The DOI matches its Crossref record; 60 of the 60 references it cites were found in a registry or an index; 35 of the 80 sources its claims cite were checked for support.
Error, signal, and the placement of Ctenophora sister to all other animals
Open accessAbstract
Elucidating relationships among early animal lineages has been difficult, and recent phylogenomic analyses place Ctenophora sister to all other extant animals, contrary to the traditional view of Porifera as the earliest-branching animal lineage. To date, phylogenetic support for either ctenophores or sponges as sister to other animals has been limited and inconsistent among studies. Lack of agreement among phylogenomic analyses using different data and methods obscures how complex traits, such as epithelia, neurons, and muscles evolved. A consensus view of animal evolution will not be accepted until datasets and methods converge on a single hypothesis of early metazoan relationships and putative sources of systematic error (e.g., long-branch attraction, compositional bias, poor model choice) are assessed. Here, we investigate possible causes of systematic error by expanding taxon sampling with eight novel transcriptomes, strictly enforcing orthology inference criteria, and progressively examining potential causes of systematic error while using both maximum-likelihood with robust data partitioning and Bayesian inference with a site-heterogeneous model. We identified ribosomal protein genes as possessing a conflicting signal compared with other genes, which caused some past studies to infer ctenophores and cnidarians as sister. Importantly, biases resulting from elevated compositional heterogeneity or elevated substitution rates are ruled out. Placement of ctenophores as sister to all other animals, and sponge monophyly, are strongly supported under multiple analyses, herein.
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
21 No full text of the sources · 21 Own result · 10 Own interpretation · 9 Partly supported · 4 Supported · 3 Own method · 2 Not supported · 2 No basis given · 1 Supported so far · 1 Sources not found · 1 Not checked yet · accuracy not yet measured
At least one cited source doesn’t support this claim or points to a different paper, and none confirmed it — see the verdicts below.
In the paper
“The argument for LBA (7-10) or saturated datasets (7, 8) as the reason past studies found ctenophores to be sister to all other animals seems to have been overstated.”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Placement of Ctenophores Sister to all Remaining Animals Is Not
What the sources say
- Not checked — no full text of the sourcecites [7] 7. Nosenko T, et al. (2013) Deep metazoan phylogeny: When different genes tell dif- ferent stories. Mol Phylogenet Evol 67(1):223-233. source
- Disputedcites [8] 8. Philippe H, et al. (2011) Resolving difficult phylogenetic questions: Why more se- quences are not enough. PLoS Biol 9(3):e1000602. sourceExperimental — accuracy not yet measured
In Box 3 (Quality Control of Phylogenomic Datasets), the paper argues that long-branch attraction probably affected Dunn et al.’s phylogeny, with fast-evolving ctenophores likely attracted to the distant outgroup. In Box 4 (Improving Phylogenetic Inference Methods), it calls the basal emergence of ctenophores an artifactual topology. The source advances the explanation the claim says was overstated, rather than questioning it. (LLM, conf=0.87)
Checked by a reasoning model — may be wrong.
- Not checked — no full text of the sourcecites [9] 9. Philippe H, et al. (2009) Phylogenomics revives traditional views on deep animal re- lationships. Curr Biol 19(8):706-712. source
- Disputedcites [10] 10. Pick KS, et al. (2010) Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships. Mol Biol Evol 27(9):1983-1987. sourceExperimental — accuracy not yet measured
The Abstract argues the opposite: it attributes the basal placement of ctenophores in earlier analyses to long-branch attraction, rather than suggesting that explanation was overstated. It also reports comparatively high saturation in the earlier dataset as a possible contributor to poor support for some nonbilaterian nodes. The supplied passages do not provide page numbers. (LLM, conf=0.90)
Checked by a reasoning model — may be wrong.
hedged- 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.
At least one cited source doesn’t support this claim or points to a different paper, and none confirmed it — see the verdicts below.
In the paper
“Therefore, LBA plausibly influenced the phylogenetic position of ctenophores in analyses of Ryan et al. (6) that recovered ctenophores-sister.”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Abstract
What the sources say
- Disputedcites [6] 6. Ryan JF, et al.; NISC Comparative Sequencing Program (2013) The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 342(6164):1242592. sourceExperimental — accuracy not yet measured
In “Phylogenetic position of Mnemiopsis leidyi” (page unavailable), Ryan et al. say their analyses without non-metazoan outgroups contradict the proposed long-branch attraction between ctenophores and the outgroup. They acknowledge sensitivity to taxon sampling and inference method, but do not present long-branch attraction as a plausible explanation for their ctenophores-sister results. (LLM, conf=0.86)
Checked by a reasoning model — may be wrong.
hedgedconditional- 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.
- Disputed
Every source the paper cites for this claim was checked and supports it.
In the paper
“We identified ribosomal protein genes as possessing a conflicting signal compared with other genes, which caused some past studies to infer ctenophores and cnidarians as sister.”
- Also stated in: § Ctenophores Sister to Other Extant Animals and Monophyletic Sponges. · plain
“Ribosomal protein genes can have conflicting signal with most other genes (32).”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Abstract
What the sources say
- Supportedcites [32] 32. Bleidorn C, et al. (2009) On the phylogenetic position of Myzostomida: Can 77 genes get it wrong? BMC Evol Biol 9(1):150. source
The Results and discussion (page unavailable) report that, for myzostomids, ribosomal-protein and mitochondrial marker sets yielded different topologies, with incongruence between the sets rather than within the ribosomal-protein set. This supports the quoted claim about conflicting signals. The passage does not address the citing authors’ separate explanation involving ctenophores and cnidarians. (LLM, conf=0.90)
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.
- Also stated in: § Ctenophores Sister to Other Extant Animals and Monophyletic Sponges. · plain
Every source the paper cites for this claim was checked and supports it.
In the paper
“In Moroz et al. (5), strong nodal support for ctenophores sister to all other extant animals disappeared when both the strictest orthology criteria were enforced and ctenophore taxon sampling increased.”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Abstract
What the sources say
- Supportedcites [5] 5. Moroz LL, et al. (2014) The ctenophore genome and the evolutionary origins of neural systems. Nature 510(7503):109-114. source
The Ctenophore phylogeny section reports that adding ten ctenophores and applying stricter orthology criteria still placed ctenophores at the base of the animal tree, but with less support. It also says the topology was unresolved when the most conserved genes were considered. Thus the claim concerns the loss of strong nodal support, not the loss of every analysis placing ctenophores basally. (LLM, conf=0.88)
boosteddirect- 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.
- Supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Inferred relationships among major sponge lineages (i.e., Demospongiae + Hexactinellida sister to Calcarea + Homoscleromorpha) were consistent with morphology (27,28) and most other molecular analyses that have recovered monophyletic sponges (datasets 1-27 in Figs. 2 and 3 and Figs.S1-S5) (4, 5, 8, 9, 28-30).”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Ctenophores Sister to Other Extant Animals and Monophyletic Sponges.
What the sources say
- Not checked — no full text of the sourcecites [27] 27. van Soest RWM (1984) Deficient Merlia normani Kirkpatrick, 1908, from the Curacao reefs, with a discussion on the phylogenetic interpretation of sclerosponges. Contrib Zool 54(2):211-219. source
- Partly supportedcites [28] 28. Gazave E, et al. (2012) No longer Demospongiae: Homoscleromorpha formal nomi- nation as a fourth class of Porifera. Hydrobiologia 687(1):3-10. sourceExperimental — accuracy not yet measured
The “New insights from molecular phylogenies/phylogenomics studies” section reports molecular support for a Homoscleromorpha–Calcarea sister relationship. The “Linnaean classification of Homoscleromorpha” section says sponge monophyly is consistent with morphological characters, and the Discussion identifies a morphological feature shared by Homoscleromorpha and Calcarea. These passages do not establish the claimed Demospongiae–Hexactinellida sister pairing or the full relationship between the two pairs. Page numbers were not available in our copy. (LLM, conf=0.85)
- Partly supportedcites [4] 4. Hejnol A, et al. (2009) Assessing the root of bilaterian animals with scalable phylo- genomic models. Proc Biol Sci 276(1802):4261-4270. sourceExperimental — accuracy not yet measured
The Discussion (§4(d), page unavailable) reports an EST study sampling all major sponge groups that placed Porifera as sister to other metazoans, supporting the monophyletic-sponges part of the claim. Our copy does not state the specified Demospongiae–Hexactinellida and Calcarea–Homoscleromorpha relationship or say that it agrees with sponge morphology. (LLM, conf=0.79)
- Partly supportedcites [5] 5. Moroz LL, et al. (2014) The ctenophore genome and the evolutionary origins of neural systems. Nature 510(7503):109-114. sourceExperimental — accuracy not yet measured
The ‘Ctenophore phylogeny’ section reports Porifera as a single sister taxon to other metazoans, supporting the claim that this molecular analysis recovered monophyletic sponges. It does not state the specified relationships among Demospongiae, Hexactinellida, Calcarea, and Homoscleromorpha. The morphology comparison is attached to other citations in the citing sentence. (LLM, conf=0.86)
- Partly supportedcites [8] 8. Philippe H, et al. (2011) Resolving difficult phylogenetic questions: Why more se- quences are not enough. PLoS Biol 9(3):e1000602. sourceExperimental — accuracy not yet measured
The Issues at the Level of Taxon Sampling section reports support for a Demospongiae + Hexactinellida clade and describes an analysis supporting sponge monophyly. It does not state that this clade is sister to Calcarea + Homoscleromorpha; the precise relationship attributed to this source is therefore unsupported by our copy. (LLM, conf=0.82)
- Not checked — no full text of the sourcecites [9] 9. Philippe H, et al. (2009) Phylogenomics revives traditional views on deep animal re- lationships. Curr Biol 19(8):706-712. source
- Supportedcites [29] 29. Dohrmann M, Janussen D, Reitner J, Collins AG, Wörheide G (2008) Phylogeny and evolution of glass sponges (Porifera, Hexactinellida). Syst Biol 57(3):388-405. source
In “Molecular Phylogeny of Hexactinellida and Relationships among Poriferans,” the paper reports a Demospongiae–Hexactinellida clade, a Homoscleromorpha–Calcarea sister grouping, and monophyletic Porifera. “Relationships of the Major Sponge Groups” reports morphological support for the Demospongiae–Hexactinellida clade, though that result becomes ambiguous when polymorphisms are allowed. The paper thus supports the cited topology as an example of a molecular analysis consistent with morphology; support for sponge monophyly was model-sensitive. (LLM, conf=0.88)
- Could not verifycites [30] 30. Voigt O, Adamski M, Sluzek K, Adamska M (2014) Calcareous sponge genomes reveal complex evolution of α-carbonic anhydrases and two key biomineralization enzymes. BMC Evol Biol 14(1):230. sourceExperimental — accuracy not yet measured
The Results (Phylogenetic analysis; page unavailable) examine carbonic anhydrase gene relationships and reconcile them with alternative hypotheses about animal phylogeny. The Methods (Sequence identification and analysis; page unavailable) say sponge-class relationships were taken from those hypotheses and previous results. Neither passage establishes the claimed sister-group relationship or its consistency with morphology and other molecular analyses. (LLM, conf=0.76)
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.
