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  1. Article: Systematic bias in phylogenetic analysis: is the Strepsiptera problem solved?

    Huelsenbeck, J P

    Systematic biology

    1998  Volume 47, Issue 3, Page(s) 519–537

    MeSH term(s) Animals ; DNA ; Insecta/classification ; Insecta/genetics ; Observer Variation ; Phylogeny ; Rodentia/classification ; Rodentia/genetics
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 1998-09
    Publishing country England
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1482572-7
    ISSN 1076-836X ; 1063-5157
    ISSN (online) 1076-836X
    ISSN 1063-5157
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  2. Article: Reply from j.p. Huelsenbeck, j.j. Bull and C.w. Cunningham.

    Huelsenbeck, J P / Bull, J J / Cunningham, C W

    Trends in ecology & evolution

    2011  Volume 11, Issue 8, Page(s) 335

    Language English
    Publishing date 2011-01-14
    Publishing country England
    Document type Letter
    ZDB-ID 284965-3
    ISSN 1872-8383 ; 0169-5347
    ISSN (online) 1872-8383
    ISSN 0169-5347
    DOI 10.1016/s0169-5347(96)91643-2
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  3. Article: Combining data in phylogenetic analysis.

    Huelsenbeck, J P / Bull, J J / Cunningham, C W

    Trends in ecology & evolution

    2011  Volume 11, Issue 4, Page(s) 152–158

    Abstract: Systematists have access to multiple sources of character information in phylogenetic analysis. For example, it is not unusual to have nucleotide sequences from several different genes, or to have molecular and morphological data. How should diverse data ...

    Abstract Systematists have access to multiple sources of character information in phylogenetic analysis. For example, it is not unusual to have nucleotide sequences from several different genes, or to have molecular and morphological data. How should diverse data be analyzed in phylogenetic analysis? Several methods have been proposed for the treatment of partitioned data: the total evidence, separate analysis, and conditional combination approaches. Here, we review some of the advantages and disadvantages of the different approaches, with special concentration on which methods help us to discern the evolutionary process and provide the most accurate estimates of phylogeny.
    Language English
    Publishing date 2011-01-14
    Publishing country England
    Document type Journal Article
    ZDB-ID 284965-3
    ISSN 1872-8383 ; 0169-5347
    ISSN (online) 1872-8383
    ISSN 0169-5347
    DOI 10.1016/0169-5347(96)10006-9
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  4. Article: Is the Felsenstein zone a fly trap?

    Huelsenbeck, J P

    Systematic biology

    1997  Volume 46, Issue 1, Page(s) 69–74

    Abstract: Although long-branch attraction, the incorrect grouping of long lineages in a phylogeny because of systematic error, has been identified as a potential source of error in phylogenetic analysis for almost two decades, no empirical examples of the ... ...

    Abstract Although long-branch attraction, the incorrect grouping of long lineages in a phylogeny because of systematic error, has been identified as a potential source of error in phylogenetic analysis for almost two decades, no empirical examples of the phenomenon exist. Here, I outline several criteria for identifying long-branch attraction and apply these criteria to 18S ribosomal DNA (rDNA) sequence data for 13 insects. Parsimony and minimum evolution with p distances group the two longest branches together (those leading to Strepsiptera and Diptera). Simulation studies show that the long branches are long enough to attract. When a tree is assumed in which Strepsiptera and Diptera are separated and many data sets are simulated for that tree (using the parameter estimates for that tree for the original data), parsimony analysis of the simulated data consistently groups Strepsiptera and Diptera. Analyses of the 18S rDNA sequences using methods that are less sensitive to the problem of long-branch attraction estimate trees in which the long branches are separate.
    MeSH term(s) Animals ; DNA, Ribosomal/genetics ; Evolution, Molecular ; Insecta/classification ; Insecta/genetics ; Phylogeny ; RNA, Ribosomal, 18S/genetics
    Chemical Substances DNA, Ribosomal ; RNA, Ribosomal, 18S
    Language English
    Publishing date 1997-03
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1482572-7
    ISSN 1076-836X ; 1063-5157
    ISSN (online) 1076-836X
    ISSN 1063-5157
    DOI 10.1093/sysbio/46.1.69
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  5. Article: The robustness of two phylogenetic methods: four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining.

    Huelsenbeck, J P

    Molecular biology and evolution

    1995  Volume 12, Issue 5, Page(s) 843–849

    Abstract: The robustness (sensitivity to violation of assumptions) of the maximum-likelihood and neighbor-joining methods was examined using simulation. Maximum likelihood and neighbor joining were implemented with Jukes-Cantor, Kimura, and gamma models of DNA ... ...

