Article | 21-July-2017
invariable sites and a gamma-shaped distribution of substitution rates (GTR + I + G) model for ITS1 and coxI. Phylogenetic analyses of ITS1 and coxI using Bayesian inference (BI) placed R. eximius and R. incultus from Tunisia in subclades that included all R. eximius and R. incultus sequences deposited in GenBank (Fig. 1), which agrees with previous results (Cantalapiedra-Navarrete et al., 2013). Morphology, morphometry, and molecular and phylogenetic data obtained from these samples were consistent with
ILHEM GUESMI-MZOUGHI,
ANTONIO ARCHIDONA-YUSTE,
CAROLINA CANTALAPIEDRA-NAVARRETE,
HAJER REGAIEG,
NAJET HORRIGUE-RAOUANI,
JUAN E. PALOMARES-RIUS,
PABLO CASTILLO
Journal of Nematology, Volume 48 , ISSUE 3, 136–138
Article | 06-July-2017
Ranjita Pandey,
Anoop Chaturvedi
Statistics in Transition New Series, Volume 17 , ISSUE 2, 211–219
research-article | 30-November-2018
alignment based on the Akaike information criterion corrected for small sample sizes (Posada, 2008). Maximum likelihood (ML) and Bayesian inference (BI) were used to estimate phylogenies for the D2-D3 and COI regions. For ML, 250 bootstraps were used and the general time reversible model with allowance for a gamma distribution of rate variation (GTR + Γ) in RaxML v8 (Stamatakis, 2014). Inferred phylogenies by BI (MrBayes v3.2.6, Ronquist et al., 2012), used the general time reversible model with
Donald Riascos-Ortiz,
Ana Teresa Mosquera-Espinosa,
Francia Varón De Agudelo,
Claudio Marcelo Gonçalves de Oliveira,
Jaime Eduardo Muñoz-Flórez
Journal of Nematology, Volume 51 , 1–13
research-article | 30-November-2020
Abbas Abdolkhani,
Sedighe Azimi
Journal of Nematology, Volume 53 , 1–10
Article | 06-July-2017
Wioletta Grzenda
Statistics in Transition New Series, Volume 17 , ISSUE 4, 763–780
Research Article | 18-March-2020
Olushina Olawale Awe,
Abosede Adedayo Adepoju
Statistics in Transition New Series, Volume 21 , ISSUE 1, 123–136
research-article | 30-November-2020
nucleotide substitution used for the phylogenetic analysis was statistically selected using jModelTest 2.1.10 (Darriba et al., 2012). Phylogenetic tree was generated with Bayesian inference (BI) method using MrBayes 3.2.6 (Huelsenbeck and Ronquist, 2001; Ronquist et al., 2012). Atetylenchus longilabiatus (Hosseinvand et al., 2020a) (MN807620) and Psilenchus hilarulus (De Man, 1921) (EU915489) were chosen as outgroups for the tree. The analysis under general time-reversible model of sequence evolution
Manouchehr Hosseinvand,
Ali Eskandari,
Joaquín Abolafia,
Reza Ghaderi
journal of Nematology, Volume 53 , 1–10
Article | 21-July-2017
phylogenetic studies based on partial sequences of 28S rDNA D2/D3 fragments, all species formed a clade with high Bayesian posterior probability in Bayesian inference, indicating the monophyly of the genus. The clade of Coslenchus spp. formed a highly supported monophyletic group, a sister clade to two species of the genus Aglenchus.
