The DOI matches its Crossref record; 42 of the 46 references it cites were found in a registry or an index; none of the 15 sources its claims cite is checked for support yet.
Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA
Open accessAbstract
We studied the evolutionary relationships among basal metazoan lineages by using complete large subunit (LSU) and small subunit (SSU) ribosomal RNA sequences for 23 taxa. After identifying competing hypotheses, we performed maximum likelihood searches for trees conforming to each hypothesis. Kishino–Hasegawa tests were used to determine whether the data (LSU, SSU, and combined) reject any of the competing hypotheses. We also conducted unconstrained tree searches, compared the resulting topologies, and calculated bootstrap indices. Shimodaira–Hasegawa tests were applied to determine whether the data reject any of the topologies resulting from the constrained and unconstrained tree searches. LSU, SSU, and the combined data strongly contradict two assertions pertaining to sponge phylogeny. Hexactinellid sponges are not likely to be the basal lineage of a monophyletic Porifera or the sister group to all other animals. Instead, Hexactinellida and Demospongia form a well-supported clade of siliceous sponges, Silicea. It remains unclear, on the basis of these data alone, whether the calcarean sponges are more closely related to Silicea or to nonsponge animals. The SSU and combined data reject the hypothesis that Bilateria is more closely related to Ctenophora than it is to Cnidaria, whereas LSU data alone do not refute either hypothesis. LSU and SSU data agree in supporting the monophyly of Bilateria, Cnidaria, Ctenophora, and Metazoa. LSU sequence data reveal phylogenetic structure in a data set with limited taxon sampling. Continued accumulation of LSU sequences should increase our understanding of animal phylogeny.
Overview
AI snapshot
Written from the paper’s full text.
TL;DR
Complete LSU and SSU rRNA sequences for 23 taxa were used to test competing hypotheses of basal metazoan phylogeny. The data strongly reject Hexactinellida as basal within a monophyletic Porifera or as sister to all other animals, support a Silicea clade of Hexactinellida plus Demospongia, and reject Ctenophora as closer to Bilateria than Cnidaria in SSU and combined analyses.
Key findings
- LSU, SSU, and combined data reject two sponge hypotheses: Porifera monophyletic with Hexactinellida basal (KH P = 0.021, 0.002, 0.000 for SSU, LSU, combined) and Hexactinellida sister to all other Metazoans (KH P = 0.028, 0.005, 0.000). Instead, Hexactinellida and Demospongia form a well-supported Silicea clade (ML bootstraps 95 and 100); whether Calcarea is closer to Silicea or to nonsponge animals remains unclear.
- SSU and combined data reject Bilateria being more closely related to Ctenophora than to Cnidaria (KH P = 0.022 and 0.033), whereas LSU alone does not (P = 1.000).
- LSU and SSU agree in supporting monophyly of Bilateria, Cnidaria, Ctenophora, and Metazoa; ML bootstraps were 100 except Cnidaria (77 and 62) and Metazoa (63 and 63), and combined data raised Cnidaria and Metazoa support to 98 and 99.
- LSU and combined data reject Hydrozoa as sister to other cnidarians (KH P = 0.004 and 0.016; SH LSU P = 0.036), and SSU data reject Choanoflagellida as sister group to Metazoa (KH P = 0.049).
Methods
- Compiled complete LSU and SSU rRNA sequences for 23 taxa; 17 LSU and 3 SSU sequences were new. LSU was sequenced from mainly nonbilaterian animals (one mesomycetozoan, two choanoflagellates, four sponges, five cnidarians, three ctenophores, two bilaterians); SSU from three cnidarians; three fungi served as outgroup.
- Final alignment contained 4,003 characters (SSU 1,595; LSU 2,408), with 1,779 variable and 1,216 parsimony-informative sites combined. Secondary structure was encoded and ambiguous regions excluded; model selection used nested likelihood ratio tests in modeltest, and analyses used paup*.
