genetree

Genetree, or gene tree, is the genealogical history of copies of a gene sampled from individuals or species. In a genetree, leaves represent sampled gene copies, internal nodes represent ancestral alleles, and the root corresponds to the most recent common ancestor of the locus. Gene trees reflect the lineage history of a particular gene rather than the history of species.

Gene trees are distinct from the species tree, which tracks species relationships. Because different evolutionary processes can affect a gene’s history, gene trees often differ from the species tree. Incomplete lineage sorting, where ancestral genetic variation is sorted differently across lineages, is a common source of discordance. Other factors include gene duplication and loss, horizontal gene transfer, and recombination within loci, which can create multiple, conflicting genealogies for the same genomic region.

Inference and analysis typically begin with sequence data from a locus. Researchers align sequences and apply phylogenetic methods—such as maximum likelihood or Bayesian inference—to estimate a tree for that locus. Recombination can complicate tree inference, so analyses may focus on nonrecombinant blocks or explicitly model recombination. In many studies, multiple loci are analyzed to compare gene trees and to infer broader evolutionary patterns, often within a multispecies coalescent framework that relates gene trees to the species tree.

Applications include dating divergence events, investigating population history and genetic diversity, and informing species delimitation. Gene trees serve as input for methods that infer species trees or demographic parameters and are central to understanding gene-level evolution and its relationship to species-level history.