Morphological redescription and molecular characterization of Trichodina matsu Basson & Van As, 1994 (Ciliophora, Mobilida, Trichodinidae) infecting Tachysurus fulvidraco (Richardson, 1846) from Chongqing, China

Zootaxa ◽  
2021 ◽  
Vol 4995 (2) ◽  
pp. 334-344
Author(s):  
QIAN ZHOU ◽  
FAHUI TANG ◽  
YUANJUN ZHAO
Keyword(s):  
Phylogenetic Analyses ◽  
Molecular Data ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Similar Species ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Morphological And Molecular Data ◽  
Tachysurus Fulvidraco

During a survey of parasitic ciliates in Chongqing, China, Trichodina matsu Basson & Van As, 1994 was isolated from gills of Tachysurus fulvidraco. Furthermore, the 18S rRNA gene and ITS-5.8S rRNA region of T. matsu were sequenced for the first time and applied for the species identification and comparison with similar species in the present study. Based on the morphological and molecular comparisons, the results indicate that T. matsu is an ectoparasite specific for the Siluriformes catfish. Based on the analyses of genetic distance, multiple sequence alignments, and phylogenetic analyses, no obvious differentiation within populations of T. matsu was found. In addition, the ‘Trichodina hyperparasitis’ (KX904933) in GenBank is a misidentification and appears to be conspecific with T. matsu according to the comparison of morphological and molecular data.  

scholarly journals SequenceBouncer: A method to remove outlier entries from a multiple sequence alignment

2020 ◽  
Author(s):  
Cory D. Dunn
Keyword(s):  
Nucleic Acid ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Phylogenetic Analyses ◽  
Protein Sequences ◽  
Mitochondrial Genomes ◽  
Dna Barcodes ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments

AbstractPhylogenetic analyses can take advantage of multiple sequence alignments as input. These alignments typically consist of homologous nucleic acid or protein sequences, and the inclusion of outlier or aberrant sequences can compromise downstream analyses. Here, I describe a program, SequenceBouncer, that uses the Shannon entropy values of alignment columns to identify outlier alignment sequences in a manner responsive to overall alignment context. I demonstrate the utility of this software using alignments of available mammalian mitochondrial genomes, bird cytochrome c oxidase-derived DNA barcodes, and COVID-19 sequences.

Phylogenetics of scolopendromorph centipedes: can denser taxon sampling improve an artificial classification?

2013 ◽  
Vol 27 (5) ◽  
pp. 578 ◽  
Author(s):  
Varpu Vahtera ◽  
Gregory D. Edgecombe ◽  
Gonzalo Giribet
Keyword(s):  
Bayesian Inference ◽  
New World ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Taxon Sampling ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Artificial Classification

Previous phylogenetic analyses of the centipede order Scolopendromorpha indicated a fundamental division into blind and ocellate clades. These analyses corroborated the monophyly of most families and tribes but suggested that several species-rich, cosmopolitan genera in traditional and current classifications are polyphyletic. Denser taxon sampling is applied to a dataset of 122 morphological characters and sequences for four nuclear and mitochondrial loci. Phylogenetic analyses including 98 species and subspecies of Scolopendromorpha employ parsimony under dynamic and static homology schemes as well as maximum likelihood and Bayesian inference of multiple sequence alignments. The monotypic Australian genera Notiasemus and Kanparka nest within Cormocephalus and Scolopendra, respectively, and the New Caledonian Campylostigmus is likewise a clade within Cormocephalus. New World Scolopendra are more closely related to Hemiscolopendra and Arthrorhabdus than to Scolopendra s.s., which is instead closely allied to Asanada; the tribe Asanadini nests within Scolopendrini for molecular and combined datasets. The generic classification of Otostigmini has a poor fit to phylogenetic relationships, although nodal support within this tribe is weak. New synonymies are proposed for Ectonocryptopinae Shelley & Mercurio, 2005 (= Newportiinae Pocock, 1896), Asanadini Verhoeff, 1907 (= Scolopendrini Leach, 1814), and Kanparka Waldock & Edgecombe, 2012 (= Scolopendra Linnaeus, 1758). Scolopendrid systematics largely depicts incongruence between phylogeny and classification rather than between morphology and molecules.

scholarly journals Relative model selection can be sensitive to multiple sequence alignment uncertainty

