The Experts below are selected from a list of 18651 Experts worldwide ranked by ideXlab platform
Lars S Jermiin - One of the best experts on this subject based on the ideXlab platform.
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a new phylogenetic protocol dealing with model misspecification and confirmation bias in molecular Phylogenetics
NAR Genomics and Bioinformatics, 2020Co-Authors: Lars S Jermiin, Renee A Catullo, Barbara R HollandAbstract:Molecular Phylogenetics plays a key role in comparative genomics and has increasingly significant impacts on science, industry, government, public health and society. In this paper, we posit that the current phylogenetic protocol is missing two critical steps, and that their absence allows model misspecification and confirmation bias to unduly influence phylogenetic estimates. Based on the potential offered by well-established but under-used procedures, such as assessment of phylogenetic assumptions and tests of goodness of fit, we introduce a new phylogenetic protocol that will reduce confirmation bias and increase the accuracy of phylogenetic estimates.
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a new phylogenetic protocol dealing with model misspecification and confirmation bias in molecular Phylogenetics
bioRxiv, 2020Co-Authors: Lars S Jermiin, Renee A Catullo, Barbara R HollandAbstract:Molecular Phylogenetics plays a key role in comparative genomics and has an increasingly-significant impact on science, industry, government, public health, and society. We report that the current phylogenetic protocol is missing two critical steps, and that their absence allows model misspecification and confirmation bias to unduly influence the phylogenetic estimates. Based on the potential offered by well-established but under-used procedures (i.e., assessment of phylogenetic assumptions and test of goodness-of-fit), we introduce a new phylogenetic protocol that will reduce confirmation bias and increase the accuracy of phylogenetic estimates.
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modelfinder fast model selection for accurate phylogenetic estimates
Nature Methods, 2017Co-Authors: Subha Kalyaanamoorthy, Lars S Jermiin, Arndt Von Haeseler, Thomas K F Wong, Bui Quang MinhAbstract:ModelFinder is a fast model-selection method that greatly improves the accuracy of phylogenetic estimates. Model-based molecular Phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.
Allen G Rodrigo - One of the best experts on this subject based on the ideXlab platform.
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pghma application of the heteroduplex mobility assay analysis in Phylogenetics and population genetics
Molecular Ecology Resources, 2021Co-Authors: Thomas K F Wong, Louis Ranjard, Allen G RodrigoAbstract:The heteroduplex mobility assay (HMA) has proven to be a robust tool for the detection of genetic variation. Here, we describe a simple and rapid application of the HMA by microfluidic capillary electrophoresis, for Phylogenetics and population genetic analyses (pgHMA). We show how commonly applied techniques in Phylogenetics and population genetics have equivalents with pgHMA: phylogenetic reconstruction with bootstrapping, skyline plots, and mismatch distribution analysis. We assess the performance and accuracy of pgHMA by comparing the results obtained against those obtained using standard methods of analyses applied to sequencing data. The resulting comparisons demonstrate that: (a) there is a significant linear relationship (R2 = .992) between heteroduplex mobility and genetic distance, (b) phylogenetic trees obtained by HMA and nucleotide sequences present nearly identical topologies, (c) clades with high pgHMA parametric bootstrap support also have high bootstrap support on nucleotide phylogenies, (d) skyline plots estimated from the UPGMA trees of HMA and Bayesian trees of nucleotide data reveal similar trends, especially for the median trend estimate of effective population size, and (e) optimized mismatch distributions of HMA are closely fitted to the mismatch distributions of nucleotide sequences. In summary, pgHMA is an easily-applied method for approximating phylogenetic diversity and population trends.
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pghma application of the heteroduplex mobility assay analysis in Phylogenetics and population genetics
Authorea Preprints, 2021Co-Authors: Thomas K F Wong, Louis Ranjard, Allen G RodrigoAbstract:The Heteroduplex mobility assay (HMA) has proven to be a robust tool for the detection of genetic variation. Here, we describe a simple and rapid application of the HMA by microfluidic capillary electrophoresis, for Phylogenetics and population genetic analyses (pgHMA). We show how commonly applied techniques in Phylogenetics and population genetics have equivalents with pgHMA: phylogenetic reconstruction with bootstrapping, skyline plots, and mismatch distribution analysis. We assess the performance and accuracy of pgHMA by comparing the results obtained against those obtained using standard methods of analyses applied to sequencing data. The resulting comparisons demonstrate that: (1) there is a significant linear relationship (R = 0.992) between heteroduplex mobility and genetic distance; (2) phylogenetic trees obtained by HMA and nucleotide sequences present nearly identical topologies; (3) clades with high pgHMA parametric bootstrap support also have high bootstrap support on nucleotide phylogenies; (4) skyline plots estimated from the UPGMA trees of HMA and Bayesian trees of nucleotide data reveal similar trends, especially for the median trend estimate of effective population size; and (5) optimized mismatch distributions of HMA are closely fitted to the mismatch distributions of nucleotide sequences. In summary, pgHMA is an easily-applied method for approximating phylogenetic diversity and population trends. KEYWORDS: bootstrap, heteroduplex mobility assay, mismatch distribution, Phylogenetics, skyline plot
Thomas K F Wong - One of the best experts on this subject based on the ideXlab platform.
