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Ronald A Jenner - One of the best experts on this subject based on the ideXlab platform.

  • the scientific status of metazoan Cladistics why current research practice must change
    Zoologica Scripta, 2004
    Co-Authors: Ronald A Jenner
    Abstract:

    Jenner, R. A. (2004). The scientific status of metazoan Cladistics: why current research practice must change. —Zoologica Scripta, 33, 293–310. Metazoan phylogenetics is bustling with activity. The use of comprehensive morphological data sets in recent phylogenetic analyses of the Metazoa indicates that morphological evidence continues to play a key role in the reconstruction of metazoan deep history. In this paper I review the scientific status of morphological metazoan Cladistics from the perspective of cladistic research cycles. Each research cycle consists of three main steps: (1) the compilation of a data matrix (2) the simultaneous evaluation of all possible cladograms in a character congruence test, and (3) the assessment of the relationship between evidence and hypothesis after finding the optimal tree. I identify a striking discrepancy between the sophistication of the analysis of given data sets (Step 2), and their compilation and the interpretation of the results (Steps 1 and 3). The latter two steps deserve far greater attention than is current practice. Uncritical and nonexplicit character selection, character coding, and character scoring seriously compromise Step 1. Careful comparative morphological study prior to data matrix construction is necessary to remedy this problem in future cladistic analyses. Step 2 is the locus of most recent advances in metazoan Cladistics through the increasing availability of computing power, and the development of increasingly efficient phylogenetic software that allows analysis of large data sets. Failure to identify problems and errors generated in Step 1 of the research cycle is testament to the general failure of Step 3. Consequently, recent progress in metazoan Cladistics is primarily analytical, while the only empirical anchor of the discipline receives surprisingly little attention. Not surprisingly, the first generation of modern metazoan phylogeneticists used computers principally as a relatively quick and easy means to generate abundant phylogenies from morphological data. The next phase should build on this foundation by critically testing these alternative hypotheses by a thorough qualitative reassessment and elaboration of morphological data matrices, and a more critical approach to data selection. A rigorous research program for metazoan Cladistics can only be established when the cladistic research cycle is properly completed, and when subsequent research cycles are effectively linked to previous efforts.

  • Unleashing the Force of Cladistics? Metazoan Phylogenetics and Hypothesis Testing
    Integrative and comparative biology, 2003
    Co-Authors: Ronald A Jenner
    Abstract:

    Abstract The accumulation of multiple phylogenetic hypotheses for the Metazoa invites an evaluation of current progress in the field. I discuss three case studies from the recent literature to assess how cladistic analyses of metazoan morphology have contributed to our understanding of animal evolution. The first case study on cleavage cross patterns examines whether a decade of unanimous character scoring across different cladistic studies can be considered a reliable indicator of accumulated wisdom. The two remaining case studies illustrate how the unique strength of cladistic analyses to arbitrate between competing hypotheses can be crippled when insufficient attention is directed towards the construction of the data matrix. The second case study discusses a recent morphological cladistic analysis aimed at providing insight into the evolution of larval ciliary bands (prototrochs) in the Spiralia, and the third case study evaluates how four subsequent morphological cladistic analyses have contributed to...

  • boolean logic and character state identity pitfalls of character coding in metazoan Cladistics
    Contributions to Zoology, 2002
    Co-Authors: Ronald A Jenner
    Abstract:

    A critical study of the morphological data sets used for the most recent analyses of metazoan Cladistics exposes a rather cavalier attitude towards character coding. Binary absence/presence coding is ubiquitous, but without any explicit justification. This uncompromising application of Boolean logic in character coding is remarkable since several recent investigations have nominated absence/presence coding as the most problematic coding method available for standard cladistic analysis. Moreover, the prevalence of unspecified “absence” character states in the published data sets introduces a discrepancy between the theoretical foundations of phylogenetic parsimony and current practices in metazoan Cladistics. Because phylogenetic parsimony assumes transformation of character states, its effective operation breaks down when not all character states are carefully delimited. Examples of resulting meaningless character state transformations are discussed in two categories: 1) when unspecified “absence” states are plesiomorphic; and 2) when unspecified “absence” states are apomorphic (character reversals). To facilitate future progress in metazoan Cladistics, the mandatory link between comparative morphology and character coding needs to be reestablished through a more explicit study of morphological variation prior to character coding, and through a more explicitly experimental approach to character coding.

