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Journal articles on the topic 'Molecular clade'

Author: Grafiati

Published: 2 June 2025

Last updated: 31 July 2025

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1

Iqbal, Mudassir, Ralf-Udo Ehlers, and Lieven Waeyenberge. "Molecular characterisation of novel isolates of entomopathogenic nematodes." Nematology 18, no. 3 (2016): 277–91. http://dx.doi.org/10.1163/15685411-00002959.

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Entomopathogenic nematodes belong to the families of Steinernematidae and Heterorhabditidae. They are obligate and lethal parasites of insects that can provide effective control of some important pests of commercial crops. A total of 53 isolates of EPN were molecularly characterised (ITS region-based) in the present study. Most of the studied isolates belong to theSteinernemagenus and only few isolates belong to theHeterorhabditisgenus. The phylogenetic relations ofSteinernemaandHeterorhabditisspecies were analysed by utilising the maximum likelihood method. In theSteinernemaphylogenetic tree,

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Conran, John G., Gunta Jaudzems, and Neil D. Hallam. "Droseraceae gland and germination patterns revisited: support for recent molecular phylogenetic studies." Carnivorous Plant Newsletter 36, no. 1 (2007): 14–20. http://dx.doi.org/10.55360/cpn361.jc170.

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Droseraceae germination and leaf gland and microgland character state patterns were re-examined in the light of new molecular phylogenetic relationships. Phanerocotylar germination is basal in the family, with cryptocotylar germination having evolved at least twice; once in Aldrovanda, and again in Drosera within the Bryastrum/Ergaleium clade. Gland patterns also support major clades; with the Bryastrum clade taxa having marginal and Rorella-type glands whereas the terminal branch of the Drosera clade had marginal glands and most of the clade possessed biseriate type 3 glands. The gland and ge

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Domán, M., L. Makrai, Gy Lengyel, R. Kovács, L. Majoros, and K. Bányai. "Molecular Diversity and Genetic Relatedness of Candida albicans Isolates from Birds in Hungary." Mycopathologia 186, no. 2 (2021): 237–44. http://dx.doi.org/10.1007/s11046-021-00527-3.

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AbstractThe molecular epidemiology of Candida albicans infections in animals has been rarely studied. In this study, multilocus sequence typing was used to characterise the genetic diversity and population structure of 24 avian origin C. albicans isolates collected from different birds with candidiasis and compared to human isolates. Fourteen diploid sequence types (DSTs) including six new DSTs were determined. Cluster analysis revealed that isolates grouped into 8 clades. Bird isolates mainly belonged to minor clades and Clade 15 with DST 172 was the most common (11 isolates; 45.8%). The rema

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CHEN, S. P. "Molecular phylogenetic and evolutionary analysis of Japanese encephalitis virus in China." Epidemiology and Infection 140, no. 9 (2011): 1637–43. http://dx.doi.org/10.1017/s095026881100255x.

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SUMMARYWe elucidated the molecular epidemiology and evolution of Japanese encephalitis virus (JEV) strains isolated from 1949 to 2009 in China in this study. Three genotypes (I, III, V) were confirmed to be co-circulating in China in both high- and low-prevalence areas. Genotype III consisted of two clades (mainland clade and Taiwan clade). Compared to the mainland clade, genotype I and the Taiwan clade were newly introduced and evolved more rapidly. We also demonstrated that JEV strains in China, especially those in the mainland clade, were not only under purifying selection, but also probabl

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Bhandari, Vaibhav, Nadia Z. Ahmod, Haroun N. Shah, and Radhey S. Gupta. "Molecular signatures for Bacillus species: demarcation of the Bacillus subtilis and Bacillus cereus clades in molecular terms and proposal to limit the placement of new species into the genus Bacillus." International Journal of Systematic and Evolutionary Microbiology 63, Pt_7 (2013): 2712–26. http://dx.doi.org/10.1099/ijs.0.048488-0.

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The genus Bacillus is a phylogenetically incoherent taxon with members of the group lacking a common evolutionary history. Comprising aerobic and anaerobic spore-forming bacteria, no characteristics are known that can distinguish species of this genus from other similar endospore-forming genera. With the availability of complete genomic data from over 30 different species from this group, we have constructed detailed phylogenetic trees to determine the relationships among Bacillus and other closely related taxa. Additionally, we have performed comparative genomic analysis for the determination

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Xuan, Yahui, Yue Wu, Peng Li, et al. "Molecular phylogeny of mulberries reconstructed from ITS and two cpDNA sequences." PeerJ 7 (December 12, 2019): e8158. http://dx.doi.org/10.7717/peerj.8158.

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Background Species in the genus Morus (Moraceae) are deciduous woody plants of great economic importance. The classification and phylogenetic relationships of Morus, especially the abundant mulberry resources in China, is still undetermined. Internal transcribed spacer (ITS) regions are among the most widely used molecular markers in phylogenetic analyses of angiosperms. However, according to the previous phylogenetic analyses of ITS sequences, most of the mulberry accessions collected in China were grouped into the largest clade lacking for phylogenetic resolution. Compared with functional IT

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Bose, C. Nitha, Anu Boswell, and Francy K. Kakkassery. "A molecular phylogeny of Zygopterans (Insecta, Odonata) of Kerala, India." Journal of Insect Biodiversity and Systematics 11, no. 1 (2025): 195–205. https://doi.org/10.61186/jibs.11.1.195.

