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| Phylogeny | The evolutionary history of a species or group of related species. |
| Systematics | A scientific discipline focused on classifying organisms and determining their evolutionary relationships. |
| Taxonomy | A scientific discipline concerned with naming and classifying the diverse forms of life. |
| Binomial | The two-part, latinized format for naming a species, consisting of the genus and specific epithet; a binomen. |
| Family | In Linnaean classification, the taxonomic category above genus. |
| Orders | In Linnaean classification, the taxonomic category above the level of family. |
| Class | In Linnaean classification, the taxonomic category above the level of order. |
| Phylum | In Linnaean classification, the taxonomic category above class. |
| Kingdoms | A taxonomic category, the second broadest after domain. |
| Domain | (1) A taxonomic category above the kingdom level. The three domains are Archaea, Bacteria, and Eukarya. (2) A discrete structural and functional region of a protein. |
| Phylogenetic Tree | A branching diagram that represents a hypothesis about the evolutionary history of a group of organisms. |
| PhyloCode | Proposed system of classification of organisms based on evolutionary relationships: Only groups that include a common ancestor and all of its descendants are named. |
| Branch Points | The representation on a phylogenetic tree of the divergence of two or more taxa from a common ancestor. A branch point is usually shown as a dichotomy in which a branch representing the ancestral lineage splits (at the branch point) into two branches, one for each of the two descendant lineages. |
| Sister Taxa | Groups of organisms that share an immediate common ancestor and hence are each other’s closest relatives. |
| Rooted | Describing a phylogenetic tree that contains a branch point (often, the one farthest to the left) representing the most recent common ancestor of all taxa in the tree. |
| Basal Taxon | In a specified group of organisms, a taxon whose evolutionary lineage diverged early in the history of the group. |
| Polytomy | In a phylogenetic tree, a branch point from which more than two descendant taxa emerge. A polytomy indicates that the evolutionary relationships between the descendant taxa are not yet clear. |
| Analogy | Similarity between two species that is due to convergent evolution rather than to descent from a common ancestor with the same trait. |
| Homoplasies | A similar (analogous) structure or molecular sequence that has evolved independently in two species. |
| Molecular Systematics | A scientific discipline that uses nucleic acids or other molecules to infer evolutionary relationships between different species. |
| Cladistics | An approach to systematics in which organisms are placed into groups called clades based primarily on common descent. |
| Clades | A group of species that includes an ancestral species and all of its descendants. |
| Monophyletic | Pertaining to a group of taxa that consists of a common ancestor and all of its descendants. A monophyletic taxon is equivalent to a clade |
| Paraphyletic | Pertaining to a group of taxa that consists of a common ancestor and some, but not all, of its descendants. |
| Polyphyletic | Pertaining to a group of taxa derived from two or more different ancestors. |
| Shared Ancestral Character | A character, shared by members of a particular clade, that originated in an ancestor that is not a member of that clade. |
| Shared Derived Character | An evolutionary novelty that is unique to a particular clade. |
| Outgroup | A species or group of species from an evolutionary lineage that is known to have diverged before the lineage that contains the group of species being studied. An outgroup is selected so that its members are closely related to the group of species being studied, but not as closely related as any study-group members are to each other. |
| Ingroup | A species or group of species whose evolutionary relationships we seek to determine. |
| Maximum Parsimony | A principle that states that when considering multiple explanations for an observation, one should first investigate the simplest explanation that is consistent with the facts. |
| Maximum Likelihood | As applied to molecular systematics, a principle that states that when considering multiple phylogenetic hypotheses, one should take into account the hypothesis that reflects the most likely sequence of evolutionary events, given certain rules about how DNA changes over time. |
| Orthologous Genes | Homologous genes that are found in different species because of speciation. |
| Paralogous Genes | Homologous genes that are found in the same genome as a result of gene duplication. |
| Molecular Clock | A method for estimating the time required for a given amount of evolutionary change, based on the observation that some regions of genomes evolve at constant rates. |
| Neutral Theory | The hypothesis that much evolutionary change in genes and proteins has no effect on fitness and therefore is not influenced by natural selection. |
| Horizontal Gene Transfer | The transfer of genes from one genome to another through mechanisms such as transposable elements, plasmid exchange, viral activity, and perhaps fusions of different organisms. |
| Taxon | A named taxonomic unit at any given level of classification. |
