Incomplete lineage sorting

Incomplete lineage sorting occurs when ancestral genetic variants persist across successive speciation events and are randomly inherited by descendant species. As a result, gene trees can differ from the species tree.

Coalescent theory: A mathematical framework that models how ancestral gene copies trace back to common ancestors in populations. It predicts the probability that ancestral variants persist through successive speciation events.
Phylogenetic discordance: Disagreement among evolutionary histories inferred from different genes, traits, or methods. Incomplete lineage sorting is one cause of disagreement among gene trees and species trees.
Introgression: The movement of genetic material between populations or species through hybridization and repeated backcrossing. Unlike lineage sorting, it transfers variants between lineages after they begin diverging.
Three-taxon problem: A basic phylogenetic scenario with three species used to study competing gene-tree histories. It shows how one species tree can produce two alternative discordant gene trees.
Gene tree: A branching diagram of the evolutionary relationships among copies of a gene. Its branching order can differ from the species tree when ancestral variants sort incompletely.
Phylogenetic network: A diagram that represents evolutionary relationships with reticulate connections as well as branching descent. Networks can help represent histories where lineage sorting and gene flow complicate a single tree.
Gene duplication: The production of an additional copy of a gene in a genome. Duplicated genes can yield misleading genealogies, but arise through copy-number change rather than ancestral sorting.
Great ape phylogeny: The evolutionary relationships among humans, chimpanzees, gorillas, and other living apes. Short ancestral intervals help explain conflicting genomic signals about early ape divergences.
Species tree: A branching diagram representing the evolutionary relationships among species. It provides the species-level history against which discordant gene trees are recognized.
Species delimitation: The process of identifying and defining distinct species from biological evidence. Shared ancestral variants can make recently diverged species appear genetically less distinct.

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