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The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics. Syst. Biol
, 2007
"... Abstract.—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 of molecular evolution. We investigated the effect of improper data partitioning on phylogenetic ac ..."
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Abstract.—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 of molecular evolution. We investigated the effect of improper data partitioning on phylogenetic accuracy, as well as the type I error rate and sensitivity of Bayes factors, a commonly used method for choosing among different partitioning strategies in Bayesian analyses. We also used Bayes factors to test empirical data for the need to divide data in a manner that has no expected biological meaning. Posterior probability estimates are misleading when an incorrect partitioning strategy is assumed. The error was greatest when the assumed model was underpartitioned. These results suggest that model partitioning is important for large data sets. Bayes factors performed well, giving a 5 % type I error rate, which is remarkably consistent with standard frequentist hypothesis tests. The sensitivity of Bayes factors was found to be quite high when the acrossclass model heterogeneity reflected that of empirical data. These results suggest that Bayes factors represent a robust method of choosing among partitioning strategies. Lastly, results of tests for the inclusion of unexpected divisions in empirical data mirrored the simulation results, although the outcome of such tests is highly dependent on accounting for rate variation among classes. We conclude by discussing other approaches for partitioning data, as well as other applications of Bayes factors. [Bayes factors; Bayesian phylogenetic inference; data partitioning; model choice; posterior probabilities.] Maximum likelihood (ML) and Bayesian methods of
Accurate branch length estimation in partitioned Bayesian analyses requires accommodation of amongpartition rate variation and attention to branch length priors. Syst Biol
, 2006
"... Molecular phylogenetic studies are making increasing use of partitioned Bayesian analyses via software tools like MrBayes, version 3 (Ronquist and Huelsenbeck, 2003). Data partitioning is important because, as long as the same topology/history underlies all of the partitions, it addresses some of t ..."
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Cited by 33 (0 self)
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Molecular phylogenetic studies are making increasing use of partitioned Bayesian analyses via software tools like MrBayes, version 3 (Ronquist and Huelsenbeck, 2003). Data partitioning is important because, as long as the same topology/history underlies all of the partitions, it addresses some of the problems associated with the combination of data sets with heterogeneous rates (Bull et al., 1993) and eliminates the need to argue the validity of tests that have been used to judge data combinability (e.g., Huelsenbeck et al., 1994; Huelsenbeck
Optimal Data Partitioning and a Test Case for RayFinned Fishes (Actinopterygii) Based on Ten Nuclear Loci' Syst Biol 57(4
, 2008
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Cited by 28 (2 self)
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This Article is brought to you for free and open access by the Department of Biology at
Bayesian mixed models and the phylogeny of pitvipers (Viperidae:
 Serpentes). Mol. Phylogenet. Evol.
, 2006
"... Abstract The subfamily Crotalinae (pitvipers) contains over 190 species of venomous snakes distributed in both the Old and New World. We incorporated an extensive sampling of taxa (including 28 of 29 genera), and sequences of four mitochondrial gene fragments (2.3 kb) per individual, to estimate th ..."
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Abstract The subfamily Crotalinae (pitvipers) contains over 190 species of venomous snakes distributed in both the Old and New World. We incorporated an extensive sampling of taxa (including 28 of 29 genera), and sequences of four mitochondrial gene fragments (2.3 kb) per individual, to estimate the phylogeny of pitvipers based on maximum parsimony and Bayesian phylogenetic methods. Our Bayesian analyses incorporated complex mixed models of nucleotide evolution that allocated independent models to various partitions of the dataset within combined analyses. We compared results of unpartitioned versus partitioned Bayesian analyses to investigate how much unpartitioned (versus partitioned) models were forced to compromise estimates of model parameters, and whether complex models substantially alter phylogenetic conclusions to the extent that they appear to extract more phylogenetic signal than simple models. Our results indicate that complex models do extract more phylogenetic signal from the data. We also address how diVerences in phylogenetic results (e.g., bipartition posterior probabilities) obtained from simple versus complex models may be interpreted in terms of relative credibility. Our estimates of pitviper phylogeny suggest that nearly all recently proposed generic reallocations appear valid, although certain Old and New World genera (Ovophis, Trimeresurus, and Bothrops) remain polyor paraphyletic and require further taxonomic revision. While a majority of nodes were resolved, we could not conWdently estimate the basal relationships among New World genera and which lineage of Old World species is most closely related to this New World group.
Modeling nucleotide evolution at the mesoscale: the phylogeny of the Neotropical pitvipers
 of the Porthidium group (Viperidae: Atropoides, Cerrophidion, Porthidium). Molecular Phylogenetics and Evolution
, 2005
"... Abstract We analyzed the phylogeny of the Neotropical pitvipers within the Porthidium group (including intraspeciWc through intergeneric relationships) using 1.4 kb of DNA sequences from two mitochondrial proteincoding genes (ND4 and cytb). We investigated how Bayesian Markov chain MonteCarlo ( ..."
