Notices
Results 1 to 13 of 13

Thread: Cave Bears of the Pleistocene

  1. #1 Cave Bears of the Pleistocene 
    Suspended
    Join Date
    Dec 2008
    Location
    Nirgendwo und Ueberall
    Posts
    1,300
    From:

    Science 22 July 2005:
    Vol. 309. no. 5734, pp. 597 - 599
    DOI: 10.1126/science.1113485



    The substitution rate we estimated for cave bears is higher than that in any other bear lineage. On the basis of results from PCR-amplified ancient mitochondrial DNA, cytosines in ancient DNA can undergo deamination to uracil, which results in an excess of G-to-A and C-to-T (GC–AT) transitions (21). The inflated substitution rate in cave bears is likely caused by an excess of such events, because many of the substitutions assigned to the cave bear lineage are GC–AT transitions (Fig. 3A). These presumably damage-induced substitutions complicate phylogenetic reconstruction and the identification of functional sequence differences between extinct and modern species.
    This is simply saying that Cave Bears underwent more genetic change than other bears and that these events make it hard to reconstruct what they looked like? The GC-AT transitions are due to uracil deanimation, which is an event that occurs often in ancient DNA? If so, why does this occur?


    We developed an amplification-independent direct-cloning approach to constructing metagenomic libraries from ancient DNA (Fig. 1). Ancient remains are obtained from natural environments in which they have resided for thousands of years, and their extracted DNA is a mixture of genome fragments from the ancient organism and sequences derived from other organisms in the environment. A metagenomic approach, in which all genome sequences in an environment are anonymously cloned into a single library, may therefore be a powerful alternative to the targeted PCR approaches that have been used to recover ancient DNA molecules. We chose to explore this strategy with the extinct cave bear instead of an extinct hominid, to unambiguously assess the issue of modern human contamination (1, 2). In addition, because of the close evolutionary relationship of bears and dogs, cave bear sequences in these libraries can be identified and classified by comparing them to the available annotated dog genome.
    How is this metagenomic library useful? Isn't the goal isolation of Cave Bear genes?


    Reply With Quote  
     

  2.  
     

  3. #2  
    Suspended
    Join Date
    Dec 2008
    Location
    Nirgendwo und Ueberall
    Posts
    1,300
    I was hoping someone would answer these questions for me...


    Reply With Quote  
     

  4. #3  
    Forum Cosmic Wizard paralith's Avatar
    Join Date
    Jun 2007
    Posts
    2,190
    gottspieler, asking questions like these is rather akin to asking homework questions, in that you should not expect people to be waiting around ready to explain everything to you. Members will answer if they feel like it, and if none are interested then none will answer.
    Man can will nothing unless he has first understood that he must count on no one but himself; that he is alone, abandoned on earth in the midst of his infinite responsibilities, without help, with no other aim than the one he sets himself, with no other destiny than the one he forges for himself on this earth.
    ~Jean-Paul Sartre
    Reply With Quote  
     

  5. #4 Re: Cave Bears of the Pleistocene 
    Forum Radioactive Isotope Paleoichneum's Avatar
    Join Date
    Oct 2008
    Location
    Washington State, USA
    Posts
    4,624
    Quote Originally Posted by gottspieler
    From:

    Science 22 July 2005:
    Vol. 309. no. 5734, pp. 597 - 599
    DOI: 10.1126/science.1113485



    The substitution rate we estimated for cave bears is higher than that in any other bear lineage. On the basis of results from PCR-amplified ancient mitochondrial DNA, cytosines in ancient DNA can undergo deamination to uracil, which results in an excess of G-to-A and C-to-T (GC–AT) transitions (21). The inflated substitution rate in cave bears is likely caused by an excess of such events, because many of the substitutions assigned to the cave bear lineage are GC–AT transitions (Fig. 3A). These presumably damage-induced substitutions complicate phylogenetic reconstruction and the identification of functional sequence differences between extinct and modern species.
    This is simply saying that Cave Bears underwent more genetic change than other bears and that these events make it hard to reconstruct what they looked like? The GC-AT transitions are due to uracil deanimation, which is an event that occurs often in ancient DNA? If so, why does this occur?
    The key word in the passage is phylogenetic. This means attempting to create a "family tree" of Ursidae (the bear family) by compairing the DNA of the different genera and then placing them on "branches" which show how closely the taxa are related. From what I can tell, it does not have anything to do with recreating what an individual cave bear looked like.

