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Molecular Phylogenetics and Systematics of the Bivalve Family Ostreidae Based on rRNA Sequence-Structure Models and Multilocus Species Tree

https://doi.org/10.1371/journal.pone.0108696
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What this work says

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

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Molecular Phylogenetics of Cupped Oysters Based on Partial 28S rRNA Gene Sequences
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Phylogenetic Analysis of Southern Hemisphere Flat Oysters Based on Partial Mitochondrial 16S rDNA Gene Sequences
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Phylogenetic Analysis of Molluscan Mitochondrial LSU rDNA Sequences and Secondary Structures
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Evolution of Parental Care and Ovulation Behavior in Oysters
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Oyster beds: Morphologic response to changing substrate conditions
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Molecular phylogenies help resolve taxonomic confusion with Asian Crassostrea oyster species
inferredcites →https://doi.org/10.1007/s10126-002-0047-4openalex-snapshot
Molecular Genetic Identification Tools for Three Commercially Cultured Oysters ( Crassostrea belcheri , Crassostrea iredalei , and Saccostrea cucullata ) in Thailand
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Molecular Taxonomy of Cupped Oysters (Crassostrea, Saccostrea, and Striostrea) in Thailand Based on COI, 16S, and 18S rDNA Polymorphism
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Crassostrea gigas in natural oyster banks in southern Brazil
inferredcites →https://doi.org/10.1016/0022-0981(95)00065-yopenalex-snapshot
Differences in mitochondrial 16S ribosomal gene sequences allow discrimination among American [Crassostrea virginica (Gmelin)] and Asian [C. gigas (Thunberg) C. ariakensis Wakiya] oyster species
inferredcites →https://doi.org/10.1016/j.gene.2004.06.049openalex-snapshot
The molecular phylogeny of oysters based on a satellite DNA related to transposons
inferredcites →https://doi.org/10.1016/j.gene.2014.05.065openalex-snapshot
ITS2, 18S, 16S or any other RNA — simply aligning sequences and their individual secondary structures simultaneously by an automatic approach
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ITS2 sequence–structure analysis in phylogenetics: A how-to manual for molecular systematics
inferredcites →https://doi.org/10.1016/j.ympev.2010.04.025openalex-snapshot
The analysis of rRNA sequence-structure in phylogenetics: An application to the family Pectinidae (Mollusca: Bivalvia)
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/j.ympev.2012.07.017openalex-snapshot
Molecular phylogenetics in 2D: ITS2 rRNA evolution and sequence-structure barcode from Veneridae to Bivalvia
inferredcites →https://doi.org/10.1016/s0044-8486(03)00215-1openalex-snapshot
Mitochondrial DNA and morphological identification of a new species of Crassostrea (Bivalvia: Ostreidae) cultured for centuries in the Pearl River Delta, Hong Kong, China
inferredcites →https://doi.org/10.1016/s1055-7903(02)00227-0openalex-snapshot
ITS2 rRNA evolution and its congruence with the phylogeny of muricid neogastropods (Caenogastropoda, Muricoidea)
inferredcites →https://doi.org/10.1016/s1055-7903(03)00013-7openalex-snapshot
Phylogenetic analysis of the subclass Pteriomorphia (Bivalvia) from mtDNA COI sequences
inferredcites →https://doi.org/10.1017/s0025315414000058openalex-snapshot
Revision of genusCrassostrea(Bivalvia: Ostreidae) of Brazil
inferredcites →https://doi.org/10.1017/s0025315414001027openalex-snapshot
Does GenBank provide a reliable DNA barcode reference to identify small alien oysters invading the Mediterranean Sea?
