Caetano-Anollés Gustavo, Claverie Jean-Michel, Nasir Arshan
Evolutionary Bioinformatics Laboratory, Department of Crop Sciences and C.R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States.
Structural and Genomic Information Laboratory (UMR7256), Mediterranean Institute of Microbiology (FR3479), IM2B, IOM, Aix Marseille University, CNRS, Marseille, France.
Front Microbiol. 2023 Aug 3;14:1240993. doi: 10.3389/fmicb.2023.1240993. eCollection 2023.
Taxonomical classification has preceded evolutionary understanding. For that reason, taxonomy has become a battleground fueled by knowledge gaps, technical limitations, and . Here we assess the current state of the challenging field, focusing on fallacies that are common in viral classification. We emphasize that viruses are crucial contributors to the genomic and functional makeup of holobionts, organismal communities that behave as units of biological organization. Consequently, viruses cannot be considered taxonomic units because they challenge crucial concepts of organismality and individuality. Instead, they should be considered processes that integrate virions and their hosts into life cycles. Viruses harbor phylogenetic signatures of genetic transfer that compromise monophyly and the validity of deep taxonomic ranks. A focus on building phylogenetic networks using alignment-free methodologies and molecular structure can help mitigate the impasse, at least in part. Finally, structural phylogenomic analysis challenges the polyphyletic scenario of multiple viral origins adopted by virus taxonomy, defeating a polyphyletic origin and supporting instead an ancient cellular origin of viruses. We therefore, prompt abandoning deep ranks and urgently reevaluating the validity of taxonomic units and principles of virus classification.
分类学分类先于进化理解。因此，分类学已成为一个由知识空白、技术限制等因素引发争议的领域。在此，我们评估这一具有挑战性领域的当前状况，重点关注病毒分类中常见的谬误。我们强调，病毒是全生物（作为生物组织单位的生物群落）基因组和功能构成的关键贡献者。因此，病毒不能被视为分类单元，因为它们挑战了生物个体性和独特性的关键概念。相反，它们应被视为将病毒粒子及其宿主整合到生命周期中的过程。病毒具有基因转移的系统发育特征，这损害了单系性以及深层分类等级的有效性。至少在一定程度上，关注使用无序列比对方法和分子结构构建系统发育网络有助于缓解这一僵局。最后，结构系统发育基因组学分析挑战了病毒分类学所采用的多种病毒起源的多系进化模式，否定了多系起源，转而支持病毒起源于古老细胞的观点。因此，我们敦促摒弃深层分类等级，并迫切重新评估病毒分类单元的有效性和分类原则。
