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22
Phylogenetic inference via sequential Monte Carlo. Systematic Biology
, 2012
"... Abstract.—Bayesian inference provides an appealing general framework for phylogenetic analysis, able to incorporate a wide variety of modeling assumptions and to provide a coherent treatment of uncertainty. Existing computational approaches to Bayesian inference based on Markov Chain Monte Carlo (MC ..."
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Abstract.—Bayesian inference provides an appealing general framework for phylogenetic analysis, able to incorporate a wide variety of modeling assumptions and to provide a coherent treatment of uncertainty. Existing computational approaches to Bayesian inference based on Markov Chain Monte Carlo (MCMC) have not, however, kept pace with the scale of the data analysis problems in phylogenetics, and this has hindered the adoption of Bayesian methods. In this paper we present an alternative to MCMC based on Sequential Monte Carlo (SMC). We develop an extension of classical SMC based on partially ordered sets, and show how to apply this framework—which we refer to as PosetSMC—to phylogenetic analysis. We provide a theoretical treatment of PosetSMC and also present experimental evaluation of PosetSMC on both synthetic and real data. The empirical results demonstrate that PosetSMC is a very promising alternative to MCMC, providing up to two orders of magnitude faster convergence. We discuss other factors favorable to the adoption of PosetSMC in phylogenetics, including its ability to estimate marginal likelihoods, its ready implementability on parallel and distributed computing platforms, and the possibility of combining with MCMC in hybrid MCMC-SMC schemes. Software for PosetSMC is available at
Bayesian Tests of Topology Hypotheses with an Example from Diving Beetles
, 2013
"... Abstract.—We review Bayesian approaches to model testing in general and to the assessment of topological hypotheses in particular.We show that the standardway of setting up Bayes factor tests of themonophyly of a group, or the placement of a sample sequence in a known reference tree, can be misleadi ..."
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Abstract.—We review Bayesian approaches to model testing in general and to the assessment of topological hypotheses in particular.We show that the standardway of setting up Bayes factor tests of themonophyly of a group, or the placement of a sample sequence in a known reference tree, can be misleading. The reason for this is related to the well-known dependency of Bayes factors on model-specific priors. Specifically, when testing tree hypotheses it is important that each hypothesis is associated with an appropriate tree space in the prior. This can be achieved by using appropriately constrained searches or by filtering trees in the posterior sample, but in a more elaborate way than typically implemented. If it is difficult to find the appropriate tree sets to be contrasted, then the posterior model odds may be more informative than the Bayes factor. We illustrate the recommended techniques using an empirical test case addressing the issue of whether two genera of diving beetles (Coleoptera: Dytiscidae), Suphrodytes and Hydroporus, should be synonymized. Our refined Bayes factor
Accelerated Rate of Molecular Evolution for Vittarioid Ferns is Strong and Not Driven by Selection
"... Abstract.—Molecular evolutionary rate heterogeneity—the violation of a molecular clock—is a prominent feature of many phylogenetic data sets. It has particular importance to systematists not only because of its biological implications, but also for its practical effects on our ability to infer and d ..."
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Abstract.—Molecular evolutionary rate heterogeneity—the violation of a molecular clock—is a prominent feature of many phylogenetic data sets. It has particular importance to systematists not only because of its biological implications, but also for its practical effects on our ability to infer and date evolutionary events. Here we show, using both maximum likelihood and Bayesian approaches, that a remarkably strong increase in substitution rate in the vittarioid ferns is consistent across the nuclear and plastid genomes. Contrary to some expectations, this rate increase is not due to selective forces acting at the protein level on our focal loci. The vittarioids bear no signature of the change in the relative strengths of selection and drift that one would expect if the rate increase was caused by altered post-mutation fixation rates. Instead, the substitution rate increase appears to stem from an elevated supply of mutations, perhaps limited to the vittarioid ancestral branch. This generalized rate increase is accompanied by extensive fine-scale heterogeneity in rates across loci, genomes, and taxa. Our analyses demonstrate the effectiveness and flexibility of trait-free investigations of rate heterogeneity within a model-
Revised systematics and higher classification of pierid butterflies (Lepidoptera: Pieridae) based on molecular data
, 2014
"... systematics and higher classification of pierid butterflies (Lepidoptera: Pieridae) based on molecular data. — Zoologica Scripta, 43, 641–650. The butterfly family Pieridae comprises approximately 1000 described species placed in 85 genera, but the higher classification has not yet been settled. We ..."
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systematics and higher classification of pierid butterflies (Lepidoptera: Pieridae) based on molecular data. — Zoologica Scripta, 43, 641–650. The butterfly family Pieridae comprises approximately 1000 described species placed in 85 genera, but the higher classification has not yet been settled. We used molecular data from eight gene regions (one mitochondrial and seven nuclear protein-coding genes) com-prising a total of ~6700 bp from 96 taxa to infer a well-supported phylogenetic hypothesis for the family. Based on this hypothesis, we revise the higher classification for all pierid genera. We resurrect the tribe Teracolini stat. rev. in the subfamily Pierinae to include the genera Teracolus, Pinacopteryx, Gideona, Ixias, Eronia, Colotis and most likely Calopieris. We transfer Hebomoia to the tribe Anthocharidini and assign the previously unplaced gen-era Belenois and Dixeia to the subtribe Aporiina. Three lineages near the base of Pierinae (Leptosia, Elodina and Nepheronia + Pareronia) remain unplaced. For each of these, we describe and delineate new tribes: Elodinini Braby tribus nova, Leptosiaini Braby tribus nova and Nepheroniini Braby tribus nova. The proposed higher classification is based on well-supported monophyletic groups and is likely to remain stable even with the addition
DOI:10.1093/sysbio/syu077 Phylogeny, Paleontology, and Primates: Do Incomplete Fossils Bias the Tree of Life?
