Phylogenetic tree

A branching diagram representing inferred evolutionary relationships among organisms, genes, or other biological entities. Its branching pattern summarizes hypotheses about shared ancestry, not necessarily the passage of time or amount of change.

Cladistics: A method of classifying organisms by shared derived traits and their inferred common ancestry. It groups taxa into clades, the lineage units represented by branches.
Clade: An ancestor and all of its descendants in an evolutionary tree. A clade is the group of lineages enclosed by a single branch point.
Molecular phylogenetics: The reconstruction of evolutionary relationships from DNA, RNA, or protein sequences. It uses sequence differences to infer trees of genes or organisms.
Cladogram: A branching diagram that shows relative branching order without encoding amounts of evolutionary change or time. A cladogram shows topology alone, unlike trees whose branch lengths carry meaning.
Gene tree–species tree reconciliation: The comparison of gene histories with species histories to explain their differences. It addresses why a gene's branching pattern may not match the species tree.
Maximum parsimony: A method that favors the evolutionary tree requiring the fewest character-state changes. It selects a tree by minimizing inferred evolutionary changes.
Most recent common ancestor: The latest ancestral population shared by two or more lineages. Each internal node represents a hypothesized common ancestor of descendant lineages.
Comparative genomics: The comparison of genome structure and sequence across organisms to study biology and evolution. Genome comparisons use evolutionary trees to interpret shared and distinct features.
Phylogram: A phylogenetic tree whose branch lengths represent estimated amounts of evolutionary change. Its branch lengths quantify change rather than merely showing branching order.
Incomplete lineage sorting: The persistence and sorting of ancestral genetic variants across successive speciation events. It can produce gene trees that disagree with the actual branching history of species.

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