Open AccessEstimating substitution rates from molecular data using the coalescent.
Author(s) -
Ron Lundstrom,
Simon Tavaré,
Ryk Ward
Publication year - 1992
Publication title -
proceedings of the national academy of sciences of the united states of america
Language(s) - English
Resource type - Journals
eISSN - 1091-6490
pISSN - 0027-8424
DOI - 10.1073/pnas.89.13.5961
Subject(s) - coalescent theory , substitution (logic) , most recent common ancestor , effective population size , population , nucleotide diversity , molecular evolution , divergence (linguistics) , biology , molecular clock , evolutionary biology , neutral theory of molecular evolution , population size , statistics , genetics , mathematics , phylogenetic tree , genetic variation , computer science , gene , demography , haplotype , linguistics , philosophy , sociology , genotype , programming language
A coalescent model is used to estimate the rate at which neutral substitutions occur in a DNA sequence, without the necessity for an independent estimate of divergence times. Given a random sample of molecular sequences from a finite population, the distribution of the time to a common ancestor can be obtained from the coalescent model. With this principle, summary statistics are developed that use the distribution of molecular diversity within the sample to estimate the relative magnitude of nucleotide substitution rates. If, in addition, the effective population size is known, absolute substitution rates can also be estimated. These techniques are illustrated by estimating the transition rates that underlie the evolution of the first 360 nucleotides of the mitochondrial control region in an Amerindian tribal population.