Planet, I showed your post to some other people. They have their own take on what you wrote. I know you will want to read it, so here it is.
The 5% difference is counting indels. Indels is short for insertions & deletions of base pairs. The study they are referring to was done by Roy Britten and appeared in the Proceedings of the National Academy of Sciences in October of 2002. Here is the abstract:
Quote:
Five Chimpanzee bacterial artificial chromosome (BAC) sequences (described in GenBank) have been compared with the best matching regions of the human genome sequence to assay the amount and kind of DNA divergence. The conclusion is the old saw that we share 98.5% of our DNA sequence with chimpanzee is probably in error. For this sample, a better estimate would be that 95% of the base pairs are exactly shared between chimpanzee and human DNA. In this sample of 779 kb, the divergence due to base substitution is 1.4%, and there is an additional 3.4% difference due to the presence of indels. The gaps in alignment are present in about equal amounts in the chimp and human sequences. They occur equally in repeated and nonrepeated sequences, as detected by REPEATMASKER (
http://ftp.genome.washington.edu/RM/RepeatMasker.html).
However, Britten goes on to state in his discussion:
Quote:
However, it now seems almost certain that chimp or bonobo is our nearest relative.
One interesting observation is that the sequence divergence between chimp and human is quite large, in excess of 20% for a few regions. Some of the larger gaps are broken by regions within them that align with appropriate segments of the other species' DNA sequence but only have distant similarity. These observations suggest that complex processes, presumably involving repeated sequences and possible conversion events, may occur that will require detailed study to understand. The uncertainty in the estimate of 3.4% indels on Table 1 cannot be directly evaluated. In the first place, the sample of 779 kb is small, and the variation between the different BACs is large. Further, there may be gaps that were missed as part of chimpanzee BAC sequences that could not be aligned with the human genome. Nevertheless, the conclusion is clear that comparison of the DNA sequences of closely related species reflects many events of insertion and deletion. It is the result of a major evolutionary process.
Now, basically the assertion that because of the measure of variation including exact indels is splitting hairs. This doesn't change the fact that we are very closely related to chimps. It gives insight into what makes the differences between us. Indels are mutations, they are the very thing that gives evolution the diversity in species that selection works off of.
As Britten, Rowen, Williams, and Cameron reported in PNAS in April of 2003:
Quote:
Human genetic evidence suggests that indels are a major source of gene defects. In one example gene defects affecting the nervous system showed a majority that were due to indels. Many data suggest that indels are a significant source of evolutionary change.
The indels are why we are different from chimps. It is the cumulative mutantions over the millions of years that made us Homo sapiens. These cumulations over the millenia are since we diverged with the chimp line from our common ancestor and in no way refutes that we are closely related to chimps at all.
Yet, in June of 2003 in the Proceedings of the National Academy of Science, Wildman, Uddin, Liu, Grossman and Goodman tested the repeatability of Britten's studies:
Quote:
A recent study has proposed that when all alignment positions in indels are counted as if a nucleotide substitution had occurred at each of these indel positions, humans and chimpanzees are only 95% similar at the DNA level. We analyzed our data in a similar manner and found that the total coding divergence between humans and chimpanzees increased from 0.9% to 1.14%. Thus, in the >90,000 coding bases examined between humans and chimpanzees, the percent of sequence difference due to indels is much less within coding regions than for average genomic DNA. Humans and chimpanzees are more similar to each other from estimates mad from protein-encoding DNA than from DNA samples in which non-coding DNA predominates. Clearly, any indel that alters the reading frame of a gene will result in that gene coding for a completely different set of amino acid residues from the indel to the end of the coding sequence. Such mutations are very likely to be detrimental and selected against by purifying selection.
Nonsynonymous change is less common than synonymous change. Human and chimpanzee divergence is <0.6% at the nonsynonymous level but 1.6% at the synonymous level. This result suggests that when all sites are considered the purifying form of natural selection acts on nonsynonymous sites but not on (or not nearly as much on) synonymous sites. Additionally, the amount of nonsynonymous change was only slightly larger on the terminal human branch than on the terminal chimpanzee branch.
So basically, they are both correct. However, Britten's study focused only on a certain part of the DNA genome with such specific focus you will get results only applicable to that area. A larger perspective can show a different story when taking into consideration the larger genome which is what this study showed. Even Britten admitted to his small sample and with his second study with a larger sample, he still focused on that certain area which, of course, would give similar results.
There is still possibility for further confirmation on the larger scale and I'm sure that research will be done in the future.
And here are the human and chimp chromosomes side by side:
Cannot get the chart up, will post it later.
Britten, R. (2002). Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels. PNAS 99, 13633-13635.
Britten, R., Rowen, L., Williams, J., and Cameron, A. (2003). Majority of divergence between closely related DNA samples is due to indels. PNAS 100, 4661-4665.
Wildman, D., Uddin, M., Liu, G., Grossman, L., and Goodman, M. (2003). Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: Enlarging genus Homo. PNAS 100, 7181-7188.
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