3,973 results match your criteria maximum-likelihood bayesian

Morphological and Molecular Data Reveal Two New Species of Viannaia (Nematoda: Viannaiidae), Parasitizing Opossums (Mammalia: Didelphidae) in Mexico.

J Parasitol 2021 May;107(3):388-403

Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México. Avenida Universidad 3000, Ciudad Universitaria, C. P. 04510, Mexico City, Mexico.

Two new species of Viannaia from the intestine of the North American opossums, Didelphis virginiana (Virginia opossum), and Philander opossum (gray four-eyed opossum), are described based on morphological and molecular data, through an integrative taxonomic approach. Maximum likelihood and Bayesian inference analyses for each dataset and the concatenated dataset were performed using a mitochondrial cytochrome c oxidase subunit 1 (COI) gene, and the nuclear ribosomal internal transcribed spacer region (ITS1-5.8S-ITS2). Read More

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The complete mitochondrial genome of the freshwater crab Türkay and Dai 1997 (Decapoda: Brachyura: Potamoidea).

Mitochondrial DNA B Resour 2021 Apr 26;6(4):1554-1556. Epub 2021 Apr 26.

School of Basic Medical Sciences, Research lab of Freshwater Crustacean Decapoda & Paragonimus, Nanchang University, Nanchang, PR China.

We report the complete mitochondrial genome of for the first time, which is found to be 17,612 base pairs in length, and contains 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA), and 1 non-coding AT-rich region known as the D-loop. In addition, the mitogenome has 17 intergenic regions ranging from 1 to 1512 bp in length. The mitochondrial genome of is the first mitochondrial genome under the genus , providing DNA data for species identification, enriching the species diversity of Brachyura. Read More

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Evaluating advanced computing techniques for predicting breeding values in Harnali sheep.

Trop Anim Health Prod 2021 May 9;53(2):313. Epub 2021 May 9.

Department of Animal Genetics and Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, 125001, India.

Advanced computing techniques have been used by animal researchers to understand the intricate data structures for deriving the most reliable allusions of populations in order to conserve genetically superior animals. The present attempt was made to evaluate the potential of two advanced techniques, artificial neural networks (ANN) and Bayesian technique (BT), for predicting breeding values (BV) of weaning weight (WWT) using data of 498 lambs born to 41 sires and 173 dams in Harnali sheep for the period from 2014 to 2019. The estimated BV for WWT was initially obtained using univariate animal model under restricted maximum likelihood procedure. Read More

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The history, taxonomy, and geographic origins of an introduced African monkey in the southeastern United States.

Primates 2021 May 8. Epub 2021 May 8.

Biological Sciences Department, Florida Atlantic University, Boca Raton, USA.

The origins and taxonomy of the introduced vervet monkey population in Dania Beach, Florida has been unconfirmed due to a lack of documentation and genetic research. Our goal was to determine the introduction history, species identification, and geographic origins of the monkeys. Through interviews, historical archives, and popular media, we traced the monkeys to an escape from the Dania Chimpanzee Farm in 1948. Read More

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Phylogenetics and historical biogeography of Solanum section Brevantherum (Solanaceae).

Mol Phylogenet Evol 2021 May 4:107195. Epub 2021 May 4.

Programa de Pós-Graduação em Biodiversidade, Universidade Federal do Oeste do Pará, Rua Vera Paz, sn, Santarém, PA, 68040-255, Brazil; Programa de Pós-Graduação em Botânica, Instituto Nacional De Pesquisas Da Amazônia, Av. André Araújo, 2936 - Aleixo, Manaus, AM, 69060-001, Brazil.

Patterns of diversification in Neotropical plants have been studied intensively over the past decades. Most studies have focused on groups that migrated to and radiated into the Neotropics, however, with little focus on understanding diversification patterns in indigenous Neotropical groups. This study focuses on Solanum section Brevantherum Seithe (Solanaceae), a group of Neotropical nightshade shrubs or treelets defined mostly by terminal inflorescences with long peduncles, plurifoliate sympodial units and porrect-stellate, dendritic-echinoid, or lepidote trichomes. Read More

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Bayesian Modal Estimation for the One-Parameter Logistic Ability-Based Guessing (1PL-AG) Model.

Appl Psychol Meas 2021 May 8;45(3):195-213. Epub 2021 Feb 8.