YOUSEF PANAHANDEH,
EBRAHIM POURJAM,
MAJID PEDRAM
Journal of Nematology, Volume 48 , ISSUE 4, 268–279
research-article | 30-November-2018
nucleotide substitution used for the phylogenetic analysis was statistically selected using jModelTest 2.1.10 (Darriba et al., 2012) and phylogenetic tree was generated with the Bayesian inference method using MrBayes 3.2.6 (Huelsenbeck and Ronquist, 2001; Ronquist et al., 2012). The analysis under GTR+I+G model was initiated with a random starting tree and run with the Markov Chain Monte Carlo (MCMC) for 1 × 106 generations. The tree was visualized and saved with FigTree 1.4.3 (Rambaut, 2014) and edited
Manouchehr Hosseinvand,
Ali Eskandari,
Reza Ghaderi
journal of nematology, Volume 51 , 1–10
Sampling Methods | 25-May-2018
Varun Agiwal,
Jitendra Kumar,
Dahud Kehinde Shangodoyin
Statistics in Transition New Series, Volume 19 , ISSUE 1, 7–23
research-article | 30-November-2020
Poleae_fw1_4_36 (5′-GACAGATTAGAATGGAATCTGTTCG-3′) and Poleae_rv1_ _525_551 (5′ATCGCTTTTGGATTCAATAATATA-3′) as described by Palomares-Rius et al. (2014). For phylogenetic analysis, obtained P. oleae sequence was aligned with related sequences from GenBank through National Center for Biotechnology Information (NCBI) BLASTn homology search, using ClustalW implemented by MEGA version 10.0. The GTR + I + G model was selected as the best by jModeltest v.2.1.10. Bayesian tree generated using the Bayesian inference
Farhad Saeidi Naeini,
Zahra Majd Taheri
Journal of Nematology, Volume 53 , 1–7
Article | 21-July-2017
SERGIO ALVAREZ-ORTEGA,
THI ANH DUONG NGUYEN,
JOAQUI´N ABOLAFIA,
MICHAEL BONKOWSKI,
REYES PEN˜A-SANTIAGO
Journal of Nematology, Volume 48 , ISSUE 2, 95–103
Article | 06-July-2017
, within spatio temporal domains subdivided by the mode of fishing. Because many of these domains have small sample sizes, small area estimation methods are developed. Bayesian inference for the circular distributions on the 24-hour clock is conducted, based on a large set of observed daily departure times from another National Marine Fisheries Service study, the Coastal Household Telephone Survey. A novel variational/Laplace approximation to the posterior distribution allows fast comparison of a large
Daniel Hernandez-Stumpfhauser,
F. Jay Breidt,
Jean D. Opsomer
Statistics in Transition New Series, Volume 17 , ISSUE 1, 91–104
research-article | 24-April-2020
invariant sites and a gamma distribution was the best fit substitution model for this data based on Bayesian information criterion. An evolutionary history was inferred based on this model using the maximum likelihood (ML) method and a consensus tree was generated using 1,000 bootstrapping replicates in MEGA. The Bayesian inference (BI) analysis was prepared in BEAUti v. 2.6.0 (Bouckaert et al., 2019) and performed in BEAST2 v. 2.6.0 (Bouckaert et al., 2019). The analysis used the HKY substitution model
Malorri R. Hughes,
Deborah A. Duffield,
Dana K. Howe,
Dee R. Denver
Journal of Nematology, Volume 52 , 1–6
Article | 01-June-2020
Barndorff-Nielsen and Shephard (2001) proposed a class of stochastic volatility models in which the volatility follows the Ornstein–Uhlenbeck process driven by a positive Levy process without the Gaussian component. The parameter estimation of these models is challenging because the likelihood function is not available in a closed-form expression. A large number of estimation techniques have been proposed, mainly based on Bayesian inference. The main aim of the paper is to present an
Piotr Szczepocki
Statistics in Transition New Series, Volume 21 , ISSUE 2, 173–187
Article | 04-December-2017
MAHYAR MOBASSERI,
MAJID PEDRAM,
EBRAHIM POURJAM
Journal of Nematology, Volume 49 , ISSUE 3, 286–294
research-article | 30-November-2019
., 2012). Phylogenetic tree was generated with a Bayesian inference method using MrBayes 3.2.6 (Huelsenbeck and Ronquist, 2001; Ronquist et al., 2012). Aphelenchus avenae Bastian, 1865 (KP527123) was chosen as outgroup for the tree according to (Bai et al., 2020; Hosseinvand et al., 2020b; Yaghoubi et al., 2015). The analysis under general time-reversible model of sequence evolution with correction for invariable sites and a gamma-shaped distribution (GTR + I + G) model was initiated with a random
Manouchehr Hosseinvand,
Ali Eskandari,
Reza Ghaderi
Journal of Nematology, Volume 52 , 1–10
research-article | 17-March-2020
homology searches. Multiple sequence comparison by log-expectation was done using Geneious version 11.0 software (Kearse et al., 2012). Bayesian inference was used to construct phylogenetic trees in the Geneious version 11.0 software. The model selected was the best fit for the SSU plus ITS1, ITS1 & ITS1 and LSU data set, the HKY + G + I (Hasegawa et al., 1985), and Helicotylenchus spp. were selected as outgroups for the data sets.
