Reversing ecology reveals ancient en...( From hair color to the ancestral lin...)

From hair color to the ancestral line of parasitic bacteria, scientists can glean a lot from genes. But imagine if genes also revealed where you lived or who you spent time with. It turns out they do, if you know where and how to look.

Stanford researchers with collaborators at Tel-Aviv University have now laid the foundation for opening such a window to the past using a technique called "reverse ecology." The technique uses genomic data to examine metabolic networks and pulls out proxies for reconstructing bacterial environments millions of years in the past. The work, published in the February issue of the Journal of Computational Biology, offers clues to the complex evolutionary interplay between organisms such as parasites and hosts.

"Based on reverse ecology, you can start with an organism-say, a certain bacterial species that you know nothing about ecologically. But by looking at its genome and metabolic network, you can recreate that past environment the organism lived in," said Elhanan Borenstein, lead author of the paper and a postdoctoral researcher in the Biology Department at Stanford. "And we've done this with hundreds of different species."

Researchers have used genomic data to study metabolic networks-the chemical reactions in metabolism that determine the physiological and biochemical properties of cells-in great detail. But Borenstein, with co-author Marcus Feldman, a professor of biology at Stanford, took this understanding a step further.

Through the metabolic network, organisms accumulate biochemical compounds from their interactions with the surrounding environment (e.g., oxygen, glutamine or sulfate). These molecules also correlate with other environmental properties like temperature and salinity. "This gives us a way to predict the biochemical environment of organisms and learn ecology from the genomic data on a large scale," Borenstein said.

The researchers collected clues about not onl
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