Gene Trees and Species Trees


A species tree is a phylogenetic tree that represents the evolutionary pathways of a group of species. A gene tree is a phylogenetic tree constructed from a single gene from each of the species under study.

Keywords: ancestral polymorphism; sequence splitting; population splitting

Figure 1.

Diagram showing that gene splitting (G) usually occurs earlier than population splitting (P) if the population is genetically polymorphic at time P. The evolutionary history of gene splitting resulting in the six alleles denoted af is shown in solid lines, and the population splitting is shown in broken lines. (From Nei .)

Figure 2.

Three possible relationships between a species tree (rectangles) and a gene tree (open circles). (a,b) The topologies of the species trees are identical to those of the gene trees. Note that in (a) the time of divergence between the genes is roughly equal to the time of divergence between the populations. In (b), on the other hand, the time of divergence between genes X and Y greatly predates the time of divergence between the respective populations. (c) The topology of the gene tree is different from that of the species tree. For neutral alleles, the probability of occurrence of each tree is given underneath the tree. t1 is the time at which the first speciation event occurred, and t2 is the time at which the second speciation event occurred. T=t2t1, and Ne is the effective population size. (From Nei .)

Figure 3.

Three possible gene trees for the three species of human, chimpanzee and gorilla. Orangutan is used as an outgroup for rooting the tree in tree reconstruction. Tree (a) is now commonly believed to be the true tree, that is, the species tree.



Chen FC and Li WH (2001) Genomic divergence between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. American Journal of Human Genetics 68: 444–456.

Nei M (1987) Molecular Evolutionary Genetics. New York, NY: Columbia University Press.

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Li, Wen‐Hsiung(Jul 2006) Gene Trees and Species Trees. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1038/npg.els.0005137]