    Quote Originally Posted by gottspieler
    We developed an amplification-independent direct-cloning approach to constructing metagenomic libraries from ancient DNA (Fig. 1). Ancient remains are obtained from natural environments in which they have resided for thousands of years, and their extracted DNA is a mixture of genome fragments from the ancient organism and sequences derived from other organisms in the environment. A metagenomic approach, in which all genome sequences in an environment are anonymously cloned into a single library, may therefore be a powerful alternative to the targeted PCR approaches that have been used to recover ancient DNA molecules. We chose to explore this strategy with the extinct cave bear instead of an extinct hominid, to unambiguously assess the issue of modern human contamination (1, 2). In addition, because of the close evolutionary relationship of bears and dogs, cave bear sequences in these libraries can be identified and classified by comparing them to the available annotated dog genome.
    How is this metagenomic library useful? Isn't the goal isolation of Cave Bear genes?
    Again if I understand the text segment correctly, it is. This is done by cloning everything and then compairing the strands to modern organizms to determine what is being looked at. This way it is easier to tell when they are (random example) looking at slime mold DNA and not cave bear DNA. They can then isolate the bear DNA and work with it.

    By the way as there are a group of related species all called "Cave bear", does the paper specify what species is being worked with?
    Reply With Quote  
     

  6. #5  
    Forum Cosmic Wizard spuriousmonkey's Avatar
    Join Date
    May 2005
    Posts
    2,193
    Quote Originally Posted by gottspieler
    I was hoping someone would answer these questions for me...
    Start by giving a link to the paper. I can't be arsed to look for the paper.
    "Kill them all and let God sort them out."

    - Arnaud Amalric

    http://spuriousforums.com/index.php
    Reply With Quote  
     

  7. #6  
    Suspended
    Join Date
    Dec 2008
    Location
    Nirgendwo und Ueberall
    Posts
    1,300
    Quote Originally Posted by paralith
    gottspieler, asking questions like these is rather akin to asking homework questions, in that you should not expect people to be waiting around ready to explain everything to you. Members will answer if they feel like it, and if none are interested then none will answer.
    Basic logic would confirm that you have a good point. However, giving a thread an occasional bump never hurts anything.
    Reply With Quote  
     

  8. #7  
    Suspended
    Join Date
    Dec 2008
    Location
    Nirgendwo und Ueberall
    Posts
    1,300
    Quote Originally Posted by spuriousmonkey
    Quote Originally Posted by gottspieler
    I was hoping someone would answer these questions for me...
    Start by giving a link to the paper. I can't be arsed to look for the paper.
    Genomic Sequencing of Pleistocene Cave Bears
    James P. Noonan,1,2 Michael Hofreiter,3 Doug Smith,1 James R. Priest,2 Nadin Rohland,3 Gernot Rabeder,4 Johannes Krause,3 J. Chris Detter,1,5 Svante Pääbo,3 Edward M. Rubin1,2*

    Despite the greater information content of genomic DNA, ancient DNA studies have largely been limited to the amplification of mitochondrial sequences. Here we describe metagenomic libraries constructed with unamplified DNA extracted from skeletal remains of two 40,000-year-old extinct cave bears. Analysis of 1 megabase of sequence from each library showed that despite significant microbial contamination, 5.8 and 1.1% of clones contained cave bear inserts, yielding 26,861 base pairs of cave bear genome sequence. Comparison of cave bear and modern bear sequences revealed the evolutionary relationship of these lineages. The metagenomic approach used here establishes the feasibility of ancient DNA genome sequencing programs.

