Selecting the Best-Fit Model of Nucleotide Substitution

Posada, David; Crandall, Keith A.
August 2001
Systematic Biology;Aug2001, Vol. 50 Issue 4, p580
Academic Journal
Despite the relevant role of models of nucleotide substitution in phylogenetics, choosing among different models remains a problem. Several statistical methods for selecting the model that best fits the data at hand have been proposed, but their absolute and relative performance has not yet been characterized. In this study, we compare under various conditions the performance of different hierarchical and dynamic likelihood ratio tests, and of Akaike and Bayesian information methods, for selecting best-fit models of nucleotide substitution. We specifically examine the role of the topology used to estimate the likelihood of the different models and the importance of the order in which hypotheses are tested. We do this by simulating DNA sequences under a known model of nucleotide substitution and recording how often this true model is recovered by the different methods. Our results suggest that model selection is reasonably accurate and indicate that some likelihood ratio test methods perform overall better than the Akaike or Bayesian information criteria. The tree used to estimate the likelihood scores does not influence model selection unless it is a randomly chosen tree. The order in which hypotheses are tested, and the complexity of the initial model in the sequence of tests, influence model selection in some cases. Model fitting in phylogenetics has been suggested for many years, yet many authors still arbitrarily choose their models, often using the default models implemented in standard computer programs for phylogenetic estimation. We show here that a best-fit model can be readily identified. Consequently, given the relevance of models, model fitting should be routine in any phylogenetic analysis that uses models of evolution.


Related Articles

  • Intraspecific variability of ITS sequences in the parasitic plant Monotropa hypopitys L. from the European Russian populations. Filyushin, M.; Reshetnikova, N.; Kochieva, E.; Skryabin, K. // Russian Journal of Genetics;Nov2015, Vol. 51 Issue 11, p1149 

    Intraspecific sequence polymorphism in the ITS region of the nuclear ribosomal operon was examined in ten populations of the parasitic plant Monotropa hypopitys from Belgorod region, Vologda region, and Kaluga region of Russia. Based on an analysis of the identified nucleotide substitutions and...

  • The Rho GTPase Family Genes in Bivalvia Genomes: Sequence, Evolution and Expression Analysis. Li, Xue; Wang, Ruijia; Xun, Xiaogang; Jiao, Wenqian; Zhang, Mengran; Wang, Shuyue; Wang, Shi; Zhang, Lingling; Huang, Xiaoting; Hu, Xiaoli; Bao, Zhenmin // PLoS ONE;12/3/2015, Vol. 10 Issue 12, p1 

    Background: Rho GTPases are important members of the Ras superfamily, which represents the largest signaling protein family in eukaryotes, and function as key molecular switches in converting and amplifying external signals into cellular responses. Although numerous analyses of Rho family genes...

  • Molecular Cloning and Evolutionary Analysis of GJB6 in Mammals. Ru, Binghua; Han, Naijian; He, Guimei; Brayer, Kathryn; Zhang, Shuyi; Wang, Zhe // Biochemical Genetics;Apr2012, Vol. 50 Issue 3/4, p213 

    GJB6 plays a crucial role in hearing. In mammals, bats use ultrasonic echolocation for orientation and locating prey. To investigate the evolution of GJB6 in mammals, we cloned the full-length coding region of GJB6 from 16 species of bats and 4 other mammal species and compared them with...

  • Analysis of sequences of ITS1 internal transcribed spacer and 5.8S ribosome gene of Malus species. Savelyeva, E.; Boris, K.; Kochieva, E.; Kudryavtsev, A. // Russian Journal of Genetics;Nov2013, Vol. 49 Issue 11, p1175 

    The nucleotide sequence of the ITS1-5.8S ribosomal DNA spacer fragment was determined for 41 samples of the Malus species. The total length of compared sequences ranged from 389 to 392 bp. The nucleotide sequence of the 5.8S gene within the genus was highly conserved. The level of polymorphism...

  • The synthesis of phosphonic acids derived from homocysteine via transesterification reactions. Pícha, Jan; Buděšínský, Miloš; Fiedler, Pavel; Jiráček, Jiří // ARKIVOC: Online Journal of Organic Chemistry;2012, p80 

    An efficient methodology for the synthesis of S-substituted derivatives of phosphonohomocysteine has been developed. It starts from the corresponding thiols and is based on a synthetic sequence consisting of (i) the Kabachnik-Fields reaction, (ii) the transesterification of the...

  • Nucleotide substitutions in dengue virus serotypes from Asian and American countries: insights into intracodon recombination and purifying selection. Behura, Susanta K.; Severson, David W. // BMC Microbiology;2013, Vol. 13 Issue 1, p1 

    Background: Dengue virus (DENV) infection represents a significant public health problem in many subtropical and tropical countries. Although genetically closely related, the four serotypes of DENV differ in antigenicity for which cross protection among serotypes is limited. It is also believed...

  • The Embedding Problem for Markov Models of Nucleotide Substitution. Verbyla, Klara L.; Yap, Von Bing; Pahwa, Anuj; Shao, Yunli; Huttley, Gavin A. // PLoS ONE;Jul2013, Vol. 8 Issue 7, p1 

    Continuous-time Markov processes are often used to model the complex natural phenomenon of sequence evolution. To make the process of sequence evolution tractable, simplifying assumptions are often made about the sequence properties and the underlying process. The validity of one such...

  • Effect of particle-induced displacements on the critical temperature of YBa2Cu3O7-δ. Summers, G. P.; Burke, E. A.; Chrisey, D. B.; Nastasi, M.; Tesmer, J. R. // Applied Physics Letters;10/2/1989, Vol. 55 Issue 14, p1469 

    The particle-induced depression of the superconducting critical temperature Tc of YBa2Cu3O7-δ is shown to be directly proportional, over seven orders of magnitude, to the nonionizing energy deposited in the lattice by primary knock-on atoms displaced by incident electrons, protons, and heavy...

  • Substituted heteropolyacids. Yadav, G. D. // Chemical Business;Nov99, Vol. 13 Issue 11, p16 

    Reports that substitution of the protons in heteropoly acids of the Keggin structure type also improves their catalytic activity and stability. Production of high surface area microporous solids.


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics