Gallus gallus aggrecan gene-based phylogenetic analysis of selected avian taxonomic groups

Genetica ◽  
2005 ◽  
Vol 124 (1) ◽  
pp. 23-32 ◽  
Author(s):  
Edward J. Smith ◽  
Li Shi ◽  
Zhijian Tu
Keyword(s):  
Phylogenetic Analysis ◽  
Gallus Gallus ◽  
Taxonomic Groups

scholarly journals Comparison of complex networks and tree-based methods of phylogenetic analysis and proposal of a bootstrap method

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4349 ◽  
Author(s):  
Aristóteles Góes-Neto ◽  
Marcelo V.C. Diniz ◽  
Daniel S. Carvalho ◽  
Gilberto C. Bomfim ◽  
Angelo A. Duarte ◽  
...  
Keyword(s):  
Biological Sciences ◽  
Phylogenetic Analysis ◽  
Complex Networks ◽  
Complex Network ◽  
Bootstrap Method ◽  
Molecular Data ◽  
Data Sets ◽  
Fungal Cell ◽  
Taxonomic Groups ◽  
Inference Methods

Complex networks have been successfully applied to the characterization and modeling of complex systems in several distinct areas of Biological Sciences. Nevertheless, their utilization in phylogenetic analysis still needs to be widely tested, using different molecular data sets and taxonomic groups, and, also, by comparing complex networks approach to current methods in phylogenetic analysis. In this work, we compare all the four main methods of phylogenetic analysis (distance, maximum parsimony, maximum likelihood, and Bayesian) with a complex networks method that has been used to provide a phylogenetic classification based on a large number of protein sequences as those related to the chitin metabolic pathway and ATP-synthase subunits. In order to perform a close comparison to these methods, we selected Basidiomycota fungi as the taxonomic group and used a high-quality, manually curated and characterized database of chitin synthase sequences. This enzymatic protein plays a key role in the synthesis of one of the exclusive features of the fungal cell wall: the presence of chitin. The communities (modules) detected by the complex network method corresponded exactly to the groups retrieved by the phylogenetic inference methods. Additionally, we propose a bootstrap method for the complex network approach. The statistical results we have obtained with this method were also close to those obtained using traditional bootstrap methods.

scholarly journals Phylogenetic analysis of different Artemisia species based on chloroplast gene rps11

2011 ◽  
Vol 63 (3) ◽  
pp. 661-665 ◽  
Author(s):  
Tariq Mahmood ◽  
Nadia Hassan ◽  
Nazia Nazar ◽  
Ishrat Naveed
Keyword(s):  
Phylogenetic Analysis ◽  
Restriction Site ◽  
Fragment Length Polymorphism ◽  
Restriction Enzymes ◽  
The Family ◽  
Artemisia Species ◽  
The Subject ◽  
Analysis System ◽  
Mixed Pattern ◽  
Taxonomic Groups

Artemisia L. of the family Astereacae is a genus with enormous economical and medicinal importance. As a result, the genus Artemisia has been the subject of diversity-focused studies. In the present study, phylogenetic analysis based on restriction fragment length polymorphism of the chloroplast rps11 gene was conducted on eight species of Artemisia that represent the major morphological subgroups. After digestion of the rps11 gene that was amplified from eight species, with six different restriction enzymes, each restriction site was observed and scored on a 12% polyacrylamide gel. The data were analyzed using the Numerical Taxonomy and Multivariate Analysis System to infer the phylogenetic relationship within the genus. A mixed pattern was observed among the species belonging to various taxonomic groups of Artemisia.

Identification of the Oligocene to early Miocene loricariid catfish †Taubateia paraiba as a member of the Rhinelepinae

2021 ◽  
pp. 1-5
Author(s):  
Jonathan W. Armbruster ◽  
Nathan K. Lujan
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Clock ◽  
Early Miocene ◽  
Primary Sources ◽  
Correct Identification ◽  
Circular Reasoning ◽  
Time Calibration ◽  
Molecular Phylogenies ◽  
Taxonomic Groups

Correct identification of fossil taxa is immensely important for dating molecular phylogenies and understanding when and how quickly modern biodiversity evolved. Fossils that are available for a clade of interest and can be directly incorporated in the phylogenetic analysis are considered primary sources of time calibration, whereas calibrations inferred from other studies are secondary (Arroyave et al., 2013). Studies of taxonomic groups that lack fossils must either expand their analyses to include fossilized outgroup lineages, use secondary calibrations, or use more problematic primary calibrations, e.g., vicariant geologic events. The use of vicariant geologic events to calibrate phylogenies poses the risk of circular reasoning, because the goal of many such studies is to determine how geologic events have affected diversification. Near et al. (2012) argued that fossil calibrations external to clades of interest, but still within the broader Actinopterygian (ray-finned fishes) tree, could be used as means of calibrating a generalized molecular clock, but internal calibrations are still valuable for refining such inferences (Arroyave et al., 2013).

