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Compensatory Base Changes in ITS2 Secondary Structures Correlate with the Biological Species Concept Despite Intragenomic Variability in ITS2 Sequences – A Proof of Concept

https://doi.org/10.1371/journal.pone.0066726
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1006/jmbi.1999.2700openalex-snapshot
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
inferredcites →https://doi.org/10.1007/pl00006143openalex-snapshot
The Internal Transcribed Spacer 2 Exhibits a Common Secondary Structure in Green Algae and Flowering Plants
inferredcites →https://doi.org/10.1007/s00239-001-0006-0openalex-snapshot
Exploring the Phylogenetic Utility of ITS Sequences for Animals: A Test Case for Abalone (Haliotis)
inferredcites →https://doi.org/10.1016/j.gene.2008.10.012openalex-snapshot
5.8S-28S rRNA interaction and HMM-based ITS2 annotation
inferredcites →https://doi.org/10.1016/j.ympev.2008.10.008openalex-snapshot
Is there a molecular key to the level of “biological species” in eukaryotes? A DNA guide
inferredcites →https://doi.org/10.1016/j.ympev.2011.08.019openalex-snapshot
Corrigendum to “Is there a molecular key to the level of “biological species” in eukaryotes? A DNA guide” [Mol. Phylogenet. Evol. 50 (2009) 197–203]
inferredcites →https://doi.org/10.1016/j.ympev.2012.01.026openalex-snapshot
ITS2 Database IV: Interactive taxon sampling for internal transcribed spacer 2 based phylogenies
inferredcites →https://doi.org/10.1016/s0168-9525(03)00118-5openalex-snapshot
ITS2 is a double-edged tool for eukaryote evolutionary comparisons
inferredcites →https://doi.org/10.1016/s1055-7903(03)00208-2openalex-snapshot
Ribosomal ITS sequences and plant phylogenetic inference
inferredcites →https://doi.org/10.1073/pnas.1104551108openalex-snapshot
Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants
inferredcites →https://doi.org/10.1073/pnas.1117018109openalex-snapshot
Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi
inferredcites →https://doi.org/10.1078/1434-4610-00002openalex-snapshot
The Significance of a Coincidence between Evolutionary Landmarks Found in Mating Affinity and a DNA Sequence
inferredcites →https://doi.org/10.1093/nar/27.23.4533openalex-snapshot
Ribosomal internal transcribed spacer 2 (ITS2) exhibits a common core of secondary structure in vertebrates and yeast
inferredcites →https://doi.org/10.1093/nar/gkl129openalex-snapshot
The internal transcribed spacer 2 database--a web server for (not only) low level phylogenetic analyses
inferredcites →https://doi.org/10.1093/nar/gkm233openalex-snapshot
Pan-eukaryote ITS2 homologies revealed by RNA secondary structure
inferredcites →https://doi.org/10.1093/nar/gkm827openalex-snapshot
The ITS2 Database II: homology modelling RNA structure for molecular systematics
inferredcites →https://doi.org/10.1093/nar/gkp966openalex-snapshot
The ITS2 Database III—sequences and structures for phylogeny
inferredcites →https://doi.org/10.1111/j.1755-0998.2008.02199.xopenalex-snapshot
Modelling cross‐hybridization on phylogenetic DNA microarrays increases the detection power of closely related species
inferredcites →https://doi.org/10.1128/mmbr.58.1.10-26.1994openalex-snapshot
Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective
inferredcites →https://doi.org/10.1186/1471-2105-7-498openalex-snapshot
4SALE – A tool for synchronous RNA sequence and secondary structure alignment and editing
inferredcites →https://doi.org/10.1186/1745-6150-5-4openalex-snapshot
Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees
inferredcites →https://doi.org/10.1186/1756-0500-1-91openalex-snapshot
Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE
inferredcites →https://doi.org/10.1261/rna.2144205openalex-snapshot
Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures
inferredcites →https://doi.org/10.1261/rna.617107openalex-snapshot
Distinguishing species
inferredcites →https://doi.org/10.1261/rna.7204505openalex-snapshot
A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota
inferredcites →https://doi.org/10.1371/journal.pone.0008613openalex-snapshot
Validation of the ITS2 Region as a Novel DNA Barcode for Identifying Medicinal Plant Species
inferredcites →https://doi.org/10.1371/journal.pone.0013102openalex-snapshot
Use of ITS2 Region as the Universal DNA Barcode for Plants and Animals
inferredcites →https://doi.org/10.1371/journal.pone.0016931openalex-snapshot
Internal Transcribed Spacer 2 (nu ITS2 rRNA) Sequence-Structure Phylogenetics: Towards an Automated Reconstruction of the Green Algal Tree of Life
inferredcites →https://doi.org/10.1371/journal.pone.0043971openalex-snapshot
Extensive Pyrosequencing Reveals Frequent Intra-Genomic Variations of Internal Transcribed Spacer Regions of Nuclear Ribosomal DNA
inferredcites →https://doi.org/10.3410/f.1163590.625341openalex-snapshot
Faculty Opinions recommendation of Is there a molecular key to the level of "biological species" in eukaryotes? A DNA guide.