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“especially considering a growing body of evidence that supports convergent evolution of many animal traits including neurons (5,6,(41)(42)(43).”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Conclusions
What the sources say
- Partly supportedcites [5] 5. Moroz LL, et al. (2014) The ctenophore genome and the evolutionary origins of neural systems. Nature 510(7503):109-114. sourceExperimental — accuracy not yet measured
The Discussion (page unavailable) proposes convergent evolution of neuro-muscular organization in ctenophores, and the Extended Data Figure 10 caption says the study supports multiple origins of neurons. The paper supports the claim about neurons, but these passages do not establish the broader claim about many animal traits. (LLM, conf=0.82)
- Partly supportedcites [6] 6. Ryan JF, et al.; NISC Comparative Sequencing Program (2013) The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 342(6164):1242592. sourceExperimental — accuracy not yet measured
The Discussion and Conclusion supports independent evolution of ctenophore mesodermal cell types and discusses independently evolved musculature. It presents independent origins of neural cell types as an unresolved alternative, however, while its genetic evidence suggests an ancestral nervous system later reduced in sponges and placozoans. Thus it does not establish convergent evolution of neurons. (LLM, conf=0.88)
- Not checked — no full text of the sourcecites [41] 41. Dunn CW, Giribet G, Edgecombe GD, Hejnol A (2014) Animal phylogeny and its evolutionary implications. Annu Rev Ecol Evol Syst 45:371-395. source
- Partly supportedcites [42] 42. Liebeskind BJ, Hillis DM, Zakon HH (2015) Convergence of ion channel genome content in early animal evolution. Proc Natl Acad Sci USA 112(8):E846-E851. sourceExperimental — accuracy not yet measured
The Discussion (page unavailable) says the findings suggest a large role for convergence in extant animal nervous systems and cites evidence for independently evolved striated muscle. But the paper says it cannot distinguish competing hypotheses about nervous-system origins; it does not establish that neurons themselves evolved convergently. (LLM, conf=0.83)
- Not checked — no full text of the sourcecites [43] 43. Moroz LL (2015) Convergent evolution of neural systems in ctenophores. J Exp Biol 218(Pt 4):598-611. source
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.
- Partly supported
The sources with a verdict support this claim; the rest weren’t checked yet, have no full text we could read, or their verdicts aren’t rated yet.
In the paper
“standard measurements of sequence saturation (7,8,25) average across the length of the sequence.”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Placement of Ctenophores Sister to all Remaining Animals Is Not
What the sources say
- Not checked — no full text of the sourcecites [7] 7. Nosenko T, et al. (2013) Deep metazoan phylogeny: When different genes tell dif- ferent stories. Mol Phylogenet Evol 67(1):223-233. source
- Supportedcites [8] 8. Philippe H, et al. (2011) Resolving difficult phylogenetic questions: Why more se- quences are not enough. PLoS Biol 9(3):e1000602. source
In ‘Issues at the Level of Gene Sampling’ (page not provided), the paper estimates one saturation level for each dataset from a regression of sequence distances. This is an alignment-wide measure rather than a position-by-position measurement, supporting the paraphrase that it averages across sequence length. (LLM, conf=0.85)
- Supportedcites [25] 25. Struck TH (2014) TreSpEx-detection of misleading signal in phylogenetic reconstruc- tions based on tree information. Evol Bioinform Online 10:51-67. source
The “Detection of saturation and phylogenetic signal” section describes standard saturation measures as a slope or R² value calculated for each gene, data set, or partition, rather than for individual positions along a sequence. The “Run-time Statistics” section says the underlying pairwise distances are calculated from the alignments. Together, these support the paraphrase that the measures summarize saturation across the sequence length; page numbers are unavailable in our copy. (LLM, conf=0.85)
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.
In the paper
“Importantly, Phylobayes (26) analyses using the CAT-GTR+Γ model also resulted in phylogenies with Ctenophora sister to all other animals with 100% posterior probability (PP), and 100% PP for sponge monophyly (datasets 6 and 16 in Figs. 2 and 3 and Fig. S5 B and C).”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Ctenophores Sister to Other Extant Animals and Monophyletic Sponges.
What the sources say
- Not checked — no full text of the sourcecites [26] 26. Lartillot N, Rodrigue N, Stubbs D, Richer J (2013) PhyloBayes MPI: Phylogenetic re- construction with infinite mixtures of profiles in a parallel environment. Syst Biol 62(4):611-615. source
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.
In the paper
“Importantly, Phylobayes (26) analyses using the CAT-GTR+Γ model also resulted in phylogenies with Ctenophora sister to all other animals with 100% posterior probability (PP), and 100% PP for sponge monophyly (datasets 6 and 16 in Figs. 2 and 3 and Fig. S5 B and C).”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Ctenophores Sister to Other Extant Animals and Monophyletic Sponges.
What the sources say
- Not checked — no full text of the sourcecites [26] 26. Lartillot N, Rodrigue N, Stubbs D, Richer J (2013) PhyloBayes MPI: Phylogenetic re- construction with infinite mixtures of profiles in a parallel environment. Syst Biol 62(4):611-615. source
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
“All maximum-likelihood analyses with outgroups resulted in topologies with strong support [≥ 97% bootstrap support (BS)] for ctenophores sister to all other extant animal lineages (datasets 1-21 in Figs. 2 and 3 and Figs.S1-S4).”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Ctenophores Sister to Other Extant Animals and Monophyletic Sponges.
boostedcorrelational- 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. 25
- Probably not a substantial claim. 12
- The quote only partly states this claim. 2
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“However, ctenophores were recovered as sister to all other extant animals in maximumlikelihood analyses with greater taxon sampling (Bayesian inference never converged for datasets with more than 19 taxa).”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Abstract
What the sources say
- Partly supportedcites [6] 6. Ryan JF, et al.; NISC Comparative Sequencing Program (2013) The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 342(6164):1242592. sourceExperimental — accuracy not yet measured
In “Phylogenetic position of Mnemiopsis leidyi” (page unavailable), the paper reports that maximum-likelihood analyses placed ctenophores sister to all other animals for both its 13-animal Genome Set and its more broadly sampled 58-animal EST Set. It also reports that none of the Bayesian analyses of the EST Set converged. It does not establish a general cutoff of more than 19 taxa for Bayesian nonconvergence. (LLM, conf=0.83)
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.
It may state two separate claims as one.
- Partly supported
Every source the paper cites for this claim was checked and supports it.
In the paper
“For example, Ryan et al. (6) recovered a sister relationship between sponges and ctenophores in analyses where taxa with high amounts of missing data were excluded, and support for this was highest in Bayesian inference with the CAT (17) substitution model.”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Abstract
What the sources say
- Supportedcites [6] 6. Ryan JF, et al.; NISC Comparative Sequencing Program (2013) The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 342(6164):1242592. source
In “Phylogenetic position of Mnemiopsis leidyi” (page not available), the Genome Set includes only complete genomes and has substantially less missing data than the EST Set. The paper reports that Bayesian analysis of the Genome Set, using the CAT model, strongly supports a Ctenophora–Porifera clade, whereas maximum-likelihood analyses give it only some support. (LLM, conf=0.91)
- Supportedcites [17] 17. Lartillot N, Brinkmann H, Philippe H (2007) Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evol Biol 7(Suppl 1):S4. source
Citation (17) identifies the CAT model, not Ryan et al.’s findings. The Background describes CAT as a site-heterogeneous mixture model implemented in a Bayesian framework, and the Results and Discussion compare its use in phylogenetic analyses with WAG. (LLM, conf=0.93)
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.
It may state two separate claims as one.
- Supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Additional sources of systematic error include poor taxon or character sampling (10,14,15), large amounts of missing data (16), and model misspecification (16,17).”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Abstract
What the sources say
- Supportedcites [10] 10. Pick KS, et al. (2010) Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships. Mol Biol Evol 27(9):1983-1987. source
This source is cited for poor taxon or character sampling, not for missing data or model misspecification. The paper argues that insufficient taxon sampling produced erroneous phylogenetic results and notes that character-rich analyses are thought to outperform character-poor ones (Abstract; page unavailable in our copy). (LLM, conf=0.91)
- Not checked — no full text of the sourcecites [14] 14. Heath TA, Hedtke SM, Hillis DM (2008) Taxon sampling and the accuracy of phylo- genetic analyses. J Syst Evol 46(3):239-257. source
- Not checked — no full text of the sourcecites [15] 15. Jeffroy O, Brinkmann H, Delsuc F, Philippe H (2006) Phylogenomics: The beginning of incongruence? Trends Genet 22(4):225-231. source
- Not checked — no full text of the sourcecites [16] 16. Roure B, Baurain D, Philippe H (2013) Impact of missing data on phylogenies inferred from empirical phylogenomic data sets. Mol Biol Evol 30(1):197-214. source
- Partly supportedcites [17] 17. Lartillot N, Brinkmann H, Philippe H (2007) Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evol Biol 7(Suppl 1):S4. sourceExperimental — accuracy not yet measured
The Background links systematic phylogenetic errors to poor taxon sampling and model misspecification, and says that more careful selection of sites or sequences improves reliability. It does not identify large amounts of missing data as a source of systematic error; a search for “missing data” found no supporting passage. (LLM, conf=0.85)
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. It may state two separate claims as one.
- Supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Other than progressive data filtering, differences between datasets analyzed here and those used in previous studies of basal metazoan relationships (3-10) are increased character sampling and less missing data compared with some studies and increased nonbilaterian taxon sampling.”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Datasets and Accounting for Biases.
What the sources say
- Not checked — no full text of the sourcecites [3] 3. Dunn CW, et al. (2008) Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452(7188):745-749. source
- Partly supportedcites [4] 4. Hejnol A, et al. (2009) Assessing the root of bilaterian animals with scalable phylo- genomic models. Proc Biol Sci 276(1802):4261-4270. sourceExperimental — accuracy not yet measured
The Results (data matrix assembly; page unavailable) describe this prior dataset as a 1,487-gene, 94-taxon matrix with 19% occupancy. The Methods (data acquisition and matrix assembly; page unavailable) identify its taxon sampling, including a sponge. These passages provide a basis for comparison, but the source cannot establish that the citing authors’ datasets had more characters, less missing data, or more nonbilaterian taxa. (LLM, conf=0.78)
- Supportedcites [5] 5. Moroz LL, et al. (2014) The ctenophore genome and the evolutionary origins of neural systems. Nature 510(7503):109-114. source
The citation identifies this paper as a previous study of basal metazoan relationships. Its Ctenophore phylogeny section reports analyses of those relationships, and its Methods describe the datasets used. The claimed improvements belong to the citing authors’ comparison of datasets, not to a finding attributed to this source. (LLM, conf=0.90)
- Partly supportedcites [6] 6. Ryan JF, et al.; NISC Comparative Sequencing Program (2013) The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 342(6164):1242592. sourceExperimental — accuracy not yet measured
In “Phylogenetic position of Mnemiopsis leidyi” (page not specified), the paper describes two earlier matrices with different taxon sampling and missing-data fractions, making it a relevant example of a previous dataset. It does not establish that the citing study’s datasets have more characters, less missing data, or more nonbilaterian taxa than its own. (LLM, conf=0.76)
- Not checked — no full text of the sourcecites [7] 7. Nosenko T, et al. (2013) Deep metazoan phylogeny: When different genes tell dif- ferent stories. Mol Phylogenet Evol 67(1):223-233. source
- Supportedcites [8] 8. Philippe H, et al. (2011) Resolving difficult phylogenetic questions: Why more se- quences are not enough. PLoS Biol 9(3):e1000602. source
The citation identifies this paper as one of the previous studies of basal metazoan relationships, rather than asking it to describe the citing authors’ new dataset. In ‘Issues at the Level of Taxon Sampling,’ the paper compares nonbilaterian sampling across earlier datasets; in ‘Box 3,’ it reports missing-data levels for an updated dataset. Those passages support its role as a prior study in the comparison. (LLM, conf=0.84)
- Not checked — no full text of the sourcecites [9] 9. Philippe H, et al. (2009) Phylogenomics revives traditional views on deep animal re- lationships. Curr Biol 19(8):706-712. source
- Partly supportedcites [10] 10. Pick KS, et al. (2010) Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships. Mol Biol Evol 27(9):1983-1987. sourceExperimental — accuracy not yet measured
In the section labeled Abstract (page unavailable), Pick et al. report adding nonbilaterian taxa to a previous dataset, supporting that part of the comparison. They say they used an identical gene set to Dunn et al.; the passages do not establish that the citing paper’s datasets had more characters or less missing data than Pick et al.’s dataset. (LLM, conf=0.84)
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.
