Classification, phylogeny and molecular evidence

Binomial nomenclature and the taxonomic hierarchy

Common names are local and unstable, and the same name can refer to different species in different places. A robin in Surrey is a small brown bird that will follow a spade around a garden; a robin in Ohio is a thrush the size of a blackbird. A buzzard in Britain is a hawk; a buzzard in Arizona is a vulture. Biology therefore uses an internationally agreed name that belongs to one species only.

The system is binomial nomenclature, set out by Linnaeus in the eighteenth century, before the reason organisms fall into groups was known. Every species has two words. The first is the genus, shared with the other species placed in that genus; the second is the specific name, and it is unique within that genus. Homo sapiens. Panthera leo. Quercus robur. The genus takes a capital letter and the specific name never does, both are printed in italics, and both are underlined in handwriting. After the first mention you may abbreviate the genus to its initial: H. sapiens.

The conventions are part of the name. homo Sapiens reverses both of them and is not a correctly written binomial.

Describe the drawing

Eight rectangles drawn one inside another, each labelled with a taxonomic rank and the group a human belongs to at that rank: domain Eukarya, kingdom Animalia, phylum Chordata, class Mammalia, order Primates, family Hominidae, genus Homo, species sapiens. A short note beside each rank gives the feature that rank picks out, and the two innermost boxes are highlighted as the binomial.

A species does not sit on its own. It is placed in a genus, the genus in a family, and so on up through eight ranks: domain, kingdom, phylum, class, order, family, genus, species. Botanists usually use division where zoologists use phylum.

Two features define the hierarchy. It is nested: every mammal is a chordate, every chordate is an animal, and there is no organism that belongs half to one class and half to another. And it has no overlap at a rank: nothing is in two orders. Both features follow from building groups by descent, because a lineage that has split does not rejoin.

Taxonomy

The naming and classifying of organisms into a hierarchy of groups.

Taxon

Any one group in the taxonomic hierarchy: Mammalia, Primates and Homo are all taxa.

Binomial

The two-part international name of a species: genus then specific name, italicised, genus capitalised.

Phylogeny

The evolutionary history of a group: which lineages split from which, and in what order.

Species concepts

The species is the only rank in the hierarchy that has been defined from first principles, and several definitions are in use. The one stated by AQA, Cambridge International and Pearson Edexcel Biology B, and assumed by the other mapped specifications, is the biological species concept: a group of organisms with similar characteristics whose members can breed with each other to produce fertile offspring.

The word fertile is doing the work. A horse and a donkey will breed and produce a mule, and the mule is almost always sterile, so horses and donkeys stay two species. Textbooks often add that members of a species occupy the same ecological niche; treat that as a common observation about species rather than part of the definition, which turns on interbreeding. In animals there is usually also a specific courtship behaviour, whether a display, a call, a scent or a dance, that lets a male and a female recognise a member of their own species, of the opposite sex, and in breeding condition. Courtship is one of the mechanisms that maintains reproductive isolation, and AQA examines it directly.

The concept has four limitations. It cannot be applied to organisms that do not reproduce sexually, which excludes bacteria and archaea and many protoctists and plants; prokaryote species are delimited instead by genome similarity, using thresholds that differ between groups and between methods rather than a single universal cut-off. It cannot be applied to fossils, which cannot be bred. It cannot resolve cases where populations form a chain around a barrier and neighbours interbreed while the two ends do not. And a substantial number of species hybridise successfully in the wild: polar and brown bears do, as do many flowering plants, in which new species have arisen from hybrids doubling their chromosomes.

The concept remains the standard definition. A question asking for a limitation is asking for one of the four situations above, and which populations count as one species can depend on the operational concept applied.

Phenetic and phylogenetic classification

A classification can be built by grouping organisms by how much they resemble one another, counting the features they share and placing the most similar together. That is a phenetic classification, and it is what Linnaeus was doing. It requires no theory of ancestry, and it has one systematic weakness.

A dolphin is streamlined, has a dorsal fin and flippers, and lives its whole life in the sea, exactly like a shark. A bat has wings and flies, exactly like a swift. A cactus and a euphorbia are both fat, spiny, green-stemmed desert plants that look almost identical, and they belong to families that are not closely related. In each case the resemblance is convergent evolution: unrelated lineages under the same selection pressure arriving at similar structures. Grouping by resemblance places the dolphin with the shark.

