scholarly journals Phylogenetic analysis of eyeworm (Oxyspirura petrowi) in northern bobwhite (Colinus virginianus) based on the nuclear 18S rDNA and mitochondrial cytochrome oxidase 1 gene (COX1)

2018 ◽  
Vol 4 ◽  
Author(s):  
Aravindan Kalyanasundaram ◽  
Kendall R. Blanchard ◽  
Cassandra Henry ◽  
Matthew Z. Brym ◽  
Ronald J. Kendall
Keyword(s):  
Phylogenetic Trees ◽  
Colinus Virginianus ◽  
Close Relation ◽  
Nematode Species ◽  
Northern Bobwhite ◽  
Cox1 Gene ◽  
Parsimony Method ◽  
Phylogenetic Relations ◽  
Maximum Parsimony Method ◽  
Mitochondrial Region

Abstract Oxyspirura petrowi is a heteroxenous nematode found in northern bobwhite (Colinus virginianus) of the Rolling Plains ecoregion of Texas. Despite its impact on this popular gamebird, genetic level studies on O. petrowi remain relatively unexplored. To accomplish this, we chose the previously studied nuclear rDNA 18S region as well as the mitochondrial COX1 gene region of O. petrowi to investigate phylogenetic relations between O. petrowi and other nematode species. In this study, we generate primers using multiple alignment and universal nematode primers to obtain a near-complete 18S and partial COX1 sequence of O. petrowi, respectively. Phylogenetic trees for O. petrowi’s 18S and COX1 gene regions were constructed using the Maximum Likelihood and Maximum Parsimony method. A comparative analysis was done based on the nuclear and mitochondrial region similarities between O. petrowi and other nematode species that infect both humans and animals. Results revealed a close relation to the zoonotic eyeworm Thelazia callipaeda as well as a close relation with filarial super family (Filarioidea) such as the human eyeworm Loa loa and Dirofilaria repens eyeworm of dog and carnivores.

scholarly journals Molecular phylogenetics of Malesian Diospyros (Ebenaceae) based trnL-F spacer sequences

2021 ◽  
Vol 22 (9) ◽  
Author(s):  
Irvan Fadli Wanda ◽  
Nina Ratna Djuita ◽  
TATIK CHIKMAWATI
Keyword(s):  
Dna Barcoding ◽  
Phylogenetic Trees ◽  
Molecular Phylogenetics ◽  
Sequence Data ◽  
Intergenic Spacer ◽  
Botanical Garden ◽  
Limited Information ◽  
Parsimony Method ◽  
Maximum Parsimony Method ◽  
Diospyros Species

Abstract. Wanda IF, Djuita NR, Chikmawati T. 2021. Molecular phylogenetics of Malesian Diospyros (Ebenaceae) based trnL-F spacer sequences. Biodiversitas 22: 4106-4114. Diospyros is a genus composed of potential species as an economic commodity with high diversity. However, there is limited information on the phylogenetic relationship of this genus in the Malesian region. This study aimed to provide information on the species diversity through a DNA barcoding approach and revealing the phylogenetic information of Diospyros spp. in the Malesian region. This study used 20 Diospyros accessions from Bogor Botanical Garden collections, 40 Diospyros accessions, and four outgroup accessions obtained from the NCBI database. The DNA barcoding primer utilized comes from plastids, trnL-F intergenic spacer. The phylogenetic trees were constructed using the Maximum-Parsimony method. A total of 20 accessions of Diospyros were validated with sequence data on the genebank. The result showed that all accessions had relationships with 44 other Diospyros species globally. Here, we reported 10 new trnL-F intergenic spacer sequences of Malesian Diospyros species. A phylogenetic tree grouped 64 monophyletic Diospyros species into seven clades. The phylogenetic results supports the biogeographic hypothesis: the Malesian region, the Malesian-Caledonian Region, and Cosmopolite species in almost all bioregions.

Phylogenetic relationships within the genus Steinernema (Nematoda: Rhabditida) as inferred from analyses of sequences of the ITS1-5.8S-ITS2 region of rDNA and morphological features

Nematology ◽  
2004 ◽  
Vol 6 (4) ◽  
pp. 547-566 ◽  
Author(s):  
Sergei E. Spiridonov ◽  
Alex P. Reid ◽  
Kasia Podrucka ◽  
Sergei A. Subbotin ◽  
Maurice Moens
Keyword(s):  
Phylogenetic Trees ◽  
Sequence Divergence ◽  
Morphological Features ◽  
Its Rdna ◽  
Data Matrix ◽  
Its2 Region ◽  
Nominal Species ◽  
Parsimony Method ◽  
Maximum Parsimony Method ◽  
Different Populations

Abstract Eighty four new and four published ITS1-5.8S-ITS2 sequences of rDNA obtained from different populations of 24 nominal species and 28 isolates of 16 putative Steinernema species were analysed using the maximum parsimony method. In most of the phylogenetic trees obtained from different ITS alignments and phylogenetic procedures, the 84 isolates formed five main, highly or moderately supported, clades, viz Clade I: 'affine-intermedium'; Clade II: 'carpocapsae-scapterisci-tami'; Clade III: 'feltiae-krausseioregonense'; Clade IV: 'bicornutum-ceratophorum-riobrave'; and Clade V: 'arenarium-glaseri-karii-longicaudum'. The ITS rDNA data were found to be of little utility in resolving relationships between these clades, but were useful in studying relationships between species within certain clades. The level of intra-specific variability was different between clades with sequence divergence of 2.4-2.8% of ITS rDNA for some species. Analysis of a combined data matrix of both molecular and morphological features was performed with six qualitative and three quantitative features.

