Coast Highway near the Oregon Dunes National Recreation Area is a humble water hole known in some biology circles as Slimy Log Pond. It was from this inauspicious pool that a water flea (Daphnia pulex) dubbed The Chosen One was plucked in 2000, and became the first crustacean to have its genome sequenced.

Analysis of The Chosen One's genome shows that this Lilliputian crustacean contains the most genes of any animal sequenced to date. It also has the potential to accelerate scientists' understanding of synthetic chemicals' effects on the environment—and human health.

The world's most common small freshwater feeder—gobbling up algae in lakes and ponds the world over—Daphnia are also a staple in fishes' diets, proving a crucial link in food webs. This miniscule animal—barely visible to the naked eye—has long been an invaluable aquatic indicator species and is used by agencies across the globe to take stock of the health of freshwater systems.

As such a well-studied species, Daphnia are poised to become a key model organism to delve deeper in the study of environmental genomics. Improved understanding of the interactions among genes and the environment could also diminish the deleterious effects of chemicals on human health as well.

The sequence details, published online February 3 in Science, turned up the most shared genes with humans of any arthropod that has been sequenced to date. This genetic overlap means that the sentinel species could also end up being "a surrogate for humans to show the effects of the chemicals on shared pathways," says John Colbourne of Indiana University Bloomington's Center for Genomics and Bioinformatics and the lead author on the new paper. "The majority of the genome is a reflection of how the animal has evolved to cope with environmental stress."

Previous genetic snapshots of Daphnia have hinted at its overall makeup. But whole genome sequences provide "much better information about the function of genes, and allow us to be much more comprehensive in understanding the effects of toxicants," says Chris Vulpe of the Nutritional Science and Toxicology group at University of California, Berkeley, who was not involved in the new study. "It really adds to your ability to understand what's going on" in the environment.

Muddy biology
Named for the Greek mythological nymph Daphne (who shuns the god Apollo's advances and in Ovid's telling was transformed into a tree), aquatic Daphnia, with its gently branching antennae, generally reproduce without males by passing along a diploid genome (a complete set of chromosomes) to offspring. This consistency creates clone lines, making them excellent candidates for laboratory study.

But like the water they often live in, these crustaceans "have a really muddy biology," Colbourne says. That murkiness, however, has turned out to be fertile territory for genetic research, he notes. "The genome is a lot more plastic and a lot more responsive to the environment than we had given it credit for."

Researchers working to sequence Daphnia—as part of the Daphnia Genomics Consortium—were expecting to find one about the size of the fruit fly, with its 14,000 genes. So they were stunned to find that the D. pulex genome contains at least 30,907 genes—nearly 8,000 more than the human genome. Some 36 percent of these genes have not previously been identified in any other organism. And researchers found that rather than being evolutionary deadweight, most of these unfamiliar genetic signatures "tend to be the genes that are most responsive to Daphnia's ecology," Colbourne says.

Not all of the crustacean's genes are active at any given time. Rather, a large portion of them are switched on or off with changes in the flea's environment. They are "more or less environment-specific," Colbourne says. Although they are "coding for the same proteins, they're being expressed differently depending on what environmental stresses you expose the animal to." And finding the genes that allow the animal to tolerate outside stressors—whether they are chemicals or UV radiation—could help researchers search for parallel pathways in humans.

Modeling complexity
One of the reasons the Daphnia genome contains so many genes, the researchers found, is because gene duplication in this species occurs at a much higher rate than in other familiar species—about 30 percent higher rate than in humans and about three times the rate in fruit flies.

"There's obviously a selective advantage to having so many genes," Colbourne says. "We were able to discover for the very first time that newly duplicated genes can acquire new functions very, very rapidly." In other species duplicate genes tend to become harmful or irrelevant and thus get weeded out quickly. Daphnia genes stick around longer, suggesting that they are often put to good use—and quickly—responding to environmental factors.

