scholarly journals A reevaluation of the basal turtle Indochelys spatulata from the Early–Middle Jurassic (Toarcian–Aalenian) of India, with descriptions of new material

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8542
Author(s):  
Walter G. Joyce ◽  
Saswati Bandyopadhyay
Keyword(s):  
Phylogenetic Analysis ◽  
Middle Jurassic ◽  
Phylogenetic Analyses ◽  
Type Locality ◽  
Recent Analysis ◽  
New Material

Background Indochelys spatulata is an extinct turtle from the Early to Middle Jurassic Kota Formation of the Pranhita–Godavari Gondwana basin, India. The holotype and previously only known specimen is a partially eroded shell that had been collected near Kota village, north of Sironcha, in Maharashtra State. Phylogenetic analyses have consistently suggested placement at the base of the clade Mesochelydia. Methods We here figure and describe the holotype of Indochelys spatulata and two new specimens, which were collected from the Kota Formation near Kistapur village, Telengana State, about 60 km NW from the type locality. We furthermore explore the relationships of this fossil turtle by updating its scoring based on all available material in the most recent analysis of basal turtle relationships. Results The revision of the holotype of Indochelys spatulata provides minor adjustments to the morphology of this specimen, in particular recognition of a transverse break across the carapace, presence of only eight neurals, of which the eight is octagonal, and presence of a pathological element located between neurals VII and VIII. The new material provides new anatomical insights, in particular presence of a broad cervical, a vertebral V that inserts deeply into vertebral IV, narrow pleurals within increasingly short posteromedial contacts with the vertebrals towards the posterior, at least three pairs of musk duct foramina, and numerous insights into the morphology of the girdles and stylopodium. In combination, all material allows affirming the validity of Indochelys spatulata with confidence. The phylogenetic analysis affirms the placement of Indochelys spatulata as a basal mesochelydian, but cannot resolve its relationships relative to the roughly coeval Condorchelys antiqua and Kayentachelys aprix.

A redefinition of the genus Troglocharinus Reitter, 1908, with description of new species (Coleoptera, Leiodidae, Cholevinae, Leptodirini)

Zootaxa ◽  
2021 ◽  
Vol 4926 (2) ◽  
pp. 151-188
Author(s):  
JAVIER FRESNEDA ◽  
VALERIA RIZZO ◽  
JORDI COMAS ◽  
IGNACIO RIBERA
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Valid Species ◽  
Distribution Area ◽  
Undescribed Species ◽  
Separate Species ◽  
Male And Female ◽  
New Material

We redefine the genus Troglocharinus Reitter, 1908 based on a phylogenetic analysis with a combination of mitochondrial and molecular data. We recovered the current Speonomites mengeli (Jeannel, 1910) and S. mercedesi (Zariquiey, 1922) as valid, separate species within the Troglocharinus clade, not directly related to Speonomites Jeannel, 1910, a finding corroborated by a detailed study of the male and female genitalia. In consequence, we reinstate Speonomus mercedesi Zariquiey, 1922 stat. nov. as a valid species, transfer both of them to the genus Troglocharinus, T. mengeli (Jeannel, 1910) comb. nov. and T. mercedesi (Zariquiey, 1922) comb. nov., and redescribe the genus. The study of new material from the distribution area of the former S. mengeli revealed the presence of two undescribed species, T. sendrai sp. nov. and T. fadriquei sp. nov., which we describe herein. We designate the lectotype of Speonomus vinyasi Escolà, 1971 to fix its identity, as among its syntypes there are two different species. In agreement with the results of the phylogenetic analyses we establish the synonymy between the genus Speonomites and Pallaresiella Fresneda, 1998 syn. nv. 

scholarly journals New material and revision ofMelanorosaurus thabanensis, a basal sauropodomorph from the Upper Triassic of Lesotho

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1639 ◽  
Author(s):  
Claire Peyre de Fabrègues ◽  
Ronan Allain
Keyword(s):  
Phylogenetic Analysis ◽  
Southern Africa ◽  
Upper Triassic ◽  
Early Jurassic ◽  
Type Locality ◽  
Late Triassic ◽  
Original Publication ◽  
Stratigraphic Position ◽  
New Material

Melanorosaurusis a genus of basal sauropodomorph that currently includes two species from Southern Africa. In this paper, we redescribe the holotype femur ofMelanorosaurus thabanensisfrom the Elliot Formation of Lesotho, as well as associated remains. The stratigraphic position of this taxon is reviewed, and it is clear that it comes from the Lower Elliot Formation being, therefore, Late Triassic in age, and not Early Jurassic as originally described. The knowledge of the anatomy of the basal sauropodomorph of Thabana Morena is enhanced by the description of six new skeletal elements from the type locality. The femur and the ilium from Thabana Morena are diagnostic and characterized by unusual proportions. The first phylogenetic analysis including both this specimen andMelanorosaurusis conducted. This analysis leads to the conclusion that the femur described in the original publication ofMelanorosaurus thabanensiscan no longer be referred toMelanorosaurus. For these reasons, we hereby createMeroktenosgen. nov. to encompassMeroktenos thabanensiscomb. nov.