    Abstract The robustness (sensitivity to violation of assumptions) of the maximum-likelihood and neighbor-joining methods was examined using simulation. Maximum likelihood and neighbor joining were implemented with Jukes-Cantor, Kimura, and gamma models of DNA substitution. Simulations were performed in which the assumptions of the methods were violated to varying degrees on three model four-taxon trees. The performance of the methods was evaluated with respect to ability to correctly estimate the unrooted four-taxon tree. Maximum likelihood outperformed neighbor joining in 29 of the 36 cases in which the assumptions of both methods were satisfied. In 133 of 180 of the simulations in which the assumptions of the maximum-likelihood and neighbor-joining methods were violated, maximum likelihood outperformed neighbor joining. These results are consistent with a general superiority of maximum likelihood over neighbor joining under comparable conditions. They extend and clarify an earlier study that found an advantage for neighbor joining over maximum likelihood for gamma-distributed mutation rates.
    MeSH term(s) DNA/genetics ; Decision Trees ; Models, Genetic ; Models, Statistical ; Phylogeny ; Probability
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 1995-09
    Publishing country United States
    Document type Comparative Study ; Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 998579-7
    ISSN 1537-1719 ; 0737-4038
    ISSN (online) 1537-1719
    ISSN 0737-4038
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    In stock of ZB MED Cologne/Königswinter

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  6. Article: Detecting positively selected amino acid sites using posterior predictive P-values.

    Nielsen, R / Huelsenbeck, J P

    Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

    2002  , Page(s) 576–588

    Abstract: Identifying positively selected amino acid sites is an important approach for making inference about the function of proteins; an amino acid site that is undergoing positive selection is likely to play a key role in the function of the protein. We ... ...

    Abstract Identifying positively selected amino acid sites is an important approach for making inference about the function of proteins; an amino acid site that is undergoing positive selection is likely to play a key role in the function of the protein. We present a new Bayesian method for identifying positively selected amino acid sites and apply the method to a data set of hemagglutinin sequences from the Influenza virus. We show that the results of the new methods are in accordance with results obtained using previous methods. More importantly, we also demonstrate how the method can be used for making further inferences about the evolutionary history of the sequences. For example, we demonstrate that sites that are positively selected tend to have a preponderance of conservative amino acid substitutions.
    MeSH term(s) Amino Acid Sequence ; Amino Acid Substitution ; Amino Acids ; Likelihood Functions ; Models, Genetic ; Mutation ; Phylogeny ; Proteins/chemistry ; Proteins/genetics ; Software
    Chemical Substances Amino Acids ; Proteins
    Language English
    Publishing date 2002-04-02
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 2335-6928
    ISSN 2335-6928
    DOI 10.1142/9789812799623_0054
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: MRBAYES: Bayesian inference of phylogenetic trees.

    Huelsenbeck, J P / Ronquist, F

    Bioinformatics (Oxford, England)

    2001  Volume 17, Issue 8, Page(s) 754–755

    Abstract: Summary: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo.: Availability: MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms ... ...

    Abstract Summary: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo.
    Availability: MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.
    MeSH term(s) Algorithms ; Bayes Theorem ; Computational Biology ; Markov Chains ; Phylogeny ; Software
    Language English
    Publishing date 2001-08
    Publishing country England
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1422668-6
    ISSN 1367-4803
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/17.8.754
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  8. Article: Empirical and hierarchical Bayesian estimation of ancestral states.

    Huelsenbeck, J P / Bollback, J P

    Systematic biology

    2001  Volume 50, Issue 3, Page(s) 351–366

    Abstract: Several methods have been proposed to infer the states at the ancestral nodes on a phylogeny. These methods assume a specific tree and set of branch lengths when estimating the ancestral character state. Inferences of the ancestral states, then, are ... ...

