The article "Phylogenetic Classification and the Universal Tree" by W. Ford Doolittle discusses the construction and implications of the "universal tree of life," a hierarchical classification of all living things based on molecular phylogenetic analyses. The tree, rooted by small subunit ribosomal RNA (SSU rRNA) sequences, has been widely accepted as a representation of organismal phylogeny. However, recent studies have raised concerns about the reliability of this tree, particularly regarding deep branchings and the rooting of the tree. Methodological issues, such as mutational saturation and long-branch attraction, have been identified as sources of uncertainty. Additionally, evidence of lateral gene transfer (LGT) has shown that many genes in archaeal and bacterial genomes come from multiple sources, challenging the concept of a "natural" hierarchical classification. The article explores the implications of LGT on the conceptual basis of phylogenetic classification, suggesting that it may not be a threat to the enterprise of classification but rather a fundamental aspect of the phylogenetic process. It concludes by discussing the potential for a more flexible approach to classification that acknowledges the role of LGT and the complexity of evolutionary history.The article "Phylogenetic Classification and the Universal Tree" by W. Ford Doolittle discusses the construction and implications of the "universal tree of life," a hierarchical classification of all living things based on molecular phylogenetic analyses. The tree, rooted by small subunit ribosomal RNA (SSU rRNA) sequences, has been widely accepted as a representation of organismal phylogeny. However, recent studies have raised concerns about the reliability of this tree, particularly regarding deep branchings and the rooting of the tree. Methodological issues, such as mutational saturation and long-branch attraction, have been identified as sources of uncertainty. Additionally, evidence of lateral gene transfer (LGT) has shown that many genes in archaeal and bacterial genomes come from multiple sources, challenging the concept of a "natural" hierarchical classification. The article explores the implications of LGT on the conceptual basis of phylogenetic classification, suggesting that it may not be a threat to the enterprise of classification but rather a fundamental aspect of the phylogenetic process. It concludes by discussing the potential for a more flexible approach to classification that acknowledges the role of LGT and the complexity of evolutionary history.