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Phylogenomic studies have resulted in controversial hypotheses placing either Placozoa (Fig. 1A) (2), ctenophores (ctenophore-sister hypothesis) (Fig. 1B) (3)(4)(5)(6)(7), or a clade of ctenophores and sponges (Fig. 1C) (6) as sister to all remaining animals.”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Abstract
What the sources say
- Partly supportedcites [2] 2. Dellaporta SL, et al. (2006) Mitochondrial genome of Trichoplax adhaerens supports placozoa as the basal lower metazoan phylum. Proc Natl Acad Sci USA 103(23): 8751-8756. sourceExperimental — accuracy not yet measured
The Abstract says the mitochondrial-protein analyses support Placozoa at the root of Metazoa, supporting the Placozoa hypothesis for which this paper is cited. But the Results and Discussion establish its basal position among the lower metazoans; when bilaterians were included, the analysis instead split bilaterians from the other sampled animals. The paper therefore does not establish Placozoa as sister to all remaining animals. (LLM, conf=0.84)
- Not matchedcites (3)(4)(5)(6)(7)
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Supportedcites [6] 6. Ryan JF, et al.; NISC Comparative Sequencing Program (2013) The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 342(6164):1242592. source
The Phylogenetic position of Mnemiopsis leidyi section (page not supplied) reports substantial support for ctenophores as sister to all other animals. It also reports that a Bayesian analysis strongly supports a ctenophore–sponge clade as sister to the remaining animals, while cautioning that the result may reflect poor taxon sampling. Those are the two hypotheses for which this paper is cited; the Placozoa hypothesis has a different citation. (LLM, conf=0.93)
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.
- Partly supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Our robust support of sponge monophyly agrees with morphology (35) and most other large molecular datasets (5,6,(8)(9)(10).”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Placement of Ctenophores Sister to all Remaining Animals Is Not
What the sources say
- Not checked — no full text of the sourcecites [35] 35. Ax P (1996) Multicellular Animals: A New Approach to the Phylogenetic Order in Nature (Springer, Berlin). source
- Supportedcites [5] 5. Moroz LL, et al. (2014) The ctenophore genome and the evolutionary origins of neural systems. Nature 510(7503):109-114. source
The Ctenophore phylogeny section (page unavailable) reports that its molecular analysis recovered Porifera as a group, with 100% bootstrap support. This supports citing the paper as one molecular dataset consistent with sponge monophyly; the separate morphology citation is not attributed to this source. (LLM, conf=0.91)
- Could not verifycites [6] 6. Ryan JF, et al.; NISC Comparative Sequencing Program (2013) The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 342(6164):1242592. sourceExperimental — accuracy not yet measured
The ‘Phylogenetic position of Mnemiopsis leidyi’ section reports support for ctenophores as sister to other animals and discusses the alternative placement of Porifera. It does not report whether sponge species form a monophyletic group. Searches for sponge and Porifera monophyly found no passage establishing the point attributed to this molecular dataset; page numbers were not available in our copy. (LLM, conf=0.70)
- Partly supportedcites [8] 8. Philippe H, et al. (2011) Resolving difficult phylogenetic questions: Why more se- quences are not enough. PLoS Biol 9(3):e1000602. sourceExperimental — accuracy not yet measured
The Issues at the Level of Taxon Sampling section reports 96% bootstrap support for sponge monophyly in one large phylogenomic analysis. But Box 2 says monophyly is not unequivocally accepted and that only that analysis recovered it with significant statistical support; the paper therefore does not support agreement with most other large molecular datasets. The morphology citation is separate from this source. (LLM, conf=0.84)
- Not checked — no full text of the sourcecites [9] 9. Philippe H, et al. (2009) Phylogenomics revives traditional views on deep animal re- lationships. Curr Biol 19(8):706-712. source
- Supportedcites [10] 10. Pick KS, et al. (2010) Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships. Mol Biol Evol 27(9):1983-1987. source
The cited paper is one of the molecular datasets invoked by the sentence. Its Abstract reports that its expanded phylogenomic analysis recovered monophyletic Porifera, supporting the claimed agreement on sponge monophyly. (LLM, conf=0.92)
boostedcorrelational- 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.
Every source the paper cites for this claim was checked and supports it.
In the paper
“Ribosomal protein genes have previously been identified as a potential source of phylogenetic error (32)”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Placement of Ctenophores Sister to all Remaining Animals Is Not
What the sources say
- Supportedcites [32] 32. Bleidorn C, et al. (2009) On the phylogenetic position of Myzostomida: Can 77 genes get it wrong? BMC Evol Biol 9(1):150. source
The Results and discussion section (page not provided) says that ribosomal proteins might mislead phylogenetic analyses because of evolutionary biases. It also warns that relying on genes from a single macromolecular complex can produce a biased phylogenetic picture. (LLM, conf=0.93)
hedgedconditional- 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.
- Supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Notably, a study focused only on myxozoan cnidarians (34) used the same matrix as Philippe et al. ( 9), but added two highly divergent cnidarians and recovered ctenophores sister to all other animals.”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Placement of Ctenophores Sister to all Remaining Animals Is Not
What the sources say
- Partly supportedcites [34] 34. Nesnidal MP, Helmkampf M, Bruchhaus I, El-Matbouli M, Hausdorf B (2013) Agent of whirling disease meets orphan worm: phylogenomic analyses firmly place Myxozoa in Cnidaria. PLoS ONE 8(1):e54576. sourceExperimental — accuracy not yet measured
Methods (Data Assembly; page unavailable) says the authors added two myxozoans to a phylogenomic dataset assembled by Philippe et al.; Results and Discussion describes their high substitution rates and places them within Cnidaria. The available text does not state that the analysis recovered ctenophores as sister to all other animals, so that outcome is unsupported. (LLM, conf=0.84)
- Not checked — no full text of the sourcecites [9] 9. Philippe H, et al. (2009) Phylogenomics revives traditional views on deep animal re- lationships. Curr Biol 19(8):706-712. source
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.
- Partly supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“extremely low mutation rates can indicate selection and result in too little phylogenetic information, both of which could lead to the inference of incorrect relationships (33).”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Placement of Ctenophores Sister to all Remaining Animals Is Not
What the sources say
- Partly supportedcites [33] 33. Edwards SV (2009) Natural selection and phylogenetic analysis. Proc Natl Acad Sci USA 106(22):8799-8800. sourceExperimental — accuracy not yet measured
In the discussion (pp. 8799–8800), Edwards says stabilizing selection lowers the overall rate of evolution, and that some forms of selection can mislead phylogenetic analysis. The paper does not say that extremely low mutation rates leave too little phylogenetic information or that low rates themselves lead to incorrect relationships; it describes stabilizing selection as not necessarily a problem for analysis. (LLM, conf=0.84)
hedgedconditional- 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.
- Partly supported
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
“Importantly, biases resulting from elevated compositional heterogeneity or elevated substitution rates are ruled out.”
- Also stated in: § Systematic Biases and Their Effect on Phylogenetic Inference. · plain
“Removing OGs with high amino acid compositional heterogeneity (datasets 7-11, 17-21, 23, and 25 in Fig. 2) also had no effect on branching order (Fig. 3 and Figs.S2 A-E, S3 E and F, S4 A-E, and S5A).”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Abstract
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.
- Also stated in: § Systematic Biases and Their Effect on Phylogenetic Inference. · plain
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
“Placement of ctenophores as sister to all other animals, and sponge monophyly, are strongly supported under multiple analyses, herein.”
- Also stated in: § Ctenophores Sister to Other Extant Animals and Monophyletic Sponges. · boosted
“All maximum-likelihood analyses with outgroups resulted in topologies with strong support [≥ 97% bootstrap support (BS)] for ctenophores sister to all other extant animal lineages (datasets 1-21 in Figs. 2 and 3 and Figs.S1-S4).”
- Also stated in: § Placement of Ctenophores Sister to all Remaining Animals Is Not · boosted
“Every analysis conducted herein strongly supported the ctenophore-sister hypothesis (Fig. 3 and Table 1).”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Abstract
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.
- Rests on an assumption: The sampled taxa adequately represent the major metazoan lineages for inferring the position of ctenophores relative to all other animals.
- Rests on an assumption: The outgroup taxa used are appropriate for rooting the animal tree.
- Also stated in: § Ctenophores Sister to Other Extant Animals and Monophyletic Sponges. · boosted
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 example, most topologies with both certain and uncertain paralogs removed had strong support for sponge monophyly (i.e., ≥ 95% BS) (datasets 12-14 and 18-20 in Figs. 2 and 3 and Figs.S2F, S3 A, B, and F, and S4 A and B), but four analyses with only certain paralogs removed recovered low support (< 90% BS) for sponge monophyly (datasets 5, 7, 9, and 10 in Figs. 2 and 3 and Figs.S1E and S2 A, D,”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Systematic Biases and Their Effect on Phylogenetic Inference.
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.
It may state two separate claims as one.
In the paper
“We also find strong support for sponge monophyly in contrast to previous reports (7,(22)(23)(24).”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Abstract
What the sources say
- Not matchedcites (7,(22)(23)(24)
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
boosted- 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.
- Not matched
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
“Analyses with all outgroup taxa removed (datasets 22-25 in Fig. 2) recovered identical relationships among major metazoan lineages as other analyses (Figs.S4 D-F and S5A). However, we observed low support for relationships among ctenophores, sponges, and placozoans in these analyses.”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Systematic Biases and Their Effect on Phylogenetic Inference.
