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Minimalist barcodes for sponges: a case study classifying African freshwater Spongillida

https://doi.org/10.1139/gen-2018-0098
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What this work says

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

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Systema Porifera. A Guide to the Classification of Sponges
inferredcites →https://doi.org/10.1007/978-1-4615-0747-5_97openalex-snapshot
Suborder Spongillina subord. nov.: Freshwater Sponges
inferredcites →https://doi.org/10.1007/bf02537358openalex-snapshot
The reef cave dwelling ultraconservative coralline demospongeAstrosclera willeyana Lister 1900 from the Indo-Pacific
inferredcites →https://doi.org/10.1007/bf02670471openalex-snapshot
RAPD analysis in flax: Optimization of yield and reproducibility using klenTaq 1 DNA polymerase, chelex 100, and gel purification of genomic DNA
inferredcites →https://doi.org/10.1007/s00239-008-9158-5openalex-snapshot
Ribosomal ITS Sequences Allow Resolution of Freshwater Sponge Phylogeny with Alignments Guided by Secondary Structure Prediction
inferredcites →https://doi.org/10.1007/s10126-005-6109-7openalex-snapshot
Status and Perspective of Sponge Chemosystematics
inferredcites →https://doi.org/10.1007/s10750-007-9000-xopenalex-snapshot
Global diversity of sponges (Porifera: Spongillina) in freshwater
inferredcites →https://doi.org/10.1007/s10750-011-0842-xopenalex-snapshot
No longer Demospongiae: Homoscleromorpha formal nomination as a fourth class of Porifera
inferredcites →https://doi.org/10.1007/s12526-017-0775-3openalex-snapshot
First records of Geodia demosponges from the New England seamounts, an opportunity to test the use of DNA mini-barcodes on museum specimens
inferredcites →https://doi.org/10.1016/0003-2697(75)90739-3openalex-snapshot
A freeze-squeeze method for recovering long DNA from agarose gels
inferredcites →https://doi.org/10.1016/0305-1978(91)90034-wopenalex-snapshot
Phylogenetic relationships within the order Hadromerida (Porifera, Demospongiae, Tetractinomorpha) as indicated by ribosomal RNA sequence comparisons
inferredcites →https://doi.org/10.1016/b978-0-12-387787-1.00007-6openalex-snapshot
Deep Phylogeny and Evolution of Sponges (Phylum Porifera)
inferredcites →https://doi.org/10.1016/j.ympev.2005.11.001openalex-snapshot
Speculation with spiculation?—Three independent gene fragments and biochemical characters versus morphology in demosponge higher classification
inferredcites →https://doi.org/10.1016/j.ympev.2007.03.004openalex-snapshot
Cryptic speciation in marine sponges evidenced by mitochondrial and nuclear genes: A phylogenetic approach
inferredcites →https://doi.org/10.1016/j.ympev.2007.09.007openalex-snapshot
Phylogenetic analysis of freshwater sponges provide evidence for endemism and radiation in ancient lakes
inferredcites →https://doi.org/10.1016/j.ympev.2010.03.034openalex-snapshot
Species boundaries and phylogenetic relationships between Atlanto-Mediterranean shallow-water and deep-sea coral associated Hexadella species (Porifera, Ianthellidae)
inferredcites →https://doi.org/10.1016/j.ympev.2011.05.021openalex-snapshot
Insights into the evolution of freshwater sponges (Porifera: Demospongiae: Spongillina): Barcoding and phylogenetic data from Lake Tanganyika endemics indicate multiple invasions and unsettle existing taxonomy
inferredcites →https://doi.org/10.1017/s0025315407058274openalex-snapshot
DNA taxonomy of sponges—progress and perspectives
inferredcites →https://doi.org/10.1017/s0025315415000521openalex-snapshot
Nothing in (sponge) biology makes sense – except when based on holotypes
inferredcites →https://doi.org/10.1038/44560openalex-snapshot
Decline in Mesozoic reef-building sponges explained by silicon limitation
inferredcites →https://doi.org/10.1071/is14060openalex-snapshot
Microscleres and gemmoscleres as phylogenetic signals in Spongillida: phylogeny and biogeography of the genus Metania Gray, 1867 (Porifera, Metaniidae)
inferredcites →https://doi.org/10.1080/10635150490522629openalex-snapshot
Frequentist Properties of Bayesian Posterior Probabilities of Phylogenetic Trees Under Simple and Complex Substitution Models
inferredcites →https://doi.org/10.1080/20442041.2017.1320507openalex-snapshot
Intraspecific and interspecific sequence variability in the ITS region of the rDNA of freshwater sponges of Lake Baikal and East Siberia
inferredcites →https://doi.org/10.1093/bioinformatics/bts199openalex-snapshot
Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data
inferredcites →https://doi.org/10.1093/icb/ict078openalex-snapshot
Phylogeny and Systematics of Demospongiae in Light of New Small-Subunit Ribosomal DNA (18S) Sequences
inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
inferredcites →https://doi.org/10.1093/nar/29.23.4793openalex-snapshot
DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA
inferredcites →https://doi.org/10.1093/nar/gku1127openalex-snapshot
Type material in the NCBI Taxonomy Database
inferredcites →https://doi.org/10.1093/sysbio/syq010openalex-snapshot
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
inferredcites →https://doi.org/10.1111/ivb.12027openalex-snapshot
Disrupted spiculogenesis in deep‐water Geodiidae (Porifera, Demospongiae) growing in shallow waters
inferredcites →https://doi.org/10.1111/j.1365-294x.2006.03171.xopenalex-snapshot
Amassing diversity in an ancient lake: evolution of a morphologically diverse parthenogenetic gastropod assemblage in Lake Malawi
inferredcites →https://doi.org/10.1111/j.1463-6409.2005.00211.xopenalex-snapshot
Phylogenetic relationships of freshwater sponges (Porifera, Spongillina) inferred from analyses of 18S rDNA, COI mtDNA, and ITS2 rDNA sequences
inferredcites →https://doi.org/10.1111/j.1471-8286.2006.01470.xopenalex-snapshot
A minimalist barcode can identify a specimen whose DNA is degraded
inferredcites →https://doi.org/10.1111/jzs.12022openalex-snapshot
The number of endemic species of freshwater sponges (Malawispongiidae; Spongillina; Porifera) from Lake Kinneret is overestimated
inferredcites →https://doi.org/10.1126/science.aac9927openalex-snapshot
Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake
inferredcites →https://doi.org/10.1128/mmbr.62.4.1435-1491.1998openalex-snapshot
Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationships among Archaebacteria, Eubacteria, and Eukaryotes
inferredcites →https://doi.org/10.1134/s1022795413080036openalex-snapshot
Investigation of nuclear and mitochondrial DNA polymorphism in closely related species of endemic Baikal sponges
inferredcites →https://doi.org/10.1139/z06-003openalex-snapshot
Systematics and evolution of Demospongiae
inferredcites →https://doi.org/10.11646/zootaxa.1668.1.10openalex-snapshot
On the molecular phylogeny of sponges (Porifera)*
inferredcites →https://doi.org/10.11646/zootaxa.3544.1.3openalex-snapshot
Biodiversity assessment in the Lower Mekong basin: First record of the genus Oncosclera (Porifera: Spongillina: Potamolepidae) from the Oriental Region
inferredcites →https://doi.org/10.11646/zootaxa.3918.1.2openalex-snapshot
Adaptive morpho-traits, taxonomy and biogeography of Metania Gray, 1867 (Porifera: Spongillina: Metaniidae) with the description of a new species from Madagascar
inferredcites →https://doi.org/10.11646/zootaxa.3957.1.2openalex-snapshot
Discovery of living Potamolepidae (Porifera: Spongillina) from Nearctic freshwater with description of a new genus
inferredcites →https://doi.org/10.11646/zootaxa.3990.1.7openalex-snapshot
Endemic Lake Baikal sponges from deep water. 1: Potential cryptic speciation and discovery of living species known only from fossils
inferredcites →https://doi.org/10.1186/1297-9686-44-21openalex-snapshot
Ancient DNA studies: new perspectives on old samples
inferredcites →https://doi.org/10.1186/s12983-015-0099-8openalex-snapshot
Proposal for a revised classification of the Demospongiae (Porifera)
inferredcites →https://doi.org/10.1371/journal.pone.0033417openalex-snapshot
Molecular Phylogenetic Evaluation of Classification and Scenarios of Character Evolution in Calcareous Sponges (Porifera, Class Calcarea)
inferredcites →https://doi.org/10.1371/journal.pone.0035105openalex-snapshot
Global Diversity of Sponges (Porifera)
inferredcites →https://doi.org/10.1371/journal.pone.0039345openalex-snapshot
Barcoding Sponges: An Overview Based on Comprehensive Sampling
inferredcites →https://doi.org/10.4039/ent103407-3openalex-snapshot
DISTRIBUTION AND ECOLOGY OF AMAZONIAN CHIRONOMIDS (DIPTERA)
inferredcites →https://doi.org/10.5281/zenodo.15145663openalex-snapshot
Table 1 in A new Gammarus species from Xinjiang Uygur Autonomous Region (China) with a key to Xinjiang freshwater gammarids (Crustacea, Amphipoda, Gammaridae)
inferredcites →https://doi.org/10.5479/si.03629236.272.1openalex-snapshot
Comprehensive Revision of a Worldwide Collection of Freshwater Sponges (Porifera, Spongillidae)

