6,123 results match your criteria phylogeny maximum-likelihood


Molecular phylogeny, classification, biogeography and diversification patterns of a diverse group of moths (Geometridae: Boarmiini).

Mol Phylogenet Evol 2021 May 11:107198. Epub 2021 May 11.

Department of Biology, Lund University, Sweden. Electronic address:

Understanding how and why some groups have become more species-rich than others, and how past biogeography may have shaped their current distribution, are questions that evolutionary biologists have long attempted to answer. We investigated diversification patterns and historical biogeography of a hyperdiverse lineage of Lepidoptera, the geometrid moths, by studying its most species-rich tribe Boarmiini, which comprises ca. 200 genera and ca. Read More

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Mitogenomics of five leafhoppers (Hemiptera: Cicadellidae: Coelidiinae) and their phylogenetic implications.

PeerJ 2021 27;9:e11086. Epub 2021 Apr 27.

Institute of Entomology, Guizhou University, Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guiyang, Guizhou Provincial, China.

Similar morphological characteristics and limited molecular data of resulted in their unknown phylogenetic statuses and equivocal relationships. To further understand the genus , we sequenced and annotated five complete mitochondrial genomes (mitogenomes). Our results show that mitogenomes range from 15,205 bp to 15,993 bp in length and include 37 typical genes (13 protein-coding genes, 22 tRNAs, and 2 rRNAs) and a control region. Read More

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Improving the phylogenetic resolution of Malaysian and Javan mahseer (Cyprinidae), Tor tambroides and Tor tambra: Whole mitogenomes sequencing, phylogeny and potential mitogenome markers.

Gene 2021 May 10:145708. Epub 2021 May 10.

GeneSEQ Sdn Bhd, Bukit Beruntung, 48300 Rawang, Selangor, Malaysia; Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia.

The true mahseer (Tor spp.) is one of the highest valued fish in the world due to its high nutritional value and great unique taste. Nevertheless, its morphological characterization and single mitochondrial gene phylogeny in the past had yet to resolve the ambiguity in its taxonomical classification. Read More

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(Urticaceae), a new species from limestone karst in Guangxi, China.

PeerJ 2021 19;9:e11148. Epub 2021 Apr 19.

Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China.

L.F. Fu, A. Read More

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The complete mitochondrial genome sequences of varieties NY18 and 088018.

Mitochondrial DNA B Resour 2021 Apr 15;6(4):1429-1430. Epub 2021 Apr 15.

Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, China.

variety NY18 and 088018 are female and male parents of the national registered variety Ningza 1818, respectively. Here, we determined the complete mitochondrial genomes of these two varieties. The genome sizes of NY18 and 088018 were 221,864 bp and 222,015 bp, respectively. Read More

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Molecular evidence and morphological aspects of and re-description of (Digenea) from the Red Sea.

Vet Res Forum 2021 15;12(1):15-24. Epub 2021 Mar 15.

Department of Biology, College of Science, Al Baha University, Al Baha, Saudi Arabia.

During a recent survey on digenean parasites infecting marine fish captured from water located along the Red Sea off Gizan Coasts, Saudi Arabia, thirty-two (29.09%) out of 110 fish were naturally infected with three different species of digenean parasites. The taxonomical status of the recovered worms was confirmed by light microscopy and molecular analysis. Read More

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Molecular-genetic characterization of human parvovirus B19 prevalent in Kerala State, India.

Virol J 2021 May 5;18(1):96. Epub 2021 May 5.

Laboratory Medicine and Molecular Diagnostics Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695585, India.

Background: Human parvovirus B19V is a DNA virus, and a member of the family Parvoviridae, that causes various clinical manifestations, from asymptomatic to persistent infection that is associated with different autoimmune diseases. The parvovirus B19 evolves with a very high mutation rate that is closer to those of existing RNA viruses. Globally circulating B19V is currently classified into three genotypes, but their distribution is not spatially and temporally correlated. Read More

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Subtyping bovine viral diarrhea virus (BVDV): Which viral gene to choose?

