Majority Does Not Rule: The Trouble with Majority‐Rule Consensus Trees

Sharkey, Michael J.; Leathers, Jason W.

doi:10.1111/j.1096-0031.2001.tb00124.x

Cited by 10 publications

(7 citation statements)

References 8 publications

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“…Bootstrapping and majority rule consensus may be a strategy for improving the structure of morphometric trees when within-taxon variation is large compared to between-taxon variation. Because of this, the issues with majority-rule and morphometric data are different from those associated with majority-rule and discrete-character cladistic trees, which were criticized by Sharkey and Leathers (2001).…”

Section: Phylogenetic Components Of Shape Variancementioning

confidence: 99%

Phylogenetic and Environmental Components of Morphological Variation: Skull, Mandible, and Molar Shape in Marmots (Marmota, Rodentia)

Caumul,

Polly

2005

Evolution

229

192

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Abstract. The phenotype is a product of its phylogenetic history and its recent adaptation to local environments, but the relative importance of the two factors is controversial. We assessed the effects of diet, habitat, elevation, temperature, precipitation, body size, and mtDNA genetic divergence on shape variation in skulls, mandibles, and molars, structures that differ in their genetic and functional control. We asked whether these structures have adapted to environment to the same extent and whether they retain the same amount of phylogenetic signal. We studied these traits in intra-and interspecific populations of Eurasian marmots whose last common ancestor lived 2-5 million years ago. Path Analysis revealed that body size explained 10% of variation in skulls, 7% in mandibles, and 15% in molars. Local vegetation explained 7% of variation in skulls, 11% in mandibles, and 12% in molars. Dietary category explained 25% of variation in skulls, 11% in mandibles, and 9% in molars. Cyt b mtDNA divergence (phylogeny) explained 15% of variation in skulls, 7% in mandibles, and 5% in molars. Despite the percentages of phylogenetic variance, maximum-likelihood trees based on molar and skull shape recovered most phylogenetic groupings correctly, but mandible shape did not. The good performance of molars and skulls was probably due to different factors. Skulls are genetically and functionally more complicated than teeth, and they had more mathematically independent components of variation (5-6-in skulls compared to 3-in molars). The high proportion of diet-related variance was not enough to mask the phylogenetic signal. Molars had fewer independent components, but they also have less ecophenotypic variation and evolve more slowly, giving each component a proportionally stronger phylogenetic signal. Molars require larger samples for each operational taxonomic unit than the other structures because the proportion of within-taxon to between-taxon variation was higher. Good phylogenetic signal in quantitative skeletal morphology is likely to be found only when the taxa have a common ancestry no older than hundreds of thousands or millions of years (1% to 10% mtDNA divergence)-under these conditions skulls and molars provide stronger signal than mandibles. The phenotype is the product both of phylogenetic history and recent adaptation to local environments, but the relative importance of the two factors in explaining morphometric variation is contested (MacLeod and Forey 2002). Some studies have concluded that morphology is an unreliable indicator of phylogenetic relationships because of capricious, adaptation-driven homoplasy (e.g., Graur et al. 1997;Collard and Wood 2001;Stone and Cook 2002) or because of lack of differentiation among genetically distinct populations (e.g., Barratt et al. 1997; Mayer and von Helvernsen 2001;Roca et al. 2004). But other studies have found significant phylogeographic structuring in morphometric data among closely related taxa (Thorpe 1976;Straney and Patton 1980;Hausser 1984;Malhotra and Thor...

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Section: Phylogenetic Components Of Shape Variancementioning

confidence: 99%

Phylogenetic and Environmental Components of Morphological Variation: Skull, Mandible, and Molar Shape in Marmots (Marmota, Rodentia)

Caumul,

Polly

2005

Evolution

229

192

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“…The MRC is a form of consensus that pre- serves all clades present in the majority (i.e., in more than 50%) of the obtained set of equally parsimonious cladograms (Margush and McMorris 1981). The 50% rule ensures that all included clades are compatible (Sharkey and Leathers 2001). In spite of some criticism (e.g., Sharkey and Leathers 2001), several authors are using MRC as a method of weighting clades to solve ambiguous strict consensus trees (e.g., Swofford 1991, Candall and Fritzpatrick 1996, Titus and Larson 1996, Lutzoni 1997.…”

Section: Methodsmentioning

confidence: 99%

Taxonomic review and phylogenetic analysis of Enchodontoidei (Teleostei: Aulopiformes)

Silva

Gallo

2011

An. Acad. Bras. Ciênc.