inferredcites →https://doi.org/10.1046/j.1095-8312.2002.00042.xopenalex-snapshot
On the use of genetic divergence for identifying species
inferredcites →https://doi.org/10.1086/399023openalex-snapshot
Recent Advances in Oyster Biology
inferredcites →https://doi.org/10.1093/bioinformatics/btm404openalex-snapshot
Clustal W and Clustal X version 2.0
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phangorn: phylogenetic analysis in R
inferredcites →https://doi.org/10.1093/jaoac/89.1.144openalex-snapshot
Species Identification of Crassostrea and Ostrea Oysters by Polymerase Chain Reaction Amplification of the 5S rRNA Gene
inferredcites →https://doi.org/10.1093/molbev/msp274openalex-snapshot
Bayesian Inference of Species Trees from Multilocus Data
inferredcites →https://doi.org/10.1093/molbev/mss075openalex-snapshot
Bayesian Phylogenetics with BEAUti and the BEAST 1.7
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MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0
inferredcites →https://doi.org/10.1093/mollus/67.2.243openalex-snapshot
Contrasting morphological and molecular variation in Coralliophila meyendorffii (Muricidae, Coralliophilinae)
inferredcites →https://doi.org/10.1093/mollus/eyl002openalex-snapshot
Morphological and mitochondrial-DNA analysis of the Indo-West Pacific rock oysters (Ostreidae: Saccostrea species)
inferredcites →https://doi.org/10.1093/mollus/eym018openalex-snapshot
Molecular phylogeny of mangrove oysters (Crassostrea) from Brazil
inferredcites →https://doi.org/10.1093/nar/16.suppl.r175openalex-snapshot
A Compilation of large subunit RNA sequences presented in a structural format
inferredcites →https://doi.org/10.1093/nar/21.13.3055openalex-snapshot
A compilation of large subunit (23S and 23S-like) ribosomal RNA structures: 1993
inferredcites →https://doi.org/10.1093/nar/27.11.2271openalex-snapshot
Evolutionarily conserved structural features in the ITS2 of mammalian pre-rRNAs and potential interactions with the snoRNA U8 detected by comparative analysis of new mouse sequences
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/gkm233openalex-snapshot
Pan-eukaryote ITS2 homologies revealed by RNA secondary structure
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040517openalex-snapshot
Relationships between gene trees and species trees.
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Gene Trees in Species Trees
inferredcites →https://doi.org/10.1093/sysbio/sys029openalex-snapshot
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
inferredcites →https://doi.org/10.1098/rstb.2005.1722openalex-snapshot
The unholy trinity: taxonomy, species delimitation and DNA barcoding
inferredcites →https://doi.org/10.1111/j.0014-3820.2003.tb00355.xopenalex-snapshot
THE SHAPES OF NEUTRAL GENE GENEALOGIES IN TWO SPECIES: PROBABILITIES OF MONOPHYLY, PARAPHYLY, AND POLYPHYLY IN A COALESCENT MODEL
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Towards integrative taxonomy
inferredcites →https://doi.org/10.1111/j.1438-8677.2012.00576.xopenalex-snapshot
‘Y’Scenedesmus (Chlorophyta, Chlorophyceae): the internal transcribed spacer 2 rRNA secondary structure re‐revisited
inferredcites →https://doi.org/10.1111/j.1755-0998.2011.03025.xopenalex-snapshot
Identifying the true oysters (Bivalvia: Ostreidae) with mitochondrial phylogeny and distance‐based DNA barcoding
inferredcites →https://doi.org/10.1146/annurev.ecolsys.36.102003.152638openalex-snapshot
Introduction of Non-Native Oysters: Ecosystem Effects and Restoration Implications
inferredcites →https://doi.org/10.1186/1471-2105-11-129openalex-snapshot
RNAstructure: software for RNA secondary structure prediction and analysis
inferredcites →https://doi.org/10.1186/1471-2105-7-11openalex-snapshot
SuperMimic – Fitting peptide mimetics into protein structures
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/10.1186/1471-2148-10-394openalex-snapshot
Unusual conservation of mitochondrial gene order in Crassostreaoysters: evidence for recent speciation in Asia
