Evolutionary Similarity Among Genes

Suchard, Marc A.; Weiss, Robert E.; Sinsheimer, Janet S.; Dorman, Karin S.; Patel, Mona; McCabe, Edward R.B.

doi:10.1198/016214503000000558

Cited by 12 publications

(8 citation statements)

References 42 publications

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“…An alternative approach utilizing prior predictive simulation exists [46] and satisfies the above criticism. However, prior predictive simulation is undefined under improper prior distributions [47] and may not offer sufficient statistical power when vague priors are employed [48,49], such is the case The ideal behaviour for p B when applied to data simulated from the null distribution would be a uniform distribution (see main text for details). This plot shows that if the true demographic history is a constant population, then p B will be a good test of neutrality.…”

Section: Resultsmentioning

confidence: 99%

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Fully Bayesian tests of neutrality using genealogical summary statistics

Drummond

Suchard

2008

BMC Genet

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Background: Many data summary statistics have been developed to detect departures from neutral expectations of evolutionary models. However questions about the neutrality of the evolution of genetic loci within natural populations remain difficult to assess. One critical cause of this difficulty is that most methods for testing neutrality make simplifying assumptions simultaneously about the mutational model and the population size model. Consequentially, rejecting the null hypothesis of neutrality under these methods could result from violations of either or both assumptions, making interpretation troublesome.

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Section: Resultsmentioning

confidence: 99%

“…This process is called posterior predictive simulation [46][47][48]56]. Model selection and critique using posterior predictive simulation has had a successful history in phylogenetics [33,49,[57][58][59].…”

Section: Methodsmentioning

confidence: 99%

Fully Bayesian tests of neutrality using genealogical summary statistics

Drummond

Suchard

2008

BMC Genet

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“…That is, even if we find strong evidence for a model allowing separate topology parameters, this might not mean strong evidence for separate gene phylogenies, as long as vital components of the substitution model are still missing. For further discussions on Bayesian approaches to combined data issues see e.g., [25,26,33]. …”

Section: Discussionmentioning

confidence: 99%

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et al. 2004

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BackgroundThe typical antbirds (Thamnophilidae) form a monophyletic and diverse family of suboscine passerines that inhabit neotropical forests. However, the phylogenetic relationships within this assemblage are poorly understood. Herein, we present a hypothesis of the generic relationships of this group based on Bayesian inference analyses of two nuclear introns and the mitochondrial cytochrome b gene. The level of phylogenetic congruence between the individual genes has been investigated utilizing Bayes factors. We also explore how changes in the substitution models affected the observed incongruence between partitions of our data set.ResultsThe phylogenetic analysis supports both novel relationships, as well as traditional groupings. Among the more interesting novel relationship suggested is that the Terenura antwrens, the wing-banded antbird (Myrmornis torquata), the spot-winged antshrike (Pygiptila stellaris) and the russet antshrike (Thamnistes anabatinus) are sisters to all other typical antbirds. The remaining genera fall into two major clades. The first includes antshrikes, antvireos and the Herpsilochmus antwrens, while the second clade consists of most antwren genera, the Myrmeciza antbirds, the "professional" ant-following antbirds, and allied species. Our results also support previously suggested polyphyly of Myrmotherula antwrens and Myrmeciza antbirds. The tests of phylogenetic incongruence, using Bayes factors, clearly suggests that allowing the gene partitions to have separate topology parameters clearly increased the model likelihood. However, changing a component of the nucleotide substitution model had much higher impact on the model likelihood.ConclusionsThe phylogenetic results are in broad agreement with traditional classification of the typical antbirds, but some relationships are unexpected based on external morphology. In these cases their true affinities may have been obscured by convergent evolution and morphological adaptations to new habitats or food sources, and genera like Myrmeciza antbirds and the Myrmotherula antwrens obviously need taxonomic revisions. Although, Bayes factors seem promising for evaluating the relative contribution of components to an evolutionary model, the results suggests that even if strong evidence for a model allowing separate topology parameters is found, this might not mean strong evidence for separate gene phylogenies, as long as vital components of the substitution model are still missing.

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“…For additional details on predictive distributions the reader is referred to the literature (e.g. Nielsen and Huelsenbeck, 2001;Bollback, 2002;Suchard et al, 2003).…”

Section: Statistical Inference Using Sampled Mutational Pathsmentioning

confidence: 99%

Estimating the history of mutations on a phylogeny

Bollback¹,

Geeleher²,

Nielsen³

2007

Ancestral Sequence Reconstruction

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Evolution has left its signature on the molecules and morphology of living organisms. Ancestral reconstruction offers an excellent tool for understanding the process of evolution using comparative information. Methods for ancestral reconstruction have generally focused on reconstructing the ancestral states at the internal nodes of a phylogeny. Often, we are not interested in particular nodes of the phylogeny but the whole history of a character. This chapter focuses on a Bayesian method for estimating these histories, or mutational paths, on phylogenies. Mutational path methods differ most notably from other approaches in their ability to estimate not only the ancestral states at the internal nodes of a phylogeny, but also the order and timing of mutational changes across the phylogeny. The chapter provides a concise introduction to the statistical tools needed for sampling mutational paths on a phylogeny.

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Evolutionary Similarity Among Genes

Cited by 12 publications

References 42 publications

Fully Bayesian tests of neutrality using genealogical summary statistics

Fully Bayesian tests of neutrality using genealogical summary statistics

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Estimating the history of mutations on a phylogeny

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