scholarly journals Evolution of developmental sequences in lepidosaurs

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3262 ◽  
Author(s):  
Tomasz Skawiński ◽  
Bartosz Borczyk
Keyword(s):  
Phylogenetic Signal ◽  
Molecular Data ◽  
Ancestral State ◽  
Continuous Analysis ◽  
Developmental Sequences ◽  
Cladistic Analyses ◽  
Phylogenetic Hypotheses ◽  
Morphological And Molecular Data

Background Lepidosaurs, a group including rhynchocephalians and squamates, are one of the major clades of extant vertebrates. Although there has been extensive phylogenetic work on this clade, its interrelationships are a matter of debate. Morphological and molecular data suggest very different relationships within squamates. Despite this, relatively few studies have assessed the utility of other types of data for inferring squamate phylogeny. Methods We used developmental sequences of 20 events in 29 species of lepidosaurs. These sequences were analysed using event-pairing and continuous analysis. They were transformed into cladistic characters and analysed in TNT. Ancestral state reconstructions were performed on two main phylogenetic hypotheses of squamates (morphological and molecular). Results Cladistic analyses conducted using characters generated by these methods do not resemble any previously published phylogeny. Ancestral state reconstructions are equally consistent with both morphological and molecular hypotheses of squamate phylogeny. Only several inferred heterochronic events are common to all methods and phylogenies. Discussion Results of the cladistic analyses, and the fact that reconstructions of heterochronic events show more similarities between certain methods rather than phylogenetic hypotheses, suggest that phylogenetic signal is at best weak in the studied developmental events. Possibly the developmental sequences analysed here evolve too quickly to recover deep divergences within Squamata.

scholarly journals Fensomea setacea, gen. & sp. nov. (Cladopyxidaceae, Dinophyceae), is neither gonyaulacoid nor peridinioid as inferred from morphological and molecular data

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Marc Gottschling ◽  
Maria Consuelo Carbonell-Moore ◽  
Kenneth Neil Mertens ◽  
Monika Kirsch ◽  
Malte Elbrächter ◽  
...  
Keyword(s):  
Molecular Data ◽  
Character Evolution ◽  
Ancestral State ◽  
Close Relationship ◽  
Regular Configuration ◽  
The Common ◽  
Morphological And Molecular Data ◽  
Rrna Sequences

AbstractDinophyte evolution is essentially inferred from the pattern of thecal plates, and two different labelling systems are used for the important subgroups Gonyaulacales and Peridiniales. The partiform hypotheca of cladopyxidoid dinophytes fits into the morphological concepts of neither group, although they are assigned to the Gonyaulacales. Here, we describe the thecate dinophyte Fensomea setacea, gen. & sp. nov., which has a cladopyxidoid tabulation. The cells displayed a Kofoidean plate formula APC, 3′, 4a, 7″, 7C, 6S, 6′′′, 2′′′′, and slender processes were randomly distributed over the echinate or baculate surface. In addition, we obtained rRNA sequences of F. setacea, gen. & sp. nov., but dinophytes that exhibit a partiform hypotheca did not show a close relationship to Gonyaulacales. Character evolution of thecate dinophytes may have progressed from the ancestral state of six postcingular plates, and two more or less symmetrically arranged antapical plates, towards patterns of only five postcingular plates (Peridiniales) or more asymmetrical configurations (Gonyaulacales). Based on our phylogenetic reconsiderations the contact between the posterior sulcal plate and the first postcingular plate, as well as the contact between an antapical plate and the distalmost postcingular plate, do not represent a rare, specialized gonyaulacoid plate configuration (i.e., the partiform hypotheca of cladopyxidoid dinophytes). Instead, these contacts correspond to the common and regular configuration of peridinioid (and other) dinophytes.

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.

Pentachondra dehiscens sp. nov. - An aberrant new member of Styphelieae

2001 ◽  
Vol 14 (4) ◽  
pp. 513 ◽  
Author(s):  
W. Cherry ◽  
P. A. Gadek ◽  
E. A. Brown ◽  
M. M. Heslewood ◽  
C. J. Quinn
Keyword(s):  
New Species ◽  
New South ◽  
New South Wales ◽  
Molecular Data ◽  
Blue Mountains ◽  
Strong Affinity ◽  
South Wales ◽  
Cladistic Analyses ◽  
Morphological And Molecular Data ◽  
A New Species

A new species of Styphelieae collected from the Blue Mountains region of New South Wales is described. Cladistic analyses of morphological and molecular data show that the species has a strong affinity with the genus Pentachondra. The genus is redefined to accommodate the following features of the new species: a drupaceous fruit with 6–11 locules in which the mesocarp splits to release the separate pyrenes at maturity and a more complex inflorescence.

