On Character Coding for Phylogeny Reconstruction

Pleijel, Fredrik

doi:10.1111/j.1096-0031.1995.tb00092.x

Cited by 165 publications

(200 citation statements)

References 10 publications

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“…139 Specimens for the molecular analyses were stored in 100% ethanol, 140 whereas vouchers and specimens used for morphological studies 141 were fixed in 2% glutaraldehyde in cacodylate buffer or 2% parafor-142 maldehyde in PBS. All the investigated material is listed in hierarchically following the principles of C-coding (Pleijel, 1995 cated, a minimum of 10-15 whole mounted specimens were mea-219 sured. All measures were taken from relaxed and fixed specimens.…”

mentioning

confidence: 99%

Molecular and morphological phylogeny of Saccocirridae (Annelida) reveals two cosmopolitan clades with specific habitat preferences

Domênico

Martínez

Lana

et al. 2014

Molecular Phylogenetics and Evolution

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mentioning

confidence: 99%

Molecular and morphological phylogeny of Saccocirridae (Annelida) reveals two cosmopolitan clades with specific habitat preferences

Domênico

Martínez

Lana

et al. 2014

Molecular Phylogenetics and Evolution

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“…In fact, dichotomizing continuous or quasicontinuous variation results in a loss of information (González-José et al 2008;Hawks 2004;Willermet 2001). Pleijel (1995) identified four distinct methods for coding data using dichotomous or multistate methods, each with distinct advantages and disadvantages, and with implications for the resulting cladistic analysis. Strait et al (1997) analyzed the effect of utilizing variable characters as data on cladistic analysis.…”

Section: Methodsmentioning

confidence: 99%

Untitled

2012

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Recognizing fossil species, and reconstructing their phylogenetic relationships, is dependent in part on our ability to accurately record and analyze continuously distributed data. We usually classify specimens into groups (whether species or populations) by using crisp set theory. Fuzzy set theory can aid analysis in situations where populations have indistinct boundaries. Two primary areas of cladistic research contain elements of fuzzinessthe species concept itself, and the variables we use to analyze phylogenetic relationships among species. Analytical determination of species boundaries can be difficult due to hybridization as well as intra-and inter-specific variability. However, cladistic analysis requires that taxa are monophyletic, and unique in their morphological patterns. Variables used in cladistic analysis must be coded using discrete character states to determine polarity. But many morphological and metric variables are continuous or quasicontinuous in distribution, and are problematic for use in cladistic analyses without some type of non-overlapping dichotomization or breakpoint. The issue of how to utilize these continuously or quasicontinuously distributed variables, whether metric or nonmetric, is an ongoing issue in phylogenetic analysis. Fuzzy set theory is a method that circumvents two problematic assumptions implicit in phylogenetic analyses-crispness of taxa and crispness of traits. Using a fuzzy analysis, multiple character states are maintained through fuzzy variable sets that maintain the fuzziness of boundaries. Additionally, fuzzy analysis calculates a measure of the degree of group membership.To illustrate this process, I analyzed nine multistate nonmetric cranial variables representing three regions of the skull on 14 Neandertals and 24 early moderns using a Mamdani Fuzzy Inference System to compare the relative performance of fuzzy and crisp variables and groups on group identification. The analysis that performed best contained both fuzzy trait groups and fuzzy taxon groups. Fuzzy analysis is useful to explore the degree to which fuzziness is present in trait variation and in taxa, and it can advance our understanding of species identification and phylogeny construction. Expanding our toolkit to include fuzzy set analysis can help us determine how crisp or fuzzy are our putative taxonomic groups. "[T]he cult of impressive technicalities or the cult of precision may get the better of us, and interfere with our search for clarity, simplicity, and truth" (Popper 1983: 60). "The closer one looks at a real-world problem, the fuzzier becomes its solution" (Zadeh 1973: 28). INTRODUCTIONT here are many areas in paleoanthropology where precision eludes us. It is uncertain how many fossil species existed in the past; fossil sample sizes are small, and the magnitude and pattern of character variation within fossil species is unknown. It is unclear to what degree many characters are correlated, or are selectively neutral. Nonmetric characters may present as a continuous distributio...

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“…Below The jaw musculature of turtles is presented following the lotus approach (modified from Werneburg 2011, see text for details) coding strategies that are used for bony structures are not applicable here. As such, several alternative character coding approaches could be developed, all of which have advantages and disadvanteges (sensu Pleijel 1995). I decided on three alternative coding strategies, and estimated their influence on character distribution.…”

Section: Methodsmentioning

confidence: 99%

“…This, however, is less likely as many clades are confirmed both by osteological and molecular data; (2) The codings of characters presented herein might not be adequate for phylogenetic reconstructions. As pointed out by Pleijel (1995), Wiens (2000), and many others, the definition of character states indeed has an important influence on the output of a phylogenetic analysis. As reviewed by those authors, and many others, none of the coding strategies (e.g.…”

Section: Using Atomised Characters For Phylogenetic Reconstructionsmentioning

confidence: 99%

Jaw musculature during the dawn of turtle evolution

Werneburg

2012

Org Divers Evol

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Using a new approach to study muscle anatomy in vertebrates, the fully differentiated jaw musculature of 42 turtle species was studied and character mappings were performed. Soft tissue arrangements were correlated to the temporal openings (emarginations) of the skull and the trochlearis system of the jaw apparatus among turtle taxa. When compared to the cranial anatomy of stem Testudines, most characters detected as diagnostic of particular extant groups have to be considered as being evolved first within Testudines. Hence, jaw muscle anatomy of extant turtles is difficult to compare to that of other reptilian taxa. Moreover, the high number of apomorphic character changes speaks for a divergating turtle and saurian morphotype of jaw musculature, which could indicate either a position of turtles outside of Sauria or a highly derived, undetectable origin within that group. In general, a low direct correlation of most soft and hard tissue characters was detected. This finding could imply that both character complexes are more integrated to each other driven by functional morphology; i.e., the composition of muscle fibre types. That condition highlights the difficulty in using gross anatomy of jaw muscle characters to interpret temporal bone arrangements among amniotes in general.

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On Character Coding for Phylogeny Reconstruction

Cited by 165 publications

References 10 publications

Molecular and morphological phylogeny of Saccocirridae (Annelida) reveals two cosmopolitan clades with specific habitat preferences

Molecular and morphological phylogeny of Saccocirridae (Annelida) reveals two cosmopolitan clades with specific habitat preferences

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Jaw musculature during the dawn of turtle evolution

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