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Systematic Review of Phylogenetic Analysis Techniques for RNA Viruses Using Bioinformatics.
Int J Mol Sci
February 2025
Polytechnic University of Coimbra, Rua da Misericórdia, Lagar dos Cortiços, S. Martinho do Bispo, 3045-093 Coimbra, Portugal.
The present paper addresses topics from various fields of biology. Its purpose is to enlarge the understanding of the usage of bioinformatics tools in the phylogenetic analysis of RNA viruses. The paper highlights the benefits of using information technology in virology, bringing the scientific community closer to unraveling the mysteries of RNA virus evolution and their adaptation to different niches and hosts and facilitating the understanding of their rapid mutation processes.
View Article and Find Full Text PDFFirst detection and molecular characterization of Chaphamaparvovirus galliform in broiler and turkey flocks in Türkiye.
BMC Vet Res
March 2025
Faculty of Veterinery Medicine, Department of Virology, Firat University, Elazig, 23110, Türkiye.
Background: A newly uncovered parvovirus, Chaphamaparvovirus, continues to be reported across various species. This study investigated the detection and genetic characterization of Chaphamaparvovirus galliform (GaChpV) in poultry, specifically broilers and turkeys, from various regions in Türkiye. To address this, comprehensive sampling and analysis were conducted to better understand the virus's distribution and impact in these avian populations.
View Article and Find Full Text PDFBioluminescence and repeated deep-sea colonization shaped the diversification and body size evolution of squaliform sharks.
Proc Biol Sci
March 2025
Institut des Sciences de l'Evolution de Montpellier, CNRS, IRD, EPHE, Université de Montpellier, Montpellier 34095, France.
Understanding the underlying mechanisms that have generated the striking biodiversity inhabiting deep-sea ecosystems remains a challenge in evolutionary biology. Here, we addressed this topic by studying the macroevolutionary dynamics that have shaped the diversification of squaliform sharks, an iconic clade of deep-sea vertebrates. Using phylogenetic comparative methods and fossil-based Bayesian diversification estimates, both at species level, we combined fossil record data with molecular phylogenies to provide a quantitative framework for understanding the evolutionary history of Squaliformes.
View Article and Find Full Text PDFShedding light on Pleurotus: An update on taxonomy, properties, and photobiology.
Microbiol Res
June 2025
Institute of Sciences of Food Production, National Research Council, Via Amendola 122/o, Bari 70126, Italy.
Pleurotus genus (Jacq.) P. Kumm comprises widely known edible mushrooms whose commercial and biotechnological exploitation has been steadily increasing worldwide.
View Article and Find Full Text PDFUse their names: there are no basal, lower, or early diverging fungi.
Mycologia
March 2025
Department of Biological Sciences, Evolutionary Studies Initiative, Vanderbilt University, VU Station B 35-1364, Nashville, Tennessee 37235, USA.
Fungal biologists have embraced phylogenies for understanding the biology of this diverse group in an evolutionary framework. In an attempt to highlight lineages of fungi that are distinct from the most speciose subphylum Dikarya (Ascomycota + Basidiomycota), the terms "early diverging fungi [lineages]" and "basal fungi" have been introduced, typically to refer to any phylum of fungi outside Dikarya. However, these terms are problematic, because they implicitly assume that the traits and taxa outside of Dikarya are ancestral by invoking a "ladder of progress.
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