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
“When all outgroups except two choanoflagellates were removed (datasets 5, 11, 15, and 21 in Fig. 2), inferred nonbilaterian relationships were identical as in analyses we performed with full outgroup sampling (datasets 5, 11, 15, and 21 in Figs. 2 and 3 and Figs.S1E, S2E, S3C, and S4C), but support for sponge monophyly decreased.”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Systematic Biases and Their Effect on Phylogenetic Inference.
plaindirect- 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
“However, Bayesian inference (Fig. S5E) recovered sponges as sister to all other metazoans, but support for this and other deep nodes were low (PP ≤ 90).”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Ctenophores Sister to Other Extant Animals and Monophyletic Sponges.
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 quote only partly states this claim.
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
“Topologies inferred with only the slowest evolving half of OGs assembled here (datasets 6 and 16 in Fig. 2) (i.e., least saturated and least prone to homoplasy; see Fig. S7 for saturation plots) recovered high support for ctenophores sister to all other animals and sponge monophyly with both maximum-likelihood (BS = 100) (Fig. 3 and Figs.S1F and S3D) and Bayesian inference using the CAT-GTR model”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Systematic Biases and Their Effect on Phylogenetic Inference.
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
“The maximum-likelihood analysis recovered strong support for ctenophores as sister to all other metazoan lineages (BS = 93) (Fig. S5D).”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Ctenophores Sister to Other Extant Animals and Monophyletic Sponges.
boostedcorrelational- 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.
The quote only partly states this claim.
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
“We found complete congruence in relationships among basal metazoan phyla in trees inferred with (datasets 1, 2, 8, 12, and 18 in Fig. 2) and without (datasets 3-7, 9-11, 13-17, 19-21, and 22-25 in Fig. 2) taxa and genes that had high LB scores, and nodal support for critical nodes showed little variation among analyses (Fig. 3 and Figs.S1-S5).”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Systematic Biases and Their Effect on Phylogenetic Inference.
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.
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 recovered position of ctenophores was identical in analyses with (datasets 1, 2, 8, 12, and 18 in Fig. 2 and Figs.S1 A and B, S2 B and F, and S3F) and without (datasets 3-7, 9-11, 13-17, and 19-25 in Fig. 2, and Figs.S1 C-F, S2 A and C-E, S3 A-E, S4, and S5 A-C) taxa and genes with high LB scores, and analyses with the slowest evolving genes (datasets 6 and 16 in Fig. 2 and Fig. S7) also”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Placement of Ctenophores Sister to all Remaining Animals Is Not
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.
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
“Although relationships among basal lineages were unaffected, removal of paralogs as identified by TreSpEx appeared to have the greatest effect on support for some critical nodes.”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Systematic Biases and Their Effect on Phylogenetic Inference.
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.
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, sponge monophyly was recovered in all of our analyses and best supported when the strictest orthology criteria were applied with TreSpEx (Fig. 3 and Table 1), which also removes sequences resulting from sample contamination (e.g., endosymbionts).”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Placement of Ctenophores Sister to all Remaining Animals Is Not
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.
It may state two separate claims as one.
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
“Inaccurate orthology assignment can also introduce systematic error into phylogenomic analyses.”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Systematic Biases and Their Effect on Phylogenetic Inference.
plaindirect- 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: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
In the paper
“This lower mutational saturation has been the primary rational for emphasizing ribosomal genes when inferring deep animal relationship (7).”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Placement of Ctenophores Sister to all Remaining Animals Is Not
What the sources say
- Not checked — no full text of the sourcecites [7] 7. Nosenko T, et al. (2013) Deep metazoan phylogeny: When different genes tell dif- ferent stories. Mol Phylogenet Evol 67(1):223-233. source
plaindirect- 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 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
“Maximum-likelihood and Bayesian inference using the CAT-GTR model of the least saturated datasets (datasets 6 and 16 in Fig. 2 and Fig. S7) recovered identical basal relationships as our other analyses (Fig. 3 and Figs.S1F, S3D, and S5 B and C), also indicating homoplasy and model choice did not bias results.”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Placement of Ctenophores Sister to all Remaining Animals Is Not
hedged- 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
“Ideally, if robust datasets are assembled and causes of systematic error are accounted for, different datasets and analytical methods will converge on a single phylogenetic hypothesis (19).”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Abstract
What the sources say
- Not checked — no full text of the sourcecites [19] 19. Philippe H, Delsuc F, Brinkmann H, Lartillot N (2005) Phylogenomics. Annu Rev Ecol Evol Syst 36:541-562. source
hedgedconditional- 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.
In the paper
“Nosenko et al. (7) analyzed a dataset without ribosomal protein genes and recovered ctenophores sister to all other animals, but a similar analysis has not been done for the original Philippe et al. (9) dataset.”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Ctenophores Sister to Other Extant Animals and Monophyletic Sponges.
What the sources say
- Not checked — no full text of the sourcecites [7] 7. Nosenko T, et al. (2013) Deep metazoan phylogeny: When different genes tell dif- ferent stories. Mol Phylogenet Evol 67(1):223-233. source
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.
It may state two separate claims as one.
In the paper
“the above indicates that ctenophores sister to cnidarians as in Philippe et al. ( 9) was caused by either limited cnidarian taxon sampling, misleading signal in ribosomal genes, or both.”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Placement of Ctenophores Sister to all Remaining Animals Is Not
What the sources say
- Not checked — no full text of the sourcecites [9] 9. Philippe H, et al. (2009) Phylogenomics revives traditional views on deep animal re- lationships. Curr Biol 19(8):706-712. source
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.
In the paper
“The AU test (31) was used to determine if a priori hypotheses of basal metazoan relationships could be rejected (Fig. 1).”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Orthology Determination and Data Filtering.
What the sources say
- Not checked — no full text of the sourcecites [31] 31. Shimodaira H (2002) An approximately unbiased test of phylogenetic tree selection. Syst Biol 51(3):492-508. source
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.
In the paper
“Convergence was also assessed with tracecomp (26) to ensure each parameter had a maximum discrepancy between chains of less than 0.3 and an effective sample size of at least 50.”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Orthology Determination and Data Filtering.
What the sources say
- Not checked — no full text of the sourcecites [26] 26. Lartillot N, Rodrigue N, Stubbs D, Richer J (2013) PhyloBayes MPI: Phylogenetic re- construction with infinite mixtures of profiles in a parallel environment. Syst Biol 62(4):611-615. 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. It may state two separate claims as one.
In the paper
“Phylobayes analyses were run with two chains until the maxdiff statistic between chains was below 0.3 as measured by bpcomp (26).”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Orthology Determination and Data Filtering.
What the sources say
- Not checked — no full text of the sourcecites [26] 26. Lartillot N, Rodrigue N, Stubbs D, Richer J (2013) PhyloBayes MPI: Phylogenetic re- construction with infinite mixtures of profiles in a parallel environment. Syst Biol 62(4):611-615. source
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.
In the paper
“Furthermore, the Porifera-sister hypothesis lacks critical evaluation and homology of many characters in these taxa still need thorough analysis (44).”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Conclusions
What the sources say
- Not checked — no full text of the sourcecites [44] 44. Halanych KM (2015) The ctenophore lineage is older than sponges? That cannot be right! Or can it? J Exp Biol 218(Pt 4):592-597. source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check 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. It may be too vague to check against evidence. The paper’s conclusions may not depend on it. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Nodal support was measured with 100 fast bootstrap replicates.”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Orthology Determination and Data Filtering.
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.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Computational demands and convergence issues prevented us from using the CAT-GTR+Γ model for most datasets.Therefore, Bayesian phylogenies are only reported for the two analyses of the slowest evolving half of OGs.”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Orthology Determination and Data Filtering.
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.
The paper relies on this without support.
The sampled taxa adequately represent the major metazoan lineages for inferring the position of ctenophores relative to all other animals.
“Here, we have assembled a more comprehensive phylogenomic dataset of metazoan lineages that branched early in animal evolution than previous studies to alleviate taxon sampling concerns.”
“Other than progressive data filtering, differences between datasets analyzed here and those used in previous studies of basal metazoan relationships (3-10) are increased character sampling and less missing data compared with some studies and increased nonbilaterian taxon sampling.”
The paper relies on this without support.
The outgroup taxa used are appropriate for rooting the animal tree.
“Because outgroup sampling has the potential to influence rooting of the animal tree, we explored outgroup sampling as well.”
The paper relies on this without support.
The orthology assignments are accurate enough that the orthologous groups reflect true gene orthology.
“Orthology filtering of transcriptome and genome data from 76 species resulted in 251 orthologous groups (OGs) and 81,008 aligned amino acid sites (Tables S1 and S2).”
“Inaccurate orthology assignment can also introduce systematic error into phylogenomic analyses.”
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 cited source doesn’t support the claim as written.
In the citing paper
“Here, we have consolidated these findings by directly showing that the primary remaining lines of evidence supporting Ctenophora sister, partitioned phylogenomics4,7 and measures of underlying support (such as ΔPSlnl values)4,40, do not do so when better-fitting site-heterogeneous models are incorporated into the analysis.”
From Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding (2021) · cites this paper as [7]
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measuredThe cited source doesn’t support the claim as written.
In the citing paper
“These results suggest that the lack of support for Coelenterata and decreased support for Porifera-sister in Whelan et al. ' s (6) reanalysis was not caused by the absence of a misleading signal specific to the generally slowly evolving ribosomal proteins but, instead, by a bias introduced by distant outgroups that becomes dominant when only the faster evolving nonribosomal proteins are retained.”
From Genomic data do not support comb jellies as the sister group to all other animals (2015) · cites this paper as [6]
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measuredThe cited source doesn’t support the claim as written.
In the citing paper
“analysis of the Whelan et al. (6) datasets gave decreased support for Ctenophora-sister because distantly related outgroups were excluded (Fig. 2 and Figs. S3 A -C and S4 A -C ). At the same time, support for Porifera-sister increased”
From Genomic data do not support comb jellies as the sister group to all other animals (2015) · cites this paper as [6]
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“A key aspect of the debate is that support for both hypotheses is generally recovered from the same dataset when different substitution models and/or taxon- and gene-sampling strategies are used (contrast [6, 10] and [42, 45], and see [7, 43, 47]).”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [10]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“The dataset we selected from [10] was dataset D20, their least compositionally heterogeneous dataset”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [10]
Experimental — accuracy not yet measured
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Studies using partitioned site-homogeneous models have always recovered comb jellies as sister to other animals3,4,6,7.”
From Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding (2021) · cites this paper as [7]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Relaxed clustering has previously shown that partitioning by gene is the best fit for the WEA15 dataset and this is the partitioning scheme that was used in the original study7.”
From Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding (2021) · cites this paper as [7]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Whelan et al. (6) assembled 25 datasets differing in protein and species selection, and recovered Ctenophora-sister with strong support from all of them”
From Genomic data do not support comb jellies as the sister group to all other animals (2015) · cites this paper as [6]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“they did not examine the combined effect of these factors. That is, all of the outgroup-subsampled datasets were analyzed exclusively using site-homogeneous substitution models, whereas the analyses using the better-fitting site-heterogeneous model were exclusively performed using the full set of outgroups, which included distantly related Fungi”
From Genomic data do not support comb jellies as the sister group to all other animals (2015) · cites this paper as [6]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“The same procedure applied to a previously published dataset [10] led to the same results, suggesting that the choice of the model of evolution, and not the dataset per se, is responsible for the effect observed (see Figure S3).”