Statistical analysis
Differences in morphological parameters among
Doreen M. Mgonja,
Gladness E. Temu,
Joseph C. Ndunguru,
Magreth F. Mziray,
Sylvester L. Lyantagaye,
Nessie D. Luambano
Journal of Nematology, Volume 52 , 1–8
research-article | 30-November-2020
sequences (Holterman et al., 2008; Mullin, 2004; van Megen et al., 2009). All sequence alignments were analyzed with Bayesian inference (BI) using MrBayes 3.1.2 (Ronquist and Huelsenbeck, 2003) under the GTR + G + I model. BI analysis was initiated with a random starting tree and was run with four chains for 8.0 × 106 generations for the D2-D3 of 28S rRNA alignment and 3.0 × 106 generations for the 18S rRNA alignment. Posterior probabilities (PP) in percentage are given on appropriate clades.
Results
Sergio Álvarez-Ortega,
Sergei A. Subbotin,
Renato N. Inserra
Journal of Nematology, Volume 53 , 1–9
research-article | 30-November-2019
was composed of 447 total characters, of which 281 characters were variable, with an average nucleotide composition of 25.8% A, 20.3% C, 31.5% G, and 22.4% T. Figure 5 represents the phylogenetic tree inferred using this data set. In this tree, the new species is in sister relation with an unidentified species of the genus (KM403370) with moderate support in Bayesian inference. Deladenus appeared non-monophyletic in this tree.
Figure 5:
Bayesian 50% majority rule consensus tree of Deladenus
Fariba Heydari,
Joaquín Abolafia,
Majid Pedram
Journal of Nematology, Volume 52 , 1–13
Research Article | 17-October-2018
duct, offset spermatheca filled with small spheroid sperm cells, 106 to 127 µm long elongate-conoid tail with filiform distal region and finely rounded tip. Molecular phylogenetic analyses were performed using a near-full length fragment of the 18S rDNA and the D2–D3 expansion segments of the 28S rDNA using Bayesian inference and maximum likelihood methods. In the inferred phylogenetic tree with 18S rDNA, the new species has a close affinity with several isolates of the type species, Labrys
Yousef Panahandeh,
Joaquín Abolafia,
Ebrahim Pourjam,
Robin M. Giblin-Davis,
Farahnaz Jahanshahi Afshar,
Majid Pedram
Journal of Nematology, Volume 50 , ISSUE 3, 343–354
Research Article | 03-September-2018
28S tree, the clade including the new species and six other species (L. attenuatus, Longidorus sp. and four above-mentioned species having molecular data for this fragment) was well supported in Bayesian inference. In the ITS1 tree, the new species formed a clade with L. euonymus, L. perangustus and L. persicus, as in 28S tree. This is one of the cases from which the morphologically similar species are separated using molecular sequences.
Farshad Gharibzadeh,
Ebrahim Pourjam,
Majid Pedram
Journal of Nematology, Volume 50 , ISSUE 2, 207–218
Article | 21-July-2017
., 2013). Alignment indicated that the D2-D3 and ITS sequences (KU059494 and KU059495, respectively) showed 99% and 100% to 99% similarity, respectively, to other sequences of S. brachyurus (type A) deposited in GenBank from the United States, Italy, and Korea (JX472037-JX472046, DQ328753, FJ485643; and JX472069, JX472070, JX472071, respectively), differing from one to six nucleotides. Phylogenetic analyses using Bayesian inference of these sequences placed the Scutellonema sp. in a
EMMANUEL A. TZORTZAKAKIS,
CAROLINA CANTALAPIEDRA-NAVARRETE,
ANTONIO ARCHIDONA-YUSTE,
JUAN E. PALOMARES-RIUS,
PABLO CASTILLO
Journal of Nematology, Volume 48 , ISSUE 1, 7–7
Article | 21-July-2017
, respectively, to other sequences of L. kuiperi deposited in GenBank from Italy and Spain (AM911623, AM905267-AM905270, respectively), with a query coverage of 99%. Similarly, D2-D3 sequence alignment from R. eximius (KX398058) showed 100% to 99% to another sequence of R. eximius deposited in GenBank from Italy and Spain (EU280794, DQ328741), differing in zero to three nucleotides, respectively, and a query coverage of 81%. Phylogenetic analyses using Bayesian Inference placed L. kuiperi in a highly
EMMANUEL A. TZORTZAKAKIS,
CAROLINA CANTALAPIEDRA-NAVARRETE,
ANTONIO ARCHIDONA-YUSTE,
JUAN E. PALOMARES-RIUS,
PABLO CASTILLO
Journal of Nematology, Volume 48 , ISSUE 3, 135–135