22.1 Classification of Living Organisms

22.1 Classification of Living Organisms

Biologists name living things so that one label means the same organism in every course and lab. The filing system in introductory biology is the Linnaean hierarchy. Its ranks run from broad to narrow: domain, kingdom, phylum, class, order, family, genus, and species. Each rank is nested inside the rank above it. Learn the eight ranks in that direction. An older memory sentence, King Philip came over for good soup, starts at kingdom and leaves domain out. Put domain in front of that list when you use the three-domain system.

The binomial

The species is written as a binomial, a two-word name. The first word is the genus. The second word is the specific epithet. In Homo sapiens, Homo is the genus and sapiens is the specific epithet. The genus is capitalized. The epithet is not. Both words are italicized. After the full name has appeared once, the genus may be shortened to an initial, as in H. sapiens. The epithet should not stand alone. Different genera can reuse a word such as vulgaris.

Humans show how the ranks nest:

• Domain: Eukarya
• Kingdom: Animalia
• Phylum: Chordata
• Class: Mammalia
• Order: Primates
• Family: Hominidae
• Genus: Homo
• Species: Homo sapiens

Family versus species

Hominidae is the family. It is a single word at a higher rank. A scientific name is not the family name alone. If a prompt gives only Hominidae, the rank is family. If it gives Homo sapiens, the rank is species. The genus plus the specific epithet is the name that stays attached to the organism.

Three domains

Carl Woese and colleagues compared ribosomal RNA, a molecule every cellular organism uses when it builds proteins. The comparisons supported three domains: Bacteria, Archaea, and Eukarya. That result replaced the habit of placing every organism without a nucleus into one kingdom. Archaea are not a subgroup of bacteria. They are not bacteria that lost a trait and remained inside the bacterial domain.

Bacteria

Bacteria have no nucleus. In this introductory scheme their cell walls contain peptidoglycan, a mesh of sugars cross-linked by short peptides. Escherichia coli, common in the human gut, is a bacterium. Cyanobacteria, which release oxygen during photosynthesis, are bacteria as well. Lacking a nucleus is not enough to call a cell a bacterium. Archaea also lack a nucleus. The peptidoglycan wall is the classroom trait that separates bacteria from archaea here.

Archaea

Archaea have no nucleus and no peptidoglycan. Many are extremophiles. Some grow in very hot water, some in very salty water, and some produce methane where oxygen is scarce. Those habitats fill textbook examples, yet archaea also live in ordinary soil and seawater. The classification point is the domain, not the temperature. Archaea are their own domain.

Use the traits on a short case. A thermophilic unicellular prokaryote without peptidoglycan is placed with Archaea in this introductory scheme. Thermophilic means the cell favors high heat. Unicellular sets aside animals, plants, and other multicellular bodies. A prokaryote has no nucleus, so the cell is not in Eukarya. Without peptidoglycan, the cell is not placed with Bacteria. This is a teaching rule for the scheme. It does not say that every archaeon is a thermophile.

Eukarya

Eukarya have a nucleus. A nuclear envelope surrounds the chromosomes. Members of this domain also tend to have other membrane-bound organelles, including mitochondria. Animals, plants, fungi, and the organisms still called protists in many first courses all sit inside Eukarya.

Kingdoms that courses still name

Introductory courses still speak of kingdoms such as animals, plants, fungi, and protists. Animals are multicellular eukaryotes that usually take in food. Plants are multicellular eukaryotes that photosynthesize with chlorophyll, and their cell walls contain cellulose. Fungi absorb food after releasing enzymes, and their cell walls contain chitin rather than cellulose. Protists are the eukaryotes left over in that older sorting, including many algae, amoebae, ciliates, and slime molds.

Protists are not one true evolutionary group. Some are closer relatives of plants, animals, or fungi than of other organisms called protists. A kingdom label can still appear on a lab list. The evolutionary claim is separate. Do not treat protists as one clade on the same footing as the animals or the plants.

Cladistics

Cladistics groups organisms by shared derived characters. A shared derived character arose in a common ancestor of a group and was passed to its descendants. Among vertebrates, hair is a shared derived character of mammals. A very old trait, such as the use of DNA, does not sort mammals from fishes, because it is shared far more widely. When cladistics asks who belongs together, it prefers the shared trait that is new for that group.

A monophyletic group is a clade. It includes an ancestor and all of its descendants. A set that leaves out some descendants is not monophyletic. A set that joins organisms from separate branches only because they look alike is not monophyletic either. Protists fail that test. Mammals, taken as their common ancestor plus every descendant, pass it.

An outgroup roots a tree. The outgroup is a lineage outside the group under study. The branch point where it joins that group gives the tree a base, so later splits can be read in order. The small diagram in this section names the three domains: Bacteria, Archaea, and Eukarya.

Reading a classification question

Test one trait at a time. A nucleus places the organism in Eukarya. No nucleus leaves Bacteria and Archaea. Peptidoglycan in the cell wall supports Bacteria in this scheme. A thermophilic unicellular prokaryote without peptidoglycan is placed with Archaea. Then read any scientific name with the binomial rule: a capital letter on the genus, a lowercase epithet, and two italicized words. A family name such as Hominidae is one word at a higher rank.