Infect Genet Evol 2021 May 1:104891. Epub 2021 May 1.

Setor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil. Electronic address:

Bovine viral diarrhea virus-1 (BVDV-1, Pestivirus A) and BVDV-2 (Pestivirus B) have been clustered into 21 and 4 subtypes, respectively. This genetic diversity, in addition to the lack of consensus on which genomic region to use for BVDV subtyping, has resulted in conflicting classifications depending on the target analyzed. Here, we investigated which genes or UTRs would reproduce the phylogeny obtained by complete genome (CG) analyses. Read More

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Root Digger: a root placement program for phylogenetic trees.

BMC Bioinformatics 2021 May 1;22(1):225. Epub 2021 May 1.

Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.

Background: In phylogenetic analysis, it is common to infer unrooted trees. However, knowing the root location is desirable for downstream analyses and interpretation. There exist several methods to recover a root, such as molecular clock analysis (including midpoint rooting) or rooting the tree using an outgroup. 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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The Population Structure of Is Reflected by a Population Division of Its Vector.

Microorganisms 2021 Apr 27;9(5). Epub 2021 Apr 27.

National Reference Center for Borrelia, Bavarian Health and Food Safety Authority, 85764 Oberschleissheim, Germany.

Populations of vector-borne pathogens are shaped by the distribution and movement of vector and reservoir hosts. To study what impact host and vector association have on tick-borne pathogens, we investigated the population structure of using multilocus sequence typing (MLST). Novel sequences were acquired from questing ticks collected in multiple North African and European locations and were supplemented by publicly available sequences at the Borrelia Pubmlst database (accessed on 11 February 2020). Read More

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Phylogenetic and Molecular Analyses of More Prevalent HCV1b Subtype in the Calabria Region, Southern Italy.

J Clin Med 2021 Apr 13;10(8). Epub 2021 Apr 13.

Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy.

Hepatitis C virus subtype 1b (HCV1b) is still the most prevalent subtype worldwide, with massive expansion due to poor health care standards, such as blood transfusion and iatrogenic procedures. Despite safe and effective new direct antiviral agents (DAA), treatment success can depend on resistance-associated substitutions (RASs) carried in target genomic regions. Herein we investigated transmission clusters and RASs among isolates from HCV1b positive subjects in the Calabria Region. 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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Complete mitochondrial DNA sequence of the (Scleractinia, Psammocoridae): mitogenome characterisation and phylogenetic implications.

Biodivers Data J 2021 19;9:e62395. Epub 2021 Apr 19.

Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China Third Institute of Oceanography, Ministry of Natural Resources Xiamen China.

Complete mitochondrial DNA sequence data have played a significant role in phylogenetic and evolutionary studies of scleractinian corals. In this study, the complete mitogenome of Gardiner, 1898, collected from Guangdong Province, China, was sequenced by next-generation sequencing for the first time. is the first species for which a mitogenome has been sequenced in the family Psammocoridae. 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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First Report of Causing Powdery Mildew on in Mexico.

Plant Dis 2021 Apr 27. Epub 2021 Apr 27.

Centro de Investigación en Alimentación y Desarrollo, Coordinación Culiacán, Carretera El Dorado Km 5.5, Campo el Diez, Culiacán, Sinaloa, Mexico, 80110;

, common sow thistle, is native to Europe, Northern Africa, and Western Asia. This plant has become a common weed throughout the world. In Mexico, this weed has become widely naturalized by replacing indigenous plants and invading many agricultural areas. Read More

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A milestone for Pentatomoidea: Grazia emet al./em 2008-What do we know and where can we go?

Zootaxa 2021 Apr 14;4958(1):zootaxa.4958.1.26. Epub 2021 Apr 14.

Laboratório de Entomologia Sistemática, Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil. Programa de Pós-Graduação em Biologia Animal da Universidade Federal do Rio Grande Sul, PPG-BAN.

