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Old 04-06-2006, 07:32 AM   #1
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Welcome To Jurassic Park?

Reconstructing extinct animal genomes by means of advanced sequencing supercomputers, very cool piece of molecular evolutionary biology.
About 100 million years ago, a creature the size of an opossum ambled through the forests of what is now South America. It was probably a ratlike thing, with coarse fur, a scrawny tail, and furtive eyes. If you went back in time with a .22, you could pick it off with one well-aimed shot. But that wouldn't be a good idea. That creature was your ancestor.

Over millions of years, an evolutionary cornucopia spilled from that unassuming ur-mammal. The species to which it belonged split into two daughter species, and then those species split, and the process repeated again and again. One line eventually led to rabbits, beavers, and mice. The members of another line began hunting in shallow bodies of water and gradually evolved into whales and dolphins. Meanwhile, with a few exceptions, the other mammals living back then - and their descendants - eventually went extinct.

In his office overlooking the redwood groves of UC Santa Cruz, David Haussler eagerly shows me our pedigree. "Here's the common ancestor," he says, writing the word Boreoeutherian at the top of a piece of paper. He draws downward-branching lines with animals at the tips. "Here's us," he says, filling in the last two labels - chimpanzee, human.

Biologists have been drawing diagrams like these since Charles Darwin sketched the first evolutionary tree in 1837. But Haussler's reconstruction process is different. Instead of examining fossils and tracing a line from extinct creatures down to those alive today, he's trying to move back up the evolutionary tree. Haussler is attempting to run evolution in reverse.

He starts by comparing the genomes of humans and other existing animals with one another, making inferences about the DNA sequences in their common ancestors. Haussler has used this technique to mathematically reassemble parts of the genome of the progenitor of chimps and humans - a shambling, hirsute, apelike creature that lived about 6 million years ago. He has reconstructed DNA sequences of the predecessor of most hoofed animals, an unprepossessing beast that had to dodge the footfalls of dinosaurs to survive. Most audaciously, Haussler and his collaborators have pieced together much of the genome of the ur-mammal itself, which they plan to release in draft form later this year. "Haussler can reconstruct its genome with a fairly high accuracy" says Eric Lander, director of the Broad Institute and a leader of the public Human Genome Project, "and that's way cool."

Haussler's unexpected success complements a frenzy of work done by researchers using other methods to determine the genetic makeup of extinct organisms. Last year, scientists working with physical DNA specimens published the sequence of a big chunk of a genetic code extracted from a frozen woolly mammoth bone. Another team recovered 40,000-year-old DNA fragments from cave bears. Other groups have gone after the DNA of extinct plants, insects, and even dinosaurs.
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