Parsimony analysis of unaligned sequence data: some clarifications

Ospina-Sarria, Jhon Jairo; Cabra-García, Jimmy

doi:10.1111/cla.12229

Cited by 3 publications

(1 citation statement)

References 32 publications

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“…Every case where the same feature is independently derived from an ancestor not having the feature, is a failure to explain the similarity in both groups as due to homology, regardless of applicability. That formulation of the problem makes it clear that maximization of explanatory power is equivalent to minimization of homoplasy also in the presence of inapplicables (see discussion in De Laet, 2015; contra Kluge and Grant, 2006;Wheeler, 2012;Ospina-Sarria and Cabra-Garc ıa, 2018). The general relationships between different proposals for inapplicables are summarized in Fig.…”

Section: Direct Counts Of Homoplasy: X-transformationsmentioning

confidence: 98%

A reconsideration of inapplicable characters, and an approximation with step‐matrix recoding

et al. 2021

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Evidence for phylogenetic analysis comes in the form of observed similarities, and trees are selected to minimize the number of similarities that cannot be accounted for by homology (homoplasies). Thus, the classical argument for parsimony directly links homoplasy with explanatory power. When characters are hierarchically related, a first character may represent a primary structure such as tail absence/presence and a secondary (subordinate) character may describe tail colour; this makes tail colour inapplicable when tail is absent. It has been proposed that such character hierarchies should be evaluated on the same logical basis as standard characters, maximizing the number of similarities accounted for by secondary homology, i.e. common ancestry. Previous evaluations of the homology of a given ancestral reconstruction contain the unintuitive quantity "subcharacters" (number of regions of applicability). Rather than counting subcharacters, this paper proposes an equivalent but more intuitive formulation, based on counting the number of changes into each separate state. In this formulation, x-transformations, the homoplasy for the reconstruction is simply the number of changes into the state beyond the first, summed over all states. There is thus no direct connection between homoplasy and number of steps, only between homoplasy and extra steps. The link between the two formulations is that, for any region of applicability of any character, a subcharacter can be interpreted as the change into the state that is plesiomorphic in that region. Although some authors have claimed that the equivalence between maximizing explanatory power and minimizing independent originations of similar features (i.e. the standard justification of parsimony) does not hold for inapplicable characters, evaluating homoplasy with x-transformations clearly connects the two sides of that equation. Furthermore, as the evaluation with x-transformations provides a direct count and a straightforward interpretation of homoplasy, it extends naturally into implied weighting, and sheds light on problems with additive, step-matrix or continuous characters. It also allows deriving transformation costs for recoding hierarchies as step-matrix characters (where recoded states correspond to permissible combinations of states in primary and secondary characters), so that homology of the original observations is properly measured. Those transformation costs set the cost of gaining the primary structure to the maximum difference between "present" states plus cost of loss, and difference between "present" states to the sum of user-defined transformation costs between secondary features. With such recoding, invoking multiple independent derivations of the structure and similar features will cost as many extra "steps" as the instances of similarities (in both original characters) that are not being homologized. The step-matrix recoding also can take into account nested dependences. We present a simple convention for naming characters, which TNT can use to automat...

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Section: Direct Counts Of Homoplasy: X-transformationsmentioning

confidence: 98%

A reconsideration of inapplicable characters, and an approximation with step‐matrix recoding

et al. 2021

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Exploring the impact of morphology, multiple sequence alignment and choice of optimality criteria in phylogenetic inference: a case study with the Neotropical orb-weaving spider genus Wagneriana (Araneae: Araneidae)

Cabra-García

Hormiga

2019

Zoological Journal of the Linnean Society

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We present a total evidence phylogenetic analysis of the Neotropical orb-weaving spider genus Wagneriana and discuss the phylogenetic impacts of methodological choices. We analysed 167 phenotypic characters and nine loci scored for 115 Wagneriana and outgroups, including 46 newly sequenced species. We compared total evidence analyses and molecular-only analyses to evaluate the impact of phenotypic evidence, and we performed analyses using the programs POY, TNT, RAxML, GARLI, IQ-TREE and MrBayes to evaluate the effects of multiple sequence alignment and optimality criteria. In all analyses, Wagneriana carimagua and Wagneriana uropygialis were nested in the genera Parawixia and Alpaida, respectively, and the remaining species of Wagneriana fell into three main clades, none of which formed a pair of sister taxa. However, sister-group relationships among the main clades and their internal relationships were strongly influenced by methodological choices. Alignment methods had comparable topological effects to those of optimality criteria in terms of ‘subtree pruning and regrafting’ moves. The inclusion of phenotypic evidence, 2.80–3.05% of the total evidence matrices, increased support irrespective of the optimality criterion used. The monophyly of some groups was recovered only after the addition of morphological characters. A new araneid genus, Popperaneus gen. nov., is erected, and Paraverrucosa is resurrected. Four new synonymies and seven new combinations are proposed.

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Systematic revision and total evidence phylogenetic analysis of the Andean family Metasarcidae Kury, 1994 (Opiliones: Laniatores), with description of two new genera and twenty new species

Benedetti¹,

Pinto‐da‐Rocha²

2022

ASP

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Metasarcidae Kury, 1994 (Gonyleptoidea) is exclusively distributed in the Andean region of South America, from northern Peru to southern Bolivia. This contribution reviews the family using traditional taxonomy and cladistics. The cladistic analysis is based on total evidence (TE), maximum likelihood (ML) and direct optimization of molecular and morphological characters. The data matrix is composed of DNA sequences from three mitochondrial loci (12S rRNA, 16S rRNA and COI), from two nuclear loci (28S rRNA and H3) and 68 phenotypic characters. The dataset consists of 25 ingroup terminals (representing 20 species of the family) and eight outgroup species. The parsimony analysis resulted in one most parsimonious tree (L=4910) that recovered a monophyletic Metasarcidae, sister-group of Cosmetidae. As a result of the taxonomic revision and cladistic hypothesis, a new classification is proposed with six genera and 38 valid species of Metasarcidae, of which two genera and 20 species are described for the first time. Additionally, the following are established: six generic name synonymies; four species synonymies; seven new species combinations; and three secondary homonym species names replaced.

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Parsimony analysis of unaligned sequence data: some clarifications

Abstract: De Laet (2015) claimed that minimization of ad hoc hypotheses of homoplasy does not lead to a preference for trivial optimizations when analysing unaligned

Cited by 3 publications

References 32 publications

A reconsideration of inapplicable characters, and an approximation with step‐matrix recoding

A reconsideration of inapplicable characters, and an approximation with step‐matrix recoding

Exploring the impact of morphology, multiple sequence alignment and choice of optimality criteria in phylogenetic inference: a case study with the Neotropical orb-weaving spider genus Wagneriana (Araneae: Araneidae)

Systematic revision and total evidence phylogenetic analysis of the Andean family Metasarcidae Kury, 1994 (Opiliones: Laniatores), with description of two new genera and twenty new species

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