Liaocheng University, Liaocheng, China.

The calibration of the one-parameter logistic ability-based guessing (1PL-AG) model in item response theory (IRT) with a modest sample size remains a challenge for its implausible estimates and difficulty in obtaining standard errors of estimates. This article proposes an alternative Bayesian modal estimation (BME) method, the Bayesian Expectation-Maximization-Maximization (BEMM) method, which is developed by combining an augmented variable formulation of the 1PL-AG model and a mixture model conceptualization of the three-parameter logistic model (3PLM). By comparing with marginal maximum likelihood estimation (MMLE) and Markov Chain Monte Carlo (MCMC) in JAGS, the simulation shows that BEMM can produce stable and accurate estimates in the modest sample size. Read More

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Mitochondrial Genome of Spirometra theileri Compared with Other Spirometra Species.

Korean J Parasitol 2021 Apr 22;59(2):139-148. Epub 2021 Apr 22.

Department of Parasitology, Parasitology Research Center and Parasite Resource Bank, Chungbuk National University, School of Medicine, Cheongju 28644, Korea.

This study was carried out to provide information on the taxonomic classification and analysis of mitochondrial genomes of Spirometra theileri. One strobila of S. theileri was collected from the intestine of an African leopard (Panthera pardus) in the Maswa Game Reserve, Tanzania. Read More

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Discovery of a new mammal species (Soricidae: Eulipotyphla) from Narcondam volcanic island, India.

Sci Rep 2021 May 3;11(1):9416. Epub 2021 May 3.

Mammal and Osteology Section, Zoological Survey of India, Kolkata, 700053, India.

We discovered a new Crocidura species of shrew (Soricidae: Eulipotyphla) from Narcondam Island, India by using both morphological and molecular approaches. The new species, Crocidura narcondamica sp. nov. Read More

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Bayesian estimation of maximum entropy model for individualized energy landscape analysis of brain state dynamics.

Hum Brain Mapp 2021 May 2. Epub 2021 May 2.

Center for Systems and Translational Brain Science, Institute of Human Complexity and Systems Science, Yonsei University, Seoul, South Korea.

The pairwise maximum entropy model (MEM) for resting state functional MRI (rsfMRI) has been used to generate energy landscape of brain states and to explore nonlinear brain state dynamics. Researches using MEM, however, has mostly been restricted to fixed-effect group-level analyses, using concatenated time series across individuals, due to the need for large samples in the parameter estimation of MEM. To mitigate the small sample problem in analyzing energy landscapes for individuals, we propose a Bayesian estimation of individual MEM using variational Bayes approximation (BMEM). Read More

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A multilevel Bayesian framework for predicting municipal waste generation rates.

Waste Manag 2021 Apr 29;127:90-100. Epub 2021 Apr 29.

Department of Economics and Business Economics, Aarhus University, Fuglesangs Allé 4, DK-8210 Aarhus V, Denmark.

Prediction of waste production is an essential part of the design and planning of waste management systems. The quality and applicability of such predictions depend heavily on model assumptions and the structure of the collected data. Ordinarily, municipal waste generation data are organized in hierarchical structures with municipal or county levels, and multilevel models can be used to generalize linear regression by directly incorporating the structure into the model. Read More

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Multi-locus phylogeny with dense Guiana Shield sampling supports new suprageneric classification of the neotropical three-barbeled catfishes (Siluriformes: Heptapteridae).

Mol Phylogenet Evol 2021 Apr 29;162:107186. Epub 2021 Apr 29.

Department of Ichthyology, American Museum of Natural History, New York, NY 10024, USA.

The catfish family Heptapteridae is ubiquitous across a range of freshwater habitats from southern Mexico to northern Argentina and contains 23 genera and 228 valid species. After a century of mostly morphology-based systematic analyses of these fishes, we provide the first molecular phylogenetic hypothesis spanning most valid Heptapteridae genera (16 of 23). We examined eight of 14 valid genera in the Nemuroglanis-subclade (Heptapterini), all valid genera in the Brachyglanis-subclade (Brachyglaniini) and most valid Brachyglaniini species (11 of 15). Read More

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Evolutionary history of H5 highly pathogenic avian influenza viruses (clade circulating in Taiwan during 2015-2018.

Infect Genet Evol 2021 Apr 28:104885. Epub 2021 Apr 28.

