This unit is about how biologists sort millions of species into groups that reflect who is related to whom, from the three domains down to a single species name. By the end, you should be able to place an organism in its domain and kingdom, write its scientific name correctly, and read a phylogenetic tree to decide which groups share the most recent common ancestor.
Read the overview first, then work through each topic note and answer its checkpoint before you look at the answer.
Earth has roughly 2 million named species and likely millions more unnamed. This unit gives you the system biologists use to organize them. Modern classification aims to group organisms by evolutionary history, which biologists study using evidence such as DNA and fossils.
Honors Biology Unit 12 covers how living things are named and classified. You learn the three-domain system (Bacteria, Archaea, and Eukarya) and why ribosomal RNA evidence split prokaryotes into two domains. You survey the major groups, including bacteria, archaea, protists, fungi, plants, and animals, plus viruses, which don't belong to any domain. You also practice binomial nomenclature, the ranks from domain to species, and reading phylogenetic trees and cladograms to identify clades and closest relatives.
In 1977 Carl Woese and George Fox used ribosomal RNA evidence to distinguish archaea from bacteria. In 1990 Woese and colleagues proposed the three-domain system: Bacteria, Archaea, and Eukarya. Domain sits one level above kingdom.
Fungi generally have chitin walls and absorb food. Most plants have cellulose walls and photosynthesize. Animals have no cell walls and generally ingest food. These traits can help identify a group, but exceptions exist and evolutionary evidence is also used.
Two species in the same genus, like Canis lupus and Canis latrans, share a common ancestor. A phylogenetic tree shows the same idea visually, with each branch point marking a common ancestor. Both are hypotheses that can change when new DNA evidence appears.
Early systems grouped organisms by looks or habitat, which put whales with fish. Modern classification groups organisms by shared ancestors, using DNA, anatomy, and fossils as evidence. Ranks, names, and trees help biologists organize organisms and describe their relationships, though names and ranks do not always reflect evolutionary history.
Domain is the broadest rank in classification, one level above kingdom.
Once you know the domains, the next step is telling the major groups apart by how they're built and how they get energy.
Taxonomy is the science of naming and classifying organisms.
Open this guide for a closer review of the topic.
Domain is the broadest rank in classification, one level above kingdom. Bacteria and Archaea are both prokaryotes, meaning their cells have no nucleus and no membrane-bound organelles. Eukarya contains every organism whose cells have a nucleus, which covers protists, fungi, plants, and animals.
Biologists used to lump all prokaryotes together. In 1977, Carl Woese and George Fox used 16S ribosomal RNA evidence to distinguish archaea from bacteria. The three-domain system was proposed in 1990. Most bacteria have cell walls containing peptidoglycan, while archaeal walls lack it. Archaeal membrane lipids also differ from those of bacteria.
Here is the surprise. Even though archaea look like bacteria under a microscope, their genes and ribosomes show they are more closely related to eukaryotes than to bacteria.
Worked example. Compare a 20-base stretch of rRNA from three microbes. A and B differ at 2 positions, so they match at sites, which is similarity. A and C differ at 7 positions, so they match at sites, which is . A is more similar to B in this stretch, which can be evidence of a closer relationship. A short sequence alone is not enough to establish the relationship, since mutation rates and chance can affect similarity.
A newly discovered single-celled organism has no nucleus and no peptidoglycan in its cell wall. Is that enough to identify its domain? (Answer: No. It could be an archaeon, but some bacteria also lack peptidoglycan. Compare evidence such as rRNA sequences to help identify it.)
| Feature | Bacteria | Archaea | Eukarya |
|---|---|---|---|
| Nucleus | No | No | Yes |
| Membrane-bound organelles | No | No | Yes |
| Peptidoglycan in cell wall | Yes | No | No |
| Ribosome size | 70S | 70S | 80S in the cytosol |
| Examples | E. coli, Streptococcus | Methanogens, halophiles | Amoebas, mushrooms, oak trees, humans |
Once you know the domains, the next step is telling the major groups apart by how they're built and how they get energy.
Bacteria are tiny prokaryotes often sorted by shape (cocci are spheres, bacilli are rods, spirilla are spirals). Archaea look similar but include extremophiles such as halophiles in salt lakes and methanogens that release methane in swamps and cow guts.
Inside Eukarya, protists are the leftovers, meaning any eukaryote that isn't a plant, animal, or fungus. That includes amoebas, paramecia, diatoms, and giant kelp. Fungi such as mushrooms, molds, and yeasts are heterotrophs that release enzymes outside their bodies and absorb the digested food. Their cell walls generally contain chitin. Many fungi form networks of threads called hyphae, while yeasts are usually single-celled.
