Classification and Taxonomy

Organisms are sorted into a hierarchy of nested groups called taxonomic ranks. Any group at any rank is called a taxon (plural taxa). From the broadest to the most specific, the eight main ranks are domain, kingdom, phylum, class, order, family, genus, species. Each rank sits inside the one above it. Moving down the hierarchy, each group holds fewer kinds of organisms, and those organisms share more features. A common memory aid is "Do Kind People Come Over For Good Soup?" To compare how closely two organisms are related, find the lowest (most specific) rank they share. A grey wolf and a human share ranks only down to class, but a wolf and a coyote (Canis latrans) share every rank down to genus, so the wolf and coyote are far closer relatives.

Every species also needs a name that works everywhere. The Swedish naturalist Carl Linnaeus made popular the system still used today: binomial nomenclature, meaning "two-part naming". Every species gets a scientific name made of its genus name followed by a specific epithet, a word that identifies that species within the genus. The rules are strict so that names are never ambiguous, and they avoid the traps of common names: a starfish is not a fish, and a koala bear is not a bear.

1. The genus is written first, with a capital letter: Canis.
2. The specific epithet comes second and is all lowercase, even when it comes from a place or person's name: Canis lupus.
3. The full name is written in italics when typed, or underlined when handwritten.
4. After the full name has appeared once, the genus may be shortened to its first letter: C. lupus. The epithet is never used alone, because lupus by itself does not identify a species.
5. Names are usually Latin or Latinized words, so they stay the same in every language.

The broadest rank is the domain. Comparisons of ribosomal RNA, led by the American microbiologist Carl Woese, showed that the organisms once lumped together as "bacteria" are really two very different groups. Life is now divided into three domains: Bacteria and Archaea, both made of prokaryotic cells (no nucleus), and Eukarya, made of eukaryotic cells (with a nucleus). Surprisingly, Archaea share a more recent common ancestor with Eukarya than with Bacteria. The genes and proteins archaea use to copy and read their DNA look more like ours than like those of bacteria. This course sorts life into six kingdoms, compared in the table below. Kingdom Protista is a grouping of convenience: it holds the eukaryotes that are not fungi, plants or animals, and some protists are more closely related to plants or animals than to other protists. Many biologists now divide protists among several separate groups instead of one kingdom, a reminder that classification changes as new evidence arrives.

A phylogenetic tree is a branching diagram of hypothesized evolutionary relationships. A cladogram is one kind of tree, built from shared derived characteristics: features that appeared in a common ancestor and were passed to all of its descendants, such as jaws, four limbs or hair. Each branching point, called a node, stands for a common ancestor. A clade is an ancestor plus all of its descendants. The organism that branches off first and lacks the derived traits is the outgroup, which serves as a reference point. Biologists use body structure (morphology), embryos and, increasingly, DNA sequences to decide where the branches go. To build a cladogram from the character table below, count each organism's derived traits. The lamprey has none, so it is the outgroup and branches off first. The perch has one (jaws), so it branches next, and so on until the mouse, which has all four. Each trait is marked on the main stem just before the branch of the first organism that has it, and everything above that mark has the trait. Reading the result, the lizard and mouse are more closely related to each other than either is to the frog, because they share a more recent common ancestor (the one that had the amniotic egg).