What points at this work

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

inferred← citeshttps://doi.org/10.11646/zootaxa.4728.3.5zenodo-depositor-declared
Two new species of freshwater sponges from Neotropical and Afrotropical Regions
inferred← citeshttps://doi.org/10.11646/zootaxa.5298.1.1zenodo-depositor-declared
Two centuries of sponges (phylum Porifera) taxonomic studies in Indonesia (1820–2021): checklist and bibliography
inferred← citeshttps://doi.org/10.11646/zootaxa.5398.1.1zenodo-depositor-declared
Correcting sponge names: nomenclatural update of lower taxa level Porifera
inferred← citeshttps://doi.org/10.1007/s10201-021-00670-2openalex-snapshot
Discovery of the freshwater sponge genus Corvospongilla Annandale (Porifera: Spongillida) in Australia with the description of a new species and phylogeographic implications
inferred← citeshttps://doi.org/10.1016/j.jglr.2019.09.028openalex-snapshot
Having the balls to colonize – The Ephydatia fluviatilis group and the origin of (ancient) lake “endemic” sponge lineages
inferred← citeshttps://doi.org/10.1038/s41598-021-88288-3openalex-snapshot
Community composition and functional prediction of prokaryotes associated with sympatric sponge species of southwestern Atlantic coast
inferred← citeshttps://doi.org/10.1038/s41598-022-26970-wopenalex-snapshot
Low genetic diversity and predation threaten a rediscovered marine sponge
inferred← citeshttps://doi.org/10.1080/00222933.2019.1694716openalex-snapshot
An overview on the freshwater sponge fauna (Demospongiae: Spongillida) of New Zealand and New Caledonia with new insights into Heterorotula from deep thermal vents of the Lake Taupo
inferred← citeshttps://doi.org/10.1080/14772000.2020.1827077openalex-snapshot
Phylogenomic inference of the interrelationships of Lake Baikal sponges
inferred← citeshttps://doi.org/10.1080/14772000.2021.1915896openalex-snapshot
Hundreds of new DNA barcodes for South African sponges
inferred← citeshttps://doi.org/10.1080/14772000.2021.1958948openalex-snapshot
Investigation of the spongillidSpongilla albaCarter, 1849 reveals a new group of brackish-water sponges
inferred← citeshttps://doi.org/10.1080/14772000.2023.2228865openalex-snapshot
Morphological and molecular analysis of Ephydatia fluviatilis (Porifera: Spongillida: Spongillidae) from Nanjing, China
inferred← citeshttps://doi.org/10.1080/14772000.2025.2491350openalex-snapshot
Taxonomy and molecular systematic position of the freshwater genus Eunapius with the descriptions of new species: more evidence in favour of the polyphyly of Spongillida
inferred← citeshttps://doi.org/10.1101/2020.04.26.062448openalex-snapshot
Phylogenetic analysis of Michigan’s freshwater sponges (Porifera, Spongillidae) using extended COI mtDNA sequences
inferred← citeshttps://doi.org/10.1134/s0006297925602977openalex-snapshot
20 Years of DNA Barcoding – Achievements and Problems
inferred← citeshttps://doi.org/10.1186/s12859-019-3205-7openalex-snapshot
Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage
inferred← citeshttps://doi.org/10.12688/wellcomeopenres.23988.1openalex-snapshot
The chromosome-level genome sequences of the freshwater sponge, Spongilla lacustris (Linnaeus, 1759) and the chlorophyte cobiont Choricystis sp., and the associated microbial metagenome sequences
inferred← citeshttps://doi.org/10.31951/2658-3518-2020-a-4-785openalex-snapshot
Study of variability of ITS1 and ITS2 spacers of rDNA of freshwater sponges (Porifera, Spongillida)
inferred← citeshttps://doi.org/10.31951/2658-3518-2022-a-5-1671openalex-snapshot
The problem of species delimitation within the endemic Lake Baikal sponges Lubomirskiidae
inferred← citeshttps://doi.org/10.3390/d14121126openalex-snapshot
The Utilityof 28S rDNA for Barcoding of Freshwater Sponges (Porifera, Spongillida)
inferred← citeshttps://doi.org/10.3390/jmse8121008openalex-snapshot
A New Species of Spongilla (Porifera, Demospongiae) from a Karst Lake in Ha Long Bay (Vietnam)
inferred← citeshttps://doi.org/10.3390/limnolrev24040034openalex-snapshot
A Revision of Dispersal Strategies in Freshwater Sponges: The Journey of the Ponto-Caspian Sponge Rosulaspongilla rhadinaea (Porifera: Spongillidae), a New Alien Species for Europe
inferred← citeshttps://doi.org/10.3897/zookeys.915.47460openalex-snapshot
Genetic analysis confirms the freshwater origin of the endemic Caspian sponges (Demospongiae, Spongillida, Metschnikowiidae)
inferred← citeshttps://doi.org/10.71161/ivb.144.2.2025.00027openalex-snapshot
Four species of freshwater sponges dominate riverine habitats of northwestern North Carolina, USA
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