Impact of interventions on mpox transmission during the 2022 outbreak in Canada: a mathematical modeling study of three different cities by Fanyu Xiu, Carla M. Doyle, Jorge Luis Flores Anato, Jesse Knight, Linwei Wang, Joseph Cox, Daniel Grace, Trevor A. Hart, Terri Zhang, Shayna Skakoon-Sparling, Milada Dvorakova, Rita Shahin, Herveen Sachdeva, Nathan Lachowsky, Hind Sbihi, Darrell H.S. Tan, Michael A. Irvine, Sharmistha Mishra, Mathieu Maheu-Giroux

“…Objectives: The global mpox (clade II) outbreak of 2022 primarily affected gay, bisexual, and other men who have sex with men (GBM) and was met with swift community and public health responses. …”
Get full text

Neurotropic Tick-Borne Flavivirus in Alpine Chamois (<i>Rupicapra rupicapra rupicapra</i>), Austria, 2017, Italy, 2023 by Norbert Nowotny, Maria Lucia Mandola, Isabella Monne, Zoltán Bagó, Chiara Nogarol, Alice Fusaro, Katharina Dimmel, Barbara Moroni, Lisa Guardone, Jolanta Kolodziejek, Elisa Palumbo, Gabriela Stanclova, Adi Steinrigl, Gabriele Fidler, Cristina Bertasio, Irene Bertoletti, Alessandro Bianchi, Mattia Calzolari, Paola Prati, Nadia Vicari, Angela Salomoni, Maria Francesca Priore, Federica Gobbo, Aitor Garcia-Vozmediano, Tom Loney, Ahmad Abou Tayoun, Alawi Alsheikh-Ali, Paola De Benedictis, Jeremy V. Camp, Zdenek Hubalek, Ivo Rudolf, Davide Lelli, Ana Moreno

“…The chamois-derived virus strains, tentatively termed “Alpine chamois encephalitis virus”, form a well-supported independent genetic clade with Spanish goat encephalitis virus, clearly separated from other LIV. …”
Get full text

Reactogenicity and Immunogenicity Against MPXV of the Intradermal Administration of Modified Vaccinia Ankara Compared to the Standard Subcutaneous Route by Valentina Mazzotta, Pierluca Piselli, Alessandro Cozzi Lepri, Giulia Matusali, Eleonora Cimini, Rozenn Esvan, Francesca Colavita, Roberta Gagliardini, Stefania Notari, Alessandra Oliva, Silvia Meschi, Rita Casetti, Giulia Micheli, Licia Bordi, Alessandro Giacinta, Germana Grassi, Saba Gebremeskel Tekle, Claudia Cimaglia, Jessica Paulicelli, Alessandro Caioli, Paola Gallì, Giulia Del Duca, Miriam Lichtner, Loredana Sarmati, Enrica Tamburrini, Claudio Mastroianni, Alessandra Latini, Paolo Faccendini, Carla Fontana, Emanuele Nicastri, Andrea Siddu, Alessandra Barca, Francesco Vaia, Enrico Girardi, Fabrizio Maggi, Andrea Antinori

“…Our data support the current WHO recommendation of using the ID route in low–medium-income countries (LMIC), although response data in people infected with the new 1b clade are urgently needed.…”
Get full text

Spatiotemporal variability in the South American mammalian fossil record and its impact on macroevolutionary inference by Pedro D. de S. Ugarte, João C. S. Nascimento, Mathias M. Pires

“…Most early South American and early immigrant clades have lower preservation rates than late immigrant clades. …”
Get full text

Phylogenetic Relationships in the Miracle Berry Genus, <i>Synsepalum</i>, Sensu Lato, and Relatives (Sapotaceae) by Daniel Potter, Mark Uleh

“…Phylogenetic trees generated for both regions (nuclear and plastid) resulted in the resolution of six clades. Four of the clades correspond to species in the genus <i>Synsepalum</i> and two clades include species of <i>Englerophytum</i>. …”
Get full text

