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RESEARCH PRODUCT

Monte Carlo simulation in phylogenies: an application to test the constancy of evolutionary rates.

Joaquín DopazoJose Carlos Adell

subject

Least-squares methodBiometryMonte Carlo methodCytochrome c GroupBiologySet (abstract data type)Hybrid Monte Carlosymbols.namesakeGeneticsAnimalsHumansComputer SimulationMolecular BiologyEcology Evolution Behavior and SystematicsMonte Carlo simulationPhylogenyPhylogenetic treeModels GeneticMolecular clockEvolutionary ratesMarkov chain Monte CarloTree (data structure)Genetic TechniquesMutationsymbolsProbability distributionCytochrome-cAlgorithmMonte Carlo MethodMonte Carlo molecular modelingParametric bootstrap

description

Monte Carlo simulation has commonly been used in phylogenetic studies to test different tree-reconstruction methods, and consequently, its application for testing evolutionary models can be considered as a natural extension of this usage. Repetitive simulation of a given evolutionary process, under the restrictions imposed by the model to be tested, along a determinate tree topology allow the estimate of probability distributions for the desired parameters. Next, the phylogenetic tree can be reconstructed again without the constraints of the model, and the parameter of interest, derived from this tree, can be compared to the corresponding probability distribution derived from the restricted, simulated trees. As an example we have used Monte Carlo simulation to test the constancy of evolutionary rates in a set of cytochrome-c protein sequences. © 1994, Springer-Verlag New York Inc. All rights reserved.

yearjournalcountryeditionlanguage
1994-03-01Journal of molecular evolution
10.1007/bf00176093https://pubmed.ncbi.nlm.nih.gov/8006998