Classification

A species is a group of organisms with similar characteristics that can interbreed (reproduce) to produce fertile offspring.

The key word is fertile: the offspring must themselves be able to reproduce, which is why a horse and a donkey — whose offspring (the mule) is sterile — count as two separate species.

(a) The genus is Canis (the first word, written with a capital initial letter); lupus is the species name.

(b) Any two of: the genus is written first with a capital letter; the species name is written entirely in lower case; the whole name is italicised (in print) or underlined (when handwritten).

(c) Binomial names are universal/international — the same name is used by scientists worldwide regardless of language — so they avoid the confusion caused by common names, which can refer to different organisms in different places (or where one organism has several common names).

From largest/most inclusive to smallest/least inclusive, the ranks are:

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

As you move down this hierarchy, each group contains fewer organisms that are more similar and more closely related.

A natural (phylogenetic) classification groups organisms according to their evolutionary relationships, that is, how closely they are related through a common ancestor. It is based on many shared features, including homologous structures — structures that have the same basic origin and development even if they now perform different functions (for example the pentadactyl limb of mammals, which is adapted into an arm, a wing or a flipper). Because it reflects evolutionary history, a natural classification is relatively stable and predictive: organisms placed in the same group are likely to share other characteristics too.

An artificial classification, by contrast, groups organisms using only a small number of convenient, easily observed features, chosen for practical reasons and without regard to evolutionary relationship. It often relies on analogous structures — features that have the same function but a different evolutionary origin (for example the wing of a bird and the wing of an insect, which both enable flight but evolved separately). Because analogous features can arise independently in unrelated organisms (convergent evolution), an artificial classification may group unrelated organisms together and can be misleading.

In short, a natural classification reflects common ancestry (homologous structures), whereas an artificial classification reflects convenience and superficial similarity (analogous structures).

In the five-kingdom system, all prokaryotes were placed together in a single kingdom (Prokaryotae/Monera). However, when scientists compared the base sequences of ribosomal RNA (rRNA) across many organisms, they discovered that the prokaryotes are not one uniform group but consist of two fundamentally different lineages. These became the domains Bacteria and Archaea, with all eukaryotes forming the third domain, Eukarya. The domain is therefore a new rank placed above kingdom.

Although Archaea superficially resemble Bacteria (both are prokaryotic and small), they differ from Bacteria in several important ways revealed by molecular and biochemical evidence:

• Archaea have different rRNA base sequences from Bacteria — the original evidence for the split.
• Archaea have no murein (peptidoglycan) in their cell walls, whereas Bacteria do.
• Archaea have different cell-membrane lipids (branched, ether-linked) compared with the straight, ester-linked lipids of Bacteria.
• Archaea differ in their enzymes for transcription and translation (for example RNA polymerase) and in several respects are more similar to eukaryotes than to Bacteria.

Because these differences are so deep, grouping Archaea and Bacteria together in one kingdom did not reflect their true evolutionary relationships. The classification was therefore revised in the light of this new molecular evidence, producing the three-domain system that more accurately represents the relatedness of organisms.

Scientific knowledge is not fixed; it is a working model that is revised as new evidence becomes available. Classification is a clear example of this process.

Early classifications were based mainly on observable (morphological) features, because these were the only data available. As new techniques developed — in particular DNA and protein (amino acid) sequencing — scientists could compare organisms at the molecular level, giving an objective measure of relatedness. This new evidence sometimes contradicted the earlier classifications based on appearance. For example, comparing ribosomal RNA base sequences showed that the prokaryotes were really two very different groups, leading to the three-domain system replacing the five-kingdom system, and the separation of Archaea from Bacteria.

Crucially, a new idea is not accepted immediately. The findings are published and then scrutinised and tested by other scientists through peer review. When the evidence is repeatable and widely accepted by the scientific community, the classification is revised to reflect it.

Because classification depends on the evidence available at the time, current schemes are always provisional — they remain open to further change if better evidence (such as new molecular data) emerges in the future. This continual testing and revision in the light of peer-reviewed evidence is exactly how scientific knowledge advances.

Molecular evidence compares organisms at the level of their molecules rather than their outward appearance. Two molecules are most often compared: the base sequences of DNA (or RNA) and the amino acid sequences of proteins, such as cytochrome c.