Phylogenetic analysis based on nuclear DNA and morphology defines a clade of eastern Australian species of Acacia s.s. (section Juliflorae): the 'Acacia longifolia group'

2010 ◽  
Vol 23 (3) ◽  
pp. 162 ◽  
Author(s):  
Gillian K. Brown ◽  
Catherine Clowes ◽  
Daniel J. Murphy ◽  
Pauline Y. Ladiges
Keyword(s):  
Nuclear Dna ◽  
Molecular Data ◽  
Herbarium Specimens ◽  
Nuclear Rdna ◽  
Flora Of Australia ◽  
Informal Group ◽  
Australian Species ◽  
Cladistic Analyses ◽  
Acacia Longifolia ◽  
Morphological And Molecular Data

Seventeen Australian, phyllodinous species of Acacia s.s. (from sections Juliflorae and Phyllodineae) were analysed to test the monophyly and relationships of ‘the Acacia longifolia group’, an informal group recognised in the Flora of Australia. Analyses were based on both morphological and molecular data, with A. triptera as an outgroup. A total of 92 herbarium specimens was investigated, with 15 phyllode, inflorescence, flower, pod and seed characters scored. The ITS and ETS regions of nuclear rDNA were sequenced and combined with a larger dataset sampled from species of all major clades of Acacia, totalling 65 accessions. Cladistic analyses provided evidence of a clade that defines the A. longifolia group as follows: A. alpina, A. axillaris, A. courtii, A. dallachiana, A. derwentiana, A. floribunda, A. longifolia subsp. longifolia and A. longifolia subsp. sophorae, A. longissima, A. maidenii, A. mucronata, A. obtusifolia, A. orites, A. oxycedrus, A. phlebophylla, A. rhigiophylla and A. riceana (all sect. Juliflorae), but excluding A. verticillata (section Juliflorae) and A. genistifolia (section Phyllodineae). The A. longifolia group is recognised as including south-eastern Australian species with cylindrically spiked inflorescences and phyllodes with prominent anastomosing venation.

Phylogeny of the Bryopsidaceae (Bryopsidales, Chlorophyta): cladistic analyses of morphological and molecular data

Phycologia ◽  
2000 ◽  
Vol 39 (6) ◽  
pp. 471-481 ◽  
Author(s):  
Geoffrey W. Woolcott ◽  
Kristin Knöller ◽  
Robert J. King
Keyword(s):  
Molecular Data ◽  
Cladistic Analyses ◽  
Morphological And Molecular Data

scholarly journals Cytogenetic analysis of Hypomasticus copelandii and H. steindachneri: relevance of cytotaxonomic markers in the Anostomidae family (Characiformes)

2021 ◽  
Vol 15 (1) ◽  
pp. 65-76
Author(s):  
Filipe Schitini Salgado ◽  
Marina Souza Cunha ◽  
Silvana Melo ◽  
Jorge Abdala Dergam
Keyword(s):  
Sex Chromosome ◽  
5S Rdna ◽  
Molecular Data ◽  
Banding Patterns ◽  
As Species ◽  
Heteromorphic Sex Chromosomes ◽  
Species Groups ◽  
Phylogenetic Hypotheses ◽  
Morphological And Molecular Data ◽  
Species Specific

Recent phylogenetic hypotheses within Anostomidae, based on morphological and molecular data, resulted in the description of new genera (Megaleporinus Ramirez, Birindelli et Galetti, 2017) and the synonymization of others, such as the reallocation of Leporinus copelandii Steindachner, 1875 and Leporinus steindachneri Eigenmann, 1907 to Hypomasticus Borodin, 1929. Despite high levels of conservatism of the chromosomal macrostructure in this family, species groups have been corroborated using banding patterns and the presence of different sex chromosome systems. Due to the absence of cytogenetic studies in H. copelandii (Steindachner, 1875) and H. steindachneri (Eigenmann, 1907), the goal of this study was to characterize their karyotypes and investigate the presence/absence of sex chromosome systems using different repetitive DNA probes. Cytogenetic techniques included: Giemsa staining, Ag-NOR banding and FISH using 18S and 5S rDNA probes, as well as microsatellite probes (CA)15 and (GA)15. Both species had 2n = 54, absence of heteromorphic sex chromosomes, one chromosome pair bearing Ag-NOR, 18S and 5S rDNA regions. The (CA)15 and (GA)15 probes marked mainly the subtelomeric regions of all chromosomes and were useful as species-specific chromosomal markers. Our results underline that chromosomal macrostructure is congruent with higher systematic arrangements in Anostomidae, while microsatellite probes are informative about autapomorphic differences between species.

