Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA

Medina, Mónica; Collins, Allen G.; Silberman, Jeffrey D.; Sogin, Mitchell L.

doi:10.1073/pnas.171316998

Cited by 395Marine Invertebrate Physiology and EcologyProtist diversity and phylogenyGenomics and Phylogenetic Studies

Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA

Open access

Medina, Mónica, Collins, Allen G., Silberman, Jeffrey D., Sogin, Mitchell L.·2001·Proceedings of the National Academy of Sciences

DOI 10.1073/pnas.171316998PMC PMC55517

Open this paper in CoChat — free account

Abstract

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.

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

Crossref · 10.1073/pnas.171316998

Cites

42 of 42 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 15 cited sources checked · 0 supported · 0 flagged

Findingown data
§ Results
The combined and SSU data reject the hypothesis that Ctenophora is more closely related to Bilateria than is Cnidaria.
“The combined and SSU data reject the hypothesis that Ctenophora is more closely related to Bilateria than is Cnidaria.”
Quote in the paperSubstantial claim
Findingown data
§ Results
A poorly supported monophyletic Porifera is the sister to all other animals in the combined ML topology.
“A poorly supported (bootstrap < 50) monophyletic Porifera is the sister to all other animals, which are broadly arranged as seen in the SSU topology.”
Quote in the paperNot a substantial claim
Findingown data
§ Discussion
Our data unequivocally contradict the hypothesis that Hexactinellida may be the sister group to all other metazoans.
“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.”
Quote in the paperSubstantial claim
Findingown data
§ Results
The SSU topology has Calcarea as the sister to nonsponge animals (Eumetazoa).
“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.”
Quote in the paperSubstantial claim
Findingown data
§ Results
The optimal SSU and LSU ML trees are consistent in suggesting monophyletic Metazoa.
“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).”
Quote in the paperSubstantial claim

