Article] Genome scan shows human-chimp differences

Robert Karl Stonjek said:

Genome scan shows human-chimp differences Variations hint at how our lifestyle is reflected in our
genes. 12 December 2003 JOHN WHITFIELD

Genes involved in smell and hearing are significantly different between humans and chimpanzees,
researchers have discovered. The finding could be a starting point for understanding what
separates us from our closest relative.

"This tells us the types of genes that are important for our differences," says Michele Cargill of
the biotech company behind the comparison, Celera Diagnostics in Alameda, California. But the list
does not tell us what makes us human, she cautions: "Just finding a change in one protein gives us
no idea of how it affects the whole animal."

The human and chimp genomes are about 99.2% identical. In the most important bits of the genome,
this figure rises to 99.5%. Yet Cargill and her colleagues believe that they have seen the
fingerprint of evolution in these small DNA differences.

The researchers compared the sequences for more than 7,500 human, chimpanzee and mouse genes,
compiled by the genome projects for each species. Matching the two primates against the mouse
revealed whether chimp or man has changed most from the ancestral starting point shared by the
three mammals.

<snip>

Can someone here tell me if this 99.2% figure is just considering DNA segments that code for
proteins, or if it includes the long stretches of DNA of unknown function?

Mitchell Timin

--
"Many are stubborn in pursuit of the path they have chosen, few in pursuit of the goal." -
Friedrich Nietzsche

annevolve.sourceforge.netannevolve.sourceforge.netOpen ↗ is what I'm into nowadays. Humans may write to me at this address:
zenguy at shaw dot ca

Exactly how is the difference meassured? I have seen some rather different numbers such as 98,5%.

Mats

SNIP: This article does not reference the original science article. It looks like they have compared
genomic sequences of 7,500 genes and of course the region around genes. I'd interpret their meaning
of "important" regions of the genome to be coding sequence and the lesser conserved to be introns
and flanking sequence.

They have done a DNA sequence comparison and not a DNA hybridization.

If you find a Chimp BAC clone in GenBank and Blast a couple thousand base-pairs at random across
the human HTG database you will find around a 99.3% sequence similarity. You have to set the return
to only 10 sequences because you are bound to pick up an Alu sequence and if you do, the return
file will be very large. I compared around 24,000 bp this way and only got a 0.7% difference. I
didn't find any large deletions and even the ALU sequences were in the same places, but insertion-
deletions do exist.

Estimates above 99% do not consider the large deletions and insertions between chiimps and humans.
These are likely due to single mutation events and you can't count a 1000 base-pair deletion as 1000
individual events. If you incorporate deletions and insertions into the data you get around a 95%
match between the chimp and human genome, but the number of mutations that differ between the two
species does not increase significantly because there are a lot more single nucleotide mutations
than insertion deletion events. It is just that you can wipe out thousands of base-pairs at a time
with a single deletion.

Ron Okimoto

Quoted message said:

Robert Karl Stonjek said:

<snip>

Can someone here tell me if this 99.2% figure is just considering DNA segments that code for
proteins, or if it includes the long stretches of DNA of unknown function?

Mitchell Timin

RKS: The human genome project only mapped Genes. Techniques to find genes among the junk is what
made the project possible. If it were called the human DNA project then they would only have managed
to get around 5% done thus far.

The comparison is of coding genes.

Kind Regards, Robert Karl Stonjek.

SeeBelo said:

Robert Karl Stonjek said:

Genome scan shows human-chimp differences Variations hint at how our lifestyle is reflected in
our genes. 12 December 2003 JOHN WHITFIELD

Genes involved in smell and hearing are significantly different between humans and chimpanzees,
researchers have discovered. The finding could be a starting point for understanding what
separates us from our closest relative.

"This tells us the types of genes that are important for our differences," says Michele Cargill
of the biotech company behind the comparison, Celera Diagnostics in Alameda, California. But the
list does not tell us what makes us human, she cautions: "Just finding a change in one protein
gives us no idea of how it affects the whole animal."

The human and chimp genomes are about 99.2% identical. In the most important bits of the genome,
this figure rises to 99.5%. Yet Cargill and her colleagues believe that they have seen the
fingerprint of evolution in these small DNA differences.

The researchers compared the sequences for more than 7,500 human, chimpanzee and mouse genes,
compiled by the genome projects for each species. Matching the two primates against the mouse
revealed whether chimp or man has changed most from the ancestral starting point shared by the
three mammals.

<snip>

Can someone here tell me if this 99.2% figure is just considering DNA segments that code for
proteins, or if it includes the long stretches of DNA of unknown function?

Mitchell Timin

The classical experiment involves cross-hybridization of genomic DNA (see references below).
Therefore it would reflect identity over all regions, coding and non-coding. The question that
remains is whether the guys at Celera refer to the classical experiment or to some database
comparison the performed themselves. If I recall correctly the original figures found in the
classical experiment are slightly lower (~98.5%).

Cheers,

Burnce

- Sibley, C.G. and Ahlquist, J.E. 1984. The phylogeny of the hominoid primates, as indicated by DNA-
DNA hybridization.
J. Mol. Evol. 20: 2-15
- Sibley, C.G. and Ahlquist, J.E. 1987. DNA hybridization evidence of hominoid phylogeny: results
from an expanded data set.
J. Mol. Evol. 26: 99-121