Researchers enter age of comparative genetics with large-scale study of vertebrate DNA

Arizona State University =>Nature ^ | 13-Aug-2003 | Skip Derra

[AdmSmith]

TEMPE, Ariz. -- An Arizona State University researcher is part of a group of scientists reporting the first large-scale comparison of the human genome to 12 other vertebrates. The work is an important step in understanding how vertebrate species are genetically similar or different from one another, and provides a glimpse into the evolutionary past of humans.

For example, the work shows that humans are more closely related to rodents than to dogs or cats.

The team, which includes Jeff Touchman -- an assistant professor of biology at Arizona State and director of the sequencing facility at the Translational Genomics Research Institute, Phoenix -- published its findings in the Aug. 14 issue of Nature.

The report, "Comparative analyses of multi-species sequences from targeted genomic regions," details the comparison of one targeted region of the human genome (a segment of the human chromosome 7, which includes the gene mutated in cystic fibrosis) to the same region of other vertebrates ranging from chimpanzees to zebrafish. Touchman directed the sequencing effort of this work while he was at the National Institutes of Health, Bethesda, Md.

"This is a significant genomic achievement," Touchman said. "We can learn a lot about the human genome by comparing it to the genomes of other species."

The team, which included 71 researchers from 10 institutions, made the comparisons of the human genome to that of the chimpanzee, baboon, cat, dog, cow, pig, rat, mouse, chicken, two species of puffer fish (fugu and tetraodon) and zebrafish.

Touchman said the work is both a technical achievement in the amount of the genome sequenced (1.8 million base pairs in each of the 12 species), as well as for what will be learned by comparing these genome sequences together. It could provide clues as to how each vertebrate evolved.

"One of the things we examined was how much of the genome sequence was 'conserved' across organisms," Touchman said.

As organisms evolved into species, specific sequences were conserved, or selected for retention in the genome, over millions of years of evolution. The sequences that were conserved are thought to be strong candidates for being biologically significant to the survival of that species.

"We already know that genes are very highly conserved across vertebrate species, but what we are finding now is that not only are genes conserved, but other anonymous sequences are conserved as well," Touchman said. "These regions are likely to control important functions such as gene expression."

Also, by studying the differences in the genome of humans compared to other vertebrates, the researchers could determine when organisms split off and headed in different evolutionary directions. For example, the work shows that genetically humans are more closely related to mice and rats than to dogs and cats.

"This has been a controversial issue," Touchman said. "We determined this by looking at the ancestral repetitive sequences that are in these genomes and compared them to each other to infer phylogenic relationships."

Touchman added that the real significance of the work might lie in the paradigm of comparing large regions of genomic sequence together, from multiple species to explore functional similarities and differences in the genetic code of those species. Because sequencing is an arduous and costly task, scientists do not have complete sequences of the genomes of many species. But they are eager to begin the comparative study of genomes.

"The work provides a first glimpse of the type of genomic studies that will occur in the future as more and more whole genomes are sequenced," Touchman said.

[AdmSmith]

Yes, some are really RATS.

[AdmSmith]

Of Mice and Men...

[PatrickHenry]

PING. [This ping list is for the evolution side of evolution threads, and sometimes for other science topics. FReepmail me to be added or dropped.]

[Question_Assumptions]

DNA is a language written in 4 letters. That means that for every double mutation (where a gene mutates twice), there should be roughly a 1 in 4 chance of the mutation being reversed. Do they take this into account?

[PatrickHenry]

Some of you may not be aware that a number of parties involved in these science threads have agreed to a standard of conduct which would encourage respectful discourse and thus avoid thread deletions, threads being relegated to Smokey Backroom and reporting of abuse on complying posters.

I respectfully ask that you read the linked agreement so that you will know what the willing parties expect of one another and their dealings with others.

[Right Wing Professor]

For example, the work shows that humans are more closely related to rodents than to dogs or cats.

Shows, but not for the first time. Our relationship to the Rodentia has been pretty clear from the dawn of gene sequencing. This looks interesting, but what we really need is a little information about a lot of species, rather than a lot of information about a few. Once you've gotten phylogenetic trees using 10 or 20 genes, I'm not sure adding another 30,000 improves things much.

[LurkedLongEnough]

"The scientists were most surprised with the comparison of Bill Clinton's DNA with that of a horny toad. While not a completely exact match, the scientists expressed optimism that such a match might be obtained using the DNA of his wife, Hillary."

[ASA Vet]

But what will they discover using DNA of Hillary's daughter?

[RightWhale]

Kind of gives a person a warm fuzzy feeling to think he's closer to rats than pigs.

[js1138]

DNA is a language written in 4 letters. That means that for every double mutation (where a gene mutates twice), there should be roughly a 1 in 4 chance of the mutation being reversed. Do they take this into account?

I get one in 16, unless there are "words" that can't occur.

[js1138]

That's from computer background. I know nothing of molecular biology.

[Doctor Stochastic]

This is true only for one base pair. If a gene consists of (for example) 40 base pairs, each of which has an equal chance of mutation, then a mutation in the first pair is 39 times more likely to be followed by a mutation in another pair than to be reversed. If a reversal takes place on the first pair later, the gene is still different.

The entire genone undergoes drift under mutation rather than reversal. It's a diffusion process.

[<1/1,000,000th%]

No moose?

[<1/1,000,000th%]

The supermarket tabloids say Chelsea's pregnant.

[PatrickHenry]

They'll get around to doing your family. These things take time.

[LurkedLongEnough]

The supermarket tabloids say Chelsea's pregnant.

She will then, like her mother, be caught on camera fleeing through the streets of Brooklyn, shielding her baby from the flying rocks of Palestinian refugees...

[AdmSmith]

It is more complex than that. The probability of a mutation varies depending on the site on the sequence and the surrounding nucleotides. Furthermore the probability of A => C is not the same as A => G or A => T etc.

The code is in triplets and the probability of a mutation with no effect is much higher for position 3 than for the first position.

[AdmSmith]

No we haver a pretty good idea on the phylogenetic tree just from the mitochondrial DNA.

[<1/1,000,000th%]

They'll get around to doing your family. These things take time.

LOL!

At some point in time, kids will have their genome recorded when they're born, instead of leaving a footprint on a piece of paper.

[Old Professer]

Kind of gives a person a warm fuzzy feeling to think he's closer to rats than pigs.

I don't believe the article said that.

Two quotes from the article:

For example, the work shows that humans are more closely related to rodents than to dogs or cats.

For example, the work shows that genetically humans are more closely related to mice and rats than to dogs and cats.

Nowhere in the above article does it say rats were closer than pigs.

If you linked all of the way to the original and paid for the article as it directs, please share the relevant passage with us that supports your statement.