Parsimony and explanatory power

Abstract

Parsimony can be related to explanatory power, either by noting that each additional requirement for a separate origin of a feature reduces the number of observed similarities that can be explained as inheritance from a common ancestor; or else by applying PopperÕs formula for explanatory power together with the fact that parsimony yields maximum likelihood trees under No Common Mechanism (NCM). Despite deceptive claims made by some likelihoodists, most maximum likelihood methods cannot be justified in this way because they rely on unrealistic background assumptions. These facts have been disputed on the various grounds that ad hoc hypotheses of homoplasy are explanatory, that they are not explanatory, that character states are ontological individuals, that character data do not comprise evidence, that unrealistic theories can be used as background knowledge, that NCM is unrealistic, and that likelihoods cannot be used to evaluate explanatory power. None of these objections is even remotely well founded, and indeed most of them do not even seem to have been meant seriously, having instead been put forward merely to obstruct the development of phylogenetic methods.

Structural Phylogenomics Retrodicts the Origin of the Genetic Code and Uncovers the Evolutionary Impact of Protein Flexibility

“…gene content in genomes and the tree of life [32]). Agreements are used to reformulate homology hypotheses in an iterative framework of maximization of explanatory power [33] that links phylogenetic analysis and the Popperian pillars of content of theories and degree of corroboration [34]. In this framework, increasing explanatory power over background knowledge is obtained through test and corroboration and not through verificationist strategies that seek to increase support of nodes in trees.…”

The Evolutionary Basis of Naturally Diverse Rice Leaves Anatomy

“…For this, each of the morphological and anatomical data was grouped into three equal portions with defined minima and maxima to determine the high, low, and intermediate values for each trait. The phylogenetic tree, created using PhyML, was used as a backbone to obtain the transition parameters for ancient and recent state reconstruction using parsimony analysis [37]. Mesquite software analyzes the character state at the terminal taxa and attempts to reconstruct the ancestral state at each node and finally reconstructs the character history.…”

Análise filogenética de ralídeos Neotropicais (Aves: Rallidae) com base em caracteres osteológicos

“…As famílias Turnicidae e Mesithornithidae foram incluídas em sua própria ordem, Turniciformes. O estudo também corrobora a relação de grupo-irmão entre Rallidae e Heliornithidae suportada por diversos autores (Fürbringer, 1888;Beddard, 1898;Lowe, 1931;Livezey, 1998;2008) afirmam que as relações evolutivas da tradicional ordem Gruiformes são problemáticas e o grupo certamente não é monofilético. Nas filogenias propostas por Ericson et al (2006) e Hackett et al (2008) são encontrados quatro clados distintos: (1) Gruiformes, composto por Aramidae, Gruidae, Psophiidae, Heliornithidae e Rallidae;…”

“…As hipóteses de relacionamento entre os Rallidae foram inferidas de acordo com as metodologias da Escola de Sistemática Cladista (Hennig 1950;1966) adotando-se o princípio da parcimônia para a análise dos dados (Wiley, 1981;Farris, 1983;Kitching et al, 1998;Farris, 2008).…”