WOOD ANATOMY OF THE TRIBE MILLETTIEAE WITH COMMENTS ON RELATED PAPILIONOID LEGUMINOSAE

IAWA Journal ◽  
2004 ◽  
Vol 25 (4) ◽  
pp. 485-545 ◽  
Author(s):  
Peter Gasson ◽  
Elspeth Wray ◽  
Brian D. Schrire
Keyword(s):  
Wood Anatomy ◽  
Secondary Growth ◽  
Molecular Data ◽  
Sensu Stricto ◽  
Axial Parenchyma ◽  
The Core ◽  
C 23 ◽  
Form Part ◽  
Cladistic Analyses ◽  
Morphological And Molecular Data

The tribe Millettieae has traditionally included some 43 to 47 genera although more recent phylogenetic evidence has shown that a smaller core-Millettieae group of c. 23 genera may form part of a recircumscribed Millettieae sensu stricto. We have examined the wood of 27 genera, 16 of which are in the core-Millettieae and the remaining 11 belong in 4 groups, mostly with closer affinities outside Millettieae s.str. The wood anatomy of the various genera is nevertheless very uniform. Most genera are diffuse porous with no predominant vessel pattern. They have paratracheal parenchyma ranging from scanty through vasicentric, aliform and confluent, and often banded. Rays are mainly up to 5 cells wide. Axial parenchyma and rays are nearly always storied. The lianas Paraderris elliptica, Derris uliginosa, Ostryocarpus cf. riparius and Wisteria spp. have alternating bands of xylem and phloem, which are also found in some Dalbergieae. Even in the genera without such anomalous secondary growth there are many similarities between the wood of Millettieae and Dalbergieae. The wood of some genera in Sophoreae and Swartzieae is also compared. Our observations will be put in the context of recent cladistic analyses on both morphological and molecular data by other authors.

scholarly journals The Culicidae (Diptera): a review of taxonomy, classification and phylogeny*

Zootaxa ◽  
2007 ◽  
Vol 1668 (1) ◽  
pp. 591-638 ◽  
Author(s):  
RALPH E. HARBACH
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Molecular Evidence ◽  
Traditional Classification ◽  
Phenetic Classification ◽  
Cladistic Analyses ◽  
Morphological And Molecular Data ◽  
Stable Classification

The taxonomy, classification and phylogeny of family Culicidae are reviewed. The application of explicit methods of phylogenetic analysis has revealed weaknesses in the traditional classification of mosquitoes, but little progress has been made to achieve a robust, stable classification that reflects evolutionary relationships. The current phenetic classification is discussed in view of phylogeny reconstructions based on cladistic analyses of morphological and molecular data. It is concluded that the generic and suprageneric relationships and the validity and monophyly of the generic and subgeneric groupings of Culicidae are in need of extensive reappraisal. If the classification is to reflect evolutionary history, changes to the nomenclature of mosquitoes are inevitable. There is strong morphological and molecular evidence that subfamily Anophelinae and tribes Aedini, Culicini and Sabethini of subfamily Culicinae are monophyletic, but the other taxonomic groupings are not demonstrably monophyletic or have not been subjected to phylogenetic analyses.

Phylogeny of Carpha and related genera (Schoeneae, Cyperaceae) inferred from morphological and molecular data

2007 ◽  
Vol 20 (2) ◽  
pp. 93 ◽  
Author(s):  
Xiufu Zhang ◽  
Jeremy J. Bruhl ◽  
Karen L. Wilson ◽  
Adam Marchant
Keyword(s):  
Phylogenetic Relationships ◽  
Molecular Data ◽  
Sensu Stricto ◽  
Morphological Data ◽  
Data Support ◽  
Cladistic Analyses ◽  
Morphological And Molecular Data ◽  
High Degree

The limits, definitions and relationships of Carpha have been controversial and unclear. This study using cladistic analyses of morphological and combined morphological and molecular data indicates that: (1) Carpha sensu latu is paraphyletic and its species form two clades, consistent with the definitions of Carpha sensu stricto and Asterochaete respectively (i.e. the data support the division of Carpha sensu latu into two genera: Carpha sensu stricto and Asterochaete); (2) the morphological data show a high degree of homoplasy within Schoeneae; (3) Schoeneae is not a monophyletic tribe; (4) Schoenus and Tricostularia are polyphyletic; (5) it is better to place Schoenoides back in Oreobolus; (6) separation of Capeobolus brevicaulis from Costularia or Tetraria is supported; and (7) both genera Costularia and Tetraria should be maintained. The study resolves some phylogenetic relationships between Carpha and its relatives. Many aspects of these relationships are in agreement with previous studies, but some of these relationships have no support. The study also resolves the phylogenetic relationships of species of Carpha, although with lack of support for some clades, highlighting the need for other sources of data.

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