Effect of Larval Density on Development of the Coconut Hispine Beetle, Brontispa longissima (Gestro) (Coleoptera: Chrysomelidae) by Mika Murata, Dang Thi Dung, Shun-ichiro Takano, Ryoko Tabata Ichiki, Satoshi Nakamura

“…Recently we found that B. longissima was divided into two monophyletic clades by genetic analysis. Therefore, we also compared the results between two populations, from Ishigaki, Japan (ISH) and Papua New Guinea (PNG), which were representative of the two monophyletic clades of B. longissima. …”
Get full text

A revised classification of Dryopteridaceae based on plastome phylogenomics and morphological evidence, with the description of a new genus, Pseudarachniodes by Zheng-Yu Zuo, Germinal Rouhan, Shi-Yong Dong, Hong-Mei Liu, Xin-Yu Du, Li-Bing Zhang, Jin-Mei Lu

“…Our analyses recovered 24 strongly supported clades grouped into seven major clades of Dryopteridaceae. …”
Get full text

Novel primers improve species delimitation in Cercospora by Mounes Bakhshi, Mahdi Arzanlou, Asadollah Babai-ahari, Johannes Z. Groenewald, Pedro W. Crous

“…The C. armoraciae s. lat. isolates are distributed over two clades, C. armoraciae s. str. and C. bizzozeriana. …”
Get full text

Fleming's penicillin producing strain is not Penicillium chrysogenum but P. rubens by J. Houbraken, J.C. Frisvad, R.A. Samson

“…Phylogenetic analysis of the most important penicillin producing P. chrysogenum isolates revealed the presence of two highly supported clades, and we show here that these two clades represent two species, P. chrysogenum and P. rubens. …”
Get full text

Using target enrichment sequencing to study the higher-level phylogeny of the largest lichen-forming fungi family: Parmeliaceae (Ascomycota) by Felix Grewe, Claudio Ametrano, Todd J. Widhelm, Steven Leavitt, Isabel Distefano, Wetchasart Polyiam, David Pizarro, Mats Wedin, Ana Crespo, Pradeep K. Divakar, H. Thorsten Lumbsch

“…We used a target enrichment data set and a qualitative selection method for 250 out of 350 genes to infer the phylogeny of the major clades in this family including 81 taxa, with both subfamilies and all seven major clades previously recognized in the subfamily Parmelioideae. …”
Get full text

Profiling Human Coronavirus Genomic Data Obtained from Patients in Belarus by M. V. Sprindzuk, A. S. Vladyko, L. P. Titov, V. I. Bernik

“…The dominant clades-clusters in Belarus and Russia are B.1 (“Basel cluster”) and B.1.1. …”
Get full text

Specialized Bacteroidetes dominate the Arctic Ocean during marine spring blooms by Álvaro Redondo-Río, Christopher J. Mundy, Javier Tamames, Carlos Pedrós-Alió

“…These specialized taxa quickly displaced the microbial clades that dominate nutrient-poor waters during early spring, such as Archaea, Alpha-and Gammaproteobacteria. …”
Get full text

Review and Phylogenetic Evaluation of Associations between Microdontinae (Diptera: Syrphidae) and Ants (Hymenoptera: Formicidae) by Menno Reemer

“…(2) Are Microdontinae associated with all ants? (3) Are particular clades of Microdontinae associated with particular clades of ants? …”
Get full text

Clarifications needed concerning the new Article 59 dealing with pleomorphic fungi by Walter Gams, Hans-Otto Baral, Walter M. Jaklitsch, Roland Kirschner, Marc Stadler

“…The new rules formulated in Article 59 of the International Code of Nomenclature for algae, fungi, and plants (ICN) will cause numerous, often undesirable, name changes, when only phylogenetically defined clades are named. Our task is to name fungal taxa and not just clades. …”
Get full text

Phylogenetic taxon definitions for Fungi, Dikarya, Ascomycota and Basidiomycota by David S. Hibbett, Meredith Blackwell, Timothy Y. James, Joseph W. Spatafora, John W. Taylor, Rytas Vilgalys