Findingown data
§ Abstract
LSU and SSU data agree in supporting the monophyly of Cnidaria.
“LSU and SSU data agree in supporting the monophyly of Bilateria, Cnidaria, Ctenophora, and Metazoa.”
Quote in the paperSubstantial claim
Findingown data
§ Results
The SH test did not yield many significant P-values.
“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.”
Quote in the paperNot a substantial claim
Findingown data
§ Results
The combined tree agrees with the LSU topology in having Anthozoa as sister to the medusa-bearing cnidarians.
“The combined tree agrees with the LSU topology in having Anthozoa as sister to the medusa-bearing cnidarians.”
Quote in the paperNot a substantial claim
Findingown data
§ Results
In the combined ML topology, Mesomycetozoa plus Choanoflagellida compose the sister group to Metazoa.
“In the combined ML topology, Mesomycetozoa plus Choanoflagellida compose the sister group to Metazoa.”
Quote in the paperSubstantial claim
Findingown data
§ Results
The SSU data do not refute any hypotheses by using the SH test.
“The SSU data do not refute any hypotheses by using this test.”
Quote in the paperSubstantial claim
Findingown data
§ Discussion
The SSU and combined data presented here suggest that the hypothetical clade Ctenophora plus Bilateria is significantly less probable than Bilateria plus Cnidaria.
“In fact, the SSU and combined data presented here suggest that the hypothetical clade Ctenophora plus Bilateria is significantly less probable than Bilateria plus Cnidaria.”
Quote in the paperSubstantial claim
Findingown data
§ Discussion
The SSU data reject the hypothesis that Choanoflagellida is most closely related to Metazoa.
“Moreover, the SSU data reject the hypothesis that Choanoflagellida is most closely related to Metazoa.”
Quote in the paperSubstantial claim
Findingown data
§ Results
The LSU and combined data both reject the two hypotheses pertaining to sponge phylogeny that were rejected by the KH tests.
“However, the LSU and combined data both reject the two hypotheses pertaining to sponge phylogeny that were rejected by the KH tests.”
Quote in the paperSubstantial claim
Findingown data
§ Results
Both topologies contradict the hypothesis that sponges form a monophyletic Porifera.
“In addition, both topologies contradict the hypothesis that sponges form a monophyletic Porifera and reveal a well-supported (bootstraps of 95 and 100) grouping of the siliceous sponges, Hexactinellida and Demospongia (Silicea).”
Quote in the paperSubstantial claim
Findingown data
§ Results
The LSU tree depicts Ctenophora plus Cnidaria as the sister group to a clade that includes sponges paraphyletically arranged at the base of the bilaterian animals.
“The LSU tree depicts Ctenophora plus Cnidaria as the sister group to a clade that includes sponges paraphyletically arranged at the base of the bilaterian animals.”
Quote in the paperSubstantial claim
Findingown data
§ Results
KH tests reject a number of a priori metazoan hypotheses.
“KH tests reject a number of a priori metazoan hypotheses (Table 4).”
Quote in the paperSubstantial claim
Findingown data
§ Discussion
In this analysis, bilaterian taxa display the longest branches.
“Nevertheless, in this analysis, bilaterian taxa display the longest branches, which are notoriously difficult for phylogenetic analyses, particularly when taxon sampling is limited.”
Quote in the paperSubstantial claim
Findingown data
§ Results
For the taxa sampled, the pattern and overall base composition of the LSU gene is very similar to that of the SSU gene.
“For the taxa we sampled, the pattern and overall base composition of the LSU gene is very similar to that of the SSU gene (Table 5).”
Quote in the paperNot a substantial claim
Findingown data
§ Results
The optimal SSU and LSU ML trees are consistent in suggesting monophyletic Bilateria.
“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).”
Quote in the paperSubstantial claim
Findingown data
§ Results
The LSU topology has Anthozoa as the sister group to the medusa-bearing cnidarians.
“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.”
Quote in the paperNot a substantial claim
Findingown data
§ Discussion
Our data unequivocally contradict the proposal that Calcarea and Demospongia form a clade.
“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.”
Quote in the paperSubstantial claim
Findingown data
§ Discussion
The SSU data do not refute either of the competing hypotheses about whether Hydrozoa is sister to other cnidarians.
“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.”
Quote in the paperSubstantial claim
Findingown data
§ Abstract
LSU and SSU data agree in supporting the monophyly of Ctenophora.
“LSU and SSU data agree in supporting the monophyly of Bilateria, Cnidaria, Ctenophora, and Metazoa.”
Quote in the paperSubstantial claim
Findingown data
§ Abstract
Hexactinellid sponges are not likely to be the basal lineage of a monophyletic Porifera.
“Hexactinellid sponges are not likely to be the basal lineage of a monophyletic Porifera or the sister group to all other animals.”
Quote in the paperSubstantial claim
Findingown data
§ Results
The SSU topology has Ctenophora as the sister group to Cnidaria plus Bilateria.
“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.”
Quote in the paperSubstantial claim
Findingown data
§ Results
The optimal SSU and LSU ML trees are consistent in suggesting monophyletic Ctenophora.
“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).”
Quote in the paperSubstantial claim
Findingown data
§ Results
Results of KH tests for all other hypotheses chosen a priori were not significant.
“Results of KH tests for all other hypotheses chosen a priori were not significant (Table 4).”
Quote in the paperSubstantial claim
Findingown data
§ Abstract
LSU and SSU data agree in supporting the monophyly of Bilateria.
“LSU and SSU data agree in supporting the monophyly of Bilateria, Cnidaria, Ctenophora, and Metazoa.”
Quote in the paperSubstantial claim
Findingown data
§ Discussion
The optimal ML tree based on the SSU sequences compiled here corresponds with Hyman's view that Hydrozoa was the ancestral group of cnidarians.
“Surprisingly, the optimal ML tree, on the basis of the SSU sequences compiled here, corresponds with Hyman's view.”
Quote in the paperNot a substantial claim
Findingown data
§ Abstract
Hexactinellida and Demospongia form a well-supported clade of siliceous sponges, Silicea.
“Instead, Hexactinellida and Demospongia form a well-supported clade of siliceous sponges, Silicea.”
- Also stated in: § Results · boosted
  “reveal a well-supported (bootstraps of 95 and 100) grouping of the siliceous sponges, Hexactinellida and Demospongia (Silicea).”
Quote in the paperSubstantial claim
Findingown data
§ Abstract
Hexactinellid sponges are not likely to be the sister group to all other animals.
“Hexactinellid sponges are not likely to be the basal lineage of a monophyletic Porifera or the sister group to all other animals.”
Quote in the paperSubstantial claim
Findingown data
§ Abstract
The SSU and combined data reject the hypothesis that Bilateria is more closely related to Ctenophora than it is to Cnidaria.
“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.”
- Also stated in: § Results · plain
  “The combined and SSU data reject the hypothesis that Ctenophora is more closely related to Bilateria than is Cnidaria.”
Quote in the paperSubstantial claim
Findingown data
§ Results
The optimal SSU and LSU ML trees are consistent in suggesting monophyletic Cnidaria.
“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).”
Quote in the paperNot a substantial claim
Findingown data
§ Results
The optimal SSU and LSU ML trees are consistent in suggesting monophyletic Choanoflagellida.
“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).”
Quote in the paperNot a substantial claim
Findingown data
§ Results
LSU, SSU, and the combined data reject two of four hypotheses dealing with sponge phylogeny.
“LSU, SSU, and the combined data reject two of four hypotheses dealing with sponge phylogeny.”
Quote in the paperSubstantial claim
Findingnone given
§ Abstract
LSU sequence data reveal phylogenetic structure in a data set with limited taxon sampling.
“LSU sequence data reveal phylogenetic structure in a data set with limited taxon sampling.”
Quote in the paperSubstantial claim
Findingown data
§ Results
All clades in common to the SSU and LSU topologies are also present in the combined ML tree.
“Not surprisingly, all clades in common to the SSU and LSU topologies are also present in the combined ML tree (Fig. 2).”
Quote in the paperNot a substantial claim
Findingown data
§ Discussion
The SSU and combined data ML trees suggest that Choanoflagellida plus Mesomycetozoa is the sister group to animals.
“The SSU and combined data ML trees (Figs. 1 and 2) suggest that Choanoflagellida plus Mesomycetozoa is the sister group to animals.”
Quote in the paperSubstantial claim
Findingown data
§ Results
The LSU and combined data reject the idea that Hydrozoa is the sister group to other cnidarians.
“The LSU and combined data reject the idea that Hydrozoa is the sister group to other cnidarians.”
Quote in the paperSubstantial claim
Findingown data
§ Results
The SH test with LSU data rejects the hypothesis that Hydrozoa is sister to the other cnidarians.
“In addition, the SH test with LSU data reject the hypothesis that Hydrozoa is sister to the other cnidarians.”
Quote in the paperSubstantial claim
Findingown data
§ Results
The combined data produce a topology that is more similar to the SSU ML tree than to the LSU reconstruction.
“The combined data produce a topology that is more similar to the SSU ML tree than to the LSU reconstruction.”
Quote in the paperNot a substantial claim
Findingown data
§ Discussion
The LSU data favor the idea that the mesomycetozoan animal parasites are the closest living relatives of animals.
“In contrast, the LSU data favor the interesting idea that the mesomycetozoan animal parasites are the closest living relatives of animals.”
Quote in the paperSubstantial claim
Findingown data
§ Results
The SSU topology has Hexactinellida plus Demospongia as the sister group to all other animals.
“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.”
Quote in the paperSubstantial claim
Findingown data
§ Results
There is a strong correspondence between the ML and MP topologies based on the combined data.
“Although not identical, there is a strong correspondence between the ML and MP topologies based on the combined data (Fig. 2).”
Quote in the paperNot a substantial claim
Findingown data
§ Abstract
LSU and SSU data agree in supporting the monophyly of Metazoa.
“LSU and SSU data agree in supporting the monophyly of Bilateria, Cnidaria, Ctenophora, and Metazoa.”
Quote in the paperSubstantial claim
Findingown data
§ Abstract
It remains unclear, on the basis of these data alone, whether the calcarean sponges are more closely related to Silicea or to nonsponge animals.
“It remains unclear, on the basis of these data alone, whether the calcarean sponges are more closely related to Silicea or to nonsponge animals.”
Quote in the paperSubstantial claim
Findingown data
§ Results
That Choanoflagellida is the sister group to Metazoa is rejected by SSU data.
“That Choanoflagellida is the sister group to Metazoa is rejected by SSU data.”
Quote in the paperSubstantial claim
Findingown data
§ Results
Both topologies reveal a well-supported grouping of the siliceous sponges, Hexactinellida and Demospongia (Silicea).
“In addition, both topologies contradict the hypothesis that sponges form a monophyletic Porifera and reveal a well-supported (bootstraps of 95 and 100) grouping of the siliceous sponges, Hexactinellida and Demospongia (Silicea).”
Quote in the paperSubstantial claim
Findingown data
§ Abstract
LSU, SSU, and combined data strongly contradict two assertions pertaining to sponge phylogeny.
“LSU, SSU, and the combined data strongly contradict two assertions pertaining to sponge phylogeny.”
Quote in the paperSubstantial claim
Findingown data
§ Abstract
LSU data alone do not refute either the hypothesis that Bilateria is more closely related to Ctenophora than to Cnidaria or the alternative.
“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.”
Quote in the paperSubstantial claim
Premisecitation
§ Abstract
SSU rRNA data suggest that Cnidaria, Placozoa, and Bilateria form a well-supported clade to the exclusion of Ctenophora.
“This view is contradicted by SSU rRNA data, which weakly suggest that sponges are paraphyletically arranged at the base of Metazoa (21, 22) and that Cnidaria, Placozoa, and Bilateria form a well-supported clade to the exclusion of Ctenophora (22, 23).”
Quote in the paperSubstantial claim0 of 2 sources checked
- cites [22] Collins A G. Proc Natl Acad Sci USA. 1998;95:15458–15463. doi: 10.1073/pnas.95.26.15458. [DOI] [PMC free article] [PubMed] [Google Scholar] source
  Not checked in the free run.
- cites [23] Kim J H, Kim W, Cunningham C W. Mol Biol Evol. 1999;16:423–427. doi: 10.1093/oxfordjournals.molbev.a026124. [DOI] [PubMed] [Google Scholar] source
  Not checked in the free run.
Interpretationown data
§ Discussion
The LSU and SSU data that we present suggest that a number of hypotheses concerning early animal phylogeny are unlikely to be true.
“The LSU and SSU data that we present suggest that a number of hypotheses concerning early animal phylogeny are unlikely to be true.”
Quote in the paperSubstantial claim
Interpretationown data
§ Results
A comparison of branch lengths in the unconstrained ML topologies based on SSU and LSU data suggests that there are lineage specific factors affecting the rate of evolution in these two genes.
“A comparison of branch lengths in the unconstrained ML topologies based on SSU and LSU data suggests that there are lineage specific factors affecting the rate of evolution in these two genes (Fig. 1).”
Quote in the paperNot a substantial claim
Study design and conductown data
§ Results
The likelihood ratio test indicated that very similar models of nucleotide evolution best fit the LSU, SSU, and combined data.
“The likelihood ratio test implemented in modeltest (30) indicated that very similar models of nucleotide evolution best fit the LSU, SSU, and combined data (Table 5).”
Quote in the paperNot a substantial claim0 of 1 sources checked
- cites [30] Posada D, Crandall K A. Bioinformatics. 1998;14:817–818. doi: 10.1093/bioinformatics/14.9.817. [DOI] [PubMed] [Google Scholar] source
  Not checked in the free run.
- Rests on an assumption: The best available model of sequence evolution selected by likelihood ratio tests is adequate for phylogenetic analysis.
Interpretationreasoning
§ Abstract
The nuclear LSU rRNA gene may have great potential as a phylogenetic marker for animals.
“The nuclear large subunit (LSU) rRNA gene may have great potential as a phylogenetic marker for animals.”
Quote in the paperSubstantial claim
- Rests on an assumption: Determining orthologs is not problematic for ribosomal genes because of the mechanisms of concerted evolution.
Interpretationown data
§ Discussion
The position of Bilateria in any of the topologies suggested by our data may potentially be artifactual.
“Therefore, the position of Bilateria in any of the topologies suggested by our data may potentially be artifactual.”
Quote in the paperSubstantial claim
Premisecitation
§ Abstract
SSU rRNA data weakly suggest that sponges are paraphyletically arranged at the base of Metazoa.
“This view is contradicted by SSU rRNA data, which weakly suggest that sponges are paraphyletically arranged at the base of Metazoa (21, 22) and that Cnidaria, Placozoa, and Bilateria form a well-supported clade to the exclusion of Ctenophora (22, 23).”
Quote in the paperSubstantial claim0 of 2 sources checked
- cites [21] Cavalier-Smith T, Allsopp M T E P, Chao E E, Boury-Esnault N, Vacelet J. Can J Zool. 1996;74:2031–2045. [Google Scholar] source
  Not checked in the free run.
- cites [22] Collins A G. Proc Natl Acad Sci USA. 1998;95:15458–15463. doi: 10.1073/pnas.95.26.15458. [DOI] [PMC free article] [PubMed] [Google Scholar] source
  Not checked in the free run.
Interpretationown data
§ Discussion
Our data set, with its relatively limited taxon sampling, may be inadequate to resolve the question of whether Choanoflagellida, Mesomycetozoa, or the two combined are the closest living relatives of animals.
“Nevertheless, our data set, with its relatively limited taxon sampling (particularly outside the fungal/animal divergence), may be inadequate to resolve this question.”
Quote in the paperSubstantial claim
Study design and conductown data
§ Results
Removing the relatively fast evolving sequences of D. tigrina had no substantive impact on the results of the constrained and unconstrained tree searches, as well as the KH and SH tests.
“Finally, removing the relatively fast evolving sequences of D. tigrina had no substantive impact on the results (not shown) of the constrained and unconstrained tree searches, as well as the KH and SH tests.”
Quote in the paperNot a substantial claim
Interpretationreasoning
§ Discussion
LSU data, especially when combined with SSU data, have significant potential to further resolve questions dealing with phylogenetic relationships within and among animal phyla.
“LSU data, especially when combined with SSU data, have significant potential to further resolve questions dealing with the phylogenetic relationships within and among animal phyla.”
Quote in the paperSubstantial claim
- Rests on an assumption: Determining orthologs is not problematic for ribosomal genes because of the mechanisms of concerted evolution.