- Constrained ML searches for a priori hypotheses were compared with Kishino–Hasegawa tests; unconstrained ML and MP searches (2:1 transversion:transition weighting) were compared with Shimodaira–Hasegawa tests; support estimated with 100 ML and 1,000 MP bootstrap pseudoreplicates and Bremer indices; analyses repeated excluding D. tigrina.
Limitations
- Stated: taxon sampling is relatively limited, particularly outside the fungal/animal divergence, and may be inadequate to resolve the closest relatives of animals; bilaterian taxa have the longest branches, so the position of Bilateria in any topology may be artifactual.
- Stated: SSU rRNA data have limitations including nucleotide compositional bias, among-site rate variation, and heterogeneous rates across lineages; LSU may share similar limitations because of similar functional constraints and genetic linkage.
- Evident from the text: the SH test did not yield many significant P-values, and SSU data did not refute any hypotheses under SH; LSU alone failed to reject the Ctenophora-sister-to-Bilateria hypothesis.
Model-written summary. Check it against the paper before relying on it.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
55 Own result · 9 Own interpretation · 7 Not checked yet · 2 No basis given · 1 Own method
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The combined and SSU data reject the hypothesis that Ctenophora is more closely related to Bilateria than is Cnidaria.”
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“A poorly supported (bootstrap < 50) monophyletic Porifera is the sister to all other animals, which are broadly arranged as seen in the SSU topology.”
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Our data unequivocally contradict this hypothesis and the proposal that Calcarea and Demospongia form a clade, leaving two hypotheses pertaining to sponge phylogeny for further consideration.”
boosted- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In contrast, the SSU topology has Hexactinellida plus Demospongia as the sister group to all other animals, Calcarea as the sister to nonsponge animals (Eumetazoa), and Ctenophora as the sister group to Cnidaria plus Bilateria.”
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“They are consistent in suggesting monophyletic Choanoflagellida, Metazoa, Bilateria, Cnidaria, and Ctenophora, with ML bootstraps of 100 except for Cnidaria (77 and 62) and Metazoa (63 and 63).”
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“LSU and SSU data agree in supporting the monophyly of Bilateria, Cnidaria, Ctenophora, and Metazoa.”
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The SH test, which was applied to all hypotheses that resulted from the constrained and unconstrained tree searches, did not yield many significant P-values.”
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The combined tree agrees with the LSU topology in having Anthozoa as sister to the medusa-bearing cnidarians.”
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In the combined ML topology, Mesomycetozoa plus Choanoflagellida compose the sister group to Metazoa.”
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The SSU data do not refute any hypotheses by using this test.”
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- It may state two separate claims as one. 10
- Probably not a substantial claim. 6
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Finally, the layout among cnidarians differs between the two topologies, with Hydrozoa being the sister group of Anthozoa plus Scyphozoa in the SSU topology and Anthozoa as the sister group to the medusa-bearing cnidarians in the LSU topology.”
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Within each gene, the loops were markedly more A-T rich than the stems.”
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The symmetric difference, or the number of clades present in only one of two trees being compared, is 6 between the combined ML topology and the SSU tree, whereas the symmetric difference between the combined and LSU trees is 10.”
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“For instance, relatively accelerated substitution rates in both genes are evident for the bilaterian taxa whereas rates are relatively low for cnidarians and ctenophores.”
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“By combining the data, bootstrap support for monophyly of Cnidaria and Metazoa increased to 98 and 99, respectively.”
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“However, the SSU data do not refute either of the competing hypotheses, and the LSU and combined data both strongly contradict the hypothesis that Hydrozoa is sister to the other cnidarian groups.”
boosted- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“The KH test is often inappropriately used to discern among hypotheses chosen a posteriori (33).”
What the sources say
- Not checked yetcites [33] Goldman N, Anderson J P, Rodrigo A G. Syst Biol. 2000;49:652–670. doi: 10.1080/106351500750049752. [DOI] [PubMed] [Google Scholar]
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Moreover, LSU is much larger than SSU and contains a greater proportion of variable regions.”
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper may give no reason why it holds. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Nevertheless, three independent sets of molecular data show sponges to be paraphyletic—SSU, LSU, and Protein Kinase C—implying that this alternative is most likely.”
hedgeddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“If true, then an animal with sponge characteristics is in the direct ancestry of nonsponge animals.”
