Monthly Archives: April 2016

The (Phylogenetic) Tree of Life


In the new issue of Nature Microbiology, a team of scientists has published a graphical representation of the evolution of organisms, a new tree of life.

The new tree shows that “bacteria make up most of life’s branches. And [the team] found that much of that diversity has been waiting in plain sight to be discovered, dwelling in river mud and meadow soils….’It is a momentous discovery — an entire continent of life forms.’”(Zimmer, 2016)

The quest to represent all of life on Earth has a long history. Aristotle’s works are filled with facts about natural history and Pliny the Elder composed a huge encyclopedia of what the Romans believed they knew about nature.

In 1859, Charles Darwin suggested that it is possible to show how the “affinities of all the beings of the same class” could be represented by a “great tree.” (Darwin, p. 203)

How Darwin’s “great tree” was made possible is in part the story of the work of a biophysicist named Carl Woese whose work created the first tree of life, one that was actually based on evolutionary principles.

The modern story of the quest for  begins with the Swedish naturalist Carl von Linné (Linnaeus) who published his Systema Naturae in 1735. The Systema was Linné’s answer to the question of how to organize the huge mass of living organisms so that it is possible to see how all the different individuals and groups fit together.

But which individuals get included in a particular class?

Both birds and bats eat insects and use their ability to fly to snatch insect food out of the air.

Do bats and birds make up a “class of beings?”

Linné’s solution was  to create a system of classification that grouped organisms by their physical traits. So plants whose flowers had similar numbers of stamens in the same grouping, or animals that got their food by predation were grouped together.

After Darwin, biologists used Linné’s system of classification (that is, grouping organisms according to their visible traits) to describe the branches on the tree of life, and by the first half of the 20th century there were five main branches: Animalia, Plantae, Fungi, Protista, and Monera.

In the 1960s biophysicist Carl Woese found this to be a highly unsatisfactory approach.

For Woese “the morphology-metabolism approach was like trying to create a genealogical history using only photographs and drawings. Are people with dimples on their right cheeks and long ring fingers all members of the same family? Maybe, but probably not.” (Arnold, 2014)

Woese observed that the “biologist has customarily structured his world in terms of…dichotomies. Classically, what was not plant was animal.” But the discovery that bacteria did not fit into the dichotomy (they resembled both plants and animals ) forced biologists to reconsider the question.  (Woese & Fox, 1977, p. 5088)

Early in his career Woese had done research on the newly discovered genetic code at the Pasteur Institute in Paris; and genes, of course, are intimately connected to evolution.  This led Woese to see that a “tree of life” could be constructed using genetic data in order to actually show the evolutionary relationships among organisms.

The creation of a tree of life defined by evolutionary connections rather than by physical similarities was what Woese had in mind when he arrived at the University of Illinois as a young professor in 1964.

“To create his evolutionary tree of life…Woese would need to choose a gene that was present in every known organism, one that was copied from generation to generation…and [which] mutated slowly…. ‘This would let him make a direct measure of evolutionary history….By tracking these gene sequences…he could calculate evolutionary distance between two organisms and make a map of how life on Earth many have evolved.”

The gene he chose is one found n the ribosome, a structure present in all living cells and which is the site of biological protein synthesis. He selected the gene labeled 16S rRNA.

In the 1960s gene sequencing was done by hand, separating genetic material using electrophoresis and then using a magnifying glass and a light box to examine the resulting bands of RNA. Woese and his colleague George Fox entered the sequences onto IBM 80 column punch cards and used them in a program that matched sequences and which allowed them to identify evolutionary connections among organisms.

It took Woese and his colleague George Fox a full ten years of work sequencing 16S rRNA in a variety of different organisms.  (Arnold, 2014)

The hard work paid off when Woese was working on a group of prokaryotes called a methanogenes. They expected to find that the group was related to the bacteria. “When they finally analyzed its fingerprint, looking nothing like any of the other bacteria Woese and Fox had previously analyzed…To fellow microbiologist Ralph Wolfe, Woese announced, ‘I don’t even think these are bacteria.’” (Arnold, 2014)

This discovery overturned the previous view that all life on Earth belonged to either the eukaryotes (animals, plants, fungi, and some single-celled animals) or the prokaryotes, organisms whose cells lack a nucleus.

In 1977,  Woese and Fox published their findings in an article entitled “Phylogenetic structure of the prokaryotic domain: The primary kingdoms.” The article was groundbreaking enough to merit a New York Times article on June 19, 1978, “Scientists Identify More Members of The ‘Third Kingdom of Life….”

In their publication, Woese and Fox made three principle points: (1) That the tree of life had three main branches, not two or five; bacteria, eucaryotes (eucarya), and archaea; (2)“An organism’s genome seems to be the ultimate record of its evolutionary history”;  and (3) “the comparative analysis of molecular sequences has become a powerful approach to determining evolutionary relationships.” (Woese & Fox, 1977)

The new tree of life is a descendant of the one constructed by Woese and Fox nearly four decades ago. By taking advantage of new understandings (molecular biology) and techniques (gene sequencing) Woese demonstrated that the prokaryote-eukaryote model (what I learned in biology a half century ago) was erroneous. By looking at organisms at the molecular level, the real evolutionary history was uncovered.


Arnold, C. (2014). The Man Who Rewrote the Tree of Life. Retrieved from http:

Darwin, C. (2016). The Origin of Species. iBooks.

Hug, L. A., Baker, B. J., Anantharaman, K., Brown, C. T., Probst, A. J., Castelle, C. J., . . . Banfield, J. F. (2016). A new view of the tree of life. Nature Microbiography, 16048. Retrieved from

Woese, C. R., & Fox, G. E. (1977). Phylogenetic structure of the prokaryotic domain: The Primary Kingdoms. Proceedings of the National Academy of Science, 74(11), 5088-5090.

Woese, C. R., Kandler, O., & Wheelis, M. L. (1990). Towards a natural system of organisms: Proposals for the domains Archae, Bacteria, and Eucarya. Proceedings of the National Academy of Science, 87, 4576-4579. Retrieved from

Zimmer, C. (2016). Scientists Unveil New ‘Tree of Life’. New York Times. Retrieved from


evolution, Carl Woese, phylogeny, tree of life, Archaea, Eucary, Bacteria, prokaryotes, eukaryotes