May combine two claims. 10
Classified as probably not a substantial claim. 6

May combine two claims.
Findingown data
§ Results
The layout among cnidarians differs between the SSU and LSU topologies, with Hydrozoa being the sister group of Anthozoa plus Scyphozoa in the SSU topology.
“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.”
Quote in the paperNot a substantial claim
Probably not a substantial claim: may not pass S3 (load-bearing).
Findingown data
§ Results
Within each gene, the loops were markedly more A-T rich than the stems.
“Within each gene, the loops were markedly more A-T rich than the stems.”
Quote in the paperNot a substantial claim
May combine two claims.
Findingown data
§ Results
The symmetric difference is 6 between the combined ML topology and the SSU tree, whereas the symmetric difference between the combined and LSU trees is 10.
“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.”
Quote in the paperNot a substantial claim
May combine two claims.
Findingown data
§ Results
Relatively accelerated substitution rates in both genes are evident for the bilaterian taxa whereas rates are relatively low for cnidarians and ctenophores.
“For instance, relatively accelerated substitution rates in both genes are evident for the bilaterian taxa whereas rates are relatively low for cnidarians and ctenophores.”
Quote in the paperNot a substantial claim
May combine two claims.
Findingown data
§ Results
By combining the data, bootstrap support for monophyly of Cnidaria and Metazoa increased to 98 and 99, respectively.
“By combining the data, bootstrap support for monophyly of Cnidaria and Metazoa increased to 98 and 99, respectively.”
Quote in the paperSubstantial claim
May combine two claims.
Findingown data
§ Discussion
The LSU and combined data both strongly contradict the hypothesis that Hydrozoa is sister to the other cnidarian groups.
“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.”
Quote in the paperSubstantial claim
Classified as probably not a substantial claim.
Premisecitation
§ Materials and Methods
The KH test is often inappropriately used to discern among hypotheses chosen a posteriori.
“The KH test is often inappropriately used to discern among hypotheses chosen a posteriori (33).”
Quote in the paperSubstantial claim0 of 1 sources checked
- cites [33] Goldman N, Anderson J P, Rodrigo A G. Syst Biol. 2000;49:652–670. doi: 10.1080/106351500750049752. [DOI] [PubMed] [Google Scholar]
  Not checked in the free run.
Probably not a substantial claim: may not pass S4 (based). May combine two claims.
Premisenone given
§ Abstract
LSU is much larger than SSU and contains a greater proportion of variable regions.
“Moreover, LSU is much larger than SSU and contains a greater proportion of variable regions.”
Quote in the paperNot a substantial claim
May combine two claims.
Interpretationreasoning
§ Discussion
Three independent sets of molecular data-SSU, LSU, and Protein Kinase C-show sponges to be paraphyletic, implying that this alternative is most likely.
“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.”
Quote in the paperSubstantial claim
Classified as probably not a substantial claim. May combine two claims.
Interpretationreasoning
§ Discussion
If sponges are paraphyletic, then an animal with sponge characteristics is in the direct ancestry of nonsponge animals.
“If true, then an animal with sponge characteristics is in the direct ancestry of nonsponge animals.”
Quote in the paperSubstantial claim
Classified as probably not a substantial claim.
Premisecitation
§ Abstract
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.
“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).”
Quote in the paperSubstantial claim0 of 2 sources checked
- cites [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 in the free run.
- cites [20] Nielsen C, Scharff N, Eibye-Jacobsen D. Biol J Linn Soc. 1996;57:385–410. [Google Scholar] source
  Not checked in the free run.
May combine two claims.
Interpretationreasoning
§ Results
The LSU data reject the SSU ML topology, presumably because it contains the cnidarian hypothesis that is rejected.
“The LSU data also reject the SSU ML topology, presumably because it contains the cnidarian hypothesis that is rejected.”
Quote in the paperNot a substantial claim
Probably not a substantial claim: may not pass S3 (load-bearing).
Premisecitation
§ Abstract
Agreement has developed for the proposal that Deuterostomia is a clade composed of just Chordata, Urochordata, Hemichordata, and Echinodermata.
“Agreement has also developed for the proposal that Deuterostomia is a clade composed of just Chordata, Urochordata, Hemichordata, and Echinodermata (17, 18).”
Quote in the paperNot a substantial claim0 of 2 sources checked
- cites [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 in the free run.
- cites [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
  Not checked in the free run.
May combine two claims.
Premisecitation
§ Abstract
Analyses of nuclear SSU rRNA sequences have limitations including nucleotide compositional bias, among site rate variation, and heterogeneous rates of evolution across lineages.
“Among the limitations noted are nucleotide compositional bias, among site rate variation, and heterogeneous rates of evolution across lineages (12–16).”
Quote in the paperSubstantial claim0 of 5 sources checked
- cites [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 in the free run.
- cites [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 in the free run.
- cites [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 in the free run.
- cites [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 in the free run.
- cites [16] Maley L E, Marshall C R. Science. 1998;279:505–506. doi: 10.1126/science.279.5350.505. [DOI] [PubMed] [Google Scholar]
  Not checked in the free run.

14 of 14

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.”

4 of 4

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?

