scholarly journals Transformation of Quotient Values for their use as Continuous Cladistic Characters

2018 ◽  
Author(s):  
Steven Uros Vidovic
Keyword(s):  
Morphological Variation ◽  
Cladistic Analysis ◽  
Two Dimensions ◽  
Morphological Data ◽  
Operational Taxonomic Units ◽  
New Methods ◽  
Cladistic Analyses ◽  
Trigonometric Solution ◽  
Continuous Character ◽  
Logarithmic Solution

Recent advances in cladistic technology have produced novel methods for introducing morphological data into cladistic analyses, such as the landmark and continuous character functions in the software TNT and RevBayes. While these new methods begin to address the problem of representing morphology, there has been little consideration of how to transform and code the operational taxonomic units’ (OTUs) dimensions into the datamatrix. Indeed, angles, serial counts, percentages and quotient values can be used as continuous characters, but little has been said about how coding these data affect the trees discovered. Logically, counts of elements and angles measured off specimens may be coded directly into continuous character matrices but percentages and quotient values are more problematic, being transformed data. Quotient values and percentages are the simplest way of representing proportional differences between two dimensions and reducing the effect of inter-taxonomic magnitude differences. However, both are demonstrated to be problematic transformations that produce continuous characters with weighted states that are non-representative of morphological variation. Thus, two OTUs may be represented as less/more similar morphologically than other OTUs that display the same degree of morphological variation. Furthermore, the researcher’s choice of which dimension is the divisor and dividend will have a similar affect. To address this problem, a trigonometric solution and a logarithmic solution have been proposed. Another solution called linear transposition scaling (LTS) was recently presented, with the intention of best representing and coding observable morphological variation. All three methods are reviewed to establish the best way to represent and code morphology in a cladistic analysis using continuous characters.

Cladistic analysis and revision of Billardiera (Pittosporaceae)

2004 ◽  
Vol 17 (1) ◽  
pp. 83 ◽  
Author(s):  
L. W. Cayzer ◽  
M. D. Crisp ◽  
I. R. H. Telford
Keyword(s):  
New Taxa ◽  
Cladistic Analysis ◽  
Species Level ◽  
Morphological Data ◽  
New Combinations ◽  
The Family ◽  
Cladistic Analyses ◽  
Definition Of ◽  
First Time

Cladistic analyses of morphological data were used to clarify the definition of Billardiera in the context of other genera of the family Pittosporaceae. These analyses indicate that Billardiera s.str. is monophyletic including the small genera Sollya and Pronaya, but excluding Marianthus and Rhytidosporum, which have been previously included in a broader concept of Billardiera. The re-circumscribed Billardiera is revised, incorporating these changes. Five taxa are reinstated at species level (B. fusiformis, B. mutabilis, B. macrantha, B. speciosa and B.�venusta). Three are new combinations (B. fraseri, B. heterophylla, B. drummondii replacing Sollya drummondii) and three new taxa are described for the first time: B. nesophila, B. rubens and B. viridiflora.

Ternatus, a new spider genus from China with a cladistic analysis and comments on its phylogenetic placement (Araneae: Linyphiidae)

Zootaxa ◽  
2012 ◽  
Vol 3358 (1) ◽  
pp. 28
Author(s):  
NING SUN ◽  
BIN LI ◽  
LIHONG TU
Keyword(s):  
New Species ◽  
New Genus ◽  
Cladistic Analysis ◽  
Sister Group ◽  
Morphological Data ◽  
Sister Group Relationship ◽  
Phylogenetic Placement ◽  
Two New Species ◽  
Cladistic Analyses

A new spider genus, Ternatus n. gen., is erected to accommodate two new erigonine species from China, Ternatus malleatusn. sp. and Ternatus siculus n. sp. Descriptions and illustrations of the new genus and new species are provided. To test the phy-logenetic placement within Linyphiidae, morphological data of the two new species were added to the matrices of two previousstudies addressing the higher level phylogeny of erigonine spiders. The results of the cladistic analyses support the monophyly of the new genus and its sister group relationship to the genus Gonatium Menge, 1868.

