Classification Changes

Some microbes that make methane look just like bacteria under a microscope. In 1977, two scientists compared one molecule inside them and found that they belong to a separate branch of life. For most of history, people sorted living things by what they could see. A microscope shows shape and size, but not ancestry. So how can a molecule overturn what our eyes tell us, and is it a problem when science changes its groups?

Explore: remodel a tree with new evidence

You start with the five-kingdom tree many biologists used in the 1970s. Then you add evidence cards one at a time: an RNA comparison, a test of cell-membrane fats and a set of gene sequences. After each card, the tree redraws itself and a note says which evidence moved which group.

RNA comparison Ribosomal RNA, which every cell has, compared across cells (Woese and Fox, 1977). Membrane fats Archaea differ from bacteria in their cell membranes. Gene sequences Protein and DNA sequences compared, such as 25 proteins in a 1993 survey.

Reset

Which evidence moved which group

In this sketch each card moves its own groups, so the order of the cards does not change the finished tree, and branch lengths are not to scale. Rule to keep: the RNA card splits Monera, membrane fats add support to that split, and gene sequences move Fungi and Protista. The number of protist groups and where they attach are schematic; the lesson says only that Protista splits into many groups. The tree is still being tested, and scientists still use the three domain names.

Try this.

1. Before you add any card, predict which kingdom you think will split first. Write your guess down, then add the RNA card.
2. Add the cards in a different order. Predict whether the final tree will be the same, then test it.
3. Watch where Fungi sit after the gene card. Did they move closer to plants or to animals?
4. Remove one card from the finished tree. Predict which branch loses its support, then check the note.

Explain: how the sorting system has changed

Classification is the sorting of living things into groups based on how they are related. The groups are nested, like folders inside folders. A kingdom is a large group, such as plants or animals. A domain is the largest group of all, above kingdom.

Biologists build these groups from several kinds of evidence:

• Structure: body parts and cell parts, such as a nucleus or a cell wall.
• Embryology: how an organism develops in its earliest stages, before birth, hatching or sprouting. Embryology is the study of that early development.
• Phylogeny: the history of ancestors and descendants. A phylogeny is that family history, often drawn as a branching tree.
• DNA and RNA: the order of the bases in an organism’s genes and other molecules.

The system has been rebuilt several times. Each date below is the year a scheme was published, not the year everyone agreed.

Year	Scheme	What changed
1735	Linnaeus, Systema naturae	Living things sorted as plants or animals (minerals too)
1866	Haeckel	Protista added as a third living kingdom
1938	Copeland	A four-kingdom system, with bacteria apart
1969	Whittaker	Five kingdoms, with Fungi apart from plants
1977	Woese and Fox	RNA evidence for three major lines of descent
1990	Woese, Kandler and Wheelis	Three domains placed above the kingdoms

Many US textbooks use six kingdoms: Archaebacteria, Eubacteria, Protista, Fungi, Plantae and Animalia. A protist is a eukaryote that is not a plant, animal or fungus. Virginia’s Biology standards (the SOL) keep Protista as a kingdom, and you will use it. Newer trees divide protists into many separate groups, because some protists are closer to animals or plants than to other protists.

Explain: a molecule every cell shares

Every cell builds proteins on ribosomes. Ribosomal RNA (rRNA) is the RNA that forms much of a ribosome. Because every cell has it, rRNA can be compared across all cellular life. Its sequence changes slowly, so even very distant groups still share enough of it to compare. Shared does not mean identical: the small differences are the evidence.

Woese and Fox cut rRNA into short pieces and listed the pieces from each organism. Then they scored how much two lists overlapped, from 0 (no overlap) to 1 (the same). Methane-making microbes scored high with each other and low with typical bacteria. In 1977 they read this as three major lines of descent.

In 1990, Woese, Otto Kandler and Mark Wheelis proposed the rank of domain, above kingdom, with three names:

• Bacteria: the domain of familiar single-celled prokaryotes, such as E. coli.
• Archaea: the domain of single-celled prokaryotes that differ from bacteria in their RNA and membranes.
• Eukarya: the domain of organisms whose cells have a nucleus, including animals, plants, fungi and protists. The 1990 paper spelled it Eucarya.

