Tree of life

[HELISA]

Can somebody explain me in a simple words what are the main points of the concept of the "tree of life" ?

[HELISA]

O.K. I have asked my previous question not exactly; therefore I have to improve it.
I’m asking about the idea of the Tree if Life, which at the beginning proposed two-domain view of life (prokaryotes and eukaryotes). After that C. Woese proposed the concept of three-domain view of life: eukaryotes, bacteria and archaea. His ribosomal RNA sequence analysis suggested that eukaryotes diverged from the archaea and additionally it explained how cells first came to possess mitochondria and chloroplasts (endosymbiont concept). Now, I have in my hand the article of W. Ford Doolittle, which proposes different view on “The Tree of Life” due to occurrence of horizontal gene transfer. I am now wondering whether the tree of life is invalided by this interpretation or if there is still value in this concept. What are your opinion guys?

[AstusAleator]

Well, there are different schools of though (as I'm sure you know). Ultimately, I believe the universal classification system for biology will be based on evolutionary lineage. This will be made easier as we become more efficient with genetic sequencing.
Horizontal gene transfer is definitely an issue of concern for anyone that uses the standard method of cladistics. The ultimate challenge comes in attempting to organize these species in a graphical sense that most accurately represents their true relationships. Since we do not know (nor will we ever) every single evolutionary relationship throughout natural history and the present, we will probably never have a full, completely accurate model.
I like to call it the vine of life. In some parts it branches out, in others it grows back into itself, but it just keeps creeping along.

[HELISA]

So, this idea doesn’t invalidate the theory of evolution, which seems to be the dominant mode of evolution for modern organisms, but indicates that another mechanism of heredity was once more common. Right?

[Khaiy]

No, evolution is still the best descriptor of the process, because the tree will still branch out more and more as time goes on from a common ancestor.

The issue with current taxonomic diagrams is that they were originally based only on physical characteristics, which does not necessarily represent their true relationships with each other.

[HELISA]

Horizontal gene transfer (HGF) is not a dominant mode of evolution, therefore it doesn’t nullify the theory of evolution, but still have important evolution consequences i.e. it shows that life spring from a community of cells, not from a single cell. What other consequences for evolution, have HGF?

[Khaiy]

Sorry! I misunderstood what you meant by HGF. But HGF just moves genes around in a population, without having to wait for successive generations. Evolution is still the change in frequency of genes in a population, so HGF is an evolutionary process, and therefore can't nullify the theory. It isn't about life springing from something.

HGF isn't really a measure of heredity, but it does present some problems with classifying prokaryotes (which frequently utilize the process even today).

[AstusAleator]

Khaiy I'm not sure if that's the way he's using horizontal gene flow. I'm pretty sure he means it as reconvergence of evolutionary lines. An example would be two prokaryotes specializing in functions, then one engulfing the other and the two becoming one through endosymbiosis. You have two seperate evolutionary lines that come back together to form a new species.
He also uses the example of colonies of cells evolving into organisms.
Hybridization could also be seen as a lesser form of horizontal gene flow.

HGF makes cladistics very difficult, as the graphical method for cladistics cannot account for reconvergence of evolutionary lines. But again, that's just a graphic representation of what we're observing.
Ultimately, what we theorize about evolutionary lineages comes from observations of homologies, based on the principle that the most related organisms will share the most similar characteristics.
This is precisely why HGF can be such a pain, as very disimilar organisms may have combined, causing their progeny to not resemble either of the evolutionary lines they came from.

The discovery of HGF changed how scientists thought of evolution. It was no longer direct heredity - genes passed from parent to child and so on - but a more ambiguous flow of genes. Fortunately, HGF is only really seen in micro-organisms, so the principles of evolution remained the same for macro-organisms.

[Khaiy]

I see. Well I apologize for my (second) misunderstanding. But I still don't think that HGF has any particular effect on evolution, aside from providing more combinations of things to be affected by natural selection.

[HELISA]

OK, so we have a consensus tree of life which is based on the assumption that life diverged first into bacteria and archaea. Eukaryotes evolved from an archaea precursor, and eukaryotes took up genes from bacteria twice, obtaining mitochondria and chloroplast. Therefore, we can identify in eukaryotic genome some genes from bacteria and some from archaea. But! there are some nuclear genes in eukaryotes which turn out to be unlike those of any known archaea and bacteria; these genes seems to come from nowhere. What are your opinions about the nowhere? Where they come from?

[AstusAleator]

Eukaryotes probably didn't JUST take in mitochondria and chloroplasts. There were probably other things as well. Again it's hard to determine cladistic relationships when HGF occurs.

[kabuto]

is "tree of life"="shrub of life"?