Animal Health Research Institute, Council of Agriculture, New Taipei City, Taiwan. Electronic address:

The highly pathogenic avian influenza (HPAI) virus A/goose/Guangdong/1/96 H5N1 (Gs/GD) lineage has been transmitted globally and has caused deaths in wild birds, poultry, and humans. Clade 2.3. Read More

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Complete chloroplast genomes of Achnatherum inebrians and comparative analyses with related species from Poaceae.

FEBS Open Bio 2021 May 1. Epub 2021 May 1.

State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, Gansu Tech Innovation Centre of Western China Grassland Industry, Centre for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, China.

This article reports the complete chloroplast genome of Achnatherum inebrians, a poisonous herb that is widely distributed in the rangelands of Northern China. The genome is 137 714 bp in total and consists of a large single-copy (81 758 bp) region and small single-copy (12 682 bp) region separated by a pair of inverted repeats (21 637 bp). The genome contains 130 genes, including 84 protein-coding genes, 38 tRNA genes and 8 ribosomal RNA genes, and the guanine + cytosine content is 36. Read More

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Bipartite molecular approach for species delimitation and resolving cryptic speciation of Exobasidium vexans within the Exobasidium genus.

Comput Biol Chem 2021 Apr 24;92:107496. Epub 2021 Apr 24.

Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India; Department of Molecular Biology and Biotechnology, Cotton University, Panbazar, Guwahati, Assam, 781001, India. Electronic address:

Exobasidium vexans, a basidiomycete pathogen, is the causal organism of blister blight disease in tea. The molecular identification of the pathogen remains a challenge due to the limited availability of genomic data in sequence repositories and cryptic speciation within its genus Exobasidium. In this study, the nuclear internal transcribed spacer rDNA region (ITS) based DNA barcode was developed for E. Read More

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Taxonomy and Phylogeny of the Wood-Inhabiting Fungal Genus with Descriptions of Three New Species from East Asia.

J Fungi (Basel) 2021 Apr 16;7(4). Epub 2021 Apr 16.

Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China.

Three new wood-inhabiting fungi, , and spp. nov., are proposed based on a combination of morphological features and molecular evidence. Read More

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Characterization of Two Complete Mitochondrial Genomes of (Hemiptera: Cicadellidae: Cicadellinae) and the Phylogenetic Implications.

Insects 2021 Apr 11;12(4). Epub 2021 Apr 11.

Institute of Entomology, Guizhou University, Guiyang 550025, China.

The complete mitochondrial genomes of and were sequenced. The results showed that the mitogenomes of these two species are 15,621 and 15,895 bp in length, with A+T contents of 78.6% and 78. Read More

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Bayesian and Frequentist Inferences on a Type I Half-Logistic Odd Weibull Generator with Applications in Engineering.

Entropy (Basel) 2021 Apr 10;23(4). Epub 2021 Apr 10.

Department of Mathematics, Faculty of Science, Mansoura University, Mansoura 35516, Egypt.

In this article, we have proposed a new generalization of the odd Weibull-G family by consolidating two notable families of distributions. We have derived various mathematical properties of the proposed family, including quantile function, skewness, kurtosis, moments, incomplete moments, mean deviation, Bonferroni and Lorenz curves, probability weighted moments, moments of (reversed) residual lifetime, entropy and order statistics. After producing the general class, two of the corresponding parametric statistical models are outlined. Read More

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Low genetic diversity and the phylogeny of Achatina fulica, an intermediate host of Angiostrongylus cantonensis in Thailand, inferred from 16S mitochondrial sequences.

Infect Genet Evol 2021 Apr 24;92:104876. Epub 2021 Apr 24.

Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand; Centre of Excellence in Medical Biotechnology (CEMB), Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand; Center of Excellence for Biodiversity, Faculty of Sciences, Naresuan University, Phitsanulok 65000, Thailand. Electronic address:

The giant African land snail, Achatina fulica, is a pulmonate land snail of the Achatinidae family. The snail is native of East Africa and has spread to tropical and subtropical areas in different parts of the world. Achatina fulica is an important agricultural pests and the intermediate host for Angiostrongylus spp. Read More

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New species and findings of emPagastia/em Oliver (Diptera: Chironomidae: Diamesinae) from Central Asia, with DNA barcoding of known species of the genus.

