scholarly journals A new phylogenetic analysis of Phytosauria (Archosauria: Pseudosuchia) with the application of continuous and geometric morphometric character coding

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5901 ◽  
Author(s):  
Andrew S. Jones ◽  
Richard J. Butler
Keyword(s):  
Phylogenetic Analyses ◽  
Late Triassic ◽  
Morphometric Character ◽  
Sister Relationship ◽  
Geometric Morphometric ◽  
Variable Position ◽  
Basal Clade ◽  
Discrete Character ◽  
Tree Topologies ◽  
Character Matrix

Phytosauria is a clade of large, carnivorous, semi-aquatic archosauromorphs which reached its peak diversity and an almost global distribution in the Late Triassic (c. 230–201 Mya). Previous phylogenetic analyses of Phytosauria have either focused primarily on the relationships of specific subclades, or were limited in taxonomic scope, and no taxonomically comprehensive dataset is currently available. We here present the most taxonomically comprehensive cladistic dataset of phytosaurs to date, based on extensive first-hand study, identification of novel characters and synthesis of previous matrices. This results in an almost twofold increase in phylogenetic information scored per taxon over previous analyses. Alongside a traditional discrete character matrix, three variant matrices were analysed in which selected characters were coded using continuous and landmarking methods, to more rigorously explore phytosaur relationships. Based on these four data matrices, four tree topologies were recovered. Relationships among non-leptosuchomorph phytosaurs are largely consistent between these four topologies, whereas those of more derived taxa are more variable. Rutiodon carolinensis consistently forms a sister relationship with Angistorhinus. In three topologies Nicrosaurus nests deeply within a group of traditionally non-Mystriosuchini taxa, leading us to redefine Mystriosuchini by excluding Nicrosaurus as an internal specifier. Two distinct patterns of relationships within Mystriosuchini are present in the four topologies, distinguished largely by the variable position of Mystriosuchus. In two topologies Mystriosuchus forms the most basal clade in Mystriosuchini, whilst in the others it occupies a highly derived position within the Machaeroprosopus clade. ‘Redondasaurus’ is consistently recovered as monophyletic; however, it also nests within the Machaeroprosopus clade. The greatest impact on tree topology was associated with the incorporation of continuous data into our matrices, with landmark characters exerting a relatively modest influence. All topologies correlated significantly with stratigraphic range estimates. Topological variability in our results highlights clades in which further investigation may better elucidate phytosaur relationships.

scholarly journals Resolving Phylogenetic Relationships within Passeriformes Based on Mitochondrial Genes and Inferring the Evolution of Their Mitogenomes in Terms of Duplications

2019 ◽  
Vol 11 (10) ◽  
pp. 2824-2849 ◽  
Author(s):  
Paweł Mackiewicz ◽  
Adam Dawid Urantówka ◽  
Aleksandra Kroczak ◽  
Dorota Mackiewicz
Keyword(s):  
Phylogenetic Analyses ◽  
Mitochondrial Genes ◽  
The Other ◽  
Phylogenetic Position ◽  
Evolutionary Relationships ◽  
Mitochondrial Genomes ◽  
Ancestral State ◽  
Phylogenetic Information ◽  
Long Time ◽  
Tree Topologies

Abstract Mitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass.

Multigene phylogenetic analyses including diverse radiolarian species support the “Retaria” hypothesis — The sister relationship of Radiolaria and Foraminifera

2011 ◽  
Vol 81 (1-2) ◽  
pp. 32-42 ◽  
Author(s):  
Yoshiyuki Ishitani ◽  
Sohta A. Ishikawa ◽  
Yuji Inagaki ◽  
Masashi Tsuchiya ◽  
Kozo Takahashi ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Sister Relationship ◽  
Relationship Of

scholarly journals Noteworthy record of the Ethiopian genet, Genetta abyssinica, (Carnivora, Viverridae) from Djibouti informs its phylogenetic position within Genetta

Mammalia ◽  
2019 ◽  
Vol 83 (2) ◽  
pp. 180-189 ◽  
Author(s):  
Adam W. Ferguson ◽  
Houssein R. Roble ◽  
Molly M. McDonough
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Alternative Hypothesis ◽  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Sister Relationship ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Molecular Phylogenetic ◽  
Relationship Of

AbstractThe molecular phylogeny of extant genets (Carnivora, Viverridae,Genetta) was generated using all species with the exception of the Ethiopian genetGenetta abyssinica. Herein, we provide the first molecular phylogenetic assessment ofG. abyssinicausing molecular sequence data from multiple mitochondrial genes generated from a recent record of this species from the Forêt du Day (the Day Forest) in Djibouti. This record represents the first verified museum specimen ofG. abyssinicacollected in over 60 years and the first specimen with a specific locality for the country of Djibouti. Multiple phylogenetic analyses revealed conflicting results as to the exact relationship ofG. abyssinicato otherGenettaspecies, providing statistical support for a sister relationship to all other extant genets for only a subset of mitochondrial analyses. Despite the inclusion of this species for the first time, phylogenetic relationships amongGenettaspecies remain unclear, with limited nodal support for many species. In addition to providing an alternative hypothesis of the phylogenetic relationships among extant genets, this recent record provides the first complete skeleton of this species to our knowledge and helps to shed light on the distribution and habitat use of this understudied African small carnivore.

scholarly journals Phylogenetic and Comparative Analyses of Complete Chloroplast Genomes of Chinese Viburnum and Sambucus (Adoxaceae)

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1143 ◽  
Author(s):  
Hang Ran ◽  
Yanyan Liu ◽  
Cui Wu ◽  
Yanan Cao
Keyword(s):  
Genomic Structure ◽  
Phylogenetic Analyses ◽  
Sister Relationship ◽  
Plastome Evolution ◽  
Chloroplast Genomes ◽  
Flora Of China ◽  
Phylogenetic Resolution ◽  
Sister Relationships ◽  
Phylogenomic Analyses ◽  
Cp Genome

Phylogenetic analyses of complete chloroplast genome sequences have yielded significant improvements in our understanding of relationships in the woody flowering genus Viburnum (Adoxaceae, Dipsacales); however, these relationships were evaluated focusing only on Viburnum species within Central and South America and Southeast Asia. By contrast, despite being a hotspot of Viburnum diversity, phylogenetic relationships of Viburnum species in China are less well known. Here, we characterized the complete chloroplast (cp) genomes of 21 Viburnum species endemic to China, as well as three Sambucus species. These 24 plastomes were highly conserved in genomic structure, gene order and content, also when compared with other Adoxaceae. The identified repeat sequences, simple sequence repeats (SSRs) and highly variable plastid regions will provide potentially valuable genetic resources for further population genetics and phylogeographic studies on Viburnum and Sambucus. Consistent with previous combined phylogenetic analyses of 113 Viburnum species, our phylogenomic analyses based on the complete cp genome sequence dataset confirmed the sister relationship between Viburnum and the Sambucus-Adoxa-Tetradoxa-Sinadoxa group, the monophyly of four recognized sections in Flora of China (i.e., Viburnum sect. Tinus, Viburnum sect. Solenotinus, Viburnum sect. Viburnum and Viburnum sect. Pseudotinus) and the nonmonophyly of Viburnum sect. Odontotinus and Viburnum sect. Megalotinus. Additionally, our study confirmed the sister relationships between the clade Valvatotinus and Viburnum sect. Pseudotinus, as well as between Viburnum sect. Opulus and the Odontotinus-Megalotinus group. Overall, our results clearly document the power of the complete cp genomes in improving phylogenetic resolution, and will contribute to a better understanding of plastome evolution in Chinese Adoxaceae.