    1 United States Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.
    2 Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
    3 Max Planck Institute for Evolutionary Anthropology, Leipzig, D-04103, Germany.
    4 Institute of Paleontology, University of Vienna, Vienna, A-1010 Austria.
    5 Biosciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.

    Published online 2 June 2005

    Include this information when citing this paper.


    * To whom correspondence should be addressed. E-mail: emrubin@lbl.gov

    Genomic DNA sequences from extinct species can help reveal the process of molecular evolution that produced modern genomes. However, the recovery of ancient DNA is technologically challenging, because the molecules are degraded and mixed with microbial contaminants, and individual nucleotides are often chemically damaged (1, 2). In addition, ancient remains are invariably contaminated with modern DNA, which amplifies efficiently compared with ancient DNA, and therefore inhibits the detection of ancient genomic sequences (1, 2). These factors have limited most previous studies of ancient DNA sequences to polymerase chain reaction (PCR) amplification of mitochondrial DNA (3–8). In exceptional cases, small amounts of single-copy nuclear DNA have been recovered from ancient remains less than 20,000 years old obtained from permafrost or desert environments, which are well suited to preserving ancient DNA (9–12). However, the remains of most ancient animals, including hominids, have not been found in such environments.

    To circumvent these challenges, we developed an amplification-independent direct-cloning approach to constructing metagenomic libraries from ancient DNA (Fig. 1). Ancient remains are obtained from natural environments in which they have resided for thousands of years, and their extracted DNA is a mixture of genome fragments from the ancient organism and sequences derived from other organisms in the environment. A metagenomic approach, in which all genome sequences in an environment are anonymously cloned into a single library, may therefore be a powerful alternative to the targeted PCR approaches that have been used to recover ancient DNA molecules. We chose to explore this strategy with the extinct cave bear instead of an extinct hominid, to unambiguously assess the issue of modern human contamination (1, 2). In addition, because of the close evolutionary relationship of bears and dogs, cave bear sequences in these libraries can be identified and classified by comparing them to the available annotated dog genome. The phylogenetic relationship of cave bears and modern bear species has also been inferred from mitochondrial sequences, providing the opportunity to compare the phylogenetic information content of cave bear mitochondrial and genomic DNA (13).




    Fig. 1. Schematic illustration of the ancient DNA extraction and library construction process. Extracts prepared from a cave bear tooth (library CB1) and a bone (library CB2) contain cave bear DNA (red) and a mixture of DNA from other organisms (gray). [View Larger Version of this Image (10K GIF file)]



    We extracted DNA from a cave bear tooth recovered from Ochsenhalt Cave, Austria, and a cave bear bone from Gamssulzen Cave, Austria, dated at 42,290 (error +970/–870) and 44,160 (+1400/–1190) years before the present, respectively, by accelerator mass spectrometry radiocarbon dating (table S1). We used these ancient DNA molecules to construct two metagenomic libraries, designated CB1 and CB2 (Fig. 1) (14). These libraries were constructed in a laboratory into which modern carnivore DNA has never been introduced. Ancient DNA molecules were blunt end–repaired before ligation but were otherwise neither enzymatically treated nor amplified. We sequenced 9035 clones [1.06 megabases (Mb)] from library CB1 and 4992 clones (1.03 Mb) from library CB2. The average insert sizes for each library were 118 base pairs (bp) and 207 bp, respectively.
    We compared each insert in these libraries to GenBank nucleotide, protein, and environmental sequences, and the July 2004 dog whole genome shotgun assembly, by using Basic Local Alignment Search Tool (BLAST) software with an expect value cutoff of 0.001 and a minimum hit size of 30 bp (14–16). 1.1% of clones in library CB1 (Fig. 2A) and 5.8% of clones in library CB2 (Fig. 2B) had significant hits to dog genome or modern bear sequences. Our direct-cloning approach produces chimeric inserts, so we defined as candidate cave bear sequence only that part of the insert that had a hit to dog or bear sequence. The average hit for the 100 clones in library CB1 with significant hits to carnivore sequence was 68 bp long and covered 58% of the insert; whereas the average hit for the 289 clones in library CB2 with significant carnivore hits was 70 bp and covered 49% of the insert. None of these clones showed homology to cave bear mitochondrial DNA sequences, which is consistent with the expected ratio of nuclear versus mitochondrial clones, given the much greater size of the nuclear genome (14). Based on the amount of cave bear genomic DNA used to construct library CB2, we estimate that it could yield >10-fold coverage of the cave bear genome if sequenced completely (14).