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Molecular phylogenetic reconstruction of the suborder Zygoptera based on sequences of the nuclear ribosomal gene 18S and mitochondrial gene COI was carried out using species collected from India. Sequence samples of 19 species belonging to 7 families of Zygoptera were used for the analysis. All the existing family levels in Zygoptera were confirmed as monophyletic clades in both analyses. While the 18S analysis resolved deep relations well, the COI analyses supported recently diverged clades. The analysis based on the COI gene showed the monophyly of families Coenagrionidae, Calopterygidae, Le

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Balashov, Sergey V., Eli Mordechai, Martin E. Adelson, and Scott E. Gygax. "Identification, quantification and subtyping of Gardnerella vaginalis in noncultured clinical vaginal samples by quantitative PCR." Journal of Medical Microbiology 63, no. 2 (2014): 162–75. http://dx.doi.org/10.1099/jmm.0.066407-0.

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Gardnerella vaginalis is an important component of the human vaginal microflora. It is proposed to play a key role in the pathogenesis of bacterial vaginosis (BV), the most common vaginal condition. Here we describe the development, validation and comparative analysis of a novel molecular approach capable of G. vaginalis identification, quantification and subtyping in noncultured vaginal specimens. Using two quantitative PCR (qPCR) assays, we analysed G. vaginalis bacterial loads and clade distribution in 60 clinical vaginal-swab samples. A very high pathogen prevalence was revealed by species

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Spiridonov, Sergei E., Alex P. Reid, Kasia Podrucka, Sergei A. Subbotin, and Maurice Moens. "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 6, no. 4 (2004): 547–66. http://dx.doi.org/10.1163/1568541042665304.

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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-

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Funk, Vicki A., Gisela Sancho, and Nádia Roque. "Nahuatlea: a new genus of compositae (Gochnatieae) from North America." PhytoKeys 91 (December 18, 2017): 105–24. https://doi.org/10.3897/phytokeys.91.21340.

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In the course of a detailed molecular study of the tribe Gochnatieae (Compositae: Gochnatioideae) it became apparent that the genus Gochnatia (sensu Cabrera) was not monophyletic but composed of a number of morphologically, geographically, and molecularly distinct clades. All but one of these clades had previously been recognized at the generic or sectional level and therefore had a name that could be applied. However, one clade, whose members are from Mexico and adjacent parts of the United States, had never been recognized as a distinct taxon. The Mexican clade is the sister group of the Car

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Hirai, Shinichiro, Eiji Yokoyama, Naoshi Ando, et al. "Another advantage of multi-locus variable-number tandem repeat analysis that can putatively subdivide enterohemorrhagic Escherichia coli O157 strains into clades by maximum a posteriori estimation." PLOS ONE 18, no. 3 (2023): e0283684. http://dx.doi.org/10.1371/journal.pone.0283684.

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Enterohemorrhagic Escherichia coli O157 (O157) strains can be subdivided into clades based on their single-nucleotide polymorphisms, but such analysis using conventional methods requires intense effort by laboratories. Although multi-locus variable-number tandem repeat analysis (MLVA), which can be performed with low laboratory burden, has been used as a molecular epidemiological tool, it has not been evaluated whether MLVA can be used the clade subdivision of O157 strains like it can for that of other pathogenic bacteria. This study aimed to establish a method for subdividing O157 strains int

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Oku, Yutaro, Kenji Iwao, Bert W. Hoeksema, et al. "Fungia fungites (Linnaeus, 1758) (Scleractinia, Fungiidae) is a species complex that conceals large phenotypic variation and a previously unrecognized genus." Contributions to Zoology 89, no. 2 (2020): 188–209. http://dx.doi.org/10.1163/18759866-20191421.

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Recent molecular phylogenetic analyses of scleractinian corals have resulted in the discovery of cryptic lineages. To understand species diversity in corals, these lineages need to be taxonomically defined. In the present study, we report the discovery of a distinct lineage obscured by the traditional morphological variation of Fungia fungites. This taxon exists as two distinct morphs: attached and unattached. Molecular phylogenetic analyses using mitochondrial COI and nuclear ITS markers as well as morphological comparisons were performed to clarify their phylogenetic relationships and taxono

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Hernández-Canchola, Giovani, and Livia León Paniagua. "About the specific status of Baiomys musculus and B. brunneus." Therya 12, no. 2 (2021): 291–301. http://dx.doi.org/10.12933/therya-21-1150.

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The southern pygmy mouse, Baiomys musculus, is distributed in arid and semiarid lowlands, from southern Nayarit and central Veracruz in México to northwestern Nicaragua, excluding the Yucatán Peninsula and the Caribbean tropical lowlands. Previous reports suggest that B. musculus includes two clades that may be eligible for specific status, although this remains uncertain. We used mitochondrial DNA (cytochrome b) and morphometric data to test whether two lineages exist within the species. Molecular data support the existence of two monophyletic groups with genetic distances of 6.69 % between t

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Lavrov, Dennis V., Maria C. Diaz, Manuel Maldonado, et al. "Phylomitogenomics bolsters the high-level classification of Demospongiae (phylum Porifera)." PLOS ONE 18, no. 12 (2023): e0287281. http://dx.doi.org/10.1371/journal.pone.0287281.

