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.…”
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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. …”
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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. …”
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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.…”
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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. …”
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Convergent evidence for the temperature-dependent emergence of silicification in terrestrial plants by Zhihao Pang, Félix de Tombeur, Sue E. Hartley, Constantin M. Zohner, Miroslav Nikolic, Cyrille Violle, Lidong Mo, Thomas W. Crowther, Dong-Xing Guan, Zhongkui Luo, Yong-Guan Zhu, Yuxiao Wang, Ping Zhang, Hongyun Peng, Caroline A. E. Strömberg, Nina Nikolic, Yongchao Liang

“…We then find that, globally, the average distribution temperature of high-Si plant clades is 1.2 °C higher than that of low-Si clades. …”
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Genomic epidemiology and antimicrobial resistance of Morganella clinical isolates between 2016 and 2023 by Wentao Zhu, Qian Liu, Jinlv Liu, Jinlv Liu, Yaqi Wang, Yaqi Wang, Hong Shen, Ming Wei, Ji Pu, Li Gu, Jing Yang, Jing Yang, Jing Yang

“…Phylogenomic analysis revealed that the 102 M. morganii isolates fell into six clades, with clades 4-6 making up the majority. Core genome multi-locus sequence type analysis indicted high genomic diversity among different hosts and relatively stability (< 10 SNPs accumulated over three years) within the same host. …”
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Cryptic species in lichen-forming fungi by A. Crespo, T.H. Lumbsch

“…In several cases, a re-examination of morphology against the background of molecular phylogenetic evidence revealed, sometimes subtle, morphological and/or chemical characters, supporting the distinction of particular clades at species level. However, there are also examples of cryptic species in which no morphological characters could be identified to distinguish between lineages. …”
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Genomic analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains isolated in Malaysia by Hooi-Leng Ser, Loh Teng-Hern Tan, Jodi Woan-Fei Law, Vengadesh Letchumanan, Nurul-Syakima Ab Mutalib, Learn-Han Lee

“… Using seven complete genomes of human SARS-CoV-2 (retrieved from GISAID) isolated in Malaysia for phylogenetic tree construction, the current study showed that these strains formed four distinct clades when compared with other representative strains from Asia, Europe and US. …”
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New information on insect nematodes from Iran: report of Distolabrellus veechi (Nematoda: Mesorhabditidae) as new species and male of Oscheius tipulae (Nematoda: Rhabditidae) by Parissa Jalalinasab, Ramin Heydari, Reza Talaei-Hassanloui, Ebrahim Shokoohi, Javad Karimi

“…The phylogenetic analyses placed these nematodes within their respective clades with high bootstrap support, confirming their identity. …”
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Protocol for a phase IV double-blind randomised controlled trial to investigate the effect of the 13-valent pneumococcal conjugate vaccine and the 23-valent pneumococcal polysaccha... by Tao Chen, Duolao Wang, Konstantinos Liatsikos, Stephen B Gordon, Hassan Burhan, Ben Morton, Tinashe K Nyazika, Bradford D Gessner, Helen Hill, Andrea Collins, Josh Hamilton, Kelly Davies, Fred Fyles, Phoebe Hazenberg, Elizabeth Begier, Angela Hyder-Wright, Sherin Pojar, Christopher Myerscough, Jesus Reine, Ryan E Robinson, Britta Urban, Elena Mitsi, Carla Solorzano, Angela Quinn, Kaijie Pan, Annaliesa S Anderson, Christian Theilacker, Daniela M Ferreira, Kelly Convey, James Court, Madlen Farrar, Lisa Hitchins, Ashleigh Howard, Lauren Kerruish, Samuel Latham, Annabel Murphy, Elissavet Nikolaou, Angelina Peterson

“…Participants randomised to PCV13 and placebo will also be randomised to one of two clinically relevant SPN3 strains from distinct lineages within clonal complex 180, clades Ia and II, creating five study groups. Following inoculation, participants will be seen on days 2, 7, 14 and 23. …”
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The trend of phylogenetic and epitope variations of SARS-CoV-2 Omicron sub-lineages in Iran by Mehdi Shabani, Ahmad Nejati, Jila Yavarian, Jila Yavarian, Kaveh Sadeghi, Sevrin Zadheidar, Akram Sadat Ahmadi, Monire Ghadirali, Arghavan Zebardast, Adel Abedi, Mohammad Hossein Najmi, Nazanin-Zahra Shafiei-Jandaghi, Talat Mokhtari-Azad

