Does choice in model selection affect maximum likelihood analysis?
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Summary
This study uses 250 phylogenetic data sets obtained from TreeBASE to examine the effects that choice in model selection has on ML estimation of phylogeny, with an emphasis on optimal topology, bootstrap support, and hypothesis testing and suggests that although choice inmodel selection has a strong impact on optimal treeTopology, it rarely affects evolutionary inferences drawn from the data.
- Type
- article
- Published
- 2008-02-01
- Cited by
- 142
- References
- 49
- Access
- Open access
- OpenAlex
- https://openalex.org/W2116210362
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:9705407
Keywords
Akaike information criterion, Model selection, Bayesian information criterion, Statistics, Selection (genetic algorithm)
References
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- Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation.
- Extensive mtDNA variation within the yellow-pine chipmunk, Tamias amoenus (Rodentia: Sciuridae), and phylogeographic inferences for northwest North America.
- Comparison of phylogenetic trees
- A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
- MODELTEST: testing the model of DNA substitution
- Different models, different trees: the geographic origin of PTLV-I.
- Model use in phylogenetics: nine key questions.
- Comparative performance of Bayesian and AIC-based measures of phylogenetic model uncertainty.
- Should phylogenetic models be trying to "fit an elephant"?
- Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests.
- Evolution of the Mitochondrial Cytochrome Oxidase II Gene in Collembola
- Accounting for uncertainty in the tree topology has little effect on the decision-theoretic approach to model selection in phylogeny estimation.
- Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference
Cited by
- Sources of error inherent in species-tree estimation: impact of mutational and coalescent effects on accuracy and implications for choosing among different methods.
- Phylogenetic Bootstrapping under Resource Constraints: Higher Model Accuracy or more Replicates?
- Understanding How Stochasticity Impacts Reconstructions of Recent Species Divergent History.
- Phylogénie, éléments transposables et évolution de la taille des génomes chez les lupins
- Phylogenetic reconstruction methods: an overview.
- Identification of ornamental fishes for biosecurity
- Flexible components of functional responses.
- Barcoding's next top model: an evaluation of nucleotide substitution models for specimen identification
- Análise de espécies crípticas do complexo Anastrepha fraterculus (Díptera: Tephritidae) no Brasil através de sequências do gene mitocondrial cytochrome oxidase I
- Theoretical And Practical Utility Of Gene Sequences in Phylogenetic and Phylogeographic Analysis
- Kakusan4 and Aminosan: two programs for comparing nonpartitioned, proportional and separate models for combined molecular phylogenetic analyses of multilocus sequence data
- Empar: EM-based algorithm for parameter estimation of Markov models on trees
- Phylogenetics and phylogeography of a long-legged harvestman (Arachnida : Opiliones) in the Brazilian Atlantic Rain Forest reveals poor dispersal, low diversity and extensive mitochondrial introgression
- Diversification and Species Boundaries of Rhinebothrium (Cestoda; Rhinebothriidea) in South American Freshwater Stingrays (Batoidea; Potamotrygonidae)
- Information-theoretic approaches to statistical analysis in behavioural ecology: an introduction
- Molecular Phylogeny and Biogeography of Percocypris (Cyprinidae, Teleostei)
- Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets
- An Optimized Reconfigurable System for Computing the Phylogenetic Likelihood Function on DNA Data
- Moisture variables, and not temperature, are responsible for climate filtering and genetic bottlenecks in the South African endemic terrestrial mollusc Prestonella (Orthalicoidea)
- The effects of partitioning on phylogenetic inference.
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