The bilaterian-cnidarian ancestor likely lived well before the Cambrian.
“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
Both molecular and morphological phylogenies indicate that the bilaterian stem lineage arose from an ancestor shared with cnidarians.
“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

Molecular cloning: A laboratory manual
Deininger, P. L. (1990) · Analytical Biochemistry · doi:10.1016/0003-2697(90)90595-z · Cited by 84,684 · see citing works
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 · see citing works
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 · see citing works
Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea
Kishino, H., & Hasegawa, M. (1989) · Journal of Molecular Evolution · doi:10.1007/bf02100115 · Cited by 3,378 · see citing works
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 · see citing works
Self-citation
Evidence 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 · see citing works
Likelihood-Based Tests of Topologies in Phylogenetics
Goldman, N., Anderson, J. P., & Rodrigo, A. G. (2000) · Systematic Biology · doi:10.1080/106351500750049752 · Cited by 1,076 · see citing works
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 · see citing works
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 653 · see citing works
Self-citation
The origins and relationships of lower invertebrates
Morris, S. C. (1983) · Lethaia · doi:10.1111/j.1502-3931.1983.tb02002.x · Cited by 605 · see citing works
Phylogeny of the Metazoa Based on Morphological and 18S Ribosomal DNA Evidence
Zrzavý, J., Mihulka, S., Kepka, P., Bezděk, A., & Tietz, D. F. (1998) · Cladistics · doi:10.1111/j.1096-0031.1998.tb00338.x · Cited by 439 · see citing works
A critical reappraisal of the fossil record of the bilaterian phyla
BUDD, G. E., & JENSEN, S. (2000) · Biological Reviews of the Cambridge Philosophical Society · doi:10.1017/s000632310000548x · Cited by 428 · see citing works
The Early Evolution of Metazoa and the Significance of Problematic Taxa.
Ghiselin, M. T., Simonetta, A. M., & Morris, S. C. (1993) · Systematic Biology · doi:10.2307/2992562 · Cited by 414 · see citing works
Evolution of the chordate body plan: New insights from phylogenetic analyses of deuterostome phyla
Cameron, C. B., Garey, J. R., & Swalla, B. J. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.9.4469 · Cited by 414 · see citing works
Origin of Bilaterian Body Plans: Evolution of Developmental Regulatory Mechanisms
Davidson, E. H., Peterson, K. J., & Cameron, R. A. (1995) · Science · doi:10.1126/science.270.5240.1319 · Cited by 381 · see citing works
Origin of the metazoan phyla: Molecular clocks confirm paleontological estimates
Ayala, F. J., Rzhetsky, A., & Ayala, F. J. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.2.606 · Cited by 342 · see citing works
Fossils, molecules and embryos: new perspectives on the Cambrian explosion
Valentine, J. W., Jablonski, D., & Erwin, D. H. (1999) · Development · doi:10.1242/dev.126.5.851 · Cited by 300 · see citing works
Class-level relationships in the phylum Cnidaria: evidence from mitochondrial genome structure.
Bridge, D., Cunningham, C. W., Schierwater, B., DeSalle, R., & Buss, L. W. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.18.8750 · Cited by 296 · see citing works
Evaluating multiple alternative hypotheses for the origin of Bilateria: An analysis of 18S rRNA molecular evidence
Collins, A. G. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.26.15458 · Cited by 252 · see citing works
Self-citation
Phylogenetic Analysis of Rhinosporidium seeberi ’s 18S Small-Subunit Ribosomal DNA Groups This Pathogen among Members of the Protoctistan Mesomycetozoa Clade
Herr, R. A., Ajello, L., Taylor, J. W., Arseculeratne, S. N., & Mendoza, L. (1999) · Journal of Clinical Microbiology · doi:10.1128/jcm.37.9.2750-2754.1999 · Cited by 247 · see citing works
Cladistic analyses of the animal kingdom
Nielsen, C., Scharff, N., & Eibye-Jacobsen, D. (1996) · Biological Journal of the Linnean Society · doi:10.1111/j.1095-8312.1996.tb01857.x · Cited by 222 · see citing works
On the origin and evolution of the lower Metazoa
Salvini-Plawen, L. V. (2009) · Journal of Zoological Systematics & Evolutionary Research · doi:10.1111/j.1439-0469.1978.tb00919.x · Cited by 217 · see citing works
Sponge phylogeny, animal monophyly, and the origin of the nervous system: 18S rRNA evidence
Cavalier-Smith, T., Allsopp, M. T. E. P., Chao, E. E., Boury-Esnault, N., & Vacelet, J. (1996) · Canadian Journal of Zoology · doi:10.1139/z96-231 · Cited by 180 · see citing works
A novel clade of protistan parasites near the animal-fungal divergence.
Ragan, M. A., Goggin, C. L., Cawthorn, R. J., Cerenius, L., Jamieson, A., Plourde, S. M., Rand, T. G., Söderhäll, K., & Gutell, R. R. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.21.11907 · Cited by 170 · see citing works
Limitations of Metazoan 18S rRNA Sequence Data: Implications for Reconstructing a Phylogeny of the Animal Kingdom and Inferring the Reality of the Cambrian Explosion
Abouheif, E., Zardoya, R., & Meyer, A. (1998) · Journal of Molecular Evolution · doi:10.1007/pl00006397 · Cited by 167 · see citing works
A new perspective on lower metazoan relationships from 18S rDNA sequences
Kim, J., Kim, W., & Cunningham, C. W. (1999) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026124 · Cited by 143 · see citing works
Phylogenetic Position of the Hexactinellida Within the Phylum Porifera Based on the Amino Acid Sequence of the Protein Kinase C from Rhabdocalyptus dawsoni
Kruse, M., Leys, S. P., Müller, I. M., & Müller, W. E. G. (1998) · Journal of Molecular Evolution · doi:10.1007/pl00006353 · Cited by 119 · see citing works
Late Precambrian bilaterians: grades and clades.
Valentine, J. W. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.15.6751 · Cited by 116 · see citing works
Phylogenetic analysis of the Hsp70 sequences reveals the monophyly of Metazoa and specific phylogenetic relationships between animals and fungi
Borchiellini, C., Boury‐Esnault, N., Vacelet, J., & Parco, Y. L. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025968 · Cited by 113 · see citing works
The significance of moulting in Ecdysozoan evolution
Valentine, J. W., & Collins, A. G. (2000) · Evolution & Development · doi:10.1046/j.1525-142x.2000.00043.x · Cited by 112 · see citing works
Self-citation
Evolution according to large ribosomal subunit RNA
Rijk, P. D., de Peer, Y. V., den Broeck, I. V., & Wächter, R. D. (1995) · Journal of Molecular Evolution · doi:10.1007/bf01215184 · Cited by 108 · see citing works
Cleavage patterns and the topology of the metazoan tree of life
Valentine, J. W. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.15.8001 · Cited by 103 · see citing works
Hyaloraphidium curvatum is not a Green Alga, but a Lower Fungus; Amoebidium parasiticum is not a Fungus, but a Member of the DRIPs
Ustinova, I., Krienitz, L., & Huss, V. A. R. (2000) · Protist · doi:10.1078/1434-4610-00023 · Cited by 90 · see citing works
Evolutionary relationships of Metazoa within the eukaryotes based on molecular data from Porifera
Schütze, J., Krasko, A., Custódio, M. R., Efremova, S. M., Müller, I. M., & Müller, W. E. G. (1999) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.1999.0605 · Cited by 86 · see citing works
The Coming of Age of Molecular Systematics
Maley, L. E., & Marshall, C. R. (1998) · Science · doi:10.1126/science.279.5350.505 · Cited by 64 · see citing works
Phylogenetic relationships of the intercellular fish pathogenIchthyophonus hoferi and fungi, choanoflagellates and the rosette agent
Spanggaard, B., Skouboe, P., Rossen, L., & Taylor, J. W. (1996) · Marine Biology · doi:10.1007/bf00571382 · Cited by 53 · see citing works
The presence of flagellar vanes in choanomeres of Porifera and their possible phylogenetic implications
Mehl, D., & Reiswig, H. M. (2009) · Journal of Zoological Systematics & Evolutionary Research · doi:10.1111/j.1439-0469.1991.tb00676.x · Cited by 51 · see citing works
Prototheca richardsi, a pathogen of anuran larvae, is related to a clade of protistan parasites near the animal-fungal divergence
Baker, G. C., Beebee, T. J. C., & Ragan, M. A. (1999) · Microbiology · doi:10.1099/13500872-145-7-1777 · Cited by 51 · see citing works
The rosette agent of chinook salmon (Oncorhynchus tshawytscha) is closely related to choanoflagellates, as determined by the phylogenetic analyses of its small ribosomal subunit RNA
Kerk, D., Gee, A., Standish, M., Wainwright, P. O., Drum, A. S., Elston, R., & Sogin, M. L. (1995) · Marine Biology · doi:10.1007/bf00348931 · Cited by 30 · see citing works
Self-citation
Sequence of the Small Subunit Ribosomal RNA Gene of Perkinsus atlanticus-like Isolated from Carpet Shell Clam in Galicia, Spain
Figueras, A. J., Lorenzo, G., Ordás, M. C., Gouy, M., & Novoa, B. (2000) · Marine Biotechnology · doi:10.1007/s101260000015 · Cited by 26 · see citing works
Untitled work
Dewel (2000) · doi:10.1002/(sici)1097-4687(200001)243:1
Untitled work
Collins, A. G. (2000) · doi:10.1666/0094-8373(2000)026

Flagged first, then by citations

4 of the 46 references couldn’t be matched to a known paper.