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Class Demospongiae is the largest in the phylum Porifera (Sponges) and encompasses nearly 8,000 accepted species in three subclasses: Keratosa, Verongimorpha, and Heteroscleromorpha. Subclass Heteroscleromorpha contains ∼90% of demosponge species and is subdivided into 17 orders. The higher level classification of demosponges underwent major revision as the result of nearly three decades of molecular studies. However, because most of the previous molecular work only utilized partial data from a small number of nuclear and mitochondrial (mt) genes, this classification scheme needs to be tested

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SHALISKO, VIACHESLAV, MICHAEL A. SUNDUE, ALMA ROSA VILLALOBOS-ARÁMBULA, MIGUEL ÁNGEL MUÑIZ-CASTRO, and J. ANTONIO VÁZQUEZ-GARCÍA. "Taxonomic novelties in grammitid ferns (Polypodiaceae) from the Neotropics and Madagascar supported by molecular data." Phytotaxa 394, no. 3 (2019): 176. http://dx.doi.org/10.11646/phytotaxa.394.3.1.

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Based on cpDNA data, we provide the phylogenetic position for 18 species of Neotropical grammitid ferns (Polypodiaceae) that were not previously included in a molecular phylogeny. These species were resolved in Alansmia, Ceradenia, Enterosora, Grammitis, Lellingeria, Lomaphlebia, Melpomene, Moranopteris, Stenogrammitis, and Terpsichore. Our results indicate that Enterosora is polyphyletic and in need of generic recircumscription. We maintain the identity of Enterosora, based on the position of E. campbellii subsp. spongiosa, a variety of the type species. This finding allowed us to conclude th

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Silvério Pena Bento, João Pedro, Edna Scremin-Dias, Flávio Macedo Alves, Vidal De Freitas Mansano, and Ângela Lúcia Bagnatori Sartori. "Phylogenetic implications of the anatomical study of the Amburaneae clade (Fabaceae: Faboideae)." Botanical Journal of the Linnean Society 194, no. 1 (2020): 69–83. http://dx.doi.org/10.1093/botlinnean/boaa019.

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Abstract Phylogenetic analyses of early-diverging Faboideae have indicated that genera previously positioned in distinct tribes are instead closely related, e.g. in the Amburaneae clade, and the relatively recent rearrangements of many genera into clades has hampered the identification of morphological synapomorphies for previously unrecognized clades. Our aims are to evaluate anatomical vegetative characters of leaflets attached to reproductive features in the Amburaneae clade, to identify new synapomorphies for the clade and subclades, to identify characters supporting intergeneric relations

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Garnica, Sigisfredo, Michael Weiß, Bernhard Oertel, and Franz Oberwinkler. "A framework for a phylogenetic classification in the genus Cortinarius (Basidiomycota, Agaricales) derived from morphological and molecular data." Canadian Journal of Botany 83, no. 11 (2005): 1457–77. http://dx.doi.org/10.1139/b05-107.

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Phylogenetic relationships in the genus Cortinarius with emphasis on European species were studied by integrating a molecular phylogenetic analysis of nuclear rDNA sequences with morphological, chemical, and ecological data. Internal transcribed spacers (ITS1 and ITS2, including 5.8S) and the D1–D2 regions of nuclear rDNA of 262 Cortinarius species including most of the recognised subgenera from Europe, South America, Australia, Tasmania, New Zealand, and Asia were sequenced and analysed by maximum likelihood and neighbour joining. Our morphological and molecular analyses showed considerable d

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CERON, KAROLINE, and DIEGO JOSÉ SANTANA. "The tadpole of Physalaemus nanus (Boulenger, 1888) (Anura, Leptodactylidae) from Southern Brazil." Zootaxa 4277, no. 2 (2017): 280. http://dx.doi.org/10.11646/zootaxa.4277.2.9.

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The genus Physalaemus Fitzinger, 1826 currently comprises 47 described species distributed from Central America (Guianas) to Uruguay (Frost 2016). The genus has been recently organized in two main clades based on molecular data, Physalaemus signifer Clade and Physalaemus cuvieri Clade (Lourenço et al. 2015). The P. signifer Clade, with 15 species, is composed by the P. deimaticus and P. signifier groups, plus P. nattereri (Steindachner, 1863) and P. maculiventris (Lutz, 1925) (Nascimento et al. 2005; Lourenço et al. 2015).

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KIRIKA, PAUL M., PRADEEP K. DIVAKAR, ANA CRESPO, et al. "Polyphyly of the genus Canoparmelia—uncovering incongruences between phenotype-based classification and molecular phylogeny within lichenized Ascomycota (Parmeliaceae)." Phytotaxa 289, no. 1 (2016): 36. http://dx.doi.org/10.11646/phytotaxa.289.1.2.

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Many phenotypical features traditionally used to classify genera in Parmeliaceae and in lichens in general have evolved several times independently, potentially limiting their taxonomic utility. Here, we aim to elucidate evolutionary relationships of Canoparmelia s. lat. among other parmotremoid taxa. A multilocus dataset (ITS, nuLSU and mtSSU rDNA sequences) was gathered and analyzed within a phylogenetic framework. Canoparmelia s. lat. was recovered as highly polyphyletic within the parmelioid clade, and three divergent lineages representing Canoparmelia s. lat. were identified in addition t

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Martínez, Jose R. W., Maria Spencer, Lina M. Rivas, et al. "666. Molecular Epidemiology of Methicillin-Resistant Staphylococcus aureus in Chile between 1999-2018." Open Forum Infectious Diseases 8, Supplement_1 (2021): S435—S436. http://dx.doi.org/10.1093/ofid/ofab466.863.