From A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals (2017) · cites this paper as [10]
The cited source says what the claim attributes to it.
In the citing paper
“In previous studies, the Porifera-sister hypothesis has tended to be better supported by smaller, manually constructed and curatedphylogenomicdatasets[1-3],whereasdatasetsfeaturing many more genes and assembled using entirely automated procedures have tended to support Ctenophora-sister (e.g., [5-10]).”
From A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals (2017) · cites this paper as [10]
The cited source says what the claim attributes to it.
In the citing paper
“Analyses of large-scale molecular superalignments assembled from genomic or transcriptomic data have failed thus far to provide a widely accepted consensus for the branching order among the five major animal lineages, i.e., sponges, placozoans, ctenophores, cnidarians, and bilaterians [1-12].”
From A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals (2017) · cites this paper as [10]
The cited source says what the claim attributes to it.
In the citing paper
“Potential causes of systematic error were controlled for by creating additional datasets that removed potentially problematic genes (Supplementary Table S3) 11 .”
From Ctenophore relationships and their placement as the sister group to all other animals (2017) · cites this paper as [11]
The cited source says what the claim attributes to it.
In the citing paper
“However, phylogenomic analyses have supported both Porifera-sister [6, 7, 39, 41-44] and Ctenophora-sister [8-12, 35, 45, 46], with some studies (like [47]) presenting both trees.”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [10]
The cited source says what the claim attributes to it.
In the citing paper
“Indeed, CAT-GTR+G analyses (with and without Dayhoff-6 recoding) of a dataset of [10] from which [11] removed ''outlier genes'' still finds support for Porifera-sister (PP = 0.98 and PP = 0.99, respectively; Figures S3I and S3J).”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [10]
The cited source says what the claim attributes to it.
In the citing paper
“however, in our analyses support for the monophyly of sponges generally tends to increase as better-fitting models are applied (Supplementary Figs. 17-19, 21-23) consistent with other analyses arguing against this hypothesis7.”
From Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding (2021) · cites this paper as [7]
The cited source says what the claim attributes to it.
In the citing paper
“Two of these, from Ryan et al.3 (REA dataset) and Whelan et al. (2015)7 (WEA15 dataset) supported Ctenophora sister under partitioned phylogenomics, but were found by Pisani and colleagues8 to support sponges as sister to other animals under CAT/CATGTR.”
From Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding (2021) · cites this paper as [7]
The cited source says what the claim attributes to it.
In the citing paper
“Thus, while strong support for Ctenophora-sister may be obtained from phylogenomic datasets (2 -6, 46, 55), our analysis suggests these results are caused by undetected systematic bias.”
From Genomic data do not support comb jellies as the sister group to all other animals (2015) · cites this paper as [6]
The cited source says what the claim attributes to it.
In the citing paper
“Taken together, our results show the datasets of Whelan et al. (6) do not support Ctenophora-sister when both distantly related outgroups are excluded and better-fitting substitution models are used”
From Genomic data do not support comb jellies as the sister group to all other animals (2015) · cites this paper as [6]
The check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“Finally, the absence of many gene families, coupled with massive lineage-specific expansions in others (6), suggests ctenophore genomes may be extremely derived compared with genomes of other animals.”
From Genomic data do not support comb jellies as the sister group to all other animals (2015) · cites this paper as [6]
Experimental — accuracy not yet measuredIn the citing paper
“Recent phylogenomic evidence suggests that ctenophores may be the sister group to the rest of animals.”
From Where is my mind? How sponges and placozoans may have lost neural cell types (2015) · cites this paper as [6]
In the citing paper
“We show that two key phylogenomic datasets that previously supported Ctenophora-sister [10, 12] display strong heterogeneity in amino acid composition across sites and taxa”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [10]
In the citing paper
“WhelanD20-Opistho, the dataset including all original outgroups from [10] (STAR Methods; Table 3; Figure S1D), supported Ctenophora-sister (PP z 1).”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [10]
In the citing paper
“Ctenophora-sister invariably emerges when site-specific amino acid differences are not modeled [10] or when site-specific amino acid differences are modeled but distant outgroups are used to root the tree [6].”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [10]
In the citing paper
“WhelanD20 was not analyzed under its optimal PF-scheme because [10] already showed that this dataset supports Ctenophora-sister when the PF-scheme is used.”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [10]
In the citing paper
“which is very similar to WhelanD20”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [10]
In the citing paper
“PFschemes were used by [10]”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [10]
In the citing paper
“The second is a dataset from [10] that had not been reassessed in [6].”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [10]
In the citing paper
“More broadly, our results demonstrate that PFschemes (strongly advocated for by [10, 28, 29, 38]) are much worse than CAT-GTR+G and are not always better than unpartitioned modeling strategies at capturing the heterogeneity of the considered datasets”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [10]
In the citing paper
“as the latter was obtained in [10] by removing genes of significant compositional heterogeneity from D16”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [10]
In the citing paper
“which apparently explicitly excludes proteins of significant compositional heterogeneity (see [10])”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [10]
In the citing paper
“Whelan et al. [38] have increased the number of ctenophoran species compared to those they used in [10].”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [10]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Each contradiction between two passages listed here was confirmed by an independent check.
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ Error, signal, and the placement of Ctenophora sister to all other animals > Systematic Biases and Their Effect on Phylogenetic Inference.
“four analyses with only certain paralogs removed recovered low support (< 90% BS) for sponge monophyly (datasets 5, 7, 9, and 10 in Figs. 2 and 3 and Figs.S1E and S2 A, D, and E).”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Orthology Determination and Data Filtering.
“| Genes with high LB scores | 9.E-41 | 9.E-05 | 2.E-04 | 2.E-66 | 99 BS | 90 BS |”
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ Error, signal, and the placement of Ctenophora sister to all other animals > Systematic Biases and Their Effect on Phylogenetic Inference.
“When all outgroups except two choanoflagellates were removed (datasets 5, 11, 15, and 21 in Fig. 2)”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Systematic Biases and Their Effect on Phylogenetic Inference.
“analyses we performed with full outgroup sampling (datasets 5, 11, 15, and 21 in Figs. 2 and 3 and Figs.S1E, S2E, S3C, and S4C)”
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ Error, signal, and the placement of Ctenophora sister to all other animals > Ctenophores Sister to Other Extant Animals and Monophyletic Sponges.
“All maximum-likelihood analyses with outgroups resulted in topologies with strong support [≥ 97% bootstrap support (BS)] for ctenophores sister to all other extant animal lineages (datasets 1-21 in Figs. 2 and 3 and Figs.S1-S4).”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Orthology Determination and Data Filtering.
“| Choanoflagellate-only | 1.E-03 | 3.E-36 | 1.E-02 | 6.E-104 | 92 BS | 82 BS |”
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ Error, signal, and the placement of Ctenophora sister to all other animals > Orthology Determination and Data Filtering.
“| Philippe et al. (7) Maximum | 0.001 | 0.010 | 0.008 | 0.075 | 93 BS | 42 BS |”
§ Error, signal, and the placement of Ctenophora sister to all other animals > References
“7. Nosenko T, et al. (2013) Deep metazoan phylogeny: When different genes tell dif- ferent stories.”
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ Error, signal, and the placement of Ctenophora sister to all other animals > Ctenophores Sister to Other Extant Animals and Monophyletic Sponges.
“Alternative hypotheses of basal animal relationships (Fig. 1) were rejected by every phylogenetic analysis as measured by the approximately unbiased (AU) (31) test (P ≤ 0.001) (Table 1).”
§ Error, signal, and the placement of Ctenophora sister to all other animals > Orthology Determination and Data Filtering.
“| Genes with high LB scores | 1.E-02 | 2.E-04 | 2.E-32 | 3.E-47 | 100 BS | 94 BS |”
Citations
Cites
R: A Language and Environment for Statistical Computing
R Core Team (2000) · doi:10.32614/r.manuals · Cited by 355,893
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
Stamatakis, A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu033 · Cited by 32,291
Haas, B. J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P. D., Bowden, J., Couger, M. B., Eccles, D., Li, B., Lieber, M., et al. (2013) · Nature Protocols · doi:10.1038/nprot.2013.084 · Cited by 8,464 · cited 1×
“Normalized Illumina reads were assembled using default parameters in Trinity v20131110 (46).”
MethodGenome sequencing in microfabricated high-density picolitre reactors
Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A., Berka, J., Braverman, M. S., Chen, Y.-J., Chen, Z., et al. (2005) · Nature · doi:10.1038/nature03959 · Cited by 7,693 · cited 1×
“Raw 454 transcriptome data were assembled with Newbler (47).”
MethodCases in which Parsimony or Compatibility Methods Will be Positively Misleading
Felsenstein, J. (1978) · Systematic Biology · doi:10.1093/sysbio/27.4.401 · Cited by 3,261
An approximately unbiased test of phylogenetic tree selection
Shimodaira, H. (2002) · Systematic Biology · doi:10.1080/10635150290069913 · Cited by 2,791 · cited 2×
“1) were rejected by every phylogenetic analysis as measured by the approximately unbiased (AU) (31) test (P ≤ 0.”
Method(1986) · Cited by 2,570
Cases in which parsimony or compatibility methods will be positively misleading.
Felsenstein, J. (1978) · Systematic Zoology · doi:10.2307/2412923 · Cited by 2,230
CONSEL: for assessing the confidence of phylogenetic tree selection
Shimodaira, H., & Hasegawa, M. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.12.1246 · Cited by 2,049 · cited 2×
“Per site log-likelihoods for trees were calculated in RAxML and AU tests were performed in Consel (57).”
MethodBroad phylogenomic sampling improves resolution of the animal tree of life
Dunn, C. W., Hejnol, A., Matus, D. Q., Pang, K., Browne, W. E., Smith, S. A., Seaver, E., Rouse, G. W., Obst, M., Edgecombe, G. D., et al. (2008) · Nature · doi:10.1038/nature06614 · Cited by 1,921 · cited 2×
“Taxa with high LB scores removed (3) 6.”
Background
Cited by
Sorted by citations
ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference
Steenwyk, J. L., Buida, T. J., Li, Y., Shen, X., & Rokas, A. (2020) · PLoS Biology · doi:10.1371/journal.pbio.3001007 · Cited by 711
“The 4 simulated datasets (Nalignments = 50 alignments per dataset or 200 total) stem from simulated nucleotide sequence evolution along the species phylogeny of 93 filamentous fungi [10] and from simulated amino acid sequence evolution along the species phylogenies of 70 metazoans [11], 46 flowering plants [12], and 9…”
BackgroundMethodMallet, J., Besansky, N. J., & Hahn, M. W. (2015) · BioEssays · doi:10.1002/bies.201500149 · Cited by 597
“Given that other major groups, such as the placental mammals [13], or the animals as a whole [82], appear also to have evolved in rapid”
BackgroundSimion, P., Philippe, H., Baurain, D., Jager, M., Richter, D. J., Di Franco, A., Roure, B., Satoh, N., Quéinnec, É., Ereskovsky, A., et al. (2017) · Current Biology · doi:10.1016/j.cub.2017.02.031 · Cited by 518
“The same procedure applied to a previously published dataset [10] led to the same results, suggesting that the choice of the model of evolution, and not the dataset per se, is responsible for the effect observed (see Figure S3).”
