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Antievolution.org Discussion Board > From the Panda's Thumb > After the Bar Closes... > Duplication of Genes May Solve Mystery

Henry J Posts: 5760 Joined: Mar. 2005 (Permalink) Posted: May 15 2006,16:08    Massive Duplication of Genes May Solve Darwin's "Abominable Mystery" about Flowering Plants   Quote Researchers from the Floral Genome Project at Penn State University, with an international team of collaborators, have proposed an answer to Charles Darwin's "abominable mystery:" the inexplicably rapid evolution of flowering plants immediately after their first appearance some 140 million years ago. [...] a previously hidden "paleopolyploidy" event Henry

sir_toejam Posts: 846 Joined: April 2005 (Permalink) Posted: May 15 2006,18:38    Hmm, I must be missing something here. botanical polyploidy has been a well known phenomenon for decades. It's not clear to me how this is anything new?

Renier Posts: 276 Joined: Jan. 2006 (Permalink) Posted: May 15 2006,21:03    Thanks, it was a very interesting article.

George Posts: 316 Joined: Feb. 2006 (Permalink) Posted: May 16 2006,02:25    The idea is that the ancient polyploidy event was somehow responsible for the rapid proliferation of angiosperms.  From the article the mechanism isn't clear.  Neither is the role of co-evolution with pollinator species, which has been suggested as an important factor in angiosperm speciation. Hybridisation + polyploidy is a not-too-uncommon method of "instant speciation" in plants.  Several species of ferns appear to have arisen this way.  But the best example is Spartina anglica which arose as a polyploid hybrid of two British species in the 1890s.  It's now dominant in much of coastal Britain, and still spreading (though humans also gave it a helping hand in its initial spread).

Chris Hyland Posts: 705 Joined: Jan. 2006 (Permalink) Posted: May 16 2006,03:17    In animals quite often we see a diversification of species following genome duplication events, for example a whole genome duplication coincides with the origin of vertebrates. It appears that it also reduces the change of a species becoming extinct, and duplication events are often preceeded by multiple extinct lineages. This is probably because a duplication of the genome equals quadruple the number of genetic interactions, so a lot of oppurtunity to generate biological novelty, which is useful if you're facing extinction.

sir_toejam Posts: 846 Joined: April 2005 (Permalink) Posted: May 16 2006,09:00    yes, and my point remains.  this mechanism has been known for years.  what, specifically, is this article contributing to our knowledge?

jeannot Posts: 1201 Joined: Jan. 2006 (Permalink) Posted: May 16 2006,09:11    Now, we know that a whole genome duplication occurred in the common ancestor of most plants, which could have contributed to their diversification. This hypothesis is based on the already known effects of genome duplications. I think this discovery deserves an article, why don't you?

sir_toejam Posts: 846 Joined: April 2005 (Permalink) Posted: May 16 2006,09:29    Edit: I see Jeannot suggests it's the contribution to unraveling partial vs. whole genome duplication. Is this correct?  Is the method for DNA fragment analysis a new contribution as well? look, you should know by now that I'm not a hollow minded AFDAVE here.  I wasn't questioning whether the article should be published, but rather attempting to elucidate what is new in it.

Henry J Posts: 5760 Joined: Mar. 2005 (Permalink) Posted: May 16 2006,09:33    Well, it contributed to my knowledge, even if professional biologists knew everything in it already. Henry

jeannot Posts: 1201 Joined: Jan. 2006 (Permalink) Posted: May 16 2006,09:34    Quote (sir_toejam @ May 16 2006,14:29) Is this article the first to use polyploidy to explain angiosperm diversification? really? Did I say that? EDIT Quote I see Jeannot suggests it's the contribution to unraveling partial vs. whole genome duplication. No I don't (see my next post).

sir_toejam Posts: 846 Joined: April 2005 (Permalink) Posted: May 16 2006,09:37    no, you didn't.  You must be missing what i meant by that. which is why i edited the comment.

jeannot Posts: 1201 Joined: Jan. 2006 (Permalink) Posted: May 16 2006,09:40    They just investigated the historical causes of the diversification of angiosperms (based on known genetic processes). That's their contribution. Edit: I remember reading a study about some genome duplications in early angiosperms (before the true angiosperms actually, they traced back to trias or something) but I don't remember where. It was several months ago.

