IB Biology HLClassification & CladisticsPaper 1 & 2~11 min read
Classification System
For a long time there were two kingdoms: plants and animals. Fungi got filed with the plants, which was wrong. Then microscopes arrived, then rRNA analysis, and it turned out that what we had been calling “bacteria” was two completely different groups of organisms.
📚 What you need to know
Taxonomy has frequently changed to match new discoveries about organisms.
The sequence: plant and animal kingdoms → fungi added (incorrectly) to plants → microscopes revealed prokaryotes and eukaryotes → five kingdoms → three domains.
The five kingdoms were plants, animals, fungi, protoctists and prokaryotes. Protoctists are eukaryotic, mostly single-celled organisms.
rRNA analysis showed there are two distinct groups of prokaryotes, leading to the three domain system.
The largest taxonomic group is now the domain. The three domains are Archaea, Eubacteria and Eukaryotes.
The Archaea are single-celled and include thermophiles in hot springs and methanophiles that metabolise methane.
They were originally grouped with bacteria because of prokaryotic cell structure, a circular chromosome, a cell wall and 70S ribosomes.
Work by Carl Woese in 1977 showed distinct features — different cell wall material, a distinct membrane lipid, and a ribosomal small subunit more similar to eukaryotes — so they became their own domain.
How the top of the hierarchy changed
Notice the trigger each time: better microscopes revealed prokaryotes, and rRNA analysis revealed that the prokaryotes were two separate things.
Historically the largest taxonomic groups were the plant and animal kingdoms. When fungi were discovered they were added to the plant kingdom, which was incorrect.
Microscopes led to the discovery of prokaryotes and eukaryotes, and the taxa were later divided into five kingdoms: plants, animals, fungi, protoctists and prokaryotes.
rRNA analysis then showed there were two distinct groups of prokaryotes. That shift in taxonomic thinking produced the three domain system.
The three domains
The largest taxonomic group is now the domain. There are three: Archaea (prokaryotes), Eubacteria (prokaryotes) and Eukaryotes.
Both the eubacteria and the archaea are prokaryotic, yet the archaea sit on the eukaryote side of the tree. Cell structure and ancestry are not the same thing.
Why the archaea were separated
The Archaea are single-celled organisms living in a wide range of habitats. Some live in extreme environments — thermophiles in hot springs, methanophiles that metabolise methane.
They were originally classified with the rest of the bacteria in one taxon, because they share several features with them:
Prokaryotic cell structure
A circular chromosome
The presence of a cell wall
70S ribosomes
Closer analysis, much of it carried out by Carl Woese in 1977, showed that some of their features were distinct from the rest of the prokaryotes:
Their cell walls are made of a different material from the walls of other bacteria.
Their cell membranes are made of a distinct type of lipid.
The small subunit of their ribosomes is more similar to eukaryotic ribosomes than to those of other prokaryotes.
Multiple DNA sequences present in bacteria are absent in methanogenic archaeans.
Those discoveries led to a change in the classification of the archaea, which became their own domain.
Feature
Archaea
Eubacteria
Eukaryotes
Cell type
Prokaryotic
Prokaryotic
Eukaryotic
Chromosome
Circular
Circular
Linear, plus circular mitochondrial and chloroplast DNA
Cell membrane lipids
Glycerol-ether lipids
Glycerol-ester lipids
Glycerol-ester lipids
Ribosomes
70S, with a small subunit more similar to eukaryotic ribosomes
70S
80S in the cytoplasm, 70S in mitochondria and chloroplasts
Cell walls
Always present, without peptidoglycan
Always present, with peptidoglycan
Sometimes present, without peptidoglycan
Histones
Yes
No
Yes
Introns
Sometimes
Rarely
Yes
Read that table down the archaea column and you can see the whole argument. Cell type and chromosome match the eubacteria. Membrane lipids are unique to them. Ribosome subunit and histones match the eukaryotes. A group that sits between two others like that does not belong in either.
🧠
Archaea look bacterial but read eukaryotic
Structure says bacteria — no nucleus, circular chromosome, 70S ribosomes. Molecules say eukaryote — histones, ether lipids, a eukaryote-like ribosomal subunit. That mismatch is exactly why they got their own domain.
Worked examples
WE 1
Outline how classification has changed
Outline how the highest levels of biological classification have changed over time. (4 marks)
Stage 1
The largest groups were originally the plant and animal kingdoms, with fungi incorrectly added to the plants.
Stage 2
Microscopes led to the discovery of prokaryotes and eukaryotes.
Stage 3
The taxa were divided into five kingdoms: plants, animals, fungi, protoctists and prokaryotes.
Stage 4
rRNA analysis showed two distinct groups of prokaryotes, producing the three domain system of Archaea, Eubacteria and Eukaryotes.
Two kingdoms, five kingdoms, three domainslink each change to the evidence that caused it, not just the date
WE 2
Justify a separate domain
Explain why the archaea are placed in a separate domain from the eubacteria. (4 marks)
Point 1: why they were grouped together
Both are prokaryotic, with a circular chromosome, a cell wall and 70S ribosomes.
Point 2: the wall and membrane
Archaeal cell walls are made of a different material and lack peptidoglycan, and their membranes contain a distinct type of lipid.
Point 3: the ribosomes
The small subunit of archaeal ribosomes is more similar to eukaryotic ribosomes than to those of other prokaryotes.
Point 4: genetic evidence
rRNA analysis and the absence of several bacterial DNA sequences showed archaea form a distinct group, so they were given their own domain.
Bacterial in structure, but distinct in wall, membrane and ribosomegive a mixture of structural and molecular evidence, not one type only
WE 3
Identify a domain from features
An organism has no nucleus, a circular chromosome, a cell wall containing no peptidoglycan and histones associated with its DNA. Deduce its domain and justify your answer. (3 marks)
Step 1: rule one out
No nucleus means it is prokaryotic, so it is not a eukaryote.
Step 2: separate the two prokaryote domains
Eubacteria always have peptidoglycan in their cell walls and have no histones, so it is not a eubacterium.
Step 3: the deduction
A cell wall without peptidoglycan, together with the presence of histones, matches the archaea.
Archaeapeptidoglycan and histones are the two features that split the prokaryote domains
💡 Exam tips
Learn the order of change and the evidence behind each step.
Name the three domains as Archaea, Eubacteria and Eukaryotes.
Say rRNA analysis when explaining why prokaryotes were split.
Learn the archaea’s distinctive features: wall material, membrane lipids, ribosomal small subunit.
Credit Carl Woese, 1977 if a question asks who established the domains.
Remember archaea are more closely related to eukaryotes than to eubacteria.
⚠ Common mistakes
Calling archaea a type of bacteria. They are a separate domain.
Giving archaea peptidoglycan walls. Their walls always lack it.
Saying all prokaryotes are equally related. Archaea sit nearer the eukaryotes.
Listing four kingdoms. The five-kingdom system included protoctists.
Putting fungi with plants. That was the historical error the system corrected.
Saying eukaryotes have only 80S ribosomes. Their mitochondria and chloroplasts contain 70S ones.
That completes Classification & Cladistics. The four notes tell one story: why we group organisms at all, how grouping by ancestry replaced grouping by appearance, what happens when the evidence overturns a group, and how that process reshaped the very top of the hierarchy.
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