    Fig. 2. Characterization of two independent cave bear genomic libraries. Predicted origin of 9035 clones from library CB1 (A) and 4992 clones from library CB2 (B) are shown, as determined by BLAST comparison to GenBank and environmental sequence databases. Other refers to viral or plasmid-derived DNAs. Distribution of sequence annotation features in 6,775 nucleotides of carnivore sequence from library CB1 (C) and 20,086 nucleotides of carnivore sequence from library CB2 (D) are shown as determined by alignment to the July 2004 dog genome assembly. [View Larger Version of this Image (31K GIF file)]




    BLAST hits to the dog genome from libraries CB1 and CB2 were on average 92.4 and 92.3% identical to dog, respectively. To confirm that these sequences were indeed those of the cave bear, we designed primers against 124 putative cave bear sequences and successfully amplified and sequenced 116 orthologous sequences from the modern brown bear. All 116 of these modern bear sequences were at least 97% identical to their cave bear orthologs, verifying that all or nearly all of the carnivore sequences in both libraries are genuine cave bear genomic sequences. Only 6 of 14,027 sequenced clones had an insert that was identical to modern human genomic DNA (Fig. 2, A and B). The average BLAST hit length to the human genome for these clones was 116 bp, and the average hit covered 76% of the insert. Although we cannot establish a formal insert length or insert coverage threshold that differentiates between ancient and modern inserts because of the limited number of modern sequences we obtained, these values are significantly greater than the corresponding values for clones with cave bear sequences (P < 0.05 for the difference in both average clone length and average insert coverage calculated by two-tailed t test). This result suggests that it may be possible to discriminate between inserts derived from short ancient DNA molecules and inserts containing modern undamaged DNA in ancient DNA libraries. This may have relevance to the application of these methods to ancient hominids, in which the ability to distinguish ancient hominid DNA from modern contamination will be essential.


    The remaining inserts with BLAST hits to sequences from known taxa were derived from other eukaryotic sources, such as plants or fungi, or from prokaryotic sources (bacteria and archaea), which provided the majority of known sequences in each library. The end-repair reaction performed on each ancient DNA extract is likely biased toward less-damaged ancient DNA fragments and modern DNA, which could contribute to the abundance of prokaryotic sequences relative to cave bear sequences in these libraries. The representation we observe in the libraries thus reflects the proportion of clonable sequences from each source, not the true abundances of such sequences in the original extracts. However, the results from both libraries demonstrate that substantial quantities of genuine cave bear genomic DNA are efficiently end-repaired and cloned, despite this possible bias. A considerable fraction of inserts in each library (17.3% in library CB1 and 11.2% in library CB2; Fig. 2) had hits only to uncharacterized environmental sequences. The majority of these clones had BLAST hits to GenBank sequences derived from a single soil sample (17), consistent with the contamination of each cave bear bone with soil bacteria from the recovery site. As in other metagenomic sequencing studies, most inserts in each library had no similarity to any sequences in the public databases.