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Cladistic analyses of morphology tend to suggest a step-wise arrangement where either Porifera or Placozoa diverge first, then Cnidaria, and finally Ctenophora, from the lineage leading to Bilateria (19, 20).”
What the sources say
- Not checked yetcites [19] Schram F R. In: The Early Evolution of Metazoa and the Significance of Problematic Taxa. Simonetta A M, Conway Morris S, editors. Cambridge, U.K.: Cambridge Univ. Press; 1991. pp. 35–46. [Google Scholar]
- Not checked yetcites [20] Nielsen C, Scharff N, Eibye-Jacobsen D. Biol J Linn Soc. 1996;57:385–410. [Google Scholar] source
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The LSU data also reject the SSU ML topology, presumably because it contains the cnidarian hypothesis that is rejected.”
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Agreement has also developed for the proposal that Deuterostomia is a clade composed of just Chordata, Urochordata, Hemichordata, and Echinodermata (17, 18).”
What the sources say
- Not checked yetcites [17] Zrzavy J, Mihulka S, Kepka P, Bezdek A, Tietz D. Cladistics. 1998;14:249–285. doi: 10.1111/j.1096-0031.1998.tb00338.x. [DOI] [PubMed] [Google Scholar]
- Not checked yetcites [18] Cameron C B, Garey J R, Swalla B J. Proc Natl Acad Sci USA. 2000;97:4469–4474. doi: 10.1073/pnas.97.9.4469. [DOI] [PMC free article] [PubMed] [Google Scholar] source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“Among the limitations noted are nucleotide compositional bias, among site rate variation, and heterogeneous rates of evolution across lineages (12–16).”
What the sources say
- Not checked yetcites [12] Rodrigo A G, Bergquist P R, Bergquist P L, Reeves R A. In: Sponges in Time and Space. van Soest R W M, van Kempen T M G, Braekman J-C, editors. Rotterdam, The Netherlands: Balkema; 1994. pp. 47–54. [Google Scholar]
- Not checked yetcites [13] Aguinaldo A M A, Turbeville J M, Linford L S, Rivera M C, Garey J R, Raff R A, Lake J A. Nature (London) 1997;387:489–493. doi: 10.1038/387489a0. [DOI] [PubMed] [Google Scholar] source
- Not checked yetcites [14] Abouheif E, Zardoya R, Meyer A. J Mol Evol. 1998;47:394–405. doi: 10.1007/pl00006397. [DOI] [PubMed] [Google Scholar] source
- Not checked yetcites [15] Ayala F J, Rzhetsky A, Ayala F J. Proc Natl Acad Sci USA. 1998;95:606–611. doi: 10.1073/pnas.95.2.606. [DOI] [PMC free article] [PubMed] [Google Scholar] source
- Not checked yetcites [16] Maley L E, Marshall C R. Science. 1998;279:505–506. doi: 10.1126/science.279.5350.505. [DOI] [PubMed] [Google Scholar]
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The authors state this as an assumption.
Comparative zoology is predicated on the assumption of a phylogenetic history.
“Comparative zoology is predicated on the assumption of a phylogenetic history.”
The paper relies on this without support.
The best measure of the validity of any hypothesis is provided by the accord or incongruence of alternative lines of evidence.
“Nevertheless, the best measure of the validity of any hypothesis is provided by the accord or incongruence of alternative lines of evidence.”
The paper relies on this without support.
Determining orthologs is not problematic for ribosomal genes because of the mechanisms of concerted evolution.
“Unlike for some protein coding genes, determining orthologs is not problematic for ribosomal genes because of the mechanisms of concerted evolution.”
The paper relies on this without support.
The best available model of sequence evolution selected by likelihood ratio tests is adequate for phylogenetic analysis.
“We performed nested likelihood ratio tests (LRT) by using modeltest version 3.0 (30) to determine the best available model of sequence evolution for the SSU, LSU, and combined data, as well as the stem and loop regions of each gene.”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“Molecular and morphological phylogenies agree that the bilaterian stem group emerged from a common ancestor of bilaterians and cnidarians, which probably existed much deeper in time (Peterson and Eernisse, 2001;Medina et al., 2001;Peterson and Davidson, 2000).”