2021 ◽  
Author(s):  
Stephanie J Spielman ◽  
Molly Miraglia
Keyword(s):  
Model Selection ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Selection Procedure ◽  
Evolutionary Model ◽  
Ancestral State ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Nucleotide Data

Multiple sequence alignments (MSAs) represent the fundamental unit of data inputted to most comparative sequence analyses. In phylogenetic analyses in particular, errors in MSA construction have the potential to induce further errors in downstream analyses such as phylogenetic reconstruction itself, ancestral state reconstruction, and divergence estimation. In addition to providing phylogenetic methods with an MSA to analyze, researchers must also specify a suitable evolutionary model for the given analysis. Most commonly, researchers apply relative model selection to select a model from candidate set and then provide both the MSA and the selected model as input to subsequent analyses. While the influence of MSA errors has been explored for most stages of phylogenetics pipelines, the potential effects of MSA uncertainty on the relative model selection procedure itself have not been explored. In this study, we assessed the consistency of relative model selection when presented with multiple perturbed versions of a given MSA. We find that while relative model selection is mostly robust to MSA uncertainty, in a substantial proportion of circumstances, relative model selection identifies distinct best-fitting models from different MSAs created from the same set of sequences. We find that this issue is more pervasive for nucleotide data compared to amino-acid data. However, we also find that it is challenging to predict whether relative model selection will be robust or sensitive to uncertainty in a given MSA. We find that that MSA uncertainty can affect virtually all steps of phylogenetic analysis pipelines to a greater extent than has previously been recognized, including relative model selection.

scholarly journals Characterization of two novel EF-hand proteins identifies a clade of putative Ca2+-binding protein specific to the Ambulacraria

2020 ◽  
Author(s):  
Arisnel Soto-Acabá ◽  
Pablo A. Ortíz-Pineda ◽  
José E. García-Arrarás
Keyword(s):  
Calcium Binding ◽  
Phylogenetic Analyses ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Significant Similarity ◽  
Significant Differential Expression ◽  
Multiple Sequence Alignments ◽  
Ef Hand ◽  
Protein Discovery

AbstractIn recent years, transcriptomic databases have become one of the main sources for protein discovery. In our studies of nervous system and digestive tract regeneration in echinoderms, we have identified several transcripts that have attracted our attention. One of these molecules corresponds to a previously unidentified transcript (Orpin) from the sea cucumber Holothuria glaberrima that appeared to be upregulated during intestinal regeneration. We have now identified a second highly similar sequence and analyzed the predicted proteins using bioinformatics tools. Both sequences have EF-hand motifs characteristic of calcium-binding proteins (CaBPs) and N-terminal signal peptides. Sequence comparison analyses such as multiple sequence alignments and phylogenetic analyses only showed significant similarity to sequences from other echinoderms or from hemichordates. Semi-quantitative RT-PCR analyses revealed that transcripts from these sequences are expressed in various tissues including muscle, haemal system, gonads, and mesentery. However, contrary to previous reports, there was no significant differential expression in regenerating tissues. Nonetheless, the identification of unique features in the predicted proteins suggests that these might comprise a novel subfamily of EF-hand containing proteins specific to the Ambulacraria clade.

scholarly journals QMaker: Fast and accurate method to estimate empirical models of protein evolution

2020 ◽  
Author(s):  
Bui Quang Minh ◽  
Cuong Cao Dang ◽  
Le Sy Vinh ◽  
Robert Lanfear
Keyword(s):  
Amino Acid ◽  
Amino Acid Substitution ◽  
Search Algorithm ◽  
Phylogenetic Analyses ◽  
Accurate Method ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Substitution Models ◽  
Protein Alignments

AbstractAmino acid substitution models play a crucial role in phylogenetic analyses. Maximum likelihood (ML) methods have been proposed to estimate amino acid substitution models, however, they are typically complicated and slow. In this paper, we propose QMaker, a new ML method to estimate a general time-reversible Q matrix from a large protein dataset consisting of multiple sequence alignments. QMaker combines an efficient ML tree search algorithm, a model selection for handling the model heterogeneity among alignments, and the consideration of rate mixture models among sites. We provide QMaker as a user-friendly function in the IQ-TREE software package (http://www.iqtree.org) supporting the use of multiple CPU cores so that biologists can easily estimate amino acid substitution models from their own protein alignments. We used QMaker to estimate new empirical general amino acid substitution models from the current Pfam database as well as five clade-specific models for mammals, birds, insects, yeasts, and plants. Our results show that the new models considerably improve the fit between model and data and in some cases influence the inference of phylogenetic tree topologies.