Pentatomoidea is the third largest superfamily in Heteroptera. The internal systematics and classification of this superfamily have an intricate history. The paper by Grazia et al. Read More

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Contribution to the molecular phylogeny of Sciaridae (Diptera) with special attention to the genera emBradysia/em and emCorynoptera/em.

Zootaxa 2021 Apr 6;4951(2):zootaxa.4951.2.12. Epub 2021 Apr 6.

Department of Ecology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria..

The systematics of the dipteran family Sciaridae is based mainly on morphological characters and has remained quite controversial. In this study, we used two mitochondrial DNA markers (CO1, 16S) and a nuclear one (28S) to take a glimpse into phylogenetic relationships of part of the North and Central European Sciaridae. A total of 91 species from 19 genera were analysed using Maximum Likelihood based phylogenetics (depending on the availability of valid sequences, 50-70 per gene). 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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Global prevalence and phylogeny of hepatitis B virus (HBV) drug and vaccine resistance mutations.

J Viral Hepat 2021 Apr 24. Epub 2021 Apr 24.

Nuffield Department of Medicine, Oxford, UK.

Vaccination and anti-viral therapy with nucleos(t)ide analogues (NAs) are key approaches to reducing the morbidity, mortality and transmission of hepatitis B virus (HBV) infection. However, the efficacy of these interventions may be reduced by the emergence of drug resistance-associated mutations (RAMs) and/or vaccine escape mutations (VEMs). We have assimilated data on the global prevalence and distribution of HBV RAMs/VEMs from publicly available data and explored the evolution of these mutations. 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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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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Genetic Diversity and Population Structure of Gynaephora qinghaiensis in Yushu Prefecture, Qinghai Province Based on the Mitochondrial COI Gene.

Biochem Genet 2021 Apr 23. Epub 2021 Apr 23.

Food and Health Engineering Research Center of State Education Ministry, School of Life Science, Sun Yat-Sen University, Guangzhou, Guangdong, China.

Gynaephora qinghaiensis (Lepidoptera: Lymantriidae: Gynaephora), a serious economic pest in alpine meadows, is mainly distributed in Yushu prefecture, Qinghai province, China. In this study, we aimed to investigate the genetic diversity and population structure of G. qinghaiensis through analyzing the sequence of 194 mitochondrial cytochrome oxidase subunit (COI) genes (658 bp in length) identified from 10 geographic populations located in three different countries, including Zhiduo, Zaduo, and Chengduo, of Yushu prefecture. Read More

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A fossil-calibrated time-tree of all Australian freshwater fishes.

Mol Phylogenet Evol 2021 Apr 20;161:107180. Epub 2021 Apr 20.

School of Life and Environmental Sciences, University of Sydney, Sydney, Australia.

Australian freshwater fishes are a relatively species-poor assemblage, mostly comprising groups derived from older repeated freshwater invasions by marine ancestors, plus a small number of Gondwanan lineages. These taxa are both highly endemic and highly threatened, but a comprehensive phylogeny for Australian freshwater fishes is lacking. This has hampered efforts to study their phylogenetic diversity, distribution of extinction risk, speciation rates, and rates of trait evolution. Read More

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Genetic Analysis of Formosan Subterranean Termite (Blattodea: Rhinotermitidae) Populations in California.

J Econ Entomol 2021 Apr 22. Epub 2021 Apr 22.

Department of Entomology, University of California, Riverside, CA.

A new infestation of the Formosan subterranean termite, Coptotermes formosanus Shiraki (Blattodea: Rhinotermitidae), was discovered in Canyon Lake, Riverside County, California. We used three mitochondrial DNA (COI, COII, and 16S) and seven polymorphic microsatellite markers to characterize the genetic relationship of the colony with two other colonies that were collected in 1992 and 2018 in La Mesa, San Diego County. Maximum likelihood phylogeny of C. 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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