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  1. Article ; Online: ANOTHER MONOPHYLY INDEX: REVISITING THE JACKKNIFE.

    Siddall, Mark E

    Cladistics : the international journal of the Willi Hennig Society

    2021  Volume 11, Issue 1, Page(s) 33–56

    Abstract: Randomization routines have quickly gained wide usage in phylogenetic systematies. Introduced a decade ago, the jackknife has rarely been applied in cladistic methodology. This data resampling technique was re-investigated here as a means to discover ... ...

    Abstract - Randomization routines have quickly gained wide usage in phylogenetic systematies. Introduced a decade ago, the jackknife has rarely been applied in cladistic methodology. This data resampling technique was re-investigated here as a means to discover the effect that taxon removal may have on the stability of the results obtained from parsimony analyses. This study shows that the removal of even a single taxon in an analysis can cause a solution of relatively few multiple equally parsimonious trees in an inclusive matrix to result in hundreds of equally parsimonious trees with the single removal of a taxon. On the other hand, removal of other taxa can stabilize the results to fewer trees. An index of clade stability, the Jackknife Monophyly Index (JMI) is developed which, like the bootstrap, applies a value to each clade according to its frequency of occurrence in jackknife pseudoreplicates. Unlike the bootstrap and earlier application of the jackknife, alternative suboptimal hypotheses are not forwarded by this method. Only those clades in the most parsimonious tree(s) are given JMI values. The behaviour of this index is investigated both in relation to a hypothetical and a real data set, as well as how it performs in comparison to the bootstrap. The JMI is found to not be influenced by uninformative characters or relative synapomorphy number, unlike the bootstrap.
    Language English
    Publishing date 2021-12-15
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1462608-1
    ISSN 1096-0031 ; 0748-3007
    ISSN (online) 1096-0031
    ISSN 0748-3007
    DOI 10.1111/j.1096-0031.1995.tb00003.x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Success of Parsimony in the Four-Taxon Case: Long-Branch Repulsion by Likelihood in the Farris Zone.

    Siddall, Mark E

    Cladistics : the international journal of the Willi Hennig Society

    2021  Volume 14, Issue 3, Page(s) 209–220

    Abstract: The accuracy of phylogenetic methods is reinvestigated for the four-taxon case with a two-edge rate and a three-edge rate. Unlike previous studies involving computer simulations, the two-edge rate relates to branches that are sister taxa in the model ... ...

    Abstract The accuracy of phylogenetic methods is reinvestigated for the four-taxon case with a two-edge rate and a three-edge rate. Unlike previous studies involving computer simulations, the two-edge rate relates to branches that are sister taxa in the model tree. As with previous studies, certain methods are found to behave inaccurately in a portion of the parameter space where the two-edge rate is proportionally large. This phenomenon, to which parsimony is immune, is termed "long-branch repulsion" and the region of poor performance is called the Farris Zone. Maximum likelihood methods are shown to be particularly prone to failure when closely related taxa have long branches. Long-branch repulsion is demonstrated with an empirical case involving Strepsiptera and Diptera.
    Language English
    Publishing date 2021-08-21
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1462608-1
    ISSN 1096-0031 ; 0748-3007
    ISSN (online) 1096-0031
    ISSN 0748-3007
    DOI 10.1111/j.1096-0031.1998.tb00334.x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: The AIDS Pandemic is New, but is HIV Not New?

    Siddall, Mark E

    Cladistics : the international journal of the Willi Hennig Society

    2021  Volume 13, Issue 3, Page(s) 267–273

    Abstract: The determinations made by Mindell, Shultz and Ewald regarding the ancestral host for immunodeficiency retroviruses, and their conclusion that monkeys acquired their infections as a result of a host-switch from humans, do not withstand rigorous scrutiny. ...