Antibiotic susceptibility of Edwardsiella hoshinae isolated from northern bobwhite quail (Colinus virginianus)

2004 ◽  
Vol 155 (1) ◽  
pp. 29-29 ◽  
Author(s):  
I. M. Singh ◽  
S. Singh ◽  
M. A. McMurphy ◽  
S. S. Crupper ◽  
F. Mills-Robertson ◽  
...  
Keyword(s):  
Antibiotic Susceptibility ◽  
Colinus Virginianus ◽  
Northern Bobwhite ◽  
Bobwhite Quail

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.

Molecular and morphometric characterisation of Xiphinema globosum Sturhan, 1978 (Nematoda: Longidoridae) from Spain

Nematology ◽  
2011 ◽  
Vol 13 (1) ◽  
pp. 17-28 ◽  
Author(s):  
Blanca Landa ◽  
Carolina Cantalapiedra-Navarrete ◽  
Juan Palomares-Rius ◽  
Pablo Castillo ◽  
Carlos Gutiérrez-Gutiérrez
Keyword(s):  
Phylogenetic Trees ◽  
18S Rrna ◽  
Matrix Representation ◽  
Natural Environments ◽  
28S Rrna ◽  
Parsimony Method ◽  
Rdna Genes ◽  
Supertree Method ◽  
The Matrix ◽  
Relationship Of

AbstractDuring a recent nematode survey in natural environments of the Los Alcornocales Regional Park narrow valleys, viz., the renowned 'canutos' excavated in the mountains that maintain a humid microclimate, in southern Spain, an amphimictic population of Xiphinema globosum was identified. Morphological and morphometric studies on this population fit the original and previous descriptions and represent the first report from Spain and southern Europe. Molecular characterisation of X. globosum from Spain using D2-D3 expansion regions of 28S rRNA, 18S rRNA and ITS1-rRNA is provided and maximum likelihood and Bayesian inference analysis were used to reconstruct phylogenetic relationships within X. globosum and other Xiphinema species. A supertree solution of the different phylogenetic trees obtained in this study and in other published studies using rDNA genes are presented using the matrix representation parsimony method (MRP) and the most similar supertree method (MSSA). The results revealed a closer phylogenetic relationship of X. globosum with X. diversicaudatum, X. bakeri and with some sequences of unidentified Xiphinema spp. deposited in GenBank.

scholarly journals Validation of a noninvasive technique to quantify stress in northern bobwhite (Colinus virginianus)

2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Jessica L Mohlman ◽  
Kristen J Navara ◽  
Michael J Sheriff ◽  
Theron M Terhune ◽  
James A Martin
Keyword(s):  
Colinus Virginianus ◽  
Population Decline ◽  
Endocrine System ◽  
Northern Bobwhite ◽  
Noninvasive Technique ◽  
Acth Challenge ◽  
Non Invasive ◽  
Management Actions ◽  
Hunting Dog ◽  
Corticosterone Metabolites

Abstract Examination of the endocrine system through non-invasive fecal sampling may improve population management more than using demographic indicators alone. By addressing the physiological mechanisms that are influencing fitness, management actions can be proactively developed to alleviate stressors. Proactive determination of vulnerable populations is critical for species of concern, such as the Northern Bobwhite (Colinus virginianus), which have suffered decades of population decline. We validated an assay to noninvasively measure the adrenocortical response of captive reared bobwhite through fecal corticosterone metabolites (FCM). All individuals received three sequential 48-hour treatments in which samples were collected every 4 hours, including a reference period, an adrenocorticotropic hormone (ACTH) challenge and a biological stressor (exposure to a hunting dog). Reference FCM values had a mean concentration of 16.75 pg/mg (95% CrI: 13.68, 19.91) with adrenocortical activity increasing by 73% for the duration of the ACTH challenge (29.00 pg/mg; CrI: 25.01, 33.78). FCM concentrations remained similar to that of the reference levels during the biological stressor (16.56 pg/mg; CrI: 13.33, 19.92). Our study validates the use of feces to detect changes in FCM levels in our subject species but also demonstrates the complexity of FCM and the importance of both physiological and biological validation prior to field implementation.

Amino acid sequence of Japanese quail (Coturnix japonica) and northern bobwhite (Colinus virginianus) myoglobin

2015 ◽  
Vol 181 ◽  
pp. 256-262 ◽  
Author(s):  
John Goodson ◽  
Robert B. Beckstead ◽  
Jason Payne ◽  
Rakesh K. Singh ◽  
Anand Mohan
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Japanese Quail ◽  
Colinus Virginianus ◽  
Northern Bobwhite ◽  
Coturnix Japonica
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