“…Abstract Phylogenetic taxon definitions (PTDs) are explicit, phylogeny-based statements that specify clades. PTDs are central to the system of rank-free classification that is governed by the PhyloCode, but they can also be used to clarify the meanings of ranked names. …”
Get full text

Ketogenic Diet‐Associated Worsening of Osteoarthritis Histologic Secerity, Increased Pain Sensitivity and Gut Microbiome Dysbiosis in Mice by Gabby Dyson, Montana Barrett, Leoni Schlupp, Emmaline Prinz, Nicholas Hannebut, Aleksander Szymczak, Cindy Miranda Brawner, Matlock A. Jeffries

“…KD induces significant gut microbiome dysbiosis in clades previously associated with murine OA.…”
Get full text

New tribe-level classification of Hypostominae (Loricariidae) based on optimization of morphological states on DNA-based relationships, with descriptions of three new tribes and tw... by Jonathan W. Armbruster, Nathan K. Lujan

“…Abstract Hypostominae tribe-level taxonomy is revised with new recognition and cladistic diagnoses of previously proposed family-level names for the Acanthicus (Acanthicini), Chaetostoma (Chaetostomatini), and Hemiancistrus (Spectracanthicini) clades. Three new tribes are described for the Peckoltia, Pseudancistrus,and ‘Pseudancistrus’ clades, with a new tribe erected for two new monotypic genera containing the sister species ‘Pseudancistrus’ sidereus and ‘P.’ pectegenitor. …”
Get full text

Comparative genomics of Aspergillus nidulans and section Nidulantes by Sebastian Theobald, Tammi Vesth, Jane L. Nybo, Jens C. Frisvad, Inge Kjærbølling, Stephen Mondo, Kurt LaButti, Sajeet Haridas, Robert Riley, Alan A. Kuo, Asaf A. Salamov, Jasmyn Pangilinan, Anna Lipzen, Maxim Koriabine, Mi Yan, Kerrie Barry, Alicia Clum, Ellen K. Lyhne, Elodie Drula, Ad Wiebenga, Astrid Müller, Ronnie J.M. Lubbers, Roland S. Kun, Ana Carolina dos Santos Gomes, Miia R. Mäkelä, Bernard Henrissat, Blake A. Simmons, Jon K. Magnuson, Jakob B. Hoof, Uffe H. Mortensen, Paul S. Dyer, Michelle Momany, Thomas O. Larsen, Igor V Grigoriev, Scott E. Baker, Ronald P. de Vries, Mikael R. Andersen

“…Whole-genome phylogeny of 34 Aspergillus species and Penicillium chrysogenum clarifies the position of clades inside section Nidulantes. Comparative genomics reveals a high genetic diversity between species with 684 up to 2433 unique protein families. …”
Get full text

Predicting climate-change impacts on the global glacier-fed stream microbiome by Massimo Bourquin, Hannes Peter, Grégoire Michoud, Susheel Bhanu Busi, Tyler J. Kohler, Andrew L. Robison, Mike Styllas, Leïla Ezzat, Aileen U. Geers, Matthias Huss, Stilianos Fodelianakis, The Vanishing Glaciers Field Team, Tom J. Battin

“…Altogether, we project a ‘greener’ future of the world’s GFSs accompanied by a loss of clades that have adapted to environmental harshness, with consequences for ecosystem functioning.…”
Get full text

Limnospira (Cyanobacteria) chemical fingerprint reveals local molecular adaptation by Théotime Roussel, Cédric Hubas, Sébastien Halary, Mathias Chynel, Charlotte Duval, Jean-Paul Cadoret, Tarik Meziane, Léa Vernès, Claude Yéprémian, Cécile Bernard, Benjamin Marie

“…Previous phylogenomic analysis of Limnospira allowed us to distinguish two major phylogenetic clades (I and II) but failed to clearly segregate strains according to their respective habitats in terms of salinity or biogeography. …”
Get full text