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The Newsletter of the Colorado Herpetological Society

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Paleontology and Evolution

Knots on the Tree of Life

By Donald L. Blanchard
CHS Editor

First of all, there are now recognized more than two kingdoms of living organisms. Bacteria were elevated to their own kingdom many years ago. Somewhat later, unicellular microorganisms and sponges were split off into a new kingdom -- the Protista. Now, recent DNA studies are revealing that not all bacteria are bacteria. Several forms previously thought to be bacteria, notably those from somewhat exotic environments like sulfurous thermal vents or near-boiling hot springs, are turning out to be as different from all other bacteria as bacteria are from plants and animals. In fact, these not-bacteria, now known as Archaea, for ancient life, turn out to share more genetic traits with plants, animals and protists than with bacteria.

That still leaves us with a symmetrical branching tree, bacteria and archaea splitting off first from some primitive ancestor, then protists branching off from the archaea, and plants and animals branching off later. But all is not so simple.

Bacteria and Archaea share a similar, rather simple cellular structure, surrounded by both a membrane and a cell wall, with the DNA loose inside. This structure is known as prokaryotic. Plants, animals, and protists share a more complex, and typically considerably larger cell structure, known as eukaryotic, where the DNA is contained securely within a nucleus, enclosed within its own membrane, and surrounded by a protein-rich salt solution known as cytoplasm, also contained within a much larger membrane. The DNA within the nucleus of eukaryotic cells is clearly more closely related to archaean DNA than it is to bacterial DNA.

However, within the cytoplasm of eukaryotic cells, there are organelles which contain their own DNA: notably mitochondria -- which provide energy for the cell, and, in the case of green algae and other plants, chloroplasts, which allow the cells to produce food from sunlight. And the DNA from mitochondria and chloroplasts is clearly more related to bacterial DNA². Thus, eukaryotic cells represent a de-facto merger between two separate lineages, with ancestry both among the bacteria and the archaea.

But wait; there is more. Archaea and bacteria do not reproduce sexually, as many multi-celled eukaryotic organisms do, but they can exchange genes between themselves, thereby accomplishing an equivalent form of genetic interchange. They can even do it between unrelated species³. And recent DNA sequencing efforts have found bacterial DNA in archaea and in eukaryotes (in addition to mitochondrial and chloroplast DNA). Apparently, some branches on the tree of life converge and merge into a single stem. In trying to plot the tree of life for individual genes, we find that different genes in the same organism follow totally different trees. It is indeed a knotty problem.

Notes:

1. Bacteria were first discovered in 1683 by the Dutch microscopist Antony van Leeuwenhoek, and were undoubtedly known to Darwin.
2. It is generally thought that chloroplasts, which resemble blue-green algae (which are bacteria), and mitochondria were originally free-living organisms which were assimilated by and eventually became symbiotic with eukaryotic cells.
3. This capacity is used by scientists doing research in gene therapy. It is also how immunity to antibiotics can be transmitted from one pathogenic bacterial strain to another.

References:
W. Ford Doolittle. "Uprooting the Tree of Life." Scientific American, February 2000, pp.90-95.