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Author Topic:   OMG!! Humans are more closely related to chimps than to other humans!!!
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 1 of 11 (365549)
11-23-2006 6:57 AM


A very interesting paper is now online at Nature. It is entitled 'Global variation in copy number in the human genome' (Redon et al., 2006). The full article is freely available online.
We have recently had a number of threads discussing human/chimp genetics and the significance of indels on measurements of divergence and their significance to evolution. This paper studied copy number variations which include indels as well as duplications and more complex genetic events.
This nature paper is a product of the haplotype mapping (HAPMAP) project which is being worked on by a number of HGP contributors such as the Sanger centre. The abstract is as follows...
Copy number variation (CNV) of DNA sequences is functionally significant but has yet to be fully ascertained. We have constructed a first-generation CNV map of the human genome through the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia (the HapMap collection). DNA from these individuals was screened for CNV using two complementary technologies: single-nucleotide polymorphism (SNP) genotyping arrays, and clone-based comparative genomic hybridization. A total of 1,447 copy number variable regions (CNVRs), which can encompass overlapping or adjacent gains or losses, covering 360 megabases (12% of the genome) were identified in these populations. These CNVRs contained hundreds of genes, disease loci, functional elements and segmental duplications. Notably, the CNVRs encompassed more nucleotide content per genome than SNPs, underscoring the importance of CNV in genetic diversity and evolution. The data obtained delineate linkage disequilibrium patterns for many CNVs, and reveal marked variation in copy number among populations. We also demonstrate the utility of this resource for genetic disease studies.
They identified 1,447 regions (CNVRs) in the genome where there were variations in copy number amongst the sampled genomes of sequences greater than 1Kb in size. These regions covered 12% of the genome altogether.
They go on to show that copy number variations can be used to identify populations with putative common ancestry from european, asian and african populations.
It would be interesting to see how these CNVRs compare to the regions of indels associated with the increased estimates in human chimp divergence. If both human and chimps can have as much as 12% variation based on CNVR's with populations then how much distinct difference do such factors present between the 2 species.
This is really phenomenal work and as more organisms are studied at the same level of detail it opens up the possibility of identifying a vast area of functionally relevant variation both within and between mammalian species and throughout the animal kingdom. This also has major implications for the study of genetic differences affecting responses to medical treatments and to disease in general.
There are at least 2 other CNV papers out related to this one, one in nature genetics (Khaja et al, 2006) and one in Genome Research which explains the technical methodology behind the comparisons in more detail(Fiegler et al., 2006)
TTFN,
WK
Edited by Wounded King, : No reason given.
Edited by Wounded King, : No reason given.

Replies to this message:
 Message 7 by mick, posted 11-24-2006 4:05 PM Wounded King has replied
 Message 9 by Minnemooseus, posted 04-05-2007 11:11 PM Wounded King has not replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 2 of 11 (365550)
11-23-2006 7:03 AM


Perhaps this needs a sexier title like 'OMG!! Humans are more closely related to chimps than to other humans!!!'.
TTFN,
WK

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 Message 3 by AdminPhat, posted 11-23-2006 7:44 AM Wounded King has replied

  
AdminPhat
Inactive Member


Message 3 of 11 (365558)
11-23-2006 7:44 AM
Reply to: Message 2 by Wounded King
11-23-2006 7:03 AM


Which Forum?
Which Forum do you want this in, WK?

This message is a reply to:
 Message 2 by Wounded King, posted 11-23-2006 7:03 AM Wounded King has replied

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 Message 4 by Wounded King, posted 11-23-2006 7:48 AM AdminPhat has not replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 4 of 11 (365561)
11-23-2006 7:48 AM
Reply to: Message 3 by AdminPhat
11-23-2006 7:44 AM


Re: Which Forum?
I'd have thought Biological Evolution was the most appropriate.
TTFN,
WK

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AdminNem
Inactive Member


Message 5 of 11 (365614)
11-23-2006 2:00 PM


Thread moved here from the Proposed New Topics forum.

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 6 of 11 (365795)
11-24-2006 3:47 PM


Blatant tabloidism
*bump* to see if a crass headline title can attract anyone's attention.
TTFN,
WK

  
mick
Member (Idle past 4987 days)
Posts: 913
Joined: 02-17-2005


Message 7 of 11 (365797)
11-24-2006 4:05 PM
Reply to: Message 1 by Wounded King
11-23-2006 6:57 AM


what is copy number variation?
Hi,
I don't have access to the literature right now, so could you explain what copy number variation is?
I am thinking microsats and duplicated genes, but perhaps i am on the wrong track.
[AbE] I know that microsatellites are the result of variation in copy number of nucleotide pairs, triplets, quadruplets, or whatever, and that the human population varies moderately in copy number. At a different order of magnitude, I know that duplicated genes might result in numerous copies of a protein-coding sequence, and that in this respect the human population is pretty constant in copy number. So I can only assume that the authors of the paper are talking about some intermediate level, perhaps variation in copy number of intronic elements or something like that?
Mick
Edited by mick, : No reason given.