Verne Grant - One of the best experts on this subject based on the ideXlab platform.

  • Incongruence between cladistic and taxonomic systems.
    American journal of botany, 2003
    Co-Authors: Verne Grant
    Abstract:

    Cladistic and taxonomic treatments of the same plant group usually exhibit a mixture of congruences and incongruences. The question arises in the case of the incongruences as to which version is right and which is wrong. Many cladists believe that Cladistics is a superior approach and gives the best results. There are several conceptual and methodological differences between Cladistics and taxonomy that cause incongruence. One important conceptual difference is the use of different criteria for grouping: order of branching vs. similarity and difference (clades vs. taxa). Another is the policy regarding paraphyletic groups: to ban them in Cladistics but ignore the ban in taxonomy. These two differences automatically lead to some incongruences. One approach is not right and the other wrong; each is operating by its own standards. However, when cladists apply the paraphyly rule to a taxonomic system and conclude that it needs revision to eliminate paraphyly, as cladists often do, they are judging the taxonomic system by a wrong standard. Several differences between the two schools in the use and handling of characters can also cause incongruence. First consider phenetic characters. Taxonomy uses a very wide range of these, whereas phenetic Cladistics sets restrictions on the selection of characters, which deprive it of potentially useful evidence. Taxonomic systems generally rest on a broader empirical foundation than phenetic cladistic systems. Next, consider molecular Cladistics, which is the leader in the use of DNA evidence. Two sources of incongruence between molecular Cladistics and taxonomic systems can come into play here. First, the molecular evidence used in Cladistics comes mainly from cytoplasmic organelles, whereas taxonomic systems are based on characters that are determined mainly by the chromosomal genome. More generally, the database in a molecular cladogram is, in itself, too narrow to serve as a foundation for an organismic classification. In cases of incongruence, the molecular evidence can be a reliable indicator of taxonomic relationships sometimes, misleading other times, and may afford no clear basis for a systematic decision. In this situation, it is helpful, indeed necessary, to integrate the molecular evidence with the phenetic evidence and bring more characters to bear on the question.

  • primary classification and phylogeny of the polemoniaceae with comments on molecular Cladistics
    American Journal of Botany, 1998
    Co-Authors: Verne Grant
    Abstract:

    The system of classification of the Polemoniaceae currently in use was published by Grant in 1959. Much new evidence concerning relationships in the family has been obtained by numerous workers since 1959, and the old system is in need of revision. A revised system down to the genus level, based on conventional and unconventional characters, including molecular evidence, is presented here. Nineteen genera are grouped into eight tribes and two subfamilies. Three new tribes are described: Acanthogilieae, Loeselieae, and Leptodactyloneae. Several genera are transferred to new groups. The phylogeny of the family is discussed in the light of both the older and new evidence. The approach used in constructing both the 1959 and new systems is that of evolutionary systematics. Two recent (1996, 1997) family-wide surveys of cpDNA and rDNA use cladistic methods of analysis to arrive at sets of major groups. Some of this molecular evidence has been adopted for the present revised system. However, much incongruence still exists between the new sets of clades, on the one hand, and the present revised system or the still-viable parts of the 1959 system on the other hand. The incongruences call for an examination and comparison of the contrasting methods of evolutionary systematics and molecular Cladistics. A fundamental flaw in the 1996 and 1997 treatments is the attempt to classify plants on the basis of single-gene gene trees.

Keith Ridgway - One of the best experts on this subject based on the ideXlab platform.