inferredcites →https://doi.org/10.1186/1471-2148-8-218openalex-snapshot
ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales)
inferredcites →https://doi.org/10.1186/1471-2148-9-300openalex-snapshot
ITS2 secondary structure improves phylogeny estimation in a radiation of blue butterflies of the subgenus Agrodiaetus (Lepidoptera: Lycaenidae: Polyommatus )
inferredcites →https://doi.org/10.1186/1742-9994-7-16openalex-snapshot
The integrative future of taxonomy
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/10.1186/1756-0500-4-400openalex-snapshot
Complete mitochondrial DNA sequence of the European flat oyster Ostrea edulis confirms Ostreidae classification
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.pgen.0020068openalex-snapshot
Discordance of Species Trees with Their Most Likely Gene Trees
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/10.1590/s1415-47572010000300030openalex-snapshot
Molecular identification, phylogeny and geographic distribution of Brazilian mangrove oysters (Crassostrea)
inferredcites →https://doi.org/10.2307/1543197openalex-snapshot
Differences in the rDNA-Bearing Chromosome Divide the Asian-Pacific and Atlantic Species ofCrassostrea(Bivalvia, Mollusca)
inferredcites →https://doi.org/10.2307/1543473openalex-snapshot
Trans-Atlantic Distribution of a Mangrove Oyster Species Revealed by 16S mtDNA and Karyological Analyses
inferredcites →https://doi.org/10.2307/2421912openalex-snapshot
The Generic Status of Living Oysters and the Scientific Name of the Common American Species
inferredcites →https://doi.org/10.2983/0730-8000(2008)27[481:iocaar]2.0.co;2openalex-snapshot
Identification of Crassostrea ariakensis and Related Oysters by Multiplex Species-Specific PCR
inferredcites →https://doi.org/10.4172/2329-9002.1000114openalex-snapshot
Phylogenetic Model Choice: Justifying a Species Tree or Concatenation Analysis
inferredcites →https://doi.org/10.5281/zenodo.16667686openalex-snapshot
SYNOPSIS OF THE SUPRASPECIFIC CLASSIFICATION OF LIVING OYSTERS (BIVALVIA, GRYPHAEIDAE AND OSTREIDAE)

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

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inferred← citeshttps://doi.org/10.1007/s00343-025-5052-xopenalex-snapshot
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Enhanced uptake of perfluorooctanoic acid by polystyrene nanoparticles in Pacific oyster (Magallana gigas)
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inferred← citeshttps://doi.org/10.1016/j.scitotenv.2019.04.450openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.tig.2015.02.005openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.ygeno.2025.111142openalex-snapshot
m6A-RNA epitranscriptomes regulate splicing and neuronal development in the Pacific oyster Crassostrea gigas
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.08.014openalex-snapshot
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inferred← citeshttps://doi.org/10.1186/s12862-015-0458-2openalex-snapshot
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inferred← citeshttps://doi.org/10.1186/s12864-025-12122-7openalex-snapshot
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inferred← citeshttps://doi.org/10.1186/s41200-016-0105-7openalex-snapshot
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inferred← citeshttps://doi.org/10.1242/jeb.183236openalex-snapshot
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inferred← citeshttps://doi.org/10.1371/journal.pone.0116014openalex-snapshot
Correction: Molecular Phylogenetics and Systematics of the Bivalve Family Ostreidae Based on rRNA Sequence-Structure Models and Multilocus Species Tree
inferred← citeshttps://doi.org/10.1508/cytologia.83.129openalex-snapshot
Karyological Analysis and Nucleolar Organizer Region of Tropical Oyster, Crassostrea iredalei (Ostreoida, Ostreidae) in Thailand
inferred← citeshttps://doi.org/10.15625/1859-3097/18275openalex-snapshot
