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# 18.29 Tree Of Life

The diversity of life on Earth is incredibly widespread. From microscopic organisms thriving in conditions similar to boiling battery acid to creatures as delicate as butterflies, there seems to be no limits to nature's imagination. But with this diversity comes the challenging task of categorizing a number of organisms on the planet that is virtually too large to count.

Prior to the 1970s, people categorized Earth's inhabitants according to a natural taxonomy that relied only on fossil records and morphology — the form and structure of an organism. The first system of classification split all the Earth's creatures into one of two categories, plants or animals. Following Charles Darwin's publication of The Origin of Species in 1859, which articulated the now well-accepted model of natural selection, scholars sought to establish a more detailed and accurate depiction of how organisms are related on Earth. In 1866, Ernst Haeckel formally challenged the pre-existing "tree of life", which at that time consisted of only two branches: plant and animal. It was during this time that protists — single-celled microorganisms — were first identified by scientists. These organisms did not fit well into either of the two categories of life. Based on this observation, Haeckel proclaimed that the tree of life should contain three branches, not two.

Although Haeckel, and eventually other scientists, continued to add branches to and therefore diversify the tree of life, the primary distinctions made between the branches was based on physical traits and characteristics of organisms, not on actual genetic relationships. By the 1970s, the tree of life had grown to include 5 main branches, called kingdoms:  Animalia, Plantae, Fungi, Protista, and Monera. Although this five kingdom designation gained rapid popularity and is still widely taught today, microbiologists have been articulating the need for a different classification based on molecular and cytological understanding of cells. For over 100 years, microbiologists have argued that the primary division of life should lie between bacteria and eukaryotes followed by the division between plants and animals. As a result, a two kingdom classification system is also commonly accepted:  Prokaryotes and Eukaryotes.

Two recent discoveries have significantly changed how we define the modern tree of life. In the 1960s, Linus Pauling and Emile Zuckerkandl introduced a new method of examining organisms, molecular phylogeny, that examined the molecular building blocks of life (such as genes and proteins) to determine actual genetic relationships amongst organisms. As a result of this type of research, in 1977 Carl Woese and George Fox announced their discovery of archaebacteria, single-celled organisms that resemble bacterial microorganisms no more than they resemble eukaryotes. This revelation upset the two kingdom classification system of Prokaryotes versus Eukaryotes. On the cellular level, archaeabacteria (now commonly known as archaea) resemble other prokaryotes as they lack membrane-bound organelles and possess circular rather than linear DNA. However, on a genetic level, archaea are no more similar to other prokaryotes as they are to eukaryotes. In 1990, Carl Woese and colleagues formally proposed a restructured tree of life. In this modern tree, there are three domains that supercede all pre-existing kingdoms:  Archaea, Bacteria, and Eukarya.

Just as the tree of life has changed over the past several hundred years, we can surely expect it to change as our understanding of true genetic relationships between organisms is expanded. Scientists are currently sequencing entire genomes of organisms and determining relationships never before anticipated. What began as an endeavor to illustrate the relationships of living creatures on Earth as depicted by Darwin's theory of natural selection and evolution has now been enlightened, and confused, by modern science  Although molecular sequencing techniques are allowing us to fill in the branches on the tree of life, we are still far from being able to trace those branches back to the ancestral root of all life on Earth.

What is complicating our search for a last common ancestor to life on Earth? According to our basic knowledge of inheritance, a particular individual possesses genetic material which it then passes on to its offspring. Sometimes during this process, an individual will develop mutations in its genetic material which can, in turn, be passed on. Regardless, the main idea is that genetic material is passed from parent to offspring in a top-down, linear manner. If this were the only mechanism for gene transfer, then it would be logical to assume that the tree of life would have a clean set of traceable limbs and branches, allowing us to easily determine a common ancestor for life on Earth. However, this is not the only mechanism. A different process, lateral or horizontal gene transfer, has profoundly influenced the development and evolution of life. This process entails the exchange of genetic material between species, not from parent to offspring. If one were to draw a picture of how this would look in an actual tree, one could imagine two branches from distant limbs on a tree to suddenly have a branch growing between them, linking them together. Horizontal gene transfer has significantly increased the complexity of creating a universal tree of life. But in our efforts to establish this tree of life, we will learn more and more about the origins and evolution of life on our planet and, hopefully, extend that knowledge to other planets or moons.