Phenetic classification

Grouping organisms by observable similarity, without regard to how they are related.

Phylogenetic classification

Grouping organisms so that each group contains a common ancestor and all of its descendants.

Homologous structures

Structures with the same underlying plan, inherited from a common ancestor, whatever they are now used for.

Analogous structures

Structures with the same function and different origins, produced by convergent evolution.

The resolution is to compare the underlying structure rather than the overall resemblance. A dolphin's flipper contains one upper arm bone, two forearm bones, a set of wrist bones and five digits: the pentadactyl limb, the same plan as a bat's wing, a horse's leg and your hand. A shark's fin has nothing of the kind. The flipper and the wing are homologous; the flipper and the shark fin are analogous. Homology is evidence of common ancestry; analogy is evidence of similar selection pressures.

A phylogenetic classification uses homology and excludes analogy. Each group it recognises is a complete section of the evolutionary tree: a common ancestor together with every descendant of that ancestor, and nothing else. On that criterion 'reptiles' is not a valid group. The ancestor of crocodiles and lizards also gave rise to birds, so a group containing the reptiles but excluding the birds omits part of the ancestor's descendants.

The three domains

For most of the twentieth century the top-level division was between prokaryotes and eukaryotes: cells without a nucleus, and cells with one. The five-kingdom scheme that grew out of Whittaker's 1969 proposal, with Prokaryotae (his Monera), Protoctista, Fungi, Plantae and Animalia, placed every organism without a nucleus in a single kingdom, on the evidence then available from microscopy.

Comparisons of small-subunit ribosomal RNA helped establish Bacteria, Archaea and Eukarya as three distinct domains. Domains and kingdoms are both taxonomic groupings informed by evolutionary relationships; the traditional kingdom Prokaryotae spans organisms now placed in two domains.

From the 1970s Carl Woese compared the base sequence of the RNA in the small subunit of the ribosome, 16S rRNA in prokaryotes and 18S in eukaryotes, across a wide range of organisms. The comparison separated the prokaryotes into two groups whose rRNA sequences differed substantially from each other. In 1990 Woese, Kandler and Wheelis proposed a rank above kingdom, the domain, and three of them: Bacteria, Archaea and Eukarya.

Describe the drawing

A rooted branching tree with three tips. The root divides first into the bacterial branch and second into a node, marked in amber, from which Archaea and Eukarya branch as a pair. Beside each tip are two lines of cell features: peptidoglycan walls and small ribosomes for Bacteria, ether-linked membrane lipids and histone-like proteins for Archaea, a nucleus and large ribosomes for Eukarya.

Ribosomal RNA was chosen for four reasons. Every cellular organism sequenced has ribosomes, so the same molecule can be compared across all cellular life. Its function, holding the ribosome together and positioning the tRNAs, is the same everywhere, so equivalent positions can be lined up against each other. Most of its sequence changes very slowly, because almost any change breaks a working ribosome, so it still carries a readable signal across billions of years. And it is long enough that the similarities are not coincidence.

Cell biology supports the split. Archaea are not a subgroup of bacteria; on several molecular features they resemble eukaryotes more closely than they resemble Bacteria.

Exam-board note. AQA names domain as the top rank of its hierarchy but states that recall of the three-domain and five-kingdom systems will not be required. OCR Biology A lists the five kingdoms and the three-domain revision, and can require a comparison of them. Cambridge International 9700 lists three domains with the eukaryotic kingdoms beneath them. In each case a classification is a hypothesis about ancestry, and new evidence can revise it.

Woese's proposal also shows how a new classification comes to be accepted, which both Pearson Edexcel specifications examine. His sequence comparisons were published in scientific journals after peer review, in which other specialists check the methods and the reasoning before a paper appears. Publication let other laboratories test the claim, and the three domains were argued over at scientific conferences, where some prominent biologists rejected them. The model became the accepted view because independent groups, comparing other genes and proteins, kept finding the same three-way split.

Viruses sit outside the whole arrangement. They are not cells, they have no ribosomes and therefore no ribosomal RNA to compare, and they carry out no metabolism of their own, so the molecule that built the tree cannot place them on it. They are classified by their own scheme, based on the kind of nucleic acid they carry and how they replicate it.