Morphological examination and phylogenetic analysis clarify the taxonomic status of Cuban Longior Travassos & Kloss, 1958 (Nematoda: Thelastomatoidea: Hystrignathidae) 

Zootaxa ◽  
2018 ◽  
Vol 4399 (4) ◽  
pp. 521
Author(s):  
JANS MORFFE ◽  
NAYLA GARCÍA ◽  
KARIN BREUGELMANS ◽  
BYRON J. ADAMS
Keyword(s):  
Phylogenetic Analysis ◽  
Taxonomic Status ◽  
Type Locality ◽  
Phylogenetic Position ◽  
Lsu Rdna ◽  
Morphological Examination ◽  
Type Host ◽  
Molecular Studies ◽  
The Status ◽  
New Material

The status of Longior alius García & Coy, 1994 (Nematoda: Thelastomatoidea: Hystrignathidae) is discussed on the basis of new material obtained from its type host Antillanax pertyi (Kaup, 1869) (Coleoptera: Passalidae) from Limonar, Guantánamo province, Cuba, near the type locality. Based on morphological and molecular studies L. alius is considered synonymous with L. longior Morffe & García, 2011. L. longior and L. similis Morffe, García & Ventosa, 2009 are redescribed and illustrated with the aid of SEM. New locality records for both species are given. The conspecificity of females and males of both species is supported by comparison of the D2-D3 segment of the 28S LSU rDNA. The inter-specific differences and phylogenetic position of L. longior and L. similis are discussed. 

scholarly journals Molecular record for the first authentication of Isaria cicadae from Vietnam

2021 ◽  
Vol 16 (1) ◽  
pp. 711-718
Author(s):  
Thuan Duc Lao ◽  
Hanh Van Trinh ◽  
Loi Vuong ◽  
Luyen Tien Vu ◽  
Thuy Ai Huyen Le ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genomic Dna ◽  
Morphological Analysis ◽  
Phylogenetic Analyses ◽  
Neighbor Joining ◽  
Pcr Assay ◽  
Parsimony Method ◽  
Maximum Parsimony Method ◽  
Cordyceps Cicadae ◽  
High Bootstrap

Abstract The entomopathogenic fungus T011, parasitizing on nymph of Cicada, collected in the coffee garden in Dak Lak Province, Vietnam, was preliminarily morphologically identified as Isaria cicadae, belonged to order Hypocreales and family Clavicipitaceae. To ensure the authenticity of T011, phylogenetic analysis of the concatenated set of multiple genes including ITS, nrLSU, nrSSU, Rpb1, and Tef1 was applied to support the identification. Genomic DNA was isolated from dried sample T011. The PCR assay sequencing was applied to amplify ITS, nrLSU, nrSSU, Rpb1, and Tef1 gene. For phylogenetic analysis, the concatenated data of both target gens were constructed with MEGAX with a 1,000 replicate bootstrap based on the neighbor-joining, maximum likelihood, maximum parsimony method. As the result, the concatenated data containing 62 sequences belonged to order Hypocreales, families Clavicipitaceae, and 2 outgroup sequences belonged to order Hypocreales, genus Verticillium. The phylogenetic analysis results indicated that T011 was accepted at subclade Cordyceps and significantly formed the monophyletic group with referent Cordyceps cicadae (Telemorph of Isaria cicadae) with high bootstrap value. The phylogenetically analyzed result was strongly supported by our morphological analysis described as the Isaria cicadae. In summary, phylogenetic analyses based on the concatenated dataset were successfully applied to strengthen the identification of T011 as Isaria cicadae.

scholarly journals Phylogenetic Analysis: Basic Concepts and Its Use as a Tool for Virology and Molecular Epidemiology

2018 ◽  
Vol 44 (1) ◽  
pp. 20
Author(s):  
Eloiza Teles Caldart ◽  
Helena Mata ◽  
Cláudio Wageck Canal ◽  
Ana Paula Ravazzolo
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Molecular Epidemiology ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Evolutionary Process ◽  
Amino Acid Sequences ◽  
Evolutionary Models ◽  
Reconstruction Methods ◽  
Basic Concepts

