On Friday, August 31, 2012 9:33:37 AM UTC-4, gecoverr wrote:
> I have one question about this paper "Initial sequence of the chimpanzee genome and comparison with the human genome" concerning the level of human-chimp similarity.
You should always actually put a complete citation in, so that people trying to respond do not have to search to find the article. This one is freely available at:
http://www.nature.com/nature/journal/v437/n7055/full/nature04072.html
But you may have failed to understand the meaning of the first words of the article: "Initial sequence..."
Initial does not mean complete. More complete analyses are available.
As we read in the Nucleotide Divergence section:
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> "Best reciprocal nucleotide-level alignments of the chimpanzee and human genomes cover ~2.4 gigabases (Gb) of high-quality sequence, including 89 Mb from chromosome X and 7.5 Mb from chromosome Y."
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> My question is: Why did they align only about 76% of human genome with chimp genome? Was it (as some creationists e.g. Jeffrey Tomkins imply) because of huge differences between these two species in the remaining 24% of the genome? Or is there some other reason?
It was NOT because of huge differences between these two species in the remaining 24% of the genome. As they point out, there are, in addition to 'point' mutation differences, differences of up to thousands of nts due to deletions and insertions (see Fig. 6) for a total of about 90 Mb (million basepairs) difference. These are the result, however, of no more than a few hundred mutation events. In addition there are known inversions and translocations that have occurred (which changes the *arrangement* of nts but not necessarily the sequence. Again, these are examples of a very few mutational events causing a big difference if you were to examine million base pair chunks across the boundary. You would get a human sequence, for example, that would have homology with DNA in two different chimpanzee chromosomes.
But what is important for evolution is the number of mutational events, not whether the mutational event causes a big "sequence change" of little consequence or causes a big "phenotypic" difference due to a single base change.
Even *before* we could sequence DNA, we *knew* this was false. If you denature DNA from two species and allow it to reanneal and then do thermal melting temperature analysis, you get a measure of DNA similarity that is similar to what you see in Fig. 3 where you examine 1 Mb segments. You get a mean difference of about 1.2%.
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> Or here -
http://www.icr.org/article/human-chimp-similarities-common-ancestry/ - Jeffrey Tomkins claims that: "One of the main problems with a comparative evolutionary analysis between human and chimp DNA is that some of the most critical DNA sequence is often omitted from the scope of the analysis. Another problem is that only similar DNA sequences are selected for analysis. As a result, estimates of similarity become biased towards the high side. An inflated level of overall DNA sequence similarity between humans and chimps is then reported to the general public, which obviously supports the case for human evolution. Since most people are not equipped to investigate the details of DNA analysis, the data remains unchallenged."
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> I would be very grateful if someone could clarify this issue for me.
If you count the 90 Mb difference as being due to 250-500 insertion/deletion events with the number of nts affected being biased by a few large mutational events and ignore translocations and inversions (at most a few dozen), you get around 5% total sequence difference rather than 1.2%. But the number of mutational events that produced all these changes (LL would only modestly increase the number of mutational event differences from the 30 million point mutation differences. All the large deletions/insertions and rearrangements amount to fewer than a few hundred *mutational* differences. The vast majority of indels are small (<700 bp). The total estimate of all such indel differences (large or small) is about 5 million "mutational events". This is biased strongly toward small events with a blip due to transposable units at around 300 bp. Humans have significantly more Alu transposable elements interspersed in their genome (7000 rather than 2300), but the sequences of these elements is still identifiable
as a transposable unit.
That said, the *only* way for someone to have claimed in 2005 that there is only 70% sequence identity between humans and chimps would be for them to ignore all previous data on DNA homology or to lie about what constitutes homology (for example, all the Alu sequences that transpose show homology to each other, but are present in different locations). It also helps to claim that we should consider a single indel of a 40,000 base pairs as a 40,000 times more important than 40,000 changes at single nt sites.
But the fact remains that nearly all of the 30-35 million mutational differences between humans and chimps are selectively neutral and due to drift. The phenotypically important mutational differences -- those that natural selection has more rapidly changed -- can *sometimes* be identified by evidence of more rapid change and *more* difference. Other selectively important mutations, those that only required a small change at the DNA level and, often, only a small change in timing or amount (one or two nt or mutational differences) may be hidden among these 30-35 million mutational differences.
Bottom line: In terms of mutational differences, the human and chimp genome differ at about 1.2-1.5% sites. About 14% of these site differences may be due to large to small indels.