scholarly journals Nodosilinea chupicuarensis sp. nov. (Leptolyngbyaceae, Synechococcales) a subaerial cyanobacterium isolated from a stone monument in central Mexico

Phytotaxa ◽  
2018 ◽  
Vol 334 (2) ◽  
pp. 167 ◽  
Author(s):  
JUAN VÁZQUEZ-MARTÍNEZ ◽  
JUAN MANUEL GUTIERREZ-VILLAGOMEZ ◽  
CITLALI FONSECA-GARCÍA ◽  
ENRIQUE RAMÍREZ-CHÁVEZ ◽  
MA. LOURDES MONDRAGÓN-SÁNCHEZ ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Its Region ◽  
Molecular Data ◽  
Central Mexico ◽  
Rrna Gene ◽  
North Central ◽  
Stone Monuments ◽  
Morphological And Molecular Data ◽  
A New Species ◽  
The 16S Rrna Gene

Microorganisms of subaerial biofilms, which develop on the surface of stone monuments, have been widely studied due to their impact on Cultural Heritage deterioration. Nevertheless, these extremophile microorganisms are poorly characterised. In this study, a cyanobacterial strain isolated from an archaeological zone in north-central Mexico was characterised through a polyphasic study based on ecological, morphological, and molecular data. Phylogenetic analyses were done using sequences of the 16S rRNA gene and the 16S-23S ITS region. Based on the polyphasic data, a new species corresponding to the genus Nodosilinea is described. This alkaliphilic species has optimum growth at pH of 9. Its fatty acid profile indicates that C18:1, 9E and C16:0 are its most abundant fatty acids. Extracellular polymeric substance production was verified on this strain. Only a few species of the genus Nodosilinea have been documented and described, and this is the first report of their presence in central Mexico. Hence the name Nodosilinea chupicuarensis sp. nov. is proposed.

A new species of Megophrys (Amphibia: Anura: Megophryidae) from Vietnam

Zootaxa ◽  
2020 ◽  
Vol 4722 (5) ◽  
pp. 401-422 ◽  
Author(s):  
TRUONG QUANG NGUYEN ◽  
CUONG THE PHAM ◽  
TAO THIEN NGUYEN ◽  
ANH MAI LUONG ◽  
THOMAS ZIEGLER
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Dorsal Surface ◽  
Molecular Data ◽  
Outer Edge ◽  
Rrna Gene ◽  
Dorsal Skin ◽  
Dorsal Ridge ◽  
Morphological And Molecular Data ◽  
A New Species

A new species of Megophrys is described from Cao Bang Province, northeastern Vietnam based on morphological and molecular data. Morphologically, the new species is distinguishable from its congeners by a combination of the following characters: Size small (SVL 34.9–38.9 mm in males); tympanum visible; vomerine teeth absent; tongue not notched posteriorly; male with a single vocal sac; toes with rudimentary webbing; subarticular tubercles and lateral fringes absent on all digits; nuptial pads present on fingers I and II in males, with spicules; dorsal skin with scattered granules and tubercles; flank with tubercles; dorsum with a X-shaped dorsal ridge; dorsolateral folds prominent; a small horn-like tubercle present at the outer edge of the eyelid; dorsal surface yellowish brown with a dark brown triangle between the eyes, and a dark brown marking along the X-shaped ridge on the back. In the phylogenetic analyses, the new species is unambiguously nested within the subgenus Panophrys with interspecific uncorrected genetic p-distances (16S rRNA gene) varying from 4.26% (compared with M. rubrimera) to 10.80% (compared with M. acuta).

Additional data on Pratylenchoides riparius (Andrássy, 1985) Luc, 1986 (Nematoda: Merliniidae) from Iran

Nematology ◽  
2019 ◽  
Vol 21 (8) ◽  
pp. 827-836 ◽  
Author(s):  
Manouchehr Hosseinvand ◽  
Ali Eskandari ◽  
Reza Ghaderi
Keyword(s):  
Taxonomic Status ◽  
Molecular Data ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Similar Species ◽  
28S Rrna ◽  
Lateral Field ◽  
Molecular Phylogenetic ◽  
Type Population ◽  
Stylet Length