From Precambrian Animal Life: Probable Developmental and Adult Cnidarian Forms from Southwest China (2002) · cites this paper as Medina et al., 2001
In the citing paper
“Molecular and morphological phylogenies agree that the bilaterian stem group emerged from a common ancestor of bilaterians and cnidarians, which probably existed much deeper in time (Peterson and Eernisse, 2001;Medina et al., 2001;Peterson and Davidson, 2000).”
From Precambrian Animal Life: Probable Developmental and Adult Cnidarian Forms from Southwest China (2002) · cites this paper as Medina et al., 2001
Citations
Cites
Molecular cloning: A laboratory manual
Deininger, P. L. (1990) · Analytical Biochemistry · doi:10.1016/0003-2697(90)90595-z · Cited by 84,684
MODELTEST: testing the model of DNA substitution.
Posada, D., & Crandall, K. A. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.9.817 · Cited by 19,820
Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference
Shimodaira, H., & Hasegawa, M. (1999) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026201 · Cited by 4,237
Kishino, H., & Hasegawa, M. (1989) · Journal of Molecular Evolution · doi:10.1007/bf02100115 · Cited by 3,310
The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions
Medlin, L. K., Elwood, H. J., Stickel, S. K., & Sogin, M. L. (1988) · Gene · doi:10.1016/0378-1119(88)90066-2 · Cited by 2,991
Self-citationEvidence for a clade of nematodes, arthropods and other moulting animals
Aguinaldo, A. M. A., Turbeville, J. M., Linford, L. S., Rivera, M. C., Garey, J. R., Raff, R. A., & Lake, J. A. (1997) · Nature · doi:10.1038/387489a0 · Cited by 1,609
Likelihood-Based Tests of Topologies in Phylogenetics
Goldman, N., Anderson, J. P., & Rodrigo, A. G. (2000) · Systematic Biology · doi:10.1080/106351500750049752 · Cited by 1,086
Early animal evolution: emerging views from comparative biology and geology
Knoll, A. H., & Carroll, S. B. (1999) · Science · doi:10.1126/science.284.5423.2129 · Cited by 821
Monophyletic Origins of the Metazoa: an Evolutionary Link with Fungi
Wainright, P. O., Hinkle, G., Sogin, M. L., & Stickel, S. K. (1993) · Science · doi:10.1126/science.8469985 · Cited by 656
Self-citationThe origins and relationships of lower invertebrates
Morris, S. C. (1983) · Lethaia · doi:10.1111/j.1502-3931.1983.tb02002.x · Cited by 605
Research works printed but not linked: 7
- A G Collins, J H Lipps, J W Valentine Paleobiology 26, 47–55 (2000). · DOI
- A G Rodrigo, P R Bergquist, P L Bergquist, R A Reeves Sponges in Time and Space, eds R W M van Soest, T M G van Kempen, J-C Braekman (Balkema, Rotterdam, The Netherlands), pp. 47–54 (1994).
- P De Rijk, Y Van De Peer, I Van Den Broeck, R De Wachter J Mol Evol 41, 366–375 (1995).
- D L Swofford paup* (Sinauer, Sunderland, MA, 2000).
- H Böger Meyniana 40, 67–90 (1988).
- J Reitner, D Mehl Verh Naturwiss Ver Hamburg 36, 5–32 (1996).
- L H Hyman The Invertebrates (McGraw–Hill, New York), pp. 726 (1940).
