The Decline and Fall of the Animal Kingdom

Wired, November 27, 2007

Some of the greatest moments in the history of biology slip from the world’s memory, their anniversaries hardly noticed among the wars, bankruptcies and celebrity detoxifications. But before this month passes, let us stop to remember one of those great moments that came 30 years ago, in November 1977: the death knell of the animal kingdom.

The animal kingdom’s decline came in the form of a three-page paper that appeared in the Proceedings of the National Academy of Sciences. Its lead author, Carl Woese, had spent the previous few years trying to find a way to figure out the relationship of all living things, including microbes. A taxonomist can classify a giraffe, a bat and a human as mammals simply by looking at them. They have hair, for example, and they nurse. But microbes are harder to make sense of. They might simply look like a rod or a sphere.

Within a microbe, however, are the same kinds of molecules you can find inside a giraffe, a bat or a human. They all have proteins, DNA and RNA — which is a single-strand version of DNA that carries out a number of jobs in the cell. Woese recognized that among these molecules he might find a universal rule for measuring the diversity of life. All living things use an assembly of proteins and RNA molecules called ribosomes to build proteins according to the sequence of the genes. Woese selected one piece of RNA from the ribosome and began to painstakingly decipher the versions of it carried by a range of species. Close relatives would have similar RNA molecules, because they shared a recent common ancestor, he reasoned.

Among the species Woese and his colleague George Fox studied were a mouse, yeast and duckweed. They also sequenced RNA from E. coli other bacterial species. When they lined up the species by kinship, they found two strange results. The mouse, the yeast and the duckweed were, relatively speaking, very closely related. They were more closely related than many species of bacteria were to one another. And the bacteria yielded other strange results. Four species of methane-producing bacteria were only distantly related to other bacteria. They were just as closely related to the mouse, the yeast and the duckweed.

To understand just how strange the results were, you have to understand how scientists have classified life for nearly 300 years. Back in 1735 Carl Linnaeus mapped out an elaborate system, assigning every species to a genus, every genus to a family, every family to an order, and so on, all the way up to a kingdom. For Linnaeus, there were only two kingdoms that a species could belong to: animal and plant.

To be an animal was to belong to a major group in the panorama of life. In the centuries that followed, scientists added new kingdoms, such as the protist kingdom comprised of creatures from which animals and plants are believed to have evolved. Mushrooms and other fungi, which Linnaeus had classified as plants, proved to be fundamentally different. They did not catch sunlight like plants, nor did they eat food and then digest it like animals. Instead, they digested first and ate later. So they earned their own kingdom as well. The protists also produced yet another kingdom. Some of them lacked a true nucleus — a sac for storing DNA. They became the kingdom of bacteria. Even if the animal kingdom was one of five, the title still carried some grandeur. After all, kingdoms were at the top of the hierarchy of life.

But Woese and Fox discovered that the animal kingdom might not be so supreme after all. If it was, then why were animals so closely related to plants and fungi compared to the relationships of bacteria to one another? Life was not split into five kingdoms, Woese and Fox argued, but three “urkingdoms” (think German). Woese later changed this label to “domains.”

Animals belonged to a domain known as the eukaryotes, along with plants, fungi and protists. Bacteria such as E. coli made up a second domain, and Woese and Fox set apart the methane-producing microbes in a domain of their own, which they called Archaea.

Earlier this month, a group of scientists gathered at the University of Illinois, where Woese teaches, to celebrate the anniversary of the discovery of three domains of life. The three-domain system was initially met with huge resistance. But when other scientists studied new species, they found support for it. You can see one of the newest versions of the tree of life at the European Molecular Biology Laboratory, or EMBL, website where the branches have been wrapped into a circle. The three colors of the tree mark Woese’s three domains. Scientists have yet to find a species that falls outside them.

While most taxonomists still use Linnaeus’s elegant system of species, genus and the rest, most also recognize Woese’s three domains.

Woese also gave scientists a way to gauge the genetic diversity of life, and as the new tree shows, the animal kingdom doesn’t make up much of it. In the early depictions of the tree of life, it took up a huge portion of its branches at its top — the crown of evolution. On the new tree, the animal kingdom (marked Metazoa) has been reduced to a small tuft of branches. The EMBL tree only shows a small sampling of life’s full diversity, and it’s certain that when scientists finally assemble the full tree of life, the animal kingdom will suffer even more humiliation.

Most of life’s genetic diversity is turning up in bacteria and archaea. A single quart of seawater can hold 60,000 different kinds of bacteria — more than 10 times all the species of mammals on Earth. And the differences among those bacteria are not superficial. A greater genetic distance than the one that divides us from duckweed may separate two bacteria that look nearly identical.

Even within our own domain, the animal kingdom is losing ground. Studies on the DNA of eukaryotes suggest that they belong to six main branches. Scientists sometimes call the branches “supergroups,” although it’s doubtful they can sing like Led Zeppelin. Our once-imperial kingdom belongs to the nearly unpronounceable Opisthokonts, into which the entire kingdom of fungi is now crammed, along with a host of single-celled protists. Scientists are discovering a staggering number of new species of eukaryotes, but most of the genetic diversity is turning up beyond the animal kingdom, among single-celled residents of the oceans.

Scientists still refer to the animal kingdom, but more out of convention than conviction. That’s not to say that animals aren’t interesting or ecologically important. But as Woese demonstrated, to understand the full reach of life, scientists will have to look far beyond our own little fiefdom.