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A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
Although reconstruction of the phylogeny of living birds has progressed tremendously in the last decade, the evolutionary history of Neoaves—a clade that encompasses nearly all living birdExpand
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When trees grow too long: investigating the causes of highly inaccurate bayesian branch-length estimates.
A surprising number of recent Bayesian phylogenetic analyses contain branch-length estimates that are several orders of magnitude longer than corresponding maximum-likelihood estimates. The levels ofExpand
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Anchored hybrid enrichment for massively high-throughput phylogenomics.
The field of phylogenetics is on the cusp of a major revolution, enabled by new methods of data collection that leverage both genomic resources and recent advances in DNA sequencing. PreviousExpand
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The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics.
As larger, more complex data sets are being used to infer phylogenies, accuracy of these phylogenies increasingly requires models of evolution that accommodate heterogeneity in the processes ofExpand
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The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference
Abstract Although an increasing number of phylogenetic data sets are incomplete, the effect of ambiguous data on phylogenetic accuracy is not well understood. We use 4-taxon simulations to study theExpand
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The metapopulation genetic algorithm: An efficient solution for the problem of large phylogeny estimation
Large phylogeny estimation is a combinatorial optimization problem that no future computer will ever be able to solve exactly in practical computing time. The difficulty of the problem is amplifiedExpand
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Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics.
In recent articles published in Molecular Phylogenetics and Evolution, Mark Springer and John Gatesy (S&G) present numerous criticisms of recent implementations and testing of the multispeciesExpand
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The importance of proper model assumption in bayesian phylogenetics.
We studied the importance of proper model assumption in the context of Bayesian phylogenetics by examining >5,000 Bayesian analyses and six nested models of nucleotide substitution. ModelExpand
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GEOLOGICAL AND CLIMATIC FORCES DRIVING SPECIATION IN THE CONTINENTALLY DISTRIBUTED TRILLING CHORUS FROGS (PSEUDACRIS)
Abstract Tertiary geological events and Quaternary climatic fluctuations have been proposed as important factors of speciation in the North American flora and fauna. Few studies, however, haveExpand
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Resolving Relationships among the Megadiverse Butterflies and Moths with a Novel Pipeline for Anchored Phylogenomics
Abstract. The advent of next‐generation sequencing technology has allowed for thecollection of large portions of the genome for phylogenetic analysis. Hybrid enrichment and transcriptomics are twoExpand
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