inferredcites →https://doi.org/10.3791/3806openalex-snapshot
The ITS2 Database
inferredcites →https://doi.org/10.5479/sil.262971.39088000323931openalex-snapshot
Jacobi Bernoulli profess. basil. & utriusque societ. ... Ars conjectandi, opus posthumum : accedit Tractatus de seriebus infinitis, et epistola Gallice scripta de ludo pilæ reticularis

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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ITS2 and 18S rDNA sequence-structure phylogeny of Chlorella and allies (Chlorophyta, Trebouxiophyceae, Chlorellaceae)
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DNA Analysis of Algal Endosymbionts of Ciliates Reveals the State of Algal Integration and the Surprising Specificity of the Symbiosis
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Phylogenetic classification and generic delineation ofCalyptosphaeriagen. nov.,Lentomitella,SpadicoidesandTorrentispora(Sordariomycetes)
inferred← citeshttps://doi.org/10.1016/j.tig.2015.02.005openalex-snapshot
ITS so much more
inferred← citeshttps://doi.org/10.1016/j.ympev.2014.06.015openalex-snapshot
Gorgonia mariae and Antillogorgia bipinnata populations inferred from compensatory base change analysis of the internal transcribed spacer 2
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Molecular phylogeny and species delimitation within the ciliate genus Spirostomum (Ciliophora, Postciliodesmatophora, Heterotrichea), using the internal transcribed spacer region
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.08.014openalex-snapshot
A consensus secondary structure of ITS2 for the diatom Order Cymatosirales (Mediophyceae, Bacillariophyta) and reappraisal of the order based on DNA, morphology, and reproduction
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Untangling a mess of worms: Species delimitations reveal morphological crypsis and variability in Southeast Asian semi-aquatic earthworms (Almidae, Glyphidrilus)
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A genomics approach reveals the global genetic polymorphism, structure, and functional diversity of ten accessions of the marine model diatom Phaeodactylum tricornutum
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Pediludiella daitoensis gen. et sp. nov. (Scenedesmaceae, Chlorophyceae), a large coccoid green alga isolated from a Loxodes ciliate
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Parasites specific to centipedes form a new major lineage of terrestrial gregarines
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Integrative taxonomy of the Pseudo-nitzschia (Bacillariophyceae) populations in the NW Adriatic Sea, with a focus on a novel cryptic species in the P. delicatissima species complex
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A new mesophilic isolate of Pleurastrosarcina , a genus previously only reported from arid habitats
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DNA-based species delimitation in algae
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Lunachloris lukesovae gen. et sp. nov. (Trebouxiophyceae, Chlorophyta), a novel coccoid green alga isolated from soil in South Bohemia, Czech Republic
inferred← citeshttps://doi.org/10.1080/09670262.2017.1386328openalex-snapshot
Biecheleria tirezensis sp. nov. (Dinophyceae, Suessiales), a new halotolerant dinoflagellate species isolated from the athalassohaline Tirez natural pond in Spain
inferred← citeshttps://doi.org/10.1080/09670262.2018.1475015openalex-snapshot
Species distinctions among closely related strains of Eustigmatophyceae (Stramenopiles) emphasizing ITS2 sequence-structure data: Eustigmatos and Vischeria
inferred← citeshttps://doi.org/10.1080/09670262.2018.1558286openalex-snapshot
Desmodesmus tropicus (Chlorophyta) in the Danube Delta – reassessing the phylogeny of the series Maximi
inferred← citeshttps://doi.org/10.1080/09670262.2019.1681519openalex-snapshot
Overlooked diversity with terrestrial lifestyle in the predominantly freshwater and snow phylogroup Chloromonadinia (Volvocales, Chlorophyceae)
inferred← citeshttps://doi.org/10.1080/09670262.2022.2076291openalex-snapshot
Hidden diversity of Chlorococcum (Chlorophyta) in a shallow temporary freshwater lake: description of Chlorococcum szentendrense sp. nov
inferred← citeshttps://doi.org/10.1080/13880209.2018.1499780openalex-snapshot
Phylogenetic analysis of Uncaria species based on internal transcribed spacer (ITS) region and ITS2 secondary structure
inferred← citeshttps://doi.org/10.1093/aob/mcz062openalex-snapshot