  • manufacturing systematics and Cladistics state of the art and generic classification
    Journal of Manufacturing Technology Management, 2017
    Co-Authors: Christen Roseanderssen, James Baldwin, Keith Ridgway
    Abstract:

    Purpose The purpose of this paper is to critically evaluate the state of the art of applications of organisational systematics and manufacturing Cladistics in terms of strengths and weaknesses and introduce new generic cladistic and hierarchical classifications of discrete manufacturing systems. These classifications are the basis for a practical web-based expert system and diagnostic benchmarking tool. Design/methodology/approach There were two stages for the research methods, with eight re-iterative steps: one for theory building, using secondary and observational data, producing conceptual classifications; the second stage for theory testing and theory development, using quantitative data from 153 companies and 510 manufacturing systems, producing the final factual cladogram. Evolutionary relationships between 53 candidate manufacturing systems, using 13 characters with 84 states, are hypothesised and presented diagrammatically. The manufacturing systems are also organised in a hierarchical classification with 13 genera, 6 families and 3 orders under one class of discrete manufacturing. Findings This work addressed several weaknesses of current manufacturing cladistic classifications which include the lack of an explicit out-group comparison, limited conceptual cladogram development, limited use of characters and that previous classifications are specific to sectors. In order to correct these limitations, the paper first expands on previous work by producing a more generic manufacturing system classification. Second, it describes a novel web-based expert system for the practical application of the discrete manufacturing system. Practical implications The classifications form the basis for a practical web-based expert system and diagnostic benchmarking tool, but also have a novel use in an educational context as it simplifies and relationally organises extant manufacturing system knowledge. Originality/value The research employed a novel re-iterative methodology for both theory building, using observational data, producing the conceptual classification, and through theory testing developing the final factual cladogram that forms the basis for the practical web-based expert system and diagnostic tool.

  • Cladistic Classification of Ancient Manufacturing Forms and Technologies
    Enabling Manufacturing Competitiveness and Economic Sustainability, 2011
    Co-Authors: Christen Rose-anderssen, James Baldwin, Keith Ridgway
    Abstract:

    The purpose of the paper is to explore ancient manufacturing forms. Ancient evolutionary steps are brought together by applying Cladistics. Earlier manufacturing cladistic research has simply presented the most ancient manufacturing forms as Ancient Craft System without reference to any characteristics. The paper tries to explore ancient forms through literature research based on archaeological and anthropological accounts. Ancient manufacturing forms can be represented by character states. Their relationships are based on the character states they share. There is a continuous adaptation to the environment.

  • Linnaean and Cladistic Classifications of Manufacturing Systems
    Enabling Manufacturing Competitiveness and Economic Sustainability, 2011
    Co-Authors: James Baldwin, Christen Rose-anderssen, Keith Ridgway
    Abstract:

    This paper addresses the advantages of applying Cladistics to explore and change manufacturing layout systems. The approach is presented as evolutionary steps by the introduction of key layout characters. These steps are brought together by applying Cladistics to classify the evolutionary relationships between manufacturing layout systems. The classifications will form a knowledge base for a web-based expert system and diagnostic tool for the rapid design and virtual prototyping of factories of the future.

  • Organisational diversity, evolution and cladistic classifications
    Omega, 2000
    Co-Authors: Ian P. Mccarthy, Michel Leseure, Keith Ridgway, Nick Fieller
    Abstract:

    Abstract This article presents a case for the construction of a formal classification of manufacturing systems using Cladistics, a technique from the biological school of classification. A seven-stage framework for producing a manufacturing cladogram is presented, along with a pilot case study example. This article describes the role that classification plays in the pure and applied sciences, the social sciences and reviews the status of existing manufacturing classifications. If organisational diversity and organisational change processes are governed by evolutionary mechanisms, studies of organisations based on an evolutionary approach such as Cladistics could have potential, because as March [March JG. The evolution of evolution. In: Baum JAC, Singh JV, editors. Evolutionary dynamics of organizations. Oxford University Press, 1994. p. 39–52], page 45, states “there is natural speculation that organisations, like species can be engineered by understanding the evolutionary processes well enough to intervene and produce competitive organisational effects”. It is suggested that a cladistic study could provide organisations with a “knowledge map” of the ecosystem in which they exist and by using this phylogenetic and situational analysis, they could determine coherent and appropriate action for the specification of change.

Kevin R. Thiele - One of the best experts on this subject based on the ideXlab platform.

