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Diagnosing Discordance: Signal in Data, Conflict in Paradigms

Quinn, Aleta (2019) Diagnosing Discordance: Signal in Data, Conflict in Paradigms. Philosophy, Theory, and Practice in Biology, 11 (17). ISSN 2475-3025


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I analyze recent debates between proponents of concatenation versus coalescence in phylogenetic inference. I argue that concatenation is the latest manifestation of a paradigm weaving through phylogenetics that has focused on a successive series of models thought to be justified by the “principle of total evidence.” I analyze the principle of total evidence as the main philosophical strand linking parsimony versus likelihood (1980s), character congruence versus consensus trees (1990s), and concatenation versus coalescence (2000–10s). My hope is to provide a foothold for philosophers to engage with contemporary phylogenetics, in the face of the discipline’s bewildering and rapidly expanding array of computational models. The basic idea of total evidence—include all data that is relevant to an analysis, that has signal with respect to the problem at hand—is extremely attractive at an intuitive level. However, the general intuition is less clear in the case that all relevant data are included in the overall study, but no single method employs the total dataset in one inferential step. Moreover, simulation studies demonstrate that there are cases in which excluding some data, even when that data provides signal, leads to a better result by a particular method. Each of these points is explored through analysis of the historical and contemporary debates.

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Item Type: Published Article or Volume
Quinn, Aleta
Keywords: Cladist Concatenation Multi-species Coalescent Parsimony Phylogenetics Total Evidence
Depositing User: Christopher Eliot
Date Deposited: 26 May 2022 02:09
Last Modified: 26 May 2022 02:09
Item ID: 20658
Journal or Publication Title: Philosophy, Theory, and Practice in Biology
Publisher: Michigan Publishing
Official URL:
DOI or Unique Handle:
Date: 2019
Volume: 11
Number: 17
ISSN: 2475-3025

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