The philosophy of total evidence and its relevance for phylogenetic inference

Rieppel, Olivier

doi:10.1590/s0031-10492005000800001

Cited by 32 publications

(33 citation statements)

References 66 publications

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“…In this study, based on the comparison of the poly morphism of intronic sequences of the ATP synthase α subunit gene, the previously published nucleotide sequences of mitochondrial genes, and the morpho logical descriptions of respective species, the first attempt to construct a phylogenetic tree of Baicaliidae combining all the traits was made, which was based on a single Bayesian approach (Rieppel, 2005;Ronquist et al, 2012).…”

Section: Genetic and Morphologicalmentioning

confidence: 99%

Genetic and morphological diversification in gastropods of the Baicaliidae family

Kovalenkova

Sitnikova

Sherbakov

2015

Russ J Genet Appl Res

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The combined ("total evidence") phylogenetic inference was based on the comparison of the intronic nucleotide sequences of the ATP synthase α subunit gene of 11 gastropod species belonging to the rapidly evolving Baikalian endemic family Baicaliidae, the morphological description of these species, and the previously published sequences of the mitochondrial gene coding the first subunit of cytochrome c oxi dase. The phylogeny based on the intron sequences agrees well with the morphology. It is shown that sister species usually have similar substrate preferences. Certain discrepancy in the phylogenetic tree topology and the taxonomy based on morphological traits is probably due to the rapid morphological evolution of mollusks of the family Baicaliidae.

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Section: Genetic and Morphologicalmentioning

confidence: 99%

Genetic and morphological diversification in gastropods of the Baicaliidae family

Kovalenkova

Sitnikova

Sherbakov

2015

Russ J Genet Appl Res

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“…An increasingly algorithmic approach to characters has become predominant in the analysis of morphological characters as well, under the paradigm of a total evidence approach that combines all available character data without critical evaluation of homology hypotheses. Indeed, the congruence of characters (coherence of character statements: Rieppel 2004) relative to a hierarchy has become accepted as the sole arbiter of homology vs. non-homology (homoplasy) by many contemporary systematists, irrespective of the nature of the data (Rieppel 2005a). In an effort to avoid theory-ladenness of character statements, systematics has moved towards an operationalist approach to character delineation (Kearney, in press), where theoretical input into the process of character conceptualization is rejected in favor of an appeal to mere congruence in the evaluation of whatever character hypothesis is being proposed (e.g.…”

Section: Introductionmentioning

confidence: 99%

The Poverty of Taxonomic Characters

Rieppel

Kearney

2006

Biol Philos

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The theory and practice of contemporary comparative biology and phylogeny reconstruction (systematics) emphasizes algorithmic aspects but neglects a concern for the evidence. The character data used in systematics to formulate hypotheses of relationships in many ways constitute a black box, subject to uncritical assessment and social influence. Concerned that such a state of affairs leaves systematics and the phylogenetic theories it generates severely underdetermined, we investigate the nature of the criteria of homology and their application to character conceptualization in the context of transformationist and generative paradigms. Noting the potential for indeterminacy in character conceptualization, we conclude that character congruence (the coherence of character statements) relative to a hierarchy is a necessary, but not a sufficient, condition for phylogeny reconstruction. Specifically, it is insufficient due to the lack of causal grounding of character hypotheses. Conceptualizing characters as homeostatic property cluster natural kinds is in accordance with the empirical practice of systematists. It also accounts for the lack of sharpness in character conceptualization, yet requires character identification and re-identification to be tied to causal processes.

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“…The new species was recovered in MP and ML nuclear trees as the sister taxon of T. cocorobensis, but placed as sister of the clade formed by (T. cocorobensis (T. catalanensis ((T. cocorobensis ((T. torquatus + T. imbituba) (T. catalanensis (T. chromatops + T. etheridgei)))) in MP and ML mitochondrial analyses. Total evidence and topological conflict: Inasmuch as separate analyses were useful for understanding differences and inferring the sources of topological conflict (Nixon and Carpenter, 1996;Peloso et al, 2015; but see Kluge, 2003, andFitzhugh, 2006, for a critique on this kind of data exploration), we favored the phylogenetic hypotheses based on the analyses of our concatenated data set following the principle of character congruence or total evidence (Carnap, 1950, who credited much earlier workers; subsequently championed by others including Kluge, 1989;Rieppel, 2005, andFitzhugh, 2006). The ML total evidence tree was preferred as the best hypothesis representing the phylogenetic relationships of tropidurines ( fig.…”

Section: Phylogeneticsmentioning

confidence: 99%

A NewTropidurus(Tropiduridae) from the Semiarid Brazilian Caatinga: Evidence for Conflicting Signal between Mitochondrial and Nuclear Loci Affecting the Phylogenetic Reconstruction of South American Collared Lizards

Carvalho

Sena

Peloso

et al. 2016

American Museum Novitates

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Tropidurus Wied, 1825, is one of the most ubiquitous lizard genera distributed in open habitats of tropical and subtropical South America. Nevertheless, the broad representation of specimens of this group in scientific collections is hardly reflected in our knowledge of its taxonomic diversity. Most species currently assigned to Tropidurus began to be uncovered in the early 1980's and additional populations in need of formal taxonomic treatment have been cataloged ever since. Herein, we name Tropidurus sertanejo, n. sp., a new species of the T. torquatus group endemic to the semiarid Brazilian Caatinga. Tropidurus sertanejo, n. sp., is currently known from two isolated populations in the municipalities of Caetité and Ibotirama Bahia, Brazil. This is the only species of the T. torquatus group lacking granular mite pockets on the lateral neck, and it is also diagnosable by having a conspicuous bronze-colored head, a light-brown dorsal body with small pale salmon spots, and small body size in comparison with most congeners. Phylogenetic analyses recovered a paraphyletic Tropidurus, but firmly supported T. sertanejo, n. sp., as member of a monophyletic T. torquatus species group. Trees generated by independent analyses of nuclear and mitochondrial sequence data conflicted with our total evidence phylogenetic hypotheses. Since topological disagreements were detected among phylogenetic trees resulting from maximum parsimony (MP) and maximum likelihood (ML) reconstructions, and MP analyses do not require distinct evolutionary models or partition schemes to be defined prior to conduction of phylogenetic reconstruction, these factors were considered unlikely to explain all the variation in the observed results, favoring the interpretation of conflicting phylogenetic signal. Because detailed information on the distribution, population size, and ecological requirements of T. sertanejo, n. sp., are currently unavailable, we recommend the species to be listed as "data deficient" following the rules proposed by IUCN.

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The philosophy of total evidence and its relevance for phylogenetic inference

Abstract: ABSTRACT

Cited by 32 publications

References 66 publications

Genetic and morphological diversification in gastropods of the Baicaliidae family

Genetic and morphological diversification in gastropods of the Baicaliidae family

The Poverty of Taxonomic Characters

A NewTropidurus(Tropiduridae) from the Semiarid Brazilian Caatinga: Evidence for Conflicting Signal between Mitochondrial and Nuclear Loci Affecting the Phylogenetic Reconstruction of South American Collared Lizards

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