The Tree of Life Consolidates

Roland Piquepaille writes "The Tree of Life is an expression first used by Charles Darwin to describe the diversity of organisms on Earth and their evolutionary history. There are only two life forms, — eukaryotes, which gather their genetic material in a nucleus, and prokaryotes, such as bacteria, which have their genetic material floating freely in the cell. Until recently, eukaryotes, which include humans, were divided into five groups. But now, based on work by European researchers, the Tree of Life has lost a branch. After doing the largest ever genetic comparison of life forms they concluded that there are only four groups of eukaryotes."

Comments

Archaea

[virology-not for com]

Let's not forget that many scientists think there are three domains (Prokaryotes, Eukaryotes and Archaea). Archaea are very similar to Prokaryotes in that they don't have a nucleus, but they also share many features with Eukaryotes, including several key enzymes. Due to their similarity to the two other lineages, it is thought that Archaea may in fact be the grand daddy of all life. http://en.wikipedia.org/wiki/Archaea

Re:Archaea

[Anonymous Coward]

Little Nit - Archaea are technically Prokayotes (meaning "before nucleus"). The distinction is not between Prokaryotes and Archaea, but between Archaea and Eubacteria.

Although you can slice and dice as Eukaryotes/Prokaryotes, it's commonly accepted that Archaea are as different genetically from Eubacteria as Eubacteria are to Eukaryotes. In fact, it is usually said that Archaea are more closely related to Eukaryotes than they are to Eubacteria, so grouping Eubacteria and Archaea together as "Prokaryotes" because they lack a nucleus makes as much sense as grouping bats and birds together because they can fly.

Re:Archaea

[reverseengineer]

The level of organization being discussed in the paper treats a subdivision of the eukaryotes into "superkingdoms." (There's actually not a completely agreed upon term for this level.) This would put these groups a level below the three domains (Eucarya, Eubacteria, Archaebacteria) proposed by Carl Woese. There's a high-level differentiation between the superkingdoms involved based on organization of flagella, with a high-level split between unikonts (one flagellum) and bikonts (two, naturally). This is of course based on evolutionary ancestry- humans are unikonts, but don't have many cells with flagella.

The unikonts contain the amoebae lineages in one grouping, and the animal and fungi together in another. The bikonts contain the plants and algaes in one grouping, and also a handful of other groupings which take care of the rest of the eukaryotes, most of which are unicellular organisms of various sort. It is the "various sort" that's being ironed out with this paper- the authors argue that on the basis of a common genetic heritage, a couple of the leftover groupings can be consolidated.

Ironically, this move would actually reunite groupings that were fairly recently separated by the argument that no firm evidence of relation existed. Back when the "five Kingdoms" (Animalia, Plantae, Fungi, Monera, Protista) were considered the top level of organization, Protista existed as a sort of "junk drawer" for simple organisms which did not clearly fit in the other categories. Now it looks as though some of these organisms really are related.

Re:First used by Darwin?

[Scrameustache]

"The Tree of Life is an expression first used by Charles Darwin"

So Charles Darwin, born in the 1809, predates the Kabbalah? That's cosmology, not biology.

Re:Not really a tree...

[Otter]

Unfortunately it has 'cycles'.

Someone helpfully linked the paper (and was modded down for his trouble); they address that concern extensively.

Re:Proof?

[LWATCDR]

No but Evolution is still mostly theory but it is the best current theory. At least some evolution has been seen in the "wild". Drug resistant bacteria is a good example of evolution in action.

Just hoopla over definitions

[chrisjbuck]

I never heard of "PLoS ONE", it claims to be a peer reviewed journal at least. If this was ground breaking I'd expect it to be published in Nature though. The "PLoS ONE" website isn't loading for me at the moment, but hopefully I'll be able to read the actual article. This seems to be hoopla over definitions though, we can sort organisms into kingdoms and phyla any way we like, this seems identical to the tug-of-war over whether Pluto is a planet or a planetoid. Is it the size of the planet? Is it if an organism has x+2 mutations in a histone protein/gene it gets slotted into one kingdom or another?

Hey the journal finally loaded, here is a link to the actual paper: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000790, although its taking a long time to load for me, and it's not even slashdotted yet. :P

Re:Just hoopla over definitions

[Seiruu]

[quote]I never heard of "PLoS ONE"[/quote]

Then you have also never heard of Open Access, because then you would certainly know what PLoS ONE is. A shame you've never heard of it, because it is a very significant and rapidly growing movement within the scientific community. It puts the emphasis on opening up the access of scientific literature to everyone by switching from reader-pays to author-pays models. And with that said, it is very likely that scholars select PLoS ONE or other OA journals (peer reviewed of course) to show that they believe in the Open Access concept and let everyone with a digital connection have access to it.