“…CD4+), protein (higher for non-spike vs. spike), and clades (higher for 21L, 22F, 23B, 23H, 23D, and 24B vs. 24A and 24C).ConclusionHerein, the increased conservation of CD8+ epitopes compared to CD4+ and B cell epitopes is probably attributable to the shorter length of the peptides associated with CD8+ epitopes. …”
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Deep cryptic diversity in the Craugastor podiciferus Species Group (Anura: Craugastoridae) of Isthmian Central America revealed by mitochondrial and nuclear data by Erick Arias, Andrew J. Crawford, Andreas Hertz, Gabriela Parra Olea

“…Molecular phylogenetic analyses showed that the group contains four major clades. All currently named species are supported by molecular data, yet species richness within the group is clearly underestimated. …”
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Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota) by Claudio G. Ametrano, Felix Grewe, Pedro W. Crous, Stephen B. Goodwin, Chen Liang, Laura Selbmann, H. Thorsten Lumbsch, Steven D. Leavitt, Lucia Muggia

“…Previous multilocus studies have investigated the taxonomic and evolutionary relationships of these taxa but often failed to resolve early diverging nodes and frequently generated inconsistent placements of some clades. Here, we use a phylogenomic approach to resolve relationships in Dothideomycetes, focusing on two genera of melanized, extremotolerant rock-inhabiting fungi, Lichenothelia and Saxomyces, that have been suggested to be early diverging lineages. …”
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New insights into the phylogeny and infrageneric taxonomy of Saussurea based on hybrid capture phylogenomics (Hyb-Seq) by Liansheng Xu, Zhuqiu Song, Tian Li, Zichao Jin, Buyun Zhang, Siyi Du, Shuyuan Liao, Xingjie Zhong, Yousheng Chen

“…For the first time, we recovered a well-resolved nuclear phylogeny of Saussurea consisting of four main clades, which was also supported by morphological data. …”
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Cryo-EM structure and evolutionary history of the conjugation surface exclusion protein TraT by Chloe Seddon, Sophia David, Joshua L. C. Wong, Naito Ishimoto, Shan He, Jonathan Bradshaw, Wen Wen Low, Gad Frankel, Konstantinos Beis

“…Plasmid-associated TraT sequences are found in multiple distinct lineages, including two separate clades incorporating TraT from Enterobacteriaceae IncF/F-like and Legionellaceae F-like plasmids. …”
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Genetic Diversity in Passiflora Species Assessed by Morphological and ITS Sequence Analysis by Shiamala Devi Ramaiya, Japar Sidik Bujang, Muta Harah Zakaria

“…The final dataset of aligned sequences from nine studied Passiflora accessions and 30 other individuals obtained from GenBank database (NCBI) yielded one most parsimonious tree with two strongly supported clades. Maximum parsimony (MP) tree showed the phylogenetic relationships within this subgenus Passiflora support the classification at the series level. …”
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Mitogenomic Phylogenetic Analyses Reveal New Insights into the Taxonomy and Evolution of Parnassiinae Swallowtail Butterflies (Lepidoptera: Papilionidae) by Lu Song, Xiaoxiao Chen, Xiushan Li, Raul Narciso C. Guedes, Youssef Dewer, Suqin Shang, Jingjiang Zhou

“…Phylogenetic analyses based on both the 13 PCGs and the complete set of 37 mitochondrial genes supported the placement of Parnassiinae as a subfamily within Papilionidae, with Parnassini and Zerynthini identified as two distinct clades within Parnassiinae. Notably, tree topologies derived from the 13 PCGs alone exhibited slight deviations from those based on the full mitogenome, underscoring the need for expanded mitogenomic data across Papilionidae to further refine evolutionary relationships.…”
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Exploring the recombinant evolution and hosts of crucivirus based on novel oyster-associated viruses by Hong-Sai Zhang, Hong-Sai Zhang, Chang Liu, Guang-Feng Liu, Yu-Yu Chen, Peng Zhu, Peng Zhu, Xin Xu, Bing-Xin Yin, Jing-Zhe Jiang, Jing-Zhe Jiang

“…The results indicate that the crucivirus genomes and replicase-associated proteins (Rep) from oysters conform to the typical characteristics of crucivirus; Crucivirus Rep appears to have a direct parallel origin from multiple clades of CRESS DNA viruses, while only the S-domain of their capsid proteins shows some evolutionary relationship with tombusvirus. …”
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A novel isothermal whole genome sequencing approach for Monkeypox Virus by Matthias Licheri, Manon Flore Licheri, Lukas Probst, Cora Sägesser, Pascal Bittel, Franziska Suter-Riniker, Ronald Dijkman

“…The latter allows multiplexing due to the efficient enrichment of the viral DNA, however, mutations or the presence of different clades can negatively influence genome coverage yield. …”
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