Archaea are not only microbes of hot springs. The 1977 samples included one that grows best at moderate temperatures. In 1992, archaea were found in ordinary coastal seawater.

The tree is still being tested. Genome studies published in 2023 and 2025 placed eukaryotes inside one branch of the archaea. Scientists still use the three domain names, but they disagree about the exact branch.

Explain: other groups that moved

DNA and protein comparisons have moved other groups too.

• Fungi and animals. In 1993, a survey of 25 proteins strongly supported fungi being closer to animals than to plants. The sampled animals and fungi shared four insertions or deletions (added or missing stretches of amino acids) that plants lacked. This does not mean animals came from mushrooms. It means animals and fungi share a more recent common ancestor.
• Two African elephants. In 2010, a study of 39,763 DNA bases from 375 places in the nuclear genome supported treating forest and savanna elephants as two species. The study had only one or two animals of each kind, so it could not settle every detail.
• Whales. DNA comparisons placed whales among the even-toed hoofed mammals, with hippos as their closest living relatives. Some biologists use one group name, Cetartiodactyla, for them all, and others simply widen Artiodactyla to include whales.
• Protists. Gene sequences split the old kingdom Protista into many groups that are not each other’s closest relatives.

Why is it fine for science to change its mind? A classification is a claim about ancestry. A good claim can be tested, and some tests show it needs fixing. The older groups were reasonable for the evidence of their time.

Elaborate: read the 1977 similarity scores

Each score compares the lists of rRNA pieces from two samples. A higher score means more overlap. The scores have no units and are not percentages of DNA.

Sample A	Sample B	Kind of pair	Similarity score (no units, 0 to 1)
Yeast (Saccharomyces cerevisiae)	Duckweed (Lemna minor)	Within eukaryotes	0.29
Escherichia coli	Bacillus firmus	Within bacteria	0.25
Methanobacterium thermoautotrophicum	M. ruminantium	Within methane makers	0.51
Yeast	E. coli	Between groups	0.05
Yeast	B. firmus	Between groups	0.08
Yeast	M. thermoautotrophicum	Between groups	0.11
Yeast	M. ruminantium	Between groups	0.11
E. coli	M. thermoautotrophicum	Between groups	0.11
E. coli	M. ruminantium	Between groups	0.12

Source: Woese and Fox, PNAS 1977, Table 1. These are laboratory rRNA samples, with the names used in 1977. We picked these nine pairs from a larger table, so they are a teaching set, not a random sample.

1. Find the mean of the three within-group scores. Then find the mean of the six between-group scores.
2. Is every within-group score higher than every between-group score?
3. Which score is higher: E. coli with B. firmus, or E. coli with a methane maker? What does that tell you about where the methane makers belong?

Design problem

You think a newly found microbe from a pond might be an archaeon, not a bacterium. Plan how you would test this with sequence comparisons.

One way to do it

• Question: Is the pond microbe’s rRNA more similar to known archaea or to known bacteria?
• Independent variable: the comparison organism (several known archaea and several known bacteria).
• Dependent variable: the similarity of the matching rRNA gene, as a percent of matching bases.
• Constants: compare the same gene and the same length of sequence, and use the same computer method for every pair.
• Control: include two known bacteria compared with each other, and two known archaea, so you know what a within-group score looks like.
• Repeated trials and sample size: sequence the pond microbe more than once, and use at least five organisms from each domain, not one.
• Second line of evidence: check a different gene or the membrane fats, because one marker can mislead.
• Safety: treat unknown microbes as possible germs; grow them only in a supervised lab.

If the pond microbe scores clearly higher with every archaeon than with every bacterium, and the second marker agrees, the evidence supports calling it an archaeon.

Evaluate: check your thinking

The methane makers looked like bacteria, but their ribosomal RNA overlapped far more with each other than with typical bacteria. That molecule showed a line of descent the microscope could not. Changing their group was science doing its job: testing a claim against better evidence and fixing it.

Science practices you used: using a model and naming its limits, calculating and comparing means from a data table, and making and judging a claim from evidence.