Plants are multicellular and generally have cellulose cell walls. Most have chloroplasts and make sugars by photosynthesis, though some parasitic plants do not photosynthesize. Nonvascular plants like mosses lack xylem and phloem, so they stay small and grow in damp places. Vascular plants include ferns, conifers, and flowering plants. Animals are multicellular heterotrophs that ingest food and have no cell walls. About 95% of animal species are invertebrates, and most of those are arthropods.
Viruses don't fit anywhere. They have no cells, no ribosomes, and no metabolism of their own, so they reproduce only inside a host cell and aren't placed in any domain.
Mushrooms grow out of the ground and don't move, so why aren't they classified as plants? (Answer: Fungi can't photosynthesize. They absorb food from their surroundings, and their cell walls are made of chitin instead of cellulose.)
| Group | Cell type | Cell wall | Nutritional mode | Examples |
|---|---|---|---|---|
| Bacteria | Prokaryotic | Peptidoglycan | Varies (autotrophs and heterotrophs) | E. coli, cyanobacteria |
| Archaea | Prokaryotic | No peptidoglycan | Varies (autotrophs and heterotrophs) | Methanogens, halophiles |
| Protists | Eukaryotic, uni- or multicellular | Varies, many have none | Varies (autotrophs and heterotrophs) | Amoeba, diatoms, kelp |
| Fungi | Eukaryotic | Chitin | Heterotroph by absorption | Mushrooms, yeast, Penicillium |
| Plants | Eukaryotic, multicellular | Cellulose | Usually autotroph by photosynthesis | Moss, ferns, oak trees |
| Animals | Eukaryotic, multicellular | None | Heterotroph by ingestion | Sponges, insects, humans |
Taxonomy is the science of naming and classifying organisms. Carl Linnaeus built the system in the 1700s around binomial nomenclature, a two-part name made of the genus plus the specific epithet. In Panthera leo (lion), the genus is capitalized, the epithet is lowercase, and both are italicized. Ranks nest from broadest to most specific as domain, kingdom, phylum, class, order, family, genus, species. The mnemonic Dear King Philip Came Over For Good Soup helps. A lion is Eukarya, Animalia, Chordata, Mammalia, Carnivora, Felidae, Panthera, Panthera leo.
A phylogenetic tree shows evolutionary relationships as branches. Each node is a common ancestor, and two groups are closest relatives if they share the most recent node. A clade is an ancestor plus all of its descendants. Trees are hypotheses, and DNA evidence often redraws them.
Worked example. Build a cladogram using a simplified set of shared derived traits. Lampreys, sharks, frogs, lizards, and humans have vertebrae. All except the lamprey have jaws; frogs, lizards, and humans have four limbs; and lizards and humans share an amniotic egg. Place each trait on the branch leading to the group that shares it. On the resulting tree, the human's closest relative among the organisms listed is the lizard, not the frog. Hair belongs on the human branch. In real analyses, biologists examine many traits because traits can also be lost or evolve independently.
Is the group 'all reptiles except birds' a clade? (Answer: No. Birds descend from the same reptile ancestor as crocodiles and lizards, so leaving them out breaks the rule that a clade includes every descendant.)
| Term | Definition |
|---|---|
| Taxonomy | The science of naming, describing, and classifying organisms into groups. |
| Domain | The broadest classification rank, with three domains named Bacteria, Archaea, and Eukarya. |
| Eukaryote | An organism whose cells have a nucleus and membrane-bound organelles, including protists, fungi, plants, and animals. |
| Species | Under the biological species concept, a group whose members can interbreed in nature and produce fertile offspring, while remaining reproductively isolated from other such groups. This definition does not apply neatly to organisms that reproduce only asexually. |
| Protist | Any eukaryote that is not a plant, animal, or fungus, such as an amoeba, a diatom, or kelp. |
| Phylogenetic tree | A branching diagram that shows a hypothesis about evolutionary relationships among organisms. |
| Cladogram | A tree diagram that shows only the branching order of groups based on shared derived traits, without showing amounts of change. |
| Monophyletic group | Another name for a clade, meaning a common ancestor plus all of its descendants. |
Both are prokaryotes and are usually single-celled, so they can look alike. Archaea differ from bacteria in their rRNA and membrane lipids, and archaeal cell walls lack peptidoglycan. Genetic evidence also links archaea more closely to eukaryotes than to bacteria.
Branches can rotate around a node without changing the tree, so side-by-side tips aren't automatically closest relatives. Trace back to the most recent shared node instead. Do not assume that one living species on a tree is the ancestor of another. A species can sometimes give rise to a new species and persist, but humans did not come from living chimps. Humans and chimps share a common ancestor.
Viruses are tiny and cause disease, so they get lumped with bacteria. Viruses have no cells, ribosomes, or metabolism, and they can only copy themselves inside a host, so they aren't placed in any domain at all.
The genus is capitalized, the epithet is lowercase, and both are italicized, as in Homo sapiens (italic in print, underlined by hand). Older notes list seven ranks starting at kingdom, but modern classification has eight because domain sits above kingdom.