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  Topic: A gene for humanity?, Nature: 16 August 2006< Next Oldest | Next Newest >  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Aug. 19 2006,23:46   

Quote
Article

Nature advance online publication 16 August 2006 | doi:10.1038/nature05113; Received 27 June 2006; Accepted 25 July 2006; Published online 16 August 2006
An RNA gene expressed during cortical development evolved rapidly in humans

Katherine S. Pollard1,7,8, Sofie R. Salama1,2,8, Nelle Lambert4,5, Marie-Alexandra Lambot4, Sandra Coppens4, Jakob S. Pedersen1, Sol Katzman1, Bryan King1,2, Courtney Onodera1, Adam Siepel1,7, Andrew D. Kern1, Colette Dehay6, Haller Igel3, Manuel Ares, Jr3, Pierre Vanderhaeghen4 and David Haussler1,2
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Abstract

The developmental and evolutionary mechanisms behind the emergence of human-specific brain features remain largely unknown. However, the recent ability to compare our genome to that of our closest relative, the chimpanzee, provides new avenues to link genetic and phenotypic changes in the evolution of the human brain. We devised a ranking of regions in the human genome that show significant evolutionary acceleration. Here we report that the most dramatic of these 'human accelerated regions', HAR1, is part of a novel RNA gene (HAR1F) that is expressed specifically in Cajal–Retzius neurons in the developing human neocortex from 7 to 19 gestational weeks, a crucial period for cortical neuron specification and migration. HAR1F is co-expressed with reelin, a product of Cajal–Retzius neurons that is of fundamental importance in specifying the six-layer structure of the human cortex. HAR1 and the other human accelerated regions provide new candidates in the search for uniquely human biology.


So Dave, if you read this, you should be reassured.

  
Ichthyic



Posts: 3325
Joined: May 2006

(Permalink) Posted: Aug. 20 2006,02:48   

Jean-

Is this the paper referenced here:

http://www.antievolution.org/cgi-bin....;t=2780

If so (and it looks like it is), I figured you would have an interest in that one.

Have you gandered at it in detail yet?

--------------
"And the sea will grant each man new hope..."

-CC

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Aug. 20 2006,04:58   

Hi, Thomas.

This is the paper, I didn't read your thread.  :(

Well, I'm interested in the genomic comparison.

In short, they searched for conserved regions between chimp and mouse-rat (at least 96% identity over 100bp), to get rid of the junk.
Then, on these 35000 conserved regions, they selected the orthologs that differ the most in humans compared to other amniotes. They performed a likelihood ratio test (don't ask me) to check the significance of the differences.
96% of these 49 "Human Accelerated Regions" are non-coding. A quarter of them are adjacent to neurodevelopmental genes (regulation regions, promoters and such things, I guess. I didn't read the whole article).

  
Ichthyic



Posts: 3325
Joined: May 2006

(Permalink) Posted: Aug. 20 2006,11:18   

Quote
They performed a likelihood ratio test (don't ask me) to check the significance of the differences.


sounds like some sort of non-paramentric chi-square test.

ahh, yes, basically that's it:

http://www.molecularevolution.org/resources/lrt.php

I'm a bit confused here though.  It seems they are focusing on genes that produce interactive RNA?  this is something new to me.  do you have any more background on these kinds of genes?

When you get around to reading it in depth, let me know if you think the specific methods warrant the conclusions in this case.

cheers

--------------
"And the sea will grant each man new hope..."

-CC

  
ericmurphy



Posts: 2460
Joined: Oct. 2005

(Permalink) Posted: Aug. 20 2006,13:38   

Quote (jeannot @ Aug. 20 2006,09:58)
In short, they searched for conserved regions between chimp and mouse-rat (at least 96% identity over 100bp), to get rid of the junk.
Then, on these 35000 conserved regions, they selected the orthologs that differ the most in humans compared to other amniotes. They performed a likelihood ratio test (don't ask me) to check the significance of the differences.

I think this would be very interesting for Dave to read, in light of his "half a lousy percent!" argument about the relatedness of humans, chimps, and gorillas. I'm not sure of the exact figures, but I believe that humans and mice are something like 90% identical genetically (does anyone know the exact figure?). If so, that sort of puts the whole "half a lousy percent!" objection in perspective, doesn't it?

I think even people a lot smarter and more clue-enhanced than Dave lose sight of how closely humans cluster, genetically, with all mammals, or even all amniotes, to say nothing of primates or great apes.

