BackgroundThis paper is a comment on the idea of matrix-free Cladistics. Demonstration of this idea’s efficiency is a major goal of the study. Within the proposed framework, the ordinary (phenetic) matrix is necessary only as “source” of Hennigian trees, not as a primary subject of the analysis. Switching from the matrix-based thinking to the matrix-free Cladistic approach clearly reveals that optimizations of the character-state changes are related not to the real processes, but to the form of the data representation.MethodsWe focused our study on the binary data. We wrote the simple ruby-based script FORESTER version 1.0 that helps represent a binary matrix as an array of the rooted trees (as a “Hennigian forest”). The binary representations of the genomic (DNA) data have been made by script 1001. The Average Consensus method as well as the standard Maximum Parsimony (MP) approach has been used to analyze the data.Principle findingsThe binary matrix may be easily re-written as a set of rooted trees (maximal relationships). The latter might be analyzed by the Average Consensus method. Paradoxically, this method, if applied to the Hennigian forests, in principle can help to identify clades despite the absence of the direct evidence from the primary data. Our approach may handle the clock- or non clock-like matrices, as well as the hypothetical, molecular or morphological data.DiscussionOur proposal clearly differs from the numerous phenetic alignment-free techniques of the construction of the phylogenetic trees. Dealing with the relations, not with the actual “data” also distinguishes our approach from all optimization-based methods, if the optimization is defined as a way to reconstruct the sequences of the character-state changes on a tree, either the standard alignment-based techniques or the “direct” alignment-free procedure. We are not viewing our recent framework as an alternative to the three-taxon statement analysis (3TA), but there are two major differences between our recent proposal and the 3TA, as originally designed and implemented: (1) the 3TA deals with the three-taxon statements or minimal relationships. According to the logic of 3TA, the set of the minimal trees must be established as a binary matrix and used as an input for the parsimony program. In this paper, we operate directly with maximal relationships written just as trees, not as binary matrices, while also using the Average Consensus method instead of the MP analysis. The solely ‘reversal’-based groups can always be found by our method without the separate scoring of the putative reversals before analyses.

Coronaviruses are highly pathogenic and therefore important human and veterinary pathogens viruses worldwide. This study is the first that produced phylogenies based on all 39 species of Coronaviridae recognized by the Coronaviridae Study Group and International Committee on Taxonomy of Viruses and has, uniquely, used several methods of cladistic analysis in combination with the Maximum Likelihood method. Resultant trees were utilized to test for monophyly of all available non-monotypic genera and infrageneric taxa of Coronaviridae. Monophyly was confirmed, thereby validating they are representative of a nature hierarchy. This study therefore presents the first natural hierarchical classification of Coronaviridae and the most accurate taxonomic representation of Coronaviridae’s relationships to date. The authors additionally seek at add to the current discussion regarding the nomenclature of viruses, demonstrating and supporting a “one-step” solution to incorporate the principles of binary nomenclature into Coronaviridae, which will aid future recognition of numerous virus species, particularly in currently monotypic subgenus Sarbecovirus. Commenting on the nature of SARS-CoV-2, the authors emphasize that no member of the Sarbecovirus clade is an ancestor of this virus, and humans are the only natural known host.

Coronaviruses are highly virulent and therefore important human and veterinary pathogens worldwide. This study presents the first natural hierarchical classification of Coronaviridae. We also demonstrate a “one-step” solution to incorporate the principles of binomial (binary) nomenclature into taxonomy of Coronaviridae. We strongly support the complete rejection of the non-taxonomic category “virus” in any future taxonomic study in virology. This will aid future recognition of numerous virus species, particularly in the currently monotypic subgenus Sarbecovirus. Commenting on the nature of SARS-CoV-2, the authors emphasize that no member of the Sarbecovirus clade is an ancestor of this virus, and humans are the only natural known host.

Recently Ulloa Ulloa et al. (2017) published a 2600-page online checklist of the New World vascular plants (the Checklist hereafter) that includes 124,993 species, 6227 genera, and 355 families associated with incomplete elementary taxonomy as well as with the distributional data provided for every species (Ulloa Ulloa et al., 2017). Givnish (2017) heralds their publically searchable database as “… a monumental achievement that will be of enormous interest to conservation biologists, ecologists, evolutionary biologists, biogeographers, land managers, and governmental officials around the world” (Givnish, 2017: 1535). Although land managers and governmental officials may indeed find the massive new Checklist useful, its utility for scientific pursuits so far is less obvious.