A3.2 Classification and cladistics [HL only]

Classification organizes organisms into named groups so observations, communication and evolutionary relationships can be compared consistently.

A useful classification reduces ambiguity in common names and links new evidence to existing groups. The best system reflects both observable traits and shared ancestry rather than relying on one convenient feature.

A classification should help with:

• identification
• communication
• prediction of traits
• testing evolutionary hypotheses

Grouping organisms by homologous structures can predict that newly found relatives share developmental features, even before their genomes are sequenced.

Classification is a model for organizing evidence, not a claim that every boundary is permanent.

The traditional taxonomic hierarchy places organisms in kingdom, phylum, class, order, family, genus and species, but its fixed ranks do not always match evolutionary branching.

Ranks impose discrete levels on a continuous history of divergence. Convergent evolution can make distantly related organisms look similar, while unequal rates of change can make close relatives look different.

When auditing a traditional group, ask whether its defining traits are homologous or analogous, whether it includes a common ancestor and all descendants, and whether molecular evidence supports the same grouping.

Bird and bat wings perform the same function but evolved independently as wings. Grouping birds and bats together from wings alone would confuse convergence with recent common ancestry.

A named rank can remain convenient for communication without representing a clade; fixed rank labels are human conventions rather than measured amounts of divergence.

Evolutionary classification groups organisms by common ancestry and shared derived characteristics, making the branching history explicit.

A shared derived character appears in a common ancestor and is inherited by its descendants. Molecular sequences, fossils and morphology can be combined to test whether a proposed group is monophyletic.

Prefer evidence that is:

• homologous rather than analogous
• derived rather than ancestral
• shared by the proposed clade
• supported by independent data

If two species share a novel DNA insertion absent from their relatives, that insertion can support a recent common ancestor.

Similarity alone is not enough; the character must be inherited from the relevant ancestor rather than evolved independently.

A clade is a group consisting of a common ancestor and all of its descendants.

Clade membership is supported by shared characteristics inherited from the common ancestor. Base sequences of genes and amino-acid sequences of proteins provide especially objective comparisons; homologous morphology can provide additional evidence.

To test a proposed clade: locate one ancestral node, include every branch descending from it, and identify shared derived evidence. Excluding a descendant makes the group paraphyletic; combining separate lineages by superficial similarity makes it polyphyletic.

If several taxa share a derived DNA sequence change absent from the outgroup, that change supports their placement in one clade when the simplest tree assigns it to their common ancestor.

A group of organisms with similar habitats or lifestyles may be an ecological category without being a clade.

A molecular clock estimates when clades diverged by relating differences in homologous DNA or amino-acid sequences to an independently calibrated rate of change.

After two lineages split, sequence differences can accumulate in both. A calibration from fossils or another dated event connects genetic distance to time, allowing an estimated divergence date.

The estimate is uncertain because mutation rates can differ with generation time, population size, selective pressure, gene and lineage. A suitable sequence, evolutionary model, calibration and uncertainty range must all be stated.

If two candidate clades show fewer differences in the same calibrated gene than another pair, the clock model supports a more recent divergence for the first pair, assuming comparable rates.

A molecular clock gives an estimate, not a direct timestamp. Genetic distance cannot be converted to time reliably without calibration and rate assumptions.

A sequence-based cladogram is a hypothesis that groups taxa according to shared differences in aligned DNA, RNA or amino-acid sequences.

Homologous sequences are aligned so each position can be compared. Candidate trees place the observed changes on branches, and parsimony selects the tree that explains the data with the smallest total number of sequence changes.

Procedure: align homologous sequences; record variable positions; use an outgroup where provided to infer ancestral states; propose alternative branching patterns; count the minimum changes required by each; select the most parsimonious supported tree.

If taxa B and C share two sequence states absent from A and the outgroup, a tree pairing B with C may require fewer independent changes than trees pairing either taxon with A.

Parsimony identifies the simplest explanation for the supplied data, not a guaranteed true history. Different genes or criteria can support a different hypothesis.

A cladogram represents relative evolutionary relationships: the root is the ancestral starting point, each node represents a hypothetical common ancestor, and terminal branches end at the taxa being compared.

Taxa whose branches meet at the most recent node are sister groups. An outgroup diverges outside the ingroup and can help identify which character states are ancestral.

Read a tree by tracing from each terminal branch back to the most recent shared node. Use node order to infer relative divergence, identify every descendant branch when naming a clade, and track labelled character changes along branches.

If B and C join at one node before their branch joins A, B and C are sister taxa and share a more recent common ancestor with each other than either shares with A.

Tip spacing and left-to-right order have no evolutionary meaning, and rotating branches around a node does not change the relationships. One modern species is not the ancestor of another tip.

Cladistics tests whether a traditional taxonomic group corresponds to evolutionary relationships by comparing its membership with a tree built from independent evidence.

Traditional classifications often emphasized morphology, but similar traits can evolve independently. Conserved gene sequences can reveal that a familiar family is not one clade, prompting species to be transferred between families.

In the figwort-family case, chloroplast sequence comparisons produced clades that conflicted with the traditional morphology-based Scrophulariaceae. The classification was revised so named families more closely matched common ancestry.

When several gene sequences consistently place a plant outside its traditional family, researchers can reclassify it rather than preserving a grouping based on convergent flower form.

Students need the logic of testing and revision, not memorized details of every transferred plant. A new tree remains a testable hypothesis that can change with better sampling or evidence.

The three-domain system classifies cellular life as Bacteria (also called Eubacteria), Archaea and Eukarya, chiefly from comparisons of ribosomal RNA base sequences.

rRNA is present in all cellular organisms and changes gradually enough to compare deep lineages. Sequence evidence showed that organisms once grouped together as prokaryotes contain two profoundly different lineages, Bacteria and Archaea.

The extra rank above kingdoms was proposed in 1977. Supporting distinctions include rRNA sequences and differences in information-processing machinery, membrane lipids, cell walls, histone associations and introns.

An organism can resemble a bacterium in shape and lack a nucleus, yet its rRNA sequence and membrane chemistry can place it in Archaea.

The absence of a nucleus distinguishes both Bacteria and Archaea from eukaryotic cells but cannot distinguish those two prokaryotic domains from each other.