--------------
2006 MVD award for most dogged defense of scientific sanity

"Atheism is a religion the same way NOT collecting stamps is a hobby." —Scott Adams

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Aug. 21 2006,00:28   

Quote (Ichthyic @ Aug. 20 2006,16:18)
Quote
They performed a likelihood ratio test (don't ask me) to check the significance of the differences.


sounds like some sort of non-paramentric chi-square test.

ahh, yes, basically that's it:

http://www.molecularevolution.org/resources/lrt.php

I'm a bit confused here though.  It seems they are focusing on genes that produce interactive RNA?  this is something new to me.  do you have any more background on these kinds of genes?

When you get around to reading it in depth, let me know if you think the specific methods warrant the conclusions in this case.

cheers

Thanks for the clarification.
My knowledge in molecular evolution will have to be improved seriously by the time I build and publish my phylogeography. Is there a book you would particularly recommend?

I don't know much about interactive RNAs in general. I know that some micro-RNAs can somehow interact with mRNAs before or during translation (or something).
Mirco-RNAs seem actively studied. Someone of my research team works on the micro-RNAs that are supposed to interact with mRNAs of genes controlling the induction of sexual forms in aphids.

Regarding the methods they used, I am afraid I won't have the time to dig into this paper, but I can send it to you, if you wish.

  
Ichthyic



Posts: 3325
Joined: May 2006

(Permalink) Posted: Aug. 21 2006,11:42   

Quote
Is there a book you would particularly recommend?


WRT to molecular evolution, alas, no.

my knowledge of what a likelihood ratio test is simply comes from the two years of statistics i took (biometry as an undergrad with Allen Stuart Oaten, and a year of pure probability and statistics at the grad level when I was at Berkeley).

if you ask me for a good statistics reference applicable to parametric and non-parametric analysis in genetics and biology as a whole, I'd have more to share.  for example:

Biometry by Robert R. Sokal (I've yet to see a better treatise on useable non-parametric statistics)

and

Zar, J.H., 1998. Biostatistical Analysis (It may be the case that I've refered to this text - well, an earlier version, anyway - more often than any other in publication - at least when doing my own research).


Molecular genetics was actually one of my worst subjects (grade wise), something one of my advisors constantly chided me on.  

It doesn't keep me from being interested and seeing the relative importance of it to my preferred field (behavioral ecology); but there are far better folks hanging about to ask for a reference than myself.

Most of the texts I have read in the field of molecular biology and evolutionary genetics are hopelessly out of date at this point.  

Quote
Someone of my research team works on the micro-RNAs that are supposed to interact with mRNAs of genes controlling the induction of sexual forms in aphids.


I seemed to recall you mentioning something to this effect at some point a while back; which is why I was asking you about the interactive RNA issue.

I can only guess that the prof who oversees your lab would have a great idea as to a good text to bring us both up to date on the issue.

Please post back here if you get a good suggestion.

Quote
Regarding the methods they used, I am afraid I won't have the time to dig into this paper, but I can send it to you, if you wish.


if you get a moment, please do.  I would very much enjoy reading the whole thing, I think.

cheers

--------------
"And the sea will grant each man new hope..."

-CC

  
ericmurphy



Posts: 2460
Joined: Oct. 2005

(Permalink) Posted: Sep. 01 2006,13:42   

More info on a possible "humanity" gene:

 
Quote
News @ nature.com: A newly discovered mystery gene may have helped build the modern human brain, researchers report today.

Scientists don't know what the gene does. But they do know that humans have more copies of it than chimpanzees, monkeys, rats and mice. And they know that the gene makes a protein that is found in the human brain. That suggests that it may help to give the human brain its unique ability to think and reason, they say.


Of course, this kind of research doesn't touch on all the "non-biological" differences (whatever that means) between humans and chimps that AF Dave supposes prove that humans and chimps are not actually related at all.

--------------
2006 MVD award for most dogged defense of scientific sanity

"Atheism is a religion the same way NOT collecting stamps is a hobby." —Scott Adams

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Sep. 01 2006,22:00   

Quote
That suggests that it may help to give the human brain its unique ability to think and reason, they say.

Don't chimps and dolphins reason?

  
Ichthyic



Posts: 3325
Joined: May 2006

(Permalink) Posted: Sep. 03 2006,20:39   

yes, something strikes me that when the news article said "they say", they really meant:

"we paraphrased for dramatic interest".

--------------
"And the sea will grant each man new hope..."

-CC

  
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