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).

Sorted by citations

The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists
Adl, S., Simpson, A., Farmer, M. A., Andersen, R., Anderson, O., Barta, J. R., Bowser, S., Brugerolle, G., Fensome, R., Fredericq, S., et al. (2005) · Journal of Eukaryotic Microbiology · doi:10.1111/j.1550-7408.2005.00053.x · Cited by 1,749 · see citing works
Systema Porifera. A Guide to the Classification of Sponges
Hooper, J. N. A., & van Soest, R. W. M. (2002) · Springer eBooks · doi:10.1007/978-1-4615-0747-5_1 · Cited by 1,191 · see citing works
Resolving difficult phylogenetic questions: Why more sequences are not enough
Philippe, H., Brinkmann, H., Lavrov, D. V., Littlewood, D. T. J., Manuel, M., Wörheide, G., & Baurain, D. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1000602 · Cited by 1,129 · see citing works
Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits
Lutzoni, F. M., Kauff, F., Cox, C. J., McLaughlin, D. J., Celio, G. J., Dentinger, B. T. M., Padamsee, M., Hibbett, D. S., James, T. Y., Baloch, E., et al. (2004) · American Journal of Botany · doi:10.3732/ajb.91.10.1446 · Cited by 816 · see citing works
Phylogenomics Revives Traditional Views on Deep Animal Relationships
Philippe, H., Derelle, R., Lopez, P., Pick, K., Borchiellini, C., Boury-Esnault, N., Vacelet, J., Renard, E., Houliston, E., Quéinnec, E., et al. (2009) · Current Biology · doi:10.1016/j.cub.2009.02.052 · Cited by 695 · see citing works
The New View of Animal Phylogeny
Halanych, K. M. (2004) · Annual Review of Ecology, Evolution, and Systematics · doi:10.1146/annurev.ecolsys.35.112202.130124 · Cited by 489 · see citing works
The Unicellular Ancestry of Animal Development
King, N. (2004) · Developmental Cell · doi:10.1016/j.devcel.2004.08.010 · Cited by 482 · see citing works
Animal phylogeny and its evolutionary implications
Dunn, C. W., Giribet, G., Edgecombe, G. D., & Hejnol, A. (2014) · Annual Review of Ecology, Evolution, and Systematics · doi:10.1146/annurev-ecolsys-120213-091627 · Cited by 401 · see citing works
The phylum Cnidaria: A review of phylogenetic patterns and diversity 300 years after Linnaeus*
Daly, M., Brugler, M. R., Cartwright, P., Collins, A. G., Dawson, M. N., Fautin, D. G., France, S. C., McFadden, C. S., Opresko, D. M., Rodríguez, E., et al. (2007) · Zootaxa · doi:10.11646/zootaxa.1668.1.11 · Cited by 514 · see citing works
Self-citation
Investigating the origins of triploblasty: `mesodermal' gene expression in a diploblastic animal, the sea anemone Nematostella vectensis (phylum, Cnidaria; class, Anthozoa)
Martindale, M. Q., Pang, K., & Finnerty, J. R. (2004) · Development · doi:10.1242/dev.01119 · Cited by 396 · see citing works
Medusozoan Phylogeny and Character Evolution Clarified by New Large and Small Subunit rDNA Data and an Assessment of the Utility of Phylogenetic Mixture Models
Collins, A. G., Schuchert, P., Marques, A. C., Jankowski, T., Medina, M., & Schierwater, B. (2006) · Systematic Biology · doi:10.1080/10635150500433615 · Cited by 382 · see citing works
Self-citation
Utility of complete large and small subunit rRNA genes in resolving the phylogeny of the Neodermata (Platyhelminthes): implications and a review of the cercomer theory
Lockyer, A. E., Olson, P. D., & Littlewood, D. T. J. (2003) · Biological Journal of the Linnean Society · doi:10.1046/j.1095-8312.2003.00141.x · Cited by 382 · see citing works
Six major steps in animal evolution: Are we derived sponge larvae?
Nielsen, C. (2008) · Evolution & Development · doi:10.1111/j.1525-142x.2008.00231.x · Cited by 343 · see citing works
Origin of the Eumetazoa: Testing ecological predictions of molecular clocks against the Proterozoic fossil record
Peterson, K. J., & Butterfield, N. J. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0503660102 · Cited by 361 · see citing works
Phylogeny of Medusozoa and the evolution of cnidarian life cycles
Collins, A. G. (2002) · Journal of Evolutionary Biology · doi:10.1046/j.1420-9101.2002.00403.x · Cited by 355 · see citing works
Self-citation
The phylogeny of the Schistosomatidae based on three genes with emphasis on the interrelationships of Schistosoma Weinland, 1858
Lockyer, A. E., Olson, P. D., ØSTERGAARD, P., Rollinson, D., Johnston, D. A., Attwood, S. W., Southgate, V. R., Horák, P., Snyder, S. D., Le, T. H., et al. (2003) · Parasitology · doi:10.1017/s0031182002002792 · Cited by 355 · see citing works
Ecdysozoan phylogeny and Bayesian inference: first use of nearly complete 28S and 18S rRNA gene sequences to classify the arthropods and their kin
Mallatt, J. M., Garey, J. R., & Shultz, J. W. (2003) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2003.07.013 · Cited by 344 · see citing works
The phylum Cnidaria: A review of phylogenetic patterns and diversity 300 years after Linnaeus *
Daly, M., Brugler, M. R., Cartwright, P., Collins, A. G., Dawson, M. N., Fautin, D. G., France, S. C., McFadden, C. S., Opresko, D. M., Rodríguez, E., et al. (2007) · KU ScholarWorks (The University of Kansas) · doi:10.5281/zenodo.180149 · Cited by 344 · see citing works
Self-citation
The Closest Unicellular Relatives of Animals
Lang, B. F., O'Kelly, C., Nerad, T., Gray, M. W., & Burger, G. (2002) · Current Biology · doi:10.1016/s0960-9822(02)01187-9 · Cited by 326 · see citing works
Maintenance of ancestral complexity and non-metazoan genes in two basal cnidarians
Technau, U., Rudd, S., Maxwell, P., Gordon, P. M. K., Saina, M., Grasso, L. C., Hayward, D. C., Sensen, C. W., Saint, R., Holstein, T. W., et al. (2005) · Trends in Genetics · doi:10.1016/j.tig.2005.09.007 · Cited by 337 · see citing works
Early evolution of animal cell signaling and adhesion genes
Nichols, S., Dirks, W., Pearse, J. S., & King, N. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0604065103 · Cited by 327 · see citing works
Cladistic analysis of Medusozoa and cnidarian evolution
Marques, A. C., & Collins, A. G. (2004) · Invertebrate Biology · doi:10.1111/j.1744-7410.2004.tb00139.x · Cited by 323 · see citing works
Self-citation
An ancient role for nuclear β-catenin in the evolution of axial polarity and germ layer segregation
Wikramanayake, A. H., Hong, M., Lee, P. N., Pang, K., Byrum, C. A., Bince, J. M., Xu, R., & Martindale, M. Q. (2003) · Nature · doi:10.1038/nature02113 · Cited by 324 · see citing works
Slow Mitochondrial COI Sequence Evolution at the Base of the Metazoan Tree and Its Implications for DNA Barcoding
Huang, D., Meier, R., Todd, P. A., & Chou, L. M. (2008) · Journal of Molecular Evolution · doi:10.1007/s00239-008-9069-5 · Cited by 321 · see citing works
No variation and low synonymous substitution rates in coral mtDNA despite high nuclear variation
Hellberg, M. E. (2006) · BMC Evolutionary Biology · doi:10.1186/1471-2148-6-24 · Cited by 320 · see citing works
The Protistan Origins of Animals and Fungi
Steenkamp, E. T., Wright, J., & Baldauf, S. L. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msj011 · Cited by 307 · see citing works
The Analysis of Eight Transcriptomes from All Poriferan Classes Reveals Surprising Genetic Complexity in Sponges
Riesgo, A., Farrar, N., Windsor, P. J., Giribet, G., & Leys, S. P. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu057 · Cited by 266 · see citing works
Genesis and Expansion of Metazoan Transcription Factor Gene Classes
Larroux, C., Luke, G. N., Koopman, P. A., Rokhsar, D. S., Shimeld, S. M., & Degnan, B. M. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn047 · Cited by 275 · see citing works
Development of a Real-Time PCR Assay for Rapid Detection and Quantification ofAlexandrium minutum(a Dinoflagellate)
Galluzzi, L., Penna, A., Bertozzini, E., Vila, M., Garcés, E., & Magnani, M. (2004) · Applied and Environmental Microbiology · doi:10.1128/aem.70.2.1199-1206.2004 · Cited by 282 · see citing works
Phylogenetics and evolution of Capitata (Cnidaria: Hydrozoa), and the systematics of Corynidae
Nawrocki, A. M., Schuchert, P., & Cartwright, P. (2009) · Zoologica Scripta · doi:10.1111/j.1463-6409.2009.00419.x · Cited by 279 · see citing works
The Evolution of Organ Systems
Schmidt‐Rhaesa, A. (2007) · doi:10.1093/acprof:oso/9780198566687.001.0001 · Cited by 262 · see citing works
Deep metazoan phylogeny: When different genes tell different stories
Nosenko, T., Schreiber, F., Adamska, M., Adamski, M., Eitel, M., Hammel, J., Maldonado, M., Müller, W. E. G., Nickel, M., Schierwater, B., et al. (2013) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2013.01.010 · Cited by 254 · see citing works
Wnt and TGF-β Expression in the Sponge Amphimedon queenslandica and the Origin of Metazoan Embryonic Patterning
Adamska, M., Degnan, S. M., Green, K. M., Adamski, M., Craigie, A., Larroux, C., & Degnan, B. M. (2007) · PLoS ONE · doi:10.1371/journal.pone.0001031 · Cited by 257 · see citing works
