Papers in this group
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We develop statistical methods for phylogenetic logistic regression in which the dependent variable is binary (0 or 1) and values are nonindependent among species, with phylogenetically related species tending to have the same value of the dependent…
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The threshold model developed by Sewall Wright in 1934 can be used to model the evolution of two-state discrete characters along a phylogeny. The model assumes that there is a quantitative character, called liability, that is unobserved and that…
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The use of molecular data for species delimitation in Anthozoa is still a very delicate issue. This is probably due to the low genetic variation found among the molecular markers (primarily mitochondrial) commonly used for Anthozoa. Ceriantharia is…
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The aim of this paper is to enable those who have never reconstructed a phylogeny to do so from scratch. The paper does not attempt to be a comprehensive theoretical guide, but describes one rigorous way of obtaining phylogenetic trees. Those who…
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Studies of character evolution often assume that a phylogeny's shape is determined independently of the characters, which then evolve as mere passengers along the tree's branches. However, if the characters help shape the tree, but this is not…
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In the absence of recent admixture between species, bipartitions of individuals in gene trees that are shared across loci can potentially be used to infer the presence of two or more species. This approach to species delimitation via molecular…
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The availability of genome-wide data provides unprecedented opportunities for resolving difficult phylogenetic relationships and for studying population genetic processes of mutation, selection, and recombination on a genomic scale. The use of…
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The evolutionary success of flowering plants has been attributed to key innovations that originated at the base of that clade. Maximum likelihood methods were used to assess whether branching rate increases were correlated with the origin of these…
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With the increasing interest in recognizing the discordance between gene genealogies, various gene tree/species tree reconciliation methods have been developed. We present here the first attempt to assess and compare two such Bayesian methods,…
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Several techniques, such as concatenation and consensus methods, are available for combining data from multiple loci to produce a single statement of phylogenetic relationships. However, when multiple alleles are sampled from individual species, it…
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Until recently, it has been common practice for a phylogenetic analysis to use a single gene sequence from a single individual organism as a proxy for an entire species. With technological advances, it is now becoming more common to collect data…
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The field of phylogenetics is entering a new era in which trees of historical relationships between species are increasingly inferred from multilocus and genomic data. A major challenge for incorporating such large amounts of data into inference of…
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The marginal likelihood is commonly used for comparing different evolutionary models in Bayesian phylogenetics and is the central quantity used in computing Bayes Factors for comparing model fit. A popular method for estimating marginal likelihoods,…
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