Background: Phylogenetic analyses are an essential part in the exploratory assessment of nucleic acid and amino acid sequences. Particularly in virology, they are able to delineate the evolution and epidemiology of disease etiologic agents and/or the evolutionary path of their hosts. The objective of this review is to help researchers who want to use phylogenetic analyses as a tool in virology and molecular epidemiology studies, presenting the most commonly used methodologies, describing the importance of the different techniques, their peculiar vocabulary and some examples of their use in virology.Review: This article starts presenting basic concepts of molecular epidemiology and molecular evolution, emphasizing their relevance in the context of viral infectious diseases. It presents a session on the vocabulary relevant to the subject, bringing readers to a minimum level of knowledge needed throughout this literature review. Within its main subject, the text explains what a molecular phylogenetic analysis is, starting from a multiple alignment of nucleotide or amino acid sequences. The different software used to perform multiple alignments may apply different algorithms. To build a phylogeny based on amino acid or nucleotide sequences it is necessary to produce a data matrix based on a model for nucleotide or amino acid replacement, also called evolutionary model. There are a number of evolutionary models available, varying in complexity according to the number of parameters (transition, transversion, GC content, nucleotide position in the codon, among others). Some papers presented herein provide techniques that can be used to choose evolutionary models. After the model is chosen, the next step is to opt for a phylogenetic reconstruction method that best fits the available data and the selected model. Here we present the most common reconstruction methods currently used, describing their principles, advantages and disadvantages. Distance methods, for example, are simpler and faster, however, they do not provide reliable estimations when the sequences are highly divergent. The accuracy of the analysis with probabilistic models (neighbour joining, maximum likelihood and bayesian inference) strongly depends on the adherence of the actual data to the chosen development model. Finally, we also explore topology confidence tests, especially the most used one, the bootstrap. To assist the reader, this review presents figures to explain specific situations discussed in the text and numerous examples of previously published scientific articles in virology that demonstrate the importance of the techniques discussed herein, as well as their judicious use.Conclusion: The DNA sequence is not only a record of phylogeny and divergence times, but also keeps signs of how the evolutionary process has shaped its history and also the elapsed time in the evolutionary process of the population. Analyses of genomic sequences by molecular phylogeny have demonstrated a broad spectrum of applications. It is important to note that for the different available data and different purposes of phylogenies, reconstruction methods and evolutionary models should be wisely chosen. This review provides theoretical basis for the choice of evolutionary models and phylogenetic reconstruction methods best suited to each situation. In addition, it presents examples of diverse applications of molecular phylogeny in virology.

scholarly journals Diversity unearthed by the estimated molecular phylogeny and ecologically quantitative characteristics of uncultured Ehrlichia bacteria in Haemaphysalis ticks, Japan

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hongru Su ◽  
Eri Onoda ◽  
Hitoshi Tai ◽  
Hiromi Fujita ◽  
Shigetoshi Sakabe ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Core Genome ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Housekeeping Genes ◽  
Pcr Screening ◽  
Taxonomic Profiling ◽  
Quantitative Characteristics

AbstractEhrlichia species are obligatory intracellular bacteria transmitted by arthropods, and some of these species cause febrile diseases in humans and livestock. Genome sequencing has only been performed with cultured Ehrlichia species, and the taxonomic status of such ehrlichiae has been estimated by core genome-based phylogenetic analysis. However, many uncultured ehrlichiae exist in nature throughout the world, including Japan. This study aimed to conduct a molecular-based taxonomic and ecological characterization of uncultured Ehrlichia species or genotypes from ticks in Japan. We first surveyed 616 Haemaphysalis ticks by p28-PCR screening and analyzed five additional housekeeping genes (16S rRNA, groEL, gltA, ftsZ, and rpoB) from 11 p28-PCR-positive ticks. Phylogenetic analyses of the respective genes showed similar trees but with some differences. Furthermore, we found that V1 in the V1–V9 regions of Ehrlichia 16S rRNA exhibited the greatest variability. From an ecological viewpoint, the amounts of ehrlichiae in a single tick were found to equal approx. 6.3E+3 to 2.0E+6. Subsequently, core-partial-RGGFR-based phylogenetic analysis based on the concatenated sequences of the five housekeeping loci revealed six Ehrlichia genotypes, which included potentially new Ehrlichia species. Thus, our approach contributes to the taxonomic profiling and ecological quantitative analysis of uncultured or unidentified Ehrlichia species or genotypes worldwide.