Cited by
Sorted by citations
Items 301–395 of 395
Santiago-Valentín, J. D., Bautista‐Guerrero, E., Rodríguez‐Troncoso, A. P., Franco-Gordo, M. D. C., Razo-López, M. A., & Godínez-Domínguez, E. (2024) · Diversity · doi:10.3390/d16070425 · Cited by 6
Zhou, C., Wu, C.-W., Guo, B.-Y., & Chen, Y. (2015) · Biochemical Systematics and Ecology · doi:10.1016/j.bse.2015.01.012 · Cited by 6
Assemblage of filamentous fungi associated with aculeate hymenopteran brood in reed galls
Heneberg, P., Bizos, J., Čmoková, A., Kolařík, M., Astapenková, A., & Bogusch, P. (2015) · Journal of Invertebrate Pathology · doi:10.1016/j.jip.2015.12.007 · Cited by 6
(2009) · doi:10.1093/acprof:oso/9780199549429.001.0001 · Cited by 7
The earliest fossil record of the animals and its significance
Budd, G. E. (2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.003.0001 · Cited by 6
The Evolutionary Origin of Animals and Fungi
Baldauf, S. L., Romeralo, M., & Carr, M. (2013) · Social and ecological interactions in the Galapagos Islands · doi:10.1007/978-1-4614-6732-8_7 · Cited by 6
Hoenigsberg, H. F., Tíjaro, M. H., & Sanabria, C. (2008) · Genetics and Molecular Research · doi:10.4238/vol7-1gmr375 · Cited by 6
Basal Metazoan Sensory Evolution
Jacobs, D. K., Gold, D. A., Nakanishi, N., Yuan, D., Camara, A., Nichols, S., & Hartenstein, V. (2010) · Science Publishers eBooks · doi:10.1201/b10425-11 · Cited by 6
Paleoclimate and Evolution: Emergence of Sponges During the Neoproterozoic
Müller, W. E. G., Wang, X., & Schröder, H. C. (2009) · Progress in molecular and subcellular biology · doi:10.1007/978-3-540-88552-8_3 · Cited by 5
Kumar, A., Chaudhary, A., Verma, C., & Singh, H. S. (2014) · Korean Journal of Parasitology · doi:10.3347/kjp.2014.52.6.701 · Cited by 5
Schmidt‐Rhaesa, A. (2007) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780198566687.003.0004 · Cited by 5
Peel, A. (2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.003.0016 · Cited by 4
Schmidt‐Rhaesa, A. (2007) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780198566687.003.0009 · Cited by 4
Genotyping of Sea Anemone during Early Development
Silva, M. A. P., & Nakanishi, N. (2019) · Journal of Visualized Experiments · doi:10.3791/59541 · Cited by 3
The origin and diversification of eukaryotes
Sogin, M. L., Patterson, D. J., & McArthur, A. G. (2007) · Cambridge University Press eBooks · doi:10.1017/cbo9780511812958.015 · Cited by 3
Self-citationBoco, S. R., Capidos, C. G. G., Fornillos, R. J. C., Sucharitakul, P., Lawley, J. W., Talacay, D., Collins, A. G., Fontanilla, I. K. C., Comendador, J., & Ladiao, F. R. (2025) · Regional Studies in Marine Science · doi:10.1016/j.rsma.2025.104033 · Cited by 3
Self-citationWang, C., Zhou, Y., Jiang, D., & Han, J. (2018) · Acta Oceanologica Sinica · doi:10.1007/s13131-018-1327-9 · Cited by 3
The origins and evolution of the Ecdysozoa
Telford, M. J., Bourlat, S. J., Economou, A. D., Papillon, D., & Rota‐Stabelli, O. (2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.003.0008 · Cited by 4
Origins of metazoan body plans: the larval revolution
Raff, R. A. (2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.003.0005 · Cited by 3
1 The Protistan Origins of Animals and Fungi
Carr, M., & Baldauf, S. L. (2011) · Springer eBooks · doi:10.1007/978-3-642-19974-5_1 · Cited by 3
Experimental reef communities persist under future ocean acidification and warmingPreprint
Jury, C. P., Bahr, K. D., Barba, E., Brainard, R. E., Cros, A., Dobson, K. L., Graham, A. T., McLachlan, R. H., Nelson, C. E., Price, J., et al. (2021) · Research Square · doi:10.21203/rs.3.rs-640089/v1 · Cited by 4
Redescription of the Sea Anemone Capnea japonica (Cnidaria: Anthozoa: Actiniaria)
Yanagi, K., & Izumi, T. (2021) · Species Diversity · doi:10.12782/specdiv.26.153 · Cited by 2
Izumi, T., Fujii, T., Yanagi, K., & Fujita, T. (2023) · Diversity · doi:10.3390/d15060773 · Cited by 2
Rahmany, W. S. E., & Blackstone, N. W. (2024) · Ecological and Evolutionary Physiology · doi:10.1086/729053 · Cited by 2
Identification of Histomonas meleagridis by in vitro microculture and polymerase chain reaction
