Jump to ContentJump to Main Navigation
Parsimony, Phylogeny, and Genomics$
Users without a subscription are not able to see the full content.

Victor A. Albert

Print publication date: 2006

Print ISBN-13: 9780199297306

Published to Oxford Scholarship Online: September 2007

DOI: 10.1093/acprof:oso/9780199297306.001.0001

Show Summary Details
Page of

PRINTED FROM OXFORD SCHOLARSHIP ONLINE (www.oxfordscholarship.com). (c) Copyright Oxford University Press, 2019. All Rights Reserved. An individual user may print out a PDF of a single chapter of a monograph in OSO for personal use. date: 17 September 2019

The logic of the data matrix in phylogenetic analysis

The logic of the data matrix in phylogenetic analysis

(p.56) (p.57) Chapter 4 The logic of the data matrix in phylogenetic analysis
Parsimony, Phylogeny, and Genomics

Brent D. Mishler

Oxford University Press

The process of phylogenetic analysis inherently consists of two phases. First a data matrix is assembled, and then a phylogenetic tree is inferred from that matrix. There is obviously some feedback between these two phases, yet they remain logically distinct parts of the overall process. One could easily argue that the first phase of phylogenetic analysis is the most important: the tree is basically just a re-representation of the data matrix with no value added. This is especially true from a parsimony viewpoint, the point of which is to maintain an isomorphism between a data matrix and a cladogram. Paradoxically, despite the logical preeminence of data matrix construction in phylogenetic analysis, by far the greatest effort in phylogenetic theory has been directed at the second phase of analysis, the question of how to turn a data matrix into a tree. This chapter deals with logical issues involving the elements of the data matrix in light of the nested and interrelated nature of terminal units (‘twigs’ of the tree) and characters. It is argued that if care is taken to construct an appropriate data matrix to address a particular question of relationships at a given level, then simple parsimony analysis is all that is needed to transform that matrix into a tree. Debates over more complicated models for tree-building may then be seen for what they are: attempts to compensate for marginal data.

Keywords:   phylogenetic tree, isomorphism, data matrix, cladogram

Oxford Scholarship Online requires a subscription or purchase to access the full text of books within the service. Public users can however freely search the site and view the abstracts and keywords for each book and chapter.

Please, subscribe or login to access full text content.

If you think you should have access to this title, please contact your librarian.

To troubleshoot, please check our FAQs , and if you can't find the answer there, please contact us .