Could Recent Genetic Findings Completely Alter The Way We Classify Life?

1837 Darwin wrote "I think" above the first evolutionary tree.

That’s a bit of a stretch, but geneticists believe they may have found evidence that could alter the foundations of the tree of love…

The first tree of life was sketched by Charles Darwin in 1837. Its purpose was to represent the how all species are related, but still connected. Darwin regarded evolution as a branching process, where populations alter over time and may speciate into separate branches or terminate by extinction. Darwin thought the most appropriate way to represent this was a large branching tree. He was right; and we still do use a tree of life,   phylogenetics is the study of how different species are related, using DNA sequencing, the subsequent relationships are represented in a phylogenetic tree.

The point where the three domains join on the tree signify the first major evolutionary divergence of very early life forms on earth, the three domains are; Archaea, Bacteria and our domain Eukarya.

Woese's three-domain system, 1990

A team of geneticists lead by Jonathan Eisen at the University of California, Davis Genome Centre along with Craig Venter of the J. Craig Venter Institute, Rockville have recently made a brave claim, they believe they may have identified genes so exceptionally unique; they are only minimally related to early cellular life, which may potentially define a new, fourth biological domain of life. The last time the domains were shifted around was only in 1990, by Carl Woses. Woses reclassified the Kingdoms Eubacteria and Archaebacteria to Bacteria and Archaea respectively, he also grouped Protista, Plantae, Fungi and Animalia into the domain Eukarya.

The majority of species on earth are very small and do not contain the quantity of DNA required for genetic analysis. So to make an accurate phylogenetic tree, the species need to be  cultured, in a lab where the colonies contain enough DNA to accurately analyse a species genome . But there’s another road block, the vast majority of these microscopic species simply will not grow in a lab.

Eisen and Venter, unable to culture the species turned to a relatively new technology, metagenomics, which provided a way to gathering genetic data by sampling directly from the environment. The technology was impressive, Eisen said, it can “sequence the crap out of any DNA samples”.

Venter's Yacht

Venter voyaged across the globe obtaining samples, using this metagenomics technology. The Global Ocean Sampling Expedition provided some very interesting results, genes called small subunits rRNA; recA, and rpoB were discovered and are almost completely dissimilar to all other known genes.

Metagenomics is a messy process; the organisms are completely destroyed while the genes were being retrived from the samples. So, we have the genes but we don’t know which organism they came from.

The team narrowed down the potential mechanisms that may have lead to the existence of these evolutionarily novel gene sequences; to be either:

1) the possible genetic sequences from novel viruses

2) the sequences may indeed be from a fourth major branch on the tree of life.

Eisen said “we do not have a conclusive explanation for the origin of these sequences. But as far as we can tell, they truly could be from a fourth major branch of cellular organisms”.

However, 4th place at the Domain table may not be Eisens for the taking.

(L to R) Archaea, Bacteria, Eukaryotes, and Giant viruses

A team of scientists in France have been studying viruses called Nucleocytoplasmic Large DNA Viruses (NCLDV). The virus is very unusual. It has >1000 genes, a huge genome for a virus, 100 times the genes of your general, every day flu virus, which has maybe 10 genes. NCLDV are indeed viruses though, they hijack host cells as all viruses do. Didier Raoult et al. compared one set of genes in giant viruses to their counterparts in other families. The genes are very different, so much so that some scientists are arguing, that the giant viruses, Mimivirus, should represent the fourth domain of life.

Perhaps the fourth domain name will go to another taxa entirely, I’m going to stick with Occam’s Razor on this one, but you never know maybe Thomas Cavalier-Smiths recent 2004 organismal classification will catch on after all, he rejects the three-domain system entirely, I wonder where that would leave us?

 

 

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The project lasted six years and the paper was published in the free online science journal research PLoS One (Reference: DOI: 10.1371/journal.pone.0018011) (Direct Link: http://tiny.cc/gx79d)

Also lead author Jonathan Eisen instead of doing a press release, blogged it: http://phylogenomics.blogspot.com/2011/03/story-behind-story-of-my-new-plosone.html