Summary The second population of Pratylenchoides riparius, including females and males, is described and illustrated based upon morphological, morphometric and molecular data. The present population from Iran is characterised by some differences with the type population of the species from Hungary in stylet length (24-26 vs 21-22 μm), slightly longer body (1002-1230 vs 830-960 μm), pharynx (202-211 vs 182-190 μm) and tail (64-85 vs 48-57 μm), areolated outer bands of the lateral field (vs non-areolated), widening of the lateral field near tail terminus (vs lateral incisures connecting each other) and presence of males (vs absent). The taxonomic status of the species with regarding the data from the type and presently recovered population, as well as the closely similar species is discussed. The newly recovered population was studied based upon its molecular phylogenetic charactes using the D2-D3 of 28S rRNA and the partial 18S rRNA gene sequences and the results revealed that it forms a clade with P. magnicauda in 28S, but occupies a distant placement from it in 18S phylogeny.

Collastoma esotericum (Neodalyellida: Umagillidae), a new species of sipunculan-inhabiting rhabdocoel from Queensland, Australia

Zootaxa ◽  
2019 ◽  
Vol 4701 (6) ◽  
pp. 563-573
Author(s):  
DANIEL C. HUSTON
Keyword(s):  
Phylogenetic Analyses ◽  
Strong Support ◽  
Molecular Data ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Distinct Genus ◽  
De Man ◽  
Relationship Of ◽  
The Relationship ◽  
Southeast Queensland

The Umagillidae Wahl, represent a group of endosymbiotic Platyhelminthes which inhabit two disparate invertebrate host groups, the echinoderms and sipunculans. Sipunculan-inhabiting umagillids are morphologically distinct from those inhabiting echinoderms and have traditionally been placed in a distinct genus and subfamily, Collastoma Dörler, and the Collastominae Wahl, respectively. Although molecular data are available for umagillid species inhabiting echinoids and holothurians, species inhabiting sipunculans have yet to be evaluated with molecular data. Collastoma esotericum n. sp. from the sipunculan Phascolosoma scolops (Selenka & de Man) collected in Moreton Bay, southeast Queensland, Australia, is described. Phylogenetic analyses based on 18S rRNA gene sequences placed C. esotericum in a clade with species of the Umagillidae and the Provorticinae Luther, with strong support. However, within this clade the relationship of C. esotericum to the Umagillidae and Provorticinae was not resolved. 

scholarly journals First Molecular Characterization of Poxviruses in Cattle, Sheep, and Goats in Botswana

2021 ◽  
Author(s):  
Boitumelo Magret Modise ◽  
Tirumala Bharani Kumar Settypalli ◽  
Tebogo Kgotlele ◽  
Dingrong Xue ◽  
Kebonyemodisa Ntesang ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Clinical Symptoms ◽  
Phylogenetic Analyses ◽  
Small Ruminants ◽  
Virus Diseases ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Lumpy Skin Disease ◽  
Multiple Sequence Alignments

Abstract BackgroundPoxviruses within the Capripoxvirus, Orthopoxvirus, and Parapoxvirus genera can infect livestock, with the two former presenting also zoonotic importance. In addition, they induce similar clinical symptoms in common host species, creating a challenge for diagnosis. Although endemic in the country, poxvirus infections of small ruminants and cattle have received little attention in Botswana, and there was no prior attempt of using molecular tools to diagnose the diseases and characterize the pathogens.MethodsA high-resolution melting (HRM) assay was used to detect and differentiate poxviruses in samples from four cattle (from Mahalapye, Kasane, and Molepolole), one sheep (from Jwaneng), and one goat (from Kasane). Molecular characterization of capripoxviruses and parapoxviruses was undertaken by sequence analysis of RPO30 and GPCR genes.ResultsThe HRM assay revealed lumpy skin disease virus (LSDV) in three cattle samples, pseudocowpox virus (PCPV) in one cattle sample, and orf virus (ORFV) in one goat and one sheep sample. The phylogenetic analyses, based on the RPO30 and GPCR, and the inspection of the multiple sequence alignments showed that the LSDV sequences of Botswana were more like those of common LSDV field isolates encountered in Africa, Asia, and Europe. The Botswana PCPV presented unique features and clustered between camel isolates and cattle isolates of the PCPV group. The Botswana ORFV from goat differed from the ORFV collected in sheep.ConclusionsThis study is the first report on the genetic characterization of pox virus diseases circulating in cattle, goats, and sheep in Botswana. It shows the importance of molecular methods to differentially diagnose pox virus diseases of ruminants.

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