scholarly journals Comparative Mitochondrial Genome Analysis of Two Ectomycorrhizal Fungi (Rhizopogon) Reveals Dynamic Changes of Intron and Phylogenetic Relationships of the Subphylum Agaricomycotina

2019 ◽  
Vol 20 (20) ◽  
pp. 5167 ◽  
Author(s):  
Qiang Li ◽  
Yuanhang Ren ◽  
Xiaodong Shi ◽  
Lianxin Peng ◽  
Jianglin Zhao ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Intron Loss ◽  
Rrna Genes ◽  
Trna Genes ◽  
Evolutionary Time ◽  
Dynamic Changes ◽  
Protein Coding ◽  
Tree Topologies ◽  
Nuclear Genomes

In the present study, we assembled and compared two mitogenomes from the Rhizopogon genus. The two mitogenomes of R. salebrosus and R. vinicolor comprised circular DNA molecules, with the sizes of 66,704 bp and 77,109 bp, respectively. Comparative mitogenome analysis indicated that the length and base composition of protein coding genes (PCGs), rRNA genes and tRNA genes varied between the two species. Large fragments aligned between the mitochondrial and nuclear genomes of both R. salebrosus (43.41 kb) and R. vinicolor (12.83 kb) indicated that genetic transfer between mitochondrial and nuclear genomes has occurred over evolutionary time of Rhizopogon species. Intronic regions were found to be the main factors contributing to mitogenome expansion in R. vinicolor. Variations in the number and type of introns in the two mitogenomes indicated that frequent intron loss/gain events occurred during the evolution of Rhizopogon species. Phylogenetic analyses based on Bayesian inference (BI) and Maximum likelihood (ML) methods using a combined mitochondrial gene set yielded identical and well-supported tree topologies, wherein Rhizopogon species showed close relationships with Agaricales species. This is the first study of mitogenomes within the genus Rhizopogon, and it provides a basis for understanding the evolution and differentiation of mitogenomes from the ectomycorrhizal fungal genus.

Mitochondrial DNA dataset suggest that the genus Sphaerirostris Golvan, 1956 is a synonym of the genus Centrorhynchus Lühe, 1911

Parasitology ◽  
2020 ◽  
Vol 147 (10) ◽  
pp. 1149-1157 ◽  
Author(s):  
Nehaz Muhammad ◽  
Suleman ◽  
Munawar Saleem Ahmad ◽  
Liang Li ◽  
Qing Zhao ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Systematic Position ◽  
Likelihood Methods ◽  
Sister Relationship ◽  
Protein Coding ◽  
Maximum Likelihood Methods ◽  
Relationship Of ◽  
First Time ◽  
Mt Genome ◽  
Rna Genes

AbstractOur present genetic data of Acanthocephala, especially the mitochondrial (mt) genomes, remains very limited. In the present study, the nearly complete mt genome sequences of Sphaerirostris lanceoides (Petrochenko, 1949) was sequenced and determined for the first time based on specimens collected from the Indian pond heron Ardeola grayii (Sykes) (Ciconiiformes: Ardeidae) in Pakistan. The mt genome of S. lanceoides is 13 478 bp in size and contains 36 genes, including 12 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and two ribosomal RNA genes (rRNAs). Moreover, in order to clarify the phylogenetic relationship of the genera Centrorhynchus and Sphaerirostris, and to test the systematic position of S. lanceoides in the Centrorhynchidae, the phylogenetic analyses were performed using Bayesian inference and maximum likelihood methods, based on concatenated nucleotide sequences of 12 PCGs, rRNAs and tRNAs. The phylogenetic results further confirmed the monophyly of the order Polymorphida and the paraphyly of the order Echinorhynchida in the class Palaeacanthocephala. Our results also challenged the validity of the genus Sphaerirostris (Polymorphida: Centrorhynchidae) and showed a sister relationship between S. lanceoides and S. picae (Rudolphi, 1819).