Alternative analyses of compensatory base changes in an ITS2 phylogeny of Corydalis (Papaveraceae)
inferred← citeshttps://doi.org/10.1093/botlinnean/boz031openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/femsec/fiw122openalex-snapshot
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inferred← citeshttps://doi.org/10.1094/pdis-05-21-0951-reopenalex-snapshot
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inferred← citeshttps://doi.org/10.1099/ijsem.0.002595openalex-snapshot
Chloromonas arctica sp. nov., a psychrotolerant alga from snow in the High Arctic (Chlamydomonadales, Chlorophyta)
inferred← citeshttps://doi.org/10.1101/176008openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/1755-0998.12325openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/1755-0998.13586openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/jeu.12633openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/jpy.12313openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/jpy.12903openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/jpy.12991openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/jpy.13183openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/jpy.13307openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/jpy.13438openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/jpy.70108openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/pre.12194openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/pre.70008openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/zsc.12528openalex-snapshot
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inferred← citeshttps://doi.org/10.1186/s12862-015-0325-1openalex-snapshot
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inferred← citeshttps://doi.org/10.1186/s12915-022-01263-wopenalex-snapshot
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inferred← citeshttps://doi.org/10.1261/rna.072660.119openalex-snapshot
Adenine·cytosine substitutions are an alternative pathway of compensatory mutation in angiosperm ITS2
inferred← citeshttps://doi.org/10.1371/journal.pone.0089769openalex-snapshot
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inferred← citeshttps://doi.org/10.1371/journal.pone.0094297openalex-snapshot
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inferred← citeshttps://doi.org/10.1371/journal.pone.0103003openalex-snapshot
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inferred← citeshttps://doi.org/10.1371/journal.pone.0149284openalex-snapshot
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inferred← citeshttps://doi.org/10.1371/journal.pone.0181491openalex-snapshot
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inferred← citeshttps://doi.org/10.1371/journal.pone.0201240openalex-snapshot
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inferred← citeshttps://doi.org/10.1371/journal.pone.0231902openalex-snapshot
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inferred← citeshttps://doi.org/10.1371/journal.pone.0283847openalex-snapshot
Characterizing nrDNA ITS1, 5.8S and ITS2 secondary structures and their phylogenetic utility in the legume tribe Hedysareae with special reference to Hedysarum
inferred← citeshttps://doi.org/10.1515/bot-2024-0039openalex-snapshot
Genus Proteomonas is not monotypic: P. agilis sp. nov. (Cryptophyceae, Geminigeraceae) from the Black Sea and hidden diversity of Proteomonas species
inferred← citeshttps://doi.org/10.1515/bot-2025-0088openalex-snapshot
Morphological characteristics and molecular identification of Pseudo-nitzschia meridionalis and Pseudo-nitzschia glacialis (Bacillariophyceae) from Antarctic waters
inferred← citeshttps://doi.org/10.1515/bot-2025-0094openalex-snapshot
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inferred← citeshttps://doi.org/10.1600/036364421x16312067913444openalex-snapshot
A Toxic Story: Phylogeny and Classification of Strychnos L. (Loganiaceae)
inferred← citeshttps://doi.org/10.18699/vjgb-24-79openalex-snapshot
Molecular genetic and morphological characteristics of Micractinium thermotolerans and M. inermum (Trebouxiophyceae, Chlorophyta) from pyroclastic deposits of the Kamchatka Peninsula (Russia)
inferred← citeshttps://doi.org/10.2216/15-015.1openalex-snapshot
Morphological diversity masks phylogenetic similarity ofEttliaandHaematococcus(Chlorophyceae)
inferred← citeshttps://doi.org/10.2216/15-115.1openalex-snapshot
New insights into the morphology and phylogeny ofHeterosigma akashiwo(Raphidophyceae), with the description ofHeterosigma minor sp. nov.