Liu, W. W., Peng, J.-Y., Li, F., Sun, H., Ding, Y., Jing, H., & Liu, Y. (2011) · Reports in Parasitology · doi:10.2147/rip.s18259 · Cited by 2
Employing BAC-reporter constructs in the sea anemone Nematostella vectensis
Fischer, A., Tulin, S., Fredman, D., & Smith, J. (2013) · Integrative and Comparative Biology · doi:10.1093/icb/ict091 · Cited by 2
Reassembling animal evolution: a four-dimensional puzzle
Telford, M. J., Timothy, D. J., & Littlewood, D. T. J. (2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.003.0018 · Cited by 2
Beldade, P., & Saenko, S. V. (2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.003.0017 · Cited by 2
Schmidt‐Rhaesa, A. (2007) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780198566687.003.0007 · Cited by 2
Schmidt‐Rhaesa, A. (2007) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780198566687.003.0014 · Cited by 2
Sponges (Porifera) and Sponge Microbes
Hoffmann, F., & Schläppy, M. (2011) · Encyclopedia of earth sciences series/Encyclopedia of earth sciences · doi:10.1007/978-1-4020-9212-1_194 · Cited by 2
Khanaychenko, A. N., Nikolaeva, O. V., Rylkova, O. A., Saburova, M. A., & Aleoshin, V. V. (2024) · Botanica Marina · doi:10.1515/bot-2024-0039 · Cited by 1
Nunley, R. M., Rutkowski, E. C., Toonen, R. J., & Vicente, J. (2025) · PeerJ · doi:10.7717/peerj.18903 · Cited by 1
Izumi, T., Yanagi, K., & Kohtsuka, H. (2025) · Diversity · doi:10.3390/d17060430 · Cited by 1
Sensory perception in marine larvae
Modepalli, V. (2025) · Advances in marine biology · doi:10.1016/bs.amb.2025.09.003 · Cited by 1
Chemical micro-environments, ventilation behaviour & microbial processes in sponges
Schläppy, M. (2008) · Cited by 1
Schmidt‐Rhaesa, A. (2007) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780198566687.003.0011 · Cited by 1
Schmidt‐Rhaesa, A. (2007) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780198566687.003.0006 · Cited by 1
Schmidt‐Rhaesa, A. (2007) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780198566687.003.0003 · Cited by 1
Allam, M., & Marie, Z. A. (2021) · Egyptian Journal of Aquatic Biology and Fisheries · doi:10.21608/ejabf.2021.138554 · Cited by 1
Ewolucja. Twórcza moc selekcji
Dzik, J. (2021) · Wydawnictwa Uniwersytetu Warszawskiego eBooks · doi:10.31338/uw.9788323541134 · Cited by 1
Leitz, T. (2015) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199682201.003.0005 · Cited by 1
Ceriantharia: a retomada de um clado esquecido
Stampar, S. N. (2012) · Digital Library of Theses and Dissertations (Universidade de São Paulo) · doi:10.11606/t.41.2012.tde-16072012-151403 · Cited by 1
Boore, J. L., & Fuerstenberg, S. I. (2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.003.0013 · Cited by 1
Kashyap, P. L., Kumar, S., Sharma, A. B., Kumar, R. S., Mahapatra, S., Jasrotia, P., & Singh, G. P. (2021) · Research Square · doi:10.21203/rs.3.rs-680979/v1 · Cited by 1
The animal in the genome: comparative genomics and evolution
Copley, R. R. (2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.003.0014 · Cited by 1
Development of Homoscleromorpha of the Order Homosclerophorida Dendy, 1905
Ereskovsky, A. V. (2010) · Springer eBooks · doi:10.1007/978-90-481-8575-7_4 · Cited by 1
Abed, C. (2011) · theses.fr (ABES) · doi:10.70675/20073443z7688z4e8azb2e5z0c9d31eaf64b · Cited by 1
Ivanišević, J. (2011) · theses.fr (ABES) · doi:10.70675/6797e502z87aaz4438z85eez039ab1ede89b · Cited by 1
Filogènia Molecular dels Bilaterals: una aproximació multigènica
Montserrat, J. P. (2008) · LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas)
Hwang, U. W. (2007) · Parasitology Research · doi:10.1007/s00436-007-0471-5
Veena, S. S., & Laxmilatha, P. (2011) · Marine Biodiversity Records · doi:10.1017/s1755267211000893
Insights from Sponge Transcriptomes & Physiology about the Early Evolution of Nervous Systems
Farrar, N. R. (2014) · ERA: Education and Research Archive (University of Alberta) · doi:10.7939/r3183485q
Cammarata, M., Trapani, M. R., & Parrinello, N. (2013) · Nova Science Publishers (Nova Science Publishers, Inc.)