The principle is that an organism's amino acid sequences are determined by its DNA base sequence. After two species diverge from a common ancestor, mutations gradually accumulate in their DNA over time, and some of these change the amino acid sequences of their proteins. Therefore the more similar the DNA base sequences or amino acid sequences of two species are, the more recently they shared a common ancestor and the more closely related they are. Counting the number of differences gives a measure of how long ago the species diverged, which can be used to build phylogenetic trees and place organisms into groups that reflect their true evolutionary relationships.

This clarifies classification because it is objective and quantitative — exact numbers of base or amino acid differences can be measured and compared — rather than relying on judgements about appearance. It is also more reliable: organisms that look alike may have evolved similar features independently (convergent evolution, giving analogous structures), but this is very unlikely to produce matching DNA or protein sequences by chance. As a result, molecular data can confirm relationships, reveal hidden ones, and correct earlier classifications based on physical features — for example, the comparison of ribosomal RNA that separated the Archaea from the Bacteria.

(a) Reading off the data, the higher the percentage similarity, the more closely related the species is to humans. In order of decreasing relatedness:

chimpanzee (98.8%) → gorilla (98.4%) → orangutan (96.9%) → gibbon (94.0%).

So the chimpanzee, with the highest DNA similarity (98.8%), is the most closely related to humans, and the gibbon, with the lowest (94.0%), is the most distantly related of the four.

(b) DNA carries the genetic code as a sequence of bases. After two species diverge from a common ancestor, mutations gradually accumulate in their DNA over time, so their base sequences become less similar. Therefore, the greater the percentage similarity of the DNA base sequences, the more recently the two species shared a common ancestor and the more closely related they are.

An advantage of using DNA base sequences (a molecular method) over physical features is that it is objective and quantitative — exact percentage similarities can be measured and compared. It also avoids being misled by convergent evolution, where unrelated organisms evolve similar physical features (analogous structures); such similarity is very unlikely to arise by chance at the level of the DNA base sequence.

Archaea were originally grouped with Bacteria because, on the surface, they are very similar: both are prokaryotic, small, single-celled, and have no membrane-bound organelles or nucleus. A classification based only on these observable features therefore placed them together.

However, molecular and biochemical evidence revealed that Archaea are fundamentally different from Bacteria:

• rRNA base sequences. Comparison of ribosomal RNA showed that the base sequences of Archaea differ greatly from those of Bacteria — in fact, in some respects Archaea are more similar to eukaryotes. This was the original and most powerful evidence.
• Cell walls. Archaea lack murein (peptidoglycan), the molecule that makes up bacterial cell walls.
• Membrane lipids. Archaea have distinctive branched, ether-linked membrane lipids, whereas Bacteria have straight, ester-linked lipids.
• Gene expression machinery. Archaea use different enzymes for transcription and translation (such as RNA polymerase), which again resemble those of eukaryotes more than those of bacteria.

Because these molecular differences are so large, they show that Archaea and Bacteria are not closely related and in fact diverged from a common ancestor a very long time ago. Grouping them together therefore did not reflect their true evolutionary relationships.

Placing Archaea in a separate domain improved the classification because it is now a more natural (phylogenetic) scheme: organisms are grouped according to genuine evolutionary relatedness rather than superficial appearance. This makes the classification more stable and more predictive, and it correctly shows that Archaea and Eukarya share a more recent common ancestor with each other than either does with Bacteria.

The interbreeding definition is useful for many sexually reproducing organisms, especially animals, because the production of fertile offspring is a clear, biologically meaningful criterion: it identifies populations whose gene pools are connected. The classic example — that the horse and donkey are separate species because their offspring (the mule) is infertile — shows the definition working well.

However, the definition has significant limitations and cannot be applied to all organisms:

• Asexual organisms (such as bacteria and many protoctists) do not interbreed, so the criterion cannot be tested at all.
• Extinct/fossil species cannot be made to interbreed, so they must be classified from preserved structures only.
• Ring species form a chain of populations in which neighbours interbreed but the two ends cannot, so there is no clear species boundary.
• Some closely related species, particularly plants, produce fertile hybrids, directly contradicting the definition.
• Geographically isolated populations may never meet in nature, so whether they could interbreed is impossible to test in practice.

Evaluation/conclusion. The biological species concept is a useful and practical definition for many sexually reproducing animals, but it is not universally applicable. For this reason biologists increasingly supplement it with molecular and genetic evidence (DNA/RNA and protein sequence similarity), which can be applied to all organisms, including asexual and extinct ones. The interbreeding definition is therefore best regarded as one valuable tool rather than a complete or universal rule.