scholarly journals Molecular and phylogenetic analysis reveals new diversity of Dunaliella salina from hypersaline environments

2021 ◽  
pp. 1-11
Author(s):  
Andrea Highfield ◽  
Angela Ward ◽  
Richard Pipe ◽  
Declan C. Schroeder
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Dunaliella Salina ◽  
Phylogenetic Analyses ◽  
Ssu Rdna ◽  
Lsu Rdna ◽  
Hypersaline Environments ◽  
Rdna Its ◽  
Β Carotene ◽  
Selection Of

Abstract Twelve hyper-β carotene-producing strains of algae assigned to the genus Dunaliella salina have been isolated from various hypersaline environments in Israel, South Africa, Namibia and Spain. Intron-sizing of the SSU rDNA and phylogenetic analysis of these isolates were undertaken using four commonly employed markers for genotyping, LSU rDNA, ITS, rbcL and tufA and their application to the study of Dunaliella evaluated. Novel isolates have been identified and phylogenetic analyses have shown the need for clarification on the taxonomy of Dunaliella salina. We propose the division of D. salina into four sub-clades as defined by a robust phylogeny based on the concatenation of four genes. This study further demonstrates the considerable genetic diversity within D. salina and the potential of genetic analyses for aiding in the selection of prospective economically important strains.

New olenelline trilobites from the Northwest Territories, Canada, and the phylogenetic placement of Judomia absita Fritz, 1973

Zootaxa ◽  
2011 ◽  
Vol 2918 (1) ◽  
pp. 15 ◽  
Author(s):  
I. WESLEY GAPP ◽  
BRUCE S. LIEBERMAN ◽  
MICHAEL C. POPE ◽  
KELLY A. DILLIARD
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Northwest Territories ◽  
Phylogenetic Analyses ◽  
Geographic Range ◽  
Early Cambrian ◽  
Phylogenetic Placement ◽  
The Subject ◽  
Three New Species ◽  
One New Species

The Early Cambrian olenelline trilobites are a diverse clade and have been the subject of several phylogenetic analyses. Here, three new species of Bradyfallotaspis Fritz, 1972 (B. coriae, B. nicolascagei, and B. sekwiensis) and one new species of Nevadia Walcott, 1910 (N. saupeae) are described from the Sekwi Formation of the Mackenzie Mountains, Northwest Territories, Canada. In addition, new specimens potentially referable to Nevadia ovalis McMenamin, 1987 were recovered that may expand that species’ geographic range, which was thought to be restricted to Sonora, Mexico. The results of a phylogenetic analysis incorporating several olenelline taxa, including Judomia absita Fritz, 1973 from the Sekwi Formation, are also presented herein. This species has been assigned to various olenelline genera, including Judomia Lermontova, 1951 and Paranevadella Palmer & Repina, 1993. Phylogenetic analysis suggests this species is closely related to Judomia tera Lazarenko, 1960 from Siberia. This phylogenetic relationship provides further support for the hypothesis that a close biogeographic relationship existed between Laurentia and Siberia during the Cambrian.

A revision of Xinjiangchelys oshanensis (Ye, 1973), and new material from the Middle Jurassic of Lufeng, Yunnan Province, China

2015 ◽  
Vol 186 (1) ◽  
pp. 43-49 ◽  
Author(s):  
Haiyan Tong ◽  
Zhiming Dong ◽  
Tao Wang
Keyword(s):  
Middle Jurassic ◽  
Yunnan Province ◽  
Shell Morphology ◽  
Single Specimen ◽  
Systematic Revision ◽  
Additional Information ◽  
New Material

Abstract Xinjiangchelys oshanensis (Ye, 1973) was originally described as Plesiochelys oshanensisYe, 1973 from the Jurassic Upper Lufeng series of Eshan, Yunnan Province, China. The species was based on a single specimen (IVPP V4444), a damaged shell with articulated carapace and plastron. This species was later referred to as Xinjiangchelys? oshanensis and X. oshanensis respectively, but has never been revised and often overlooked in the studies of Asian Mesozoic turtles. In this paper, we provide the systematic revision of X. oshanensis (Ye, 1973) after new restoration of the specimen. Five additional shells from the Middle Jurassic Chuanjie Formation of Lufeng, Yunnan Province, China are referred to this species. Our study confirms the validity of the species and its assignment to the genus Xinjiangchelys. The study of the new material completes the shell morphology of X. oshanensis and provides additional information about its age.

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