inferred← citeshttps://doi.org/10.2216/15-33.1openalex-snapshot
Revisiting the taxonomic significance of aplanozygote morphologies of two cosmopolitan snow species of the genusChloromonas(Volvocales, Chlorophyceae)
inferred← citeshttps://doi.org/10.2216/15-55.1openalex-snapshot
Species diversity in EuropeanHaematococcus pluvialis(Chlorophyceae, Volvocales)
inferred← citeshttps://doi.org/10.31857/s0320965224060033openalex-snapshot
Two New Species of the Genus Cryptomonas (Cryptophyta: Cryptophyceae) from Cat Tien National Park (Vietnam)
inferred← citeshttps://doi.org/10.3389/fmars.2021.693093openalex-snapshot
Variation and Diagnostic Power of the Internal Transcribed Spacer 2 in Mediterranean and Atlantic Eolid Nudibranchs (Mollusca, Gastropoda)
inferred← citeshttps://doi.org/10.3389/fmicb.2020.00569openalex-snapshot
Variation in Snow Algae Blooms in the Coast Range of British Columbia
inferred← citeshttps://doi.org/10.3389/fmicb.2021.775570openalex-snapshot
Multi-Gene Phylogeny of the Ciliate Genus Trachelostyla (Ciliophora, Hypotrichia), With Integrative Description of Two Species, Trachelostyla multinucleata Spec. nov. and T. pediculiformis (Cohn, 1866)
inferred← citeshttps://doi.org/10.3389/fpls.2021.662298openalex-snapshot
Revealing the Characteristics of the Antarctic Snow Alga Chlorominima collina gen. et sp. nov. Through Taxonomy, Physiology, and Transcriptomics
inferred← citeshttps://doi.org/10.3390/app14041415openalex-snapshot
DNA Barcoding as a Plant Identification Method
inferred← citeshttps://doi.org/10.3390/d15070863openalex-snapshot
Morphological and Phylogenetic Study of Protococcidians Sheds Light on the Evolution of Epicellular Parasitism in Sporozoa (Apicomplexa), with the Description of Eleutheroschizon planoratum sp. nov
inferred← citeshttps://doi.org/10.3390/ijms21176395openalex-snapshot
Phylogenetic Utility of rRNA ITS2 Sequence-Structure under Functional Constraint
inferred← citeshttps://doi.org/10.3390/jof8020163openalex-snapshot
Detection and Molecular Phylogenetic-Morphometric Characterization of Rhizoctonia tuliparum, Causal Agent of Gray Bulb Rot of Tulips and Bulbous Iris
inferred← citeshttps://doi.org/10.3390/jof9090894openalex-snapshot
Compensatory Base Changes in ITS2 Secondary Structure Alignment, Modelling, and Molecular Phylogeny: An Integrated Approach to Improve Species Delimitation in Tulasnella (Basidiomycota)
inferred← citeshttps://doi.org/10.3390/life11030211openalex-snapshot
Compensatory Base Changes Reveal Sexual Incompatibility among Members of the Anopheles subpictus Sensu Lato (Diptera: Culicidae) Species Complex in Sri Lanka
inferred← citeshttps://doi.org/10.3390/microorganisms14102224openalex-snapshot
Halotetraselmis gen. nov. and Halotetraselmis indica comb. nov. (Chlorodendrophyceae, Chlorophyta): New Halophilic Green Algae from Geographically Distant Hypersaline Habitats
inferred← citeshttps://doi.org/10.3390/microorganisms7110493openalex-snapshot
Ciliate Environmental Diversity Can Be Underestimated by the V4 Region of SSU rDNA: Insights from Species Delimitation and Multilocus Phylogeny of Pseudokeronopsis (Protist, Ciliophora)
inferred← citeshttps://doi.org/10.3390/plants11070929openalex-snapshot
Compensatory Base Changes and Varying Phylogenetic Effects on Angiosperm ITS2 Genetic Distances
inferred← citeshttps://doi.org/10.3390/plants11233363openalex-snapshot
A New Cryptic Species of the Genus Mychonastes (Chlorophyceae, Sphaeropleales)
inferred← citeshttps://doi.org/10.3390/plants9091150openalex-snapshot
Applied Barcoding: The Practicalities of DNA Testing for Herbals
inferred← citeshttps://doi.org/10.3906/bot-1911-4openalex-snapshot
Structural characterization of ITS2 and CBC species concept applications in the tribe Coluteocarpeae (Brassicaceae)
inferred← citeshttps://doi.org/10.46341/pi2020034openalex-snapshot
Short notice concerning the current conservation status of dark-barked birch taxa and the proposed changes to the next edition of the Red Book of Ukraine
inferred← citeshttps://doi.org/10.53447/communc.820287openalex-snapshot
CHARACTERIZATION OF ITS1 SECONDARY STRUCTURE IN TEN SPECIES OF COLUTEOCARPEAE (BRASSICACEAE) AND ITS TAXONOMICAL UTILITY
inferred← citeshttps://doi.org/10.53846/goediss-5497openalex-snapshot
Green algae in soil: assessing their biodiversity and biogeography with molecular-phylogenetic methods based on cultures
inferred← citeshttps://doi.org/10.5507/fot.2016.010openalex-snapshot
Selenastraceae (Sphaeropleales, Chlorophyceae): rbcL, 18S rDNA and ITS-2 secondary structure enlightens traditional taxonomy, with description of two new genera, Messastrum gen. nov. and Curvastrum gen. nov.
