THREE STEPS OF HOMOLOGY ASSESSMENT

@article{Brower1996THREESO,
  title={THREE STEPS OF HOMOLOGY ASSESSMENT},
  author={Andrew V. Z. Brower and Valerie Schawaroch},
  journal={Cladistics},
  year={1996},
  volume={12}
}
Abstract — In 1991 de Pinna (Cladistics 7: 367–394) coined the term primary homology as the putative homology statements prior to tree reconstruction. However, some confusion still exists regarding the conjectural nature of homology and to the analysis of DNA sequences. By dividing de Pinna's term primary homology into topographical identity and character state identity, we emphasize the sequential refinement of putative homology statements. We discuss the problem of transformational versus… 

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References

SHOWING 1-10 OF 34 REFERENCES

PARSIMONY, HOMOLOGY AND THE ANALYSIS OF MULTISTATE CHARACTERS

Abstract— The order of states in a transformation series describes an internested set of synapomorphies. States adjacent to each other in the transformation series thus share a degree of homology not

CONCEPTS AND TESTS OF HOMOLOGY IN THE CLADISTIC PARADIGM

Logical equivalence between the notions of homology and synapomorphy is reviewed and supported, and a general theoretical solution is proposed to determine evolution of characters with ambiguous distributions, based on the notion of maximization ofHomology propositions.

Philosophy and the Transformation of Cladistics

The main principles of the Hennigian system are that the basic process of organic evolution is the splitting of an ancestral species into two descendant species and that each dichotomy should be taken as marking the origin of two new units of classification; and that the hierarchic level of such units should be determined by the geological time when the dichotomy occurred.

Molecular Versus Morphological Approaches to Systematics

This review outlines the advantages of both morphological and molecular approaches to systematics and discusses some common differences in assumptions and methods of analysis that can lead to spurious conflict between studies, especially those concerning phylogenetic reconstruction.

Homology in classical and molecular biology.

There are more kinds of homologous relation between molecular sequences than in morphology, and the terms paraxenology and plerology are proposed for two of these kinds--respectively, the consequence of multiple xenology and of gene conversion.

CHARACTER DEFINITIONS AND CHARACTER STATE DELINEATION: THE BETE NOIRE OF PHYLOGENETIC INFERENCE

Abstract— Currently characters are static concepts whose definition and state delineations seldom undergo any scrutiny. Common systematic practice tends to synthesize character slates by combining or

Philosophical Foundations of Classical Evolutionary Classification

Application of the Popperian philosophy of the demarcation and methodology of science to classification suggests that a major task is the development of severe tests of falsification by which classifications can be tried.

ON THE INDEPENDENCE OF SYSTEMATICS

  • R. Brady
  • Biology
    Cladistics : the international journal of the Willi Hennig Society
  • 1985
Abstract— Before the publication of On the Origin of Species the standing patterns of natural history—common plan, homology, ontogenetic parallelism, and the hierarchy of groups — were taken as

Sources of ambiguity in nucleic acid sequence alignment.

The discussion of molecular sequence alignment is becoming more prominent in studies of molecular systematics and evolution, and several possible solutions to the difficult situation of non-unique alignments are discussed.

SEQUENCE ALIGNMENT, PARAMETER SENSITIVITY, AND THE PHYLOGENETIC ANALYSIS OF MOLECULAR DATA

The dependence of the results of molecular phylogenetic sequence analysis (both align­ ment and cladogram construction) on variation in analytical parameters is examined and procedures for robust and liberal hypothesis choice are proposed using congruence as an optimality criterion.