From conviction to anti‐superfluity: old and new justifications of parsimony in phylogenetic inference

Abstract

Traditional justifications of parsimony in phylogenetic inference assume a correspondence between character-state similarity and steps (character transformation events). In addition to similarity, justifying arguments appeal to conviction, descriptive efficiency, ad hoc hypotheses of homoplasy and frequentist probability. Each of these rationales fails in so far as the arguments are incoherent or logically inconsistent with the ontological status of what is assumed and being explained historically. An ideographic justification of parsimony, where character-states constitute transformation events, does, however, allow for a rational preference of most parsimonious phylogenetic hypotheses by invoking the anti-superfluity principle (ASP). According to ASP, explanatory power is maximized by minimizing the number of transformation events required to explain the character-states of the terminal taxa as hypotheses of homology, where the concept homology is restricted to just those inherited ''things'' shared by species. The empirical significance of this rationale is exemplified with the method of direct optimization, which can identify more parsimonious hypotheses than can be confirmed with an analysis of character-state similarities.

Supplemental Material for 'Phylogenetic systematics of dart-poison frogs and their relatives (Amphibia, Athesphatanura, Dendrobatidae). (Bulletin of the AMNH ; no. 299)'

“…Two equally parsimonious explanations may have different CIs and RIs, and explanations with the same CI and RI may have different costs. For details, see Kluge and Grant (2006). (108, 0 R 1), and the origin of toe trembling (Character 115, 0 R 1).…”

“…Operational considerations aside (e.g., tree-space searching capabilities), disagreements between the results of unweighted parsimony analysis and the other methods are due to the increased patristic distance required to accommodate the additional assumptions. Kluge and Grant (2006) reviewed the justifications for parsimonious phylogenetic inference previously considered sufficient, namely, conviction (Hennig, 1966), descriptive efficiency (Farris, 1979), minimization of ad hoc hypotheses of homoplasy (Farris, 1983), and statistical, model-based inference (maximum likelihood, Sober, 1988). Finding significant inconsistencies in all of those justifications, Kluge and Grant (2006) proposed a novel justification for parsimony.…”

“…Kluge and Grant (2006) reviewed the justifications for parsimonious phylogenetic inference previously considered sufficient, namely, conviction (Hennig, 1966), descriptive efficiency (Farris, 1979), minimization of ad hoc hypotheses of homoplasy (Farris, 1983), and statistical, model-based inference (maximum likelihood, Sober, 1988). Finding significant inconsistencies in all of those justifications, Kluge and Grant (2006) proposed a novel justification for parsimony. Drawing on recent advances in the understanding of phylogenetics as a strictly ideographic, historical science and parsimonious inference generally in the philosophy of science literature (e.g., Barnes 2000;Baker, 2003), they argued that by minimizing globally the transformation events postulated to explain the character-states of terminal taxa, equally weighted parsimony analysis maximizes explanatory power.…”

Description and Phylogenetic Relationships of a New Genus and Species of Lizard (Squamata, Gymnophthalmidae) from the Amazonian Rainforest of Northern Brazil

“…However, since the PAR topology is almost identical to the majority rule consensus tree of the BA (Clade-Bayes, sensu Wheeler and Pickett, 2008), the criterion chosen has little implication on the overall phylogenetic hypothesis presented herein. Arguments for the use of parsimony were given and discussed extensively in Farris (1983), Goloboff (2003), and Kluge and Grant (2006). Separate and combined analyses of morphology and molecular data were performed to determine the phylogenetic placement of Marinussaurus curupira among major clades of Gymnophthalminae.…”

Systematics of the Neotropical GenusLeptodactylusFitzinger, 1826 (Anura: Leptodactylidae): Phylogeny, the Relevance of Non-molecular Evidence, and Species Accounts

“…On the basis of the arguments of Padial et al (2014), we employed tree-alignment (e.g., Sankoff, 1975;Wheeler, 1996;Wheeler, 2012, 2013) in POY 4.1.3 (Varón et al, 2010), which tests hypotheses of nucleotide homology dynamically by optimizing unaligned DNA sequences directly onto alternative topologies (Kluge and Grant, 2006;Wheeler et al, 2006;Grant and Kluge, 2009) while simultaneously optimizing prealigned transformation series as standard static matrices.…”