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Abstract Background The global spread of methicillin-resistant Staphylococcus aureus (MRSA) is associated with distinct genetic lineages that predominate in specific geographical regions. Available evidence suggests the Chilean-Cordobes clone (ChC), an ST5-SCCmecI lineage, has largely predominated in Chilean hospitals since its first description in the late 1990’s. Although the circulation of other MRSA lineages, including community-associated clones, has been well documented, the dynamics of clonal replacement over time has not been explored. Therefore, we aimed to study the molecular epidemi

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AOKI, SATOSHI, TETSUO OHI-TOMA, PAN LI, CHENGXIN FU, and JIN MURATA. "Phylogenetic, cytological and morphological comparisons of Oxalis subsect. Oxalis (Oxalidaceae) in East Asia." Phytotaxa 324, no. 3 (2017): 266. http://dx.doi.org/10.11646/phytotaxa.324.3.3.

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To assess the classification of East Asian taxa in Oxalis subsect. Oxalis, samples from a wide geographical area were examined using molecular phylogenetic, cytological and morphological analyses. The phylogenetic analysis showed the early branching of O. leucolepis and O. obtriangulata in East Asia, followed by that of O. acetosella and O. oregana in North America. The remaining Eurasian samples were divided into four clades: taxa from Mainland China and Taiwan (Clade A); O. acetosella from Eurasia including Japan (Clade B); O. griffithii from Japan (Clade C); and O. griffithii plus some O. a

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Lestari, Wenni Setyo, Bayu Adjie, Tassanai Jaruwatanaphan, Yasuyuki Watano, and Made Pharmawati. "MOLECULAR PHYLOGENY OF MAIDENHAIR FERN GENUS ADIANTUM (PTERIDACEAE) FROM LESSER SUNDA ISLANDS INDONESIA BASED ON RBCL AND TRNL-F." REINWARDTIA 14, no. 1 (2014): 143. http://dx.doi.org/10.14203/reinwardtia.v14i1.409.

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The Lesser Sunda Islands of Indonesia are composed of small islands scattered from Bali to Timor Island. We analyzed a molecular phylogeny of Adiantum collected from Lesser Sunda Islands to reveal its phylogenetic relationships. A total of 12 species of Adiantum from this region and seven species from Java Island were collected and used in this study. Two cpDNA regions (rbcL and trnL-F) were chosen as markers and phylogenetic analyses were conducted using Neighbour-Joining (NJ) and Maximum Parsimony (MP) methods. The tree topologies reconstructed by NJ and MP from specimens used in this study

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Noisumdaeng, Pirom, Juthamas Phadungsombat, Sasrinakarn Weerated, Witthawat Wiriyarat, and Pilaipan Puthavathana. "Genetic evolution of hemagglutinin and neuraminidase genes of H5N1 highly pathogenic avian influenza viruses in Thailand." PeerJ 10 (November 30, 2022): e14419. http://dx.doi.org/10.7717/peerj.14419.

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Background Ongoing outbreaks of H5N1 highly pathogenic avian influenza (HPAI) viruses and the emergence of the genetic-related hemagglutinin (HA) gene of reassortant H5Nx viruses currently circulating in wild birds and poultries pose a great global public health concern. In this study, we comprehensively analyzed the genetic evolution of Thai H5N1 HA and neuraminidase (NA) genes between 2003 and 2010. The H5N1 Thailand virus clade 2.3.4 was also genetically compared to the currently circulating clade 2.3.4.4 of H5Nx viruses. Methods Full-length nucleotide sequences of 178 HA and 143 NA genes o

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Layton, K. K. S., C. P. K. Warne, A. Nicolai, A. Ansart, and J. R. deWaard. "Molecular evidence for multiple introductions of the banded grove snail (Cepaea nemoralis) in North America." Canadian Journal of Zoology 97, no. 4 (2019): 392–98. http://dx.doi.org/10.1139/cjz-2018-0084.

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Global identification and monitoring programs for invasive species aim to reduce imminent impacts to biodiversity, ecosystem services, agriculture, and human health. This study employs a 658 base pair fragment of the cytochrome c oxidase subunit I (COI) gene to identify and categorize clades of the banded grove snail (Cepaea nemoralis (Linnaeus, 1758)) from native (European) and introduced (North American) ranges using a maximum-likelihood phylogeny and haplotype networks. This work corroborates the existence of eight clades within C. nemoralis and further identified three clades that were com

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SGOUROS, KATHERINE, LAWRENCE M. PAGE, SARAH A. ORLOFSKE, and ROBERT C. JADIN. "A revised molecular phylogeny reveals polyphyly in Schistura (Teleostei: Cypriniformes: Nemacheilidae)." Zootaxa 4559, no. 2 (2019): 349. http://dx.doi.org/10.11646/zootaxa.4559.2.8.

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There is a general consensus that the genus Schistura (Nemacheilidae), currently with 241 species, is not monophyletic. However, weak morphological synapomorphies and a lack of genetic data for most species of Schistura and their presumptive relatives have prevented meaningful diagnoses of species groups within this genus. To aid in deciphering evolutionary relationships, sequence data from two mitochondrial genes (cytochrome b and D-loop) were implemented in phylogenetic analyses for species of Schistura and other nemacheilids for which data from earlier studies and recently collected materia

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Song, Jeong-Hun, and Kee-Jeong Ahn. "Molecular phylogeny reveals multiple origins of seashore colonisation in the genus Aleochara Gravenhorst (Coleoptera : Staphylinidae : Aleocharinae)." Invertebrate Systematics 27, no. 2 (2013): 239. http://dx.doi.org/10.1071/is12040.

