Distributions of gene tree branch lengths under coalescence

Author: Degnan, J.; Kubatko, L.

Date: 2008

Publisher: University of Canterbury. Mathematics and Statistics

Type: Conference Contributions - Other

Link to this item using this URL: http://hdl.handle.net/10092/3849


In Bayesian phylogenetic inference, commonly used prior distributions for branch lengths are the uniform, exponential, and gamma distributions. We derive the exact distributions of branch lengths of gene trees under a fixed species tree using the coalescent model. We find that the distributions of branch lengths depend on both the shape and branch lengths of the species tree, which depend on the population genetic parameters of ancestral population sizes and divergence times. Distributions of branch lengths are formed by mixtures depending on the ancestral populations in which coalescent events occur (coalescent histories). For some sets of moderately short branches, these mixtures can lead to distributions of branch lengths which are not well approximated by uniform, exponential, or gamma distributions, thus suggesting that a prior based on a mixture of distributions might be more appropriate for inferring branch lengths on some gene trees.

Subjects: Mathematical Sciences, Other Mathematical Sciences, Biological Mathematics, Biological Sciences, Genetics

Marsden Codes: 230000, 239900, 239901, 270000, 270200

Citation: ["Degnan, J., Kubatko, L. (2008) Distributions of gene tree branch lengths under coalescence. Barcelona, Spain: Annual Meeting of the Society for Molecular Biology and Evolution (SMBE 08), 5-8 Jun 2008."]

Copyright: http://library.canterbury.ac.nz/ir/rights.shtml