What you'll learn

• Why biologists classify organisms and what a species is.
• How the taxonomic hierarchy works, from domain to species.
• How DNA, RNA and protein sequences are used in molecular phylogeny.
• How to interpret simple phylogenetic trees without falling into common traps.

Why classify living organisms?

There are millions of described species on Earth, and many more are still undiscovered. Classification gives biologists a shared system for organising this variety of life, communicating clearly, and making predictions about organisms based on their relatives.

For example, if a newly discovered plant is classified in the same family as a known medicinal plant, scientists might investigate whether it makes similar useful chemicals.

The species concept

The basic unit of classification is the species.

“Fertile offspring” means the offspring can also reproduce. For example, horses and donkeys can mate to produce mules, but mules are usually infertile, so horses and donkeys are treated as different species.

The taxonomic hierarchy

Classification is hierarchical: large groups are split into smaller and more specific groups. The usual order is:

Domain → Kingdom → Phylum → Class → Order → Family → Genus → Species

The diagram below shows how one organism, the human, fits into increasingly specific taxa.

A useful way to remember the hierarchy is: Dear King Philip Came Over For Good Soup.

Binomial naming

Each species is given a two-part scientific name using the binomial system.

The genus starts with a capital letter, the species name starts with a lower-case letter, and the whole name is written in italics when typed. If handwriting, underline it instead.

For example:

• Human: Homo sapiens
• Domestic cat: Felis catus
• The bacterium often used in genetic engineering: Escherichia coli

Natural and phylogenetic classification

Early classification systems often used obvious features, such as body shape, colour or habitat. These can be useful, but they can also be misleading because unrelated organisms may evolve similar features.

For example, sharks and dolphins both have streamlined bodies because both are adapted for swimming, but dolphins are mammals and sharks are fish. This is an example of convergent evolution, where similar selection pressures lead to similar adaptations in unrelated groups.

A clade is a group containing a common ancestor and all of its descendants. Modern classification aims to reflect clades rather than just superficial similarities.

The three-domain system

Molecular evidence, especially comparisons of ribosomal RNA, led to the three-domain system. A domain is the highest taxonomic rank, above kingdom.

Archaea were once grouped with bacteria because both are prokaryotic. Molecular data showed that archaea are a separate domain.

Molecular phylogeny

Molecular phylogeny uses molecular evidence, such as DNA base sequences, RNA sequences or amino acid sequences, to infer evolutionary relationships.

The logic is simple: closely related organisms usually have more similar sequences because they have had less time to accumulate mutations since sharing a common ancestor.

A typical molecular phylogeny method is:

1. Choose the same homologous gene, RNA molecule or protein in each organism.
2. Determine the sequence.
3. Align the sequences so corresponding bases or amino acids are compared.
4. Count similarities and differences.
5. Use the pattern of differences to infer which organisms share the most recent common ancestors.

For a simple comparison, percentage similarity can be calculated using:

$$percentage\; similarity=\frac{number\; of\; matching\; positions}{total\; positions\; compared}\times 100$$

Phylogenetic trees

A phylogenetic tree is a branching diagram showing inferred evolutionary relationships. Branch points represent common ancestors, and the tips usually represent present-day species or groups.

In a tree, the key question is not “which species are drawn next to each other?” but “which species share the most recent common ancestor?”

If a branch length has a scale, it may represent time or amount of genetic change. If there is no scale, do not assume a longer drawn branch means “more evolved” or “older”.

Why molecular evidence is powerful

Molecular data can reveal relationships that are not obvious from appearance. It is especially useful when organisms have few visible features, when fossils are incomplete, or when convergent evolution has made unrelated organisms look similar.

Using several genes or proteins gives stronger evidence than using one sequence alone. If multiple independent molecules suggest the same relationship, scientists can be more confident in the phylogeny.