inferred← citeshttps://doi.org/10.5507/fot.2017.010openalex-snapshot
Chloromonas nivalis subsp. tatrae, subsp. nov. (Chlamydomonadales, Chlorophyta): re-examination of a snow alga from the High Tatra Mountains (Slovakia)
inferred← citeshttps://doi.org/10.5507/fot.2019.003openalex-snapshot
Evaluating amplicon high-throughput sequencing data of microalgae living in melting snow: improvements and limitations
inferred← citeshttps://doi.org/10.5507/fot.2020.004openalex-snapshot
Taxonomic studies of Cryptomonas lundii clade (Cryptophyta: Cryptophyceae) with description of a new species from Vietnam
inferred← citeshttps://doi.org/10.5507/fot.2020.012openalex-snapshot
Mychonastes frigidus sp. nov. (Sphaeropleales/Chlorophyceae), a new species described from a mountain stream in the Subpolar Urals (Russia)
inferred← citeshttps://doi.org/10.5507/fot.2021.019openalex-snapshot
Rhodomonas storeatuloformis sp. nov. (Cryptophyceae, Pyrenomonadaceae), a new cryptomonad from the Black Sea: morphology versus molecular phylogeny
inferred← citeshttps://doi.org/10.5817/cpr2024-2-18openalex-snapshot
Is a newly reported presence of Stictis radiata in Svalbard a result of global climate change, or is it due to the availability of a suitable substrate?
inferred← citeshttps://doi.org/10.5943/cream/9/1/20openalex-snapshot
Molecular characterization of fungal endophytes associated with medicinal plant, Ficus racemosa
inferred← citeshttps://doi.org/10.6026/97320630015046openalex-snapshot
Molecular characterization of leaf spot fungi using internal transcribed spacer (ITS) based phylogenetic inference
inferred← citeshttps://doi.org/10.70675/4a282259z23fdz4dedz805bz0fa9e3948fbdopenalex-snapshot
Exploration de la diversité et du potentiel pour la reproduction sexuée au sein du complexe d’espèces Amoebophrya ceratii (Syndiniales), parasites de dinoflagellés marins
inferred← citeshttps://doi.org/10.7287/peerj.3354v0.1/reviews/1openalex-snapshot
Peer Review #1 of "A new view on the morphology and phylogeny of eugregarines suggested by the evidence from the gregarine Ancora sagittata (Leuckart, 1860) Labbé, 1899 (Apicomplexa: Eugregarinida) (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.3354v0.1/reviews/2openalex-snapshot
Peer Review #2 of "A new view on the morphology and phylogeny of eugregarines suggested by the evidence from the gregarine Ancora sagittata (Leuckart, 1860) Labbé, 1899 (Apicomplexa: Eugregarinida) (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.3354v0.2/reviews/2openalex-snapshot
Peer Review #2 of "A new view on the morphology and phylogeny of eugregarines suggested by the evidence from the gregarine Ancora sagittata (Leuckart, 1860) Labbé, 1899 (Apicomplexa: Eugregarinida) (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.3354v0.3/reviews/1openalex-snapshot
Peer Review #1 of "A new view on the morphology and phylogeny of eugregarines suggested by the evidence from the gregarine Ancora sagittata (Leuckart, 1860) Labbé, 1899 (Apicomplexa: Eugregarinida) (v0.3)"
inferred← citeshttps://doi.org/10.7717/peerj.10889openalex-snapshot
ITS secondary structure reconstruction to resolve taxonomy and phylogeny of the Betula L. genus
inferred← citeshttps://doi.org/10.7717/peerj.3354openalex-snapshot
A new view on the morphology and phylogeny of eugregarines suggested by the evidence from the gregarine Ancora sagittata (Leuckart, 1860) Labbé, 1899 (Apicomplexa: Eugregarinida)
inferred← citeshttps://doi.org/10.7872/crya/v38.iss4.2017.285openalex-snapshot
Cryptic Cyanobacterial Diversity in the Giant Cave (Trieste, Italy): The New Genus Timaviella (Leptolyngbyaceae)
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.