Contentious relationships in phylogenomic studies can be driven by a handful of genes
Shen, X.-X., Hittinger, C. T., & Rokas, A. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0126 · Cited by 520
Ancient gene linkages support ctenophores as sister to other animals
Schultz, D. T., Haddock, S. H. D., Bredeson, J. V., Green, R. E., Simakov, O., & Rokhsar, D. S. (2023) · Nature · doi:10.1038/s41586-023-05936-6 · Cited by 362
Xenacoelomorpha is the sister group to Nephrozoa
Cannon, J. T., Vellutini, B. C., Smith, J., Ronquist, F., Jondelius, U., & Hejnol, A. (2016) · Nature · doi:10.1038/nature16520 · Cited by 364
A genome-scale phylogeny of the kingdom Fungi
Li, Y., Steenwyk, J. L., Chang, Y., Wang, Y., James, T. Y., Stajich, J., Spatafora, J. W., Groenewald, M., Dunn, C. W., Hittinger, C. T., et al. (2021) · Current Biology · doi:10.1016/j.cub.2021.01.074 · Cited by 371
“Top100_slow-evolving – data matrix #8 This data matrix was constructed by retaining the 100 BUSCO genes with the lowest values of average pairwise patristic distance, which has previously been used to evaluate if fast-evolving genes bias phylogenetic inference 29,79 .”
The origin of Metazoa: a unicellular perspective
Sebé-Pedrós, A., Degnan, B. M., & Ruiz-Trillo, I. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2017.21 · Cited by 332
Revisiting metazoan phylogeny with genomic sampling of all phyla
Laumer, C. E., Fernández, R., Lemer, S., Combosch, D., Kocot, K. M., Riesgo, A., Andrade, S. C. S., Sterrer, W., Sørensen, M. V., & Giribet, G. (2019) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2019.0831 · Cited by 360
“It has been claimed that support for Ctenophora in this position even in taxonomically well-sampled datasets [9,10] is an artefact, which can be ameliorated by some combination of using adequately complex substitution models (such as CAT þ GTR) [11], deleting compositionally biased, distant outgroups, and/ or recoding…”
MethodSelf-citationGenomic data do not support comb jellies as the sister group to all other animals
Pisani, D., Pett, W., Dohrmann, M., Feuda, R., Rota-Stabelli, O., Philippe, H., Lartillot, N., & Wörheide, G. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1518127112 · Cited by 319
“(6), and identify several problems in these studies, specifically the combined use of relatively simplistic models of molecular”
BackgroundMethodResultInfluentialReddy, S., Kimball, R. T., Pandey, A., Hosner, P. A., Braun, M. J., Hackett, S. J., Han, K.-L., Harshman, J. S., Huddleston, C. J., Kingston, S. E., et al. (2017) · Systematic Biology · doi:10.1093/sysbio/syx041 · Cited by 292
“Indeed, two studies have reported that the phylogenetic signal associated with ribosomal proteins conflict with the signal associated with other proteins (Nosenko et al. 2013; Whelan et al. 2015), and another noted a difference between introns and UTRs (Bonilla et al.”
BackgroundImproved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals
Feuda, R., Dohrmann, M., Pett, W., Philippe, H., Rota-Stabelli, O., Lartillot, N., Wörheide, G., & Pisani, D. (2017) · Current Biology · doi:10.1016/j.cub.2017.11.008 · Cited by 291
“The second is that protein-specific amino acid replacement patterns across WhelanD20 and Chang could not be captured by the empirical substitution matrices considered in the PartitionFinder analyses of [10]”
InfluentialCtenophore relationships and their placement as the sister group to all other animals
Whelan, N. V., Kocot, K. M., Moroz, T. P., Mukherjee, K., Williams, P., Paulay, G., Moroz, L. L., & Halanych, K. M. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0331-3 · Cited by 263
Self-citationLavrov, D. V., & Pett, W. (2016) · Genome Biology and Evolution · doi:10.1093/gbe/evw195 · Cited by 234
“The relationships among nonbilaterian phyla and bilaterian animals remain contentious (Pisani et al. 2015; Whelan et al. 2015), but are largely irrelevant to the present study.”
BackgroundGenome-wide interrogation advances resolution of recalcitrant groups in the tree of life
Arcila, D., Ortí, G., Vari, R., Armbruster, J. W., Stiassny, M. L. J., Ko, K. D., Sabaj, M. H., Lundberg, J., Revell, L. J., & Betancur-R., R. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-016-0020 · Cited by 243
Phylogenomics of Lophotrochozoa with Consideration of Systematic Error
Kocot, K. M., Struck, T. H., Merkel, J., Waits, D. S., Todt, C., Brannock, P. M., Weese, D., Cannon, J. T., Moroz, L. L., Lieb, B., et al. (2016) · Systematic Biology · doi:10.1093/sysbio/syw079 · Cited by 209
Self-citationReconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data
Shen, X., Zhou, X., Kominek, J., Kurtzman, C. P., Hittinger, C. T., & Rokas, A. (2016) · G3 Genes Genomes Genetics · doi:10.1534/g3.116.034744 · Cited by 214
“Individually estimated ML gene trees were used as input to estimate the coalescent-based phylogenies for the AA and C12 data matrices using the ASTRAL software, version 4.7.7 (Mirarab et al. 2014).”
InfluentialEvolutionary History of Chemosensory-Related Gene Families across the Arthropoda
Eyun, S., Soh, H. Y., Posavi, M., Munro, J. B., Hughes, D., Murali, S. C., Qu, J., Dugan, S., Lee, S. L., Chao, H., et al. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx147 · Cited by 210
“1) (Moroz et al. 2014; Whelan et al. 2015), we can infer that the GRs evolved after the emergence of metazoans (850–550 Ma) and during the early stages of animal evolution (fig.”
BackgroundFidler, A. L., Boudko, S. P., Rokas, A., & Hudson, B. G. (2018) · Journal of Cell Science · doi:10.1242/jcs.203950 · Cited by 238
“…candidates to be the sister-groups to the rest of animals, based on phylogenetic analyses of genomic and transcriptomic data and cell-type evolution (Ryan et al., 2013; Moroz et al., 2014; Pisani et al., 2015; Whelan et al., 2015; Telford et al., 2016; King and Rokas, 2017; Feuda et al., 2017).”
BackgroundPhylogenomic Insights into Animal Evolution
Telford, M. J., Budd, G. E., & Philippe, H. (2015) · Current Biology · doi:10.1016/j.cub.2015.07.060 · Cited by 213
OMA standalone: orthology inference among public and custom genomes and transcriptomesPreprint
Altenhoff, A., Levy, J., Zarowiecki, M., Tomiczek, B., Vesztrocy, A. W., Dalquen, D. A., Müller, S., Telford, M. J., Glover, N. M., Dylus, D., et al. (2019) · Genome Research · doi:10.1101/gr.243212.118 · Cited by 166
Collagen IV and basement membrane at the evolutionary dawn of metazoan tissues
Fidler, A. L., Darris, C. E., Chetyrkin, S. V., Pedchenko, V. K., Boudko, S. P., Brown, K. L., Jerome, W. G., Hudson, J. K., Rokas, A., & Hudson, B. G. (2017) · eLife · doi:10.7554/elife.24176 · Cited by 197
“Collectively, we propose a model for collagen IV gene evolution that incorporates both Ctenophora-first and Porifera-first hypotheses (Figure 11).”
BackgroundInfluentialThe origin of animals: an ancestral reconstruction of the unicellular-to-multicellular transition
Ros-Rocher, N., Pérez-Posada, A., Leger, M. M., & Ruiz‐Trillo, I. (2021) · Open Biology · doi:10.1098/rsob.200359 · Cited by 169
Kapli, P., & Telford, M. J. (2020) · Science Advances · doi:10.1126/sciadv.abc5162 · Cited by 162
Dong, W., Xu, C., Wu, P., Cheng, T., Yu, J. Q., Zhou, S., & De‐Yuan, H. (2018) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2018.04.033 · Cited by 132
Dynamics of genomic innovation in the unicellular ancestry of animals
Grau‐Bové, X., Torruella, G., Donachie, S. P., Suga, H., Leonard, G., Richards, T. A., & Ruiz‐Trillo, I. (2017) · eLife · doi:10.7554/elife.26036 · Cited by 171
“…et al., 2016), Fungi (Torruella et al., 2015), the contentious hypotheses for the root of eukaryotes (namely, ‘Opimoda-Diphoda’ or ‘Excavata-first’) (Derelle et al., 2015; He et al., 2014) and the earliest-branching animal group (Porifera or Ctenophora) (Whelan et al., 2015; Simion et al., 2017).”
BackgroundBallesteros, J. A., & Sharma, P. P. (2019) · Systematic Biology · doi:10.1093/sysbio/syz011 · Cited by 167
Borowiec, M. L., Lee, E. K., Chiu, J. C., & Plachetzki, D. C. (2015) · doi:10.1101/013946 · Cited by 172
“This is true especially of sponges, where branches subtending this group could be dramatically shortened [1, 6, 9] with additional sampling.”
BackgroundResultInfluentialZhou, X., Shen, X.-X., Hittinger, C. T., & Rokas, A. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msx302 · Cited by 164
“2015], and WhelA6 [Whelan et al. 2015] cover mammals, vertebrates, and metazoans, respectively); and 4) they consist of sequence data derived from different technologies (e.”
MethodIndependent origins of neurons and synapses: insights from ctenophores
Moroz, L. L., & Kohn, A. B. (2016) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2015.0041 · Cited by 171
Self-citationEvolutionary conservation of the antimicrobial function of mucus: a first defence against infection
Bakshani, C. R., Morales‐Garcia, A. L., Althaus, M., Wilcox, M. D., Pearson, J. P., Bythell, J. C., & Burgess, J. G. (2018) · npj Biofilms and Microbiomes · doi:10.1038/s41522-018-0057-2 · Cited by 173
“The Ctenophora are a sistergroup to the Cnidaria and represent the most distant animal relatives of humans.(17) Analogous to the Cnidaria, they are diploblastic and radially symmetrical(18) and are known more commonly as comb jellies.”
BackgroundNew deep-sea species of Xenoturbella and the position of Xenacoelomorpha
Rouse, G. W., Wilson, N. G., Carvajal, J. I., & Vrijenhoek, R. C. (2016) · Nature · doi:10.1038/nature16545 · Cited by 150
Embracing Uncertainty in Reconstructing Early Animal Evolution
King, N., & Rokas, A. (2017) · Current Biology · doi:10.1016/j.cub.2017.08.054 · Cited by 145
“In contrast, analyses employing site-heterogeneous models (and in particular the CAT model [47]) typically recover sponges as the sister branch ([34–37,41,42], but see [38,40,48]).”