Re:Just hoopla over definitions

[FleaPlus]

PLoS ONE is indeed a peer-reviewed journal

Mm... not exactly. Perhaps you're thinking of PLoS Biology? Articles submitted to PLoS ONE undergo some very cursory peer review, but in a sense it's undergoing it's primary peer review -now-, with the article out in the open and readers commenting on it. From a news item in Nature:

http://www.nature.com/nature/journal/v445/n7123/full/445009a.html

Every paper submitted to the journal is reviewed by at least one member of PLoS One's editorial board of over 200 researchers, but only to check for serious flaws in the way the experiment was conducted and analysed. In contrast to almost all other journals, referees ignore the significance of the result. Notable papers will instead be highlighted by the attention they attract after publication.

Visitors to the PLoS One website can, for example, attach comments to specific parts of a paper and rate the paper as a whole. Data from those systems, as well as download and citation statistics, will then allow PLoS One's editors to identify and promote the papers that researchers are talking about. "We're trying to make a journal where papers are not the end point, they are the start of a discussion," says PLoS One managing editor Chris Surridge, based in Cambridge, UK.

Re:Just hoopla over definitions

[Anonymous Coward]

I never heard of "PLoS ONE", it claims to be a peer reviewed journal at least. If this was ground breaking I'd expect it to be published in Nature though.

I'm actually surprised you haven't heard of PLoS journals.

PLoS is an open-access publisher of science journals. Basically, the journals are free to access, and content is published under a creative-commons-type license.

PLoS journals are excellent, and rival the best journals in their content. There is no "general" science journal like Science or Nature, but there are topical journals like PLoS Biology, PLoS Medicine, etc. I'd argue that the content in these topic journals are comparable to Nature and Science publications.

PLoS One is a relatively experimental journal published by PLoS that attempts to push the open access model to its limits, by making the peer-review process completely open, where anyone is allowed to comment.

If anything, the fact that this article was published in a PLoS journal raised rather than lowered my expectations regarding its quality.

Re:two?

[wizardforce]

it depends on what you're going after in regard to categorization. three domainss: eucaryotes are cells with nuclei where as procaryotes are cells without nuclei with the third group being archea because of the large genetic and structural differences in comparison with bacteria [eubacteria]. although you could also classify them into archea+eubacteria [from the now defunct monera (5 kingdom classification)], protista, animalia, plantae, fungi under the 6 kingdom classification

Rather, you haven't been keeping up.

[IdahoEv]

When I was in 9th grade (I guess about 10 years ago!), there were five "kingdoms": bacteria, protista, fungi, plantae, and animalia.

What's happened is that better information has rapidly come to the fore as genetic analysis have been done during the last 15 years. The tree has been revised several times.

The five kingdom model was already known to be wrong 10 years ago, but that information hadn't propagated to gradeschool and highschool textbooks yet. If you'd studied biology in college, your information would be more up to date.

These days there are three superkingdoms: Bacteria, Archaea, and Eukarya. (Bacteria and Archaea were formerly grouped together as "monera" or "bacteria" before it was realized that genetically they are as distinct from each other as they are from Eukarya.) Eukarya is broken into a number of kingdoms, and that number has just changed from 5 to 4. Even the 5 they were last year weren't exactly same ones that you learned in school.

Re:Not really a tree...

[Anonymous Coward]

Tree != Directed, acyclic graph.

In a tree, each node has exactly one parent. Even if links are bidirectional, non-trivial cycles cannot exist. In a DAG, nodes can have multiple parents; making links bidirectional could create cycles. Every (unidirectional) tree is a DAG, but not every DAG is a tree.

The "tree of life" IS a directed acyclic graph - even when considering retroviruses, since "higher" organisims have more than one parent. Retroviruses allow gene transfer between individuals of different species, thus allowing organisms to have more than two parents. A cycle would mean that some individual received genetic material from one of its descendents. If you define an individual as a set of genes that is available to pass on to descendents, then a cycle, by definition, cannot exist.

Re:Three levels of truth (maybe more...)

[yali]

When religion doesn't get it right, people abandon it completely.

No they don't. They just reinterpret the primary tenets of the religion to suit their current desired conclusions.

A good demonstration of this is in the classic study When Prophecy Fails. A group of social psychologists studied a doomsday cult whose leader had predicted the end of the world. When the predicted date passed and the world didn't end, people did not leave the cult. Instead, they found reasons to explain it away (God was so impressed with their devotion that he put off the apocalypse on their behalf). The end result was that their beliefs were strengthened, not weakened, by disconfirmatory evidence.

(As a sidenote, the study was an important early test of Leon Festinger's theory of cognitive dissonance; Festinger had predicted the cult's response based on his theory.)

Re:So, what you are saying is.....

[Tablizer]

For the most part, these viral sequences are in neutral or junk genome stretches, so they don't have any influence on the organism.

I saw an interesting article on speculation that placental mammals may have "learned" how to share fluids between fetus and mother by borrowing immune-suppression genes from a virus that used such tricks to escape the immune system.

Unlike what the poster is saying, these don't make producing the tree more difficult

Only in newer and complex species does a fairly clear tree path appear. However, for simpler organisms and perhaps further back in time, cross-gene transfer seems to be more common such that tree-ness may get really murky. Bacteria, for example, create plasmids whose sole purpose appears to be to share genes with other strains.