scholarly journals Morphology, genetic characterization and molecular phylogeny of pinworm Skrjabinema longicaudatum n. sp. (Oxyurida: Oxyuridae) from the endangered Tibetan antelope Pantholops hodgsonii (Abel) (Artiodactyla: Bovidae)

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Yi-Fan Cao ◽  
Hui-Xia Chen ◽  
Yang Li ◽  
Dang-Wei Zhou ◽  
Shi-Long Chen ◽  
...  
Keyword(s):  
New Species ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Small Subunit ◽  
Sister Relationship ◽  
Tibetan Antelope ◽  
A New Species

Abstract Background The Tibetan antelope Pantholops hodgsonii (Abel) (Artiodactyla: Bovidae) is an endangered species of mammal endemic to the Qinghai-Tibetan Plateau. Parasites and parasitic diseases are considered to be important threats in the conservation of the Tibetan antelope. However, our present knowledge of the composition of the parasites of the Tibetan antelope remains limited. Methods Large numbers of nematode parasites were collected from a dead Tibetan antelope. The morphology of these nematode specimens was observed using light and scanning electron microscopy. The nuclear and mitochondrial DNA sequences, i.e. small subunit ribosomal DNA (18S), large subunit ribosomal DNA (28S), internal transcribed spacer (ITS) and cytochrome c oxidase subunit 1 (cox1), were amplified and sequenced for molecular identification. Moreover, phylogenetic analyses were performed using maximum likelihood (ML) inference based on 28S and 18S + 28S + cox1 sequence data, respectively, in order to clarify the systematic status of these nematodes. Results Integrated morphological and genetic evidence reveals these nematode specimens to be a new species of pinworm Skrjabinema longicaudatum (Oxyurida: Oxyuridae). There was no intraspecific nucleotide variation between different individuals of S. longicaudatum n. sp. in the partial 18S, 28S, ITS and cox1 sequences. However, a high level of nucleotide divergence was revealed between the new species and its congeners in 28S (8.36%) and ITS (20.3–23.7%) regions, respectively. Molecular phylogenetic results suggest that the genus Skrjabinema should belong to the subfamily Oxyurinae (Oxyuroidea: Oxyuridae), instead of the subfamily Syphaciidae or Skrjabinemiinae in the traditional classification, as it formed a sister relationship to the genus Oxyuris. Conclusions A new species of pinworm Skrjabinema longicaudatum n. sp. (Oxyurida: Oxyuridae) is described. Skrjabinema longicaudatum n. sp. represents the first species of Oxyurida (pinworm) and the fourth nematode species reported from the Tibetan antelope. Our results contribute to the knowledge of the species diversity of parasites from the Tibetan antelope, and clarify the systematic position of the genus Skrjabinema.

Do genomic datasets resolve the correct relationship among the placental, marsupial and monotreme lineages?

2009 ◽  
Vol 57 (4) ◽  
pp. 167 ◽  
Author(s):  
Gavin Huttley
Keyword(s):  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Protein Coding ◽  
Substitution Models ◽  
True Tree ◽  
Molecular Phylogenetic ◽  
Tree Topologies ◽  
Mammal Evolution ◽  
Genome Projects

Did the mammal radiation arise through initial divergence of prototherians from a common ancestor of metatherians and eutherians, the Theria hypothesis, or of eutherians from a common ancestor of metatherians and prototherians, the Marsupionta hypothesis? Molecular phylogenetic analyses of point substitutions applied to this problem have been contradictory – mtDNA-encoded sequences supported Marsupionta, nuclear-encoded sequences and RY (purine–pyrimidine)-recoded mtDNA supported Theria. The consistency property of maximum likelihood guarantees convergence on the true tree only with longer alignments. Results from analyses of genome datasets should therefore be impervious to choice of outgroup. We assessed whether important hypotheses concerning mammal evolution, including Theria/Marsupionta and the branching order of rodents, carnivorans and primates, are resolved by phylogenetic analyses using ~2.3 megabases of protein-coding sequence from genome projects. In each case, only two tree topologies were being compared and thus inconsistency in resolved topologies can only derive from flawed models of sequence divergence. The results from all substitution models strongly supported Theria. For the eutherian lineages, all models were sensitive to the outgroup. We argue that phylogenetic inference from point substitutions will remain unreliable until substitution models that better match biological mechanisms of sequence divergence have been developed.

