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  • Statistics In Transition

 

Article

First Report of the Spiral Nematode Rotylenchus incultus (Nematoda: Hoplolaimidae) from Cultivated Olive in Tunisia, with Additional Molecular Data on Rotylenchus eximius

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 , ISSUE 3, 136–138

Article

BAYESIAN INFERENCE FOR STATE SPACE MODEL WITH PANEL DATA

Ranjita Pandey, Anoop Chaturvedi

Statistics in Transition New Series , ISSUE 2, 211–219

research-article

Morpho-molecular characterization of Colombian and Brazilian populations of Rotylenchulus associated with Musa spp

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 , 1–13

Article

INFORMATIVE VERSUS NON-INFORMATIVE PRIOR DISTRIBUTIONS AND THEIR IMPACT ON THE ACCURACY OF BAYESIAN INFERENCE

Wioletta Grzenda

Statistics in Transition New Series , ISSUE 4, 763–780

Research Article

Change-point detection in CO2 emission-energy consumption nexus using a recursive Bayesian estimation approach

Olushina Olawale Awe, Abosede Adedayo Adepoju

Statistics in Transition New Series , ISSUE 1, 123–136

Article

Data on Some Species of the Genus Coslenchus Siddiqi, 1978 (Rhabditida, Tylenchidae) from Iran

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 , ISSUE 4, 268–279

research-article

Morphological and Molecular Characterization of Coslenchus paramaritus n. sp. and C. cancellatus (Cobb, 1925) Siddiqi, 1978 (Nematoda: Tylenchidae) from Iran

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 , 1–10

Sampling Methods

A BAYESIAN INFERENCE OF MULTIPLE STRUCTURAL BREAKS IN MEAN AND ERROR VARIANCE IN PANEL AR (1) MODEL

Varun Agiwal, Jitendra Kumar, Dahud Kehinde Shangodoyin

Statistics in Transition New Series , ISSUE 1, 7–23

Article

Sectonema caobangense sp. n. from Vietnam (Nematoda, Dorylaimida, Aporcelaimidae)

SERGIO ALVAREZ-ORTEGA, THI ANH DUONG NGUYEN, JOAQUI´N ABOLAFIA, MICHAEL BONKOWSKI, REYES PEN˜A-SANTIAGO

Journal of Nematology , ISSUE 2, 95–103

Article

A New Species of the Rare Genus Anguillonema Fuchs, 1938 (Nematoda: Hexatylina, Sphaerularioidea) with Its Molecular Phylogenetic Study

MAHYAR MOBASSERI, MAJID PEDRAM, EBRAHIM POURJAM

Journal of Nematology , ISSUE 3, 286–294

research-article

Morphological and molecular characterization of two species of Neothada Khan, 1973 (Nematoda: Tylenchidae) from Iran, with notes on N. cancellata

., 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 , 1–10

Article

VARIATIONAL APPROXIMATIONS FOR SELECTING HIERARCHICAL MODELS OF CIRCULAR DATA IN A SMALL AREA ESTIMATION APPLICATION

, 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 , ISSUE 1, 91–104

research-article

First report of molecular characterization and phylogeny of Trichuris fossor Hall, 1916 (Nematoda: Trichuridae)

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 , 1–6

Article

Application of iterated filtering to stochastic volatility models based on non-Gaussian Ornstein-Uhlenbeck process

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 , ISSUE 2, 173–187

research-article

Molecular approach to confirm traditional identification of Radopholus similis sampled in Tanzania

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 , 1–8

research-article

Description of Deladenus brevis n. sp. (Sphaerularioidea: Neotylenchidae) from Iran: a morphological and molecular phylogenetic study

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 , 1–13

Research Article

Morphological and Molecular Characterization of Labrys filiformis n. sp. (Rhabditida: Tylenchidae) from Iran

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 , ISSUE 3, 343–354

Research Article

Description of Longidorus azarbaijanensis n. sp. (Dorylaimida: Longidoridae) from Iran

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 , ISSUE 2, 207–218

Article

First Report of the Carolina Spiral Nematode, Scutellonema brachyurus, from Soil of a Garden in Crete, Greece

., 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 , ISSUE 1, 7–7

Article

First Report of Longidorus kuiperi and Rotylenchus eximius from Coastal Sand Dunes in Crete, Greece

, 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 , ISSUE 3, 135–135

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