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A revised molecular phylogeny of the genus Aleochara Gravenhorst is presented. The dataset comprised partial mitochondrial cytochrome c oxidase I (COI) (1373 bp), COII (577 bp), and the complete sequences of tRNA leucine (71 bp) between them, for 56 Aleochara species and 8 outgroups. We added 15 populations of 8 coastal species: A. fucicola Sharp, A. littoralis (Mäklin), A. nubis (Assing), A. puetzi (Assing), A. squalithorax Sharp, A. sulcicollis Mannerheim, A. trisulcata Weise and A. zerchei (Assing). All phylogenetic analyses strongly supported the monophyly of the genus Aleochara, a curtula

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Tate, Jennifer A., M. Cristina Acosta, Joshua McDill, Eduardo A. Moscone, Beryl B. Simpson, and Andrea A. Cocucci. "Phylogeny and Character Evolution in Nierembergia (Solanaceae): Molecular, Morphological, and Cytogenetic Evidence." Systematic Botany 34, no. 1 (2009): 198–206. http://dx.doi.org/10.1600/036364409787602249.

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Nierembergia (Solanaceae) contains 21 species found primarily in South America, with one species occurring disjunctly in Mexico. Among other features, a pollination system not found elsewhere in the Solanaceae typifies this genus. In most species, nectaries are absent, but oil-producing elaiophores are present on the corolla limb and these attract oil-collecting bees. Molecular phylogenetic hypotheses based on nuclear ITS and chloroplast rpl16 intron data support the monophyly of Nierembergia, which is sister to a clade composed of Bouchetia plus Hunzikeria. The data reconstruct two clades wit

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Salmaki, Yasaman, Günther Heubl, and Maximilian Weigend. "Towards a new classification of tribe Stachydeae (Lamiaceae): naming clades using molecular evidence." Botanical Journal of the Linnean Society 190, no. 4 (2019): 345–58. http://dx.doi.org/10.1093/botlinnean/boz021.

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AbstractStachydeae, comprising c. 470 species, are one of the most diverse and taxonomically puzzling groups in Lamioideae. In the present study, the phylogenetic relationships in the Eurystachys clade (a phylogenetic name for all genera attributed to Stachydeae except Melittis) were reconstructed utilizing nuclear ribosomal DNA sequences (nrETS, 5S-NTS) from 148 accessions in 12 genera. Our phylogenetic results recovered Stachys as paraphyletic with numerous traditionally recognized genera nested in it. A broadly defined Eurystachys clade, however, was monophyletic. Unlike previous studies, t

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Klicka, John, and Garth M. Spellman. "A Molecular Evaluation of the North American “Grassland” Sparrow Clade." Auk 124, no. 2 (2007): 537–51. http://dx.doi.org/10.1093/auk/124.2.537.

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Abstract Because they share several morphological and ecological characters, the North American sparrow (Emberizidae) genera Ammodramus, Passerculus, and Xenospiza have historically been considered members of a well-defined “grassland” sparrow assemblage. Relationships among the 11 members of this group have been the subject of much taxonomic debate, yet no comprehensive molecular assessment of relationships has been done. We investigated these relationships using mitochondrial DNA sequence data that included complete cytochrome-b and ND2 genes. Phylogenetic reconstructions derived via parsimo

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Xiao, Yan-Ping, Xian-Lin Guo, Megan Price, Wei Gou, Song-Dong Zhou, and Xing-Jin He. "New insights into the phylogeny of Sinocarum (Apiaceae, Apioideae) based on morphological and molecular data." PhytoKeys 175 (March 17, 2021): 13–32. http://dx.doi.org/10.3897/phytokeys.175.60592.

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Sinocarum is a Sino-Himalayan endemic genus of Apiaceae and distributed in high-elevations from Nepal to SW China. In this study, morphological characteristics were combined with nuclear internal transcribed spacer (ITS) and two chloroplast DNA (cpDNA) intron sequences (rpl16 and rps16) to determine the phylogenetic placement of Sinocarum and the infrageneric relationships between five Sinocarum species. The results confirmed that Sinocarum was a polyphyletic group separated into two clades, Acronema and East Asia clades. S. coloratum, the generic type of Sinocarum, S. cruciatum, S. vaginatum

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Xiao, Yan-Ping, Xian-Lin Guo, Megan Price, Wei Gou, Song-Dong Zhou, and Xing-Jin He. "New insights into the phylogeny of Sinocarum (Apiaceae, Apioideae) based on morphological and molecular data." PhytoKeys 175 (March 17, 2021): 13–32. https://doi.org/10.3897/phytokeys.175.60592.

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Sinocarum is a Sino-Himalayan endemic genus of Apiaceae and distributed in high-elevations from Nepal to SW China. In this study, morphological characteristics were combined with nuclear internal transcribed spacer (ITS) and two chloroplast DNA (cpDNA) intron sequences (rpl16 and rps16) to determine the phylogenetic placement of Sinocarum and the infrageneric relationships between five Sinocarum species. The results confirmed that Sinocarum was a polyphyletic group separated into two clades, Acronema and East Asia clades. S. coloratum, the generic type of Sinocarum, S. cruciatum, S. vaginatum

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Warwick, Suzanne I., Connie A. Sauder, and Ihsan A. Al-Shehbaz. "Phylogenetic relationships in the tribe Alysseae (Brassicaceae) based on nuclear ribosomal ITS DNA sequences." Botany 86, no. 4 (2008): 315–36. http://dx.doi.org/10.1139/b08-013.