Concatenated Analysis Sheds Light on Early Metazoan Evolution and Fuels a Modern “Urmetazoon” Hypothesis
Schierwater, B., Eitel, M., Jakob, W., Osigus, H.-J., Hadrys, H., Dellaporta, S. L., Kolokotronis, S.-O., & DeSalle, R. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000020 · Cited by 260 · see citing works
Testing the New Animal Phylogeny: First Use of Combined Large-Subunit and Small-Subunit rRNA Gene Sequences to Classify the Protostomes
Mallatt, J. M., & Winchell, C. J. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004082 · Cited by 257 · see citing works
Mitochondrial genome of Trichoplax adhaerens supports Placozoa as the basal lower metazoan phylum
Dellaporta, S. L., Xu, A., Sagasser, S., Jakob, W., Moreno, M. A., Buss, L. W., & Schierwater, B. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0602076103 · Cited by 252 · see citing works
Molecular phylogeny of Demospongiae: implications for classification and scenarios of character evolution
Borchiellini, C., Chombard, C., Manuel, M., Alivon, E., Vacelet, J., & Boury‐Esnault, N. (2004) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2004.02.021 · Cited by 248 · see citing works
A phylogenetic analysis of myosin heavy chain type II sequences corroborates that Acoela and Nemertodermatida are basal bilaterians
Ruiz‐Trillo, I., Paps, J., Loukota, M., Ribera, C., Jondelius, U., Baguñà, J., & Riutort, M. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.172390199 · Cited by 243 · see citing works
Pre-Bilaterian Origins of the Hox Cluster and the Hox Code: Evidence from the Sea Anemone, Nematostella vectensis
Ryan, J. F., Mazza, M. E., Pang, K., Matus, D. Q., Baxevanis, A. D., Martindale, M. Q., & Finnerty, J. R. (2007) · PLoS ONE · doi:10.1371/journal.pone.0000153 · Cited by 241 · see citing works
A receptor tyrosine kinase from choanoflagellates: Molecular insights into early animal evolution
King, N., & Carroll, S. B. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.261477698 · Cited by 234 · see citing works
Induction of gametogenesis in the basal cnidarian Nematostella vectensis (Anthozoa)
Fritzenwanker, J. H., & Technau, U. (2002) · Development Genes and Evolution · doi:10.1007/s00427-002-0214-7 · Cited by 218 · see citing works
Added resolution among ordinal level relationships of tapeworms (Platyhelminthes: Cestoda) with complete small and large subunit nuclear ribosomal RNA genes
Waeschenbach, A., Webster, B. L., Bray, R. A., & Littlewood, D. T. J. (2007) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2007.03.019 · Cited by 214 · see citing works
Cnidarians and the evolutionary origin of the nervous system
Watanabe, H., Fujisawa, T., & Holstein, T. W. (2009) · Development, Growth & Differentiation · doi:10.1111/j.1440-169x.2009.01103.x · Cited by 206 · see citing works
Choanoflagellates, choanocytes, and animal multicellularity
Maldonado, M. (2004) · Invertebrate Biology · doi:10.1111/j.1744-7410.2004.tb00138.x · Cited by 207 · see citing works
The evolution of metazoan axial properties
Martindale, M. Q. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1725 · Cited by 204 · see citing works
Poriferan paraphyly and its implications for Precambrian palaeobiology
Sperling, E. A., Pisani, D., & Peterson, K. J. (2007) · Geological Society, London, Special Publications · doi:10.1144/sp286.25 · Cited by 206 · see citing works
The Origin of GPCRs: Identification of Mammalian like Rhodopsin, Adhesion, Glutamate and Frizzled GPCRs in Fungi
Krishnan, A., Almén, M. S., Fredriksson, R., & Schiöth, H. B. (2012) · PLoS ONE · doi:10.1371/journal.pone.0029817 · Cited by 204 · see citing works
A placozoan affinity for Dickinsonia and the evolution of late Proterozoic metazoan feeding modes
Sperling, E. A., & Vinther, J. (2010) · Evolution & Development · doi:10.1111/j.1525-142x.2010.00404.x · Cited by 194 · see citing works
Intragenomic Variation of Fungal Ribosomal Genes Is Higher than Previously Thought
Simon, U. K., & Weiss, M. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn188 · Cited by 194 · see citing works
Sponge Systematics Facing New Challenges
Cárdenas, P., Pérez, T., & Boury‐Esnault, N. (2012) · Advances in marine biology · doi:10.1016/b978-0-12-387787-1.00010-6 · Cited by 193 · see citing works
Nervous systems of the sea anemone Nematostella vectensis are generated by ectoderm and endoderm and shaped by distinct mechanisms
Nakanishi, N., Renfer, E., Technau, U., & Rentzsch, F. (2012) · Development · doi:10.1242/dev.071902 · Cited by 188 · see citing works
A WNT of things to come: Evolution of Wnt signaling and polarity in cnidarians
LEE, P., PANG, K., Matus, D. Q., & Martindale, M. Q. (2006) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2006.05.002 · Cited by 185 · see citing works
The cnidarian-bilaterian ancestor possessed at least 56 homeoboxes: evidence from the starlet sea anemone, Nematostella vectensis
Ryan, J. F., Burton, P. M., Mazza, M. E., Kwong, G. K., Mullikin, J. C., & Finnerty, J. R. (2006) · Genome biology · doi:10.1186/gb-2006-7-7-r64 · Cited by 185 · see citing works
Where's the glass? Biomarkers, molecular clocks, and microRNAs suggest a 200‐Myr missing Precambrian fossil record of siliceous sponge spicules
SPERLING, E. A., ROBINSON, J. M., PISANI, D., & PETERSON, K. J. (2010) · Geobiology · doi:10.1111/j.1472-4669.2009.00225.x · Cited by 182 · see citing works
An evaluation of support for order-level monophyly and interrelationships within the class Demospongiae using partial data from the large subunit rDNA and cytochrome oxidase subunit I
Nichols, S. (2005) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2004.08.019 · Cited by 179 · see citing works
Developmental expression of transcription factor genes in a demosponge: insights into the origin of metazoan multicellularity
Larroux, C., Fahey, B., Liubicich, D., Hinman, V. F., Gauthier, M., Gongora, M., Green, K., Wörheide, G., Leys, S. P., & Degnan, B. M. (2006) · Evolution & Development · doi:10.1111/j.1525-142x.2006.00086.x · Cited by 173 · see citing works
Mitochondrial Genomes of Two Demosponges Provide Insights into An Early Stage of Animal Evolution
Lavrov, D. V., Forget, L., Kelly, M., & Lang, B. F. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi108 · Cited by 176 · see citing works
Tempo and mode of early animal evolution: inferences from rocks, Hox, and molecular clocks
Peterson, K. J., McPeek, M. A., & Evans, D. A. D. (2005) · Paleobiology · doi:10.1666/0094-8373(2005)031[0036:tamoea]2.0.co;2 · Cited by 173 · see citing works
Evolution of striated muscle: Jellyfish and the origin of triploblasty
Seipel, K., & Schmid, V. (2005) · Developmental Biology · doi:10.1016/j.ydbio.2005.03.032 · Cited by 172 · see citing works
FGF signalling controls formation of the apical sensory organ in the cnidarianNematostella vectensis
Rentzsch, F., Fritzenwanker, J. H., Scholz, C. B., & Technau, U. (2008) · Development · doi:10.1242/dev.020784 · Cited by 166 · see citing works
Asymmetric expression of the BMP antagonists chordin and gremlin in the sea anemone Nematostella vectensis: Implications for the evolution of axial patterning
Rentzsch, F., Anton, R., Saina, M., Hammerschmidt, M., Holstein, T. W., & Technau, U. (2006) · Developmental Biology · doi:10.1016/j.ydbio.2006.06.003 · Cited by 170 · see citing works
Lophotrochozoan phylogeny assessed with LSU and SSU data: Evidence of lophophorate polyphyly
Passamaneck, Y. J., & Halanych, K. M. (2006) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2006.02.001 · Cited by 169 · see citing works
Phylogenetic-signal dissection of nuclear housekeeping genes supports the paraphyly of sponges and the monophyly of Eumetazoa
Sperling, E. A., Peterson, K. J., & Pisani, D. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp148 · Cited by 172 · see citing works
Phylogeny and Systematics of Demospongiae in Light of New Small-Subunit Ribosomal DNA (18S) Sequences
Redmond, N. E., Morrow, C. C., THACKER, R. W., Díaz, M. C., Boury‐Esnault, N., Cárdenas, P., Hajdu, E., Lôbo‐Hajdu, G., PICTON, B. E., Pomponi, S. A., et al. (2013) · Integrative and Comparative Biology · doi:10.1093/icb/ict078 · Cited by 167 · see citing works
Self-citation
Current advances in the phylogenetic reconstruction of metazoan evolution. A new paradigm for the Cambrian explosion?
Giribet, G. (2002) · Molecular Phylogenetics and Evolution · doi:10.1016/s1055-7903(02)00206-3 · Cited by 167 · see citing works
Deep Phylogeny and Evolution of Sponges (Phylum Porifera)
Wörheide, G., Dohrmann, M., Erpenbeck, D., Larroux, C., Maldonado, M., Voigt, O., Borchiellini, C., & Lavrov, D. V. (2012) · Advances in Marine Biology · doi:10.1016/b978-0-12-387787-1.00007-6 · Cited by 166 · see citing works
