scholarly journals Trichuris trichiura isolated from Macaca sylvanus: morphological, biometrical, and molecular study

2020 ◽  
Vol 16 (1) ◽  
Author(s):  
Julia Rivero ◽  
Ángela María García-Sánchez ◽  
Antonio Zurita ◽  
Cristina Cutillas ◽  
Rocío Callejón
Keyword(s):  
Phylogenetic Trees ◽  
Evolutionary Relationship ◽  
Molecular Study ◽  
Trichuris Trichiura ◽  
Pca Analysis ◽  
Public Health Importance ◽  
Macaca Sylvanus ◽  
Molecular Sequence ◽  
Reservoir Hosts ◽  
Molecular Sequence Analysis

Abstract Background Recent studies have reported the existence of a Trichuris species complex parasitizing primate. Nevertheless, the genetic and evolutionary relationship between Trichuris spp. parasitizing humans and Non-Human Primates (NHP) is poorly understood. The hypothesised existence of different species of Trichuris in primates opens the possibility to evaluate these primates as reservoir hosts of human trichuriasis and other putative new species of whipworms. Results In this paper, we carried out a morphological, biometrical and molecular study of Trichuris population parasitizing Macaca sylvanus from Spain based on traditional morpho-biometrical methods, PCA analysis and ribosomal (ITS2) and mitochondrial (cox1 and cob) DNA sequencing. Morphological results revealed that Trichuris sp. from M. sylvanus is Trichuris trichiura. Ribosomal datasets revealed that phylogenetic relationships of populations of Trichuris sp. from M. sylvanus were unresolved. The phylogeny inferred on mitochondrial datasets (partitioned and concatenated) revealed similar topologies; Thus, phylogenetic trees supported the existence of clear molecular differentiation between individuals of Trichuris sp. from M. sylvanus appearing in two different subclades. Conclusions Based on morphological parameters, biometrical measurements, and molecular sequence analysis, we conclude that the whipworms isolated from M. sylvanus were T. trichiura. Further, the evolutionary relationship showed that these worms belonged to two genotypes within the T. trichiura lineage. Since T. trichiura is of public health importance, it is important to carry out further studies to improve the understanding of its hosts range, evolution and phylogeography.

scholarly journals Correction to: Trichuris trichiura isolated from Macaca sylvanus: morphological, biometrical, and molecular study

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Julia Rivero ◽  
Ángela María García-Sánchez ◽  
Antonio Zurita ◽  
Cristina Cutillas ◽  
Rocío Callejón
Keyword(s):  
Molecular Study ◽  
Trichuris Trichiura ◽  
Macaca Sylvanus

An amendment to this paper has been published and can be accessed via the original article.

scholarly journals Complete mitochondrial genomes confirm the generic placement of the plateau vole, Neodon fuscus

2019 ◽  
Vol 39 (8) ◽  
Author(s):  
Jian-Qiu Li ◽  
Li Li ◽  
Bao-Quan Fu ◽  
Hong-Bin Yan ◽  
Wan-Zhong Jia
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Evolutionary Relationship ◽  
Sister Group ◽  
Trna Genes ◽  
Mammal Species ◽  
Qinghai Province ◽  
Loop Region ◽  
Mt Genome

AbstractThe plateau vole, Neodon fuscus is endemic to China and is distributed mainly in Qinghai Province. It is of public health interest, as it is, a potential reservoir of Toxoplasma gondii and the intermediate host of Echinococcus multilocularis. However, genetic data of this species are lacking, and its name and taxonomy are still a controversy. In the present study, we determined the nucleotide sequence of the entire mitochondrial (mt) genome of N. fuscus and analyzed its evolutionary relationship. The mitogenome was 16328 bp in length and contained 13 protein-coding genes, 22 genes for transfer RNAs (tRNA), two ribosomal RNA genes and two major noncoding regions (OL region and D-loop region). Most genes were located on the heavy strand. All tRNA genes had typical cloverleaf structures except for tRNASer (GCU). The mt genome of N. fuscus was rich in A+T (58.45%). Maximum likelihood (ML) and Bayesian methods yielded phylogenetic trees from 33 mt genomes of Arvicolinae, in which N. fuscus formed a sister group with Neodon irene and Neodon sikimensis to the exclusion of species of Microtus and other members of the Arvicolinae. Further phylogenetic analyses (ML only) based on the cytb gene sequences also demonstrated that N. fuscus had a close relationship with N. irene. The complete mitochondrial genome was successfully assembled and annotated, providing the necessary information for the phylogenetic analyses. Although the name Lasiopodomys fuscus was used in the book ‘Wilson & Reeder’s Mammal Species of the World’, we have confirmed here that its appropriate name is N. fuscus through an analysis of the evolutionary relationships.

scholarly journals Efficient algorithms for molecular sequence analysis.