Zootaxa 2021 Apr 7;4951(3):zootaxa.4951.3.8. Epub 2021 Apr 7.

Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far East Branch of the Russian Academy of Sciences, 100 let Vladivostoku 159, 690022 Vladivostok, Russia..

Chironomids of the genus Pagastia Oliver (Diamesinae, Diamesini) from the mountains of Central Asia are revised using both morphological characters and molecular data. Illustrated descriptions of the adult male Pagastia (P.) caelestomontana sp. Read More

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Molecular phylogenetics, PCA, and MFA recover a new species of Cyrtodactylus (Squamata: Gekkonidae) from an isolated sandstone massif in northwestern Cambodia.

Zootaxa 2021 Mar 25;4949(2):zootaxa.4949.2.3. Epub 2021 Mar 25.

Herpetology Laboratory, Department of Biology, La Sierra University, 4500 Riverwalk Parkway, Riverside, California 92515, USA..

The integrated results of maximum likelihood (ML) and Bayesian inference (BI) analyses, principal component analyses (PCA), and a multiple factor analysis (MFA) recover a new, widely allopatric species of the Cyrtodactylus intermedius species group. Cyrtodactylus kulenensis sp. nov is endemic to the Phnom Kulen sandstone massif of the Phnom Kulen National Park, Siem Reap Province, in the lowlands of northwestern Cambodia. Read More

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Multi-character taxonomic review, systematics, and biogeography of the Black-capped/Tawny-bellied Screech Owl (emMegascops/em ematricapilla/em-emM. watsonii/em) complex (Aves: Strigidae).

Zootaxa 2021 Mar 26;4949(3):zootaxa.4949.3.1. Epub 2021 Mar 26.

1Zoology Graduate Program, Universidade Federal do Pará/Museu Paraense Emilio Goeldi, Belém-PA, Brazil. Department of Zoology, Museu Paraense Emílio Goeldi, Belém-PA, Brazil..

Megascops is the most species-rich owl genus in the New World, with 21 species currently recognized. Phylogenetic relationships within this genus are notoriously difficult to establish due to the considerable plumage similarity among species and polymorphism within species. Previous studies have suggested that the widespread lowland Amazonian M. Read More

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Voxel-wise and spatial modelling of binary lesion masks: Comparison of methods with a realistic simulation framework.

Neuroimage 2021 Apr 22;236:118090. Epub 2021 Apr 22.

Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Population Health, University of Oxford, OX3 7LF, UK. Electronic address:

Objectives: White matter lesions are a very common finding on MRI in older adults and their presence increases the risk of stroke and dementia. Accurate and computationally efficient modelling methods are necessary to map the association of lesion incidence with risk factors, such as hypertension. However, there is no consensus in the brain mapping literature whether a voxel-wise modelling approach is better for binary lesion data than a more computationally intensive spatial modelling approach that accounts for voxel dependence. Read More

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Mitochondrial analysis of oribatid mites provides insights into their atypical tRNA annotation, genome rearrangement and evolution.

Parasit Vectors 2021 Apr 23;14(1):221. Epub 2021 Apr 23.

Department of Health Inspection and Quarantine, Wannan Medical College, Wuhu, Anhui Province, 241002, People's Republic of China.

Background: The mitochondrial (mt) genomes of Sarcoptiformes mites typically contain 37 genes. Although the loss of genes is rare in Sarcoptiformes mite mitogenomes, two of the six previously reported oribatid mites (Acariforms: Sarcoptiformes) are reported to have lost parts of their tRNA genes. To confirm whether the tRNA genes were indeed lost and whether the loss is universal, we re-annotated the available oribatid mite sequences and sequenced the mitogenome of Oribatula sakamorii. Read More

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Bayesian and maximum likelihood estimations of the Dagum parameters under combined-unified hybrid censoring.

Math Biosci Eng 2021 03;18(3):2930-2951

Department of Statistics and Operations Research, College of Science, King Saud University, P.O.Box 2455, Riyadh 11451, Saudi Arabia.

In this paper, we introduce a new form of hybrid censoring sample, that is called COMBINED-UNIFIED (C-U) hybrid sample. In this unified approach, we merge the combined hybrid censoring sampling that considered by Huang and Yang [1] and unified hybrid censoring sampling that considered by Balakrishnan et al. [2]. Read More

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Phylogenomics resolves deep subfamilial relationships in Malvaceae s.l.