Precambrian Animal Life: Probable Developmental and Adult Cnidarian Forms from Southwest China
Chen, J.-Y., Oliveri, P., Gao, F., Dornbos, S. Q., Li, C.-W., Bottjer, D. J., & Davidson, E. H. (2002) · Developmental Biology · doi:10.1006/dbio.2002.0714 · Cited by 165 · see citing works
Investigation of molluscan phylogeny using large-subunit and small-subunit nuclear rRNA sequences
Passamaneck, Y. J., Schänder, C., & Halanych, K. M. (2004) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2003.12.016 · Cited by 164 · see citing works
Genomic inventory and expression of Sox and Fox genes in the cnidarian Nematostella vectensis
Magie, C. R., Pang, K., & Martindale, M. Q. (2005) · Development Genes and Evolution · doi:10.1007/s00427-005-0022-y · Cited by 158 · see citing works
Reconstructing ordinal relationships in the Demospongiae using mitochondrial genomic data
Lavrov, D. V., Wang, X., & Kelly, M. (2008) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2008.05.014 · Cited by 158 · see citing works
The origin of Metazoa: a transition from temporal to spatial cell differentiation
Mikhailov, K. V., Константинова, А. В., Nikitin, M. A., Troshin, P. V., Rusin, L. Y., Lyubetsky, V., Panchin, Y. V., Mylnikov, A. P., Moroz, L. L., Kumar, S., et al. (2009) · BioEssays · doi:10.1002/bies.200800214 · Cited by 151 · see citing works
Phylogeny and Evolution of Calcareous Sponges: Monophyly of Calcinea and Calcaronea, High Level of Morphological Homoplasy, and the Primitive Nature of Axial Symmetry
Manuel, M., Borchiellini, C., Alivon, E., Parco, Y. L., Vacelet, J., & Boury‐Esnault, N. (2003) · Systematic Biology · doi:10.1080/10635150309322 · Cited by 158 · see citing works
Larval development in the Homoscleromorpha (Porifera, Demospongiae)
Boury‐Esnault, N., Ereskovsky, A. V., Bézac, C., & Tokina, D. B. (2003) · Invertebrate Biology · doi:10.1111/j.1744-7410.2003.tb00084.x · Cited by 156 · see citing works
Articulated sponges from the Lower Cambrian Hetang Formation in southern Anhui, South China: their age and implications for the early evolution of sponges
Xiao, S., Hu, J., Yuan, X., Parsley, R. L., & Cao, R. (2005) · Palaeogeography, Palaeoclimatology, Palaeoecology · doi:10.1016/j.palaeo.2002.02.001 · Cited by 152 · see citing works
Combined large and small subunit ribosomal RNA phylogenies support a basal position of the acoelomorph flatworms
Telford, M. J., Lockyer, A. E., Cartwright–Finch, C., & Littlewood, D. T. J. (2003) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2003.2342 · Cited by 151 · see citing works
Putative cross-kingdom horizontal gene transfer in sponge (Porifera) mitochondria
Rot, C., Goldfarb, I., Ilan, M., & Huchon, D. (2006) · BMC Evolutionary Biology · doi:10.1186/1471-2148-6-71 · Cited by 149 · see citing works
Phylogeny and evolution of glass sponges (Porifera, Hexactinellida)
Dohrmann, M., Janussen, D., Reitner, J., Collins, A. G., & Wörheide, G. (2008) · Systematic Biology · doi:10.1080/10635150802161088 · Cited by 143 · see citing works
Self-citation
Embracing Uncertainty in Reconstructing Early Animal Evolution
King, N., & Rokas, A. (2017) · Current Biology · doi:10.1016/j.cub.2017.08.054 · Cited by 144 · see citing works
Concatenated SSU and LSU rDNA data confirm the main evolutionary trends within myxosporeans (Myxozoa: Myxosporea) and provide an effective tool for their molecular phylogenetics
Bartošová‐Sojková, P., Fiala, I., & Hypša, V. (2009) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2009.05.018 · Cited by 145 · see citing works
Molecular evidence that phoronids are a subtaxon of brachiopods (Brachiopoda: Phoronata) and that genetic divergence of metazoan phyla began long before the early Cambrian
COHEN, B., & Weydmann‐Zwolicka, A. (2005) · Organisms Diversity & Evolution · doi:10.1016/j.ode.2004.12.002 · Cited by 142 · see citing works
Reassessment of the phylogenetic position of conulariids (?Ediacaran‐Triassic) within the subphylum medusozoa (phylum cnidaria)
Van Iten, H., de Moraes Leme, J., Simões, M. G., Marques, A. C., & Collins, A. G. (2006) · Journal of Systematic Palaeontology · doi:10.1017/s1477201905001793 · Cited by 138 · see citing works
Self-citation
vasa and nanos expression patterns in a sea anemone and the evolution of bilaterian germ cell specification mechanisms
Extavour, C. G., Pang, K., Matus, D. Q., & Martindale, M. Q. (2005) · Evolution & Development · doi:10.1111/j.1525-142x.2005.05023.x · Cited by 144 · see citing works
The phylogenetic position of the comb jellies (Ctenophora) and the importance of taxonomic sampling
Wållberg, A., Thollesson, M., Farris, J. S., & Jondelius, U. (2004) · Cladistics · doi:10.1111/j.1096-0031.2004.00041.x · Cited by 141 · see citing works
Early development and axis specification in the sea anemone Nematostella vectensis
Fritzenwanker, J. H., Genikhovich, G., Kraus, Y. A., & Technau, U. (2007) · Developmental Biology · doi:10.1016/j.ydbio.2007.07.029 · Cited by 140 · see citing works
BMPs and Chordin regulate patterning of the directive axis in a sea anemone
Saina, M., Genikhovich, G., Renfer, E., & Technau, U. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0900151106 · Cited by 138 · see citing works
Adding resolution to ordinal level relationships of tapeworms (Platyhelminthes: Cestoda) with large fragments of mtDNA
Waeschenbach, A., Webster, B. L., & Littlewood, D. T. J. (2012) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2012.02.020 · Cited by 135 · see citing works
Asymmetric developmental potential along the animal–vegetal axis in the anthozoan cnidarian, Nematostella vectensis, is mediated by Dishevelled
Lee, P. N., Kumburegama, S., Marlow, H. Q., Martindale, M. Q., & Wikramanayake, A. H. (2007) · Developmental Biology · doi:10.1016/j.ydbio.2007.05.040 · Cited by 135 · see citing works
Incidence and identity of photosynthetic symbionts in Caribbean coral reef sponge assemblages
Erwin, P. M., & THACKER, R. W. (2007) · Journal of the Marine Biological Association of the United Kingdom · doi:10.1017/s0025315407058213 · Cited by 134 · see citing works
Myosin superfamily evolutionary history
Thompson, R. F., & Langford, G. (2002) · The Anatomical Record · doi:10.1002/ar.10160 · Cited by 118 · see citing works
Bauplan of Urmetazoa: Basis for Genetic Complexity of Metazoa
Müller, W. E. G., Wiens, M., Adell, T., Gamulin, V., Schröder, H. C., & Müller, I. M. (2004) · International review of cytology · doi:10.1016/s0074-7696(04)35002-3 · Cited by 133 · see citing works
Localized expression of a dpp / BMP2 / 4 ortholog in a coral embryo
Hayward, D. C., Samuel, G., Pontynen, P. C., Catmull, J., Saint, R., Miller, D. J., & Ball, E. E. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.112021499 · Cited by 132 · see citing works
Gastrulation in the cnidarian Nematostella vectensis occurs via invagination not ingression
Magie, C. R., Daly, M., & Martindale, M. Q. (2007) · Developmental Biology · doi:10.1016/j.ydbio.2007.02.044 · Cited by 132 · see citing works
Intragenomic variation of the rDNA internal transcribed spacers in sponges (Phylum Porifera): implications for phylogenetic studies
Wörheide, G., Nichols, S., & Goldberg, J. (2004) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2004.07.005 · Cited by 131 · see citing works
Developmental Signaling in Hydra: What Does It Take to Build a “Simple” Animal?
Steele, R. E. (2002) · Developmental Biology · doi:10.1006/dbio.2002.0744 · Cited by 129 · see citing works
Dorso/Ventral Genes Are Asymmetrically Expressed and Involved in Germ-Layer Demarcation during Cnidarian Gastrulation
Matus, D. Q., Thomsen, G. H., & Martindale, M. Q. (2006) · Current Biology · doi:10.1016/j.cub.2006.01.052 · Cited by 129 · see citing works
Phylogeny of elasmobranchs based on LSU and SSU ribosomal RNA genes
Winchell, C. J., Martin, A. P., & Mallatt, J. M. (2003) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2003.07.010 · Cited by 128 · see citing works
Conflicting phylogenetic signals at the base of the metazoan tree
Rokas, A., King, N., Finnerty, J. R., & Carroll, S. B. (2003) · Evolution & Development · doi:10.1046/j.1525-142x.2003.03042.x · Cited by 125 · see citing works
A simple plan-Cnidarians and the origins of developmental mechanisms
Ball, E. E., Hayward, D. C., Saint, R., & Miller, D. J. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1402 · Cited by 123 · see citing works
Molecular Phylogenetics of the Siphonophora (Cnidaria), with Implications for the Evolution of Functional Specialization
Dunn, C. W., Pugh, P. R., & Haddock, S. H. D. (2005) · Systematic Biology · doi:10.1080/10635150500354837 · Cited by 118 · see citing works
Early evolution of symmetry and polarity in metazoan body plans
Manuel, M. (2008) · Comptes Rendus Biologies · doi:10.1016/j.crvi.2008.07.009 · Cited by 123 · see citing works