Alpha-taxonomy and phylogeny of African Junoniini butterflies based on morphological data, with an emphasis on genitalia, and COI barcode (Lepidoptera: Nymphalidae)

Zootaxa ◽  
2021 ◽  
Vol 4991 (3) ◽  
pp. 401-433
Author(s):  
TOMASZ W. PYRCZ ◽  
KLAUDIA FLORCZYK ◽  
STEVE COLLINS ◽  
SZABOLCS SÁFIÁN ◽  
OSCAR MAHECHA-J. ◽  
...  
Keyword(s):  
Male Genitalia ◽  
Morphological Analysis ◽  
Cladistic Analysis ◽  
Central Africa ◽  
Molecular Data ◽  
Morphological Data ◽  
East African ◽  
East African Coast ◽  
Afrotropical Region ◽  
Close Relationship

The tribe Junoniini is a predominantly Paleotropical group of the cosmopolitan butterfly subfamily Nymphalinae (Nymphalidae), with highest diversity in the Afrotropical region. Its systematics and relationships are not entirely resolved. Question marks remain concerning the validity of some genera; and the apparently close relationship between the Indo-Australian genus Yoma and the Afrotropical Protogoniomorpha, as evidenced by molecular phylogenies, remains a puzzle. Here, we present a cladistic analysis, based on 42 characters of the male and female genitalia of 41 species of Junoniini belonging to six genera, nearly all of them continental Afrotropical, and 3 species of two Indo-Australian genera Yoma and Rhinopalpa. A ML COI-based tree is produced for 36 species of Afrotropical Junoniini and Yoma. The molecular data are consistent with previous studies. However, morphological analysis does not confirm a close relationship between Protogoniomorpha and Yoma. Despite the evolution of a number of modifications, the male genitalia within all genera and species of the Junoniini share a cohesive build plan, in particular a transformed sacculus, from which Yoma is highly divergent. The position of the genus Kamilla, previously synonymized with Junonia, is discussed. Three East African coast taxa, Junonia elgiva stat. reinst., Protogoniomorpha nebulosa stat. reinst. and Salamis amaniensis stat. reinst., and one from central Africa, Precis silvicola stat. reinst. are raised to species level, based on comparative analysis of their male genitalia.  

scholarly journals Comparative Cladistics: Fossils, Morphological Data Partitions and Lost Branches in the Fossil Tree of Life

2017 ◽  
Author(s):  
Ross Mounce
Keyword(s):  
Large Scale ◽  
Phylogenetic Signal ◽  
Scientific Progress ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Sets ◽  
Phylogenetic Groups ◽  
Use Of Data ◽  
Wide Range ◽  
Cladistic Analyses

In this thesis I attempt to gather together a wide range of cladistic analyses of fossil and extant taxa representing a diverse array of phylogenetic groups. I use this data to quantitatively compare the effect of fossil taxa relative to extant taxa in terms of support for relationships, number of most parsimonious trees (MPTs) and leaf stability. In line with previous studies I find that the effects of fossil taxa are seldom different to extant taxa – although I highlight some interesting exceptions. I also use this data to compare the phylogenetic signal within vertebrate morphological data sets, by choosing to compare cranial data to postcranial data. Comparisons between molecular data and morphological data have been previously well explored, as have signals between different molecular loci. But comparative signal within morphological data sets is much less commonly characterized and certainly not across a wide array of clades. With this analysis I show that there are many studies in which the evidence provided by cranial data appears to be be significantly incongruent with the postcranial data – more than one would expect to see just by the effect of chance and noise alone. I devise and implement a modification to a rarely used measure of homoplasy that will hopefully encourage its wider usage. Previously it had some undesirable bias associated with the distribution of missing data in a dataset, but my modification controls for this. I also take an in-depth and extensive review of the ILD test, noting it is often misused or reported poorly, even in recent studies. Finally, in attempting to collect data and metadata on a large scale, I uncovered inefficiencies in the research publication system that obstruct re-use of data and scientific progress. I highlight the importance of replication and reproducibility – even simple reanalysis of high profile papers can turn up some very different results. Data is highly valuable and thus it must be retained and made available for further re-use to maximize the overall return on research investment.

The phylogenetic position of the tuatara, Sphenodon (Sphenodontida, Amniota), as indicated by cladistic analysis of the ultrastructure of spermatozoa

1992 ◽  
Vol 335 (1274) ◽  
pp. 207-219 ◽  
Keyword(s):  
Cladistic Analysis ◽  
Sister Group ◽  
Sister Taxon ◽  
Phylogenetic Position ◽  
Sister Group Relationship ◽  
Usual Concept ◽  
Cladistic Analyses ◽  
Relationship Of