sir_toejam Posts: 846 Joined: April 2005 (Permalink) Posted: May 16 2006,10:05    Hmm, I'm not sure about that.  the historical perspective on polyploidy and speciation has been covered before. I tend to think any real significance to the scientific community might be more related to the specific methods used in this paper, which is what i was kind of hoping someone would expound upon.   I should always be more specific when in this forum. this is what i want to focus on: Quote But because of the rapid, massive gene loss after a whole-genome duplication, these events are notoriously difficult to detect after millions of years. So dePamphilis and colleagues relied on a statistical filter to hunt for ancient duplications. It's their new (?) analytical technique used to examine DNA fragments from whole genome polyploidy events that appears to be significant here, but isn't exactly covered in detail in the news article.  IS it new?   I was hoping that someone more conversant with the literature in this area could shed light on the significance of the technique used.  Is this technique amenable to analysis of other genome datasets?   It appears the full text of the article is locked to everybody but journal subscribers, so I personally can't check out the methods used. OT: as a side note, I do hope that the open journal standard starts to catch on a bit more. here's a list of open journals: http://www.doaj.org/ /OT

jeannot Posts: 1201 Joined: Jan. 2006 (Permalink) Posted: May 16 2006,10:27    I may have access to the article, but I can't find it. Am I dumb or what?

sir_toejam Posts: 846 Joined: April 2005 (Permalink) Posted: May 16 2006,10:30    actually, re-reading the report, it says it's in a JUNE issue of the journal, so it may not have made it online yet.  I was looking at another article there that was locked, so it too would have been locked of course. so it ain't you that's "dumb".  blame it on me. You have a subscription to that journal?

jeannot Posts: 1201 Joined: Jan. 2006 (Permalink) Posted: May 16 2006,10:36    Apparently, my lab has access to this journal.

jeannot Posts: 1201 Joined: Jan. 2006 (Permalink) Posted: May 16 2006,10:47    Quote (jeannot @ May 16 2006,14:40) Edit: I remember reading a study about some genome duplications in early angiosperms (before the true angiosperms actually, they traced back to trias or something) but I don't remember where. It was several months ago. It was in TREE.

sir_toejam Posts: 846 Joined: April 2005 (Permalink) Posted: May 16 2006,10:57    Quote Apparently, my lab has access to this journal. ah, well I guess i would humbly ask that if you get the time, revive this topic when the issue is released?

jeannot Posts: 1201 Joined: Jan. 2006 (Permalink) Posted: May 16 2006,11:00    No problem. If I forget, send me a PM.

sir_toejam Posts: 846 Joined: April 2005 (Permalink) Posted: May 16 2006,11:05    It really sucks not having direct online access to a university library these days. *sigh* for me these days, it means an hour and half drive to UC Riverside if i want to check out recent periodicals. there's gotta be a better way.

jeannot Posts: 1201 Joined: Jan. 2006 (Permalink) Posted: May 16 2006,11:30    (off topic) With our authentification system, I can access online articles from any computer, anywhere (provided I set some connexion parameters in every computer). Do your system check your IP adress for authentification?

sir_toejam Posts: 846 Joined: April 2005 (Permalink) Posted: May 16 2006,12:04    does your authentication system not require you to utilize a password system somewhere along the line? or does it just assign specific IP blocks as default access? if the latter, i assume you have to get an ip assigned by your department, or the university IT dept.? that would be a common way of limiting access. It used to be that i could access any of the UC systems externally with a simple password access thru any UC bio library. but of course to get my password, I had to be affiliated officially with the university in some way, which i no longer am. I could ask acquaintaces at berkeley or santa cruz or santa barbara to give me a copy of their password, but somehow I never felt comfortable doing this.  Trivial issue, but I wouldn't want them to be responsible if something ridiculous happened. I guess it's high time i did something to increase my access though.   I wanted to start an offical paper discussion group here on ATBC (using a different moderated forum), but my problem is i would need better access to be a productive contributor myself ).

jeannot Posts: 1201 Joined: Jan. 2006 (Permalink) Posted: May 16 2006,12:14    Quote (sir_toejam @ May 16 2006,17:04) does your authentication system not require you to utilize a password system somewhere along the line? Yes, I have a personal password that is sent to a proxy server at each connexion.

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