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Author | Topic: Cytachrome C and neutral drift | |||||||||||||||||||||||
Wounded King Member Posts: 4149 From: Cincinnati, Ohio, USA Joined: |
This paper is about Cytochrome C Oxidase (COX), not about Cytochrome C. I don't know that it makes any difference in terms of the current discussion but I thought it was a neccessary distinction to make.
TTFN, WK This message has been edited by Wounded King, 03-23-2005 05:31 AM
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pink sasquatch Member (Idle past 6051 days) Posts: 1567 Joined: |
I was under the impression that the various versions of Cytochrome C were used as evidence of common descent. That they display a kind of nested heirarchy. Hi judge, I think this is an important point - the reason Cytochrome C is commonly used to examine common descent doesn't really have anything to do with whether or not genetic change is exclusively the result of neutral drift. The reason Cytochrome C is used is because it is required for life in all prokaryotes and eukaryotes, and is simply available for comparison. That is, most other genes would simply not exist in a portion of the "Tree of Life", and thus would make analysis of the Tree of Life incomplete. Also, Cytochrome C is not the only gene used to examine common descent; other genetic data is used.
If there is no evidence that Cytochrome C does in fact undergo neutral drift within species then this may question whether it ever really neutrally drifts at all, and hence whether it can be used as evidence for common descent. Perhaps more importantly, the examination of common descent does not require solely neutral mutations. In fact, researchers have little way of knowing if mutations are detrimental, beneficial, or neutral - unless they perform extensive functional studies, and these are not done for most such common descent studies. In any case, the existence of a detrimental or beneficial mutation in two related species is just as much evidence for common descent as a neutral mutation. An oft-cited example is the "GLO" gene, which is mutated to non-functionality in four known species - fruit bats, guinea pigs, chimps, and humans. Humans and chimps have an identical detrimental mutation in the GLO gene, which is a different mutation than the one in the GLO gene of the fruit bats and the guinea pigs. This is evidence for humans and chimps being more closely related than to other species without that specific mutation. Thus a non-neutral mutation also can demonstrate common descent. Perhaps you are confusing the idea of determining the "molecular clock" with that of determing common descent. The molecular clock method does use assumed neutral mutations to determine when two species diverged from a common ancestor (but not whether or not they did so...) Hopefully this is helpful, let me know if you have questions.
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judge Member (Idle past 6472 days) Posts: 216 From: australia Joined: |
quote: Firstly thanks for all the replies. I was looking at a creationist site so i wanted to check the ideas there. http://www.evolutionisdegeneration.com/...ption.htm#6.4.2.9g As you can see
quote: This creationist seems to argue that Cytachrome C indicates common descent is not true, but it is difficult for me to know whether what he writes is correct as I am an amateur in this area.
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Sylas Member (Idle past 5288 days) Posts: 766 From: Newcastle, Australia Joined: |
No, the writer is not correct.
First, sharks are not a species; they are many species. Second, sharks most certainly have changed over millions of years. They are very successful in their niche, and so ancient sharks are still very clearly sharks, so the basic body form we recognize as "shark" has been around for a long time; but it is not unchanging. Third, I would expect there will be some minor differences in cytochrome C sequences within some species; but that this will be unusual. This is because the sequence is so highly conserved. To test this would require many sequences from a single species. I do not believe the writer has such data. Most species, however, will tend to have a single uniform cytochrome C sequence, because of the strong conservation. Fourth, actually, I think there is cytochrome C variation within sharks. As has been pointed out, your other reference was actually for COX (I missed that, oops!). I can't find a reference for several shark species and cytochrome C; but someone with a bit of time might like to trawl the databases and find out directly. There is certainly variation in cytochrome B; reported in Protein evolution in different cellular environments: cytochrome b in sharks and mammals, by AP Martin and SR Palumbi, in Molecular Biology and Evolution, Vol 10, 873-891. (July 1993). Cheers -- Sylas
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NosyNed Member Posts: 9004 From: Canada Joined: |
Oh well I did disclaim to death about my knowledge.
It seems reading should have been included. Thanks.
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Ooook! Member (Idle past 5843 days) Posts: 340 From: London, UK Joined: |
Hi judge,
This statement in the paragraph you quoted rang alarm bells for me :
quote: The author seems to have based it on information that probably doesn't exist. How do they know that cytochrome C doesn't vary within the same species of shark? What study is this based on? How much individual sequence data is there on the shark genome? Cytochrome C seems to vary in humans for example. I've just queried "cytochrome C NOT oxidase" here and I found that items 7-49 had variations in the cytochrome C gene (the first 6 were from another gene with cytochrome C in it's name). That's quite a lot of variation for genetic drift to play with. I would add that I am not a geneticist so I may have committed a horrendous error here (people are welcome to correct me and make me look daft ), but I'd still want to see the studies that show that no variation is seen within species. Cheers
Edit: Dikshunrees, hoo needs 'em? This message has been edited by Ooook!, 24-03-2005 11:02 AM
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Wounded King Member Posts: 4149 From: Cincinnati, Ohio, USA Joined: |
A better way to view the data is with the cSNP facility. Here is the cSNP view of CYCS.
TTFN, WK This message has been edited by Wounded King, 03-24-2005 06:25 AM
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Ooook! Member (Idle past 5843 days) Posts: 340 From: London, UK Joined: |
Yeah...
well... that is of course another way of doing it. If you wanted to make it easier to do and much more easy to understand. Cheers Wounded. Sometimes I wonder why I bother (Shuffles away sheepishly to get back to some real work)
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Wounded King Member Posts: 4149 From: Cincinnati, Ohio, USA Joined: |
I shouldn't be embarrased if I was you, I've been looking at the CYC1 gene all this time instead of CYCS.
TTFN, WK
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sfs Member (Idle past 2562 days) Posts: 464 From: Cambridge, MA USA Joined: |
Note that of the variant sites listed for the human CYCS coding sequence, not one has been validated, i.e. seen more than once. The detection method used for finding all of these SNPs is not the most reliable, so it is likely that some of these sites are not really variant, and possible that none of them are. Keep in mind that CYCS is a small gene, with only 312 base pairs of sequence. Even if there were no constraints, you'd only expect to find one reasonably high frequency (> 1%) variant in such a small bit of sequence; in coding sequence there's no reason to expect even one.
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Wounded King Member Posts: 4149 From: Cincinnati, Ohio, USA Joined: |
Note that of the variant sites listed for the human CYCS coding sequence, not one has been validated This is true but if you go to the 'in gene region' view, rather than just looking at the coding sequence, there are a number of validated polymorphisms in the 3' and 5' UTRs. TTFN, WK
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