scholarly journals A comprehensive anatomical and phylogenetic evaluation of Dilophosaurus wetherilli (Dinosauria, Theropoda) with descriptions of new specimens from the Kayenta Formation of northern Arizona

2020 ◽  
Vol 94 (S78) ◽  
pp. 1-103 ◽  
Author(s):  
Adam D. Marsh ◽  
Timothy B. Rowe
Keyword(s):  
Phylogenetic Analyses ◽  
Cervical Vertebrae ◽  
Pop Culture ◽  
Single Species ◽  
Axial Skeleton ◽  
Late Triassic ◽  
Monophyletic Clade ◽  
Navajo Nation ◽  
Northern Arizona ◽  
Nasal Process

AbstractDilophosaurus wetherilli was the largest animal known to have lived on land in North America during the Early Jurassic. Despite its charismatic presence in pop culture and dinosaurian phylogenetic analyses, major aspects of the skeletal anatomy, taxonomy, ontogeny, and evolutionary relationships of this dinosaur remain unknown. Skeletons of this species were collected from the middle and lower part of the Kayenta Formation in the Navajo Nation in northern Arizona. Redescription of the holotype, referred, and previously undescribed specimens of Dilophosaurus wetherilli supports the existence of a single species of crested, large-bodied theropod in the Kayenta Formation. The parasagittal nasolacrimal crests are uniquely constructed by a small ridge on the nasal process of the premaxilla, dorsoventrally expanded nasal, and tall lacrimal that includes a posterior process behind the eye. The cervical vertebrae exhibit serial variation within the posterior centrodiapophyseal lamina, which bifurcates and reunites down the neck. Iterative specimen-based phylogenetic analyses result in each of the additional specimens recovered as the sister taxon to the holotype. When all five specimens are included in an analysis, they form a monophyletic clade that supports the monotypy of the genus. Dilophosaurus wetherilli is not recovered as a ceratosaur or coelophysoid, but is instead a non-averostran neotheropod in a grade with other stem-averostrans such as Cryolophosaurus ellioti and Zupaysaurus rougieri. We did not recover a monophyletic ‘Dilophosauridae.’ Instead of being apomorphic for a small clade of early theropods, it is more likely that elaboration of the nasals and lacrimals of stem-averostrans is plesiomorphically present in early ceratosaurs and tetanurans that share those features. Many characters of the axial skeleton of Dilophosaurus wetherilli are derived compared to Late Triassic theropods and may be associated with macropredation and an increase in body size in Theropoda across the Triassic-Jurassic boundary.

Pleurotheciella nilotica sp. nov. (Pleurotheciales, Ascomycota) from freshwater habitats in Egypt

Nova Hedwigia ◽  
2020 ◽  
Vol 110 (1) ◽  
pp. 91-98
Author(s):  
Faten A. Abdel-Aziz ◽  
Ali H. Bahkali ◽  
Abdallah M. Elgorban ◽  
Mohamed A. Abdel-Wahab
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Distinct Species ◽  
Lsu Rdna ◽  
River Nile ◽  
Basal Clade ◽  
Molecular Phylogenetic ◽  
Freshwater Habitats ◽  
A New Species

A new species, Pleurotheciella nilotica is described and illustrated from the River Nile, Sohag, Egypt. Molecular phylogenetic analyses of the combined SSU and LSU rDNA placed the new species within Pleurotheciella as a phylogenetically distinct species. P. nilotica formed a basal clade to a node containing P. krabiensis and P.tropica. The new species is characterized by its conidial dimensions being smaller than those recorded in the eleven described species of Pleurotheciella.

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