The role of HyBMP5-8b, a BMP5-8 orthologue, during axial patterning and tentacle formation in Hydra
Reinhardt, B. (2006) · Multimedialen Archiv und Publikationsserver der Christian-Albrechts-Universität zu Kiel (Christian-Albrechts-Universität zu Kiel)
New TheoryA genomic parasite in the evolution of metazoan development
Hoenigsberg, H. F., & Sanabria, C. (2009) · Genetics and Molecular Research · doi:10.4238/vol8-3gmr571
Schmidt‐Rhaesa, A. (2007) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780198566687.003.0002
Towards understanding a holobiont: host-microbe interactions in Hydra
Fraune, S. (2009) · MACAU: Open Access Repository of Kiel University (University Library Kiel)
Assmann, M., & Gründer, S. (2014) · RWTH Publications (RWTH Aachen)
Ritmo circadiano e melatonina em Porifera
dos Santos, J. C. (2018) · Digital Library of Theses and Dissertations (Universidade de São Paulo) · doi:10.11606/d.41.2018.tde-16042018-110044
Molecular phylogenetics of the Metazoan clade Lophotrochozoa
Passamaneck, Y. J. (2003) · doi:10.1575/1912/2452
(2021) · Elsevier eBooks · doi:10.1016/b978-0-12-822655-1.16001-5
Schmidt‐Rhaesa, A. (2007) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780198566687.003.0013
Lowe, C. J. (2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.003.0010
Schmidt‐Rhaesa, A. (2007) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780198566687.003.0012
Schmidt‐Rhaesa, A. (2007) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780198566687.003.0005
Schmidt‐Rhaesa, A. (2007) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780198566687.003.0008
Schmidt‐Rhaesa, A. (2007) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780198566687.003.0010
(2004) · Encyclopedic Dictionary of Genetics, Genomics and Proteomics · doi:10.1002/0471684228.egp04227
(2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.002.0004
(2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.002.0003
(2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.002.0007
(2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.002.0008
(2007) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780198566687.002.0006
(2007) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780198566687.002.0003
(2007) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780198566687.002.0004
Cruz‐Barraza, J. A., Carballo, J. L., & Aguilar-Camacho, J. M. (2023) · Zoological Journal of the Linnean Society · doi:10.1093/zoolinnean/zlad036
Diversification of Cnidarian Mechanosensory Neurons Across Life Cycle Phases: Evidence from Hydrozoa
Nakanishi, N., Takahashi, M., & Kumano, G. (2025) · Integrative and Comparative Biology · doi:10.1093/icb/icaf027
Genetic Characterization of Schistosoma Species from Goats in Pakistan Using the 28S rDNA Region
Khan, M. A., Afshan, K., Firasat, S., Ullah, M. F., Khan, M., & Abduvalieva, D. (2025) · Indian Journal of Microbiology · doi:10.1007/s12088-025-01502-y
Supplemental Data: Placozoa No Longer a Phylum of One
Voigt, O., Collins, A. G., Pearse, V. B., Pearse, J. S., Ender, A., Hadrys, H., & Schierwater, B. (2004) · Smithsonian Digital Repository (Smithsonian Institution)
Self-citationAdditional file 1 of Forcing external constraints on tree inference using ASTRAL
Rabiee, M., & Mirarab, S. (2020) · Figshare · doi:10.6084/m9.figshare.12144273