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Sequence data from the nuclear ribosomal internal transcribed spacer (ITS) region of 85 species (131 accessions) were used to determine the tribal limits, monophyly status, and phylogenetic intra-tribal relationships of genera within the tribe Alysseae (Brassicaceae). Both maximum parsimony and maximum likelihood analyses support the recognition of the tribe Alysseae s. str. (12 genera: Alyssoides , Alyssum , Aurinia , Berteroa , Bornmuellera , Clastopus , Clypeola , Degenia , Fibigia , Galitzkya , Hormathophylla , and Physoptychis ). Six well-supported clades were recognized within the Alysse

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Joshi, Bhavesh M., Mrugesh M. Patel, Rudra B. Parmar, N. K. Singh, and P. V. Tapre. "Molecular Characterization of Plant Growth Promoting Pseudomonas from Rhizosphere of Euphorbia caducifolia Haines." International Journal of Bio-resource and Stress Management 13, no. 11 (2022): 1240–51. http://dx.doi.org/10.23910/1.2022.3262.

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A study was conducted during kharif 2020 at the Department of Microbiology, Chimanbhai Patel College of Agriculture, S. D. Agricultural University for molecular characterization of plant growth promoting Pseudomonas isolates from rhizosphere of Euphorbia caducifolia. Twenty Pseudomonas isolates (designated as PsEc1 to PsEc20) were axenically isolated from rhizospheric soil sample of Euphorbia caducifolia using Pseudomonas Isolation Agar Base (a selective medium). These isolates were tested gram negative, rod shaped, and oxidase positive. All 20 isolates were positive for utilization of maltose

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JIANG, HAIJUN, CHANGKUN FU, KEYI TANG, et al. "Molecular phylogenetics and diversity of the Himalayan shrew ( Soriculus nigrescens Gray, 1842) (Eulipotyphla, Soricidae) in Southwest China." Zootaxa 5263, no. 1 (2023): 061–78. http://dx.doi.org/10.11646/zootaxa.5263.1.3.

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The Himalayan shrew, Soriculus nigrescens Gray, 1842, belongs to the monotypic genus Soriculus, which is distributed mainly in the Himalayan region. Previous authors have studied its classification based on morphological and molecular data. However, no comprehensive study of the diversity and phylogeny of this species has been performed. In this study, we investigated the molecular phylogeny, genetic diversity, and species divergence of S. nigrescens based on one mitochondrial gene and three nuclear genes. A total of 124 samples from 27 sites in Southwest China were analyzed. Our molecular phy

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Hsiao, C., S. W. L. Jacobs, N. P. Barker, and N. J. Chatterton. "A molecular phylogeny of the subfamily Arundinoideae (Poaceae) based on sequences of rDNA." Australian Systematic Botany 11, no. 1 (1998): 41. http://dx.doi.org/10.1071/sb97001.

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Phylogenetic relationships of the whole Poaceae family inferred from the sequence data of rDNA (ITS) support the hypothesis that the arundinoids are monophyletic, not polyphyletic as previously proposed. The ITS sequence phylogeny of 42 arundinoid species demonstrates an early divergence of the Aristideae and three major groupings, corresponding loosely to the tribes Aristideae, Arundineae and Danthonieae. The Arundineae are resolved into two paraphyletic clades. In one clade, Arundo, Monachather, and Dregeochloa are the sister group to Amphipogon and Diplopogon. In the other clade, Phragmites

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Dawson, Michael N. "Morphologic and molecular redescription of Catostylus mosaicus conservativus (Scyphozoa: Rhizostomeae: Catostylidae) from south-east Australia." Journal of the Marine Biological Association of the United Kingdom 85, no. 3 (2005): 723–31. http://dx.doi.org/10.1017/s002531540501163x.

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Two reciprocally monophyletic mitochondrial clades of the commercially valuable jellyfish Catostylus mosaicus are endemic to south-eastern Australia. Here, medusae in the two clades are shown to differ also in colour and in the dimensions of their papillae, oral disk, and bell depth. They are referred to two varieties recognized in 1884 by von Lendenfeld. The clade occupying localities adjacent to Bass Strait is redescribed as subspecies C. mosaicus conservativus; the clade from New South Wales and southern Queensland spans the type locality (Port Jackson) of C. mosaicus and is designated C. m

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Hanh, Trinh Van, Vu Tien Luyen, Pham Huu Hung, et al. "Construction of a dataset for the gene nrLSU to support the identification of cantharellus at Langbian Mountain, Lam Dong." ENGINEERING AND TECHNOLOGY 8, no. 2 (2020): 14–21. http://dx.doi.org/10.46223/hcmcoujs.tech.en.8.2.342.2018.

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Fungal species of Cantharellales order are found worldwide including Europe, Africa, Asia, and North America. This clade includes two smaller, separate, but closely related genera Cantharellus and Craterellus. Cantharellus was firstly identified in the middle of the 17th century. Besides traditional classification based on morphology, molecular phylogeny of the nuclear ribosomal large subunit gene (nrLSU) can be an effective tool to provide more information during species identification for this group. In this current report, a dataset of the nrLSU gene including 60 sequences of Canthare

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Sun, Ping, John C. Clamp, Dapeng Xu, Bangqin Huang, Mann Kyoon Shin, and Franziska Turner. "An ITS-based phylogenetic framework for the genus Vorticella : finding the molecular and morphological gaps in a taxonomically difficult group." Proceedings of the Royal Society B: Biological Sciences 280, no. 1771 (2013): 20131177. http://dx.doi.org/10.1098/rspb.2013.1177.

