Selecting the best-fit model of nucleotide substitution.

By David Posada, Keith A. Crandall. Systematic Biology, 2001

969 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/2723f054b319bf5a42f5f842b27d4883edeb654d

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Citations in the corpus

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules (2016, background): “Different models can result in different estimations of the phylogeny and evolutionary rate (42,43).”
Phylogeny and evolution of Staphyliniformia and Scarabaeiformia: forest litter as a stepping stone for diversification of nonphytophagous beetles (2015, methodology): “0.1 (Lanfear et al., 2012) to select a partitioning scheme and best-fitting substitution model for each partition using the Bayesian information criterion (Posada & Crandall, 2001).”
Comparative molecular and morphological phylogenetic analyses of taxa in the Chaetocerotaceae (Bacillariophyta) (2010, methodology): “Our treatment also differs from that in Rines & Theriot (2003) in a priori assumptions about what constitutes homologous structures.”
Molecular systematics of armadillos (Xenarthra, Dasypodidae): contribution of maximum likelihood and Bayesian analyses of mitochondrial and nuclear genes. (2003, neutral): “…were appropriate to best describe the underlying evolutionary process of these eight datasets: TrN+Γ for ADRA2B, TrN+I+Γ for ND1, TVM+Γ for BRCA1 and NUC, GTR+Γ for 12S rRNA, and the GTR+I+Γ model for VWF, MITO and COMB (see Posada and Crandall, 2001 for a detailed description of these models).”
Amphi-Atlantic cold-seep Bathymodiolus species complexes across the equatorial belt (2007, methodology): “Substitution models used in phylogenies were selected according to Modeltest 3.7 ( Posada and Crandall, 2001 ) with the Bayesian Information Criterion (BIC) at a level of significance a of 0.01.”
Ecological diversification and phylogeny of emydid turtles (2003, result): “The starting model and parameter-addition hierarchy used by Modeltest corresponds to hLRT 1 of Posada & Crandall, 2001), which was shown in their simulation study to have accuracy similar or superior to that of the other model selection procedures evaluated.”
Probabilistic historical biogeography: new models for founder-event speciation, imperfect detection, and fossils allow improved accuracy and model-testing (2013, positive): “… the transition-‐ transversion rate ratio; eventually an entire family of models was produced, and model selection procedures are now used routinely pick the best substitution models and to improve phylogenetic inference as a result (Posada & Crandall 2001).”
Estimating Divergence Times from Molecular Data on Phylogenetic and Population Genetic Timescales (2002, methodology): “Although the use of LRTs is well represented in the phylogenetic literature (Posada & Crandall 2001), various other approaches to model selection are also available.”
Phylogenetic analysis of morphology in Prunus reveals extensive homoplasy (2006, methodology): “To select the model of evolution that best explains the data we used the Akaike information criterion (Akaike 1974) as implemented in the program Modeltest 3.6 ( Posada and Crandall 1998, 2001 ) Table 1. Continued”
Using Phylogenetic, Functional and Trait Diversity to Understand Patterns of Plant Community Productivity (2009, methodology): “We then selected best-fit maximum likelihood models of nucleotide substitution for each gene using the Akaike Information Criterion, as implemented in Modeltest [34,35].”
Evolutionary history and the effect of biodiversity on plant productivity (2008, methodology): “We then selected best-fit models of nucleotide substitution for each gene by using the Akaike Information Criterion, as implemented in Modeltest and MrModeltest (45, 46).”
Using information theory as a substitute for stepwise regression in ecology and behavior (2010, neutral): “Second, we can compare the best model to other nested models in the candidate set by means of likelihood ratio tests, which involve classical NHT and critical P values (Posada and Crandall 2001; but see Burnham and Anderson 2002).”
Molecular evidence that phoronids are a subtaxon of brachiopods (Brachiopoda: Phoronata) and that genetic divergence of metazoan phyla began long before the early Cambrian (2005, methodology): “06 (Posada and Crandall 1998; Posada 2001; Posada and Buckley 2004); subsequent ML heuristic analyses were performed with a neighbor-joining starting tree, followed by TBR branch exchange.”
Using MODELTEST and PAUP* to Select a Model of Nucleotide Substitution (2003, methodology): “model of evolution or another may change the outcome of the phylogenetic analysis (Leitner et al., 1997; Sullivan and Swofford, 1997; Cun-ningham et al., 1998; Kelsey et al., 1999; Posada and Crandall, 2001b).”
ALEXANDRIUM TAMUTUM SP. NOV. (DINOPHYCEAE): A NEW NONTOXIC SPECIES IN THE GENUS ALEXANDRIUM 1 (2004, methodology): “ML phylogenies were reconstructed with PAUP* 4.0b8 (Swofford 1998) constrained with the following Modeltest parameters. hLRTs gave a general time reversible (GTR) model, allowing for invariant sites and a gamma distribution (GTR þ I þ G) as the model that fit best the data set.”