The Foundations of Concordance Views of Phylogeny
Joel D. Velasco, Department of Philosophy, Texas Tech University, 2500 Broadway, Lubbock, Texas 79409, USA
email: joel@joelvelasco.net
SUBJECT TERMS
Clade, Concordance Tree, Phylogeny, Plurality Consensus
PTPBIO
Volume 11, No. 020, 2019
Received 21 November 2017; Revised 25 November 2018; Accepted 8 March 2019
Abstract
Despite the enormous importance and widespread use of the term, it is unclear exactly what a phylogeny is and what a phylogenetic tree represents. A natural thought is that a phylogeny should represent the “dominant history” of the flow of genetic information. Here, I will focus on methods in which a tree is determined by input gene trees. I compare various possibilities of how to do this including consensus trees, the R* triplet method, and concordance methods. I make precise the notion of a concordance factor and then compare concordance trees to species trees, which attempt to track population histories through time. I show that even in the most idealized circumstances, it is possible for the primary concordance tree to differ from the species tree. I argue that when these trees differ, there are reasons to think of the primary concordance tree as a better representation of phylogenetic history than the species tree and that when these highly idealized conditions break down, it is especially plausible that we should take concordance trees seriously as an interpretation of phylogeny and as the basis for taxonomic grouping.
Part of the special issue Species in the Age of Discordance, guest-edited by Matthew H. Haber and Daniel J. Molter.
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