Actinobacteria as the Base of the Evolutionary Tree

[n2doc]

ScienceDaily (July 26, 2012) — Ever since Darwin first published The Origin of the Species, scientists have been striving to identify a last universal common ancestor of all living species. Paleontological, biochemical, and genomic studies have produced conflicting versions of the evolutionary tree. Now a team of researchers, led by a professor at the State University of New York at Buffalo and including area high school students, has developed a novel method to search the vast archives of known gene sequences to identify and compare similar proteins across the many kingdoms of life. Using the comparisons to quantify the evolutionary closeness of different species, the researchers have identified Actinobacteria, a group of single membrane bacteria that include common soil and water life forms, as the base of the evolutionary tree.


They will present their findings at the annual meeting of the American Crystallographic Association (ACA), held July 28 -- Aug. 1 in Boston, Mass.

"Today the gene banks are enormous. They contain more than 600,000 genes from the genomes of more than 6,000 species," says William Duax, a physical chemist and lead researcher on the team. However, many of the gene sequences, and the proteins they encode, are not systematically identified. Proteins that are structurally similar and perform the same function could be labeled with different numbers that obscure the fact that they belong to the same protein family. "Our first challenge is to make sure that we are comparing apples to apples and oranges to oranges," says Duax.

Duax and his team have developed efficient ways to search through the gene banks looking for all copies of the same family of protein. They concentrated their efforts on proteins that are found on the surface of cell components called ribosomes. The ribosomal proteins are among the most accurately identified proteins, and because they are not transferred between individuals independent of reproduction, are good candidates for tracing the evolution of all species.


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http://www.sciencedaily.com/releases/2012/07/120726112729.htm

[Surya Gayatri]

1. Always appreciate your science posts, n2doc. Thanks!

Who knew? Our oldest genetic relatives are not Adam and Eve! Don't let the creationists hear that...

[Tikki]

2. This is so interesting.....

Thanks
Tikki

[arendt]

3. The evolutionary "tree" is really a "bush"

The approach in this paper is obsolete. I wrote an entire diary about a theory that has much more evidence than this at DKos:

Horizontal Gene Transfer(HGT) is another hot idea from 25 years ago that is now the conventional wisdom. We now know that bacteria share genetic material across species (which is why GMO crops with pesticide resistance genes are such a bad idea).

So, during the Origins of Life, in the absence of cell wall barriers, HGT was dominant. The new scientific thinking is that the "tree of evolution" does not have a single root; but, rather, it goes back to a "bush" formed by a mass of cells heavily interconnected by HGT. The conclusion of "bush, not single root" is clearly visible in the genetic comparisons that Woese used to delineate archaea from bacteria. Woese is still at work. In 2006, he followed the logic of his earlier work to propose collective evolution

We argue that the universality of the code is a generic consequence of early communal evolution mediated by HGT, and that HGT enhances optimality. Our arguments are backed up by computer simulation studies, which are necessary to probe the complex interactions between the variety of collective mechanisms that we shall present. We show that there are virtuous cycles of cooperativity: (i) the more similar the genetic codes, the greater the intensity of HGT, and the stronger the tendency for codes to become more similar; and (ii) HGT helps the codes to optimize, and optimization enforces universality and compatibility between translational machineries...

Our framework fits naturally the recently proposed picture that early evolution was dominated by HGT... The broader implication of this scenario is that innovation-sharing led to the emergence of modern cell designs from a communal state, not a unique, shared ancestor. Such a communal state existed before the point of emergence of vertical evolution, which has been termed the Darwinian transition. The defining property of the communal state was that it was capable of tolerating and using ambiguity, as reflected in the pervasive role of HGT. A Darwinian transition corresponds to a state of affairs when sufficient complexity has arisen that the state is incapable of tolerating ambiguity, and so there is a distinct change in the nature of the evolutionary dynamics (to vertical descent).