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Vorticella includes more than 100 currently recognized species and represents one of the most taxonomically challenging genera of ciliates. Molecular phylogenetic analysis of Vorticella has been performed so far with only sequences coding for small subunit ribosomal RNA (SSU rRNA); only a few of its species have been investigated using other genetic markers owing to a lack of similar sequences for comparison. Consequently, phylogenetic relationships within the genus remain unclear, and molecular discrimination between morphospecies is often difficult because most regions of the SSU rRNA gene a

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Ohi-Toma, Tetsuo, Takashi Sugawara, Hiroko Murata, Stefan Wanke, Christoph Neinhuis, and Jin Murata. "Molecular Phylogeny of Aristolochia sensu lato (Aristolochiaceae) based on Sequences of rbcL, matK, and phyA Genes, with Special Reference to Differentiation of Chromosome Numbers." Systematic Botany 31, no. 3 (2006): 481–92. http://dx.doi.org/10.1600/036364406778388656.

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The genus Aristolochia sensu lato contains over 400 species from warm temperate to tropical regions worldwide. Taxonomic treatments of Aristolochia have been ambiguous and controversial. In a recent cladistic analysis based on morphological characters, it was proposed that the genus should be divided into four genera in two subtribes. To reconsider the systematics of Aristolochia sensu lato, we reconstructed its phylogeny based on nucleotide sequences of the chloroplast rbcL gene and the nuclear-encoded phytochrome A (phyA) gene for 19 representative species and the chloroplast matK gene of ov

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Wrobel, Lauren, Julia K. Whittington, Claude Pujol, et al. "Molecular Phylogenetic Analysis of a Geographically and Temporally Matched Set of Candida albicans Isolates from Humans and Nonmigratory Wildlife in Central Illinois." Eukaryotic Cell 7, no. 9 (2008): 1475–86. http://dx.doi.org/10.1128/ec.00162-08.

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ABSTRACT This study explored whether wildlife species serve as the reservoir for human Candida albicans strains in a given geographic area. C. albicans isolates were collected from nonmigratory wildlife admitted to the University of Illinois Wildlife Medical Clinic. A geographically and temporally matched set of C. albicans oral isolates was collected from healthy human volunteers. Multilocus sequence typing was used to assign strains to genetic clades. Clade 1 isolates, particularly diploid sequence type 69 (DST 69), were most common in humans. Clade 1 strains were less frequently recovered f

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Atceken, Nazente, Sara Asghari Dilmani, Ahmed Choukri Abdullah, et al. "Development and Validation of LAMP Assays for Distinguishing MPXV Clades with Fluorescent and Colorimetric Readouts." Biosensors 15, no. 1 (2025): 23. https://doi.org/10.3390/bios15010023.

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Human monkeypox (Mpox) is a zoonotic disease caused by the Monkeypox virus (MPXV). As of 14 August 2024, the World Health Organization (WHO) has declared it a global health emergency. For Mpox, this was the second public health emergency of global significance in the past two years. MPXV belongs to the Poxviridae family and is phylogenetically and epidemically divided into two clades: the Congo Basin (Clade-I) and the West African (Clade-II) clades. Clade-I has been associated with more severe disease progression and higher mortality compared to Clade-II, and thus the differentiation between c

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NADLER, S. A., R. A. CARRENO, H. MEJÍA-MADRID, et al. "Molecular phylogeny of clade III nematodes reveals multiple origins of tissue parasitism." Parasitology 134, no. 10 (2007): 1421–42. http://dx.doi.org/10.1017/s0031182007002880.

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SUMMARYMolecular phylogenetic analyses of 113 taxa representing Ascaridida, Rhigonematida, Spirurida and Oxyurida were used to infer a more comprehensive phylogenetic hypothesis for representatives of ‘clade III’. The posterior probability of multiple alignment sites was used to exclude or weight characters, yielding datasets that were analysed using maximum parsimony, likelihood, and Bayesian inference methods. Phylogenetic results were robust to differences among inference methods for most high-level taxonomic groups, but some clades were sensitive to treatments of characters reflecting diff

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Lyson, Tyler R., Gabe S. Bever, Bhart-Anjan S. Bhullar, Walter G. Joyce, and Jacques A. Gauthier. "Transitional fossils and the origin of turtles." Biology Letters 6, no. 6 (2010): 830–33. http://dx.doi.org/10.1098/rsbl.2010.0371.

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The origin of turtles is one of the most contentious issues in systematics with three currently viable hypotheses: turtles as the extant sister to (i) the crocodile–bird clade, (ii) the lizard–tuatara clade, or (iii) Diapsida (a clade composed of (i) and (ii)). We reanalysed a recent dataset that allied turtles with the lizard–tuatara clade and found that the inclusion of the stem turtle Proganochelys quenstedti and the ‘parareptile’ Eunotosaurus africanus results in a single overriding morphological signal, with turtles outside Diapsida. This result reflects the importance of transitional fos

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Li, Shuxian, Yan Kit Tam, and Glen L. Hartman. "Molecular Differentiation of Fusarium solani f. sp. glycines from Other F. solani Based on Mitochondrial Small Subunit rDNA Sequences." Phytopathology® 90, no. 5 (2000): 491–97. http://dx.doi.org/10.1094/phyto.2000.90.5.491.