5 Comments

1. 1. JacobSilver 02:42 PM 2/5/11

   With earnest and devoted effort, scientists will be able to determine the effect of some toxins on Daphnia, and will be able to propose these findings to humans. That would be good science, but it does not directly address the problem. There is no, and that is no, reason to use or distribute toxins in the atmosphere or the waters. We can have wind, sun, nuclear,and tide produced electricity. We can grow enough food for our people, without using herbicides or pesticides. We can reforest on a massive scale. We can make paper, fabric, and even building materials out of the stalks of commercial hemp. If we art determined to live healthfully, to preserve life on earth, we can do it. It will require control of chemical companies, especially the biggest of them. These death organization have no role in a healthy world.

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2. 2. macgrant 02:53 PM 2/7/11

   JacobSilver:
   
   While your sentiments are admirable, your statements are not. I challenge you to present verifiable and tested ways to feed even the current population, not to mention the much larger one that will result absent a world-wide plague, without the use of herbicides or pesticides WHILE ALSO taking 'massive' amounts of arable land out of food production and putting it back into forest. And of course one also has to ask where all of the hemp you advocate using is going to be grown if arable land is removed from agriculture. And finally it would be good if you provided some actual data on how wind, solar, tidal and nuclear power can address the need for a high density, easily portable, and most likely liquid, transportation fuel without all of those nasty chemicals you are so against.
   
   Sentiments are good. Opinions are good. But data trumps both of them every time.

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3. 3. cathstuff 01:57 AM 2/8/11

   macgrant,
   I like data too. But what you're asking for is far too much to post here, these are incredibly complicated issues.
   As for providing food - perhaps read up on Vertical Farming: http://www.verticalfarm.com/more
   Also JacobSilver said "we can reforest on a massive scale" - he didn't say that NO arable land will be used for agriculture.
   All he's trying to say is that we can do things so much more efficiently and dramatically reduce the toxins in our air and water - what's wrong with that? It's true. We already have the technology, we're just being slow about implementing it.
   I don't know if it's possible to have NO toxins though, that claim is a bit 'out there' for my liking. Maybe in the future, but not with current technology, as far as I know.
   
   

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4. 4. the Gaul 05:36 PM 2/9/11

   "The majority of the genome is a reflection of how the animal has evolved to cope with environmental stress."
   So, if we continue to produce and dump toxins, apparently our genome will add the components necessary to allow humans to develop a chitinous shell, and other elements required for us to cope with environmental stress.
   Data may trump sentiment when those with no sentiment are the producers. Unfortunately for the majority of us, there's this thing called Congress that allows the producers of those toxins to buy the laws that allow them to destroy our land - and us along with it. Personally, I think all emissions should filter through Congress before they're released into the environment.

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5. 5. macgrant 02:42 PM 3/1/11

   Cathstuff, jacobsilver et al.
   
   Thanks for your comments. However I stand by my statements. There is no currently even theoretical way to feed the current world's population, not to mention the almost 2E9 more people who will need food in the next few decades, AND "reforest on a massive scale" AND eliminate pesticide and herbicide use AND grow very large amounts of hemp for all of our fiber and non-mineral construction needs. Vertical farming, at least as currently proposed, is neither economically or energetically viable - do the math. And I also challenge anyone to present an economically viable and SCALABLE way to use "wind, sun, nuclear,and tide produced electricity" to produce the truly enormous amounts of high density and portable fuels needed for transportation.
   
   I'm not anti-green or anti-anything else. What I am is a professional scientist and a realist. I most assuredly want to find a path forward that accomplishes the goals you have described. I just don't think any of the ideas put forward so far will actually accomplish them - they are far too expensive or they don't scale well from the lab to the real world or they take far too long to implement or one of any number of other complications.
   
   It's all well and good to rail about evil chemical companies or venal politicians. But until you can propose concrete, viable and proven alternatives all this accomplishes is to make you feel virtuous without actually solving anthing.

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