G3 (Bethesda) 2021 Apr 23. Epub 2021 Apr 23.

Institute of Parasitology, Biology Centre CAS, Branišovská 1160/31, 37005 České Budějovice, Czech Republic.

Malvaceae s.l., the most diverse family within Malvales, includes well-known species of great economic importance like cotton, cacao, and durian. Read More

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MEGA11: Molecular Evolutionary Genetics Analysis version 11.

Mol Biol Evol 2021 Apr 23. Epub 2021 Apr 23.

Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, 19122.

The Molecular Evolutionary Genetics Analysis (MEGA) software has matured to contain a large collection of methods and tools of computational molecular evolution. Here, we describe new additions that make MEGA a more comprehensive tool for building timetrees of species, pathogens, and gene families using rapid relaxed-clock methods. Methods for estimating divergence times and confidence intervals are implemented to use probability densities for calibration constraints for node-dating and sequence sampling dates for tip-dating analyses, which will be supported by new options for tagging sequences with spatiotemporal sampling information, an expanded interactive Node Calibrations Editor, and an extended Tree Explorer to display timetrees. Read More

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Revisiting the phylogeny of microsporidia.

Int J Parasitol 2021 Apr 21. Epub 2021 Apr 21.

Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9016, New Zealand.

Canonical microsporidians are a group of obligate intracellular parasites of a wide range of hosts comprising ~1,300 species of >220 genera. Microsporidians are related to fungi, and many characterised and uncharacterized groups closely related to them have been discovered recently, filling the knowledge gaps between them. These groups assigned to the superphylum Opisthosporidia have provided several important insights into the evolution of diverse intracellular parasitic lineages within the tree of eukaryotes. Read More

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Shared ancestry of core-histone subunits and non-histone plant proteins containing the Histone Fold Motif (HFM).

J Bioinform Comput Biol 2021 Apr 21;19(2):2140001. Epub 2021 Apr 21.

National Institute of Plant Genome Research, New Delhi, India.

The three helical Histone Fold Motif (HFM) of core histone proteins provides an evolutionarily favored site for the protein-DNA interface. Despite significant variation in sequence, the HFM retains a distinctive structural fold that has diversified into several non-histone protein families. In this work, we explore the ancestry of non-histone HFM containing families in the plant kingdom. Read More

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Multiple-marker phylogeny and morphological evidence reveal two new species in Steccherinaceae (Polyporales, Basidiomycota) from Asia.

MycoKeys 2021 5;78:169-186. Epub 2021 Apr 5.

CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China.

Two new wood-inhabiting fungi, and , are proposed and described from Asia based on ITS, nrLSU and molecular phylogeny and morphological characteristics. is characterized by a stipitate basidiocarp, velutinate pileal surface concentrically zoned, hydnoid hymenophore, a dimitic hyphal system in spine trama and monomitic in context, absence of gloeocystidia, presence of cystidioles and the non-amyloid, cylindrical to ellipsoid basidiospores. is characterized by a laterally stipitate basidiocarp with flabelliform to semicircular pileus, hirtellous pileal surface with appressed coarse hair and concentrically zoned and sulcate, tiny pores (10-12 per mm), a dimitic hyphal system, absence of any type of cystidia, short clavate basidia and thin-walled, smooth, cylindrical to allantoid basidiospores. Read More

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First mitogenome of subfamily Langiinae (Lepidoptera: Sphingidae) with its phylogenetic implications.

Gene 2021 Apr 18;789:145667. Epub 2021 Apr 18.

Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu, Anhui 241000, China. Electronic address:

To date, a relatively complete classification of Sphingidae (Lepidoptera) has been generated, but the phylogeny of the family remains need to be fully resolved. Some phylogenetic relationships within Sphingidae still remains uncertain, especially the taxonomic status of the subfamily Langiinae and its sole included genus and species, Langia zenzeroides. To begin to address this problem, we generated nine new complete mitochondrial genomes, including that of Langia, and together with that of Theretra oldenlandiae from our previous study and 25 other Sphingidae mitogenomes downloaded from GenBank, analyzed the phylogenetic relationships of Sphingidae and investigated the mitogenomic differences among members of the Langiinae, Sphinginae, Smerinthinae and Macroglossinae. Read More

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