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Fusarium solani is a soilborne plant pathogen that infects many different hosts. Within the species, there is some specialization, and a number of forma specialis have been described based on host affiliation. One of these, F. solani f. sp. glycines, infects soybean and causes sudden death syndrome. To differentiate between F. solani f. sp. glycines and other F. solani isolates, a partial sequence of the mitochondrial small subunit (mtSSU) rRNA gene was amplified by polymerase chain reaction and sequenced from 14 F. solani f. sp. glycines and 24 F. solani isolates from various plant hosts. All

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Fukutani, Kazumi, Masafumi Matsui, Dung Van Tran, and Kanto Nishikawa. "Genetic diversity and demography of Bufo japonicus and B. torrenticola (Amphibia: Anura: Bufonidae) influenced by the Quaternary climate." PeerJ 10 (June 8, 2022): e13452. http://dx.doi.org/10.7717/peerj.13452.

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The Quaternary climate affected the present species richness and geographic distribution patterns of amphibians by limiting their activities during the glacial period. The present study examined the phylogenetic relationships of Japanese toads (Bufo japonicus and B. torrenticola) and the demography of each lineage from the past to the present based on mitochondrial sequences and ecological niche models. Japanese toads are a monophyletic group with two main clades (clades A and B). Clade A represents B. j. formosus, including three clades (clades A1, A2, and A3). Clade B contains three clades,

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Deepak, V., Varad B. Giri, Mohammad Asif, et al. "Systematics and phylogeny of Sitana (Reptilia: Agamidae) of Peninsular India, with the description of one new genus and five new species." Contributions to Zoology 85, no. 1 (2016): 67–111. http://dx.doi.org/10.1163/18759866-08501004.

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We revise the taxonomy of the agamid genus Sitana Cuvier, 1829, a widely distributed terrestrial lizard from the Indian subcontinent based on detailed comparative analyses of external morphology, osteology and molecular data. We sampled 81 locations spread over 160,000 km2 in Peninsular India including type localities, which represented two known and five previously undescribed species. Based on general similarity in body shape and dewlap all species were hitherto identified as members of the genus Sitana. However, Sitana deccanensis and two other morphotypes, which are endemic to north Karnat

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Alfredo Holley, J., Juliana Sterli, and Néstor G. Basso. "Dating the origin and diversification of Pan-Chelidae (Testudines, Pleurodira) under multiple molecular clock approaches." Contributions to Zoology 89, no. 2 (2020): 146–74. http://dx.doi.org/10.1163/18759866-20191419.

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Pan-Chelidae (Testudines, Pleurodira) is a group of side-necked turtles with a currently disjointed distribution in South America and Australasia and characterized by two morphotypes: the long-necked and the short-necked chelids. Both geographic groups include both morphotypes, but different phylogenetic signals are obtained from morphological and molecular data, suggesting the monophyly of the long-necked chelids or the independent evolution of this trait in both groups. In this paper, we addressed this conflict by compiling and editing available molecular and morphological data for Pan-Cheli

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Ladner, Jason T., Jonathan M. Palmer, Cassandra L. Ettinger, et al. "The population genetics of the causative agent of snake fungal disease indicate recent introductions to the USA." PLOS Biology 20, no. 6 (2022): e3001676. http://dx.doi.org/10.1371/journal.pbio.3001676.

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Snake fungal disease (SFD; ophidiomycosis), caused by the pathogen Ophidiomyces ophiodiicola (Oo), has been documented in wild snakes in North America and Eurasia, and is considered an emerging disease in the eastern United States of America. However, a lack of historical disease data has made it challenging to determine whether Oo is a recent arrival to the USA or whether SFD emergence is due to other factors. Here, we examined the genomes of 82 Oo strains to determine the pathogen’s history in the eastern USA. Oo strains from the USA formed a clade (Clade II) distinct from European strains (

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Horak, Egon, P. Brandon Matheny, Dennis E. Desjardin, and Kasim Soytong. "The genus Inocybe (Inocybaceae, Agaricales, Basidiomycota) in Thailand and Malaysia." Phytotaxa 230, no. 3 (2015): 201. http://dx.doi.org/10.11646/phytotaxa.230.3.1.

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Twenty-five species of Inocybaceae are reported from Thailand and Malaysia. Thirteen are described as new from four different major clades of the family: I. errata from the Mallocybe clade, I. bicolorata and I. proxima from the Inosperma clade, I. neglecta from the Pseudosperma clade, and I. brevisquamulosa, I. fragilissima, I. latibulosa, I. lineata, I. ornata, I. parvibulbosa, I. pileosulcata, I stellata and I. thailandica from Inocybe sensu stricto. Nineteen species are documented in full, circumscribed by morphological and molecular (ITS and nLSU sequences) features. Six additional lineage

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Arnuphapprasert, Apinya, Elizabeth Riana, Thongchai Ngamprasertwong, et al. "First molecular investigation of haemosporidian parasites in Thai bat species." International Journal for Parasitology: Parasites and Wildlife 13 (June 7, 2020): 51–61. https://doi.org/10.5281/zenodo.14821173.

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(Uploaded by Plazi for the Bat Literature Project) Malaria parasites in the phylum Apicomplexa (Order: Haemosporida) infect diverse vertebrates and invertebrate hosts. At least seven genera of haemosporidian parasites have been described to exclusively infect bats. Most of these parasites remain enigmatic with a poorly known host range. Here, we investigated 271 bats belonging to 21 species and seven families from six provinces of Thailand. Overall, 124 out of 271 bats (45.8%) were positive for haemosporidian parasites, while none had Plasmodium, based on microscopic examination of blood smear

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