Sphenodon has traditionally been regarded as a little changed survivor of the Permo-Triassic thecodont or eosuchian ‘stem reptiles’ but has alternatively been placed in the Lepidosauria as the plesiomorphic or even apomorphic sister-taxon of the squamates. A cladistic analysis of 16 characters from spermatozoal ultrastructure of Sphenodon and other amniotes unequivocally confirms its exceedingly primitive status. The analysis suggests that monotremes are the sister-group of birds; squamates form the sister-group of a bird + monotreme clade while the three sister-groups successively below the bird + monotreme + squa- mate assemblage are the caiman, the tuatara and the outgroup (turtles). The monotreme + bird couplet, supports the concept of the Haemothermia, but can only be regarded heuristically. The usual concept of mammals as a synapsid-derived outgroup of all other extant amniotes is not substantiated spermatologically. All cladistic analyses made, and a separate consideration of apomorphies, indicate that Sphenodon is spermatologically the most primitive amniote, excepting the Chelonia. It is advanced (apomorphic) for the amniotes in only two of the 16 spermatozoal characters considered. A close, sister-group relationship of Sphenodon with squamates is not endorsed.

scholarly journals Towards a phylogeny of the Metazoa: evaluating alternative phylogenetic positions of Platyhelminthes, Nemertea, and Gnathostomulida, with a critical reappraisal of cladistic characters

2004 ◽  
Vol 73 (1-2) ◽  
pp. 3-163 ◽  
Author(s):  
Ronald A. Jenner
Keyword(s):  
Sister Group ◽  
Morphological Characters ◽  
Total Evidence ◽  
Morphological Data ◽  
Future Research ◽  
Sister Group Relationship ◽  
Cladistic Analyses ◽  
Phylogenetic Hypotheses ◽  
Data Matrices

This paper critically assesses all morphological cladistic analyses of the Metazoa that were published during the last one and a half decades. Molecular and total evidence analyses are also critically reviewed. This study focuses on evaluating alternative phylogenetic positions of the ‘acoelomate’ worms: Platyhelminthes, Nemertea, and Gnathostomulida. This paper consists of two parts. In Part I, all recently proposed sister group hypotheses and the supporting synapomorphies for these phyla are evaluated. Discrepancies in the treatment of corresponding characters in different cladistic analyses are identified, and where possible, resolved. In Part II, the overall phylogenetic significance across the Metazoa of all characters relevant for placing the ‘acoelomate’ worms is examined. The coding and scoring of these characters for other phyla are evaluated, and uncertainties in our understanding are pointed out in order to guide future research. The characters discussed in this paper are broadly categorized as follows: epidermis and cuticle, reproduction and sexual condition, development, larval forms, coeloms and mesoderm source, nervous system and sensory organs, nephridia, musculature, digestive system, and miscellaneous characters. Competing phylogenetic hypotheses are compared in terms of several criteria: 1) taxon sampling and the fulfillment of domain of definition for each character; 2) character sampling; 3) character coding; 4) character scoring and quality of primary homology; 5) quality of the proposed diagnostic synapomorphies as secondary homologies. On the basis of this study I conclude that a sister group for the Platyhelminthes has not yet been unambiguously established. A clade minimally composed of Neotrochozoa (Mollusca, Sipuncula, Echiura, Annelida) emerges as the most likely sister group of the Nemertea on the basis of morphological and total evidence analyses. Finally, morphological data currrently favor a sister group relationship of Gnathostomulida and Syndermata (probably plus Micrognathozoa). In contrast, molecular or total evidence analyses have not identified a reliable sister group of Gnathostomulida.Further progress in our understanding of metazoan phylogeny crucially depends on the improvement of the quality of currently adopted cladistic data matrices. A thorough reassessment of many of the more than 70 morphological characters discussed here is necessary. Despite the recent compilation of comprehensive data matrices, the power to test competing hypotheses of higher-level metazoan relationships is critically compromised due to uncritical data selection and poor character study in even the most recently published cladistic analyses.

The skull of Cochleosaurus bohemicus Frič, a temnospondyl from the Czech Republic (Upper Carboniferous) and cochleosaurid interrelationships

2003 ◽  
Vol 94 (1) ◽  
pp. 21-43 ◽  
Author(s):  
Sandra E. K. Sequeira
Keyword(s):  
Czech Republic ◽  
Cladistic Analysis ◽  
Ventral Surface ◽  
Morphological Data ◽  
Ontogenetic Change ◽  
The Czech Republic ◽  
Upper Carboniferous

ABSTRACTThe cranial anatomy of the primitive Carboniferous temnospondyl Cochleosaurus bohemicus is described herein from several large, presumably adult, skulls. This new morphological data modifies earlier descriptions by Frič (=Fritsch in post-1876 publications), Romer and Steen, which were based almost entirely on small, subadult Cochleosaurus bohemicus specimens. Recognition of a new autapomorphy for Cochleosaurus bohemicus, (pitting on the ventral surface of the postorbitals) which is independent of ontogenetic change, has facilitated more accurate intra-specific comparisons between cochleosaurids. Cladistic analysis reveals a clear dichotomy separating the Edopoidea from the more derived clade of the remaining temnospondyls, which includes Balanerpeton and Dendrerpeton. The Edopoidea are only weakly supported as a superfamily in this analysis. The Cochleosauridae are a monophyletic family comprising the genera Procochleosaurus, Adamanterpeton, Cochleosaurus and Chenoprosopus.

scholarly journals Phylogenetic relationships of Lecythidaceae: a cladistic analysis using rbcL sequence and morphological data

1997 ◽  
Vol 84 (4) ◽  
pp. 530-540 ◽  
Author(s):  
Cynthia M. Morton ◽  
Scott A. Mori ◽  
Ghillean T. Prance ◽  
Ken G. Karol ◽  
Mark W. Chase
Keyword(s):  
Phylogenetic Relationships ◽  
Cladistic Analysis ◽  
Morphological Data ◽  
Rbcl Sequence

Phylogeny reconstruction and the tempo of speciation in cheilostome Bryozoa

Paleobiology ◽  
1994 ◽  
Vol 20 (4) ◽  
pp. 407-423 ◽  
Author(s):  
Jeremy B. C. Jackson ◽  
Alan H. Cheetham
Keyword(s):  
Effective Means ◽  
Morphological Variability ◽  
Genetic Distances ◽  
Morphological Data ◽  
Phylogeny Reconstruction ◽  
High Confidence ◽  
Skeletal Morphology ◽  
Living Species ◽  
Cladistic Analyses ◽  
Tight Correlation

We compared phylogenies derived from morphological data for two cheilostome bryozoan genera, Stylopoma and Metrarabdotos, with genetic differences between species (Stylopoma) and the stratigraphic occurrence of fossils (both genera). Correspondence between species of Stylopoma defined by protein electrophoresis and on preservable skeletal morphology is excellent, despite great morphological variability within colonies and the predominance of quantitative over discrete characters. Moreover, agreement between genetic and morphological classifications increased greatly when morphological discrimination was pushed to the limit, despite inability to consistently assign all specimens to species with high confidence. This “splitting” strategy also maximized the correlation between genetic distances and the distances between species in cladistically derived phylogenies.Fossil and living species of both genera are sufficiently abundant and widespread to provide credible limits for inferred ancestral relationships. Inclusion of fossils in cladistic analyses of Stylopoma increased the consistency of cladistic hypotheses by up to 30% and provided a more effective means of rooting trees than comparison with living species of the most closely related genus (“outgroup”). Moreover, in the case of Metrarabdotos, failure to incorporate stratigraphic information turned the cladogram virtually upside down, so that postulated ancestors first appear in the fossil record 6–16 m.y. after their putative descendants became extinct.Stratigraphically rooted trees suggest that most well-sampled Metrarabdotos and Stylopoma species originated fully differentiated morphologically and persisted unchanged for > 1 to > 16 m.y., typically alongside their putative ancestors. Moreover, the tight correlation between phenetic, cladistic, and genetic distances among living Stylopoma species suggests that changes in all three variables occurred together during speciation. All of these observations support the punctuated equilibrium model of speciation.

scholarly journals A molecular method for a qualitative analysis of potentially coding sequences of DNA

2004 ◽  
Vol 64 (3a) ◽  
pp. 383-398
Author(s):  
M. L. Christoffersen ◽  
M. E. Araújo ◽  
M. A. M. Moreira
Keyword(s):  
Amino Acid ◽  
Phylogenetic Analyses ◽  
A Priori ◽  
Morphological Data ◽  
Computer Algorithms ◽  
Protein Coding ◽  
Tree Topologies ◽  
Alternative Amino Acid ◽  
Cladistic Analyses ◽  
Transformation Series

Total sequence phylogenies have low information content. Ordinary misconceptions are that character quality can be ignored and that relying on computer algorithms is enough. Despite widespread preference for a posteriori methods of character evaluation, a priori methods are necessary to produce transformation series that are independent of tree topologies. We propose a stepwise qualitative method for analyzing protein sequences. Informative codons are selected, alternative amino acid transformation series are analyzed, and most parsimonious transformations are hypothesized. We conduct four phylogenetic analyses of philodryanine snakes. The tree based on all nucleotides produces least resolution. Trees based on the exclusion of third positions, on an asymmetric step matrix, and on our protocol, produce similar results. Our method eliminates noise by hypothesizing explicit transformation series for each informative protein-coding amino acid. This approaches qualitative methods for morphological data, in which only characters successfully interpreted in a phylogenetic context are used in cladistic analyses. The method allows utilizing character information contained in the original sequence alignment and, therefore, has higher resolution in inferring a phylogenetic tree than some traditional methods (such as distance methods).

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