    Fig. 3. (A) Phylogenetic relationship of cave bear and modern bear sequences obtained by maximum-likelihood estimation using 3201 aligned sites. (B) Phylogeny obtained using all sites from (A), excluding cave bear and orthologous modern bear sites corresponding to two heavily damaged cave bear clones (table S3). Substitution rates, total substitutions (black), and GC–AT transitions (red) for each branch are shown. Orthologous dog sequence was used to root the trees. Percent support for internal nodes is also shown. [View Larger Version of this Image (11K GIF file)]



    To annotate cave bear genomic sequences, we aligned each cave bear sequence to the dog genome assembly using BLAST-like alignment tool (BLAT) (18). 6.1% of 6775 cave bear nucleotides from library CB1 and 4.1% of 20,086 cave bear nucleotides from library CB2 aligned to predicted dog RefSeq exons, in a total of 21 genes distributed throughout the dog genome (Fig. 2, C and D, and table S2). 4.1% and 6.2% of cave bear nucleotides, respectively, from library CB1 and library CB2 aligned to constrained nonexonic positions in the dog genome with phastCons conservation scores 0.8 (conserved noncoding, Fig. 2, C and D) (14). The majority of cave bear sequence in each library, however, aligned to dog repeats or regions of the dog genome with no annotated sequence features. These latter sequences are likely fragments of neutrally evolving, nonrepetitive sequence from the cave bear genome. Constrained sequences are slightly overrepresented in our set: Only 1.7% of bases in the dog genome assembly were annotated as RefSeq exons, and 10% of the cave bear sequences we obtained appear to be constrained overall, whereas 5 to 8% of positions in sequenced mammalian genomes are estimated to be under constraint (19). This discrepancy may be caused by our use of BLAST sequence similarity to identify cave bear sequences, an approach that is biased in favor of more-constrained sequences. Nevertheless, coding sequences, conserved noncoding sequences, and repeats appear in both cave bear genomic libraries at frequencies roughly proportional to what has been observed in modern mammalian genomes.
    To determine whether the cave bear sequences we obtained contain sufficient information to reconstruct the phylogeny of cave bears and modern bears, we generated and aligned 3201 bp of orthologous sequences from cave bears and modern black, polar, and brown bears and estimated their phylogeny by maximum likelihood (Fig. 3A) (20). This phylogeny is topologically equivalent to phylogenies previously obtained using cave bear and modern bear mitochondrial DNA (13). This result further indicates that our libraries contain genuine cave bear sequences and demonstrates that we can obtain sufficient ancient sequences from those libraries to estimate the evolutionary relationships between ancient and modern lineages.

    The substitution rate we estimated for cave bears is higher than that in any other bear lineage. On the basis of results from PCR-amplified ancient mitochondrial DNA, cytosines in ancient DNA can undergo deamination to uracil, which results in an excess of G-to-A and C-to-T (GC–AT) transitions (21). The inflated substitution rate in cave bears is likely caused by an excess of such events, because many of the substitutions assigned to the cave bear lineage are GC–AT transitions (Fig. 3A). These presumably damage-induced substitutions complicate phylogenetic reconstruction and the identification of functional sequence differences between extinct and modern species. However, these substitutions are not randomly distributed among all cave bear sequences but are clustered on a few clones from library CB2. Thus, two clones from library CB2 have three and four GC–AT transitions specific to cave bears, an observation that is extremely unlikely given that the occurrence of true randomly arising substitutions on cave bear clones should follow a Poisson distribution (table S3). When these two clones are excluded from the analysis (Fig. 3B), the apparent substitution rate and the excess of GC–AT transitions in cave bears are reduced, with little impact on estimates of substitution rates in the modern bear lineages. Although we cannot distinguish individual GC–AT substitutions from deamination-induced damage, these observations provide a quantitative means to identify cloned ancient DNA fragments with an excess of cytosine deamination events. It is also likely that heavily degraded ancient DNA fragments are poorly end-repaired and will therefore appear at reduced frequency in ancient DNA genomic libraries.

