Coalescent theory

Coalescent theory is a mathematical framework for tracing sampled gene copies backward through time until they share common ancestors. It connects patterns of genetic variation to population history.

Genealogy: A branching account of relationships among entities through descent or ancestry. A coalescent genealogy records the ancestral relationships among sampled gene copies.
Bayesian skyline plot: A Bayesian method that estimates changes in effective population size through time from genetic sequence data. It uses coalescent intervals to infer past population-size changes.
Genetic drift: Random changes in allele frequencies caused by finite sampling of gene copies across generations. Drift creates the random ancestry that coalescent models describe backward in time.
Structured coalescent: A coalescent model in which lineages occupy subpopulations and migrate between them. Unlike the panmictic model, it represents migration among distinct populations.
Kingman coalescent: A stochastic process in which pairs of lineages merge backward in time at a constant rate. It is the standard coalescent model for neutral, diploid populations.
Phylogenetics: The study of evolutionary relationships among organisms, genes, or other biological entities. Coalescent models help infer gene trees within broader evolutionary histories.
Gene tree: A branching history of genetic copies that traces their descent from ancestral copies. Coalescent theory models how gene trees form within populations.
Multiple-merger coalescent: A family of coalescent processes that allows several ancestral lineages to merge in one event. It replaces pairwise-only mergers in populations with highly skewed reproductive success.
Effective population size: The size of an idealized population that would experience genetic drift at the same rate as a real population. It determines the rate at which ancestral lineages coalesce.
Molecular clock: A method that uses rates of molecular change to estimate evolutionary divergence times. Coalescent ancestry helps distinguish gene divergence from population separation.

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