1988 ◽  
Vol 85 (3) ◽  
pp. 841-845 ◽  
Author(s):  
S. Karlin ◽  
M. Morris ◽  
G. Ghandour ◽  
M. Y. Leung
Keyword(s):  
Sequence Analysis ◽  
Efficient Algorithms ◽  
Molecular Sequence ◽  
Molecular Sequence Analysis

scholarly journals Biosystematic study of the genus Lallemantia (Lamiaceae): species delimitation and relationship

2020 ◽  
Vol 63 (2) ◽  
pp. 157-168
Author(s):  
Fahimeh Koohdar ◽  
Masoud Sheidai
Keyword(s):  
Phylogenetic Trees ◽  
Molecular Study ◽  
Morphological Characters ◽  
Issr Markers ◽  
Evolutionary Analysis ◽  
Species Relationship ◽  
Beast Analysis ◽  
Cpdna Markers ◽  
Components Analysis ◽  
Relationship Of

Lallemantia (Lamiaceae) is a small genus with 5 species. In general, little biosystematics and molecular study has been performed on the genus Lallemantia. Moreover, the studies used only some of the species; none of them has considered all 5 species as a whole in one specific approach. Therefore, the species inter-relationship or nexus in the genus is not thoroughly probed. The present study investigated the molecular phylogeny and species relationship of all five species in the genus Lallemantia, using ribosomal protein L16 and the multilocus ISSR markers. It also compared their morphometric, anatomical and seed results. The species were efficaciously delimited by the morphological, anatomical and seed characters, as well as by ISSR and cpDNA markers. The PCA (Principal components analysis) plot of the species based upon the morphological characters, the MDS (Multidimensional Scaling) plot of the species based on the nutlet and anatomical characters, the NJ (neighbor joining) tree plot of ISSR dataand the ML tree of cpDNA revealed closer affinity between L. iberica and L. canescens and L. peltata was placed at some distance from these species. The phylogenetic trees displayed monophyly of the genus Lallemantia. The Bayesian Evolutionary Analysis by Sampling Trees (BEAST) analysis unveiled that the studied Lallemantia species started to diverge about 25 million years ago.

scholarly journals Mathematical Understanding of Sequence Alignment and Phylogenetic Algorithms: A Comprehensive Review of Methods

2020 ◽  
Author(s):  
Rashid Saif ◽  
Sadia Nadeem ◽  
Ali Iftekhar ◽  
Alishba Khaliq ◽  
Saeeda Zia
Keyword(s):  
Phylogenetic Tree ◽  
Sequence Alignment ◽  
Phylogenetic Trees ◽  
Evolutionary Relationship ◽  
Biological Sequences ◽  
Pairwise Sequence Alignment ◽  
Phylogenetic Tree Construction ◽  
Local Sequence Alignment ◽  
Tree Construction ◽  
Local Sequence

Abstract Context: Pairwise sequence alignment is one of the ways to arrange two biological sequences to identify regions of resemblance that may suggest the functional, structural, and/or evolutionary relationship (proteins or nucleic acids) between the sequences. There are two strategies in pairwise sequence alignment: Local sequence Alignment (Smith-waterman algorithm) and Global sequence Alignment (Needleman-Wunsch algorithm). In local sequence alignment, two sequences that may or may not be related are aligned to find regions of local similarities in large sequences whereas in global sequence alignment, two sequences same in length are aligned to identify conserved regions. Similarities and divergence between biological sequences identified by sequence alignment also have to be rationalized and visualized in the sense of phylogenetic trees. The phylogenetic tree construction methods are divided into distance-based and character-based methods. Evidence Acquisition: In this article, different algorithms of sequence alignment and phylogenetic tree construction were studied with examples and compared to establish the best among them to look into background of these methods for the better understanding of computational phylogenetics.Conclusions: Pairwise sequence alignment is a very important part of bioinformatics to compare biological sequences to find similarities among them. The alignment data is visualized through phylogenetic tree diagram that shows evolutionary history among organisms. Phylogenetic tree is constructed through various methods some are easier but does not provide accurate evolutionary data whereas others provide accurate evolutionary distance among organism but are computationally exhaustive.