Monthly variation in the lipid composition and content of Pacific oysters, \(\textit{Crassostrea gigas}\), cultured in Van Don, Quang Ninh
inferred← citeshttps://doi.org/10.2983/035.036.0208openalex-snapshot
Classification and Taxonomic Revision of Two Oyster Species from Peru: Ostrea megodon (Hanley, 1846) and Crassostrea talonata (Li & Qi, 1994)
inferred← citeshttps://doi.org/10.2983/035.036.0301openalex-snapshot
The Proposed Dropping of the Genus Crassostrea for All Pacific Cupped Oysters and Its Replacement by a New Genus Magallana: A Dissenting View
inferred← citeshttps://doi.org/10.2983/035.037.0407openalex-snapshot
Diversity and Evolution of Living Oysters
inferred← citeshttps://doi.org/10.2983/035.038.0109openalex-snapshot
Monsoonally Driven Reproduction in the Tropical Black-Lip Rock Oyster Saccostrea echinata (Quoy & Gaimard, 1835) in Northern Australia
inferred← citeshttps://doi.org/10.2983/035.038.0210openalex-snapshot
Classification of Small Flat Oysters of Ostrea stentina Species Complex and a New Species Ostrea neostentina sp. nov. (Bivalvia: Ostreidae)
inferred← citeshttps://doi.org/10.2983/035.040.0107openalex-snapshot
Identification of Saccostrea mordax and a New Species Saccostrea mordoides sp. nov. (Bivalvia: Ostreidae) from China
inferred← citeshttps://doi.org/10.2983/035.040.0203openalex-snapshot
Morphological and Mitochondrial DNA Analyses of Oysters in the Northern Bay of Bengal, Bangladesh
inferred← citeshttps://doi.org/10.3354/meps12991openalex-snapshot
Developing an eDNA toolkit to quantify broadcast spawning events of the sea scallop Placopecten magellanicus: moving beyond fertilization assays
inferred← citeshttps://doi.org/10.3354/meps13538openalex-snapshot
Larval energetics of the Sydney rock oyster Saccostrea glomerata and Pacific oyster Magallana gigas
inferred← citeshttps://doi.org/10.33714/masteb.668529openalex-snapshot
First molecular record of the alien species Pacific oyster (Crassostrea gigas, Thunberg 1793) in the Marmara Sea, Turkey
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/fmars.2021.741455openalex-snapshot
Yet Another Mitochondrial Genome of the Pacific Cupped Oyster: The Published Mitogenome of Alectryonella plicatula (Ostreinae) Is Based on a Misidentified Magallana gigas (Crassostreinae)
inferred← citeshttps://doi.org/10.3389/fmars.2025.1600021openalex-snapshot
Three new sequences of Ostrea stentina and the evolution of the mitogenome of the Ostreinae clams (Ostreidae, Bivalvia)
inferred← citeshttps://doi.org/10.3389/fmars.2025.1602823openalex-snapshot
Species identity and spatial patterns of common oysters at oyster reefs of Guangdong, China
inferred← citeshttps://doi.org/10.3390/ani16182934openalex-snapshot
High Intraspecific mtDNA Polymorphisms and Mitonuclear Discordance: A Case Study of the Cadlina laevis (Linnaeus, 1767) Species Complex
inferred← citeshttps://doi.org/10.3390/biology13090702openalex-snapshot
Genetic Variability in Mediterranean Coastal Ecosystems: Insights into Ostrea spp. (Bivalvia: Ostreidae)
inferred← citeshttps://doi.org/10.3390/fishes7060317openalex-snapshot
The Complete Mitochondrial Genome of Hyotissa hyotis (Bivalvia: Gryphaeidae) Reveals a Unique Gene Order within Ostreoidea
inferred← citeshttps://doi.org/10.3390/jmse10020237openalex-snapshot
Population Genomics, Transcriptional Response to Heat Shock, and Gut Microbiota of the Hong Kong Oyster Magallana hongkongensis
inferred← citeshttps://doi.org/10.3390/life11060583openalex-snapshot
Looking at the Nudibranch Family Myrrhinidae (Gastropoda, Heterobranchia) from a Mitochondrial ‘2D Folding Structure’ Point of View
inferred← citeshttps://doi.org/10.3391/bir.2021.10.4.08openalex-snapshot
First record, DNA identification and morphometric characterization of Pacific oyster, Crassostrea gigas (Thunberg, 1793) in the southern Black Sea
inferred← citeshttps://doi.org/10.33936/at.v1i1.2147openalex-snapshot
Are 45 years of reproductive isolation enough to prevent the amplification of mitochondrial genes in the Pacific oyster?