"... Abstract.—Paleontological systematics relies heavily on morphological data that have undergone decay and fossilization. Here,weapplyaheuristicmeans toassesshowa fossil’s incompletenessdetracts frominferring itsphylogenetic relationships. We compiled a phylogenetic matrix for primates and simulated t ..."
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Abstract.—Paleontological systematics relies heavily on morphological data that have undergone decay and fossilization. Here,weapplyaheuristicmeans toassesshowa fossil’s incompletenessdetracts frominferring itsphylogenetic relationships. We compiled a phylogenetic matrix for primates and simulated the extinction of living species by deleting an extant taxon’s molecular data and keeping only those morphological characters present in actual fossils. The choice of characters present in a given living taxon (the subject) was defined by those present in a given fossil (the template). By measuring congruence between a well-corroborated phylogeny to those incorporating artificial fossils, and by comparing real vs. random character distributions and states, we tested the information content of paleontological datasets and determined if extinction of a living species leads to bias in phylogeny reconstruction. We found a positive correlation between fossil completeness and topological congruence.Real fossil templates sampled for 36ormoreof the 360 availablemorphological characters (including dental) performed significantly better than similarly complete templates with random states. Templates dominated by only one partition performed worse than templates with randomly sampled characters across partitions. The template based on the Eocene primate Darwinius masillae performs better than most other templates with a similar number of sampled
Phylogeny, Paleontology, and Primates: Do Incomplete Fossils Bias the Tree of Life?
"... Abstract.—Paleontological systematics relies heavily on morphological data that have undergone decay and fossilization. Here,weapplyaheuristicmeans toassesshowa fossil’s incompletenessdetracts frominferring itsphylogenetic relationships. We compiled a phylogenetic matrix for primates and simulated t ..."
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Abstract.—Paleontological systematics relies heavily on morphological data that have undergone decay and fossilization. Here,weapplyaheuristicmeans toassesshowa fossil’s incompletenessdetracts frominferring itsphylogenetic relationships. We compiled a phylogenetic matrix for primates and simulated the extinction of living species by deleting an extant taxon’s molecular data and keeping only those morphological characters present in actual fossils. The choice of characters present in a given living taxon (the subject) was defined by those present in a given fossil (the template). By measuring congruence between a well-corroborated phylogeny to those incorporating artificial fossils, and by comparing real vs. random character distributions and states, we tested the information content of paleontological datasets and determined if extinction of a living species leads to bias in phylogeny reconstruction. We found a positive correlation between fossil completeness and topological congruence.Real fossil templates sampled for 36ormoreof the 360 availablemorphological characters (including dental) performed significantly better than similarly complete templates with random states. Templates dominated by only one partition performed worse than templates with randomly sampled characters across partitions. The template based
Information Technology Research (ITR): Building the Tree of Life—A National Resource for Phyloinformatics and Computational Phylogenetics
"... (Information Technology Research) award from the National Science Foundation, and which was funded by no-cost extensions. The objective of the project is to design, develop, and implement a hardware and software infrastructure to facilitate work with phylogenies and, in particular, to support an att ..."
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(Information Technology Research) award from the National Science Foundation, and which was funded by no-cost extensions. The objective of the project is to design, develop, and implement a hardware and software infrastructure to facilitate work with phylogenies and, in particular, to support an attempt at assembling the Tree of Life, the phylogeny of all organisms on the planet. The original CIPRES team was made of five lead institutions and another eight affiliated ones, comprising a total of 33 faculty researchers. The team has since grown to 16 institutions and gained additional faculty conducting research in algorithm design, database design, software architecture design, and modelling and simulation, developing a central software library with well defined and fully documented APIs, setting up a high-performance central compute and database server, and preparing a wide range of outreach tools. Initially Bernard Moret was the director of the project, but Tandy Warnow became the director of the project upon Moret’s departure for EPFL in Switzerland. She works with the Executive Committee to set directions, evaluate progress, and assign responsibilities.
METHODOLOGY ARTICLE Open Access
"... framework to estimate diversification rates and their variation through time and space Daniele Silvestro 1,2,3* † , Jan Schnitzler 1,2 † and Georg Zizka 1,2,3 Background: Patterns of species diversity are the result of speciation and extinction processes, and molecular phylogenetic data can provide ..."
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framework to estimate diversification rates and their variation through time and space Daniele Silvestro 1,2,3* † , Jan Schnitzler 1,2 † and Georg Zizka 1,2,3 Background: Patterns of species diversity are the result of speciation and extinction processes, and molecular phylogenetic data can provide valuable information to derive their variability through time and across clades. Bayesian Markov chain Monte Carlo methods offer a promising framework to incorporate phylogenetic uncertainty when estimating rates of diversification. Results: We introduce a new approach to estimate diversification rates in a Bayesian framework over a distribution of trees under various constant and variable rate birth-death and pure-birth models, and test it on simulated phylogenies. Furthermore, speciation and extinction rates and their posterior credibility intervals can be estimated while accounting for non-random taxon sampling. The framework is particularly suitable for hypothesis testing using Bayes factors, as we demonstrate analyzing dated phylogenies of Chondrostoma (Cyprinidae) and Lupinus (Fabaceae). In addition, we develop a model that extends the rate estimation to a meta-analysis framework in which different data sets are combined in a single analysis to detect general temporal and spatial trends in
Average likelihood =
"... marginal likelihood estimation In ML model selection we judge models by their ML score and the number of parameters. In Bayesian context we: • Use model averaging if we can “jump ” between models (reversible jump ..."
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marginal likelihood estimation In ML model selection we judge models by their ML score and the number of parameters. In Bayesian context we: • Use model averaging if we can “jump ” between models (reversible jump