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“…The strict consensus is often deemed too strict, or insensitive, especially when taxa with a significant amount of missing data (e.g., fossils) are considered (e.g., Wilkinson 1994Wilkinson , 2003. Concerning the majority-rule consensus, it has been demonstrated that when ambiguity is rampant within a data matrix, especially because of missing data, biases in the method may drive the consensus tree toward the most ambiguous set of topologies (Sharkey & Leathers 2001;Sumrall et al 2001). Finally, the interpretation of the Adams consensus if often ambiguous because it does not represent common components/clades as strict and majority-rule consensus do, but common nestings (see Wilkinson 1994 andKitching et al 1998 for an introduction to the literature relating to consensus trees).…”

Section: Interpretation Of Consensus Treesmentioning

confidence: 99%

Reassessment of the phylogenetic interrelationships of basal turtles (Testudinata)

Anquetin¹

2017

Preprint

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Recent discoveries from the Late Triassic and Middle Jurassic have significantly improved the fossil record of early turtles. These new forms offer a unique opportunity to test the interrelationships of basal turtles. Nineteen fossil species are added to the taxon sample of the most comprehensive morphological phylogenetic analysis of the turtle clade. Among these additional species are recently discovered forms (e.g., Odontochelys semitestacea, Eileanchelys waldmani, Condorchelys antiqua), taxa generally omitted from previous analyses (e.g., chengyuchelyids, Sichuanchelys chowi) and species included in a phylogenetic analysis for the first time (Naomichelys speciosa and Siamochelys peninsularis). The coding of several characters is reassessed in light of recent observations, but also in order to reduce unwarranted assumptions on character and character state homologies. Additional characters from previous analyses, as well as five new ones, are also included, resulting in a data matrix of 178 characters scored for 86 turtle species and 7 fossil outgroups.The data set resolves the relationships of most newly included taxa, with the exception of Sichuanchelys chowi and 'Chengyuchelys' dashanpuensis. The phylogenetic placement of Heckerochelys romani, Condorchelys antiqua and Eileanchelys waldmani as stem turtles more derived than Kayentachelys aprix but more basal than Meiolania platyceps and Mongolochelys efremovi is corroborated. The relationships of chengyuchelyids remain unclear and more investigation is needed regarding these forms, yet interestingly they are unstable with respect to stem turtles. In contrast to previous analyses, Arundelemys dardeni is placed within pleurosternids. Siamochelys peninsularis falls within xinjiangchelyids. Perhaps the most salient conclusion of the present study is the placement of Naomichelys speciosa as a basal member of a clade uniting meiolaniids, Mongolochelys efremovi and Otwayemys cunicularius. This clade of rather large stem turtles was spread worldwide during the Mesozoic at least and persisted up until the Pleistocene with meiolaniids.This work is licensed under the Creative Commons Attribution 4.0 International License.CC-BY 4.0

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Majority Does Not Rule: The Trouble with Majority‐Rule Consensus Trees

Abstract: The use of majority‐rule consensus trees as a means of resolving ambiguity in phylogenetic analyses is investigated. It is shown to be an inappropriate method for this purpose.

Cited by 10 publications

References 8 publications

Phylogenetic and Environmental Components of Morphological Variation: Skull, Mandible, and Molar Shape in Marmots (Marmota, Rodentia)

Phylogenetic and Environmental Components of Morphological Variation: Skull, Mandible, and Molar Shape in Marmots (Marmota, Rodentia)

Taxonomic review and phylogenetic analysis of Enchodontoidei (Teleostei: Aulopiformes)

Reassessment of the phylogenetic interrelationships of basal turtles (Testudinata)

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