Module 4: Classification and Phylogenetics
These free OCR A Level Biology Classification and Phylogenetics revision notes have been written for specification point 4.2.2(d).
Classification
Classification is the process of placing organisms into groups.
Classification helps scientists to:
- Identify and name organisms
- Predict shared characteristics
- Organise biological knowledge
- Understand evolutionary relationships
Organisms can be classified by:
- Observable characteristics such as limbs or flower colour.
- Cellular features such as the presence of a nucleus.
- Molecular traits such as DNA and RNA sequences.
- Physiological processes (e.g. respiration type)
Artificial vs Natural Classification
The table below outlines the characteristics of artificial and natural selection:
| Feature | Artificial Classification | Natural Classification |
|---|---|---|
| Based on | A selection of observable traits | A wide range of characteristics with a focus on genetic evidence |
| Reflects evolutionary history? |  No |  Yes |
| Stability | Relatively constant | Changes with new molecular data |
| Example | Grouping plants by leaf shape | Grouping by DNA sequence similarity |
Natural Classification: Molecular Evidence
Natural classification emphasises the classification of organisms based on their evolutionary relationships and common ancestry using the following molecules:
| Molecule | Use in Classification | Example Use |
|---|---|---|
| DNA | Compares gene sequences to reveal evolutionary relationships | Comparing conserved genes like Hox or 16S rRNA |
| RNA |
– rRNA used for ancient divergence – mRNA to study gene expression |
– 18S rRNA for eukaryotes, 16S for prokaryotes – mRNA profiles in related species |
| Protein | Compares amino acid sequences for functional similarity | Cytochrome c (respiratory protein) sequence comparison in animals |
The Taxonomic Hierarchy
Taxonomic ranks (also known as taxonomic levels) are hierarchical groups into which organisms are sorted (hierarchical classification) to reflect their relative ‘closeness’ to each other.
Binomial nomenclature (also known as the binomial system) is a two-part naming system that uses the genus and species names from the taxonomic hierarchy to produce a unique two-part name for identifying a species.
Each organism is given a two-part Latin name:
Genus (capitalised) + species (lowercase)
e.g. Homo sapiens
The binomial name is traditionally written in italics, but is commonly underlined when handwritten.
The advantages of the binomial naming system included:
- Universality: Latin was the common language (of the time), avoiding confusion across different languages, and even within different regions of the same country.
- Precision: Identifies a single species without ambiguity.
- Relationships: Including the genus shows the evolutionary relationships between species.
The table below outlines the groups you need to recall at each taxonomic level:
| Rank | Groups |
|---|---|
| Domain |
– Bacteria (Kingdom: Eubacteria) – Archaea (Kingdom: Archaebacteria) – Eukarya (Kingdoms: animals, plants, fungi, protists) |
| Kingdom |
– Animalia (animals) – Plantae (plants) – Fungi (mushrooms, yeasts) – Protoctista (also known as Protista or protists) (unicellular eukaryotes) – Eubacteria (‘true’ bacteria) – Archaebacteria (‘ancient’ bacteria)* |
| Phylum |
Not expected to recall, but hopefully familiar with: – Chordata (vertebrates) – Arthropoda (insects, spiders, crustaceans) |
| Class |
Not expected to recall, but hopefully familiar with: – Mammalia (mammals) – Insecta (insects) – Reptilia (reptiles) – Aves (birds) – Amphibia (amphibians) |
| Order |
Not expected to recall, but hopefully familiar with: – Primates (apes, humans) – Carnivora (dogs, cats, bears) |
| Family |
Not expected to recall, but hopefully familiar with: – Hominidae (great apes) – Felidae (cats) – Canidae (dogs) – Muridae (mice) |
| Genus |
Not expected to recall, but hopefully familiar with: – Homo (humans) – Canis (dogs, wolves) – Felis (cats) |
| Species |
Not expected to recall, but hopefully familiar with: – Homo sapiens (humans) – Canis lupus (grey wolf) – Felis catus (domestic cat) |
*Archaebacteria is a misleading name, as Eubacteria appear to be the older evolutionary lineage.
You are expected to know and place organisms in the correct Domain and Kingdom with some provided information, but you do not need to recall the groups of the lower ranks beyond expected general knowledge (which has been included in the table for convenience).
A commonly used mnemonic to recall the order of these ranks is:
Dear King Philip Came Over For Good Soup
The Five Kingdoms System
The 5 Kingdoms system was the 1960s taxonomic system that arose from centuries of research:
| Kingdom | Features |
|---|---|
| Animalia | No cell wall, heterotrophic, motile, multicellular |
| Fungi | Chitin cell wall, saprophytic, extracellular digestion |
| Plantae | Cellulose cell wall, autotrophic, multicellular |
| Protoctista | Mostly unicellular, some plant-like or animal-like |
| Prokaryotae* | No nucleus, unicellular, peptidoglycan cell wall |
*Not to be confused with the term prokaryote/prokaryotic, which describes a cell without membrane-bound organelles, not what kingdom it belongs to.
At this point in time, archaea had not been discovered/recognised yet, and the domain level of classification had not been invented.
The features used to classify organisms into the ‘correct’ Kingdom are outlined in the table below:
| Feature | Animalia | Plantae | Fungi | Protoctista | Prokaryotae* |
|---|---|---|---|---|---|
| Cell type | Eukaryotic | Prokaryotic | |||
| Nucleus | Present | Absent | |||
| DNA | Linear chromosomes with histones | Loop of naked DNA | |||
| Membrane-bound organelles | Present | Absent | |||
| Ribosomes | 80s | 75s | |||
| Reproduction | Sexual and/or asexual | Asexual | |||
| Unicellular or multicellular | Multicellular | Unicellular (e.g. yeasts) or multicellular (e.g. mycelium) | Mostly unicellular (some multicellular algae) | Unicellular | |
| Cell wall | None | Yes (cellulose) | Yes (chitin) | Some (peptidoglycan) | |
| Nutrition | Heterotrophic | Autotrophic | Heterotrophic | Autotrophic or heterotrophic | |
| Mobility | Most can | Can’t | Some can | ||
*These features do not apply to the archaea, whose discovery ended the 5 Kingdoms system.
The Three-Domain System
By 1990 Carl Woese’s research had revealed significant differences between organisms within the 5 Kingdom’s prokaryotae group.
Structural differences between the bacteria and archaea can be found in their:
- Cell membrane
- Cell wall
- DNA replication
- Flagella
- Genetic material (bacteria lack histone-like proteins)
- RNA synthesis (they have different enzymes)
The structural similarities between the archaea and eukarya include:
- DNA replication (similar mechanisms and enzymes)
- Genetic material (both have histone-like proteins)
- RNA synthesis (similar enzymes/RNA polymerase)
The differences observed between bacterial and archaea cells, and the similarities shared between the archaea and eukaryotes, provided substantial evidence that the archaea were more closely related to the eukaryotes than bacteria are. This insight led Woese to propose the 3 domain system above the traditional kingdom ranks which, after initial opposition, was widely accepted.
Phylogeny
Phylogeny is the study of evolutionary relationships between organisms.
Phylogeny defines a species as a group of organisms that are very similar genetically (and subsequently), metabolically, physiologically and anatomically.
This definition avoids many of the problems with the traditional definition of a species, which does not apply to asexually reproducing organisms.
Phylogenetics is a scientific field of research that determines and reconstructs the evolutionary relationships between organisms.
These relationships are often shown as phylogenetic trees:
- Tips: present-day species
- Nodes: common ancestors
- Closer branches: more recent common ancestor