We traditionally think about the tree of life in terms of Kingdoms: plants, animals, fungi, bacteria, etc. Genetics has really revolutionized the way we think about the tree of life and, because our classifications should reflect ancestry (that is, who is more closely related to whom), it has actually called into question a lot of our traditional classifications. Most biologists split up life into three domains: Archaea, Bacteria, and Eucarya (the last of which includes animals, plants, fungi, etc.).

The three domains of life. From Carl Zimmer's blog The Loom.

Science writer Carl Zimmer has an interesting post on his blog about how the newest genetic data may even call this classification into question by adding a fourth domain. From his post:

There’s a lot of debate about whether eukaryotes actually split off from within the archaea, or just branched off from a common ancestor. Nevertheless, the two forms of life are quite distinct. For one thing, the common ancestor of living eukaryotes acquired oxygen-consuming bacteria that became a permanent part of their cells, called mitochondria. They’re keeping you alive right now.

A lot of scientists wonder how all the new species that scientists are discovering are going to change the shape of this tree. Will its three-part structure endure, with each part simply growing denser with new branches? Or have we been missing entire swaths of the tree of life?

It’s possible–but just possible at this point–that we have missed a big part of it.

Genetics are indicating that the fourth domain is represented by Nucleocytoplasmic Large DNA Viruses (NCLDV), or, as Zimmer comically refers to them, “Giant Viruses” (because they’re big and they have many more genes, >1,000, than “regular” viruses, which only have around 10 or so). It turns out that the genes from these “Giant Viruses” are so different that some researchers suggest they should be grouped in their own domain.

New research is looking at tons of genes from these sorts of organisms. Here is a video based on the work of Jonathan A. Eisen and his colleagues:

References

Wu, D., et al. (2011). Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees. PLoS Online 6.

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