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Abstract We analyzed the phylogeny of the Neotropical pitvipers within the Porthidium group (including intraspeciWc through intergeneric relationships) using 1.4 kb of DNA sequences from two mitochondrial proteincoding genes (ND4 and cytb). We investigated how Bayesian Markov chain MonteCarlo (MCMC) phylogenetic hypotheses based on this 'mesoscale' dataset were aVected by analysis under various complex models of nucleotide evolution that partition models across the dataset. We develop an approach, employing three statistics (Akaike weights, Bayes factors, and relative Bayes factors), for examining the performance of complex models in order to identify the bestWt model for data analysis. Our results suggest that: (1) model choice may have important practical eVects on phylogenetic conclusions even for mesoscale datasets, (2) the use of a complex partitioned model did not produce widespread increases or decreases in nodal posterior probability support, and (3) most diVerences in resolution resulting from model choice were concentrated at deeper nodes. Our phylogenetic estimates of relationships among members of the Porthidium group (genera: Atropoides, Cerrophidion, and Porthidium) resolve the monophyly of the three genera. Bayesian MCMC results suggest that Cerrophidion and Porthidium form a clade that is the sister taxon to Atropoides. In addition to resolving the intraspeciWc relationships among a majority of Porthidium group taxa, our results highlight phylogeographic patterns across Middle and South America and suggest that each of the three genera may harbor undescribed species diversity.
American
, 2006
"... www.elsevier.com/locate/ympev Phylogeographic structure and historical demography of the western diamondback rattlesnake (Crotalus atrox): A perspective on North ..."
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www.elsevier.com/locate/ympev Phylogeographic structure and historical demography of the western diamondback rattlesnake (Crotalus atrox): A perspective on North
Phylogeography and systematic revision of the Egyptian cobra (Serpentes: Elapidae: Naja haje) species complex, with the description of a new species from West Africa
"... We use a combination of phylogenetic analysis of mtDNA sequences and multivariate morphometrics to investigate the phylogeography and systematics of the Egyptian cobra (Naja haje) species complex. Phylogenetic analysis of mitochondrial haplotypes reveals a highly distinct clade of haplotypes from th ..."
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We use a combination of phylogenetic analysis of mtDNA sequences and multivariate morphometrics to investigate the phylogeography and systematics of the Egyptian cobra (Naja haje) species complex. Phylogenetic analysis of mitochondrial haplotypes reveals a highly distinct clade of haplotypes from the Sudano–Sahelian savanna belt of West Africa, and that the haplotypes of Naja haje arabica form the sister group of North and East African N. h. haje. Multivariate morphometrics confirm the distinctness of the Arabian populations, which are consequently recognised as a full species, Naja arabica Scortecci. The SudanoSahelian populations are also found to represent a morphologically distinct taxon, and thus a separate species, which we describe as Naja senegalensis sp. nov. The new species differs from all other members of the N. haje complex by a combination of colour pattern and scalation characteristics (especially higher numbers of scale rows around the neck), and the possession of a unique clade of mtDNA haplotypes. The distribution of the new species includes savanna areas of West Africa, from Senegal to western Niger and Nigeria.
A GENOMESCALE APPROACH TO PHYLOGENY OF RAY FINNED FISH (ACTINOPTERYGII) AND MOLECULAR SYSTEMATICS OF CLUPEIFORMES
, 2007
"... Part of the Life Sciences Commons This Article is brought to you for free and open access by the Biological Sciences, School of at DigitalCommons@University of Nebraska Lincoln. It has been accepted for inclusion in Dissertations and Theses in Biological Sciences by an authorized administrator of D ..."
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Part of the Life Sciences Commons This Article is brought to you for free and open access by the Biological Sciences, School of at DigitalCommons@University of Nebraska Lincoln. It has been accepted for inclusion in Dissertations and Theses in Biological Sciences by an authorized administrator of DigitalCommons@University of Nebraska Lincoln. Li, Chenhong, "A Genomescale Approach to Phylogeny of Rayfinned Fish (Actinopterygii) and Molecular Systematics of
UvADARE (Digital Academic Repository) Link to publication Citation for published version (APA)
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DOI: 10.1080/10635150490522629 Frequentist Properties of Bayesian Posterior Probabilities of Phylogenetic Trees Under Simple and Complex Substitution Models
"... Abstract. — What does the posterior probability of a phylogenetic tree mean? This simulation study shows that Bayesian posterior probabilities have the meaning that is typically ascribed to them; the posterior probability of a tree is the probability that the tree is correct, assuming that the model ..."
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Abstract. — What does the posterior probability of a phylogenetic tree mean? This simulation study shows that Bayesian posterior probabilities have the meaning that is typically ascribed to them; the posterior probability of a tree is the probability that the tree is correct, assuming that the model is correct. At the same time, the Bayesian method can be sensitive to model misspecification, and the sensitivity of the Bayesian method appears to be greater than the sensitivity of the nonparametric bootstrap method (using maximum likelihood to estimate trees). Although the estimates of phylogeny obtained by use of the method of maximum likelihood or the Bayesian method are likely to be similar, the assessment of the uncertainty of inferred trees via either bootstrapping (for maximum likelihood estimates) or posterior probabilities (for Bayesian estimates) is not likely to be the same. We suggest that the Bayesian method be implemented with the most complex models of those currently available, as this should reduce the chance that the method will concentrate too much probability on too few trees. [Bayesian estimation; Markov chain Monte Carlo; posterior probability; prior probability.] Quantifying the uncertainty of a phylogenetic estimate is at least as important a goal as obtaining the phylogenetic estimate itself. Measures of phylogenetic reliability not only point out what parts of a tree can be trusted when interpreting the evolution of a group, but can guide