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1. An ANI gap within bacterial species that advances the definitions of intra-species units

   https://doi.org/10.1128/mbio.02696-23  

   Rodriguez-R, Luis M; Conrad, Roth E; Viver, Tomeu; Feistel, Dorian J; Lindner, Blake G; Venter, Stephanus N; Orellana, Luis H; Amann, Rudolf; Rossello-Mora, Ramon; Konstantinidis, Konstantinos T (January 2024, mBio)

   Jouline, Igor B (Ed.)

   ABSTRACT Large-scale surveys of prokaryotic communities (metagenomes), as well as isolate genomes, have revealed that their diversity is predominantly organized in sequence-discrete units that may be equated to species. Specifically, genomes of the same species commonly show genome-aggregate average nucleotide identity (ANI) >95% among themselves and ANI <90% to members of other species, while genomes showing ANI 90%–95% are comparatively rare. However, it remains unclear if such “discontinuities” or gaps in ANI values can be observed within species and thus used to advance and standardize intra-species units. By analyzing 18,123 complete isolate genomes from 330 bacterial species with at least 10 genome representatives each and available long-read metagenomes, we show that another discontinuity exists between 99.2% and 99.8% (midpoint 99.5%) ANI in most of these species. The 99.5% ANI threshold is largely consistent with how sequence types have been defined in previous epidemiological studies but provides clusters with ~20% higher accuracy in terms of evolutionary and gene-content relatedness of the grouped genomes, while strains should be consequently defined at higher ANI values (>99.99% proposed). Collectively, our results should facilitate future micro-diversity studies across clinical or environmental settings because they provide a more natural definition of intra-species units of diversity. IMPORTANCEBacterial strains and clonal complexes are two cornerstone concepts for microbiology that remain loosely defined, which confuses communication and research. Here we identify a natural gap in genome sequence comparisons among isolate genomes of all well-sequenced species that has gone unnoticed so far and could be used to more accurately and precisely define these and related concepts compared to current methods. These findings advance the molecular toolbox for accurately delineating and following the important units of diversity within prokaryotic species and thus should greatly facilitate future epidemiological and micro-diversity studies across clinical and environmental settings. 

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2. Could a Focus on the “Why” of Taxonomy Help Taxonomy Better Respond to the Needs of Science and Society?

   https://doi.org/10.3389/fmicb.2022.887310  

   Pritchard, Leighton; Brown, C. Titus; Harrington, Bailey; Heath, Lenwood S.; Pierce-Ward, N. Tessa; Vinatzer, Boris A. (May 2022, Frontiers in Microbiology)

   Genomics has put prokaryotic rank-based taxonomy on a solid phylogenetic foundation. However, most taxonomic ranks were set long before the advent of DNA sequencing and genomics. In this concept paper, we thus ask the following question: should prokaryotic classification schemes besides the current phylum-to-species ranks be explored, developed, and incorporated into scientific discourse? Could such alternative schemes provide better solutions to the basic need of science and society for which taxonomy was developed, namely, precise and meaningful identification? A neutral genome-similarity based framework is then described that could allow alternative classification schemes to be explored, compared, and translated into each other without having to choose only one as the gold standard. Classification schemes could thus continue to evolve and be selected according to their benefits and based on how well they fulfill the need for prokaryotic identification. 

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3. Phylogenomic investigation of lampreys (Petromyzontiformes)

   https://doi.org/10.1016/j.ympev.2023.107942  

   Smith, Brianna; Walling, Alexandra; Schwartz, Rachel (December 2023, Molecular Phylogenetics and Evolution)

   The history of lamprey evolution has been contentious due to limited morphological differentiation and limited genetic data. Available data has produced inconsistent results, including in the relationship among northern and southern species and the monophyly of putative clades. Here we use whole genome sequence data sourced from a public database to identify orthologs for 11 lamprey species from across the globe and build phylogenies. The phylogeny showed a clear separation between northern and southern lamprey species, which contrasts with some prior work. We also find that the phylogenetic relationships of our samples of two genera, Lethenteron and Eudontomyzon, deviate from the taxonomic classification of these species, suggesting that they require reclassification. 