This message is a reply to:
 Message 1 by Wounded King, posted 11-23-2006 6:57 AM Wounded King has replied

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 8 of 11 (365805)
11-24-2006 4:33 PM
Reply to: Message 7 by mick
11-24-2006 4:05 PM


Re: what is copy number variation?
I don't have access to the literature right now
The paper is available without a subscription at the moment so you should be able to download it or read it online.
So I can only assume that the authors of the paper are talking about some intermediate level, perhaps variation in copy number of intronic elements or something like that?
No and yes. Copy nuber variation can encompass both expansion of repeat as in microsatellites and gene duplications. As I briefly mentioned in the OP it is simply any sequence of 1Kb or greater and which varies in representation from a base genome. They go on to characterise further...
A CNV can be simple in structure, such as tandem duplication, or may involve complex gains or losses of homologous sequences at multiple sites in the genome
Over half of the identified CNVs overlap genes identified in the refseq database and more than 99% overlap highly convserved non-coding regions (but not ultra-conserved elements).
TTFN,
WK

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Minnemooseus
Member
Posts: 3941
From: Duluth, Minnesota, U.S. (West end of Lake Superior)
Joined: 11-11-2001
Member Rating: 10.0


Message 9 of 11 (393609)
04-05-2007 11:11 PM
Reply to: Message 1 by Wounded King
11-23-2006 6:57 AM


Bump - Care to take a stab at explaining this to us non-biologicsts
Found this while bumbling around the older topics bin. I have recollections of having asked about this sort of topic before, but it doesn't seem to be in this topic.
Could we get the "Biology for Absolute Dummys" version? What human/human gap is larger than what human/chimp gap?
Moose

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 Message 1 by Wounded King, posted 11-23-2006 6:57 AM Wounded King has not replied

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Doddy
Member (Idle past 5910 days)
Posts: 563
From: Brisbane, Australia
Joined: 01-04-2007


Message 10 of 11 (394210)
04-10-2007 9:40 AM
Reply to: Message 9 by Minnemooseus
04-05-2007 11:11 PM


Re: Bump - Care to take a stab at explaining this to us non-biologicsts
What human/human gap is larger than what human/chimp gap?
I just skimmed through the full text of the cited paper, and I can't see any answer to that. My thinking is that Wounded King is deliberately misleading us...
I did see a study while I was searching around, by Perry, GH et al titled Hotspots for copy number variation in chimpanzees and humans (PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 103 (21): 8006-8011 MAY 23 2006). It seemed to be more on comparing the human/human and the chimp/chimp gap though:
quote:
We have identified an average of 31 CNVs in each of the 20 chimpanzees studied, compared to an average of 12.4 CNVs per person among the 55 human genomes interrogated in the Iafrate et al. study. This finding implies that overall chimpanzee genetic diversity may be more extensive than was previously thought; a notion that is based on estimates of general nuclear DNA sequence diversity among the western chimpanzee subspecies being similar to that of the human species as a whole. It is unclear whether this unexpected difference between chimpanzees and humans reflects species-level differences in selective pressures on copy number variation or higher duplication/deletion mutation rates in chimpanzees or both. Detailed studies on the evolutionary histories of specific CNV loci in both humans and chimpanzees may help resolve this issue.
Maybe WK can explain where he got the idea for the title from?

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 Message 9 by Minnemooseus, posted 04-05-2007 11:11 PM Minnemooseus has not replied

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 11 of 11 (394220)
04-10-2007 10:40 AM
Reply to: Message 10 by Doddy
04-10-2007 9:40 AM


Re: Bump - Care to take a stab at explaining this to us non-biologicsts
I chnaged the title from its original sober incarnation, which I can no longer recall, as a cheap way of attracting peole to the thread, a move which still singularly failed to excite much interest.
The basis of the title was the conflation by anti-evolutionist of virtually any measure of genetic distance as equivalent to any other and virtually interchangeable.
When you look at the arguments of people like Eggasai who complain that because sequence similarity measured by a crude biochemical measure is not the same as when measured by a direct comparison of the genetic sequence, or that one based on SNPs is different from one based on indels, that there is some sort of cover up being perpetrated.
Therefore published data suggesting a potential for divergence in ~12% of the genome between humans seems a prime target for the same sort of misconstruction.
TTFN,
WK

This message is a reply to:
 Message 10 by Doddy, posted 04-10-2007 9:40 AM Doddy has not replied

  
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