Cardoso, D. C., & Cristiano, M. P. (2026) · Comparative Cytogenetics · doi:10.3897/compcytogen.20.162616
The fossil record of siliceous sponge spicules can be taken at face valuePreprint
Cui, S., Mizrahi, N., Rahman, S., Nichols, S., Karim, T. S., & Simpson, C. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.27.702024
Lapébie, P. (2010) · theses.fr (ABES) · doi:10.70675/29fb5e58z95e7z4353z8498zaa306e8a2449
Pratlong, M. (2016) · theses.fr (ABES) · doi:10.70675/2f48e6ddza822z455eza9d5zf10fc679949c
Étude génétique et moléculaire d'éponges marines de la Martinique
Piron, J. (2021) · theses.fr (ABES) · doi:10.70675/dcf20327z74e4z4595z9839z5758bc9f3ceb
Lewis, P. A., Horowitz, Z., Shribak, M. I., & Echeverri, K. (2026) · Developmental Dynamics · doi:10.1002/dvdy.70173
A morphological phylogenetic approach to the evolution of symmetry in animals
McDermott, J., Dunn, F. S., Marlétaz, F., & Rahman, I. A. (2026) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2026.1111
Saburova, M. A., Khanaychenko, A. N., Nikolaeva, O. V., Rylkova, O. A., Efimova, T. V., Berdieva, M. A., Meger, Y. V., & Aleoshin, V. V. (2026) · European Journal of Phycology · doi:10.1080/09670262.2026.2696474
Multigene datasets for deep phylogeny
Jones, M. O. (2007) · ERA
Metadata
- Authors
- Medina, M., Collins, A. G., Silberman, J. D., & Sogin, M. L.
- Affiliations
- Marine Biological Laboratory (US)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2001-08-14
- Volume
- 98
- Issue
- 17
- Pages
- 9707-9712
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC55517
- OpenAlex
- W2028169893
- Semantic Scholar
- f694ef75b9f27240d665cb7d43dedb376b9ed7f2
- Cited by
- 395
- References
- 46
- Citations by year
- 2026: 5 · 2025: 7 · 2024: 5 · 2023: 4 · 2022: 2 · 2021: 11 · 2020: 5 · 2019: 4 · 2018: 5 · 2017: 4 · 2016: 10 · 2015: 7 · 2014: 9 · 2013: 10 · 2012: 16
- FWCI
- 23.98
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Smithsonian Digital Repository (Smithsonian Institution) (submittedVersion)
- Funders
- National Science Foundation (9814845)
- National Aeronautics and Space Administration
- Florida International University
- National Institutes of Health (5r01gm032964-17, GM32964)
- National Institute of General Medical Sciences (GM32964)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Marine Invertebrate Physiology and Ecology
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Protist diversity and phylogeny
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- sponge phylogeny, Hexactinellida, Demospongiae, Silicea, calcareous sponges, sponges, Bilateria, Ctenophora, Cnidaria, monophyly, large subunit rRNA, small subunit rRNA, phylogenetic incongruence
- MeSH terms
- Animals, Animal Population Groups, Aplysia, Cnidaria, Echinodermata, Fungi, Models, Biological, Molecular Sequence Data, Phylogeny, Platyhelminths, Porifera, RNA, Fungal, RNA, Ribosomal, Sequence Homology, Nucleic Acid, Species Specificity, Urochordata, Xenopus laevis, Polymerase Chain Reaction, Sequence Alignment, Sequence Analysis, RNA, Evolution, Molecular
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
A language model drew the claims from the paper on 2026-10-06, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-10-06 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