inferred← citeshttps://doi.org/10.3856/vol52-issue4-fulltext-3213openalex-snapshot
Effect of diet on larval settlement, growth, and spat survival of the oyster Crassostrea gigas (Thunberg, 1793)
inferred← citeshttps://doi.org/10.3897/bdj.11.e101333openalex-snapshot
The complete mitochondrial genome of Hyotissa sinensis (Bivalvia, Ostreoidea) indicates the genetic diversity within Gryphaeidae
inferred← citeshttps://doi.org/10.3897/mbmg.5.67862openalex-snapshot
Revision and annotation of DNA barcode records for marine invertebrates: report of the 8th iBOL conference hackathon
inferred← citeshttps://doi.org/10.3897/zookeys.1043.66992openalex-snapshot
Molecular and morphological systematics of a new, reef forming, cupped oyster from the northern Arabian Gulf: Talonostrea salpinx new species
inferred← citeshttps://doi.org/10.3989/scimar.04479.09aopenalex-snapshot
Sympatric sibling species: the case of Caloria elegans and Facelina quatrefagesi (Gastropoda: Nudibranchia)
inferred← citeshttps://doi.org/10.4003/006.033.0206openalex-snapshot
Phylogeny and Species Diversity of Gulf of California Oysters (Ostreidae) Inferred from Mitochondrial DNA*
inferred← citeshttps://doi.org/10.4202/app.00387.2017openalex-snapshot
Late Jurassic–Early Cretaceous oysters from Siberia: A systematic review
inferred← citeshttps://doi.org/10.4274/turkjorthod.2023.2022.98openalex-snapshot
Outcomes of Presurgical Nasoalveolar Molding using Modified Nostril Retainers in Patients with Unilateral Cleft Lip and Palate at an Average Follow-up of 2 Years
inferred← citeshttps://doi.org/10.5194/bg-13-1223-2016openalex-snapshot
Age structure, carbonate production and shell loss rate in an Early Miocene reef of the giant oyster Crassostrea gryphoides
inferred← citeshttps://doi.org/10.70675/12f4d23eze28fz49f9z86faz2a6cf38b847bopenalex-snapshot
Mise en place de la sélection génomique chez l’huître creuse Crassostrea gigas
inferred← citeshttps://doi.org/10.70675/4a46558dz18d6z467bz8385zc982fde415e4openalex-snapshot
Évolution de la virulence de V. crassostreae en lien avec l’huître en tant qu’hôte et les phages en tant que prédateurs
inferred← citeshttps://doi.org/10.70675/50d0e728zd86bz49bcza31az5a36a417957bopenalex-snapshot
Perturbations comportementales, physiologiques et cellulaires chez des mollusques bivalves exposés à un pétrole brut dans un contexte mono ou multistress.
inferred← citeshttps://doi.org/10.70675/594fda00z839ez49c6zb265z45ff8b8032ccopenalex-snapshot
Caractérisation de la voie de l’autophagie chez l’huître creuse Crassostrea gigas en réponse à une infection par le virus OsHV-1
inferred← citeshttps://doi.org/10.70675/950a9e40z4490z45b5za8d7zd7081953da6fopenalex-snapshot
Currently used pesticides and their mixtures : what are the risks to non-target aquatic organisms? Laboratory and in situ approaches.
inferred← citeshttps://doi.org/10.70675/a0965fd6zfeacz4715z92faz52b24c0cd7c5openalex-snapshot
Étude de la toxicité de pesticides seuls et en mélanges sur des microalgues marines et la larve d'huître creuse : approche combinant des tests miniaturisés en laboratoire avec l'utilisation d'extraits d'échantillonneurs passifs de type POCIS
inferred← citeshttps://doi.org/10.70675/abb219f0z223az44ecz91a7zc106d177ee28openalex-snapshot
Le déterminisme sexuel de l'huître crassostrea gigas : du phénotype aux facteurs moléculaires sous-jacents
inferred← citeshttps://doi.org/10.70675/b7022254zbb59z4cd4z958dz57b05fc79dffopenalex-snapshot
Recreational boating as a major vector of spread of nonindigenous species around the Mediterranean
inferred← citeshttps://doi.org/10.7717/peerj.12205openalex-snapshot
Genetic diversity across the mitochondrial genome of eastern oysters ( Crassostrea virginica ) in the northern Gulf of Mexico
inferred← citeshttps://doi.org/10.7717/peerj.3954openalex-snapshot
A massive update of non-indigenous species records in Mediterranean marinas
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