In the past, diploid Daphnia have been bred in the lab to cut down on extraneous genetic material that, in the wild, is necessary for their mainly mateless reproductive strategy. But this artificial inbreeding is less than desirable for researchers who are looking to study gene-environment interactions. So members of the research project launched a transcontinental search to find a specimen that was naturally inbred. What they found in The Chosen One was just that—a Daphnia in which "nature has gotten rid of all the bad alleles," simplifying the genome without losing its ecologically attuned adaptations, Colbourne says.
This little arthropod and her progeny received such a grand nickname as another Slimy Log Pond candidate line—now known as The Rejected One—was being sidelined. In preliminary analyses The Rejected One was found to have a genome that is quite heterozygous (with more differentiated alleles), Colbourne recalls. Its radical differences, however, did allow for some useful comparison with The Chosen One. "There was actually some great science that was done because of the Rejected One, although it created quite a heart attack in the community," he says.
Although D. pulex is the most common species, others, such as D. magna and Ceriodaphnia dubia are usually called on in standardized water quality tests. The D. magna genome sequence is currently in the pipeline, says Vulpe, who uses that species in his research and is part of the larger consortium. For his research, the D. pulex genome "has been an incredible boon to be able to compare and help us understand what's happening" in the D. magna genetics.
With its substantial genome now decoded, Daphnia might soon play an even more integral role in environmental assessment—beyond simple tests for dissolved oxygen or excessive chlorine.
Only a small fraction of tens of thousands of man-made chemicals have been tested for safety, and then they are usually only tested as isolated compounds—rather than in more realistic amalgamations as they often crop up in the environment. "We have so many damn chemicals," Vulpe says. "We're concerned about their effect on humans and on ecosystems."
But with so much analysis that remains to be done, "there's no way that our current methods of screening for the danger of these chemicals can catch up," Colbourne says. If Daphnia prove to be a solid model organism to study the effects of chemicals and environment on genes, they could enable a more efficient high-throughput process for assessing chemicals.
The relatively new field of "ecotoxicogenomics"—which Vulpe admits "doesn't really roll off the tongue very well"—is working to catch up to more biologically based genetics. But with the genome sequence of Daphnia, he hopes that it will allow the field to catch up. "We have the sequence of the mouse and human—and we can use genomics in a very powerful way—but unfortunately this has lagged behind in these eco-indicator species."
Bringing a genomic approach to studying toxicology promises to create a more "mechanistic understanding" of the field, Colbourne says. Vulpe explains that toxicology has relied on the "kill 'em and count 'em" approach, in which death was the primary endpoint in a chemical's dosage assessment: "We previously asked the question: Did they die?" he says. As researchers are now starting to be able to suss out particular genetic pathways, "it might help us consider endpoints that we hadn't considered," Vulpe adds, such as how chemicals are having more nuanced effects on reproductive or immune systems.
Daphnia are of course not a perfect foil for studying chemicals' potential effects on human biology, and their use as screening organisms will have to be validated by further research. "But it's certainly exciting that there is a similarity," Vulpe says. "Who would have thought that a little crab would have been similar to people?"