scholarly journals Utilizing RADseq data for phylogenetic analysis of challenging taxonomic groups: A case study inCarexsect.Racemosae

2016 ◽  
Vol 103 (2) ◽  
pp. 337-347 ◽  
Author(s):  
Rob Massatti ◽  
Anton A. Reznicek ◽  
L. Lacey Knowles
Keyword(s):  
Phylogenetic Analysis ◽  
Taxonomic Groups

scholarly journals Prevalence, Characterization and Mycotoxin Production Ability of Fusarium species on Korean Adlay (Coix lacrymal-jobi L.) Seeds

2016 ◽  
Author(s):  
Tae Jin An ◽  
Kyu Seop Shin ◽  
Narayan Chandra Paul ◽  
Young Guk Kim ◽  
Seon Woo Cha ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Quantitative Analysis ◽  
Fusarium Species ◽  
Morphological Characteristics ◽  
Test Tube ◽  
Analysis Method ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Quantitative Analysis Method ◽  
Taxonomic Groups

Adlay seed samples were collected from 3 adlay growing regions (Yeoncheon, Jeonnam and Eumseong regions) in Korea during 2012. Among all the samples collected, 400 seeds were tested for fungal occurrence by standard blotter and test tube agar methods and different taxonomic groups of fungal genera were detected. The most predominant fungal genera encountered were Fusarium, Phoma, Alternaria, Cladosporium, Curvularia, Cochliobolus and Leptosphaerulina. The occurrence of Fusarium species were 45.6% and based on the combined sequences of two protein coding genes, EF-1a, Beta-tubulin and phylogenetic analysis, 10 species were characterized as F. incarnatum (11.67%), F. kyushense (10.33%), F. fujikuroi (8.67%), F. concentricum (6.00%), F. asiaticum (5.67%), F. graminearum (1.67%), F. miscanthi (0.67%), F. polyphialidiom (0.33%), F. armeniacum (0.33%) and F. thapsinum (0.33%). The ability of these isolates to produce mycotoxins fumonisin (FUM) and zeralenone (ZEN) were tested by ELISA quantitative analysis method. The result revealed that fumonisin (FUM) was produced only by F. fujikuroi and zeralenone (ZEN) by F. asiaticum & F. graminearum. Mycotoxigenic species were then examined for their morphological characteristics to confirm their identity. Morphological observations of the species correlated well with their molecular identification and confirmed as F. asiaticum, F. fujikuroi and F. graminearum.

scholarly journals Mitochondrial genome and phylogenetic analysis of Gaojiao chicken (Gallus gallus)

2020 ◽  
Vol 5 (3) ◽  
pp. 2124-2125
Author(s):  
Lili Liu ◽  
Kui Ren ◽  
Yuanchang Jin ◽  
Huimin Zeng
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Genome ◽  
Gallus Gallus

The isolation of heavy-metal resistant culturable bacteria and resistance determinants from a heavy-metal-contaminated site

Biologia ◽  
2011 ◽  
Vol 66 (1) ◽  
Author(s):  
Edita Karelová ◽  
Jana Harichová ◽  
Tatjana Stojnev ◽  
Domenico Pangallo ◽  
Peter Ferianc
Keyword(s):  
Heavy Metal ◽  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rdna ◽  
Minimal Medium ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Rich Medium ◽  
Resistance Determinants ◽  
Taxonomic Groups

AbstractIn this study we performed a phylogenetic analysis of a culturable bacterial community isolated from heavymetal-contaminated soil from southwest Slovakia using 16S rRNA (16S rDNA) and heavy-metal resistance genes. The soil sample contained high concentrations of nickel (2,109 mg/kg), cobalt (355 mg/kg) and zinc (177 mg/kg), smaller concentrations of iron (35.75 mg/kg) and copper (32.2 mg/kg), and a trace amount of cadmium (<0.25 mg/kg). A total of 100 isolates were grown on rich (Nutrient agar No. 2) or minimal (soil-extract agar medium) medium. The isolates were identified by phylogenetic analysis using partial sequences of their 16S rRNA (16S rDNA) genes. Representatives of two broad taxonomic groups, Firmicutes and Proteobacteria, were found on rich medium, whereas four taxonomic groups, Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria, were represented on minimal medium. Forty-two isolates grown on rich medium were assigned to 20 bacterial species, while 58 bacteria grown on minimal medium belonged to 49 species. Twenty-three isolates carried czcA- and/or nccA-like heavy-metal-resistance determinants. The heavy-metalresistance genes of nine isolates were identified by phylogenetic analysis of their protein sequences.

Sign in / Sign up

Export Citation Format

Share Document