scholarly journals Prevalence and Molecular Characterization of Toxocara cati Infection in Feral Cats in Alexandria City, Northern Egypt

2021 ◽  
Author(s):  
Mahmoud Abdelnaby El-Seify ◽  
Naema Mohammed Marey ◽  
Neveen Satour ◽  
Nagwa Mohammed Elhawary ◽  
Khaled Sultan
Keyword(s):  
Phylogenetic Trees ◽  
Cross Sectional Study ◽  
Morphological Features ◽  
Toxocara Cati ◽  
Public Health Importance ◽  
Cross Sectional ◽  
Feral Cats ◽  
Molecular Approaches ◽  
Alexandria City ◽  
Nad1 Gene

Background: This study was performed to determine the prevalence and to identify precisely Toxocara spp., which infects feral cats in Alexandria, Egypt based on morphological and molecular approaches. Methods: This cross-sectional study was carried out on 100 feral cats trapped from different areas of Alexandria during 2018. Adult male and female worms were recovered from small intestinal contents after euthanasia and dissection of cats. Distinct morphological features were initially determined using available keys, and then after amplification and sequencing of the mitochondrial NADH dehydrogenase subunit 1 (nad1) gene was carried out and phylogenetic trees were constructed. Results: Forty out of 100 cats were infected with Toxocara spp. Intensity of infection ranged from 1 to 9 worms/cat, with a mean of 2.27±1.6. All isolates were confirmed as T. cati based on morphological features and the sequence of nad1 gene. Results of the current study clearly show that Egyptian T. cati isolate examined herein is genetically similar to those recorded in other countries. Conclusion: The current work revealed high prevalence of T. cati in feral cats in the study area. This is the first genetic study that confirms T. cati from feral cats in Egypt. In addition, it demonstrated the suitability and need of genetic markers such as nad1 for identification of Toxocara spp. Furthermore highlights the public health importance of T. cati in Egypt.

scholarly journals PHYLOGENETIC ANALYSIS ON FOUR SPECIES OF TILAPIA (Oreochromis niloticus, Tilapia zilli, Sarotherodon galilaeus, Sarotherodon melanotheron) IN NIGERIA

2017 ◽  
Vol 16 (2) ◽  
pp. 61-68
Author(s):  
O. T. AGBEBI ◽  
J. ECHEFU
Keyword(s):  
Oreochromis Niloticus ◽  
Phylogenetic Trees ◽  
Common Ancestor ◽  
Clarias Gariepinus ◽  
Evolutionary Relationship ◽  
Pcr Amplification ◽  
Fta Cards ◽  
Loop Region ◽  
Sarotherodon Galilaeus ◽  
Sarotherodon Melanotheron

An investigation into evolutionary history of four species of Tilapia species was carried out as a taxonomy tool to relate most tilapia species found within the Nigerian waters. These species are (Oreochromis niloticus, Tilapia zilli, Sarotherodon galilaeus, Sarotherodon melanotheron). Blood samples from the four species of tilapia were collected and preserved on Fast Technology for Analysis (FTA) cards for DNA extraction and PCR amplification. The various nucleotide sequences of the four Tilapia species found in the Mitochondria D-loop region were copied and aligned with the use of BioEdit and Mega 6.0 softwares. Three phylogenetic trees were drawn to show the evolutionary relationship amongst the four species of tilapia. The results indicated that Sarotherodon galilaeus and Sarotherodon melanotheron are sister texa and share a common ancestor with Oreochromis niloticus. Tilapia zilli is an out group which is the most distantly related to the three species (Oreochromis niloticus, Sarotherodon galilaeus Sarotherodon melanotheron). Tilapia zilli (Israel) and Tilapia zilli are sister texa and share a common ancestor in Tilapia sparmanii. The study also revealed ancestry relationship among other species of fish Cyprinus caprio and Clarias gariepinus formed a clade with the three tilapia species (Tilapia zilli, Tilapia zilli (Israel) and Tilapia sparmanii), which share an unknown but common ancestor.