    Abstract The determinations made by Mindell, Shultz and Ewald regarding the ancestral host for immunodeficiency retroviruses, and their conclusion that monkeys acquired their infections as a result of a host-switch from humans, do not withstand rigorous scrutiny. Their hypothesis requires the complete uniformativeness of third position transitions and of gapped regions in the alignment. When all of the data are permitted to corroborate or refute relationships, optimizing hosts on the viral phylogeny renders either equivocal statements or an unequivocal simian ancestry. However, merely optimizing hosts as characters on the viral phylogeny is illogical. Not only does this treat hosts as dependent on the viruses (instead of the reverse) but it ignores 15 years of methodological developments specifically designed to answer questions regarding cospeciation or host-switching.
    Language English
    Publishing date 2021-12-01
    Publishing country United States
    Document type Letter
    ZDB-ID 1462608-1
    ISSN 1096-0031 ; 0748-3007
    ISSN (online) 1096-0031
    ISSN 0748-3007
    DOI 10.1111/j.1096-0031.1997.tb00319.x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Problems with the Cladistic Use of Riboprinting.

    Siddall, Mark E

    Cladistics : the international journal of the Willi Hennig Society

    2021  Volume 17, Issue 3, Page(s) 290–297

    Language English
    Publishing date 2021-12-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1462608-1
    ISSN 1096-0031 ; 0748-3007
    ISSN (online) 1096-0031
    ISSN 0748-3007
    DOI 10.1111/j.1096-0031.2001.tb00126.x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Forum. Stratigraphic Fit to Phylogenies: A Proposed Solution.

    Siddall, Mark E

    Cladistics : the international journal of the Willi Hennig Society

    2021  Volume 14, Issue 2, Page(s) 201–208

    Abstract: Three measures intended to assess the fit of stratigraphic age to the fossil record have been suggested previously: the Spearman Rank Correlation (SRC), the Stratigraphic Consistency Index (SCI) and the Relative Completeness Index (RCI). The original ... ...

    Abstract Three measures intended to assess the fit of stratigraphic age to the fossil record have been suggested previously: the Spearman Rank Correlation (SRC), the Stratigraphic Consistency Index (SCI) and the Relative Completeness Index (RCI). The original formulation of SRC is intractable to all but pectinate trees and the corrective pruning procedure that circumvents this precludes whole-tree estimates of fit. SCI, though it has been claimed otherwise, is strongly biased by tree shape, particularly as one adds more information. RCI is a measure of the amount of gap in the fossil record but has awkward consequences for evolutionary biology when it is maximized. A new approach, the Manhattan Stratigraphic Measure, uses the Manhattan distance between stratigraphic ages to determine fit to a tree. It is not biased by tree shape, it is sensitive to the magnitude of age discrepancy and there is an obvious significance test.
    Language English
    Publishing date 2021-12-15
    Publishing country United States
    Document type Letter
    ZDB-ID 1462608-1
    ISSN 1096-0031 ; 0748-3007
    ISSN (online) 1096-0031
    ISSN 0748-3007
    DOI 10.1111/j.1096-0031.1998.tb00333.x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Uneconomical Diagnosis of Cladograms: Comments on Wheeler and Nixon's Method for Sankoff Optimization.

    Swofford, David L / Siddall, Mark E

    Cladistics : the international journal of the Willi Hennig Society

    2021  Volume 13, Issue 1-2, Page(s) 153–159

    Abstract: We provide three simple examples demonstrating that Wheeler and Nixon's method of recoding "stepmatrix' characters can fail to yield most parsimonious reconstructions of character evolution under specified cost (transformation-weight) schemes. These ... ...

    Abstract We provide three simple examples demonstrating that Wheeler and Nixon's method of recoding "stepmatrix' characters can fail to yield most parsimonious reconstructions of character evolution under specified cost (transformation-weight) schemes. These examples variously indicate undercounting or overcounting of tree lengths due to an inappropriate assumption of independence among the recoded characters. Their method is therefore not equivalent to Sankoff's dynamic programming algorithm, contrary to their claim.
    Language English
    Publishing date 2021-12-15
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1462608-1
    ISSN 1096-0031 ; 0748-3007
    ISSN (online) 1096-0031
    ISSN 0748-3007
    DOI 10.1111/j.1096-0031.1997.tb00249.x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Probabilism and Phylogenetic Inference.