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pghma application of the heteroduplex mobility assay analysis in Phylogenetics and population genetics
Molecular Ecology Resources, 2021Co-Authors: Thomas K F Wong, Louis Ranjard, Allen G RodrigoAbstract:The heteroduplex mobility assay (HMA) has proven to be a robust tool for the detection of genetic variation. Here, we describe a simple and rapid application of the HMA by microfluidic capillary electrophoresis, for Phylogenetics and population genetic analyses (pgHMA). We show how commonly applied techniques in Phylogenetics and population genetics have equivalents with pgHMA: phylogenetic reconstruction with bootstrapping, skyline plots, and mismatch distribution analysis. We assess the performance and accuracy of pgHMA by comparing the results obtained against those obtained using standard methods of analyses applied to sequencing data. The resulting comparisons demonstrate that: (a) there is a significant linear relationship (R2 = .992) between heteroduplex mobility and genetic distance, (b) phylogenetic trees obtained by HMA and nucleotide sequences present nearly identical topologies, (c) clades with high pgHMA parametric bootstrap support also have high bootstrap support on nucleotide phylogenies, (d) skyline plots estimated from the UPGMA trees of HMA and Bayesian trees of nucleotide data reveal similar trends, especially for the median trend estimate of effective population size, and (e) optimized mismatch distributions of HMA are closely fitted to the mismatch distributions of nucleotide sequences. In summary, pgHMA is an easily-applied method for approximating phylogenetic diversity and population trends.
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pghma application of the heteroduplex mobility assay analysis in Phylogenetics and population genetics
Authorea Preprints, 2021Co-Authors: Thomas K F Wong, Louis Ranjard, Allen G RodrigoAbstract:The Heteroduplex mobility assay (HMA) has proven to be a robust tool for the detection of genetic variation. Here, we describe a simple and rapid application of the HMA by microfluidic capillary electrophoresis, for Phylogenetics and population genetic analyses (pgHMA). We show how commonly applied techniques in Phylogenetics and population genetics have equivalents with pgHMA: phylogenetic reconstruction with bootstrapping, skyline plots, and mismatch distribution analysis. We assess the performance and accuracy of pgHMA by comparing the results obtained against those obtained using standard methods of analyses applied to sequencing data. The resulting comparisons demonstrate that: (1) there is a significant linear relationship (R = 0.992) between heteroduplex mobility and genetic distance; (2) phylogenetic trees obtained by HMA and nucleotide sequences present nearly identical topologies; (3) clades with high pgHMA parametric bootstrap support also have high bootstrap support on nucleotide phylogenies; (4) skyline plots estimated from the UPGMA trees of HMA and Bayesian trees of nucleotide data reveal similar trends, especially for the median trend estimate of effective population size; and (5) optimized mismatch distributions of HMA are closely fitted to the mismatch distributions of nucleotide sequences. In summary, pgHMA is an easily-applied method for approximating phylogenetic diversity and population trends. KEYWORDS: bootstrap, heteroduplex mobility assay, mismatch distribution, Phylogenetics, skyline plot
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modelfinder fast model selection for accurate phylogenetic estimates
Nature Methods, 2017Co-Authors: Subha Kalyaanamoorthy, Lars S Jermiin, Arndt Von Haeseler, Thomas K F Wong, Bui Quang MinhAbstract:ModelFinder is a fast model-selection method that greatly improves the accuracy of phylogenetic estimates. Model-based molecular Phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.
Allan Larson - One of the best experts on this subject based on the ideXlab platform.
