Model Selection in Phylogenetics

Sullivan, Jack; Joyce, Paul

doi:10.1146/annurev.ecolsys.36.102003.152633

Cited by 371 publications

(256 citation statements)

References 77 publications

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“…Briefly, the methods used in the subsequent analysis of the data are summarized. Model selection is important, and to perform well, it must strike a balance between biological realism and statistical tractability (47). To identify the model most appropriate for analyzing our data, 24 models were considered, ranging from simple (Jukes-Cantor) to complex (GTR + Γ + I; the general time-reversible model of sequence evolution with Γ-distributed rate variation across sites and an estimated proportion of invariable sites) (48).…”

Section: Methodsmentioning

confidence: 99%

Source identification in two criminal cases using phylogenetic analysis of HIV-1 DNA sequences

Scaduto

Brown

Haaland

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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Phylogenetic analysis has been widely used to test the a priori hypothesis of epidemiological clustering in suspected transmission chains of HIV-1. Among studies showing strong support for relatedness between HIV samples obtained from infected individuals, evidence for the direction of transmission between epidemiologically related pairs has been lacking. During transmission of HIV, a genetic bottleneck occurs, resulting in the paraphyly of source viruses with respect to those of the recipient. This paraphyly establishes the direction of transmission, from which the source can then be inferred. Here, we present methods and results from two criminal cases, State of Washington v Anthony Eugene Whitfield , case number 04-1-0617-5 (Superior Court of the State of Washington, Thurston County, 2004) and State of Texas v Philippe Padieu , case numbers 219-82276-07, 219-82277-07, 219-82278-07, 219-82279-07, 219-82280-07, and 219-82705-07 (219th Judicial District Court, Collin County, TX, 2009), which provided evidence that direction can be established from blinded case samples. The observed paraphyly from each case study led to the identification of an inferred source (i.e., index case), whose identity was revealed at trial to be that of the defendant.

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Section: Methodsmentioning

confidence: 99%

Source identification in two criminal cases using phylogenetic analysis of HIV-1 DNA sequences

Scaduto

Brown

Haaland

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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“…Selection of a suitable partitioning strategy and suitable models for the various partitions used the Bayesian Information Criterion (BIC) as a selection criterion (e.g., Sullivan and Joyce, 2005). The guide tree used during the entire procedure was obtained by maximum likelihood (ML) analysis of the concatenated data with a JC69 model with rate variation among sites following a discrete gamma distribution with 8 categories (JC69 + C 8 ) inferred with PhyML (Guindon and Gascuel, 2003).…”

Section: Partitioning and Model Selectionmentioning

confidence: 99%

A multi-locus time-calibrated phylogeny of the siphonous green algae

Verbruggen

Ashworth

LoDuca

et al. 2009

Molecular Phylogenetics and Evolution

150

160

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“…Both in turn are highly dependent on the evolutionary models used in the phylogenetic analyses, especially when studying a reduced dataset of highly divergent sequences (Sullivan and Joyce, 2005;Sheffield et al, 2009). In our case, most of the nodes were stable and highly supported, regardless of the data source (nucleotide or AA), phylogenetic reconstruction method (Bayesian probabilities or ML fast algorithms), partition scheme (by gene or by codon position) or evolutionary model used (GTR+I+G, CAT or CAT-BP).…”

Section: Phylogenetic Reconstruction Of Coleopteran Subordersmentioning

confidence: 99%

Nucleotide substitution rates for the full set of mitochondrial protein-coding genes in Coleoptera

Pons

Ribera

Bertranpetit

et al. 2010

Molecular Phylogenetics and Evolution

148

120

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The ages of cladogenetic events in Coleoptera are frequently estimated with mitochondrial protein coding genes (MPCGs) and the -standard‖ mitochondrial nucleotide substitution rate for arthropods. This rate has been used for different mitochondrial gene combinations and time scales despite it was estimated on short mitochondrial sequences from few comparisons of close related species. These shortcomings may cause greater impact at deep phylogenetic levels as errors in rates and ages increase with branch lengths. We use the full set of MPCGs of 15 species of beetles (two of them newly sequenced here) to estimate the nucleotide evolutionary rates in a reconstructed phylogeny among suborders, paying special attention to the effect of data partitioning and model choices on these estimations. The optimal strategy for nucleotide data, as measured with Bayes factors, was partitioning by codon position. This retrieved Adephaga as a sister group to Myxophaga with strong support (expected likelihood weights test 0.94-1) and both sisters to Polyphaga, in contradiction with the most currently accepted views. The hypothesis of Archostermata being sister to the remaining Coleoptera, which is in agreement with morphology, was increasingly supported when third codon sites were recoded or completely removed, sequences were analyzed as AA, and heterogeneous models were implemented but the support levels remained low. Nucleotide substitution rates were strongly affected by the choice of data partitioning (codon position versus individual genes), with up to sixfold levels of variation, whereas differences in the molecular clock algorithm produced changes of only about 20%. The global mitochondrial protein coding rate using codon partitioning and an estimated age of 250 million years (MY) for the origin of the Coleoptera was 1.34% per branch per MY, which closely matches the ‗standard' clock of 1.15% per MY. The estimation of the rates on alternative topologies gave similar results. Using local molecular clocks, the evolutionary rate in the Polyphaga and Archostemata was estimated to be nearly twice as fast as in the Adephaga and Myxophaga (1.03% versus 0.53% per MY). Rates across individual genes varied from 0.55% to 8.61% per MY. Our results suggest that cox1 might not be an optimal gene for implementing molecular clocks in deep phylogenies for beetles because it shows relatively slow rates at first and second codon positions but very fast rates at third ones. In contrast, nad5, nad4 and nad2 perform better, as they exhibit more homogeneous rates among codon positions.

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Model Selection in Phylogenetics

Cited by 371 publications

References 77 publications

Source identification in two criminal cases using phylogenetic analysis of HIV-1 DNA sequences

Source identification in two criminal cases using phylogenetic analysis of HIV-1 DNA sequences

A multi-locus time-calibrated phylogeny of the siphonous green algae

Nucleotide substitution rates for the full set of mitochondrial protein-coding genes in Coleoptera

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