    Abstract Several methods have been proposed to infer the states at the ancestral nodes on a phylogeny. These methods assume a specific tree and set of branch lengths when estimating the ancestral character state. Inferences of the ancestral states, then, are conditioned on the tree and branch lengths being true. We develop a hierarchical Bayes method for inferring the ancestral states on a tree. The method integrates over uncertainty in the tree, branch lengths, and substitution model parameters by using Markov chain Monte Carlo. We compare the hierarchical Bayes inferences of ancestral states with inferences of ancestral states made under the assumption that a specific tree is correct. We find that the methods are correlated, but that accommodating uncertainty in parameters of the phylogenetic model can make inferences of ancestral states even more uncertain than they would be in an empirical Bayes analysis.
    MeSH term(s) Animals ; Bayes Theorem ; DNA/genetics ; Humans ; Likelihood Functions ; Markov Chains ; Models, Genetic ; Monte Carlo Method ; Phylogeny
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2001-06
    Publishing country England
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1482572-7
    ISSN 1076-836X ; 1063-5157
    ISSN (online) 1076-836X
    ISSN 1063-5157
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  9. Article: Phylogeny, genome evolution, and host specificity of single-stranded RNA bacteriophage (family Leviviridae).

    Bollback, J P / Huelsenbeck, J P

    Journal of molecular evolution

    2001  Volume 52, Issue 2, Page(s) 117–128

    Abstract: Bacteriophage of the family Leviviridae have played an important role in molecular biology where representative species, such as Q beta and MS2, have been studied as model systems for replication, translation, and the role of secondary structure in gene ... ...

    Abstract Bacteriophage of the family Leviviridae have played an important role in molecular biology where representative species, such as Q beta and MS2, have been studied as model systems for replication, translation, and the role of secondary structure in gene regulation. Using nucleotide sequences from the coat and replicase genes we present the first statistical estimate of phylogeny for the family Leviviridae using maximum-likelihood and Bayesian estimation. Our analyses reveal that the coliphage species are a monophyletic group consisting of two clades representing the genera Levivirus and Allolevivirus. The Pseudomonas species PP7 diverged from its common ancestor with the coliphage prior to the ancient split between these genera and their subsequent diversification. Differences in genome size, gene composition, and gene expression are shown with a high probability to have changed along the lineage leading to the Allolevivirus through gene expansion. The change in genome size of the Allolevivirus ancestor may have catalyzed subsequent changes that led to their current genome organization and gene expression.
    MeSH term(s) Allolevivirus/classification ; Allolevivirus/genetics ; Allolevivirus/physiology ; Animals ; Bayes Theorem ; Capsid/genetics ; Caulobacter/virology ; Confidence Intervals ; Escherichia coli/virology ; Evolution, Molecular ; Genome, Viral ; Leviviridae/classification ; Leviviridae/genetics ; Leviviridae/physiology ; Levivirus/classification ; Levivirus/genetics ; Levivirus/physiology ; Likelihood Functions ; Phylogeny ; Pseudomonas/virology ; RNA Nucleotidyltransferases/genetics ; RNA Replicase/genetics ; RNA, Viral/genetics ; Software
    Chemical Substances RNA, Viral ; RNA Nucleotidyltransferases (EC 2.7.7.-) ; RNA Replicase (EC 2.7.7.48)
    Language English
    Publishing date 2001-02
    Publishing country Germany
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 120148-7
    ISSN 1432-1432 ; 0022-2844
    ISSN (online) 1432-1432
    ISSN 0022-2844
    DOI 10.1007/s002390010140
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 1129: Show issues Location:
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  10. Article: Effect of nonindependent substitution on phylogenetic accuracy.

    Huelsenbeck, J P / Nielsen, R

    Systematic biology

    1999  Volume 48, Issue 2, Page(s) 317–328

    Abstract: All current phylogenetic methods assume that DNA substitutions are independent among sites. However, ample empirical evidence suggests that the process of substitution is not independent but is, in fact, temporally and spatially correlated. The ... ...

    Abstract All current phylogenetic methods assume that DNA substitutions are independent among sites. However, ample empirical evidence suggests that the process of substitution is not independent but is, in fact, temporally and spatially correlated. The robustness of several commonly used phylogenetic methods to the assumption of independent substitution is examined. A compound Poisson process is used to model DNA substitution. This model assumes that substitution events are Poisson-distributed in time and that the number of substitutions associated with each event is geometrically distributed. The asymptotic properties of phylogenetic methods do not appear to change under a compound Poisson process of DNA substitution. Moreover, the rank order of the performance of different methods does not change. However, all phylogenetic methods become less efficient when substitution follows a compound Poisson process.
    MeSH term(s) Base Composition ; Base Sequence ; DNA/chemistry ; Models, Genetic ; Models, Statistical ; Phylogeny ; Reproducibility of Results
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 1999-06
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S.
    ZDB-ID 1482572-7
    ISSN 1076-836X ; 1063-5157
    ISSN (online) 1076-836X
    ISSN 1063-5157
    DOI 10.1080/106351599260319
    Database MEDical Literature Analysis and Retrieval System OnLINE

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