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4. Extensive paraphyly in the typical owl family (Strigidae)

   https://doi.org/10.1093/auk/ukz070  

   Salter, Jessie F.; Oliveros, Carl H.; Hosner, Peter A.; Manthey, Joseph D.; Robbins, Mark B.; Moyle, Robert G.; Brumfield, Robb T.; Faircloth, Brant C. (December 2019, The Auk)

   Abstract The typical owl family (Strigidae) comprises 194 species in 28 genera, 14 of which are monotypic. Relationships within and among genera in the typical owls have been challenging to discern because mitochondrial data have produced equivocal results and because many monotypic genera have been omitted from previous molecular analyses. Here, we collected and analyzed DNA sequences of ultraconserved elements (UCEs) from 43 species of typical owls to produce concatenated and multispecies coalescent-based phylogenetic hypotheses for all but one genus in the typical owl family. Our results reveal extensive paraphyly of taxonomic groups across phylogenies inferred using different analytical approaches and suggest the genera Athene, Otus, Asio, Megascops, Bubo, and Strix are paraphyletic, whereas Ninox and Glaucidium are polyphyletic. Secondary analyses of protein-coding mitochondrial genes harvested from off-target sequencing reads and mitochondrial genomes downloaded from GenBank generally support the extent of paraphyly we observe, although some disagreements exist at higher taxonomic levels between our nuclear and mitochondrial phylogenetic hypotheses. Overall, our results demonstrate the importance of taxon sampling for understanding and describing evolutionary relationships in this group, as well as the need for additional sampling, study, and taxonomic revision of typical owl species. Additionally, our findings highlight how both divergence and convergence in morphological characters have obscured our understanding of the evolutionary history of typical owls, particularly those with insular distributions. 

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5. A natural ANI gap that can define intra-species units of bacteriophages and other viruses

   https://doi.org/10.1128/mbio.01536-24  

   Aldeguer-Riquelme, Borja; Conrad, Roth E; Antón, Josefa; Rossello-Mora, Ramon; Konstantinidis, Konstantinos T (August 2024, mBio)

   Cooper, Vaughn S (Ed.)

   ABSTRACT Despite the importance of intra-species variants of viruses for causing disease and/or disrupting ecosystem functioning, there is no universally applicable standard to define these. A (natural) gap in whole-genome average nucleotide identity (ANI) values around 95% is commonly used to define species, especially for bacteriophages, but whether a similar gap exists within species that can be used to define intra-species units has not been evaluated yet. Whole-genome comparisons among members of 1,016 bacteriophage (Caudoviricetes) species revealed a region of low frequency of ANI values around 99.2%–99.8%, showing threefold or fewer pairs than expected for an even distribution. This second gap is prevalent in viruses infecting various cultured or uncultured hosts from a variety of environments, although a few exceptions to this pattern were also observed (3.7% of total species) and are likely attributed to cultivation biases or other factors. Similar results were observed for a limited set of eukaryotic viruses that are adequately sampled, including SARS-CoV-2, whose ANI-based clusters matched well with the WHO-defined variants of concern, indicating that our findings from bacteriophages might be more broadly applicable and the ANI-based clusters may represent functionally and/or ecologically distinct units. These units appear to be predominantly driven by (high) ecological cohesiveness coupled to either frequent recombination for bacteriophages or selection and clonal evolution for other viruses such as SARS-CoV-2, indicating that fundamentally different underlying mechanisms could lead to similar diversity patterns. Accordingly, we propose the ANI gap approach outlined above for defining viral intra-species units, for which we propose the term genomovars. IMPORTANCEViral species are composed of an ensemble of intra-species variants whose individual dynamics may have major implications for human and animal health and/or ecosystem functioning. However, the lack of universally accepted standards to define these intra-species variants has led researchers to use different approaches for this task, creating inconsistent intra-species units across different viral families and confusion in communication. By comparing hundreds of mostly bacteriophage genomes, we show that there is a widely distributed natural gap in whole-genome average nucleotide identity values in most, but not all, of these species that can be used to define intra-species units. Therefore, these results advance the molecular toolbox for tracking viral intra-species units and should facilitate future epidemiological and environmental studies. 

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