The Loom

Resurrecting Genomes

mammaltree.gifIn tomorrow’s New York Times, I have an article about how to reconstruct a genome that’s been gone for 80 million years. The genome in question belongs to the common ancestor of humans and many other mammals (fancy name: Boreoeutheria). In a paper in this month’s Genome Research, scientists compared the same chunk of DNA in 19 species of mammals. (The chunk is 1.1 million base pairs long and includes ten genes and a lot of junk.) The researchers could work their way backwards to the ancestral genetic chunk, and then showed they could be 98.5% certain of the accuracy of the reconstruction.

There are some pretty astonishing implications of this work. For one thing, it should be possible to synthesize this chunk of DNA and put it in a lab animal to see how it worked in our ancestor. For another, the scientists are now confident that they will be able to use the same technique to reconstruct the entire genome in the next few years, if the sequencing of mammal genomes continues apace. Could scientists some day clone a primordial Boreoeutherian? It’s not impossible.

On the down side, this method will not work for just any group of animals you want to pick. Mammal evolution was rather peculiar 80 million years ago: a lot of branches sprouted off in different directions in a geologically short period of time. That makes the 19 species the scientists studied like 19 different fuzzy images of the same picture. Other groups of species had a very different evolutionary history, and one that may make genome reconstruction impossible. If you yearn for the day when Jurassic Park becomes real, you will have to conect yourself with a swarm of shrew-like critters. If they did somehow manage to break out of a lab, I suspect they would get eaten by the first cat to cross their path.


  1. #1 Tim Ogilvie
    December 7, 2004

    Seems like the species with the smallest changes in this gene would have similarly small changes throughout the genome. So I would expect that the species most resembling the ancient ancestor (rodents), would have the smallest amount of loss.

    Instead, it appears that they have the most loss. Humans and horses have the least loss, and seem physically very different. What am I missing? (apart from a degree ;-))

  2. #2 Carl Zimmer
    December 7, 2004

    A lot of evidence indicates that relatively small changes to DNA can produce dramatic changes in body size, etc. That’s because many genes come with tiny switches that determine when and where they will make proteins. Change the switch, change the role of the gene. So the link between the number of nucleotides that change and visible differences in bodies is a complicated one.

  3. #3 otey
    December 7, 2004

    Your links on the right are over-lapping your text in the middle of the page. Please adjust your macros.

    Thanks. Enjoy your blog. I am a regular visitor and read your stuff when I can see it through your links.

  4. #4 William Gruzenski
    December 7, 2004

    A journey back through time to a point where we can find out who we are. Can this be done? Indeed, it is being done–by all of us. Life itself is but the retracing of our steps on a journey that was over the moment it began. Do not believe for a second that this results in a fence we call the body that wards us off from an imaginary external world. “Is the cat dead or alive,” asked Schroedinger in one of his famous thought experiments on the theoretical implications of Quantum Mechanics. ‘Neither’ was his answer. It has a tendency, a probability of being when the observer looks. Possible, probable and, in the end, the undoing must be certain.

  5. #5 Sarah Dempsey
    December 7, 2004

    Is it possible to retrace the same steps in reverence, remembrance and hope to remind children of days past? What we should be doing is encouraging them to embrace the power of their dreams and tell them to lead with their heart. God has everything planned for us, regardless of what it looks like in any given moment. So the real question is how do we return from a journey? We don’t. We carry it with us journey forever. Let’s face it, anything is possible if you believe.

  6. #6 vernaculo
    December 7, 2004

    Carl, your reply to Tim Ogilvie was a perfect example of what it is I come here to find. Clear, unbiased science news, in relatively non-technical lucid prose.
    And in mozilla your links don’t overlap at all.

  7. #7 Steve Russell
    December 8, 2004

    I don’t have a relevant degree either, :=), but I have heard that a parent language “evolves” more radically over time in the languages’s homeland than the daughter languages do as the speakers migrate further from home. Thus, to find the most “conservative” languages, the ones that have changed least by comparison with the parent language, you want to investigate the communities of speakers that have migrated furthest from the center. I’ve heard a similar “rule” for human genetic history: that the greatest genetic diversity is found in the populations remaining in the ancestral homeland and that this is one piece of evidence validating the Out of Africa hypothesis. I wonder if there might be a similar “fringe” versus “center” conservation rule applying to genomes? If so, then the descendant population that has continued to exploit (approximately) the same niche as the common ancestor may exhibit the greatest number of “random” (non-adaptation driven) genetic changes, while the populations that have changed niches the most may exhibit fewer changes of this kind.

  8. #8 coturnix
    December 9, 2004

    Off-topic, but, speaking of genomes, this is really cool: