Quantitative Cladistic Analyses of Chromosomal Banding Data Among Species in Three Orders of Mammals: Hominoid Primates, Felids and Arvicolid Rodents

1988 ◽  
pp. 215-242 ◽  
Author(s):  
William S. Modi ◽  
Stephen J. O’Brien
Keyword(s):  
Cladistic Analyses ◽  
Chromosomal Banding

scholarly journals Discovery of Lebambromyia in Myanmar Cretaceous Amber: Phylogenetic and Biogeographic Implications (Insecta, Diptera, Phoroidea)

Insects ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 354
Author(s):  
Davide Badano ◽  
Qingqing Zhang ◽  
Michela Fratini ◽  
Laura Maugeri ◽  
Inna Bukreeva ◽  
...  
Keyword(s):  
Early Cretaceous ◽  
Late Cretaceous ◽  
Phase Contrast ◽  
First Record ◽  
Geographic Range ◽  
X Ray ◽  
Monophyletic Lineage ◽  
Cladistic Analyses

Lebambromyia sacculifera sp. nov. is described from Late Cretaceous amber from Myanmar, integrating traditional observation techniques and X-ray phase contrast microtomography. Lebambromyia sacculifera is the second species of Lebambromyia after L. acrai Grimaldi and Cumming, described from Lebanese amber (Early Cretaceous), and the first record of this taxon from Myanmar amber, considerably extending the temporal and geographic range of this genus. The new specimen bears a previously undetected set of phylogenetically relevant characters such as a postpedicel sacculus and a prominent clypeus, which are shared with Ironomyiidae and Eumuscomorpha. Our cladistic analyses confirmed that Lebambromyia represented a distinct monophyletic lineage related to Platypezidae and Ironomyiidae, though its affinities are strongly influenced by the interpretation and coding of the enigmatic set of features characterizing these fossil flies.

scholarly journals SINE Insertions in Cladistic Analyses and the Phylogenetic Affiliations of Tarsius bancanus to Other Primates

Genetics ◽  
2001 ◽  
Vol 157 (2) ◽  
pp. 777-784
Author(s):  
Jürgen Schmitz ◽  
Martina Ohme ◽  
Hans Zischler
Keyword(s):  
New World ◽  
World Monkey ◽  
Old World ◽  
Alu Elements ◽  
Alu Sequences ◽  
Short Interspersed Elements ◽  
Divergence Point ◽  
Tarsius Bancanus ◽  
Cladistic Analyses ◽  
The Common

Abstract Transpositions of Alu sequences, representing the most abundant primate short interspersed elements (SINE), were evaluated as molecular cladistic markers to analyze the phylogenetic affiliations among the primate infraorders. Altogether 118 human loci, containing intronic Alu elements, were PCR analyzed for the presence of Alu sequences at orthologous sites in each of two strepsirhine, New World and Old World monkey species, Tarsius bancanus, and a nonprimate outgroup. Fourteen size-polymorphic amplification patterns exhibited longer fragments for the anthropoids (New World and Old World monkeys) and T. bancanus whereas shorter fragments were detected for the strepsirhines and the outgroup. From these, subsequent sequence analyses revealed three Alu transpositions, which can be regarded as shared derived molecular characters linking tarsiers and anthropoid primates. Concerning the other loci, scenarios are represented in which different SINE transpositions occurred independently in the same intron on the lineages leading both to the common ancestor of anthropoids and to T. bancanus, albeit at different nucleotide positions. Our results demonstrate the efficiency and possible pitfalls of SINE transpositions used as molecular cladistic markers in tracing back a divergence point in primate evolution over 40 million years old. The three Alu insertions characterized underpin the monophyly of haplorhine primates (Anthropoidea and Tarsioidea) from a novel perspective.

Systematic studies in Paniceae (Poaceae): Homopholis and Whalleya gen. et sp. nov.

2000 ◽  
Vol 13 (3) ◽  
pp. 437 ◽  
Author(s):  
Karen E. Wills ◽  
R. D. B. Whalley ◽  
Jeremy J. Bruhl
Keyword(s):  
Sister Group ◽  
The Other ◽  
Sister Species ◽  
Parsimonious Tree ◽  
The Third ◽  
Putative Species ◽  
Anatomical Data ◽  
Cladistic Analyses

The taxonomy ofHomopholis C.E.Hubb. is revised, and anew genus Whalleya K.E.Wills & J.J.Bruhl isdescribed. Relationships among the known species ofHomopholis (H. belsonii C.E.Hubb.,H. proluta F.Muell., and a putative species,H. sp. nov.), and the relationships betweenHomopholis and other genera within the Paniceae were investigated. Morphological and anatomical data forHomopholis and selected species ofDigitaria and Panicum were analysed phenetically and cladistically. The value and contribution ofcharacters to the findings were assessed. In the phenetic analyses, threedistinct clusters of species were formed. The first cluster includedDigitaria coenicola (F.Muell.) Hughes,D. divaricatissima (R.Br.) Hughes andD. papposa (R.Br.) P.Beauv.; the second,Panicum effusum R.Br.,P. queenslandicum Domin var.queenslandicum and P. simileDomin; and the third, H. sp. nov.,H. proluta, H. belsonii andP. subxerophilum Domin. Specimens ofH. belsonii noticeably separated from the other threespecies. For the cladistic analyses, species ofEntolasia and Thyridolepis were used as outgroup taxa. One most parsimonious tree was produced.Homopholis belsonii was well supported as the most basalmember of the ingroup. The three species ofDigitariaformed a well-supported clade.Panicum effusum, P. queenslandicumvar. queenslandicum and P. simileformed a well-supported clade, and were the sister group toEntolasia marginata (R.Br.) Hughes andE. stricta (R.Br.) Hughes.Panicum subxerophilum was in a clade (=Whalleya) with H. sp. nov. andH. proluta, with P. subxerophilumand H. proluta as sister species.

scholarly journals Pericentric Inversion Events in Karyotypic Distinction of Brazilian Lizards of Genus Pliyllopezus (Squamata, Gekkonidae) Detected by Chromosomal Banding Patterns

Hereditas ◽  
2004 ◽  
Vol 127 (3) ◽  
pp. 255-262 ◽  
Author(s):  
Katia Cristina Machado Pellegrino ◽  
Sanae Kasahara ◽  
Miguel Trefaut Rodrigues ◽  
Yatiyo Yonenaga-Yassuda
Keyword(s):  
Pericentric Inversion ◽  
Banding Patterns ◽  
Chromosomal Banding

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.

Herpetological higher taxa nomina. 6. Gymnophiona Rafinesque, 1814

Bionomina ◽  
2021 ◽  
Vol 21 (1) ◽  
pp. 39-72
Author(s):  
ALAIN DUBOIS ◽  
THIERRY FRÉTEY
Keyword(s):  
Rank Order ◽  
The Other ◽  
Distinct Class ◽  
Higher Taxa ◽  
Senior Synonym ◽  
Cladistic Analyses ◽  
Made In

A taxon, traditionally referred to the rank order, encompassing all recent taxa of caecilians and their close fossil relatives, is highly supported as holophyletic in all recent cladistic analyses of Amphibia. Under the Duplostensional Nomenclatural System, among 12 nomina available in the literature, only one, Gymnophiona Rafinesque, 1814, qualifies as a sozodiaphonym and should be used for this amphibian taxon. We show here that the authorship of this nomen, as well as of 32 other nomina published in 1814, is ‘Rafinesque’, not ‘Rafinesque-Schmaltz’.            The nomen Apoda Oppel, 1811, that has often been used for this taxon, proves to be a distagmonym and a junior homonym of Apodes Linnaeus, 1758 and five other distagmonyms, and as such it is invalid under DONS.            In total, we identified 34 distinct class-series nomina derived from the stems ἄπους (apous) or Apus in 13 distinct zoological groups, only two of which are valid under DONS Criteria: Apodiformia Wetmore, 1947, for the suborder of Aves currently known as Apodi Wetmore, 1947, and Apodomorpha Sibley, Ahlquist & Monroe, 1988 for the order of Aves currently known as Apodiformes Peters, 1940.                Several other nomenclatural findings were made in the course of this study: [1] in the Teleostei, the nomina "Eupercaria" and "Syngnatharia", like all the other new nomina proposed in the paper by Betancur-R. et al. (2017) are anoplonyms and cannot be used as valid; [2] in the Mammalia, the nomina Cetus and Cetacea should be credited to Brisson (1759); [3] in the Holothuroidea, the nomen Apoda Claus, 1868, currently considered valid under the apograph Apodida, is invalid and should be replaced by the nomen Paractinopoda Ludwig, 1891; [4] in the Isopoda, the subordinal nomen Cymothoida Wägele, 1989 should be replaced by its senior synonym Darwinida Lakshminarayana & Rama Rao, 1977.

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.

Egg ultrastructure of two species of Galgupha Amyot & Serville, with a discussion of the eggs and oviposition patterns of thyreocorid and allied groups (Hemiptera: Heteroptera: Pentatomoidea: Thyreocoridae)

Zootaxa ◽  
2012 ◽  
Vol 3247 (1) ◽  
pp. 43 ◽  
Author(s):  
VIVIANA CAUDURO MATESCO ◽  
FILIPE MICHELS BIANCHI ◽  
LUIZ ALEXANDRE CAMPOS ◽  
JOCELIA GRAZIA
Keyword(s):  
Electron Microscopy ◽  
Maternal Care ◽  
Oviposition Behavior ◽  
Rio Grande ◽  
Immature Stages ◽  
Rio Grande Do Sul ◽  
Egg Morphology ◽  
Cladistic Analyses ◽  
Phylogenetic Framework ◽  
Scanning Electron

Immature stages are known in only 11 species of the Thyreocoridae. In this paper, the eggs of Galgupha (Euryscytus)difficilis (Breddin) and Galgupha (Gyrocnemis) fossata McAtee & Malloch are described and illustrated. Egg morphologyand oviposition habit in the Thyreocoridae and Cydnidae are reviewed. Adults of both species were collected in SãoFrancisco de Paula municipality, state of Rio Grande do Sul, Brazil, and maintained in the laboratory for oviposition. Theeggs were examined by stereomicroscopy and scanning electron microscopy and photographed. In G. (E.) difficilis, theeggs were laid singly or in pairs; each egg is cylindrical (0.8 x 0.5 mm) and white and the chorion is shiny, translucent,and smooth; the micropylar processes (2–4) are short and stalked. In G. (G.) fossata, the eggs were laid singly; each eggis cylindrical (0.9 x 0.6 mm) and white and the chorion is shiny, translucent, and granulated; the micropylar processes (4–10) are short, stalked, and transversely constricted. The eggs of both species are similar to those of other thyreocorids,especially of other corimelaenines. The Thyreocoridae in the broadest sense (including the Parastrachiinae) is not auniform group concerning egg morphology, oviposition behavior, and maternal care. Within the Pentatomoidea, based onegg morphology, the Cydnidae is the group nearest to the Thyreocoridae. The evolution of the eggs in the Pentatomoidea should be investigated within a phylogenetic framework, including egg characters, in future cladistic analyses.

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