scholarly journals Taxon sampling unequally affects individual nodes in a phylogenetic tree: consequences for model gene tree construction in SwissTree

2017 ◽  
Author(s):  
Brigitte Boeckmann ◽  
David Dylus ◽  
Sebastien Moretti ◽  
Adrian Altenhoff ◽  
Clément-Marie Train ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Signal ◽  
Gene Tree ◽  
Evolutionary Relationship ◽  
Taxon Sampling ◽  
Gene Trees ◽  
Data Types ◽  
Large Gene ◽  
Tree Construction ◽  
Taxonomic Range

AbstractMedium to large phylogenetic gene trees constructed from datasets of different species density and taxonomic range are rarely topologically consistent because of missing phylogenetic signal, non-phylogenetic signal and error. In this study, we first use simulations to show that taxon sampling unequally affects nodes in a gene tree, which likely contributes to controversial conclusions from taxon sampling experiments and contradicting species phylogenies such as for the boreoeutherians. Hence, because it is unlikely that a large gene tree can be reconstructed correctly based on a single optimized dataset, we take a two-step approach for the construction of model gene trees. First, stable and unstable clades are identified by comparing phylogenetic trees inferred from multiple datasets and data types (nucleotide, amino acid, codon) from the same gene family. Subsequently, data subsets are optimized for the analysis of individual uncertain clades. Results are summarized in form of a model tree that illustrates the evolutionary relationship of gene loci. A case study shows how a seemingly complex gene phylogeny becomes increasingly consistent with the reference species tree by attentive taxon sampling and subtree analysis. The procedure is progressively introduced to SwissTree (http://swisstree.vital-it.ch), a resource of high confidence model gene (locus) trees. Finally we demonstrate the usefulness of SwissTree for orthology benchmarking.

scholarly journals Short Communication: Molecular study on mt-DNA COX2 gene of Sumatran elephant (Elephas maximus sumatranus)

2021 ◽  
Vol 22 (2) ◽  
Author(s):  
Deny Setyo Wibowo ◽  
Rini Widiyanti ◽  
Machmud Asvan ◽  
Prista Dwi Restanti ◽  
Hery Wijayanto
Keyword(s):  
Genetic Distance ◽  
Phylogenetic Trees ◽  
Short Communication ◽  
Molecular Study ◽  
Elephas Maximus ◽  
Individual Species ◽  
Parameter Method ◽  
Exploratory Research ◽  
Mt Dna ◽  
Asian Elephants

Abstract. Wibowo DS, Widiyanti R, Asvan M, Restanti PD, Wijayanto H. 2021. Short Communication: Molecular study on mt-DNA COX2 gene of Sumatran elephant (Elephas maximus sumatranus). Biodiversitas 22: 1063-1068. Sumatran elephant is the only subspecies of Asian elephants that receives a critically endangered status from the International Union for Conservation and Nature Resources (IUCN). Identifying the genetic marker of Sumatran elephants is, therefore, important for their conservation. This study aimed to identify the Sumatran elephant based on specific mitochondrial DNA markers of the Cytochrome c oxidase subunit II (COX2) gene. It is an exploratory research considering the limited data and research about the genetic, especially the COX2 of Sumatran elephant (Elephas maximus sumatranus). Forward and reverse sequencing of PCR products was conducted using the primary COX2 from Sumatran elephant samples. The results of the subsequent gene sequencing were aligned with the sequences of other Asian elephants from Genbank using Clustal W software and analyzed using the MEGA program version 6.06. The analysis of genetic distance based on COX2 constituent nucleotides calculated with Kimura’s two-parameter method showed that the genetic distance between Elephas maximus sumatranus and Elephas maximus outside of Sumatra was 0.25%. The phylogenetic trees analyzed using the maximum-likelihood based on nucleotide sequences showed a high homogeneity. The ratio of Elephas maximus sumatranus with Elephas maximus shows levels of nucleotide mutations which are nine nucleotides and four nucleotides. These results indicated that the COX2 gene could not identify the individual species of Sumatran elephant because of the high intraspecies homogeneity, but it detected the interspecies divergence clustered in Asian elephant clade.

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