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The Species Problem in the Genomic Era: A Review of Conceptual Debates, Microbial Challenges, and Evolving Frameworks

https://doi.org/10.2139/ssrn.5356679
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Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/mlf2.12088openalex-snapshot
Sequence‐discrete species for prokaryotes and other microbes: A historical perspective and pending issues
inferredcites →https://doi.org/10.1016/j.celrep.2024.114046openalex-snapshot
A global survey of host, aquatic, and soil microbiomes reveals shared abundance and genomic features between bacterial and fungal generalists
inferredcites →https://doi.org/10.1086/383542openalex-snapshot
The Impact of Species Concept on Biodiversity Studies
inferredcites →https://doi.org/10.1093/gbe/evx026openalex-snapshot
Biological Species Are Universal across Life’s Domains
inferredcites →https://doi.org/10.1093/nsr/nwae168openalex-snapshot
Advancements in prokaryotic systematics and the role of Bergey's International Society for Microbial Systematicsin addressing challenges in the meta-data era
inferredcites →https://doi.org/10.1093/sysbio/syw117openalex-snapshot
Species Delimitation with Gene Flow
inferredcites →https://doi.org/10.1111/1755-0998.13444openalex-snapshot
Opening a next‐generation black box: Ecological trends for hundreds of species‐like taxa uncovered within a single bacterial >99% 16S rRNA operational taxonomic unit
inferredcites →https://doi.org/10.1111/brv.12676openalex-snapshot
A paradigm shift in our view of species drives current trends in biological classification
inferredcites →https://doi.org/10.1111/cobi.13454openalex-snapshot
A framework for evaluating the impact of the IUCN Red List of threatened species
inferredcites →https://doi.org/10.1111/csp2.12809openalex-snapshot
Conservation of rare and cryptic species: Challenges of uncertainty and opportunities for progress
inferredcites →https://doi.org/10.1111/j.1463-6409.2008.00381.xopenalex-snapshot
Deciphering the products of evolution at the species level: the need for an integrative taxonomy
inferredcites →https://doi.org/10.1111/mam.12121openalex-snapshot
Mammals and meaningful taxonomic units: the debate about species concepts and conservation
inferredcites →https://doi.org/10.1111/mec.14486openalex-snapshot
Cryptic species as a window into the paradigm shift of the species concept
inferredcites →https://doi.org/10.1128/msystems.00731-19openalex-snapshot
Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries
inferredcites →https://doi.org/10.1146/annurev-genet-110711-155529openalex-snapshot
Evolutionary Implications of Horizontal Gene Transfer
inferredcites →https://doi.org/10.1146/annurev.ecolsys.35.112202.130128openalex-snapshot
Operational Criteria for Delimiting Species
inferredcites →https://doi.org/10.12688/wellcomeopenres.21143.1openalex-snapshot
A DNA barcoding framework for taxonomic verification in the Darwin Tree of Life Project
inferredcites →https://doi.org/10.1371/journal.pone.0280870openalex-snapshot
Reliability of species detection in 16S microbiome analysis: Comparison of five widely used pipelines and recommendations for a more standardized approach
inferredcites →https://doi.org/10.3389/fcimb.2022.977591openalex-snapshot
Metagenomic next-generation sequencing indicates more precise pathogens in patients with pulmonary infection: A retrospective study
inferredcites →https://doi.org/10.3389/fmicb.2020.01569openalex-snapshot
Horizontal Gene Transfer as a Source of Conflict and Cooperation in Prokaryotes
inferredcites →https://doi.org/10.3390/genes11070756openalex-snapshot
ShadowCaster: Compositional Methods under the Shadow of Phylogenetic Models to Detect Horizontal Gene Transfers in Prokaryotes
inferredcites →https://doi.org/10.3390/jof7090703openalex-snapshot
Current Insight into Culture-Dependent and Culture-Independent Methods in Discovering Ascomycetous Taxa
inferredcites →https://doi.org/10.3897/biss.7.111135openalex-snapshot
Genome Taxonomy Database and SeqCode: Microbial Taxonomy and Nomenclature in the Age of Big Sequence Data
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