Ancient fossil specimens of extinct species are genetically more distant to an outgroup than extant sister species are
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- The Burnham Institute, La Jolla, CA 92037
This manuscript is a preprint. A published version is available at:
http://www.tilgher.it/(iklpkj451kczv145kvc4c3vj)/index.aspx?lang=eng&tpr=4&act=abs&id=3757 (Peer Reviewed) Published in Rivista di Biologia / Biology Forum 2008 Jan-Apr;101(1):93-108.- Document Type:
- Manuscript
- Date:
- Received 23 July 2008 16:14 UTC; Posted 25 July 2008
- Subjects:
- Bioinformatics, Evolutionary Biology
- Abstract:
There exists a remarkable correlation between genetic distance as measured by protein or DNA dissimilarity and time of species divergence as inferred from fossil records. This observation has provoked the molecular clock hypothesis. However, data inconsistent with the hypothesis have steadily accumulated in recent years from studies of extant organisms. Here the published DNA and protein sequences from ancient fossil specimens were examined to see if they would support the molecular clock hypothesis. The hypothesis predicts that ancient specimens cannot be genetically more distant to an outgroup than extant sister species are. Also, two distinct ancient specimens cannot be genetically more distant than their extant sister species are. The findings here do not conform to these predictions. Neanderthals are more distant to chimpanzees and gorillas than modern humans are. Dinosaurs are more distant to frogs than extant birds are. Mastodons are more distant to opossums than other placental mammals are. The genetic distance between dinosaurs and mastodons is greater than that between extant birds and mammals. Therefore, while the molecular clock hypothesis is consistent with some data from extant organisms, it has yet to find support from ancient fossils. Far more damaging to the hypothesis than data from extant organisms, which merely question the constancy of mutation rate, the study of ancient fossil organisms here challenges for the first time the fundamental premise of modern evolution theory that genetic distances had always increased with time in the past history of life on Earth.
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3 comments
Thank for you this opportunity to address a common mistaken reaction to my paper. I will also here respond to the recent Cell paper (Cell 134, 416-426, 2008) on Neanderthal complete mtDNA that has provided independent confirmation of my paper and show that your interpretation of my result is invalid. I can only be brief here because of length limit on this platform. For a full response, visit my blog here
Your comments indicate that you have not read my paper carefully, since my paper has addressed your point. Your mistake is to think that a variable clock would cause violations of the genetic equidistance result. But, none of the results showing variable clocks violated the genetic equidistance result. See my paper posted here ‘The genetic equidistance result is independent of mutation rates.’ The equidistance result is not an outcome of a constant clock and is independent of clock variations. Most of the variable clock results interpreted minor deviations from exact equidistance as being meaningful when they are in fact not. In short, the genetic equidistance result has no known violations among all extant organisms but is violated by all three ancient fossils for which we have sequence data. Such violations cannot be explained by variable molecular clock since the equidistance result has nothing to do with clock rate variations. I have shown that genes or organisms with variable clocks still do not violate the equidistance result.
Your comment suggests that you want to explain away my finding by the non-testable ad hoc speculation of a faster mutation rate for the Neanderthals. Unfortunately for you, such speculation has been proven wrong by the recent Cell paper, which shows that neutral/synonymous mutations have normal mutation rate in the Neanderthals while non-synonymous mutation rate seem to be higher. It is not possible to imagine that a fast mutation rate should only apply to non-synonymous sites but not to synonymous sites. Probably for this reason, the authors of the Cell paper did not invoke the variable clock idea to explain their data.
Instead, they interpreted their ‘striking observation’, which of course has already been found previously by my paper, by another equally wild and speculative ad hoc idea of less purifying selection due to an imagined smaller population size for the Neandertals than modern humans. Such idea is not testable and hence not scientific. It can never be proven correct. And there are already contradictions to it (visit my blog for details).
For a true explanation of the equidistance result and the fossil violations of the result, see my paper on the MGD (maximum genetic diversity) hypothesis posted here: ‘Inverse relationship between genetic diversity and epigenetic complexity.’ The main idea of this paper has now been published as a peer reviewed book chapter: Huang, S. (2008) Histone methylation and the initiation of cancer. Cancer Epigenetics, Ed. Tollefsbol, T., CRC Press.
On the collagen sequence of the Campanian hadrosaurs (duck-billed dinosaur) B. Canadensis
Collagen sequences from an 80 million year old dinosaur were published recently.
Schweitzer et al., 2009, Biomolecular Characterization and Protein Sequences of the Campanian Hadrosaur B. Canadensis, Science, 5927, pp. 626 – 631Below I analyzed the 8 peptide sequences reported. My analysis showed that B. Canadensis is an outgroup to a T.rex-bird clade, consistent with morphological data but different from the conclusion of Schweitzer et al. Also, the analysis confirmed the major findings of my early fossil sequence paper.