    Although small amounts of genomic sequence have previously been obtained by amplification from <20,000-year-old remains (12), the direct cloning strategy employed here has yielded considerably more genomic DNA sequence from much older samples. Based on our results, ancient DNA sequencing programs for extinct Pleistocene species, including hominids, are feasible using a metagenomic approach. By revealing the phylogenomic terrain of recent mammalian evolution, these efforts should help identify the molecular events underlying adaptive differences among modern species.


    References and Notes


    1. S. Pääbo et al., Annu. Rev. Genet. 38, 645 (2004). [CrossRef] [ISI] [Medline]
    2. M. Hofreiter, D. Serre, H. N. Poinar, M. Kuch, S. Pääbo, Nat. Rev. Genet. 2, 353 (2001). [CrossRef] [ISI] [Medline]
    3. C. Hänni, V. Laudet, D. Stehelin, P. Taberlet, Proc. Natl. Acad. Sci. U.S.A. 91, 12336 (1994).[Abstract/Free Full Text]
    4. M. Krings et al., Cell 90, 19 (1997). [CrossRef] [ISI] [Medline]
    5. M. Krings, H. Geisert, R. W. Schmitz, H. Krainitzki, S. Pääbo, Proc. Natl. Acad. Sci. U.S.A. 96, 5581 (1999).[Abstract/Free Full Text]
    6. M. Hofreiter et al., Mol. Biol. Evol. 19, 1244 (2002).[Abstract/Free Full Text]
    7. D. Serre et al., PLoS Biol. 2, 313 (2004).
    8. M. Hofreiter et al., Proc. Natl. Acad. Sci. U.S.A. 101, 12963 (2004).[Abstract/Free Full Text]
    9. P. Goloubinoff, S. Pääbo, A. C. Wilson, Proc. Natl. Acad. Sci. U.S.A. 90, 1997 (1993).[Abstract/Free Full Text]
    10. A. D. Greenwood, C. Capelli, G. Possnert, S. Pääbo, Mol. Biol. Evol. 16, 1466 (1999).[Abstract]
    11. V. Jaenicke-Després et al., Science 302, 1206 (2003).[Abstract/Free Full Text]
    12. H. Poinar, M. Kuch, G. McDonald, P. Martin, S. Pääbo, Curr. Biol. 13, 1150 (2003). [CrossRef] [Medline]
    13. O. Loreille et al., Curr. Biol. 11, 200 (2001). [CrossRef] [ISI] [Medline]
    14. Materials and methods are available as supporting material on Science Online.
    15. The dog genome sequence generated by the Broad Institute and Agencourt Biosciences was obtained from the University of California at Santa Cruz Dog Genome Browser (http://genome.ucsc.edu).
    16. S. F. Altschul et al., Nucleic Acids Res. 25, 3389 (1997).[Abstract/Free Full Text]
    17. S. G. Tringe et al., Science 308, 554 (2005).[Abstract/Free Full Text]
    18. W. J. Kent, Genome Res. 12, 656 (2002).[Abstract/Free Full Text]
    19. G. M. Cooper et al., Genome Res. 14, 539 (2004).[Abstract/Free Full Text]
    20. We cannot formally exclude alternative topologies, given the small number of nucleotide sites in the analysis and the limited divergence among these bear species, which also accounts for the low percent support for the internal nodes. Damage-induced substitutions in cave bears also perturb the phylogeny. The topology with the next-best likelihood score has cave bears as the outgroup to the modern bears due to an excess of GC–AT substitutions in several library CB2 sequences.
    21. M. Hofreiter, V. Jaenicke, D. Serre, A. von Haeseler, S. Pääbo, Nucleic Acids Res. 29, 4793 (2001).[Abstract/Free Full Text]
    22. Data have been deposited into GenBank with accession numbers CZ551658 to CZ552046. We thank members of the Rubin and Pääbo laboratories for insightful discussions and support. This work was performed under the auspices of the U.S. Department of Energy's Office of Science Biological and Environmental Research Program and by the University of California; Lawrence Berkeley National Laboratory; Lawrence Livermore National Laboratory; and Los Alamos National Laboratory under contract numbers DE-AC03-76SF00098, W-7405-Eng-48, and W-7405-ENG-36, respectively, with support from NIH grants U1 HL66681B and T32 HL07279 and at the Max Planck Institute for Evolutionary Anthropology.
    Reply With Quote  
     

  9. #8  
    Forum Professor Zwirko's Avatar
    Join Date
    Sep 2008
    Location
    55° N, 3° W
    Posts
    1,086
    The paper (quite old for a study in paleogenomics) outlines why a metagenomic approach was used.