    Siddall, Mark E / Kluge, Arnold G

    Cladistics : the international journal of the Willi Hennig Society

    2021  Volume 13, Issue 4, Page(s) 313–336

    Abstract: The maximum likelihood approach to phylogenetics rests on frequency probability theory. This stands in stark contrast to the logical probability of corroboration-based cladistic parsimony. History is particular and cannot be described in terms of ... ...

    Abstract The maximum likelihood approach to phylogenetics rests on frequency probability theory. This stands in stark contrast to the logical probability of corroboration-based cladistic parsimony. History is particular and cannot be described in terms of universal statements about abstract generalities, the task of the historical sciences being one of explanation, not prediction. Thus, frequency probability methods of estimation are inappropriate for making historical inferences. Maximum likelihood estimation procedures are deconstructed from numerous perspectives in spite of their supposed impressive technicalities. Charges of parsimony's inconsistency are rendered mute, because its justification lies elsewhere, yet maximum likelihood is still subject to Wald's dilemma if realism is of any interest. Although all epistemologies make assumptions, the models employed by maximum likelihood are problematic and deterministic, as opposed to the unproblematic background knowledge characteristic of cladistics. Apart from issues of logical and sampling dependencies, the requirements of frequency probability theory are non-trivial and the maximum likelihood estimation of phylogeny can neither escape, nor satisfy the tenets of calculus independence (e.g. i.i.d.) inherent in the multiplicative relations of the method. If phylogeneticists are to maintain a rational foundation for their epistemology, neo-justificationist appeals to some metaphysical truth must be abandoned in favour of the realism of sophisticated falsification.
    Language English
    Publishing date 2021-12-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1462608-1
    ISSN 1096-0031 ; 0748-3007
    ISSN (online) 1096-0031
    ISSN 0748-3007
    DOI 10.1111/j.1096-0031.1997.tb00322.x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Biases in Maximum Likelihood and Parsimony: A Simulation Approach to a 10-Taxon Case.

    Pol, Diego / Siddall, Mark E

    Cladistics : the international journal of the Willi Hennig Society

    2021  Volume 17, Issue 3, Page(s) 266–281

    Abstract: Biases present in maximum likelihood and parsimony are investigated through a simulation study in a 10-taxon case in which several long branches coexist with short branches in the modeled topology. The performance of these methods is explored while ... ...

    Abstract Biases present in maximum likelihood and parsimony are investigated through a simulation study in a 10-taxon case in which several long branches coexist with short branches in the modeled topology. The performance of these methods is explored while increasing the length of the long branches with different amounts of data. Also, simulations with different taxonomic sampling schemes are examined through this study. The presence of a strong bias in parsimony is corroborated: the well-known long-branch attraction. Likelihood performance is found to be sensitive to the mere presence extreme of branch length disparity, retrieving topologies compatible with long-branch attraction and long-branch repulsion, irrespective of the correctness of the model used.
    Language English
    Publishing date 2021-12-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1462608-1
    ISSN 1096-0031 ; 0748-3007
    ISSN (online) 1096-0031
    ISSN 0748-3007
    DOI 10.1111/j.1096-0031.2001.tb00123.x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: LETTER TO THE EDITOR.

    Siddall, Mark E / Kluge, Arnold G

    Cladistics : the international journal of the Willi Hennig Society

    2021  Volume 15, Issue 4, Page(s) 439–440

    Language English
    Publishing date 2021-12-15
    Publishing country United States
    Document type Letter
    ZDB-ID 1462608-1
    ISSN 1096-0031 ; 0748-3007
    ISSN (online) 1096-0031
    ISSN 0748-3007
    DOI 10.1111/j.1096-0031.1999.tb00281.x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Presidential Address: Reinvention and Resolve.

    Siddall, Mark E

    The Journal of parasitology

    2016  Volume 102, Issue 6, Page(s) 566–571

    Language English
    Publishing date 2016-12
    Publishing country United States
    Document type Journal Article
    ZDB-ID 300870-8
    ISSN 1937-2345 ; 0022-3395
    ISSN (online) 1937-2345
    ISSN 0022-3395
    DOI 10.1645/16-113
    Database MEDical Literature Analysis and Retrieval System OnLINE

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