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evolution and phylogenetic information content of mitochondrial genomic structural features illustrated with acrodont lizards
Systematic Biology, 2000Co-Authors: Robert J. Macey, James A. Schulte, Allan LarsonAbstract:DNA sequences from 195 squamate reptiles indicate that mitochondrial gene order is the most reliable phylogenetic character establishing monophyly of acrodont lizards and of the snake families Boidae, Colubridae, and Viperidae. Gene order shows no evidence of evolutionary paral- lelisms or reversals in these taxa. Derived secondary structures of mitochondrial tRNAs also prove to be useful phylogenetic characters showing no reversals. Parallelisms for secondary structures of tRNAs are restricted to deep lineages that are separated by at least 200 million years of independent evolution. Presence of a stem-and-loop structure between the genes encoding tRNA Asn and tRNA c y s , where the replication origin for light-strand synthesis is typically located in vertebrate mi- tochondrial genomes, is found to undergo at least three and possibly as many as seven evolutionary shifts, most likely parallel losses. This character is therefore a less desirable phylogenetic marker than the other structural changes examined. Sequencing regions that contain multiple genes, in- cluding tRNA genes, may be preferable to the common practice of obtaining single-gene fragments for phylogenetic inference because it permits observation of major structural changes in the mito- chondrial genome. Such characters may occasionally provide phylogenetic information on rela- tively short internal branches for which base substitutional changes are expected to be relatively uninformative. (Acrodonta; gene organization; mitochondrial DNA, Phylogenetics; replication; Reptilia; tRNA.)
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molecular Phylogenetics of desmognathine salamanders caudata plethodontidae a reevaluation of evolution in ecology life history and morphology
Systematic Biology, 1996Co-Authors: Tom A Titus, Allan LarsonAbstract:1 - 2 4 Abstract.—Phylogenetic relationships were reconstructed for salamanders of the plethodontid sub- family Desmognathinae to examine evolution of morphology, ecology, and life history. Mitochon- drial DNA sequences encoding 12S and 16S ribosomal RNA and the valine transfer RNA provided 259 phylogenetically informative sites from approximately 1,200 nucleotide positions for 21 spec- imens representing 15 species and subspecies. These data were analyzed in conjunction with 13 morphological and reproductive characters to generate phylogenetic hypotheses. The directly de- veloping terrestrial desmognathines Phaeognathus hubrichti and Desmognathus wrighti represent, respectively, the first and second phylogenetic branching events within the subfamily, and the remaining terrestrial lineage, D. aeneus, also branches near the base of the phylogenetic tree. These results challenge earlier hypotheses that within Desmognathus the small nonmetamorphosing spe- cies, D. aeneus and D. wrighti, represent the end of a graded phylogenetic decrease in size and decrease in use of aquatic habitats. In contrast to previous hypotheses, our results suggest that desmognathine evolution includes transformations in the direction of larger body sizes, lengthened larval periods, and greater use of aquatic habitats. (Desmognathinae; ecology; life history; mito- chondrial DNA; molecular Phylogenetics; ribosomal DNA; salamanders.)
Thomas R Buckley - One of the best experts on this subject based on the ideXlab platform.
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model selection and model averaging in Phylogenetics advantages of akaike information criterion and bayesian approaches over likelihood ratio tests
Systematic Biology, 2004Co-Authors: David Posada, Thomas R BuckleyAbstract:Model selection is a topic of special relevance in molecular Phylogenetics that affects many, if not all, stages of phylogenetic inference. Here we discuss some fundamental concepts and techniques of model selection in the context of Phylogenetics. We start by reviewing different aspects of the selection of substitution models in Phylogenetics from a theoretical, philosophical and practical point of view, and summarize this comparison in table format. We argue that the most commonly implemented model selection approach, the hierarchical likelihood ratio test, is not the optimal strategy for model selection in Phylogenetics, and that approaches like the Akaike Information Criterion (AIC) and Bayesian methods offer important advantages. In particular, the latter two methods are able to simultaneously compare multiple nested or nonnested models, assess model selection uncertainty, and allow for the estimation of phylogenies and model parameters using all available models (model-averaged inference or multimodel inference). We also describe how the relative importance of the different parameters included in substitution models can be depicted. To illustrate some of these points, we have applied AIC-based model averaging to 37 mitochondrial DNA sequences from the subgenus Ohomopterus (genus Carabus) ground beetles described by Sota and Vogler (2001). (AIC; Bayes factors; BIC; likelihood ratio tests; model averaging; model uncertainty; model selection; multimodel inference.) It is clear that models of nucleotide substitution (henceforth models of evolution) play a significant role in molecular Phylogenetics, particularly in the context of distance, maximum likelihood (ML), and Bayesian es- timation. We know that the use of one or other model affects many, if not all, stages of phylogenetic inference. For example, estimates of phylogeny, substitution rates, bootstrap values, posterior probabilities, or tests of the molecular clock are clearly influenced by the model of evolution used in the analysis (Buckley, 2002; Buckley