    Degraded DNA present in a background of enviromental and human contaminants has been notoriously difficult to study. One solution is to just admit that your sample is hopelessly contaminated, sequence everything you've got and then try to remove unwanted sequences by comparing your data with known sequences Hopefully you end up with the sequences of interest. The study presents itself as a"powerful alternative to the targeted PCR approaches".

    Two of the authors of that paper - Svante Pääbo and James Noonan - have also been sequencing a lot of the Neanderthal genome lately.
    Reply With Quote  
     

  10. #9  
    Forum Cosmic Wizard spuriousmonkey's Avatar
    Join Date
    May 2005
    Posts
    2,193
    I still rather have a link so I can see figures and such.
    "Kill them all and let God sort them out."

    - Arnaud Amalric

    http://spuriousforums.com/index.php
    Reply With Quote  
     

  11. #10  
    Suspended
    Join Date
    Dec 2008
    Location
    Nirgendwo und Ueberall
    Posts
    1,300
    Quote Originally Posted by spuriousmonkey
    I still rather have a link so I can see figures and such.
    http://www.sciencemag.org/cgi/conten...i;309/5734/597
    Reply With Quote  
     

  12. #11  
    Forum Cosmic Wizard spuriousmonkey's Avatar
    Join Date
    May 2005
    Posts
    2,193
    This is simply saying that Cave Bears underwent more genetic change than other bears and that these events make it hard to reconstruct what they looked like? The GC-AT transitions are due to uracil deanimation, which is an event that occurs often in ancient DNA? If so, why does this occur?
    The paper stated that the phenomenon only occurred in specific clones. In the other clones the substitution rate was comparable to 'normal' bear rates, but the authors noted that it is impossible to distinguish between the proper substitutions and the chemically induced substitutions.

    As to the why this occurs: This original paper refers to another paper. And this paper refers to a 1996 paper.

    The Croonian Lecture, 1996: Endogenous Damage to DNA

    http://rstb.royalsocietypublishing.o.../1529.full.pdf

    Point 4 is on the deamination of cytosine to uracil.

    After reading that I am not quite sure on the why, other than it is a biochemical property of the molecule to do so.

    Both links were free papers and could have been following by the interested reader.
    "Kill them all and let God sort them out."

    - Arnaud Amalric

    http://spuriousforums.com/index.php
    Reply With Quote  
     

  13. #12  
    Forum Professor Zwirko's Avatar
    Join Date
    Sep 2008
    Location
    55° N, 3° W
    Posts
    1,086
    Slightly off-topic (a video lecture by the one of the authors of the cave bear paper).

    If anyone is interested, you can watch a video of Svante Pääbo's plenary lecture at the 2009 AAAS meeting. In it he discusses many of the problems ecountered on the Neanderthal genome project. He also spends a fair bit of time talking about the problems of contamination and how they were largely (hopefully) overcome.

    Video is 50 minutes long and is in the pesky Real Video foramat (at bottom of page).
    Reply With Quote  
     

  14. #13  
    Suspended
    Join Date
    Dec 2008
    Location
    Nirgendwo und Ueberall
    Posts
    1,300
    Thanks! I'll check it out when I get home from work tonight.
    Reply With Quote  
     

Bookmarks
Bookmarks
Posting Permissions
  • You may not post new threads
  • You may not post replies
  • You may not post attachments
  • You may not edit your posts
  •