MethodRooting the Animal Tree of Life
Li, Y., Shen, X.-X., Evans, B., Dunn, C. W., & Rokas, A. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab170 · Cited by 146
Redmond, A. K., & McLysaght, A. (2021) · Nature Communications · doi:10.1038/s41467-021-22074-7 · Cited by 139
“Two of these, from Ryan et al.3 (REA dataset) and Whelan et al. (2015)7 (WEA15 dataset) supported Ctenophora sister under partitioned phylogenomics, but were found by Pisani and colleagues8 to support sponges as sister to other animals under CAT/ CATGTR.”
Early metazoan life: divergence, environment and ecology
Erwin, D. H. (2015) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2015.0036 · Cited by 154
“Nonetheless, this new study evaluated these problems through increased taxon sampling and other improvements, and found support for ctenophores at the base of metazoans [14,15].”
BackgroundSearching the Evolutionary Origin of Epithelial Mucus Protein Components—Mucins and FCGBP
Lang, T., Klasson, S., Larsson, E., Johansson, M., Hansson, G. C., & Samuelsson, T. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw066 · Cited by 135
“In conclusion, we have identified proteins with properties of gel-forming mucins in Ctenophora, a group shown to be sister to all other animals (Whelan et al. 2015).”
BackgroundPhylogenomic Subsampling and the Search for Phylogenetically Reliable Loci
Koch, N. M. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab151 · Cited by 126
“…size of phylogenomic data sets is to discard loci that seem most affected by potential sources of bias (Nesnidal et al. 2010; Borowiec et al. 2015; Whelan et al. 2015; Kocot et al. 2017; Mongiardino Koch et al. 2018; Marl etaz et al. 2019), including high levels of saturation and heterogeneities…”
BackgroundMethodNeural versus alternative integrative systems: molecular insights into origins of neurotransmitters
Moroz, L. L., Romanova, D. Y., & Kohn, A. B. (2021) · Philosophical Transactions of the Royal Society B · doi:10.1098/rstb.2019.0762 · Cited by 130
Self-citationHejnol, A., & Lowe, C. J. (2015) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2015.0045 · Cited by 105
“Further development of the methodology and larger taxon sampling demonstrate the potential to resolve the position of even the most problematic taxa and to address long-branch attraction (LBA) artefacts caused by fast-evolving sequences and rapid radiations [100–102].”
BackgroundMethodOn the evolution of bilaterality
Genikhovich, G., & Technau, U. (2017) · Development · doi:10.1242/dev.141507 · Cited by 118
Early sponge evolution: A review and phylogenetic framework
Botting, J. P., & Muir, L. A. (2018) · Palaeoworld · doi:10.1016/j.palwor.2017.07.001 · Cited by 125
Sperling, E. A., & Stockey, R. G. (2018) · Integrative and Comparative Biology · doi:10.1093/icb/icy088 · Cited by 122
The Multispecies Coalescent Model Outperforms Concatenation Across Diverse Phylogenomic Data Sets
Jiang, X., Edwards, S. V., & Liu, L. (2020) · Systematic Biology · doi:10.1093/sysbio/syaa008 · Cited by 103
“2018) 10/90 4709/5162 CDS Mammal2017 (Scornavacca and Galtier 2017) 10/97 108/110 CDS Metazoan2015 (Whelan et al. 2015) 10/76 36/115 CDS Shrew (Giarla and Esselstyn 2015) 10/19 966/1112 UCE Squirrel (McLean et al.”
BackgroundA congruent topology for deep gastropod relationships
Cunha, T. J., & Giribet, G. (2019) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2018.2776 · Cited by 109
Simion, P., Belkhir, K., Francois, C. M., Veyssier, J., Rink, J. C., Manuel, M., Philippe, H., & Telford, M. J. (2018) · BMC Biology · doi:10.1186/s12915-018-0486-7 · Cited by 101
“One of these problematic relationships has been recovered with maximal support in four recent studies based on dataset A [22, 35 – 37].”
ResultSupport for a clade of Placozoa and Cnidaria in genes with minimal compositional bias
Laumer, C. E., Gruber-Vodicka, H., Hadfield, M. G., Pearse, V. B., Riesgo, A., Marioni, J. C., & Giribet, G. (2018) · eLife · doi:10.7554/elife.36278 · Cited by 112
Whelan, N. V., & Halanych, K. M. (2016) · Systematic Biology · doi:10.1093/sysbio/syw084 · Cited by 96
Self-citationComparative genomics and the nature of placozoan species
Eitel, M., Francis, W. R., Varoqueaux, F., Daraspe, J., Osigus, H., Krebs, S., Vargas, S., Blum, H., Williams, G. A., Schierwater, B., et al. (2018) · PLoS Biology · doi:10.1371/journal.pbio.2005359 · Cited by 93
Rooting the tree of life: the phylogenetic jury is still out
Gouy, R., Baurain, D., & Philippe, H. (2015) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2014.0329 · Cited by 96
Betancur‐R, R., Arcila, D., Vari, R. P., Hughes, L. C., Oliveira, C., Sabaj, M. H., & Ortı́, G. (2018) · Evolution · doi:10.1111/evo.13649 · Cited by 99
“…studies show that phylogenomics can lead to strong support for conflicting hypotheses, indicating that incongruence remains a problem in the era of big genomic data (e.g., Ryan et al. 2013; Dunn et al. 2014; Pisani et al. 2015; Whelan et al. 2015; Arcila et al. 2017; Chakrabarty et al. 2017).”
BackgroundInfluentialAncestral state reconstruction of ontogeny supports a bilaterian affinity for Dickinsonia
Gold, D. A., Runnegar, B., Gehling, J. G., & Jacobs, D. K. (2015) · Evolution & Development · doi:10.1111/ede.12168 · Cited by 99
“Other phylogenomic datasets have also failed to recover the Coelenterata (Pick et al. 2010; Ryan et al. 2013; Moroz et al. 2014; Whelan et al. 2015)—and ctenophores lack a significant number of molecular features conserved between cnidarians and bilaterians (Ryan et al.”
BackgroundInfluentialWang, H.-C., Susko, E., & Roger, A. J. (2019) · Systematic Biology · doi:10.1093/sysbio/syz021 · Cited by 85
Zhao, Y., Vinther, J., Parry, L. A., Wei, F., Green, E., Pisani, D., Hou, X., Edgecombe, G. D., & Cong, P. (2019) · Current Biology · doi:10.1016/j.cub.2019.02.036 · Cited by 89
A developmental perspective on the evolution of the nervous system
Martín-Durán, J. M., & Hejnol, A. (2019) · Developmental Biology · doi:10.1016/j.ydbio.2019.10.003 · Cited by 67
Tikhonenkov, D. V., Hehenberger, E., Сергеевич, Е. А., Belyakova, O. I., Mazei, Y., Mylnikov, A. P., & Keeling, P. J. (2020) · BMC Biology · doi:10.1186/s12915-020-0762-1 · Cited by 90
“…lineages of animals on phylogenetic trees is still debated: some consider either sponges (Porifera) [4 – 6] or Ctenophora [7 – 9] or Placozoa [10, 11] to be the first branch of extant metazoans (although most data show the latter scenario to be the least realistic of these possibilities [2, 12]).”
BackgroundA New Orthology Assessment Method for Phylogenomic Data: Unrooted Phylogenetic Orthology
Ballesteros, J. A., & Hormiga, G. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw069 · Cited by 74
Wang, J., Zhang, L., Lian, S., Qin, Z., Zhu, X., Dai, X., Huang, Z., Ke, C., Zhou, Z., Wei, J., et al. (2020) · Nature Ecology & Evolution · doi:10.1038/s41559-020-1138-1 · Cited by 65
Evolution of glutamatergic signaling and synapses
Moroz, L. L., Nikitin, M. A., Poličar, P. G., Kohn, A. B., & Romanova, D. Y. (2021) · Neuropharmacology · doi:10.1016/j.neuropharm.2021.108740 · Cited by 81
Self-citationSenatore, A., Raiss, H., & Le, P. (2016) · Frontiers in Physiology · doi:10.3389/fphys.2016.00481 · Cited by 77
“These findings were corroborated in an expanded effort, where the authors sought to curtail potential systematic errors in phylogenetic inference (Whelan et al., 2015).”
BackgroundJindrich, K., & Degnan, B. M. (2016) · BMC Evolutionary Biology · doi:10.1186/s12862-016-0598-z · Cited by 82
“Notably, ctenophores, which are deemed to be the earliest branching metazoan phyletic lineage [14], exhibit a higher level of bZIP gene loss than any other metazoan lineage (Fig.”
BackgroundRichards, E. J., Brown, J. M., Barley, A. J., Chong, R. A., & Thomson, R. C. (2018) · Systematic Biology · doi:10.1093/sysbio/syy013 · Cited by 79
“Several cases are now known where different genomic data sets support conflicting phylogenetic hypotheses with very high statistical support (e.g., Dunn et al. 2008; Philippe et al. 2009; Schierwater et al. 2009; Whelan et al. 2015), sometimes implying very different scenarios for the evolution of important traits (e.”
BackgroundA Total-Evidence Dated Phylogeny of Echinoidea Combining Phylogenomic and Paleontological Data
Koch, N. M., & Thompson, J. R. (2020) · Systematic Biology · doi:10.1093/sysbio/syaa069 · Cited by 68
de, A. N., Barley, A. J., Meza-Lázaro, R. N., García‐Vázquez, U. O., Zamora‐Abrego, J. G., Thomson, R. C., & Leaché, A. D. (2016) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2016.09.001 · Cited by 74
“In some circumstances, different approaches to analyzing phylogenetic datasets can have profound impacts on phylogenetic inference (e.g., Leaché et al., 2015b; Pisani et al., 2015; Shaffer et al., 2013; Whelan et al., 2015).”
BackgroundWhere is my mind? How sponges and placozoans may have lost neural cell types
Ryan, J. F., & Chiodin, M. (2015) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2015.0059 · Cited by 73
Sharma, P. P., Baker, C. M., Cosgrove, J. G., Johnson, J. E., Oberski, J. T., Raven, R. J., Harvey, M. S., Boyer, S. L., & Giribet, G. (2018) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2018.01.003 · Cited by 67
Complex Homology and the Evolution of Nervous Systems
Liebeskind, B. J., Hillis, D. M., Zakon, H. H., & Hofmann, H. A. (2015) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2015.12.005 · Cited by 72
“Although this placement remains controversial [17], several independent studies have arrived at this conclusion [14–16,18].”
Smith, C. L., Reese, T. S., Govezensky, T., & Barrio, R. A. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1815655116 · Cited by 62
Singhal, S., Colston, T. J., Grundler, M. R., Smith, S. A., Costa, G. C., Colli, G. R., Moritz, C. C., Pyron, R. A., & Rabosky, D. L. (2020) · Systematic Biology · doi:10.1093/sysbio/syaa054 · Cited by 64
Telford, M. J., Moroz, L. L., & Halanych, K. M. (2016) · Nature · doi:10.1038/529286a · Cited by 65
Self-citationLücking, R. (2019) · Critical Reviews in Plant Sciences · doi:10.1080/07352689.2019.1650517 · Cited by 68
Moroz, L. L., & Kohn, A. B. (2015) · Integrative and Comparative Biology · doi:10.1093/icb/icv104 · Cited by 61
“The two most recent phylogenetic analyses strongly support the placement of ctenophores as the sister group to all other animals (Borowiec et al. 2015; Whelan et al. 2015).”
