Another Big Example of Reductive Evolution?
by MikeGeneDavid Penny continues to make the case that bacteria are derived from a more complex, eukaryotic-like state:
Instead, the data suggest that eukaryote cells with all their bells and whistles are probably as ancient as bacteria and archaea, and may have even appeared first, with bacteria and archaea appearing later as stripped-down versions of eukaryotes, according to David Penny, a molecular biologist at Massey University in New Zealand…..If the first eukaryotes were a fusion of ancient bacteria and archaea, as some scientists suspect, there should be clues in the eukaryote genome and proteome that point back toward these putative ancestors. Penny and colleagues say those clues simply aren't there. Instead, the say the fusion theory is "surprisingly uninformative" when it comes explaining the special genetic and cellular features of eukaryotes. Most of the proteins that eukaryotes and bacteria share, for instance, are only distantly related and probably came from the common ancestor of both bacteria and eukaryotes.
Related analyses are found here and here.
May 19th, 2006 at 5:12 pm
Then eukaryotes came from…?
Comment by Bilbo — May 19, 2006 @ 5:12 pm
May 19th, 2006 at 7:44 pm
Bilbo,
A real scientist would not ask that question.
Comment by Douglas — May 19, 2006 @ 7:44 pm
May 20th, 2006 at 1:12 am
This is HUGE! Why is it getting so little posting activity. If the eukaryotes came before the archaea, the science of abiogenesis is in a whole lot more trouble than it is already in!
Though this post is about reductive evolution, the real story is in the most recent common ancestor to life on earth. Am I not right when I say that the simplest eukaryote is a heck of a lot more complex than the archaea is?
Comment by bFast — May 20, 2006 @ 1:12 am
May 20th, 2006 at 3:03 am
The many proteins unique to eukaryotes raise the question of whether bacteria and eukaryotes even had a common ancestor. I plan on writing a longer piece on this later, but don't hold me to it.
Comment by Krauze — May 20, 2006 @ 3:03 am
May 20th, 2006 at 3:32 am
These findings are saying that prokaryotes, archaea and eukaryotes share a common ancestor, and that prokaryotes are not necessarily the direct ancestors of eukaryotes.
It doesn't mean that 'eukaryotes came before archaea' at all. It means they share a common ancestor, which would have been neither a eukaryote nor an archaea. (What you are saying is the same as 'humans came from chimps', which of course they didn't. Humans and chimps share a common ancestor, which was neither human nor chimp).
I do find it fascinating that the archaea are more closely related to the eukaryotes than the prokaryotes though.
Comment by Odd Digit — May 20, 2006 @ 3:32 am
May 20th, 2006 at 3:55 am
Just a clarification: Both bacteria and archaeons are prokaryotes, so named because they lack the nucleus ("karyon") that characterizes eukaryotes. Tara Smith has a good post about this, including a persuasive argument for scouring the word "prokaryote" from your vocabulary.
Comment by Krauze — May 20, 2006 @ 3:55 am
May 20th, 2006 at 4:22 am
You're quite correct I should have said 'archaea are more closely related to the eukaryotes than the rest of the prokaryotes'.
Archaea have been seen as separate from the (ahem) 'rest of the prokaryotes' for quite some time now, but they were still thought to have been more closely related to bacteria than the eukaryotes, and still grouped under the heading 'prokaryotes'.
I've seen Tara's post, and she's quite right, we might have to rename prokaryotes now!
Comment by Odd Digit — May 20, 2006 @ 4:22 am
May 20th, 2006 at 4:50 am
Hi Odd Digit,
"Archaea have been seen as separate from the (ahem) 'rest of the prokaryotes' for quite some time now, but they were still thought to have been more closely related to bacteria than the eukaryotes,"
Umm, no they weren't. The traditional tree of life, with archaeons and eukaryotes as sister groups and bacteria as the outgroup, dates back to Woese's work on ribosomal RNA in the 70's (see the tree here).
What's interesting about this study is that it challenges a widely held hypothesis that Eucarya arose out of the fusion of a bacterium with an archaeon (also known as the endosymbiotic origin of the nucleus, not to be confused with the endosymbiotic origin of mitochondria and chloroplasts). The authors dispute this, based on the high number of proteins unique with eukaryotes:
Comment by Krauze — May 20, 2006 @ 4:50 am
May 20th, 2006 at 5:21 am
Umm, yes they were. Just look at the tree and see how close the archaea are to the bacteria… as opposed to the much more distant eukaryotes… i.e. 'more closely related'. Duh.
My understanding is that the traditional view of the origin of the nucleus states that the nuclear genome originated through direct evolution from an archaebacterial ancestor. I've seen Golding and Gupta's 'chimeric model' as well. I don't think the endosymbiosis theory for the origin of the nucleus was that widely held…
So the most interesting thing about this is that the archaeal branch has suddenly moved a couple of centimeters to the right on that diagram. And therefore the traditional view of what 'prokaryotes' are has now changed, because 'half' the prokaryotes are actaully closer to eukaryotes that the they are to the other 'half' of the prokaryotes. Which is the point that Tara was making.
Comment by Odd Digit — May 20, 2006 @ 5:21 am
May 20th, 2006 at 9:50 am
bFast:
Actually, what you have is an on-going debate about the origin of eukarya. Penny has been arguing that bacteria are derived, stream-lined states for some time now and he is clearly advancing the ball in his favor. However, other scientists use the same data to argue that there was a third lineage that engulfed archaea and bacteria and the eukaryotic-specific proteins are the only remnants of this now-extinct lineage. And the fusion hypothesis still remains rather popular.
Comment by MikeGene — May 20, 2006 @ 9:50 am
May 20th, 2006 at 12:01 pm
Hi Krauze,
Interesting article over at ARN:
Genomics and the Irreducible Nature of Eukaryote Cells
Comment by Mung — May 20, 2006 @ 12:01 pm
May 20th, 2006 at 5:05 pm
Hi Odd Digit,
"I don't think the endosymbiosis theory for the origin of the nucleus was that widely held"¦"
Let me just say that my own interaction with researchers of the field suggest something else.
"And therefore the traditional view of what 'prokaryotes' are has now changed, because 'half' the prokaryotes are actaully closer to eukaryotes that the they are to the other 'half' of the prokaryotes."
But as I explained before, that archaeons are closer related to eukaryotes than they are to bacteria was already advocated by Woese in the 70's. You're reading things into the paper (and Tara's post) that simply aren't there, underestimating its true novelty. One of the interesting things about the paper is its very lack of a phylogeny. The closest thing they come to one is this (sorry about the small size). Does it show Archaea as being closer related to Eukarya than to Bacteria? Not unless my eyesight is failing.
Instead, here is the much more interesting message I hear coming out of the mouths of the researchers: "Sure, all lifeforms share a common ancestor. We aren't creationists or anything! But this ancestor didn't look like bacteria nor archaeons. In fact, it probably wasn't even a single organism, but more like a community of organisms, containing autotrophs, heterotrophs, saprotrophs, and phagotrophs. Yeah, we know that that pretty much describes every organism currently living on the planet, but we're having a hard time tying the common ancestor down to some particulars."
Comment by Krauze — May 20, 2006 @ 5:05 pm