1
GLTGPIGPPGPAGAPGDKGEAGPSGPPGPTGAR
100% identical to mouse2
GSAGPPGATGFPGAAGR
100% T. rex, 100% chicken, and 100% mammals, 17/17, 100% mammut3
GATGAPGIAGAPGFPGAR
100% T. rex, 100% chicken, 100% rana. 18/18, 17/18 homo, 17/18 mammut4
GETGPAGPAGPPGPAGAR100% Chicken, 17/18 rana, 17/18 homo, 16/18 mus, 13/18 match in mammut,
5
GATGAPGIAGAPGFPGAR
100% T. rex, 100% chicken, 100% frog/newt/rana, 17/18 homo, 17/18 mammut6
GPSGPQGPSGAPGPK
100% Chicken, 100% rat, and 100% opossum. 14/15 mus, 13/15 homo, 12/15 mammut7
GSNGEPGSAGPPGPAGLR
Collagen a2(1)
100% Chicken, and 17/18 Taeniopygia guttata, 15/18, homo, 13/18 mammut8
GLPGESGAVGPAGPPGSR
Collagen a2(1)
17/18 T. rex, 17/18 chicken, 16/18, Taeniopygia, 17/18 between chicken and Taeniopygia. Much less to others. 18/18 between chicken and T. rex.Some questions:
1. Is B. canadensis more related to T. rex than chicken is?
No. It is equidistant to chicken and T. rex. And chicken is closer to T. rex than Bc is to T. rex. The informative peptide in this case is #8. Of 4 peptides whose sequences are known in Bc, Tr, and chicken, three (peptide #2, #3, #5) are non informative as they are identical among the three species.2. Is B. canadensis more related to birds than to other animals?
Yes, informative peptides 4, 7, 8 show B. canadensis more similar to chicken than to frog or mammals or any other.3. Is B. canadensis more related to bird than T. rex is?
The only informative peptide is #8. For this peptide, Tr is 18/18 to chicken and 17/18 to Tg (Taeniopygia guttata). Bc is 17/18 to chicken, and 16/18 to Taeniopygia. So, Tr is more related to birds than Bc is.4. Is B. canadensis more distant to the outgroup frog than bird/mammal are?
Not a single informative peptide. Seven of the 8 peptides are not unique to Bc. Peptide 8 is unique but not very conserved in extant animals.5. Is the distance between B. canadensis and mammut greater than that between extant birds and extant mammals?
Yes. Of 6 informative peptides (1-6 of collagen A1t1), 4 and 6 show that distance between Bc and mammut (25/33) is greater than that between birds and mammals (29/33). The distance between extant birds and mammut is also greater than between extant birds and extant mammals. This result confirms the previous finding on the distance between Tr and mammuts. Only the MGD but not the molecular clock hypothesis can predict such result.Conclusion: Bc is the outgroup to a Tr-bird clade
Schweitzer et al stated: “However, on the basis of well-established morphological analyses (25), we predict that T. rex is more closely related to birds than it is to the ornithischian hadrosaur B. canadensis.” 25. D. Pisani et al., Proc. R. Soc. London Ser. B Biol. Sci. 269, 915 (2002).
Yet their molecular analysis based on certain statistical methods suggest that the two dinosaurs belong to a clade to the exclusion of birds. Such a conclusion is false because it is based on the completely mistaken paradigm of molecular clock and neutral theory. So, my analysis shows Bc as the outgroup to a clade containing birds and Tr. This conclusion is more consistent with morphological analysis. The fact that Tr is closer to a bird Gg than a bird Gg is to another bird Tg may be due to the fact that Tr has 60 million years less time to mutate than extant birds are, or that Tg had a different dinosaur ancestor.
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Huang, Shi. Ancient fossil specimens of extinct species are genetically more distant to an outgroup than extant sister species are. Available from Nature Precedings <http://hdl.handle.net/10101/npre.2008.1676.2> (2008)
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Published version:
http://www.tilgher.it/(iklpkj451kczv145kvc4c3vj)/index.aspx?lang=eng&tpr=4&act=abs&id=3757 (Peer Reviewed) Published in Rivista di Biologia / Biology Forum 2008 Jan-Apr;101(1):93-108. -
Other versions of this document in Nature Precedings
Version number Document title Date v1 Posted 12 March 2008 Other versions of this document elsewhere on the web
leigh van valen on 22 August 2008 14:13 UTC
There is ample evidence for a variable clock. Unless the divergence from constancy here is greater than what is found elsewhere, the paper unfortunately adds nothing useful.