Biologists have formally described and named about two million species, and new ones are added every year. Estimates of how many exist in total range from several million to far more, because most insects, fungi and microbes have never been studied. Making sense of this variety requires a system.

Linnaeus and scientific names

The Swedish botanist Carl Linnaeus (1707 to 1778) brought order to naming. In his Systema Naturae, first published in 1735 and expanded over many editions, he grouped organisms into nested ranks. He also made standard the system of two-part Latin names, giving each species a genus and a species name: Homo sapiens for humans, Quercus alba for the white oak. A common name such as “robin” means different birds in Britain and America; a scientific name means one species everywhere.

The ranks used today run, from broadest to narrowest: domain, kingdom, phylum, class, order, family, genus, species.

The tree of life

Linnaeus grouped organisms by visible similarities, and he did not think species evolved. After Darwin, biologists came to see classification differently: groups should reflect shared ancestry. Modern classification builds family trees, called phylogenies, from features inherited from common ancestors and, increasingly, from DNA comparisons. Some surprises followed. Fungi turn out to be more closely related to animals than to plants. Birds are living dinosaurs, descended from the same branch as Tyrannosaurus.

Three domains

For most of history, people divided life into plants and animals. Microscopes revealed bacteria and other microbes, and by the mid-twentieth century many biologists used five kingdoms. Then in 1977 the American microbiologist Carl Woese, comparing ribosomal RNA, a molecule found in every cell, discovered that some single-celled organisms long lumped in with bacteria were as different from bacteria as bacteria are from us. In 1990 he proposed dividing life into three domains:

• Bacteria: prokaryotes found almost everywhere, from soil to your gut.
• Archaea: prokaryotes first found in extreme places such as boiling hot springs and very salty lakes, now known to live in ordinary soils, oceans and human bodies too.
• Eukarya: organisms whose cells have a nucleus, including animals, plants, fungi and protists. “Protist” is a catch-all term for eukaryotes that are not animals, plants or fungi, such as amoebas and many algae, rather than a natural family group.

A microbial planet

Most of life's diversity is microscopic. Microbes ran the planet for billions of years before animals appeared. Photosynthesizing bacteria called cyanobacteria began filling the atmosphere with oxygen around 2.4 billion years ago, changing the planet for every creature since.

Microbes also live on and inside us, a community called the microbiome. An old and often repeated claim held that bacterial cells in the body outnumber human cells ten to one. A careful 2016 estimate found the ratio is closer to one to one. Most of these bacteria are harmless or helpful, aiding digestion and crowding out harmful microbes.

Viruses

Viruses appear in none of the three domains. A virus is genetic material, DNA or RNA, wrapped in a protein coat. It has no cells and no metabolism of its own, and it cannot reproduce without taking over a host cell. That is why biologists debate whether viruses are alive. It is also why antibiotics, which attack features of bacterial cells, do nothing against viral illnesses such as colds and flu.

What is a species?

The most widely used definition, the biological species concept proposed by the biologist Ernst Mayr in 1942, defines a species as a group of populations that can interbreed in nature and produce fertile offspring. Horses and donkeys can mate, but their offspring, mules, are almost always sterile, so horses and donkeys remain separate species. The definition has limits. It does not fit bacteria, which reproduce by dividing, or extinct species known only from fossils, so biologists use other definitions in those cases.

Worked example: is a whale a fish?

A whale lives in the sea, has a streamlined body and swims with fins. Many early naturalists grouped whales with fish. Modern classification asks a different question: which features did whales inherit from which ancestors?

• Whales breathe air through lungs, while fish breathe with gills.
• Female whales feed their young on milk, and whales have traces of hair, features found in mammals.
• A whale's flipper holds the same bones as a human arm.
• Fossils and DNA show that whales descended from land mammals related to today's hippos.

A whale is a mammal. Its fish-like shape is an example of convergence, in which unrelated animals evolve similar forms because they face similar challenges, here moving fast through water. Similar reasoning places mushrooms, once called plants, on the branch nearer to animals. Classification by ancestry is less obvious than classification by appearance, but it tells us more about how living things are actually related.