The most recent ancestor shared by the stated descendant lineages. In population history it is important to distinguish a shared ancestral population from the common ancestor of copies at a particular genetic locus.

Similarity of character states not explained simply by inheritance of that state from the relevant common ancestor. Independent origins and evolutionary reversals can make a single feature misleading.

A shared derived character supporting a particular branch of a phylogenetic tree. Its level depends on inferred character polarity; a trait shared ancestrally across a wider group need not diagnose a smaller clade.

In the cladistic sense, inclusion of an ancestor and all its descendants. Such a group is a clade.

Inclusion of an ancestor while excluding some descendants. Traditional reptiles with birds excluded provide an example; the status depends on the stated group definition.

Assembly of separate lineages without including their relevant connecting ancestry, often using independently acquired similar features. Selected tips alone do not always distinguish this from paraphyly; the ancestry included and the interpretation of characters matter.

The historical difficulty of placing turtles among reptiles, including conflict between a roofed temporal skull and evidence for diapsid ancestry. It exposes the difference between character similarity and inferred descent.

Correlation among species observations caused by shared evolutionary history. Comparative tests must distinguish replicated evolutionary changes from repeated sampling of the same ancestral trait.

Inference of evolutionary relationships from molecular data. Structural correspondence is most persuasive when evaluated alongside alignments, sequence profiles and taxonomic distributions.

Inference combining evidence types such as morphological characters and molecular sequences, with explicit assumptions about homology, missing data and evolution.

Phylogenomics uses genome-scale evidence to investigate evolutionary relationships and gene histories. Many sampled loci can improve resolution, but their histories need not be identical: incomplete lineage sorting, duplication and introgression can make a gene tree differ from a species tree.

Adding sequences therefore creates a modeling question as well as a larger dataset. Concatenating all loci assumes a shared history in a way that methods explicitly representing variation among gene trees need not. Strong support conditional on a model does not by itself validate that model's account of the evolutionary process.

Naming clades by explicit ancestry-based definitions. A definition fixes the rule connecting a name to ancestry; an inferred phylogenetic tree determines which organisms satisfy that rule.

A lineage outside the focal group used to inform rooting and character polarity. An extant outgroup is not an unchanged ancestor.

A branching diagram representing a hypothesis of relationships. Branch geometry need not encode elapsed time or amount of anatomical change.

A heritable feature represented by distinct states in a comparative analysis. State definitions, homology assumptions, uncertainty and correlations among characters affect the reconstruction.

A device that collects electrical current from photosynthetic organisms or their products. Electron transfer across cellular envelopes and to an electrode links biological reducing power with an external circuit; light absorption alone does not establish that current reaches the electrode.^[ref]

Non-photochemical quenching describes pathways that reduce chlorophyll fluorescence through routes other than photochemical charge separation. Rapid protective components can dissipate excitation as heat, but a fluorescence decrease alone does not uniquely identify the pathway.

The xanthophyll cycle reversibly changes antenna-associated xanthophyll composition with light conditions. Lumen-acidification-dependent de-epoxidation towards zeaxanthin can support photoprotective quenching in plants.

Photosynthetic control refers to regulation of electron flow, especially lumen-pH-dependent restriction at the cytochrome b6f complex. Slowing electron delivery can protect downstream acceptors from excessive reduction.

Cyclic electron flow around photosystem I returns photosystem-I-derived electrons to the intersystem electron-transport chain. It can support proton-gradient formation without net NADPH production, helping adjust ATP supply and photoprotection.