BackgroundSelf-citationNew animal phylogeny: future challenges for animal phylogeny in the age of phylogenomics
Giribet, G. (2015) · Organisms Diversity & Evolution · doi:10.1007/s13127-015-0236-4 · Cited by 67
Evolution of the Chlorophyta: Insights from chloroplast phylogenomic analyses
Fang, L., Leliaert, F., Zhang, Z., Penny, D., & Zhong, B. (2017) · Journal of Systematics and Evolution · doi:10.1111/jse.12248 · Cited by 59
“Inaccurate phylogenetic relationships are often inferred when the nucleotide or amino acid data poorly fit to the substitution model (Philippe et al., 2011; Whelan et al., 2015).”
BackgroundEvolutionary origin of synapses and neurons – Bridging the gap
Burkhardt, P., & Sprecher, S. G. (2017) · BioEssays · doi:10.1002/bies.201700024 · Cited by 60
Construction of a Species-Level Tree of Life for the Insects and Utility in Taxonomic Profiling
Chesters, D. (2016) · Systematic Biology · doi:10.1093/sysbio/syw099 · Cited by 61
The evolution of animal genomes
Dunn, C. W., & Ryan, J. F. (2015) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2015.08.006 · Cited by 58
DNA Methylation in Basal Metazoans: Insights from Ctenophores
Dabe, E. C., Sanford, R. S., Kohn, A. B., Bobkova, Y. V., & Moroz, L. L. (2015) · Integrative and Comparative Biology · doi:10.1093/icb/icv086 · Cited by 59
“…strongly suggests the placement of ctenophores as a sister group to all other metazoans (Ryan et al. 2013; Moroz et al 2014; Borowiec et al. 2015; Whelan et al. 2015a, 2015b) with a possibility that the ctenophore lineage independently evolved many metazoan characteristics such as neurons,…”
BackgroundSelf-citationThe Mitochondrial Genomes of a Myxozoan Genus Kudoa Are Extremely Divergent in Metazoa
Takeuchi, F., Sekizuka, T., Ogasawara, Y., Yokoyama, H., Kamikawa, R., Inagaki, Y., Nozaki, T., Sugita‐Konishi, Y., Ohnishi, T., & Kuroda, M. (2015) · PLoS ONE · doi:10.1371/journal.pone.0132030 · Cited by 47
“A fast mitochondrial evolutionary rate is known for Ctenophora, which is the oldest lineage of Metazoa and has evolved a neural system in parallel with the Bilateria+Cnidaria clade [13,14,25,26].”
BackgroundThe phylogeny of insects in the data‐driven era
Chesters, D. (2019) · Systematic Entomology · doi:10.1111/syen.12414 · Cited by 58
“An approach taken recently is formation of individual matrices filtered for different sources of bias (Whelan et al. , 2015; Garrison et al. , 2016; Cunha & Giribet, 2019), although it is not implicit how any incongruence between trees of different matrices should be interpreted.”
BackgroundThe Role of Homology and Orthology in the Phylogenomic Analysis of Metazoan Gene Content
Pett, W., Adamski, M., Adamska, M., Francis, W. R., Eitel, M., Pisani, D., & Wörheide, G. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz013 · Cited by 57
Naser-Khdour, S., Bui, M., & Lanfear, R. (2021) · Systematic Biology · doi:10.1093/sysbio/syab067 · Cited by 53
“previous studies have sensibly used ratio likelihood tests such as the Shimodaira–Hasegawa (SH) test (Shimodaira and Hasegawa 1999) and the approximately unbiased (AU) test (Shimodaira 2002) to compare a small set of potential root placements, rejecting some alternative root placements in favor of the ML root placemen…”
MethodNeuromuscular organization of the Ctenophore Pleurobrachia bachei
Norekian, T. P., & Moroz, L. L. (2018) · The Journal of Comparative Neurology · doi:10.1002/cne.24546 · Cited by 52
“…muscles in ctenophores is congruent with any outcome of the ongoing discussion about the Ctenophora-sister (Arcila et al., 2017; Shen et al., 2017; Whelan et al., 2015b; Whelan et al., 2017) vs. Porifera-sister (Feuda et al., 2017; Pisani et al., 2015; Simion et al., 2017) phylogenetic hypotheses.”
BackgroundSelf-citationPresnell, J. S., Vandepas, L. E., Warren, K. J., Swalla, B. J., Amemiya, C. T., & Browne, W. E. (2016) · Current Biology · doi:10.1016/j.cub.2016.08.019 · Cited by 51
Oxygen and the Energetic Requirements of the First Multicellular Animals
Leys, S. P., & KAHN, A. S. (2018) · Integrative and Comparative Biology · doi:10.1093/icb/icy051 · Cited by 46
“about which group of animals—ctenophores or sponges—arose first (Dunn et al. 2008; Philippe et al. 2009; Nosenko et al. 2013; Ryan et al. 2013; Moroz et al. 2014; Whelan et al. 2015; Feuda et al. 2017).”
BackgroundA reconstruction of sexual modes throughout animal evolution
Sasson, D. A., & Ryan, J. F. (2017) · BMC Evolutionary Biology · doi:10.1186/s12862-017-1071-3 · Cited by 54
Getting Nervous: An Evolutionary Overhaul for Communication
Varoqueaux, F., & Fasshauer, D. (2017) · Annual Review of Genetics · doi:10.1146/annurev-genet-120116-024648 · Cited by 47
How and Why to Build a Unified Tree of Life
McTavish, E. J., Drew, B. T., Redelings, B., & Cranston, K. (2017) · BioEssays · doi:10.1002/bies.201700114 · Cited by 49
Evolution of Animal Neural Systems
Liebeskind, B. J., Hofmann, H. A., Hillis, D. M., & Zakon, H. H. (2017) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev-ecolsys-110316-023048 · Cited by 55
Zhao, L., Li, X., Zhang, N., Zhang, S., Yi, T., Mā, H., Guo, Z., & Li, D.-Z. (2016) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2016.06.007 · Cited by 52
“, 2013; Simmons, 2014), LBA (anomaly zone) (He et al., 2016; Linkem et al., 2016; Whelan et al., 2015), substitution saturation (fast evolution sites) (Chiari et al.”
BackgroundInfluentialHernandez, A. M., & Ryan, J. F. (2019) · doi:10.1101/729103 · Cited by 52
Moroz, L. L., Romanova, D. Y., Nikitin, M. A., Sohn, D., Kohn, A. B., Neveu, É., Varoqueaux, F., & Fasshauer, D. (2020) · Scientific Reports · doi:10.1038/s41598-020-69851-w · Cited by 51
Self-citationPrasanna, A. N., Gerber, D., Kijpornyongpan, T., Aime, M. C., Doyle, V. P., & Nagy, L. G. (2019) · Systematic Biology · doi:10.1093/sysbio/syz029 · Cited by 46
“poor model fit, biased taxon or gene sampling, orthology inference) (Dunn et al. 2008; Hejnol et al. 2009; Simon et al. 2012; Misof et al. 2013; Dell’Ampio et al. 2014; Lanfear et al. 2014; Yang and Smith 2014; Chen et al. 2015; Pisani et al. 2015; Smith et al. 2015; Whelan et al. 2015; Hosner et al. 2016), both of wh…”
BackgroundNew insights into the physiology and pathophysiology of the atypical sodium leak channel NALCN
Monteil, A., Guérineau, N. C., Gil‐Nagel, A., Parra‐Díaz, P., Lory, P., & Senatore, A. (2023) · Physiological Reviews · doi:10.1152/physrev.00014.2022 · Cited by 49
Phylogenomic analyses recover a clade of large-bodied decapodiform cephalopods
Anderson, F. E., & Lindgren, A. R. (2020) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2020.107038 · Cited by 51
A Screen for Gene Paralogies Delineating Evolutionary Branching Order of Early Metazoa
Erives, A., & Fritzsch, B. (2020) · G3 Genes|Genomes|Genetics · doi:10.1534/g3.119.400951 · Cited by 49
Endosymbiont genomes yield clues of tubeworm success
Li, Y., Liles, M. R., & Halanych, K. M. (2018) · The ISME Journal · doi:10.1038/s41396-018-0220-z · Cited by 43
“Resulting OG clusters were then filtered from each bacterial genome following modified bioinformatics pipelines of [5, 40].”
MethodSelf-citationEdiacaran origin and Ediacaran-Cambrian diversification of Metazoa
Carlisle, E. M., Yin, Z., Pisani, D., & Donoghue, P. C. J. (2024) · Science Advances · doi:10.1126/sciadv.adp7161 · Cited by 57
“The trees represent alternative resolutions for the root of Metazoa, placing either Ctenophora (comb jellies) ( 128–132 ) or Porifera (sponges) ( 127 , 133–138 ) as the sister of all other animals.”
Li, Y., Kocot, K. M., Whelan, N. V., Santos, S. R., Waits, D. S., Thornhill, D. J., & Halanych, K. M. (2016) · Zoologica Scripta · doi:10.1111/zsc.12201 · Cited by 43
“The ability to utilize genome-scale data for phylogenetic analyses, or ‘phylogenomics’, has significantly improved our understanding of metazoan evolution (Delsuc et al. 2005; Matus et al. 2006; Dunn et al. 2008; Kocot et al. 2011; Bond et al. 2014; Misof et al. 2014; Weigert et al. 2014; Whelan et al. 2015).”
BackgroundMethodInfluentialSelf-citationThe promise and pitfalls of synteny in phylogenomics
Steenwyk, J. L., & King, N. (2024) · PLoS Biology · doi:10.1371/journal.pbio.3002632 · Cited by 49
Metadata
- Authors
- Whelan, N. V., Kocot, K. M., Moroz, L. L., & Halanych, K. M.
- Affiliations
- Auburn University (US)
- The University of Queensland (AU)
- University of Florida (US)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2015-04-20
- Volume
- 112
- Issue
- 18
- Pages
- 5773-5778
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC4426464
- OpenAlex
- W2001496905
- Cited by
- 331
- References
- 60
- Citations by year
- 2026: 7 · 2025: 17 · 2024: 22 · 2023: 21 · 2022: 24 · 2021: 26 · 2020: 26 · 2019: 40 · 2018: 40 · 2017: 42 · 2016: 42 · 2015: 24
- FWCI
- 37.29
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Aeronautics and Space Administration (NASA-NNX13AJ31G)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Marine Invertebrate Physiology and Ecology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Protist diversity and phylogeny
- Keywords
- Ctenophora, animal phylogeny, sponges, systematic errors, long-branch attraction, compositional heterogeneity, ribosomal protein genes, orthology inference, transcriptome, gene tree discordance
- MeSH terms
- Algorithms, Animals, Bayes Theorem, Cnidaria, Biological Evolution, Phylogeny, Porifera, Ribosomal Proteins, Likelihood Functions, Genome, Cell Lineage, Genomics, Databases, Genetic, Ctenophora, Transcriptome
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 2026-10-11, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-10-11 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
Cited sources are checked with a language model’s help (gpt-6-sol).
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
