That disgusting layer of bug guts plastered across your bumper after a road trip could also be a great way to analyze the biodiversity of where you've been.
After a long-distance drive to a conference yielded a tremendous number of squashed bugs on his bumper, genomics researcher Anton Nekrutenko of Pennsylvania State University decided to try an experiment: Why not apply the tools of metagenomics, which is the study of DNA taken directly from an environmental sample, to the collection of insects decorating his car?
"How many species inhabit our immediate surroundings?" wrote Nekrutenko and colleagues in a paper published Thursday in *Genome Research. *"A straightforward collection technique suitable for answering this question is known to anyone who has ever driven a car at highway speeds."
By sequencing DNA taken from the bug splatter generated by two different car trips, one from Pennsylvania to Connecticut and the other from Maine to New Brunswick, Canada, the researchers discovered significant differences in insect diversity between the two regions.
In addition to proving that bug carnage can provide valuable information about biodiversity, the experiment served as proof-of-principle for a new kind of metagenomic analsyis. Until now, metagenomics had been used primarily to study mixed samples of bacteria, such as the microbes that inhabit the human gut or live on the surface of our skin. But scientists are increasingly interested in applying the same shotgun analysis of genetic material to answer questions about higher organisms.
For instance, researchers have debated for decades just how many different kinds of insects are out there, with estimates ranging from 10 million to 30 million. Of those, only a few hundred thousand have been cataloged by biologists. But analysis of insect diversity from environmental DNA samples is incredibly complex, and the researchers say our current computational tools aren't quite up to the task.
"It's somewhat easier with bacteria because normally bacteria have small genomes, and their genomes are packed with genes that produce proteins," Nekrutenko said. Higher organisms are more complicated because they tend to have larger genomes and more "junk" DNA that doesn't code for proteins. To handle analysis of the massive amounts of data necessary to screen even a simple collection, like bugs scraped from a car, the group had to create new tools.
"One of our main goals was technology development," Nekrutenko said. "In general, life sciences are becoming kind of like physics, very data-driven, but most biologists are not trained in data-driven research." Along with colleagues from the University of California, San Diego and Emory University, Nekrutenko's group developed a straightforward, web-based program called Galaxy that walks scientists through the steps of metagenomic analysis, from obtaining raw sequencing data to drawing up an evolutionary tree.
Some biologists who have already started using Galaxy give it rave reviews. "My lab would be lost without it," said biologist Ross Hardison of Pennsylvania State University, who has collaborated with Nekrutenko but was not involved in this research. "We are dependent on Galaxy for a very large fraction of the analyses we do."
Even more importantly, Nekrutenko said, Galaxy allows researchers to publish their entire dataset and methods so that other researchers can reproduce their results. "Metagenomics is kind of a parameter-dependent science," Nekrutenko said. "You run certain tools, and they have dials, and depending how you set these dials you can get completely different results. Through our system, you can see exactly how we set these dials."
That means other researchers can repeat Nekrutenko's analysis and see if they get the same results. For instance, someone might want to double-check a particularly bizarre feature of the data: In addition to finding plenty of insect and bacterial DNA, the group uncovered genetic material from the genus Homo.
Nekrutenko said the unexpected result probably represents an artifact: Because current databases of eukaryotic DNA sequences are dominated by the human genome, spurious human results are likely to pop up. "Precise species ID from mixed samples like this is very, very challenging," he said. "We have sequences that map to human DNA, even though I’m pretty sure we didn’t kill anybody."
Image 1: Flickr/John Beales. Image 2: A photograph of Nekrutenko's bumper after one of the bug collection trials*/Anton Nekrutenko*.
See Also:
- Universal 'Death Stench' Repels Bugs of All Types
- Honey Bees Give Clues on Virus Spread
- The Metagenomic Frontier
- Heavy-Duty Hardware Hauls Bacteria From the Bottom of the Sea ...
- Wired Magazine: The Plague Fighters: Stopping the Next Pandemic ...
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