Phylogenetic position of Placozoa based on large subunit (LSU) and small subunit (SSU) rRNA genes
da Silva, F. B., Muschner, V. C., & Bonatto, S. L. (2007) · Genetics and Molecular Biology · doi:10.1590/s1415-47572007000100022 · Cited by 42 · see citing works
Testing the New Animal Phylogeny: First Use of Combined Large-Subunit and Small-Subunit rRNA Gene Sequences to Classify the Protostomes
Mallatt, J. M., & Winchell, C. J. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004082 · Cited by 257 · see citing works
Investigation of molluscan phylogeny using large-subunit and small-subunit nuclear rRNA sequences
Passamaneck, Y. J., Schänder, C., & Halanych, K. M. (2004) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2003.12.016 · Cited by 164 · see citing works
Molecular evolution of rDNA in early diverging Metazoa: First comparative analysis and phylogenetic application of complete SSU rRNA secondary structures in Porifera
Voigt, O., Erpenbeck, D., & Wörheide, G. (2008) · BMC Evolutionary Biology · doi:10.1186/1471-2148-8-69 · Cited by 39 · see citing works
Evaluating Hypotheses of Deuterostome Phylogeny and Chordate Evolution with New LSU and SSU Ribosomal DNA Data
Winchell, C. J., Sullivan, J. M., Cameron, C. B., Swalla, B. J., & Mallatt, J. M. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004134 · Cited by 253 · see citing works

Authors: Medina, M., Collins, A. G., Silberman, J. D., & Sogin, M. L.
Affiliations: Marine Biological Laboratory (US)
ORCID: Medina, Mónica
Collins, Allen G.
Silberman, Jeffrey D.
Sogin, Mitchell L.
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
DOI: 10.1073/pnas.171316998
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: Physical Sciences › Earth and Planetary Sciences › Paleontology › Marine Invertebrate Physiology and Ecology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › 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.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-06.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-06.

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

Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA

Abstract

AI snapshot

TL;DR

Key findings

Methods

Limitations

Integrity signals

Claims the paper makes

Claims other papers make about this one

Cites

Cited by

Related

Record

About these checks