Molecular evidence of relatedness

Anatomical comparison has limits: prokaryotes offer few distinguishing structures, and whether a structure is homologous can be disputed. Molecules provide sequences of discrete units that can be counted, so relatedness can be quantified.

DNA base sequence. The direct comparison. Align the same gene from two species and count the positions where the bases differ. Fewer differences means less time has passed since the two lineages separated, because mutations accumulate steadily once two populations stop exchanging genes. Whole-genome comparison is now routine and has rearranged several parts of the tree.

DNA hybridisation. The older technique, still examined. Heat DNA from two species so the strands separate, mix them, and let hybrid double strands form. The more similar the sequences, the more hydrogen bonds hold the hybrid together, and the higher the temperature needed to separate it again.

Amino acid sequence. Compare the same protein, of which cytochrome c and the haemoglobin chains are the standard examples, and count the positions that differ. This is a slightly blunter tool than DNA comparison, because the genetic code is degenerate: a base can change without changing the amino acid, so some differences are invisible at the protein level.

Gel electrophoresis. The same gene, or the same stretch of DNA, from several species is cut with the same restriction enzyme and the fragments are separated by length on a gel, as in DNA profiling. A difference in base sequence can remove a restriction site or create one, so each species gives its own pattern of bands. Species whose patterns share more bands have more similar sequences and are more closely related, and a sample whose pattern matches none of the known species may belong to a separate one.

Immunological comparison. Inject a rabbit with human blood serum. The rabbit makes antibodies against the human proteins, and the serum containing those antibodies is collected. Now add that antiserum to serum from another species: the antibodies bind wherever the other species' proteins are similar enough to human ones, and the amount of precipitate formed measures how similar they are. More precipitate means a closer relative. The numbers below are idealised to show the pattern rather than taken from a particular study.

Molecular clocks. If substitutions accumulate at a roughly steady rate in a given molecule, then the number of differences between two species is a measure of the time since they diverged. Calibrate the rate against a split whose date is known from the fossil record, and the same molecule will date splits that left no useful fossils.

Interpreting a cladogram

A cladogram is a diagram of branching order. Each line is a lineage, each fork is a point where one ancestral population split into two that stopped interbreeding, and each tip is a taxon. A clade is any fork together with everything above it: an ancestor and all of its descendants.

Describe the drawing

A cladogram of five animals (lamprey, salmon, frog, lizard and mouse) built up in five steps. It begins as a single node with five branches leaving it, because no character has been used yet. Adding jaws splits the lamprey off first. Adding four limbs splits the salmon off next. Adding the amniotic egg splits the frog off and leaves lizard and mouse as a pair, which resolves the tree completely. The final step marks each character with an amber dot on the branch where it appears and draws a dashed line through all five tips to show that every one of them is living now, so no tip descends from another.

The tree is built from shared derived characters: features that are new in a group and inherited from that group's common ancestor. Jaws are a shared derived character of everything except the lamprey in that animation; four limbs are a shared derived character of the tetrapods; the amniotic egg, with its membranes that let an egg be laid on dry land, is shared by lizard and mouse. Analogous characters, such as the streamlining of a dolphin and a shark, are excluded.

A cladogram asserts three things. It asserts the order of branching: which lineages separated before which. It asserts common ancestry at every fork. It asserts a set of nested groups.

It does not assert the following. It does not say how long each branch is in years unless the diagram is explicitly drawn to a time scale. It does not say how much change happened along a branch. A lineage may have changed enormously or hardly at all. It does not say that any tip is descended from any other tip; all five animals in that animation are alive now, and none of them is the ancestor of the others. And it carries no direction of improvement. The two branches at any fork can be exchanged without changing what the tree asserts, so the order of the tips along the bottom of the diagram carries no information. One further limitation: the diagram is strictly branching, so it cannot record hybridisation or, in prokaryotes, horizontal gene transfer, both of which reconnect lineages the tree shows as separate.

A cladogram does not rank living species as more or less evolved. Every extant species has a continuous line of ancestors extending back through the same elapsed time. A modern fish is not a human ancestor; humans and modern fish share an ancestral population further back in time.