  • Regular ArticleThe Holy Grail of the Perfect Character: the Cladistic Treatment of Morphometric Data
    Cladistics, 1993
    Co-Authors: Kevin R. Thiele
    Abstract:

    —Data scored for cladistic analyses may be quantitative or qualitative, continuous or discrete, and show overlapping or non-overlapping values between taxa. Quantitative and qualitative are modes of expression of data, while continuous or discrete refer to properties of the set of numbers that express the data; both these pairs of terms have been confused with overlapping and non-overlapping. The degree of overlap of values between taxa is often used to filter characters in cladistic analyses: if a minimum amount of overlap is exceeded, or a minimum amount of disjunction not reached, characters are rejected as "not cladistic". However, this rests on a confusion between features of taxa and features of individual organisms (attributes). Cladistic characters are features of taxa, and comprise frequency distributions of attribute values over individuals of a taxon. Cladistic characters logically cannot overlap, although taxa may have overlapping attribute values. Thus, a priori rejection of characters that have overlapping attribute values is non-sensical. Such data may still be rejected from consideration for cladistic analysis if it could be demonstrated that they contain little recoverable phylogenetic signal. Few published analyses have empirically tested this. An analysis of overlapping morphometric data from three series of Banksia suggests that, at least in these cases, they map phylogeny almost as accurately as more conventional, qualitative morphological data. While more such tests are required, morphometric data should not be rejected a priori from cladistic analyses.

  • THE HOLY GRAIL OF THE PERFECT CHARACTER: THE CLADISTIC TREATMENT OF MORPHOMETRIC DATA
    Cladistics, 1993
    Co-Authors: Kevin R. Thiele
    Abstract:

    Abstract Abstract —Data scored for cladistic analyses may be quantitative or qualitative, continuous or discrete, and show overlapping or non-overlapping values between taxa. Quantitative and qualitative are modes of expression of data, while continuous or discrete refer to properties of the set of numbers that express the data; both these pairs of terms have been confused with overlapping and non-overlapping. The degree of overlap of values between taxa is often used to filter characters in cladistic analyses: if a minimum amount of overlap is exceeded, or a minimum amount of disjunction not reached, characters are rejected as "not cladistic". However, this rests on a confusion between features of taxa and features of individual organisms (attributes). Cladistic characters are features of taxa, and comprise frequency distributions of attribute values over individuals of a taxon. Cladistic characters logically cannot overlap, although taxa may have overlapping attribute values. Thus, a priori rejection of characters that have overlapping attribute values is non-sensical. Such data may still be rejected from consideration for cladistic analysis if it could be demonstrated that they contain little recoverable phylogenetic signal. Few published analyses have empirically tested this. An analysis of overlapping morphometric data from three series of Banksia suggests that, at least in these cases, they map phylogeny almost as accurately as more conventional, qualitative morphological data. While more such tests are required, morphometric data should not be rejected a priori from cladistic analyses.

Kevin C Nixon - One of the best experts on this subject based on the ideXlab platform.

  • paleobotany in Cladistics and Cladistics in paleobotany enlightenment and uncertainty
    Review of Palaeobotany and Palynology, 1996
    Co-Authors: Kevin C Nixon
    Abstract:

    Abstract Data on fossil taxa can, and should, be incorporated into cladistic analyses. Potential problems with such analyses include large amounts of missing data, and uncertainty about homology of parts that are present. Ambiguity of character data may also occur with extant taxa, but rarely to the extent that it occurs in fossil data. Such ambiguity reduces the strength of the test of character congruence among taxa, in effect relaxing the criterion of parsimony. In order to minimize such effects, composite fossil taxa should be avoided when possible, and polymorphisms reduced by breaking terminals into monomorphic subunits. When results including fossils differ radically from those that exclude fossils, such differences should be approached with caution, keeping in mind the reduced strength of the parsimony analysis when large numbers of cells in a matrix are scored as ambiguous. At this point, there is no simple way to compare the “strength” of parsimony between two data sets that have different numbers of characters and/or taxa in relation to missing data. However, methods under development may provide ways to incorporate the effect of missing values into relative measures of group support such as Bremer support, character removal, and the bootstrap.