10.15–10.18: An overview of the diversity of life on earth: organisms are divided into three domains.

The flower hat jellyfish (Olindias formosa), a rare species that lives in the oceans off Brazil, Argentina, and southern Japan.

Biological diversity can be humbling. At the very least, it makes it harder to believe that humans are particularly special. We are not at the center of earth’s “family tree.” Nor are we at its peak. We are simply one branch.

When Linnaeus first put together his system of classification, he saw a clear and obvious split: all living organisms were either plant or animal. Plants could not move and could make their own food. Animals could move but could not make their own food. So in Linnaeus’s original classification, all organisms were put in either the animal kingdom or the plant kingdom (his third, “mineral” kingdom, now abandoned, included only non-living matter).

With the refinement of microscopes and subsequent discovery of the rich world of microbes—microscopic organisms—the two-kingdom system was inadequate. Where did the microbes belong? Some could move, but many of those could also make their own food, seeming to put them somewhere between plants and animals. And the problems didn’t stop with the microbes: mushrooms and molds, among other organisms originally categorized as plants, didn’t move but they didn’t make their own food either—they digested the decaying plant and animal material around them.

The two-kingdom system gave way in the 1960s to a five-kingdom system. At its core, the new system was a division based on the distinction between prokaryotic cells (those without nuclei) and eukaryotic cells (those with nuclei). The prokaryotes were put in one kingdom, where the only residents were the bacteria: single-celled organisms with no nucleus, no organelles, and genetic material in the form of a circular strand of DNA. The eukaryotes—having a nucleus, compartmentalized organelles, and individual, linear pieces of DNA—were divided into four separate kingdoms: plants, animals, fungi, and protists.

The classification of organisms took a huge leap forward in the 1970s and 1980s, and the five-kingdom system had to be discarded. Until that point, organisms had been classified primarily based on their appearance. But because the ultimate goal of classification had changed to reconstructing phylogenetic trees that reflected the evolutionary history of earth’s diversity, Carl Woese, an American biologist, and his colleagues began classifying organisms by their nucleotide sequences.

Woese assumed that the more similar the genetic sequences were between two species, the more closely related they were, and he built phylogenetic trees accordingly. The only way Woese could compare the evolutionary relatedness of all the organisms present on earth today was by examining one molecule that was found in all living organisms and looking at the degree to which it differed from species to species. He discovered a perfect candidate for this role: a molecule called ribosomal RNA, which helps translate genes into proteins (see Chapter 5). Ribosomal RNA has the same function in all organisms on earth, almost certainly because it comes from a common ancestor. Over time, however, its genetic sequence (i.e., the DNA that codes for it) has changed a bit. Tracking these changes makes it possible to reconstruct the process of diversification and change that has taken place.

The trees that Woese’s genetic sequence data generated had some big surprises. First and foremost, the sequences revealed that the biggest division in the diversity of life on earth was not between plants and animals. It wasn’t even between prokaryotes and eukaryotes. The new trees revealed instead that the diversity among microbes was much, much greater than ever imagined—particularly because of the discovery of a completely new group of prokaryotes called archaea (sing. archaeon), which thrive in some of the most extreme environments on earth and differ greatly from bacteria. The tree of life was revised to show three primary branches, called domains: the bacteria, the archaea, and the eukarya (FIGURE 10-27). The domain names are often capitalized: Bacteria, Archaea, and Eukarya.

Figure 10.27: All living organisms are classified into one of three groups.

Woese put the domains above the kingdom level in the Linnaean system. In Woese’s new system, which is the most widely accepted classification scheme today, the bacteria and archaea domains each have one kingdom and the eukarya domain has four. Because both bacteria and archaea are microscopic, it can be hard to believe that the two domains are as different from each other as either domain is from the eukarya. However, each of the three domains is monophyletic, meaning that each contains species that share a common ancestor and includes all descendants of that ancestor. Close inspection even reveals that the archaea are more closely related to the eukarya than they are to the bacteria.

The three-domain, six-kingdom approach is not perfect and is still subject to revision. As we saw earlier, for example, within the eukarya, the single-celled protists have turned out to be much more diverse than initially thought and, problematically, are not a monophyletic group. Increasingly, it is recognized that they should be split into multiple kingdoms. Also problematic is that bacteria sometimes engage in horizontal gene transfer, which means that, rather than passing genes simply from “parent” to “offspring,” they transfer genetic material directly into another species. This process complicates the attempt to determine phylogenies based on sequence data, because it creates situations in which two organisms might have a similar genetic sequence not because they share a common ancestor, but as a result of a direct transfer of the sequence from one species to another.

Additionally, a fourth group of incredibly diverse and important biological entities, the viruses, is not even included in the tree of life, because they are not considered to be living organisms. Viruses can replicate, but they can have metabolic activity only by taking over the metabolic processes of another organism. Their lack of metabolic activity puts viruses just outside the definition of life that we use in this book, but some scientists do view viruses as living.

The most commonly accepted tree of life suggests that, after the origin of life, the following sequence of events occurred (FIGURE 10-28):

• 1. The bacteria arose from the first self-replicating, metabolizing cells.
• 2. There was a split between the bacteria and a line that gave rise to the archaea and eukarya.
• 3. The fusion of a bacterium and an archaeon-like prokaryote gave rise to the eukarya, which then split from the archaea line.

Figure 10.28: From self-replicating, metabolizing cells to complex organisms. The biggest branches on the tree of life separate the three domains.

The next three sections introduce each of the three domains, surveying the broad diversity that has evolved within each domain and the common features that link all the members of each. Chapters 11, 12, and 13 cover the domains in greater detail.